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Results for “Functional potential”

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At least 721 records · Page 40Linked to original sources

PubMed2002

Endoplasmic reticulum (ER) stress: hepatitis C virus induces an ER-nucleus signal transduction pathway and activates NF-kappaB and STAT-3.

Human hepatitis C virus (HCV) is the leading cause of chronic hepatitis, which often results in liver cirrhosis and hepatocellular carcinoma. The HCV RNA genome codes for at least ten proteins. The HCV non-structural protein 5A (NS5A) has generated considerable interest due to its effect on interferon sensitivity via binding and inactivating the cellular protein kinase, PKR. It has been shown that NS5A engages in the endoplasmic reticulum (ER)-nucleus signal transduction pathway. The expression of NS5A in the ER induces an ER stress ultimately leading to the activation of STAT-3 and NF-kappaB. This pathway is sensitive to inhibitors of Ca(2+) uptake in the mitochondria (ruthenium red), Ca(2+) chelators (TMB-8, EGTA-AM), and antioxidants (PDTC, NAC, Mn-SOD). The inhibitory effect of protein tyrosine kinase (PTK) inhibitors indicates the involvement of PTK in NF-kappaB activation by NS5A. This implicates an alternate pathway of NF-kappaB activation by NS5A. The actions of NS5A have also been studied in the context of an HCV subgenomic replicon inducing a similar intracellular event. Thus, activation of NF-kappaB leads to the induction of cellular genes, which are largely antiapoptotic in function. These studies suggest a potential function of NS5A in inducing chronic liver disease and hepatocellular carcinoma associated with HCV infection.

Animals↗

PubMedDate not supplied

Functional status and therapeutic intensity during inpatient rehabilitation.

The objective of this study was to describe the relationships between functional status at discharge and intensity of therapies received during inpatient medical rehabilitation. The sample was comprised of 140 patients with traumatic brain injury and 106 patients with spinal cord injury at eight hospitals that subscribe to the Uniform Data System for Medical Rehabilitation. Data included linear measures of motor and cognitive ability derived from the Functional Independence Measure at admission to and discharge from rehabilitation. Multiple regression was used to predict intensity of therapies, discharge motor and cognitive function, the extent to which potential functional gains were achieved, and the efficiency of gains. Intensities of occupational, physical, and speech therapies were not significant predictors of outcomes for either group, controlling linearly for admission function, psychology intensity, length of stay, onset to admission interval, age, and interrupted stays. Only intensity of psychology services seemed to have any relation to functional gain (in cognition for patients with traumatic brain injury). The apparent lack of benefit related to intensity of therapies may be due to factors such as spontaneous recovery, goals not measured by the Functional Independence Measure, limited modulation of therapy intensity according to likely patient responsiveness, or therapies focused on impairment or other goals rather than disability. We suggest that efficiently staged rehabilitation should vary the intensity and nature of services according to patients' functional status, impairments, comorbid conditions, and other clinical factors.

Adult↗

PubMed2005

A combined approach exploring gene function based on worm-human orthology.

BACKGROUND: Many aspects of the nematode Caenorhabditis elegans biology are conserved between invertebrates and vertebrates establishing this particular organism as an excellent genetic model. Because of its small size, large populations and self-fertilization of the hermaphrodite, functional predictions carried out by genetic modifications as well as RNAi screens, can be rapidly tested. RESULTS: In order to explore the function of a set of C. elegans genes of unknown function, as well as their potential functional roles in the human genome, we performed a phylogenetic analysis to select the most probable worm orthologs. A total of 13 C. elegans genes were subjected to down-regulation via RNAi and characterization of expression profiles using GFP strains. Previously unknown distinct expression patterns were observed for four of the analyzed genes, as well as four visible RNAi phenotypes. In addition, subcellular protein over-expression profiles of the human orthologs for seven out of the thirteen genes using human cells were also analyzed. CONCLUSION: By combining a whole-organism approach using C. elegans with complementary experimental work done on human cell lines, this analysis extends currently available information on the selected set of genes.

Animals↗

PubMed1993

A role for the Drosophila segment polarity gene armadillo in cell adhesion and cytoskeletal integrity during oogenesis.

The epithelial sheet is a structural unit common to many tissues. Its organization appears to depend on the function of the multi-protein complexes that form adherens junctions. Elegant cell biological experiments have provided support for hypotheses explaining the function of adherens junctions and of their components. These systems, however, lack the ability to test function within an entire organism during development. The realization that the product of the Drosophila segment polarity gene armadillo is related to the vertebrate adhesive junction components plakoglobin and beta-catenin led to the suggestion that armadillo might provide a genetic handle to study adhesive junction structure and function. An examination of the potential function of Armadillo in cell-cell adhesive junctions was initiated using the Drosophila ovary as the model system. We examined the distribution of Armadillo in the Drosophila ovary and demonstrated that this localization often parallels the location of cell-cell adhesive junctions. The consequences of removing armadillo function from the germ-line cells of the ovary were also examined. Germ-line armadillo mutations appear to disrupt processes requiring cell adhesion and integrity of the actin cytoskeleton, consistent with a role for Armadillo in cell-cell adhesive junctions. We have also used armadillo mutations to examine the effects on ovarian development of altering the stereotyped cell arrangements of the ovary. The implications of these results for the role of adhesive junctions during development are discussed.

Animals↗

PubMed2005

Mechanism of positive allosteric modulators acting on AMPA receptors.

Ligand-gated ion channels involved in the modulation of synaptic strength are the AMPA, kainate, and NMDA glutamate receptors. Small molecules that potentiate AMPA receptor currents relieve cognitive deficits caused by neurodegenerative diseases such as Alzheimer's disease and show promise in the treatment of depression. Previously, there has been limited understanding of the molecular mechanism of action for AMPA receptor potentiators. Here we present cocrystal structures of the glutamate receptor GluR2 S1S2 ligand-binding domain in complex with aniracetam [1-(4-methoxybenzoyl)-2-pyrrolidinone] or CX614 (pyrrolidino-1,3-oxazino benzo-1,4-dioxan-10-one), two AMPA receptor potentiators that preferentially slow AMPA receptor deactivation. Both potentiators bind within the dimer interface of the nondesensitized receptor at a common site located on the twofold axis of molecular symmetry. Importantly, the potentiator binding site is adjacent to the "hinge" in the ligand-binding core "clamshell" that undergoes conformational rearrangement after glutamate binding. Using rapid solution exchange, patch-clamp electrophysiology experiments, we show that point mutations of residues that interact with potentiators in the cocrystal disrupt potentiator function. We suggest that the potentiators slow deactivation by stabilizing the clamshell in its closed-cleft, glutamate-bound conformation.

Allosteric Regulation↗

PubMed2001

[Relationship between type and amount of treatment and functional improvement in first-stroke during in-patients rehabilitation].

The effectiveness of ongoing rehabilitation services for post-acute stroke patients is poorly documented. The aim of the present study was describe the relationships between functional status at discharge and intensity of therapies, including occupational therapy, physical therapy, speech therapy and nursing care, during inpatient medical rehabilitation. All patients (30) admitted after a first stroke. The functional status of patients was observed by using the Functional Independence Measure on patient admission to rehabilitation and time per week during the hospitalisation. The neurological status of patients was observed by using the NIH Stroke Scale on patient admission to rehabilitation and at discharge. The study population included 30 patients of average 64.4 years; 60% were men; length of stay was 74 days. Statistical analysis were performed to check for intensity of therapies, discharge motor and cognitive function, the extent to which potential functional gains were achieved. Intensities of physical and speech therapies were not significant predictors of outcomes. Intensity of occupational therapy was significant predictor of outcomes (P = 0.04). We suggest that efficiently staged rehabilitation should vary the intensity and nature of services according to patients functional status, impairments, comorbid conditions and other clinical factors.

Activities of Daily Living↗

PubMed2005

Direct-potential-fit analysis of new infrared and UV/visible A 1Sigma+-X 1Sigma+ emission spectra of AgH and AgD.

New high-resolution infrared and UV/visible spectra of (107)AgH, (109)AgH, (107)AgD, and (109)AgD have been recorded with a Fourier transform spectrometer. The new line positions are combined with published microwave and older electronic A (1)Sigma(+)-X (1)Sigma(+) data and used, first in a decoupled analysis of the X state alone, and then in a global multi-isotopologue analysis which yields comprehensive descriptions of both the X (1)Sigma(+) and A (1)Sigma(+) states of all four isotopologues of AgH. While the A state was long believed to be heavily perturbed, it is shown that its irregular spectrum merely reflects an unusual potential function shape. A direct fit of all data to appropriate radial Hamiltonians yields analytic potential-energy functions and Born-Oppenheimer breakdown radial functions for the ground X (1)Sigma(+) and A (1)Sigma(+) states.

Journal Article↗

PubMed1985

Brain arachidonic acid metabolites. Functions and interactions with ethanol.

The formation and potential function of arachidonic acid metabolites in brain are reviewed briefly. Cyclooxygenase metabolites of arachidonic acid are formed in brain, but the lipoxygenase derivatives have not been demonstrated. Evidence clearly indicates that the cyclooxygenase products act as neuromodulators. Possible effects of leukotrienes on brain function remain in doubt, although several studies have suggested a role for the leukotrienes and it appears that these agents have a long-lasting effect. Potential interactions between ethanol and brain arachidonic acid metabolites have received minimal attention. Several studies indicate that pretreatment with prostaglandin synthetase inhibitors produces antagonism of ethanol's behavioral effects. These observations may be related to preliminary findings that ethanol increases brain prostaglandin content.

Animals↗

PubMed2006

SNP Function Portal: a web database for exploring the function implication of SNP alleles.

MOTIVATION: Finding the potential functional significance of SNPs is a major bottleneck in understanding genome-wide SNP scanning results, as the related functional data are distributed across many different databases. The SNP Function Portal is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, the SNP Function Portal includes a powerful search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, our system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments. AVAILABILITY: http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/snpfunc.aspx.

Alleles↗

PubMed1999

The effect of queuosine on tRNA structure and function.

Computational modeling was performed to determine the potential function of the queuosine modification of tRNA found in wobble position 34 of tRNAasp, tRNAasn, tRNAhis, and tRNAtyr. Using the crystal structure of tRNAasp and a tRNA-tRNA-mRNA complex model, we show that the queuosine modification serves as a structurally restrictive base for tRNA anticodon loop flexibility. An extended intraresidue and intramolecular hydrogen bonding network is established by queuosine. The quaternary amine of the 7-aminomethyl side chain hydrogen bonds with the base's carbonyl oxygen. This positions the dihydroxycyclopentenediol ring of queuosine in proper orientation for hydrogen bonding with the backbone of the neighboring uridine 33 residue. The interresidue association stabilizes the formation of a cross-loop hydrogen bond between the uridine 33 base and the phosphoribosyl backbone of the cytosine at position 36. Additional interactions between RNAs in the translation complex were studied with regard to potential codon context and codon bias effects. Neither steric nor electrostatic interaction occurs between aminoacyl- and peptidyl-site tRNA anticodon loops that are modified with queuosine. However, there is a difference in the strength of anticodon/codon associations (codon bias) based on the presence or lack of queuosine in the wobble position of the tRNA. Unmodified (guanosine-containing) tRNAasp forms a very stable association with cytosine (GAC), but is much less stable in complex with a uridine-containing codon (GAU). Queuosine-modified tRNAasp exhibits no bias for either of cognate codons GAC or GAU and demonstrates a lower binding energy similar to the wobble pairing of guanosine-containing tRNA with a GAU codon. This is proposed to be due to the inflexibility of the queuosine-modified anticodon loop to accommodate proper positioning for optimal Watson-Crick type associations. A preliminary survey of codon usage patterns in oncodevelopmental versus housekeeping gene transcripts suggests a significant difference in bias for the queuosine-associated codons. Therefore, the queuosine modification may have the potential to influence cellular growth and differentiation by codon bias-based regulation of protein synthesis for discrete mRNA transcripts.

Anticodon↗

PubMed2004

Introduction to the reviews on neuropeptide Y.

Neuropeptide Y (NPY) was first reported as an abundant peptide in brain tissue in 1982. Shortly thereafter, NPY was found to be a member of a peptide family consisting of the endocrine peptides pancreatic polypeptide (PP) and peptide YY (PYY). These peptides exert most of their biological effects through five G-protein coupled receptors termed Y1, Y2, Y4, Y5 and y6 that mediate either inhibition adenylate cyclase or increases in intracellular calcium. Since the discovery of NPY, a robust a body of literature has developed around the potential functions of this peptide. While initial findings identified NPY is an important contributor to the regulation of feeding, body weight and blood pressure, more recent work as revealed more subtle functions of this peptide and its potential role in affective disorders, bone formation and cravings. The accompanying twelve reviews detail important developments in our understanding of the functional role of NPY.

Animals↗

PubMed2000

The rat liver Na(+)/bile acid cotransporter. Importance of the cytoplasmic tail to function and plasma membrane targeting.

To understand the potential functions of the cytoplasmic tail of Na(+)/taurocholate cotransporter (Ntcp) and to determine the basolateral sorting mechanisms for this transporter, green fluorescent protein-fused wild type and mutant rat Ntcps were constructed and the transport properties and cellular localization were assessed in transfected COS 7 and Madin-Darby canine kidney (MDCK) cells. Truncation of the 56-amino acid cytoplasmic tail demonstrates that the cytoplasmic tail of rat Ntcp is involved membrane delivery of this protein in nonpolarized and polarized cells and removal of the tail does not affect the bile acid transport function of Ntcp. Using site-directed mutagenesis, two tyrosine residues, Tyr-321 and Tyr-307, in the cytoplasmic tail of Ntcp have been identified as important for the basolateral sorting of rat Ntcp in transfected MDCK cells. Tyr-321 appears to be the major basolateral-sorting determinant, and Tyr-307 acts as a supporting determinant to ensure delivery of the transporter to the basolateral surface, especially at high levels of protein expression. When the two Tyr-based basolateral sorting motifs have been removed, the N-linked carbohydrate groups direct the tyrosine to alanine mutants to the apical surface of transfected MDCK cells. The major basolateral sorting determinant Tyr-321 is within a novel beta-turn unfavorable tetrapeptide Y(321)KAA, which has not been found in any naturally occurring basolateral sorting motifs. Two-dimensional NMR spectroscopy of a 24-mer peptide corresponding to the sequence from Tyr-307 to Thr-330 on the cytoplasmic tail of Ntcp confirms that both the Tyr-321 and Tyr-307 regions do not adopt any turn structure. Since the major motif YKAA contains a beta-turn unfavorable structure, the Ntcp basolateral sorting may not be related to the clathrin-adaptor complex pathway, as is the case for many basolateral proteins.

Amino Acid Sequence↗

PubMed2004

Hydrolysis of a two-membered silica ring on the amorphous silica surface.

We have combined density functional theory (DFT) with classical interatomic potential functions to model hydrolysis of amorphous silica surfaces. The water-silica interaction is described by DFT with incorporation of a long-range elastic field described by classical interatomic potentials. Both physisorption and chemisorption of water on a surface site, known as the two-membered silica ring, are studied in detail. The hybrid quantum-mechanical and classical mechanical method enables more realistic treatment of chemical processes on an extended surface than previous methods. We have studied cooperative events in the hydrolytic reactions and discovered a new reaction pathway that involves a double proton transfer process. In addition, the evaluation of the total energy in a hybrid quantum-mechanical and classical mechanical system is discussed.

Journal Article↗

PubMed2002

Detection and characterization of hibernating myocardium.

Since Tennant and Wiggers observed that coronary occlusion caused a reduction in cardiac contractile function, a lot has been written about the concept of hibernating myocardium. Known as the 'smart heart', hibernating myocardium is characterized by a persistent ventricular myocardial dysfunction with preserved viability, which improves with the relief of the ischaemia; this chronic downregulation in contractile function being a protective mechanism to reduce oxygen demand and thus ensure myocyte survival. This improvement usually results in an enrichment in the quality of life as well as enhanced ventricular function. In fact, it has been observed that the cardiac event rate in patients with viable dysfunctional left ventricular segments who are medically treated, is higher than the event rate in patients with comparable viability who are revascularized. Different degrees of histological alteration have been seen in hibernating myocardium, ranging from cellular de-differentiation (fetal phenotype) to cellular degeneration. Cellular de-differentiation has been associated with repetitive stunning. On the other hand, cellular degeneration (with more extensive fibrosis) has been associated with chronic low myocardial blood flow and a longer time to recovery after revascularization. These histological patterns may suggest an evolution from cellular de-differentiation to degeneration, which ends in scar formation if no revascularization is performed. In fact, several studies have described the clinical value of identifying and revascularizing hibernating segments as early as possible, to minimize fibrosis and morbidity from adverse events. Detection of hibernating myocardium still remains an important clinical problem. Imaging modalities to assess myocardial viability must differentiate potentially functional tissue from myocardium with no potential for functional recovery. These techniques fall into three broad categories: ventricular function assessment, myocardial perfusion imaging and myocardial metabolic imaging. PET imaging with fluorine-18 fluorodeoxyglucose (18F-FDG) and 11C-acetate, single photon emission computed tomography (SPECT) with thallium and 99mTc-sestamibi, dobutamine echocardiograpy, magnetic resonance imaging (MRI) and fast computed tomography (CT) have been used for this purpose. PET imaging, in both perfusion and glucose metabolic activity, has become a standard for myocardial viability assessment, however, similar information may be available from carefully performed studies with perfusion tracers alone.

Coronary Artery Disease↗

PubMedDate not supplied

Cortical sensory evoked potentials and communicative forebrain functions.

Cortical evoked potentials were measured to visual, auditory and somatosensory stimuli in 20 subjects with serious neurodevelopmental impairments due to various etiologies. The results were compared with behavioral observations to find out whether the absence/presence of the responses corresponded to the level of social functioning. No cortical evoked potentials were elicited in two subjects, responses to the stimulation of one modality were missing in three subjects (retinal b-waves and brainstem auditory and somatosensory evoked potentials were, however, preserved in them). No communicative behavior was observed in subjects with absent responses. Ten subjects had marked deviations in the evoked potentials, the behavioral observations in them, ranging from no communication to sentenced speech. Five subjects had normal response patterns and they showed a great variety of communicative skills, including speech. The results support the view that bilateral loss of cortical somatosensory, visual, and auditory evoked potentials is a sign of loss of neural substrates of communication.

Adolescent↗

PubMed2026

Activity of natural single nucleotide variants of human alkyladenine DNA glycosylase AAG R145H, G163S and R197C involved in DNA binding.

Alkyladenine DNA glycosylase (AAG) is a critical enzyme in the base excision repair (BER) pathway that safeguards genome integrity by removing structurally diverse alkylated and deaminated purine lesions from DNA. It serves as a primary defense against alkylation-induced mutations, which are linked to cancer development, chronic inflammation, and neurodegenerative diseases. Single nucleotide variants (SNVs) in the gene coding region have the potential to alter the enzyme's functionality, potentially modulating the repair capacity and affecting response and prognosis following chemoradiotherapy. In our study, we investigated three SNVs that lead to amino acid class changes in regions involved in DNA substrate coordination: R145H, G163S, and R197C using an in vitro approach. Using biochemical assays and molecular dynamics simulations, we evaluated the thermal stability, DNA binding affinity, and glycosylase activity of AAG variants toward hypoxanthine (Hx) and 1,N6-ethenoadenosine (εA) containing substrates. The G163S variant showed reduced thermal stability due to the conformational strain in the β-hairpin loop that intercalates in DNA, but retained εA excision activity comparable to that of wild-type AAG, while losing activity against Hx-containing DNA. The R197C variant had a four-fold reduction in DNA binding affinity for both substrates, and was catalytically inactive, unable to excise either damaged bases. This loss of function correlated with the rearrangement of the 201-210 loop and the reorientation of Arg-201 and Arg-207, which disrupts critical DNA contacts. However, the R145H variant retained near-wild-type thermal stability and activity on both substrates, despite bioinformatic predictions of deleterious effect. Molecular dynamics simulations revealed variant-specific structural disruptions. The data obtained underscore the importance of experimental validation in assessing the functional impact SNVs.

DNA Glycosylases↗

PubMed2004

At the crossroads of myocardial signaling: the role of Z-discs in intracellular signaling and cardiac function.

Understanding the molecular interactions among components of cardiac Z-discs and their role in signaling has become pivotal in explaining long- and short-term regulation of cardiac function. In striated muscle, the ends of the thin filaments from opposing sarcomeres overlap and are cross-linked by an elaborate array of proteins to form a highly ordered, yet dynamic network that is the Z-disc. We review here a current picture of the function and structure of the Z-disc of mammalian cardiac myocytes. We emphasize provocative findings that advance new theories about the place of cardiac Z-discs in myocardial intra- and intercellular signaling in myocardial physiology and pathology. Relatively new approaches, especially yeast two-hybrid screens, immunoprecipitation, and pull down assays, as well as immunohistochemical analysis have significantly altered previous views of the protein content of the Z-disc. These studies have generally defined domain structure and binding partners for Z-disc proteins, but the functional significance of the binding network and of the domains in cardiac cell biology remains an unfolding story. Yet, even at the present level of understanding, perceptions of potential functions of the Z-disc proteins are expanding greatly and leading to new and exciting experimental approaches toward mechanistic understanding. The theme of the following discussion of these Z-disc proteins centers on their potential to function not only as a physical anchor for myofilament and cytoskeletal proteins, but also as a pivot for reception, transduction, and transmission of mechanical and biochemical signals.

Animals↗

PubMed2000

How to generate improved potentials for protein tertiary structure prediction: a lattice model study.

Success in the protein structure prediction problem relies heavily on the choice of an appropriate potential function. One approach toward extracting these potentials from a database of known protein structures is to maximize the Z-score of the database proteins, which represents the ability of the potential to discriminate correct from random conformations. These optimization methods model the entire distribution of alternative structures, reducing their ability to concentrate on the lowest energy structures most competitive with the native state and resulting in an unfortunate tendency to underestimate the repulsive interactions. This leads to reduced accuracy and predictive ability. Using a lattice model, we demonstrate how we can weight the distribution to suppress the contributions of the high-energy conformations to the Z-score calculation. The result is a potential that is more accurate and more likely to yield correct predictions than other Z-score optimization methods as well as potentials of mean force.

Algorithms↗