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Results for “Functional potential”

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PubMed2004

A LIM protein, Hic-5, functions as a potential coactivator for Sp1.

Hic-5 is a LIM protein with striking similarity to paxillin, and shuttles between focal adhesions and the nucleus. Our previous study suggested that Hic-5 participates in the transcriptional control of several genes such as the c-fos and p21 genes. In the present study, we examined the function of Hic-5 in the nucleus using the transcriptional promoter region of the p21 gene. When localized to the nucleus, Hic-5 was found to transactivate the p21 promoter through two of five Sp1 sites in the region proximal to the TATA box. The Hic-5 effect was mediated by a transactivation domain of Sp1 and functional interaction with p300 through the LIM4 domain. Hic-5 was also shown to interact functionally and physically with Smad3 through the LIM domains and to potentiate p21 promoter activity together with Smad3 and Sp1. These properties were confirmed in an artificial system using GAL4-fusion protein. Thus, Hic-5 was suggested to have a potential function as a cofactor in the transcriptional complex that contains Sp1, playing a role in gene transcription in the nucleus as well as in integrin signaling at focal adhesion sites.

Animals↗

PubMed1995

Coagulation factor XIa cleaves the RHDS sequence and abolishes the cell adhesive properties of the amyloid beta-protein.

Amyloid beta-protein (A beta) is the major constituent of senile plaques and cerebrovascular amyloid deposits in Alzheimer's disease and is proteolytically derived from its transmembrane parent protein the amyloid beta-protein precursor (A beta PP). Although the physiological role(s) of secreted A beta PPs are not fully understood, several potential functions have been described including the regulation of hemostatic enzymes factors XIa and IXa and a role in cell adhesion. In the present study, we investigated the proteolytic processing of A beta PP by factor XIa (FXIa). Incubation of the human glioblastoma cell line U138 stably transfected to overexpress the 695 isoform of A beta PP with FXIa (2.5-5 nM) resulted in proteolytic cleavage of secreted A beta PP. Higher concentrations of FXIa (> 25 nM) resulted in loss in cell adherence. Coincubation of FXIa with purified, recombinant Kunitz protease inhibitor domain of A beta PP blocked both the proteolytic processing of A beta PP and the loss of cell adhesion. The RHDS cell adhesion site of A beta PP resides within residues 5-8 of the A beta domain. Incubation of synthetic A beta 1-40 peptide with increasing concentrations of FXIa resulted in cleavage of A beta between Arg5 and His6 within the cell adhesion domain of the peptide. FXIa-digested A beta 1-40 or A beta PP695 lost their abilities to serve as cell adhesion substrates consistent with cleavage through this cell adhesion site. Together, these results suggest a new potential biological function for FXIa in the modulation of cell adhesion. In addition, we have shown that FXIa can proteolytically alter A beta and therefore possibly modify its physiological and perhaps pathological properties.

Amino Acid Sequence↗

PubMed2003

Troglitazone antagonizes tumor necrosis factor-alpha-induced reprogramming of adipocyte gene expression by inhibiting the transcriptional regulatory functions of NF-kappaB.

Troglitazone (TGZ), a member of the thiazolidinedione class of anti-diabetic compounds and a peroxisome proliferator activator receptor-gamma (PPAR-gamma) agonist, restores systemic insulin sensitivity and improves the full insulin resistance syndrome in vivo. The mechanisms underlying its in vivo function are not understood. Here we investigated the potential functional interaction between PPAR-gamma and NF-kappaB in adipocytes. We show that TGZ selectively blocked tumor necrosis factor-alpha-induced and NF-kappaB-dependent repression of multiple adipocyte-specific genes and induction of growth phase and other genes. This occurs without interfering with NF-kappaB expression, activation, nuclear translocation, or DNA binding and without suppressing NF-kappaB-dependent survival signals. Notably, the expressions of some tumor necrosis factor-alpha-induced genes in adipocytes were unaffected by PPAR-gamma activation. In reporter gene assays in HeLa cells, ectopic expression of PPAR-gamma abolished induction of a NF-kappaB-responsive reporter gene by the p65 subunit (RelA) of NF-kappaB, and the inhibition was further enhanced in the presence of TGZ. Conversely, overexpression of p65 inhibited induction of a PPAR-gamma-responsive reporter gene by activated PPAR-gamma in a dose-dependent manner. The inhibitory effect was independent of the presence of NF-kappaB-binding sites in the promoter region. Other NF-kappaB family members, p50 and c-Rel as well as the S276A mutant of p65, blocked PPAR-gamma-mediated gene transcription less effectively. Thus, p65 antagonizes the transcriptional regulatory activity of PPAR-gamma in adipocytes, and PPAR-gamma activation can at least partially override the inhibitory effects of p65 on the expression of key adipocyte genes. Our data suggest that inhibition of NF-kappaB activity is a mechanism by which PPAR-gamma agonists improve insulin sensitivity in vivo and that adipocyte NF-kappaB is a potential therapeutic target for obesity-linked type 2 diabetes.

3T3 Cells↗

PubMed1996

A human transforming growth factor-beta type II receptor that contains an insertion in the extracellular domain.

In the signal transduction of transforming growth factor-beta (TGF-beta), the TGF-beta type II receptor (betaR-II) binds TGF-beta, presents the ligand to type I receptor, and forms a heterodimeric receptor complex that functions as an active signaling receptor. We isolated cDNA clones encoding an isoform of human betaR-II from vascular endothelial cells by RT-PCR. The deduced structure of the isoform designated as betaR-IIb contained a 25-amino-acid residue inserted at the extracellular region. The insert exhibited 73% homology to a similar insertion found in a mouse betaR-II variant. BetaR-IIb mRNA was ubiquitously expressed in all human cell lines examined. BetaR-IIb as well as betaR-II stably expressed in betaR-II deficient DR26 cells acted as a functional receptor transducing signals from TGF-beta for growth inhibition and the transcriptional activation of the plasminogen activator inhibitor-1 promoter. These results indicated that the betaR-IIb expressed in mammalian cells functions indistinguishably from in betaR-II. The potential function of betaR-IIb is discussed.

Amino Acid Sequence↗

PubMed1996

Nonparametric density estimation applied to population pharmacokinetics.

Kinetic parameters are estimated to assess absorption, distribution, metabolism, and elimination of a drug in a subject. In a group of subjects, pharmacokinetic population studies are developed to describe the variability and to detect particular subsets by establishing the relationships between kinetic parameters and easily measurable subject characteristics, the covariates (age, body weight, etc.). The usually proposed methods are based on linear regression equations relating kinetic parameters to the covariates. We propose to measure these dependencies and describe the interindividual variability through the joint probability density function. This function is estimated by a nonparametric method superposing potential functions or kernels over the sample. In this estimation, the Shannon information theory was applied to determine the number of individuals needed to describe the variability reliably and to screen informative covariates with respect to the kinetic parameters. This approach was used to obtain the nonparametric conditional probability density functions of the kinetic parameters, given the covariates. These functions supplied prior information for a Bayesian estimation. The feasibility of the global approach was illustrated by a simulation in which nonlinear relations link covariates and pharmacokinetic parameters. The performance of this new estimator using covariates was compared with that of the usual Bayesian estimation.

Animals↗

PubMed2002

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models.

Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical structure and receptor docking mechanism are still not well understood. The conformational dynamics of this neuron peptide in liquid water are studied here by using all-atom molecular dynamics (MD) and implicit water Langevin dynamics (LD) simulations with AMBER potential functions and the three-site transferable intermolecular potential (TIP3P) model for water. To achieve the same simulation length in physical time, the full MD simulations require 200 times as much CPU time as the implicit water LD simulations. The solvent hydrophobicity and dielectric behavior are treated in the implicit solvent LD simulations by using a macroscopic solvation potential, a single dielectric constant, and atomic friction coefficients computed using the accessible surface area method with the TIP3P model water viscosity as determined here from MD simulations for pure TIP3P water. Both the local and the global dynamics obtained from the implicit solvent LD simulations agree very well with those from the explicit solvent MD simulations. The simulations provide insights into the conformational restrictions that are associated with the bioactivity of the opiate peptide dermorphin for the delta-receptor.

Biophysical Phenomena↗

PubMed2003

Common behavioral dilemmas of the school-aged child.

PCPs are typically the first professionals to come into contact with children who have behavioral or developmental problems. The most common behavioral concerns that PCPs encounter in the pediatric primary care setting include noncompliance, temper tantrums, and problems with eating and sleeping routines. To adequately detect these types of problems, it essential that PCPs incorporate behavioral assessment procedures (eg, clinical interviews, behavior rating scales, ABC recording form) into the consultation process. Behavioral assessment procedures are useful in identifying the environmental events (ie, antecedents and consequences) that may be maintaining the problem behavior. Data that are collected from behavioral assessment can be used to develop a tentative hypothesis on functions of the behavioral problem. By identifying the potential function of the behavior, more effective behavioral management strategies can be developed. An existing model of behavioral consultation can be used by PCPs during office visits to more effectively identify and manage many of the common and less severe behavioral problems.

Adolescent↗

PubMed2000

Terminal bronchiolar duct ending number does not increase post-natally in normal infants.

Organ development may be assessed by estimating the total number of functional units within an organ over time; the potential functional capacity of that organ may be represented by the total number of functional units present in the fully developed, mature organ. Relative development of the lung at birth is essential to provide sufficient oxygenation of body tissues and so maintain ex utero life. Estimation of the number of one type of functional unit of the lung - terminal bronchiolar duct endings - provides important information regarding development of the lung. This investigation used stereological techniques, specifically Cavalieri's Principle and the "physical disector", to estimate total number of terminal bronchiolar duct endings in the upper lobe of the right lung of a group of 14 control infants between 0 and 66 weeks post-natal age. Results demonstrate that total terminal bronchiolar duct ending number does not increase significantly over the first 24 weeks of post-natal life in normal infants (P=0.997). The unbiased, design-based techniques used in this paper confirm previous model-based research that indicates that terminal bronchiolar duct ending development is completed before birth.

Aging↗

PubMed1983

Theory and application of molecular potential energy fields in molecular shape analysis: a quantitative structure--activity relationship study of 2,4-diamino-5-benzylpyrimidines as dihydrofolate reductase inhibitors.

A general formalism, based upon molecular mechanics pairwise potential functions, has been developed to compute the molecular potential energy fields inherent to a given molecule in a given conformation. Molecular descriptors are derived from the potential energy fields, which can be used in QSAR studies based upon molecular shape analysis. These descriptors have been computed for a set of 2,4-diamino-5-benzylpyrimidines that are dihydrofolate reductase (DHFR) inhibitors. A QSAR is derived in which DHFR inhibition activity can be explained in terms of molecular shape, as represented by differences in molecular potential energy fields between pairs of superimposed molecules, and the sum of the pi constants of substituents on the 3- and 4-position of the benzyl ring. This QSAR is superior to one developed earlier (Hopfinger, A. J. J. Med. Chem. 1981, 24, 818) in which molecular shape is described by common overlap steric volume. Ancillary information defining the "active" conformation and electrostatic nature of the binding site are realized in the construction of the QSAR.

Escherichia coli↗

PubMedDate not supplied

Cortical area and species differences in dendritic spine morphology.

Dendritic spines receive most excitatory inputs in the neocortex and are morphologically very diverse. Recent evidence has demonstrated linear relationships between the size and length of dendritic spines and important features of its synaptic junction and time constants for calcium compartmentalisation. Therefore, the morphologies of dendritic spines can be directly interpreted functionally. We sought to explore whether there were potential differences in spine morphologies between areas and species that could reflect potential functional differences. For this purpose, we reconstructed and measured thousands of dendritic spines from basal dendrites of layer III pyramidal neurons from mouse temporal and occipital cortex and from human temporal cortex. We find systematic differences in spine densities, spine head size and spine neck length among areas and species. Human spines are systematically larger and longer and exist at higher densities than those in mouse cortex. Also, mouse temporal spines are larger than mouse occipital spines. We do not encounter any correlations between the size of the spine head and its neck length. Our data suggests that the average synaptic input is modulated according to cortical area and differs among species. We discuss the implications of these findings for common algorithms of cortical processing.

Adult↗

PubMed2004

Estrogens and the hair follicle.

While it is undisputed that estrogens (1 beta-estradiol, E2) are mainly involved in skin physiology and operate as potent hair growth modulators, our knowledge about the estrogen target cells in skin and exact signaling pathways is still very limited. The current review provides an overview of estrogen effects on hair follicle cycling, cutaneous expression of estrogen receptors, and potential functions of estrogens in hair biology. We discuss potential target genes of estrogen receptor-mediated signaling in the skin, explore the interplay of estrogens with other hormones, growth factors and enzymes, and define major open questions in this intriguing and far too long neglected area of hair research.

Animals↗

PubMed2001

MRG15 activates the B-myb promoter through formation of a nuclear complex with the retinoblastoma protein and the novel protein PAM14.

The MORF4-Related Gene on chromosome 15 (MRG15) is a member of a novel family of genes originally identified in studies to reveal cell senescence-inducing factors. MRG15 contains several predicted protein motifs, including a nuclear localization signal, a helix-loop-helix region, a leucine zipper, and a chromodomain. These motifs are commonly associated with transcription factors, suggesting that MRG15 may likewise function as a transcriptional regulator. To examine the potential function(s) of MRG15, we sought to identify cellular factors associated with this MRG family member. In this regard, we have found that both the retinoblastoma tumor suppressor (Rb) and a novel nuclear protein PAM14 (Protein Associated with MRG, 14 kDa) specifically associate with MRG15. We have further demonstrated that these interactions require the helix-loop-helix and leucine zipper domains of MRG15. Interestingly we have found all three proteins present in a multiprotein complex, suggesting that at least some of their functions may be interdependent. Although the functions of PAM14 have yet to be elucidated, Rb has several well characterized activities, including repression of E2F-activated promoters such as that of B-myb. Significantly we have demonstrated that MRG15 blocks the Rb-induced repression of this promoter, leading to B-myb promoter activation. Collectively these results suggest that MRG15 regulates transcription through interactions with a cellular protein complex containing Rb and PAM14.

Amino Acid Sequence↗

PubMed1981

Theoretical studies of the structure and energies of base-paired nucleotides and the dissociation kinetics of a proflavine-dinucleotide complex.

We presented calculations of base-paired dinucleoside phosphates and hexanucleoside pentaphosphates of varying compositions. Complete energy minimizations were performed for (a) the ten base-pair combinations of dinucleoside phosphates, starting from a B-DNA conformation, (b) six hexanucleoside pentaphosphates--base-paired CGCGCG, GCGCGC, G6-C6, TATATA, ATATAT, and A6-T6--starting with a B-DNA geometry, and (c) the four hexanucleoside pentaphosphates that have alternating pyrimidine-purine sequences, starting with a Z-DNA geometry. In addition, we studied the proflavine-base-paired CpG complex, using both complete energy minimization and energetic constraints to force the drug to dissociate from the dinucleoside phosphate. In many of these calculations, we examined the dependence of the calculated energies and structures on the potential function, focusing mainly on the effect of nonbonded potentials, the effective dielectric constant, and the role of counterions. These calculations allow us to explain why pur-(3',5')-pyr sequence isomers are more stable than pyr-(3'-5')-pur isomers. Both base-base and base-backbone energies are important in this differentiation, with the former being mainly van der Waals attraction and the latter mainly electrostatic energies. The calculations also allow us to understand the differences in double helical stabilities found by Wells et al. These differences, caused by electrostatic interactions between those bases not Watson-Crick hydrogen bonded, allow us to explain the following experimental data: poly(dG-dC) melts 12 degrees C higher than poly dG-poly dC, poly(dA-dT) melts 6 degrees C lower than poly dA-poly dT, and poly(dA-dG)-poly(dC-dT) melts 6 degrees C lower than poly(dA-dC)-poly(dT-dG). These results have interesting implications for drug binding: they imply that simple intercalators, such as ethidium, will exhibit a greater affinity for hetero- than for homopolymers and that this preference will be greater in the AT polymers than it is in the GC polymers. Our calculations allow us to explain the fact that Z-DNA is more stable than B-DNA under high salt conditions and to suggest some sequence dependence for the Z to B transition. We found that the activation energy for proflavine dissociating from dCpG is almost equal to the dissociation energy.

Acridines↗

PubMed1988

The role of monopolar stimulation during computed-tomography-guided stereotactic biopsies.

44 patients underwent intraoperative stimulation with a monopolar electrode prior to computed tomography (CT)-guided stereotactic biopsy. Stimulation at 2-100 Hz resulted in functional responses in 6/21 patients with subcortical or callosal lesions, 4/6 with basal ganglion lesions, 8/10 with thalamic and 4/4 with brainstem lesions. In all but 2 patients with mesencephalic lesions, where limited biopsy sites were available, an alternative biopsy site was used if a functional response was obtained. No morbidity was seen among these patients, although postbiopsy CT scans demonstrated small 3- to 7-mm hematomas in 5/11 patients. Retrospective review of 79 patients who underwent biopsies without stimulation demonstrated hematomas in 6/10 patients and a 3.3% transient surgical morbidity. These data indicate that postbiopsy hematomas are a relatively common occurrence, that intraoperative electrical stimulation within abnormal lesions can identify functional potential, and that avoidance of biopsies within these functional areas may be associated with reduced morbidity.

Biopsy↗

PubMed2026

Oral bacteriome in pediatric patients with malignancies prior to chemotherapy: a pilot study using full-length 16S rRNA sequencing.

OBJECTIVE: To characterize the composition, diversity, and ecological features of the oral bacteriome in pediatric patients with malignancies prior to chemotherapy initiation. METHODS: In this prospective pilot study,supragingival plaque samples were collected from 10 pediatric cancer patients prior to the initiation of chemotherapy. Bacterial genomic DNA was extracted from each sample, and the full-length 16S rRNA gene was amplified and sequenced on the PacBio Sequel II platform using circular consensus sequencing (CCS). Raw CCS reads were quality-filtered and denoised into amplicon sequence variants (ASVs) using DADA2, and taxonomic assignment was performed against the SILVA 138 reference database. Alpha diversity was assessed using the Chao1, Shannon, Simpson, and Faith's phylogenetic diversity (PD whole tree) indices, while beta diversity was evaluated through principal coordinate analysis (PCoA), and non-metric multidimensional scaling (NMDS). Microbial co-occurrence networks were constructed to characterize bacterial interactions, and functional potential was predicted using PICRUSt2, and BugBase. RESULTS: A total of 614,473 high-quality CCS reads were generated, yielding 1,697 ASVs. Alpha diversity analysis revealed substantial inter-individual variation in microbial richness and diversity among the pediatric cancer patients. The bacterial community was dominated by the phyla Firmicutes, Proteobacteria, Bacteroidota, Actinobacteriota. At the genus level, Streptococcus, Prevotella, Neisseria, and Haemophilus were the most abundant taxa. Beta diversity analysis revealed distinct clustering patterns, indicating highly individualized microbial profiles. Co-occurrence network analysis identified several keystone taxa and potential pathogenic associations within the supragingival plaque community. Functional prediction indicated that the dominant metabolic pathways were related to amino acid metabolism, carbohydrate metabolism, and membrane transport. CONCLUSION: These preliminary findings reveal a taxonomically diverse, highly individualized pre-chemotherapy oral bacteriome, providing foundational baseline profiles to guide future longitudinal investigations of chemotherapy-induced dysbiosis and personalized interventions.

Humans↗

PubMed1999

Use of contiguity on the chromosome to predict functional coupling.

The availability of a growing number of completely sequenced genomes opens new opportunities for understanding of complex biological systems. Success of genome-based biology will, to a large extent, depend on the development of new approaches and tools for efficient comparative analysis of the genomes and their organization. We have developed a technique for detecting possible functional coupling between genes based on detection of potential operons. The approach involves computation of "pairs of close bidirectional best hits", which are pairs of genes that apparently occur within operons in multiple genomes. Using these pairs, one can compose evidence (based on the number of distinct genomes and the phylogenetic distance between the orthologous pairs) that a pair of genes is potentially functionally coupled. The technique has revealed a surprisingly rich and apparently accurate set of functionally coupled genes. The approach depends on the use of a relatively large number of genomes, and the amount of detected coupling grows dramatically as the number of genomes increases.

Algorithms↗

PubMed1998

Tertiary structure prediction of mixed alpha/beta proteins via energy minimization.

We describe an improved algorithm for protein structure prediction, assuming that the location of secondary structural elements is known, with particular focus on prediction for proteins containing beta-strands. Hydrogen bonding terms are incorporated into the potential function, supplementing our previously developed residue-residue potential which is based on a combination of database statistics and an excluded volume term. Two small mixed alpha/beta proteins, 1-CTF and BPTI, are studied. In order to obtain native-like structures, it is necessary to allow the beta-strands in BPTI to distort substantially from an ideal geometry, and an automated algorithm to carry this out efficiently is presented. Simulated annealing Monte Carlo methods, which contain a genetic algorithm component as well, are used to produce an ensemble of low-energy structures. For both proteins, a cluster of structures with low RMS deviation from the native structure is generated and the energetic ranking of this cluster is in the top 2 or 3 clusters obtained from simulations. These results are encouraging with regard to the possibility of constructing a robust procedure for tertiary folding which is applicable to beta-strand containing proteins.

Algorithms↗

PubMed1992

Synaptic potentials and transfer functions of lamprey spinal neurons.

1. Electrotonic and chemical synaptic potentials were measured as a function of frequency of presynaptic action potentials. Over the frequency range from 0.02 to 10 Hz, the electrotonic synaptic potential was constant, while the chemical synaptic potential decreased in magnitude. Above 10 Hz, both synaptic events decreased in magnitude consistent with filtering by the dendritic structures. 2. Electrotonic synaptic transfer functions from 0.5 to 100 Hz were measured for the I1 reticulospinal Müller axon to spinal neuron electrotonic synaptic junction of the lamprey spinal cord using paired recordings from the pre-synaptic terminals and the post-synaptic neurons. In addition to this two-point synaptic transfer function, individual single point impedance functions of both the post-synaptic soma and the pre-synaptic axon terminal were measured. 3. The measured functions were interpreted with a computational model based on a three dimensional reconstruction of a Lucifer yellow filled motoneuron. Simulations of the model for a synaptic location of the I1 synapse were consistent with the measured synaptic transfer functions. 4. Synaptic potentials were simulated for inputs on dendrites near the I1 axon as well as distal dendritic regions. The high frequency filtering increased as the synaptic location was moved from the soma to the periphery, but the potential response on distal dendrites was larger than would have been predicted from the end of the equivalent cylinder of a Rall model that was used to fit soma impedance functions. 5. Electrotonic post-synaptic potentials were enhanced by the activation of a TTX-sensitive negative conductance.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗