Gp41 coordinates - Homology model (PDB 598 kb)
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T CD4+ cells are central to the adaptive immune response against pathogens. Their activation is induced by the engagement of the T-cell receptor by antigens, and of co-stimulatory receptors by molecules also expressed on antigen... more
T CD4+ cells are central to the adaptive immune response against pathogens. Their activation is induced by the engagement of the T-cell receptor by antigens, and of co-stimulatory receptors by molecules also expressed on antigen presenting cells. Then, a complex network of intracellular events reinforce, diversify and regulate the initial signals, including dynamic metabolic processes that strongly influence both the activation state and the differentiation to effector cell phenotypes. The regulation of cell metabolism is controlled by the nutrient sensor adenosine monophosphate-activated protein kinase (AMPK), which drives the balance between oxidative phosphorylation (OXPHOS) and glycolysis. Herein, we put forward a 51-node continuous mathematical model that describes the temporal evolution of the early events of activation, integrating a circuit of metabolic regulation into the main routes of signaling. The model simulates the induction of anergy due to defective co-stimulation, ...
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Type 2 diabetes develops due to beta cell exhaustion with accompanying decrease in insulin secretion, leading to hyperglycemia and eventual damage of nerve, kidney, and eye tissues. It is usually preceded by metabolic alterations related... more
Type 2 diabetes develops due to beta cell exhaustion with accompanying decrease in insulin secretion, leading to hyperglycemia and eventual damage of nerve, kidney, and eye tissues. It is usually preceded by metabolic alterations related to insulin signaling, inflammatory pathways, or intracellular glucose processing, encompassed as metabolic syndrome. We propose a regulatory network for components of pancreatic-beta cells playing an essential role in the disease. The network interactions are expressed as continuous fuzzy logic propositions. The dynamical modeling of the network allows to portray the disease progression as a transit between steady states associated to health, metabolic syndrome, and diabetes, each state defined by specific expression patterns of the network components. Transitions between equilibrium states are due to altered expression or functional exhaustion associated to modifications of characteristic decay rates of cellular components. This approach let us ide...
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The interaction of the envelope glycoprotein of HIV-1 (gp120/gp41) with coreceptor molecules has important implications for specific cellular targeting and pathogenesis. Experimental and theoretical evidences have shown a role for gp41 in... more
The interaction of the envelope glycoprotein of HIV-1 (gp120/gp41) with coreceptor molecules has important implications for specific cellular targeting and pathogenesis. Experimental and theoretical evidences have shown a role for gp41 in coreceptor tropism, although there is no consensus about the positions involved. Here we analyze the association of physicochemical properties of gp41 amino acid residues with viral tropism (X4, R5, and R5X4) using a large set of HIV-1 sequences. Under the assumption that conserved regions define the complex structural features essential for protein function, we focused our search only on amino acids in the gp41 variable regions. Gp41 amino acid sequences of 2823 HIV-1 strains from all clades with known coreceptor tropism were retrieved from Los Alamos HIV Database. Consensus sequences were constructed for homologous sequences (those obtained from the same patient and having the same tropism) in order to avoid bias due to sequence overrepresentatio...
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The scalar quantum field uniformly moving plates in three dimensional space is studied. Field equations for Dirichlet boundary conditions are solved exactly. Comparison of the resulting wavefunctions with their instantaneous static... more
The scalar quantum field uniformly moving plates in three dimensional space is studied. Field equations for Dirichlet boundary conditions are solved exactly. Comparison of the resulting wavefunctions with their instantaneous static counterpart is performed via Bogolubov coefficients. Unlike the one dimensional problem, 'particle' creation as well as squeezing may occur. The time dependent Casimir energy is also evaluated.
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We present a theoretical study of the Casimir interaction between heavy Fermi metals that show strong electronic correlations below a critical temperature T c . Unlike noble metals like Au, these correlations lower the plasma frequency... more
We present a theoretical study of the Casimir interaction between heavy Fermi metals that show strong electronic correlations below a critical temperature T c . Unlike noble metals like Au, these correlations lower the plasma frequency and damping rate due to an increase in the electronic effective mass. Furthermore, the effective mass and damping are frequency dependent and related by causal relations, thus a zero damping or plasma-like description in the dielectric function of these materials is not possible. In this work we consider the heavy metals UPd2Al3 and UNi2Al3 and the compound CePd3, whose dielectric properties are constructed from available experimental data. In all cases, the magnitude of the Casimir force is measurable using current experimental devices.
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Recent interests in using Casimir forces for driving micro-machines and the precise measurement of these forces, has prompted an intense study of how is the Casimir effect affected by the geometry and dielectric properties of the... more
Recent interests in using Casimir forces for driving micro-machines and the precise measurement of these forces, has prompted an intense study of how is the Casimir effect affected by the geometry and dielectric properties of the surrounding media. Recent studies include the thermodynamic cycles of possible Casimir engines and the variation on the Casimir force due to the use of
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We studied the quantization of the electromagnetic field between moving boundaries in four dimensional spacetime. We considered the particular case of a field confined between two infinite conducting plates moving with constant relative... more
We studied the quantization of the electromagnetic field between moving boundaries in four dimensional spacetime. We considered the particular case of a field confined between two infinite conducting plates moving with constant relative velocity [1]. This motion produces a distortion of vacuum that can be interpreted as “particle production” . The work necessary is done at the expense of the Casimir energy of the system [2]. We evaluated the energy momentum tensor and its spectrum from the field correlations. We have also found that a vacuum or coherent state between the plates becomes squeezed. Analytic formulas for the Bogolubov and the squeezing coefficients [3] have been obtained. We analyzed the interaction of the “emitted photons” with a realistic quantum detector [4] and we have come to the conclusion that there is no spontaneous excitation of the detector. However, the spontaneous decay ratio shows strong oscillations as compared with the free case.
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Hawking radiaton by black holes [1] can be understood in terms of the Doppler distortion undergone by the modes of a quantum vacuum field in the presence of a gravitational source [2]. A very different phenomenum, the Casimir effect [3],... more
Hawking radiaton by black holes [1] can be understood in terms of the Doppler distortion undergone by the modes of a quantum vacuum field in the presence of a gravitational source [2]. A very different phenomenum, the Casimir effect [3], arises from the distortion of the vacuum produced by boundaries. Both phenomena have a common origin: they are manifestations of the restrictions that event horizons or physical boundaries impose to a quantum vacuum field. Such restrictions may confer to the vacuum state a complex structure. The vacuum structure will be analysed here for inertial and non-inertial observers in vacua confined by boundaries. Gravitational effects will be analysed elsewhere in this book by A. Sarmiento.
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ABSTRACTWe present a theoretical study of vacuum effects in systems of length scales of micrometers and nanometers. In particular, we calculate the Casimir force between dielectric plates with different compositions. We show that by an... more
ABSTRACTWe present a theoretical study of vacuum effects in systems of length scales of micrometers and nanometers. In particular, we calculate the Casimir force between dielectric plates with different compositions. We show that by an appropriate choice and configurations of materials, the Casimir forces develop noticeable changes than could be used to inhibit or modulate the action of vacuum fluctuations in MEMS and NEMS.
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ABSTRACTWe present a theoretical study of the modification of Casimir forces between nanocomposite slabs that exhibit a metal-dielectric transition. In particular, we consider slabs made of VO2 precipitates in sapphire, whose effective... more
ABSTRACTWe present a theoretical study of the modification of Casimir forces between nanocomposite slabs that exhibit a metal-dielectric transition. In particular, we consider slabs made of VO2 precipitates in sapphire, whose effective dielectric function is calculated within a mean field approximation. The results for the Casimir force as a function of the separation of the slabs, show that at a fixed separation the magnitude of the force changes as temperature increases from 300 K to 355 K. The possible applications of these results to Casimir devices is discussed.
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The thermodynamical properties of a quantized electromagnetic field inside a box with perfectly conducting walls are studied using a regularization scheme that permits to obtain finite expressions for the thermodynamic potentials. The... more
The thermodynamical properties of a quantized electromagnetic field inside a box with perfectly conducting walls are studied using a regularization scheme that permits to obtain finite expressions for the thermodynamic potentials. The source of ultraviolet divergences is directly isolated in the expression for the density of modes, and the logarithmic infrared divergences are regularized imposing the uniqueness of vacuum and, consequently, the vanishing of the entropy in the limit of zero temperature. We thus obtain corrections to the Casimir energy and pressures, and to the specific heat that are due to temperature effects; these results suggest effects that could be tested experimentally.
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We propose a systematic methodology to construct a probabilistic epigenetic landscape of cell-fate attainment associated with N-node Boolean genetic regulatory networks. The general derivation proposed here is exemplified with an... more
We propose a systematic methodology to construct a probabilistic epigenetic landscape of cell-fate attainment associated with N-node Boolean genetic regulatory networks. The general derivation proposed here is exemplified with an Arabidopsis thaliana network underlying floral organ determination grounded on qualitative experimental data.
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... How to Cite. Esquivel-Sirvent, R., Villarreal, C., Mochan, W. and Cocoletzi, G. (2002), Casimir Forces in Nanostructures. ... doi: 10.1002/1521-3951(200204)230:2<409::AID-PSSB409>3.0.CO; 2-M.... more
... How to Cite. Esquivel-Sirvent, R., Villarreal, C., Mochan, W. and Cocoletzi, G. (2002), Casimir Forces in Nanostructures. ... doi: 10.1002/1521-3951(200204)230:2<409::AID-PSSB409>3.0.CO; 2-M. Author Information. 1 ... Email: R. Esquivel-Sirvent (raul@fenix.fisica.unam.mx). ...
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We obtain expressions for the Casimir energy and force following an approach which may be applied to cavities made up of arbitrary materials. In the case of planar cavities we obtain the well known Lifshitz formula. The approach is easily... more
We obtain expressions for the Casimir energy and force following an approach which may be applied to cavities made up of arbitrary materials. In the case of planar cavities we obtain the well known Lifshitz formula. The approach is easily generalizable to other geometries.
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The quantum fluctuations of the electromagnetic field between two parallel plates at zero or finite temperature are analysed. The spectrum of the energy-momentum tensor and the two-point correlations of the field are obtained in analytic... more
The quantum fluctuations of the electromagnetic field between two parallel plates at zero or finite temperature are analysed. The spectrum of the energy-momentum tensor and the two-point correlations of the field are obtained in analytic form through the use of Hertz potentials in the Lorentz gauge. In particular, the general expression for the transition probability of atomic systems is explicitly
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Background Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes... more
Background Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of WOX5 and CLE40, also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN) models and addre...
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HIV-1 viral load is used to monitor AIDS progression and effect of antiretroviral therapy (ART). Several reports have indicated that the HIV-1 viral load of infected individuals is lower in females than in males. There are no reports... more
HIV-1 viral load is used to monitor AIDS progression and effect of antiretroviral therapy (ART). Several reports have indicated that the HIV-1 viral load of infected individuals is lower in females than in males. There are no reports exploring this issue in the Mexican population. We analyzed the relationship between sex and viral load in Mexican patients differing in CD4 T-cell count, age and treatment status. A retrospective study was performed in 3949 male and 696 female HIV-1-infected individuals. Statistical distributions were compared using the Mann-Whitney U nonparametric test. Among the antiretroviral-untreated group, females had a significantly lower viral load than males (0.52 female/male median viral load ratio, p = 0.008). When classified according to different ranges of CD4⁺ T cell counts, females had consistently lower viral loads than males, although statistical significance was achieved only for the group in the range of 201-350 (p = 0.014). Patients with the lowest CD4⁺ T-cell counts showed similar viral loads for both sexes. No differences were observed in the ART group. This study demonstrates a baseline difference in viral load between male and female ART-untreated Mexican patients. The overall tendency indicating a lower viral load in females in the same ranges of CD4⁺ T-cell counts than males, suggests that the lower viral load in females is not indicative of a lower risk of developing AIDS. These observations suggest a significant influence of sex on viral dynamics and immune response despite variations in demographic factors.
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The thermodynamical properties of a quantized electromagnetic field inside a box with perfectly conducting walls are studied using a regularization scheme that permits to obtain finite expressions for the thermodynamic potentials. The... more
The thermodynamical properties of a quantized electromagnetic field inside a box with perfectly conducting walls are studied using a regularization scheme that permits to obtain finite expressions for the thermodynamic potentials. The source of ultraviolet divergences is directly isolated in the expression for the density of modes, and the logarithmic infrared divergences are regularized imposing the uniqueness of vacuum and,
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Interactionin vitrobetween cells infected with human immunodeficiency virus (HIV) and surrounding, uninfected, target cells often leads to cell fusion and the formation of multinucleated cells, called syncytia. The presence in... more
Interactionin vitrobetween cells infected with human immunodeficiency virus (HIV) and surrounding, uninfected, target cells often leads to cell fusion and the formation of multinucleated cells, called syncytia. The presence in HIV-infected individuals of virus strains able to induce syncytia in cultures of T cells is associated with disease progression and AIDS. Even in the asymptomatic stage of infection, multinucleated cells have been observed in different organs, indicating that fused cells may be generated and remain viable in the tissues of patients. We used lymphocytic cells transfected for the expression of the HIV-envelope (Env) glycoproteins to develop a method for the direct quantification of fusion events by flow cytometry (Huerta et al., 2006,J. Virol. Methods138, 17–23; López-Balderas et al., 2007,Virus Res.123, 138–146). The method involves the staining of fusion partners with lipophilic probes and the use of fluorescence resonance energy transfer (FRET) to distinguish...