We propose an efficient and simple method for fast conformational sampling by introducing the sol... more We propose an efficient and simple method for fast conformational sampling by introducing the solvent viscosity as a parameter to the conventional temperature replica exchange molecular dynamics (T-REMD) simulation method. The method, named V-REMD (V stands for viscosity), uses both low solvent viscosity and high temperature to enhance sampling for each replica; therefore it requires fewer replicas than the T-REMD method. To reduce the solvent viscosity by a factor of λ in a molecular dynamics simulation, one can simply reduce the mass of solvent molecules by a factor of λ2. This makes the method as simple as the conventional method. Moreover, thermodynamic and conformational properties of structures in replicas are still useful as long as one has sufficiently sampled the Boltzmann ensemble. The advantage of the present method has been demonstrated with the simulations of the trialanine, deca-alanine, and a 16-residue β-hairpin peptides. It shows that the method could reduce the number of replicas by a factor of 1.5 to 2 as compared with the T-REMD method.
One of the serious challenges is to develop a methodology for accurately estimating the configura... more One of the serious challenges is to develop a methodology for accurately estimating the configurational entropy of macromolecules. We propose an effective scheme by using a variable transformation approach in combination with the independent component analysis concept. The validity of the new approach is demonstrated by presenting results of alanine and β-hairpin peptides in aqueous solution. It is shown that the new method is very fast, simple but yields estimates of the entropy which are much closer to the exact entropy than previously available techniques.Developing a new method for calculating configurational entropy of complex molecules.
... Ellen HG Backus1, Phuong H. Nguyen2, Virgiliu Botan1, Rolf Pfister1, Alessandro Moretto3, Mar... more ... Ellen HG Backus1, Phuong H. Nguyen2, Virgiliu Botan1, Rolf Pfister1, Alessandro Moretto3, Marco Crisma3, Claudio Toniolo3, Gerhard Stock2, and Peter ... 3 Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzola 1, I ...
Molecular dynamic simulation has been done to determine the dynamic and local structure of liquid... more Molecular dynamic simulation has been done to determine the dynamic and local structure of liquid alumina at 3000K. Fourteen different systems at densities ranging from 2.5 to 4.5gcm−3 was prepared by compressing the low-density melt. Two kinds of pore aggregation, pore cluster and pore tube, were examined. Clear evidence was found of structural transformation from a tetrahedral to an octahedral
It has been shown in a recent analysis of the temperature dependence of the dc conductivity of th... more It has been shown in a recent analysis of the temperature dependence of the dc conductivity of the quasi-one-dimensional conductor (fluoranthene)2PF6 that in spite of the occurrence of the Peierls transition to a charge-density-wave ground state (formally implicating polarons as excitations), the dc conduction is essentially due to electron-hole transport in bands and acoustical phonon scattering of the carriers. The
The respiratory activities of oral streptococci grown in biofilms were found to be markedly repre... more The respiratory activities of oral streptococci grown in biofilms were found to be markedly repressed compared with those of cells from aerobic culture, or for Streptococcus mutans GS-5, even for those grown in static culture. Respiration rates generally reflected levels of NADH oxidase activities in cell extracts. Superoxide dismutase levels were somewhat reduced in biofilm cells. However, sensitivities to oxidative damage caused by H2O2, t-butylhydroperoxide, or 8-hydroxyquinoline were not greatly different for cells from suspension cultures and those from either intact or dispersed biofilms. The capacities of S. sanguis and S. gordonii to produce H2O2 also were markedly repressed by biofilm growth, and presumably this repression would affect the ecology of dental plaque by reducing oxidative stresses under crowded conditions.
Pregnane steroids have sedative and neuroprotective effects on the brain, due to interactions wit... more Pregnane steroids have sedative and neuroprotective effects on the brain, due to interactions with the steroid-binding site of the GABAA receptor. In the adult brain, synthesis of the pregnane steroids is increased in response to stress. Therefore, we have used umbilicoplacental embolization to mimic chronic placental insufficiency during late gestation in sheep, to investigate the expression of the steroidogenic enzymes p450scc, 5alpha-reductase type I (5alphaRI), 5alpha-reductase type II (5alphaRII), and allopregnanolone (AP) content in the fetal brain. Umbilicoplacental embolization was induced from 114 d gestation (term approximately 147 d) by daily injection of inert microspheres into the umbilical artery and continued for 17-23 d. Fetal arterial oxygen saturation was reduced to approximately 60% of the preembolization value in each fetus, with a significant reduction in blood arterial Po2, pH, and plasma glucose concentrations (p < 0.05) and a significant increase in blood arterial Pco2 and plasma lactate concentrations (p…
Neuroactive steroids may be synthesised in the brain either de novo from cholesterol or from bloo... more Neuroactive steroids may be synthesised in the brain either de novo from cholesterol or from blood-borne precursors. Concentrations of a GABA A receptor agonist, allopregnanolone, in the fetal brain exceed those in the circulation, and are markedly higher than adult brain concentrations. We used fetal hypophysectomy or adrenalectomy to elucidate the contribution of hypothalamic-pituitary factors and adrenal steroid secretion to the overall neuroactive steroid level in both the fetal brain and the fetal circulation. Hypophysectomy or adrenalectomy was performed between 108 and 112 days of gestation (term 147 days) and fetal tissues were collected at 140 days of gestation. Immunoreactive (ir) ACTH and cortisol in the plasma were significantly reduced after hypophysectomy, whereas adrenalectomy led to increased irACTH but significantly decreased cortisol concentrations, as expected. Brain concentrations of allopregnanolone, progesterone and pregnenolone did not change significantly in fetuses that underwent either hypophysectomy or adrenalectomy; however, concentrations in the plasma and content in the adrenal gland were decreased. Expression of cytochrome P450 scc and 5 -reductase type II (5 RII) in the brain, measured by western immunoblotting, did not change after either hypophysectomy or adrenalectomy but, after hypophysectomy, expression of P450 scc in the adrenal gland was significantly decreased and that of 5 RII remained unchanged. These findings suggest that the regulation of the neuroactive steroid content in the fetal brain is independent of adrenal steroidogenesis and hypothalamic-pituitary factors. Furthermore, the absence of a change in enzyme expression in the brain suggests that the control of the expression of these enzymes is independent of hypothalamic-pituitary factors. Thus local control mechanisms within the brain may be responsible for maintaining the high neurosteroid content present during fetal life, as these mechanisms are independent of adrenal steroid production.
A replica exchange molecular dynamics (REMD) simulation of a bicyclic azobenzene peptide in expli... more A replica exchange molecular dynamics (REMD) simulation of a bicyclic azobenzene peptide in explicit dimethyl sulfoxide solution is presented in order to characterize the conformational structures and energy landscape of a photoswitchable peptide. It is shown that an enhanced-sampling technique such as the REMD method is essential to obtain a converged conformational sampling of the peptide at room temperature. This is because conventional MD simulations of less than approximately 100-ns length are either trapped in local minima (at 295 K) or-if run at high temperature-do not resemble the room-temperature REMD results. Calculating various nuclear Overhauser effects (NOEs) and (3)J-couplings, a good overall agreement between the REMD simulations and the NMR experiments of Renner et al. (Biopolymers 2000;54:501-514) is found. In particular, the REMD study confirms the general picture drawn by Renner et al. that the trans-isomer of the azobenzene peptide exhibits a well-defined structure, while the cis-isomer is a conformational heterogeneous system; that is, the trans-isomer occurs in 2 well-defined conformers, while the cis-isomer represents an energetically frustrated system that leads to an ensemble of conformational structures. Employing a principal component analysis of the REMD data, the free energy landscape of the systems is studied at various temperatures. The implications for the folding and unfolding pathways of the system are discussed.
The anaerobic degradation of tetradecylamine and other long-chain alkylamines by a newly isolated... more The anaerobic degradation of tetradecylamine and other long-chain alkylamines by a newly isolated denitrifying bacterium was studied. Strain ZN6 was isolated from a mixture of soil and active sludge and was identified as representing Pseudomonas stutzeri, based on partial 16S rRNA gene sequence analysis. Strain ZN6 was a mesophilic, motile, Gram-negative rod-shaped bacterium and was able to grow on a variety of compounds including even-numbered primary fatty amines with alkyl chains ranging from C 4 to C 18 coupled to nitrate reduction. Alkylamines were used as sole carbon, energy and nitrogen source and were completely mineralized. Nitrate was dissimilated by ZN6 to nitrite. When strain ZN6 was grown under nitrate limitation, nitrite was slowly dissimilated further. When cocultivated with the complete denitrifier Castellaniella defragens ZN3, anaerobic degradation under denitrifying of alkylamines by strain ZN6 was slightly faster. Strain ZN3 is a complete denitrifier, unable to convert tetradecylamine, and was copurified from the same enrichment culture as strain ZN6. The proposed pathway for the degradation of alkylamines in strain ZN6 starts with C-N cleavages to alkanals and further oxidation to the corresponding fatty acids.
Despite technical advancement, treatment of congenital alveolar clefts has remained controversial... more Despite technical advancement, treatment of congenital alveolar clefts has remained controversial. Currently, primary alveolar cleft repair (i.e., gingivoperiosteoplasty) has a 41 to 73 percent success rate. However, the remaining patients have persistent alveolar bone defects requiring secondary grafting procedures. Morbidity of secondary procedures includes pain, graft resorption, extrusion or infection, and graft or tooth loss. The authors present a novel rat alveolar defect model designed to facilitate investigation of therapeutics aimed at improving bone formation following primary alveolar cleft repair in humans. Sixteen 8-week-old Sprague-Dawley rats underwent creation of a 7 x 4 x 3-mm complete alveolar defect from the maxillary incisors to the zygomatic arch. Four animals were humanely killed at each of the following time points: 0, 4, 8, and 12 weeks. Morphometric analysis of the alveolar defect was determined by means of micro-computed tomography and histology. Micro-computed tomography demonstrated that new bone filled 43 +/- 5.6 percent of the alveolar defect at 4 weeks, 53 +/- 8.3 percent at 8 weeks, and 48 +/- 3.5 percent at 12 weeks. Histologically, at 4 weeks, proliferating fibroblasts and polymorphonuclear cells were scattered throughout the disorganized collagen in the intercalary gap. By 8 weeks, nascent woven bone spicules extended from the edges of the defect. At 12 weeks, the woven spicules had remodeled, with scant additional bone deposition. This model creates a critical-size alveolar defect that is similar in size and location to human alveolar defects and is suitable for studying proposed therapeutics.
Toxicological sciences : an official journal of the Society of Toxicology, 2010
We employed the suppressive subtractive hybridization to identify 41 up-and downregulated transcr... more We employed the suppressive subtractive hybridization to identify 41 up-and downregulated transcripts in Jurkat cells after benzo[a]pyrene (BaP) treatment. Among the 21 downregulated transcripts, we found that BaP suppresses the Keap1 transcript by 7.5-fold. Subsequent analyses revealed that BaP significantly suppresses the Keap1 message and protein levels to about 40 and 60%, respectively, of the vehicle controls in Jurkat cells without reactive oxygen species involvement. In addition, the nuclear Nrf2 (nuclear factor erythroid 2-related factor) protein content is significantly increased by 2.6-fold. The same BaP treatment to Hepa1c1c7 cells also downregulates the Keap1 message and protein levels to a similar extent. When we treated Jurkat cells with 3-(4-morpholinyl)propyl isothiocyanate, which is known to increase the amount of the Nrf2 content, we found that there is no change in the Keap1 message, but the amount of the Keap1 (kelch-like ECH-associated protein 1) protein is reduced to 75% of the vehicle controls. Although both Nrf2 target messages nqo1 and gstp1 are upregulated by BaP in Jurkat cells, only GSTP1 is upregulated at the protein level. Unlike Hepa1c1c7 cells, Jurkat cells have no detectable aryl hydrocarbon receptor and BaP metabolites, minimal CYP1A1 activity, and no quinone oxidoreductase 1 (NQO1) activity. We concluded that BaP, but not its metabolites, increases the amount of the nuclear Nrf2 protein by downregulating the Keap1 message in Jurkat cells.
Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society
Diabetes is characterized by several poorly understood phenomena including dysfunctional wound he... more Diabetes is characterized by several poorly understood phenomena including dysfunctional wound healing and impaired vasculogenesis. P53, a master cell cycle regulator, is upregulated in diabetic wounds and has recently been shown to play regulatory roles in vasculogenic pathways. We have previously described a novel method to topically silence target genes in a wound bed with siRNA. We hypothesized that silencing p53 results in improved diabetic wound healing and augmentation of vasculogenic mediators. Paired 4-mm stented wounds were created on diabetic db/db mice. Topically applied p53 siRNA, evenly distributed in an agarose matrix, was applied to wounds at post-wound day 1 and 7 (matrix alone and nonsense siRNA served as controls). Animals were sacrificed at post-wound days 10 and 24. Wound time to closure was photometrically assessed, and wounds were harvested for histology, immunohistochemistry, and immunofluorescence. Vasculogenic cytokine expression was evaluated via western blot, RT-PCR, and ELISA. ANOVA/t-test was used to determine significance (p<=0.05). Local p53 silencing resulted in faster wound healing with wound closure at 18 ± 1.3d in the treated group versus 28 ± 1.0d in controls. The treated group demonstrated improved wound architecture at each time point while demonstrating near complete local p53 knockdown. Moreover, treated wounds showed a 1.92 fold increase in CD31 endothelial cell staining over controls. Western blot analysis confirmed near complete p53 knockdown in treated wounds. At day 10, VEGF secretion (ELISA) was significantly increased in treated wounds (109.3 ± 13.9 pg/ml) versus controls (33.0 ± 3.8 pg/ml) while RT-PCR demonstrated a 1.86 fold increase in SDF-1 expression in treated wounds versus controls. This profile was reversed after treated wounds healed and prior to closure of controls (day 24). Augmented vasculogenic cytokine profile and endothelial cell markers are associated with improved diabetic wound healing in topical gene therapy with p53 siRNA.
The loss of E-cadherin and the gain of N-cadherin expression are known as &amp;amp;amp;amp;am... more The loss of E-cadherin and the gain of N-cadherin expression are known as &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;cadherin…
The increasing prevalence of dental caries is making it more of a major world health problem. Car... more The increasing prevalence of dental caries is making it more of a major world health problem. Caries is the direct result of acid production by cariogenic oral bacteria, especially Streptococcus mutans. New and better antimicrobial agents active against cariogenic bacteria are badly needed, especially natural agents derived directly from plants. We have evaluated the inhibitory actions of α-mangostin, a xanthone purified from ethanolic extracts of the tropical plant Garcinia mangostana L., by repeated silica gel chromatography. α-Mangostin was found to be a potent inhibitor of acid production by S. mutans UA159, active against membrane enzymes, including the F(H+)-ATPase and the phosphoenolpyruvate - sugar phosphotransferase system. α-Mangostin also inhibited the glycolytic enzymes aldolase, glyceraldehyde-3-phosphate dehydrogenase, and lactic dehydrogenase. Glycolysis by intact cells in suspensions or biofilms was inhibited by α-mangostin at concentrations of 12 and 120 µmol·L⁻¹, respectively, in a pH-dependent manner, with greater potency at lower pH values. Other targets for inhibition by α-mangostin included (i) malolactic fermentation, involved in alkali production from malate, and (ii) NADH oxidase, the major respiratory enzyme for S. mutans. The overall conclusion is that α-mangostin is a multitarget inhibitor of mutans streptococci and may be useful as an anticaries agent.
SOJOURN: Journal of Social Issues in Southeast Asia, 2002
... 221-48 Looking Beyond Bien Che: The Considerations of Young Vietnamese Graduates When Seeking... more ... 221-48 Looking Beyond Bien Che: The Considerations of Young Vietnamese Graduates When Seeking Employment in the Doi Moi Era ... the conceptof bien che. To start with a definition, bienche is &amp;quot;the number of people who officially work in an organization, or a state-...
We consider optimal control problems for convection-diffusion equations with a pointwise control ... more We consider optimal control problems for convection-diffusion equations with a pointwise control or a control localized on a smooth manifold. We prove optimality conditions for the control variable and for the position of the control. We do not suppose that the coefficient of the convection term is regular or bounded, we only suppose that it has the regularity of strong solutions of the Navier-Stokes equations. We consider functionals with an observation on the gradient of the state. To obtain optimality conditions we have to prove that the trace of the adjoint state on the control manifold belongs to the dual of the control space. To study the state equation, which is an equation with measures as data, and the adjoint equation, which involves the divergence of L p -vector fields, we first study equations without convection term, and we next use a fixed point method to deal with the complete equations.
We propose an efficient and simple method for fast conformational sampling by introducing the sol... more We propose an efficient and simple method for fast conformational sampling by introducing the solvent viscosity as a parameter to the conventional temperature replica exchange molecular dynamics (T-REMD) simulation method. The method, named V-REMD (V stands for viscosity), uses both low solvent viscosity and high temperature to enhance sampling for each replica; therefore it requires fewer replicas than the T-REMD method. To reduce the solvent viscosity by a factor of λ in a molecular dynamics simulation, one can simply reduce the mass of solvent molecules by a factor of λ2. This makes the method as simple as the conventional method. Moreover, thermodynamic and conformational properties of structures in replicas are still useful as long as one has sufficiently sampled the Boltzmann ensemble. The advantage of the present method has been demonstrated with the simulations of the trialanine, deca-alanine, and a 16-residue β-hairpin peptides. It shows that the method could reduce the number of replicas by a factor of 1.5 to 2 as compared with the T-REMD method.
One of the serious challenges is to develop a methodology for accurately estimating the configura... more One of the serious challenges is to develop a methodology for accurately estimating the configurational entropy of macromolecules. We propose an effective scheme by using a variable transformation approach in combination with the independent component analysis concept. The validity of the new approach is demonstrated by presenting results of alanine and β-hairpin peptides in aqueous solution. It is shown that the new method is very fast, simple but yields estimates of the entropy which are much closer to the exact entropy than previously available techniques.Developing a new method for calculating configurational entropy of complex molecules.
... Ellen HG Backus1, Phuong H. Nguyen2, Virgiliu Botan1, Rolf Pfister1, Alessandro Moretto3, Mar... more ... Ellen HG Backus1, Phuong H. Nguyen2, Virgiliu Botan1, Rolf Pfister1, Alessandro Moretto3, Marco Crisma3, Claudio Toniolo3, Gerhard Stock2, and Peter ... 3 Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzola 1, I ...
Molecular dynamic simulation has been done to determine the dynamic and local structure of liquid... more Molecular dynamic simulation has been done to determine the dynamic and local structure of liquid alumina at 3000K. Fourteen different systems at densities ranging from 2.5 to 4.5gcm−3 was prepared by compressing the low-density melt. Two kinds of pore aggregation, pore cluster and pore tube, were examined. Clear evidence was found of structural transformation from a tetrahedral to an octahedral
It has been shown in a recent analysis of the temperature dependence of the dc conductivity of th... more It has been shown in a recent analysis of the temperature dependence of the dc conductivity of the quasi-one-dimensional conductor (fluoranthene)2PF6 that in spite of the occurrence of the Peierls transition to a charge-density-wave ground state (formally implicating polarons as excitations), the dc conduction is essentially due to electron-hole transport in bands and acoustical phonon scattering of the carriers. The
The respiratory activities of oral streptococci grown in biofilms were found to be markedly repre... more The respiratory activities of oral streptococci grown in biofilms were found to be markedly repressed compared with those of cells from aerobic culture, or for Streptococcus mutans GS-5, even for those grown in static culture. Respiration rates generally reflected levels of NADH oxidase activities in cell extracts. Superoxide dismutase levels were somewhat reduced in biofilm cells. However, sensitivities to oxidative damage caused by H2O2, t-butylhydroperoxide, or 8-hydroxyquinoline were not greatly different for cells from suspension cultures and those from either intact or dispersed biofilms. The capacities of S. sanguis and S. gordonii to produce H2O2 also were markedly repressed by biofilm growth, and presumably this repression would affect the ecology of dental plaque by reducing oxidative stresses under crowded conditions.
Pregnane steroids have sedative and neuroprotective effects on the brain, due to interactions wit... more Pregnane steroids have sedative and neuroprotective effects on the brain, due to interactions with the steroid-binding site of the GABAA receptor. In the adult brain, synthesis of the pregnane steroids is increased in response to stress. Therefore, we have used umbilicoplacental embolization to mimic chronic placental insufficiency during late gestation in sheep, to investigate the expression of the steroidogenic enzymes p450scc, 5alpha-reductase type I (5alphaRI), 5alpha-reductase type II (5alphaRII), and allopregnanolone (AP) content in the fetal brain. Umbilicoplacental embolization was induced from 114 d gestation (term approximately 147 d) by daily injection of inert microspheres into the umbilical artery and continued for 17-23 d. Fetal arterial oxygen saturation was reduced to approximately 60% of the preembolization value in each fetus, with a significant reduction in blood arterial Po2, pH, and plasma glucose concentrations (p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.05) and a significant increase in blood arterial Pco2 and plasma lactate concentrations (p…
Neuroactive steroids may be synthesised in the brain either de novo from cholesterol or from bloo... more Neuroactive steroids may be synthesised in the brain either de novo from cholesterol or from blood-borne precursors. Concentrations of a GABA A receptor agonist, allopregnanolone, in the fetal brain exceed those in the circulation, and are markedly higher than adult brain concentrations. We used fetal hypophysectomy or adrenalectomy to elucidate the contribution of hypothalamic-pituitary factors and adrenal steroid secretion to the overall neuroactive steroid level in both the fetal brain and the fetal circulation. Hypophysectomy or adrenalectomy was performed between 108 and 112 days of gestation (term 147 days) and fetal tissues were collected at 140 days of gestation. Immunoreactive (ir) ACTH and cortisol in the plasma were significantly reduced after hypophysectomy, whereas adrenalectomy led to increased irACTH but significantly decreased cortisol concentrations, as expected. Brain concentrations of allopregnanolone, progesterone and pregnenolone did not change significantly in fetuses that underwent either hypophysectomy or adrenalectomy; however, concentrations in the plasma and content in the adrenal gland were decreased. Expression of cytochrome P450 scc and 5 -reductase type II (5 RII) in the brain, measured by western immunoblotting, did not change after either hypophysectomy or adrenalectomy but, after hypophysectomy, expression of P450 scc in the adrenal gland was significantly decreased and that of 5 RII remained unchanged. These findings suggest that the regulation of the neuroactive steroid content in the fetal brain is independent of adrenal steroidogenesis and hypothalamic-pituitary factors. Furthermore, the absence of a change in enzyme expression in the brain suggests that the control of the expression of these enzymes is independent of hypothalamic-pituitary factors. Thus local control mechanisms within the brain may be responsible for maintaining the high neurosteroid content present during fetal life, as these mechanisms are independent of adrenal steroid production.
A replica exchange molecular dynamics (REMD) simulation of a bicyclic azobenzene peptide in expli... more A replica exchange molecular dynamics (REMD) simulation of a bicyclic azobenzene peptide in explicit dimethyl sulfoxide solution is presented in order to characterize the conformational structures and energy landscape of a photoswitchable peptide. It is shown that an enhanced-sampling technique such as the REMD method is essential to obtain a converged conformational sampling of the peptide at room temperature. This is because conventional MD simulations of less than approximately 100-ns length are either trapped in local minima (at 295 K) or-if run at high temperature-do not resemble the room-temperature REMD results. Calculating various nuclear Overhauser effects (NOEs) and (3)J-couplings, a good overall agreement between the REMD simulations and the NMR experiments of Renner et al. (Biopolymers 2000;54:501-514) is found. In particular, the REMD study confirms the general picture drawn by Renner et al. that the trans-isomer of the azobenzene peptide exhibits a well-defined structure, while the cis-isomer is a conformational heterogeneous system; that is, the trans-isomer occurs in 2 well-defined conformers, while the cis-isomer represents an energetically frustrated system that leads to an ensemble of conformational structures. Employing a principal component analysis of the REMD data, the free energy landscape of the systems is studied at various temperatures. The implications for the folding and unfolding pathways of the system are discussed.
The anaerobic degradation of tetradecylamine and other long-chain alkylamines by a newly isolated... more The anaerobic degradation of tetradecylamine and other long-chain alkylamines by a newly isolated denitrifying bacterium was studied. Strain ZN6 was isolated from a mixture of soil and active sludge and was identified as representing Pseudomonas stutzeri, based on partial 16S rRNA gene sequence analysis. Strain ZN6 was a mesophilic, motile, Gram-negative rod-shaped bacterium and was able to grow on a variety of compounds including even-numbered primary fatty amines with alkyl chains ranging from C 4 to C 18 coupled to nitrate reduction. Alkylamines were used as sole carbon, energy and nitrogen source and were completely mineralized. Nitrate was dissimilated by ZN6 to nitrite. When strain ZN6 was grown under nitrate limitation, nitrite was slowly dissimilated further. When cocultivated with the complete denitrifier Castellaniella defragens ZN3, anaerobic degradation under denitrifying of alkylamines by strain ZN6 was slightly faster. Strain ZN3 is a complete denitrifier, unable to convert tetradecylamine, and was copurified from the same enrichment culture as strain ZN6. The proposed pathway for the degradation of alkylamines in strain ZN6 starts with C-N cleavages to alkanals and further oxidation to the corresponding fatty acids.
Despite technical advancement, treatment of congenital alveolar clefts has remained controversial... more Despite technical advancement, treatment of congenital alveolar clefts has remained controversial. Currently, primary alveolar cleft repair (i.e., gingivoperiosteoplasty) has a 41 to 73 percent success rate. However, the remaining patients have persistent alveolar bone defects requiring secondary grafting procedures. Morbidity of secondary procedures includes pain, graft resorption, extrusion or infection, and graft or tooth loss. The authors present a novel rat alveolar defect model designed to facilitate investigation of therapeutics aimed at improving bone formation following primary alveolar cleft repair in humans. Sixteen 8-week-old Sprague-Dawley rats underwent creation of a 7 x 4 x 3-mm complete alveolar defect from the maxillary incisors to the zygomatic arch. Four animals were humanely killed at each of the following time points: 0, 4, 8, and 12 weeks. Morphometric analysis of the alveolar defect was determined by means of micro-computed tomography and histology. Micro-computed tomography demonstrated that new bone filled 43 +/- 5.6 percent of the alveolar defect at 4 weeks, 53 +/- 8.3 percent at 8 weeks, and 48 +/- 3.5 percent at 12 weeks. Histologically, at 4 weeks, proliferating fibroblasts and polymorphonuclear cells were scattered throughout the disorganized collagen in the intercalary gap. By 8 weeks, nascent woven bone spicules extended from the edges of the defect. At 12 weeks, the woven spicules had remodeled, with scant additional bone deposition. This model creates a critical-size alveolar defect that is similar in size and location to human alveolar defects and is suitable for studying proposed therapeutics.
Toxicological sciences : an official journal of the Society of Toxicology, 2010
We employed the suppressive subtractive hybridization to identify 41 up-and downregulated transcr... more We employed the suppressive subtractive hybridization to identify 41 up-and downregulated transcripts in Jurkat cells after benzo[a]pyrene (BaP) treatment. Among the 21 downregulated transcripts, we found that BaP suppresses the Keap1 transcript by 7.5-fold. Subsequent analyses revealed that BaP significantly suppresses the Keap1 message and protein levels to about 40 and 60%, respectively, of the vehicle controls in Jurkat cells without reactive oxygen species involvement. In addition, the nuclear Nrf2 (nuclear factor erythroid 2-related factor) protein content is significantly increased by 2.6-fold. The same BaP treatment to Hepa1c1c7 cells also downregulates the Keap1 message and protein levels to a similar extent. When we treated Jurkat cells with 3-(4-morpholinyl)propyl isothiocyanate, which is known to increase the amount of the Nrf2 content, we found that there is no change in the Keap1 message, but the amount of the Keap1 (kelch-like ECH-associated protein 1) protein is reduced to 75% of the vehicle controls. Although both Nrf2 target messages nqo1 and gstp1 are upregulated by BaP in Jurkat cells, only GSTP1 is upregulated at the protein level. Unlike Hepa1c1c7 cells, Jurkat cells have no detectable aryl hydrocarbon receptor and BaP metabolites, minimal CYP1A1 activity, and no quinone oxidoreductase 1 (NQO1) activity. We concluded that BaP, but not its metabolites, increases the amount of the nuclear Nrf2 protein by downregulating the Keap1 message in Jurkat cells.
Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society
Diabetes is characterized by several poorly understood phenomena including dysfunctional wound he... more Diabetes is characterized by several poorly understood phenomena including dysfunctional wound healing and impaired vasculogenesis. P53, a master cell cycle regulator, is upregulated in diabetic wounds and has recently been shown to play regulatory roles in vasculogenic pathways. We have previously described a novel method to topically silence target genes in a wound bed with siRNA. We hypothesized that silencing p53 results in improved diabetic wound healing and augmentation of vasculogenic mediators. Paired 4-mm stented wounds were created on diabetic db/db mice. Topically applied p53 siRNA, evenly distributed in an agarose matrix, was applied to wounds at post-wound day 1 and 7 (matrix alone and nonsense siRNA served as controls). Animals were sacrificed at post-wound days 10 and 24. Wound time to closure was photometrically assessed, and wounds were harvested for histology, immunohistochemistry, and immunofluorescence. Vasculogenic cytokine expression was evaluated via western blot, RT-PCR, and ELISA. ANOVA/t-test was used to determine significance (p<=0.05). Local p53 silencing resulted in faster wound healing with wound closure at 18 ± 1.3d in the treated group versus 28 ± 1.0d in controls. The treated group demonstrated improved wound architecture at each time point while demonstrating near complete local p53 knockdown. Moreover, treated wounds showed a 1.92 fold increase in CD31 endothelial cell staining over controls. Western blot analysis confirmed near complete p53 knockdown in treated wounds. At day 10, VEGF secretion (ELISA) was significantly increased in treated wounds (109.3 ± 13.9 pg/ml) versus controls (33.0 ± 3.8 pg/ml) while RT-PCR demonstrated a 1.86 fold increase in SDF-1 expression in treated wounds versus controls. This profile was reversed after treated wounds healed and prior to closure of controls (day 24). Augmented vasculogenic cytokine profile and endothelial cell markers are associated with improved diabetic wound healing in topical gene therapy with p53 siRNA.
The loss of E-cadherin and the gain of N-cadherin expression are known as &amp;amp;amp;amp;am... more The loss of E-cadherin and the gain of N-cadherin expression are known as &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;cadherin…
The increasing prevalence of dental caries is making it more of a major world health problem. Car... more The increasing prevalence of dental caries is making it more of a major world health problem. Caries is the direct result of acid production by cariogenic oral bacteria, especially Streptococcus mutans. New and better antimicrobial agents active against cariogenic bacteria are badly needed, especially natural agents derived directly from plants. We have evaluated the inhibitory actions of α-mangostin, a xanthone purified from ethanolic extracts of the tropical plant Garcinia mangostana L., by repeated silica gel chromatography. α-Mangostin was found to be a potent inhibitor of acid production by S. mutans UA159, active against membrane enzymes, including the F(H+)-ATPase and the phosphoenolpyruvate - sugar phosphotransferase system. α-Mangostin also inhibited the glycolytic enzymes aldolase, glyceraldehyde-3-phosphate dehydrogenase, and lactic dehydrogenase. Glycolysis by intact cells in suspensions or biofilms was inhibited by α-mangostin at concentrations of 12 and 120 µmol·L⁻¹, respectively, in a pH-dependent manner, with greater potency at lower pH values. Other targets for inhibition by α-mangostin included (i) malolactic fermentation, involved in alkali production from malate, and (ii) NADH oxidase, the major respiratory enzyme for S. mutans. The overall conclusion is that α-mangostin is a multitarget inhibitor of mutans streptococci and may be useful as an anticaries agent.
SOJOURN: Journal of Social Issues in Southeast Asia, 2002
... 221-48 Looking Beyond Bien Che: The Considerations of Young Vietnamese Graduates When Seeking... more ... 221-48 Looking Beyond Bien Che: The Considerations of Young Vietnamese Graduates When Seeking Employment in the Doi Moi Era ... the conceptof bien che. To start with a definition, bienche is &amp;quot;the number of people who officially work in an organization, or a state-...
We consider optimal control problems for convection-diffusion equations with a pointwise control ... more We consider optimal control problems for convection-diffusion equations with a pointwise control or a control localized on a smooth manifold. We prove optimality conditions for the control variable and for the position of the control. We do not suppose that the coefficient of the convection term is regular or bounded, we only suppose that it has the regularity of strong solutions of the Navier-Stokes equations. We consider functionals with an observation on the gradient of the state. To obtain optimality conditions we have to prove that the trace of the adjoint state on the control manifold belongs to the dual of the control space. To study the state equation, which is an equation with measures as data, and the adjoint equation, which involves the divergence of L p -vector fields, we first study equations without convection term, and we next use a fixed point method to deal with the complete equations.
Uploads
Papers by Phuong Nguyen