Biomedical subjects

Hua Guo

Publications and source records attributed to Hua Guo.

At least 19 recordsLinked to original sources

PubMed2006

Quantum dynamics of the H + O2 --> O + OH reaction on an accurate ab initio potential energy surface.

We report exact time-dependent and time-independent quantum mechanical studies of the title reaction on an accurate ab initio potential energy surface of Xu et al. (J. Chem. Phys. 2005, 122, 24305). The J = 0 reaction probabilities for several reactant states show sharp resonance structures superimposed on relatively low backgrounds, and they are remarkably different from existing quantum results on an earlier potential energy surface (DMBE-IV). The new findings reported here suggest that our current understanding of this important reaction might require significant revision.

Letter↗

PubMed2006

Time squared: repeated measures on phylogenies.

Studies of gene expression profiles in response to external perturbation generate repeated measures data that generally follow nonlinear curves. To explore the evolution of such profiles across a gene family, we introduce phylogenetic repeated measures (PR) models. These models draw strength from 2 forms of correlation in the data. Through gene duplication, the family's evolutionary relatedness induces the first form. The second is the correlation across time points within taxonic units, individual genes in this example. We borrow a Brownian diffusion process along a given phylogenetic tree to account for the relatedness and co-opt a repeated measures framework to model the latter. Through simulation studies, we demonstrate that repeated measures models outperform the previously available approaches that consider the longitudinal observations or their differences as independent and identically distributed by using deviance information criteria as Bayesian model selection tools; PR models that borrow phylogenetic information also perform better than nonphylogenetic repeated measures models when appropriate. We then analyze the evolution of gene expression in the yeast kinase family using splines to estimate nonlinear behavior across 3 perturbation experiments. Again, the PR models outperform previous approaches and afford the prediction of ancestral expression profiles. To demonstrate PR model applicability more generally, we conclude with a short examination of variation in brain development across 4 primate species.

Algorithms↗

PubMed2006

Hypoxia influences vasculogenic mimicry channel formation and tumor invasion-related protein expression in melanoma.

BACKGROUND: Hypoxia can enhance tumor cell invasion and metastasis. The cause and the molecular mechanism are still not clear. METHODS: In our study, mouse melanoma B16 cells were inoculated into mouse ischemic limbs and non-ischemic controls and the engrafted melanomas were subsequently observed. Vasculogenic mimicry channels in melanoma tumors of the two groups were counted and the expression of HIF-1alpha, MMP-2, MMP-9 and VEGF was assessed by immunohistochemical staining. Formalin-fixed, paraffin-embedded tissues were used for immunohistochemical staining. RESULTS: In the early stage of engrafted melanoma growth, the size of melanomas in ischemic limbs increased slower than in the controls. However, later there was no obvious difference in their size. Melanoma tumors in the ischemic group had more vasculogenic mimicry channels than those in the controls (P=0.039). Similarly, the expression of HIF-1alpha, MMP-2, MMP-9 and VEGF was higher in the ischemic group than in the non-ischemic controls (P=0.024, 0.047, 0.007 and 0.025, respectively). There was a positive association in melanoma cells of the ischemic group between expression of HIF-1alpha and VEGF, and also between MMP-9 and MMP-2. In the ischemic group, there was statistical significance for the correlation between HIF-1alpha and VEGF expression (r=0.456, P=0.038). Furthermore, MMP-2 expression was positively correlated with MMP-9 and VEGF expression (r=0.589 and 0.502, P=0.008 and 0.024, respectively). CONCLUSIONS: Melanoma cells in a hypoxic microenvironment increased HIF-1alpha expression and induced the formation of vasculogenic mimicry channels to acquire an adequate blood supply. On the other hand, the expression of MMP-2 and MMP-9 in tumor tissue increased to enhance the invasiveness. HIF-1alpha, MMP-2 and MMP-9 may be associated with the failure of stop-flow perfusion in some patients with melanoma.

Animals↗

PubMed2006

Revelation of non-statistical behavior in HO2 vibration by a new ab initio potential energy surface.

The hydroperoxyl radical (HO2) has long been considered as a prototype for statistical vibrational dynamics. In this work, however, it is shown that the bound state energy levels (up to the dissociation threshold) and low-lying resonances of the HO2 system (J=0) obtained on a new ab initio potential energy surface exhibit surprisingly large regularity. The implications of the non-statistical behavior of the HO2 system in unimolecular and bimolecular reactions are discussed.

Journal Article↗

PubMed2006

Enantio- and diastereoselective Michael addition reactions of unmodified aldehydes and ketones with nitroolefins catalyzed by a pyrrolidine sulfonamide.

Chiral (S)-pyrrolidine trifluoromethanesulfonamide has been shown to serve as an effective catalyst for direct Michael addition reactions of aldehydes and ketones with nitroolefins. A wide range of aldehydes and ketones as Michael donors and nitroolefins as acceptors participate in the process, which proceeds with high levels of enantioselectivity (up to 99 % ee) and diastereoselectivity (up to 50:1 d.r.). The methodology has been employed successfully in an efficient synthesis of the potent H(3) agonist Sch 50917. In addition, a practical three-step procedure for the preparation of (S)-pyrrolidine trifluoromethanesulfonamide has been developed. The high levels of stereochemical control attending Michael addition reactions catalyzed by this pyrrolidine sulfonamide, have been investigated by using ab initio and density functional methods. Transition state structures for the rate-limiting C--C bond-forming step, corresponding to re- and si-face addition to the reactive conformation of the key enamine intermediates have been calculated. Analysis of these structures indicates that hydrogen bonding plays an important role in catalysis and that the energy barrier for si-face attack in reactions of aldehydes to form 2R,3S products is lower than that for the re-face attack leading to 2S,3R products. In contrast, the energy barrier for re-face addition is lower than that for si-face addition in reactions of ketones. The computational results, which are in good agreement with the experimental observations, are discussed in the context of the stereochemical course of these Michael addition reactions.

Journal Article↗

PubMed2006

Quantum statistical study of O + O2 isotopic exchange reactions: cross sections and rate constants.

Using a wave packet based statistical model, we compute cross sections and thermal rate constants for various isotopic variants of the O + O2 exchange reaction on a recently modified ab initio potential energy surface. The calculation predicts a highly excited rotational distribution and relatively cold vibrational distribution for the diatomic product. A small but important threshold effect was identified for the (16)O + 18O2 reaction, which is suggested to contribute to the experimentally observed negative temperature dependence of the rate ratio, k(18O + 16O2)/k(16O + 18O2). Despite reasonable agreement with quasiclassical trajectory results, however, the calculated thermal rate constants are smaller than experimental measurements by a factor from 2 to 5. The experimentally observed negative temperature dependence of the rate constants is not reproduced. Possible reasons for the theory-experiment discrepancies are discussed.

Journal Article↗

PubMed2006

Localized persistent interstitial pulmonary emphysema presenting as a spontaneous tension pneumothorax in a full term infant.

Persistent interstitial pulmonary emphysema (PIPE) is a syndrome characterized by air-leakage in the perivascular tissues of the lung, primarily affecting mechanically ventilated neonates. Reports in the literature of infants developing PIPE with no history of respiratory distress syndrome (RDS) or mechanical ventilation are scarce. Here, we present a case of a 3-month-old former full term male infant with no history of RDS or mechanical ventilation who presented with focal cystic lung disease associated with spontaneous tension pneumothorax. He was ultimately found to have PIPE based on pathologic evaluation of the resected cystic region. We believe that focal PIPE should be included in the differential diagnosis of cystic lung disease in a full term, unventilated infant, even when spontaneous pneumothorax is the presenting entity.

Humans↗

PubMed2006

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes.

Motivated by the long-term goal of understanding vectorial biological processes such as proton transport (PT) in biomolecular ion pumps, a number of developments were made to establish combined quantum mechanical/molecular mechanical (QM/MM) methods suitable for studying chemical reactions involving significant charge separation in the condensed phase. These developments were summarized and discussed with representative problems. Specifically, free energy perturbation and boundary potential methods for treating long-range electrostatics were implemented to test the robustness of QM/MM results for protein systems. It was shown that consistent models with sufficient sampling were able to produce quantitatively satisfactory results, such as pKa for titritable groups in the interior of T4-lysozyme, while an inconsistent treatment of electrostatics or lack of sufficient sampling may produce incorrect results. Modifications were made to an approximate density functional theory (SCC-DFTB) to improve the description of proton affinity and hydrogen-bonding, which are crucial for the treatment of PT in polar systems. Test calculations on water autoionization showed clearly that both improvements are necessary for quantitatively reliable results. Finally, the newly established SCC-DFTB/MM-GSBP protocol was used to explore mechanistic issues in carbonic anhydrase (CA). Preliminary results suggest that PT in CA occurs mainly through short water wires containing two water molecules in a thermally activated fashion. Although longer water wires occur with similar frequencies, PT along those pathways, on average, has substantially higher barriers, a result not expected based on previous studies. The fluctuations of water molecules peripheral to the water wire were found to make a larger impact on the PT energetics compared to polar protein residues in the active site, which are largely pre-organized and therefore have less tendency to reorganize during the reaction.

Computer Simulation↗

PubMed2006

Quantum mechanical rate constants for H + O2 <--> O + OH and H + O2 --> HO2 reactions.

Canonical rate constants for both the forward and reverse H + O(2) <--> O + OH reactions were calculated using a quantum wave packet-based statistical model on the DMBE IV potential energy surface of Varandas and co-workers. For these bimolecular reactions, the results show reasonably good agreement with available experimental and theoretical data up to 1500 K. In addition, the capture rate for the H + O(2) --> HO(2) addition reaction at the high-pressure limit was obtained on the same potential using a time-independent quantum capture method. Excellent agreement with experimental and quasi-classical trajectory results was obtained except for at very low temperatures, where a reaction threshold was found and attributed to the centrifugal barrier of the orbital motion.

Journal Article↗

PubMed2006

Kinetic analysis of Pseudomonas aeruginosa arginine deiminase mutants and alternate substrates provides insight into structural determinants of function.

L-Arginine deiminase from Pseudomonas aeruginosa (PaADI) catalyzes the hydrolysis of arginine to citrulline and ammonia. PaADI belongs to the guanidino group-modifying enzyme superfamily (GMSF), which conserves backbone fold and a Cys-, His-, and Asp-based catalytic core. In this paper the contributions made by the PaADI core residues Cys406, His278, and Asp166 and the contribution from the neighboring Asp280 (conserved in most but not all GMSF members) to catalysis of the formation and hydrolysis of the Cys406-alkyluronium intermediate were accessed by kinetic analysis of site-directed mutants. In addition, solution hydrolysis in a chemical model of the S-alkylthiouronium intermediate was examined to reveal the importance of general base catalysis in the enzymatic reaction. Substitutions of the active site gating residue Arg401, the l-arginine C(alpha)NH(3)(+)(COO(-)) binding residues, Arg185, Arg243, and Asn160, or the His278 hydrogen bond partner, Glu224, were found to cause dramatic reductions in the enzyme turnover rate. These results are interpreted to suggest that electrostatic interactions play a dominant role in PaADI catalysis. Structural variations observed in P. aeruginosa GMSF enzymes PaADI, agmatine deiminase (PaAgDI), and N(omega),N(omega)-dimethylarginine dimethylaminohydrolase (PaDDAH) indicate an early divergence of the encoding genes. Arginine analogues that are known substrates for PaAgDI and PaDDAH were tested with PaADI to define clear boundaries of biochemical function in the three hydrolases. The conservation of a catalytic core associated with the common chemical function and the divergence of substrate-binding residues (as well as one key catalytic residue) to expand the substrate range provide insight into the evolution of the catalysts that form the GMSF.

Binding Sites↗

PubMed2006

Exact quantum dynamics of N(2D) + H2 --> NH + H reaction: cross-sections, rate constants, and dependence on reactant rotation.

Using an exact Chebyshev wave packet method, initial state-specified (upsilon(i)=0, j(i)=0,2) integral cross-sections and rate constants are obtained for the title reaction on the latest ab initio potential energy surface. Reaction probabilities up to J=29 are dependent on the reactant rotation and show mild oscillations superimposed on a broad background. Due to a barrier in the entrance channel, the cross sections increase with energy with clear thresholds and the rate constants vary with temperature in the Arrhenius form. The calculated canonical rate constant is in good agreement with the experimental measurements. Our results also indicate that the quasiclassical trajectory method underestimates the rate due to the neglect of tunneling, while the quantum statistical approach overestimates because of the short lifetime of the reaction intermediate.

Journal Article↗

PubMed2006

Catalytic mechanism of class B2 metallo-beta-lactamase.

The initial nucleophilic substitution step of biapenem hydrolysis catalyzed by a subclass B2 metallo-beta-lactamase (CphA from Aeromonas hydrophila) is investigated using hybrid quantum mechanical/molecular mechanical methods and density functional theory. We focused on a recently proposed catalytic mechanism that involves a non-metal-binding water nucleophile in the active site of the monozinc CphA. Both theoretical models identified a single transition state featuring nearly concomitant nucleophilic addition and elimination steps, and the activation free energy from the potential of mean force calculations was estimated to be approximately 14 kcal/mol. The theoretical results also identified the general base for activating the water nucleophile to be the metal-binding Asp-120 rather than His-118, as suggested earlier. The protonation of Asp-120 leads to cleavage of the O(delta2)-Zn coordination bond, whereas the negatively charged nitrogen leaving group resulting from the ring opening replaces Asp-120 as the fourth ligand of the sole zinc ion. The electrophilic catalysis by the metal ion provides sufficient stabilization for the leaving group to avoid a tetrahedral intermediate. The theoretical studies provided detailed insights into the catalytic strategy of this unique metallo-beta-lactamase.

Aeromonas hydrophila↗

PubMed2006

Contributions of long-range electrostatic interactions to 4-chlorobenzoyl-CoA dehalogenase catalysis: a combined theoretical and experimental study.

It is well established that electrostatic interactions play a vital role in enzyme catalysis. In this work, we report theory-guided mutation experiments that identified strong electrostatic contributions of a remote residue, namely, Glu232 located on the adjacent subunit, to 4-chlorobenzoyl-CoA dehalogenase catalysis. The Glu232Asp mutant was found to bind the substrate analogue 4-methylbenzoyl-CoA more tightly than does the wild-type dehalogenase. In contrast, the kcat for 4-chlorobenzoyl-CoA conversion to product was reduced 10000-fold in the mutant. UV difference spectra measured for the respective enzyme-ligand complexes revealed an approximately 3-fold shift in the equilibrium of the two active site conformers away from that inducing strong pi-electron polarization in the ligand benzoyl ring. Increased substrate binding, decreased ring polarization, and decreased catalytic efficiency indicated that the repositioning of the point charge in the Glu232Asp mutant might affect the orientation of the Asp145 carboxylate with respect to the substrate aromatic ring. The time course for formation and reaction of the arylated enzyme intermediate during a single turnover was measured for wild-type and Glu232Asp mutant dehalogenases. The accumulation of arylated enzyme in the wild-type dehalogenase was not observed in the mutant. This indicates that the reduced turnover rate in the mutant is the result of a slow arylation of Asp145, owing to decreased efficiency in substrate nucleophilic attack by Asp145. To rationalize the experimental observations, a theoretical model is proposed, which computes the potential of mean force for the nucleophilic aromatic substitution step using a hybrid quantum mechanical/molecular mechanical method. To this end, the removal or reorientation of the side chain charge of residue 232, modeled respectively by the Glu232Gln and Glu232Asp mutants, is shown to increase the rate-limiting energy barrier. The calculated 23.1 kcal/mol free energy barrier for formation of the Meisenheimer intermediate in the Glu232Asp mutant represents an increase of 6 kcal/mol relative to that of the wild-type enzyme, consistent with the 5.6 kcal/mol increase calculated from the difference in experimentally determined rate constants. On the basis of the combination of the experimental and theoretical evidence, we hypothesize that the Glu232(B) residue contributes to catalysis by providing an electrostatic force that acts on the Asp145 nucleophile.

Amino Acid Substitution↗

PubMed2006

Clusterin expression and univariate analysis of overall survival in human breast cancer.

The aim of this research is to investigate the significance of clusterin (CLU) expression as a risk factor for breast cancer through tissue microarray technology and univariate analysis of overall survival. Formalin-fixed, paraffin-embedded tissues from 158 cases of breast cancer and 31 cases of normal adjacent tissues assembled into a tissue microarray. Cytoplasmic CLU expression in tumor tissues was measured by immunochemistry. Survival analysis was used to investigate the relationship between CLU expression and prognosis, tumor volume, pathological classification, and recurrence. Survival time of patients with CLU expression, lymph node metastasis, and limited post-surgery chemotherapy (<6 cycles of treatment) was significantly shorter than that of patients with no detectable CLU expression (P=0.000), without lymph node metastasis (P=0.000) and more comprehensive post-surgery chemotherapy (>/=6 cycles of treatment) (P=0.035). CLU expression in tumor cells was higher than in normal adjacent breast epithelial cells (P=0.03). The CLU expression staining coefficient of cancer tissues with lymph node metastasis was higher than those without lymph node metastasis (P=0.000). Cytoplasmic CLU expression was found to be a prognostic factor for human breast cancer.

Adult↗

PubMed2006

Segmental heterogeneity of epithelial ion transport induced by stimulants in rat distal colon.

Mammalian colon plays an important role in electrolyte and water balance, and exhibits significant segmental heterogeneity. The different responses to stimulants even exist in different segments of rat distal colon. The present study focus on the segmental heterogeneity of epithelial responses to different stimulants and investigates the possible mechanism by using short circuit current recording technique. Baseline I(SC) in the segment 4 of distal colon (DC(4), 20.8+/-2.8 microA.cm(-2)) was significantly lower than that in the segment 1 of distal colon (DC(1), 40.5+/-1.9 microA.cm(-2)). Basolateral application of indomethacin induced a larger reduction of the baseline I(SC) in DC(4) (-28.2+/-3.9 microA.cm(-2)) than that in DC(1) (-10.1+/-3.9 microA.cm(-2)). Moreover DC(4) are more sensitive to foskolin (a cAMP activator, apical side), Ach (basolateral side) and 5-HT (basolateral side) than DC(1), which was not affected by pretreatment with amiloride, a blocker of epithelial Na(+) channel. Basolateral pretreatment with atropine (muscarinic cholinergic receptor antagonist) for 10 min, Ach-induced DeltaI(SC) increases in both DC(1) and DC(4 )were totally blocked. Otherwise, 5-HT(4) receptor antagonist GR113808 (basolateral side) and SB-204070 (basolateral side) completely inhibited 5-HT-induced I(SC) increases in both DC(1) and DC(4). Taken together, the results suggested that the segmental heterogeneity of epithelial responses to different stimulants exists in rat distal colon. And it is more likely related to the dissimilar distribution of membrane proteins involved in the ion transports within different segments of rat distal colon.

Acetylcholine↗

PubMed2006

Morphologic research of microcirculation patterns in human and animal melanoma.

OBJECTIVE: The pattern and distribution of microcirculation of malignant melanoma were studied in human malignant melanoma tumor samples and in an animal model by staining of paraffin-embedded sections and transelectron microscopy. METHODS: Blood supply models for melanoma were studied with immunohistochemical and periodic acid-Schiff (PAS) double-staining technique. New sections were made from 190 paraffin-embedded melanoma samples, and immunohistochemical staining of the platelet-endothelial cell adhesive molecule (CD31 antigen) and PAS staining were conducted to confirm different microcirculation patterns of melanoma. Furthermore, malignant melanoma cells B16 and LiBr were injected into the groin of C57 mice and into the abdominal cavity of SCID mice, respectively. Tumors with vasculogenic mimicry (VM) were stained with PAS and CD31 to study the morphology and distribution of VM in mice melanoma. A diluted suspension of activated carbon was injected into the circulation of mice previously inoculated in the groin with B16 melanoma cells. Tumor tissue with VM was observed under electron microscopy. RESULTS: There were three kinds of microcirculation pattern in human and animal melanoma. The walls of VM were positive for PAS staining and negative for CD31 staining in the tumor tissues. The distribution of VM and mosaic vessels was not uniform and appeared in patches. VM along with endothelium-dependent vessels and mosaic vessels sustained the blood supply for the tumors. The results from electron microscopy validated the presence of three patterns. CONCLUSIONS: The results obtained using activated carbon as a tracer showed that VM and mosaic vessels connect with the host blood circulation. VM and mosaic vessels exist in malignant melanoma. Tumor cells can obtain oxygen and nutriment through VM and mosaic vessels besides endothelium-dependent vessels.

Animals↗

PubMed2006

Microcirculation patterns in different stages of melanoma growth.

Several microcirculation patterns in tumors have been reported, including vasculogenic mimicry (VM), mosaic vessels (MV) and endothelium-dependent vessels. To investigate the sources of blood supply during different tumor stages, we studied the correlation between expression of vasculogenic mimicry (VM), mosaic vessels (MV) and endothelium-dependent vessels in a mouse melanoma xenograph. Sixty C57 mice were divided into 12 groups (5 mice per group) and inoculated with B16 melanoma cells. Eleven days later, the average tumor size was approximately 0.2 to 0.3 cm. From days 11 to 22, one group per day was randomly sacrificed, and the density of vasculogenic mimicry, mosaic vessels and endothelium-dependent vessels was measured in tumor tissue sections. Immunohistochemical dual-staining and electronic microscopy were also used to confirm the vessel types. All three types of microcirculation patterns were observed during tumor development. In the early stage of tumor growth, vasculogenic mimicry is the main pattern of blood supply. As the area of tumor tissue expands and the number of endothelium increase, vasculogenic mimicry is replaced by endothelium-dependent vessels. Mosaic vessels might be the interim state between vasculogenic mimicry and endothelium-dependent vessels. The number of endothelium-dependent vessels correlated with the size of the tumor (r=0.718, P=0.009), while the number of vasculogenic mimicry was inversely correlated (r=0.77, P=0.003). In conclusion, the number of vasculogenic mimicry decreased and the number of endothelial-dependent vessels increased during tumor growth.

Animals↗

PubMed2006

Vasculogenic mimicry is associated with high tumor grade, invasion and metastasis, and short survival in patients with hepatocellular carcinoma.

Vasculogenic mimicry (VM) has increasingly been recognized as a form of angiogenesis. In VM, epithelial cells are integrated into the malignant tumor vasculature. An association has been observed between VM and poor clinical prognosis in some malignant tumors. However, whether VM is present and clinically significant in hepatocellular carcinoma (HCC) is unknown. In this study, we determined whether VM was present in HCC and whether it was associated with tumor grade, invasion and metastasis, and survival duration. We collected paraffin-embedded HCC tumor samples, along with complete clinical and pathologic data for all the cases, and performed immunohistochemical staining for CD31, CD105 (endoglin), hepatocyte, vascular endothelial growth factor, matrix metalloproteinase (MMP)-2, and MMP-9. The VM status was compared with the clinical and pathological data using statistical tests. Kaplan-Meier survival analysis and log-rank test were used to compare survival durations between patients with and without VM. The VM vessel cells were CD31 and CD105-negative and hepatocyte and vascular endothelial growth factor-positive, showing that they were not derived from endothelial cells but were HCC tumor cells. Patients with VM had a higher metastasis rate than did those without VM (P=0.003). Consistent with this finding, MMP-2 and MMP-9 were present in all the VM cases but were found less frequently in non-VM cases (P<0.05). The Kaplan-Meier survival analysis showed that patients in the VM group had a significantly shorter survival duration than did those in the non-VM group. In conclusion, VM is a marker of poor clinical prognosis in HCC: Its presence may be associated with a high tumor grade, invasion and metastasis, and short survival.

Aged↗