Biomedical subjects
Y Zhu
Publications and source records attributed to Y Zhu.
Immunological adjuvants promote activated T cell survival via induction of Bcl-3.
Injection of soluble protein antigen into animals causes abortive proliferation of the responding T cells. Immunological adjuvants boost T cell responses at least in part by increasing the survival of activated T cells during and after the initial proliferative phase of their clonal expansion. To understand how adjuvants promote T cell survival, we used gene microarrays to analyze gene expression in T cells activated either with antigen alone or in the presence of two different adjuvants. Among the genes whose expression was increased by both adjuvants was the IkappaB family member Bcl-3. Retroviral infection experiments showed that expression of Bcl-3 increased survival of activated T cells in vitro and in vivo. Adjuvants may therefore improve survival of activated T cells via induction of Bcl-3.
A neural circuit for circadian regulation of arousal.
An unknown aspect of behavioral state regulation is how the circadian oscillator of the suprachiasmatic nucleus (SCN) regulates sleep and waking. In this report, we describe the necessary elements for a circuit that provides circadian regulation of arousal. Trans-synaptic retrograde tracing revealed a prominent indirect projection from the SCN to the noradrenergic nucleus locus coeruleus (LC), a brain arousal system. Double-labeling experiments revealed several possible links between the SCN and the LC, including the dorsomedial (DMH) and paraventricular hypothalamic nuclei (PVN), as well as medial and ventrolateral pre-optic areas. Lesion studies confirmed that the DMH is a substantial relay in this circuit. Next, neurophysiology experiments revealed circadian variations in LC impulse activity. Lesions of the DMH eliminated these circadian changes in LC activity, confirming the functionality of the SCN-DMH-LC circuit. These results reveal mechanisms for regulation of circadian and sleep-waking functions.
High-density lipoprotein binding to scavenger receptor-BI activates endothelial nitric oxide synthase.
Atherosclerosis is the primary cause of cardiovascular disease, and the risk for atherosclerosis is inversely proportional to circulating levels of high-density lipoprotein (HDL) cholesterol. However, the mechanisms by which HDL is atheroprotective are complex and not well understood. Here we show that HDL stimulates endothelial nitric oxide synthase (eNOS) in cultured endothelial cells. In contrast, eNOS is not activated by purified forms of the major HDL apolipoproteins ApoA-I and ApoA-II or by low-density lipoprotein. Heterologous expression experiments in Chinese hamster ovary cells reveal that scavenger receptor-BI (SR-BI) mediates the effects of HDL on the enzyme. HDL activation of eNOS is demonstrable in isolated endothelial-cell caveolae where SR-BI and eNOS are colocalized, and the response in isolated plasma membranes is blocked by antibodies to ApoA-I and SR-BI, but not by antibody to ApoA-II. HDL also enhances endothelium- and nitric-oxide-dependent relaxation in aortae from wild-type mice, but not in aortae from homozygous null SR-BI knockout mice. Thus, HDL activates eNOS via SR-BI through a process that requires ApoA-I binding. The resulting increase in nitric-oxide production might be critical to the atheroprotective properties of HDL and ApoA-I.
Reciprocal regulation of endothelial substrate adhesion and barrier function.
OBJECTIVE: To examine how cell-substrate adhesion is regulated during barrier changes produced by exposure to inflammatory mediators. METHODS: Lung microvascular endothelial monolayers were treated with test agents +/- blockers, and barrier was measured by transendothelial resistance; cell-substrate adhesion was assessed by surface area conservation after trypsin treatment of monolayers. Protein phosphorylation and distribution were assayed by immunoblotting and fluorescent microscopy, respectively. RESULTS: H2O2, histamine, bradykinin, and thrombin, decreased endothelial barrier function, and enhanced adhesion to the substratum. H2O2 enhanced cell adhesion to the substrate in a concentration (0-1 mM)- and time (0-60 minutes)-dependent fashion. This effect of H2O2 reversed within 120 minutes of removal of H2O2 and was blocked by the mean arterial pressure (MAP) kinase inhibitor, PD98059 and by chelating cytoplasmic Ca2+ but not PKC or PKG inhibition. H2O2 also stimulated tyrosine phosphorylation of several proteins and increased the association of the focal adhesive proteins paxillin, talin, and vinculin with the cytoskeleton and may promote localization of these proteins to junctions. CONCLUSIONS: Our data indicate that inflammatory mediators reduce cell-cell contact, contributing to reduced solute barrier and simultaneously enhanced substrate binding, which may be reciprocal events in barrier regulation in vitro and in vivo.
Study on the co-luminescence system of Dy-Gd-1,6-bis(1'-phenyl-3'-methyl-5'-pyrazol-4'-one)hexanedionecetyltrimethylammonium bromide and its analytical application.
Dy-1,6-bis(1'-phenyl-3'-methyl-5'-pyrazol-4'-one)hexanedione-cetyltrimethylammonium bromide (Dy-BPMPHD-CTMAB) ion association system has strong fluorescence intensity. In this system, some rare earth ions such as Gd3+, Y3+ and La3+ can exert a fluorescence enhancement effect, leading to a newly found co-luminescence system. From this, a rapid, simple and sensitive method was developed for the determination of trace amounts of Dy3+. The results indicate that the fluorescence intensity of the system is linearly related to the concentration of Dy3+ in the range 1.0 x 10(-7)-1.2 x 10(-5) mol L(-1) and the detection limit (S/N = 3) is 3.0 x 10(-8) mol L(-1). The luminescence mechanism of the system is discussed.
Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis.
Mutations in clpP and clpX have pleiotropic effects on growth and developmentally regulated gene expression in Bacillus subtilis. ClpP and ClpX are needed for expression of comK, encoding the competence transcription factor required for the expression of genes within the competence regulon. ClpP, in combination with the ATPase ClpC, degrades the inhibitor of ComK, MecA. Proteolysis of MecA is stimulated by a small protein, ComS, which interacts with MecA. Suppressor mutations (cxs) were isolated that bypass the requirement for clpX for comK expression. These were found also to overcome the defect in comK expression conferred by a clpP mutation. These mutations were identified as missense mutations (cxs-5, -7 and -12) and a nonsense (UAG) codon substitution (cxs-10) in the yjbD coding sequence in a locus linked to mecA. That a yjbD disruption confers the cxs phenotype, together with its complementation by an ectopically expressed copy of yjbD, indicated that the suppressor alleles bear recessive, loss-of-function mutations of yjbD. ClpP- and ClpX-independent comK expression rendered by inactivation of yjbD was still medium-dependent and required ComS. MecA levels in a clpP-yjbD mutant were lower that those of clpP mutant cells and ComK protein concentration in the clpP mutant was restored to wild-type levels by the yjbD mutation. Consequently, the yjbD mutation bypasses the defect in competence development conferred by clpP and clpX. YjbD protein is barely detectable in wild-type cells, but is present in large amounts in the clpP mutant cells. The results suggest that the role of ClpP in competence development is to degrade YjbD protein so that ComS can productively interact with the MecA-ClpC-ComK complex. Alternatively, the result could suggest that YjbD has a negative effect on regulated proteolysis and that MecA is degraded independently of ClpP when YjbD is absent.
Expression of penicillin G acylase from the cloned pac gene of Escherichia coli ATCC11105. Effects of pacR and temperature.
The structural gene pac in Eschericia coli ATCC11105 encodes penicillin G acylase (PGA). Within the pac gene, there is a regulatory gene pacR, which is transcribed in the opposite direction. Site-directed mutagenesis was performed at base 1045 of pac by replacing a T with a C. This substitution did not alter the amino-acid sequence of PGA, but changed the translation start codon of pacR from AUG to GUG. The expression of the mutant pacR decreased dramatically and the lacZ transcriptional fusion analysis showed that GUG was an extremely poor initiation codon for pacR. The pacR mutation caused PGA expression to be constitutive rather than inductive in two strains (E. coli A56, DH10B). The pac inducer phenylacetic acid (PAA) gave significant induction of PGA production at a concentration of 0.2% in wild type, but PAA at this concentration inhibited both cell growth and PGA production in the pacR mutated strains. The temperature-dependent expression character of pac is preserved in the pacR translation-initiation mutant and the optimum temperature of PGA production was 22 degrees C in both wild type and mutant. At a higher temperature of 37 degrees C, the PGA precursor polypeptide could not be matured into subunits and formed inclusion bodies, as revealed by western blot analysis. Our investigations confirmed the hypothesis of pacR-mediated PAA induction for PGA expression and clarified the inhibitory effect of high temperature upon the post-translational processing of the PGA precursor polypeptide.
Developmental expression of metabotropic P2Y(1) and P2Y(2) receptors in freshly isolated astrocytes from rat hippocampus.
There are at least three subtypes of cloned metabotropic P2 receptors linked to intracellular Ca(2+) rises in rat brain cells, namely, P2Y(1), P2Y(2) and P2Y(4). In this study we explore the subtypes of the metabotropic P2 receptors seen in freshly isolated astrocytes (FIAs) from P8-P25 rats. We found by single cell RT-PCR that in process-bearing FIAs from hippocampi of P8-P12 rats, 31% of the glial fibrillary acidic protein (GFAP) mRNA (+) cells expressed P2Y(1) mRNA while only 5% of the cells tested expressed P2Y(2) mRNA. The expression of P2Y(1) receptor mRNA was not changed in FIAs from the hippocampi of P18-P25 rats, but 38% of the GFAP mRNA (+) cells in the P18-P25 age group then showed P2Y(2) mRNA. We also studied whether the mRNA was expressing functional receptor protein by measuring Ca(2+) responses to specific agonists for P2Y(1) and P2Y(2). We found that similar proportions of GFAP mRNA (+) FIAs responded to ATP or UTP as showed mRNAs for P2Y (1) and P2Y(2,) respectively. Total tissue RNA from P9 and P24 rat hippocampus showed a 2.8-fold increase in P2Y(2) mRNA levels from P9 to P24 with a decrease in P2Y(1) mRNA. Thus, this study shows a marked up-regulation of mRNA for P2Y(2) from 9 to 24 days in rat hippocampus, and some of this increase is likely due to the protoplasmic astrocytes which is being translated into functional receptor protein in these cells.
Effect of anti-transforming growth factor-beta antibodies in cyclosporine-induced renal dysfunction.
BACKGROUND: Several experimental and clinical studies have implicated a role for transforming growth factor-beta (TGF-beta) in mediating the nephrotoxic effects of cyclosporine (CsA). To test this hypothesis, we administered neutralizing anti-TGF-beta antibodies (alpha-TGF-beta) in a well-described rat model of chronic CsA nephrotoxicity. METHODS: We studied three groups (N = 9 per group) of adult, male Sprague-Dawley rats that received a low-salt diet (0.05% sodium). Normal controls were given vehicle subcutaneously and an alternate-day intraperitoneal injection of 3 mg of nonspecific mouse IgG (MIgG) for 28 days. The CsA group received 15 mg/kg/day of CsA subcutaneously and 3 mg of MIgG intraperitoneally on alternate days for 28 days. The CsA/alpha-TGF-beta group received CsA and alternate-day alpha-TGF-beta (3 mg) for 28 days. At the end of 28 days, creatinine clearance was measured by 24-hour urine collection. Histologic assessment was performed for tubulointerstitial damage and arteriolar hyalinosis. Northern analysis was performed for alpha 1(I) collagen and TGF-beta 1 gene expression, and quantitative reverse transcription-polymerase chain reaction was performed to measure levels of tissue inhibitor of metalloproteinase-1 (TIMP-1), TIMP-2, plasminogen activator inhibitor-1 (PAI-1), matrix metalloproteinase-2 (MMP-2), and MMP-9. RESULTS: CsA-treated rats had significantly lower creatinine clearance as compared with normal controls (0.43 +/- 0.07 vs. 0.67 +/- 0.14 mL/min, P = 0.0002), increased interstitial damage and afferent arteriolar hyalinosis (P = 0.0001), and increased alpha1(I) collagen (4-fold) and TGF-beta 1 (2.5-fold) mRNA expression. CsA-treated rats also had significantly increased TIMP-1 (7.4-fold, P < 0.001), MMP-2, and PAI-1 (all approximately 2-fold, P < 0.02) and decreased MMP-9 (85% reduction, P < 0.001) as compared with controls. Treatment with alpha-TGF-beta in CsA-treated rats significantly prevented the reduction in creatinine clearance (0.58 +/- 0.03 mL/min, P = 0.009 vs. CsA alone), the increase in afferent arteriolar hyalinosis (P < 0.05 vs. CsA alone), normalized alpha 1(I) collagen mRNA levels, and attenuated CsA effects on TGF-beta1, TIMP-1, and MMP-9. CONCLUSIONS: In this rat model of CsA-induced nephrotoxicity, renal insufficiency and characteristic histologic changes are associated with altered expression of matrix and matrix-regulating molecules. Based on our results with alpha-TGF-beta antibodies, many but not all of these nephrotoxic effects of CsA are mediated by TGF-beta.
Na(+) occupancy and Mg(2+) block of the n-methyl-d-aspartate receptor channel.
The effect of extracellular and intracellular Na(+) on the single-channel kinetics of Mg(2+) block was studied in recombinant NR1-NR2B NMDA receptor channels. Na(+) prevents Mg(2+) access to its blocking site by occupying two sites in the external portion of the permeation pathway. The occupancy of these sites by intracellular, but not extracellular, Na(+) is voltage-dependent. In the absence of competing ions, Mg(2+) binds rapidly (>10(8) M(-1)s(-1), with no membrane potential) to a site that is located 0.60 through the electric field from the extracellular surface. Occupancy of one of the external sites by Na(+) may be sufficient to prevent Mg(2+) dissociation from the channel back to the extracellular compartment. With no membrane potential; and in the absence of competing ions, the Mg(2+) dissociation rate constant is >10 times greater than the Mg(2+) permeation rate constant, and the Mg(2+) equilibrium dissociation constant is approximately 12 microM. Physiological concentrations of extracellular Na(+) reduce the Mg(2+) association rate constant approximately 40-fold but, because of the "lock-in" effect, reduce the Mg(2+) equilibrium dissociation constant only approximately 18-fold.
K(+) occupancy of the N-methyl-d-aspartate receptor channel probed by Mg(2+) block.
The single-channel kinetics of extracellular Mg(2+) block was used to probe K(+) binding sites in the permeation pathway of rat recombinant NR1/NR2B NMDA receptor channels. K(+) binds to three sites: two that are external and one that is internal to the site of Mg(2+) block. The internal site is approximately 0.84 through the electric field from the extracellular surface. The equilibrium dissociation constant for this site for K(+) is 304 mM at 0 mV and with Mg(2+) in the pore. The occupancy of any one of the three sites by K(+) effectively prevents the association of extracellular Mg(2+). Occupancy of the internal site also prevents Mg(2+) permeation and increases (by approximately sevenfold) the rate constant for Mg(2+) dissociation back to the extracellular solution. Under physiological intracellular ionic conditions and at -60 mV, there is approximately 1,400-fold apparent decrease in the affinity of the channel for extracellular Mg(2+) and approximately 2-fold enhancement of the apparent voltage dependence of Mg(2+) block caused by the voltage dependence of K(+) occupancy of the external and internal sites.
A global optimization method for three-dimensional conformal radiotherapy treatment planning.
Multiple local minima exist in almost every coplanar or non-coplanar radiotherapy treatment planning problem. We used a global optimization method based on topographical information about the distribution of local minima to find all local minima and select the best as the global minimum. We uniformly select N random points from search regions and construct a topographical graph, from which M (M << N) starting points are selected to launch a local search. Because every seed point was at or near the local minimum, the solutions found by the local search could be used as the final optimization results. We verified this algorithm by applying it to three different clinical cases and comparing the results with those obtained by a local optimization method (sequential quadratic programming). The results show that this algorithm is feasible and efficient.
An algorithm for stereotactic localization by computed tomography or magnetic resonance imaging.
Stereotactic localization of an intracranial lesion by computed tomography or magnetic resonance imaging requires the use of a head frame that is fixed to the skull of the patient. To such head frames are attached either N-shaped or V-shaped localization rods. Because of patient positioning, the transverse imaging slices may not be parallel to the frame base; a coordinate transformation algorithm that takes this possibility into consideration is crucial. Here we propose such an algorithm for a head frame with V-shaped localization rods. Our algorithm determines the transformation matrix between the image coordinate system of a transverse image and the frame coordinate system. The determining procedure has three steps: (a) calculation of the oblique angles of a transverse image relative to the head frame and calculation of the image magnification factor; (b) determination of the coordinates of four central markers in both coordinate systems; and (c) determination of the 3 x 3 transformation matrix by using the coordinates of the four markers. This algorithm is robust in principle and is useful for improving the accuracy of localization.
An optimization method for importance factors and beam weights based on genetic algorithms for radiotherapy treatment planning.
We propose a new method for selecting importance factors (for regions of interest like organs at risk) used to plan conformal radiotherapy. Importance factors, also known as weighting factors or penalty factors, are essential in determining the relative importance of multiple objectives or the penalty ratios of constraints incorporated into cost functions, especially in dealing with dose optimization in radiotherapy treatment planning. Researchers usually choose importance factors on the basis of a trial-and-error process to reach a balance between all the objectives. In this study, we used a genetic algorithm and adopted a real-number encoding method to represent both beam weights and importance factors in each chromosome. The algorithm starts by optimizing the beam weights for a fixed number of iterations then modifying the importance factors for another fixed number of iterations. During the first phase, the genetic operators, such as crossover and mutation, are carried out only on beam weights, and importance factors for each chromosome are not changed or 'frozen'. In the second phase, the situation is reversed: the beam weights are 'frozen' and the importance factors are changed after crossover and mutation. Through alternation of these two phases, both beam weights and importance factors are adjusted according to a fitness function that describes the conformity of dose distribution in planning target volume and dose-tolerance constraints in organs at risk. Those chromosomes with better fitness are passed into the next generation, showing that they have a better combination of beam weights and importance factors. Although the ranges of the importance factors should be set in advance by using this algorithm, it is much more convenient than selecting specific numbers for importance factors. Three clinical examples are presented and compared with manual plans to verify this method. Three-dimensional standard displays and dose-volume histograms are shown to demonstrate that this method is feasible, automatic and convenient.
Verification of the super-omni wedge concept.
This study verifies the concept of the super-omni wedge by validating its equations for effective wedge orientation and wedge angle and by comparing the dose distributions it produces with those produced by other wedge techniques. To validate the equations, we calculated dose distributions for 20 combinations of wedge orientations and wedge angles: we then determined the differences between the wedge orientations and angles predicted by the equations and those calculated by a three-dimensional treatment-planning system. To compare the super-omni wedge concept with other techniques, we calculated the dose and position differences between the dose distributions produced by the super-omni wedge concept and those produced by other wedge techniques. The error of wedge orientations ranged from -0.5 degrees to 0.4 degrees, and that of wedge angles ranged from -0.6 degrees to 1.7 degrees. The dose distributions produced by the super-omni wedge were similar and therefore equivalent to those produced by other wedge techniques. Serving as an intermediate step in treatment-planning optimization. the super-omni wedge is a reliable method for producing wedged dose distributions with arbitrary wedge orientations and wedge angles.
NBP is the p53 homolog p63.
We previously identified a non-p53, p53-responsive DNA element (p53RE)-binding protein named NBP, functionally analogous to p53, from human cervical carcinoma Hela cells. Here we report a biochemical study demonstrating that this activity is the recently cloned p53 analog p63. NBP was purified through conventional and DNA affinity chromatography to apparent homogeneity with a prominent polypeptide migrating in between the 43 and 68 kDa positions on a SDS gel. This polypeptide immunoreacted with monoclonal anti-p63 but not anti-p53 or anti-p73 antibodies. Also, NBP co-purified with p63 through each step of fractionation, as detected with anti-p63 antibodies. DNA-protein complexes formed with purified NBP and p53RE-containing oligomers derived from the p21(waf1) promoter were supershifted by anti-p63 but not anti-p53 antibodies. Thus, these results demonstrate that NBP is encoded by the p53 homolog p63 gene.
An amplified fragment length polymorphism map of the silkworm.
The silkworm (Bombyx mori L.) is a lepidopteran insect with a long history of significant agricultural value. We have constructed the first amplified fragment length polymorphism (AFLP) genetic linkage map of the silkworm B. mori at a LOD score of 2.5. The mapping AFLP markers were genotyped in 47 progeny from a backcross population of the cross no. 782 x od100. A total of 1248 (60.7%) polymorphic AFLP markers were detected with 35 PstI/TaqI primer combinations. Each of the primer combinations generated an average of 35.7 polymorphic AFLP markers. A total of 545 (44%) polymorphic markers are consistent with the expected segregation ratio of 1:1 at the significance level of P = 0.05. Of the 545 polymorphic markers, 356 were assigned to 30 linkage groups. The number of markers on linkage groups ranged from 4 to 36. There were 21 major linkage groups with 7-36 markers and 9 relatively small linkage groups with 4-6 markers. The 30 linkage groups varied in length from 37.4 to 691.0 cM. The total length of this AFLP linkage map was 6512 cM. Genetic distances between two neighboring markers on the same linkage group ranged from 0.2 to 47 cM with an average of 18.2 cM. The sex-linked gene od was located between the markers P1T3B40 and P3T3B27 at the end of group 3, indicating that AFLP linkage group 3 was the Z (sex) chromosome. This work provides an essential basic map for constructing a denser linkage map and for mapping genes underlying agronomically important traits in the silkworm B. mori L.