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Gu Y, Zheng C, Zhao Y, Ke H, Fan H. A new iterative procedure for combining direct methods with solvent flattening - dealing with the phase ambiguity in protein crystallography. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2005; 53:792-4. [PMID: 15299873 DOI: 10.1107/s090744499700680x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A new procedure for combining direct methods with the solvent-flattening technique is proposed for phasing single isomorphous replacement (SIR) or one-wavelength anomalous scattering (OAS) data of proteins. The new procedure differs from the previous one [Zheng, Zheng, Gu, Mo, Fan & Hao (1997). Acta Cryst. D53, 49-55] in that the direct method not only provides input phases to but also accepts feedback phases from solvent flattening, thus forming an iterative process for breaking the ambiguities and refining the values of phases. The new procedure was tested with the experimental SIR data of the known structure ribonuclease Sa. For the strongest 1000 of the total 7264 reflections, the mean F(obs)-weighted phase error is 7.5 and 9.4 degrees lower than that of the previous procedure and that of solvent flattening alone, respectively.
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Gu Y. Comparisons Between Oral Pulse Alfacalcidol Therapy and Daily Therapy in Maintenance Hemodialysis Patients with Secondary Hyperparathyroidism: A Randomized, Controlled, and Multicenter Study. Ren Fail 2005. [DOI: 10.1081/jdi-200049538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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378
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Gu Y, Ding F, Chen N, Mei CL, Qian JQ, Wang XY, Shi W, Hou FF, Li XW, Wang M, Chen YP. Comparisons between oral pulse alfacalcidol therapy and daily therapy in maintenance hemodialysis patients with secondary hyperparathyroidism: a randomized, controlled, and multicenter study. Ren Fail 2005; 27:205-12. [PMID: 15807187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
OBJECTIVE To investigate the efficacy and safety of 1alpha-(OH)-D3 high-dose pulse therapy or daily low-dose therapy in secondary hyperthyroidism in maintenance hemodialysis patients in China. METHODS Maintenance hemodialysis patients of both gender with intact parathyroid hormone (iPTH) level above 200 pg/mL were randomly divided into a pulse group and a daily group. They were treated for 20 weeks, with 2 microg oral Alfacalcidol twice weekly or thrice weekly in the pulse group, and 0.5 microg oral Alfacalcidol per day in the daily group. The therapeutic end point was parathyroid hormone level < 200 pg/ mL. The iPTH levels during the study were monitored, and parameters representative of calcium and phosphate metabolism and side effects were also observed. RESULTS One hundred and fifty-eight patients were initially enrolled, 91 in the pulse therapy group and 67 in the daily therapy group. There was no significant difference in age, hemodialysis duration, proportion of diabetic nephropathy and systemic diseases, proportion of patients who had received active vitamin D therapy previously, mean initial iPTH level (pulse group 570.47 +/- 295.86 pg/mL; daily group 498.33 +/- 207.84 pg/mL), serum calcium, serum phosphate, alkaline phosphatase (AKP), and albumin between two groups. In the pulse therapy group there were more patients with iPTH levels of 500 to approximately 1,000 pg/mL and > 1,000 pg/mL, so stratified analysis according to iPTH level was used. In therapeutic end point, iPTH levels in both groups were significantly lower compared with those before therapy (pulse group 261.29 +/- 234.97 pg/mL, P < .01; daily group 262.17 +/- 274.82 pg/mL, P < .01). After 4 weeks, the ratio of reaching end point in the pulse group was 35.2%, which was significantly higher than that (19.4%) in the daily group (P < .05). More obvious change was seen in the 200 to approximately 500 pg/mL subgroup by stratified analysis (P < .05), whereas there was no significant difference between the 500 to approximately 1,000 pg/mL and > 1,000 pg/mL subgroup (P > .05). At therapeutic end point, the total ratio of reaching end point did not differ between the two groups, and there were no obvious differences between each subgroup. In the iPTH 200 to approximately 500 pg/mL subgroup, mean iPTH%/week in the pulse group was significantly higher than that in the daily group, and no obvious difference was seen in other subgroups. AKP levels decreased significantly in both groups at therapeutic end point (pulse group 98.42 +/- 54.52 vs. 74.21 +/- 30.68 IU/L, P < .01; daily group 103.3 +/- 68.04 vs. 75.40 +/- 34.12 IU/L, P < .01). On the 4th week, AKP level in pulse group (82.39 +/- 35.23 IU/L) was significantly lower than the initial level (98.42 +/- 54.52 IU/L, P < .05), whereas in the daily group there was no difference between each week. The mean serum calcium, phosphate, and [Ca2+] x [P3+] levels in both groups did not change greatly. Nine patients in the pulse group (9.9%) and 8 patients in the daily group (11.9%) suffered hypercalcemia at least once. Persistent hypercalcemia occurred in 8 patients in the pulse group (8.8%) and 9 patients in the daily group (13.4%), but the difference in proportion did not show statistical significance. The serum phosphate in the daily group was higher after the therapy (1.74 +/- 0.36 vs. 1.89 +/- 0.36 mmol/L, P < .05), whereas that in the pulse group remained unchanged. At therapeutic end point, [Ca2+] x [P3+] level in the daily group was higher than that before the therapy (48.04 +/- 11.71 vs. 55.46 +/- 12.66, P < .05), whereas in the pulse group there was no significant difference. Side effects for both groups were minimal and well tolerated. CONCLUSIONS Alfacalcidol [1alpha-(OH)-D3] has good and safe effects on secondary hyperparathyroidism in maintenance hemodialysis patients. The efficacy and early effects of pulse therapy are superior to those of daily therapy in moderate hyperparathyroidism patients.
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Gu Y. Comparisons Between Oral Pulse Alfacalcidol Therapy and Daily Therapy in Maintenance Hemodialysis Patients with Secondary Hyperparathyroidism: A Randomized, Controlled, and Multicenter Study. Ren Fail 2005. [DOI: 10.1081/jdi-49538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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380
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Peng A, Gu Y, Lin SY. Herbal treatment for renal diseases. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2005; 34:44-51. [PMID: 15726219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Renal fibrosis is a common consequence of chronic kidney diseases (CKD). Standard therapy to prevent progression of CKD in western medicine includes dietary protein restriction, blood pressure control, angiotensin-converting enzyme inhibition and angiotensin receptor blockade. However, little is known about the renoprotective effects of Chinese herbal medicine. Cumulative evidence suggests that some Chinese herbal medicines, including Astragalus and a mixture of Astragalus plus Angelica, Ligusticum, Triptolide and Rhubarb, have a beneficial role in slowing the progression of CKD. This effect is multi-functional and multi-targeted, and is often associated with a reduction in proteinuria and the amelioration of dyslipidaemia, but not with changes in systemic blood pressure. These mechanisms include anti-inflammation and inhibition of TGF-b overproduction. On the other hand, some Chinese herbal medicines may be hazardous to patients with renal diseases. In this review, we discuss recent advances in the research of some Chinese herbs for pharmacological intervention of progressive renal diseases and kidney-related injuries.
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Yun LB, Ying BW, Fang YQ, Sun XM, Gu Y, Shi MS, Zhang J, Liang ZH, Li YB, Wu J, Hou YP. Polymorphism of three STR loci in Chinese population. J Forensic Sci 2005; 50:235. [PMID: 15831030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
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382
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Yun LB, Ying BW, Gu Y, Fang YQ, Sun XM, Huang J, Zhang J, Li YB, Wu J, Hou YP. Polymorphism data of two STR loci DYS632 and DYS634 in a Chinese Han population. J Forensic Sci 2004; 49:1373. [PMID: 15568721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
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383
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Gu Y, Kirkman-Brown JC, Korchev Y, Barratt CLR, Publicover SJ. Multi-state, 4-aminopyridine-sensitive ion channels in human spermatozoa. Dev Biol 2004; 274:308-17. [PMID: 15385161 DOI: 10.1016/j.ydbio.2004.06.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2003] [Revised: 05/20/2004] [Accepted: 06/24/2004] [Indexed: 11/30/2022]
Abstract
Although ion channels are known to be pivotal to sperm function, the technical difficulty of applying electrophysiological techniques to spermatozoa has prevented significant progress in this area. This is due to the cell size and angular shape in combination with their motility. Using a refined technique, specifically for patch clamping spermatozoa, we have made recordings from human cells. This technique permitted approaches which enable functional analysis of sperm ion channels, including acquisition of inside-out patches, generation of averaged currents, and observation of the effects of pharmacological manipulation during prolonged recordings. As well as a low conductance (7 pS) channel and a 25-pS channel, the most striking finding was the presence of very high conductance, 4-aminopyridine-sensitive multistate channels resembling the non-selective cation channel of sea urchin and mouse spermatozoa. Application of 2 mM 4-aminopyridine (a dose sufficient to cause channel blockade) caused an instant and dramatic transition of motility in the sperm population increasing hyperactivated motility by more than 10-fold as assessed by computer-assisted semen analysis. Combined application of patch clamp and pharmacological investigation of mature sperm cells and will permit rapid advances in our understanding the role of ion channels in sperm function.
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Gu Y, Di WL, Kelsell DP, Zicha D. Quantitative fluorescence resonance energy transfer (FRET) measurement with acceptor photobleaching and spectral unmixing. J Microsc 2004; 215:162-73. [PMID: 15315503 DOI: 10.1111/j.0022-2720.2004.01365.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence resonance energy transfer (FRET) by acceptor photobleaching is a simple but effective tool for measurements of protein-protein interactions. Until recently, it has been restricted to qualitative or relative assessments owing to the spectral bleed-through contamination resulting from fluorescence overlap between the donor and the acceptor. In this paper, we report a quantitative algorithm that combines the spectral unmixing technique with FRET by acceptor photobleaching. By spectrally unmixing the emissions before and after photobleaching, it is possible to resolve the spectral bleed-through and retrieve the FRET efficiency/interaction distance quantitatively. Using a human keratinocyte cell line transfected with cyan fluorescent protein (CFP)- and yellow fluorescent protein (YFP)-tagged Cx26 connexins as an example, FRET information at homotypic gap junctions is measured and compared with well-established methods. Results indicate that the new approach is sensitive, flexible, instrument independent and solely FRET dependent. It can achieve FRET estimations similar to that from a sensitized emission FRET method. This approach has a great advantage in providing the relative concentrations of the donor and the acceptor; this is, for example, very important in the comparative study of cell populations with variable expression levels.
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385
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Gu Y, Angelaki DE, DeAngelis GC. Visual and Vestibular Contributions to 3D Heading Selectivity in Area MSTd. J Vis 2004. [DOI: 10.1167/4.8.708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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386
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Karlsson H, Gu Y, DePierre J, Nässberger L. Induction of apoptosis in proliferating lymphocytes by tricyclic antidepressants. Apoptosis 2003; 3:255-60. [PMID: 14646489 DOI: 10.1023/a:1009609224936] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have previously found that tricyclic antidepressants (TCAs) induce apoptosis in quiescent human lymphocytes. The aim of the present study was to evaluate if TCAs induce apoptosis in proliferating human lymphocytes and in established blastoid lymphocytes also. The development of conA-induced lymphoblast populations was followed by measuring the CD25 membrane expression. Three TCA compounds were run with the following concentrations: imipramine (10, 20, 30, 40, 60 microM), clomipramine (1, 10, 20, 30, 40 microM) and citalopram (40, 60, 80, 100, 180 microM). They all induced a dose-dependent apoptosis both in continuously transformed, as well as in established lymphoblasts. Preincubation of the TCA up to 48 h did not significantly increase induction of apoptosis. The three drugs tested were found to be potent inducers of apoptosis in proliferating lymphocytes. Furthermore, we found that the apoptotic populations in proliferating and in established blastoid lymphocytes were of fairly the same magnitude than in the corresponding population in TCA-incubated resting lymphocytes. In conclusion, we demonstrate that TCAs induce apoptosis in proliferating lymphocytes, as they do in quiescent lymphocytes. Furthermore, the extent of apoptosis was even more pronounced in TCA-incubated lymphoblasts compared to TCA-treated resting lymphocytes.
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387
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Li CZ, Cheng LF, Wang ZQ, Gu Y. Photodynamic therapy of esophageal varices: experimental studies in animal veins, and first clinical cases. Endoscopy 2003; 35:1043-8. [PMID: 14648419 DOI: 10.1055/s-2003-44600] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
BACKGROUND AND STUDY AIMS Endoscopic injection sclerotherapy and endoscopic variceal ligation have been found to have shortcomings in the treatment of esophageal varices. In this study the effectiveness of photodynamic therapy (PDT) in the obliteration of veins was investigated to evaluate its potential in the treatment of esophageal varices. METHODS Auricular margin veins of rabbits were irradiated by copper vapor laser after intravenous injection of 10 mg/kg of hematoporphyrin monomethyl ether (which is a hematoporphyrin derivative) into the rabbits. Control groups included rabbits that received irradiation only, that received injection of photosensitizer only, and that received injection sclerotherapy (using sodium morrhuate). The treated areas were observed macroscopically and also identified using with ultrasonic miniprobe. Biopsies were performed and the specimens were examined microscopically after hematoxylin-eosin staining and Victoria blue staining. In addition, two patients with newly visible veins within the esophageal wall after endoscopic injection sclerotherapy underwent PDT. Intravenous injection of 5 mg/kg of hematoporphyrin monomethyl ether was given, and the newly visible veins were endoscopically irradiated by copper vapor laser. Endoscopic re-examination was performed 1 month later to evaluate the therapeutic effect. RESULTS Thrombi of the auricular margin vein were formed and blood flow was obstructed after PDT. Thrombus formation and diffused necrosis of adjacent tissue was found after injection of sodium morrhuate. On ultrasonic examination, the lumina of the veins showed a slightly higher echo after PDT compared with a lower echo before treatment, which was another sign of thrombus formation. The rabbit ears showed a diffused low echo after injection of sodium morrhuate, indicating diffuse necrosis. On microscopic observation, destruction of the endothelium and formation of thrombus was seen after PDT. Further observation of specimens stained with Victoria blue showed that the layer of elastic fiber was intact. After injection of sodium morrhuate, extensive necrosis of tissue was seen microscopically. No macroscopic, ultrasonic, or microscopic change was found in the rabbits that received irradiation only or injection of photosensitizer only. The rate of thrombus formation in rabbits that received PDT was significantly higher than that in the rabbits that received irradiation only or injection of photosensitizor only ( P = 0.015, P = 0.015), and comparable to that in the rabbits that received sclerotherapy ( P = 0.467). In the clinical study, at endoscopy 1 month after PDT both the number and the "red sign" of newly visible veins were found to have decreased. No adverse effect was found. CONCLUSION PDT can destroy the endothelium of the vein, result in thrombus formation, and eventually obliterate the vein. It is potentially a new method for the treatment of esophageal varices.
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388
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Gu Y, Nelson DL. FMR2 function: insight from a mouse knockout model. Cytogenet Genome Res 2003; 100:129-39. [PMID: 14526173 DOI: 10.1159/000072847] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2003] [Accepted: 02/28/2003] [Indexed: 11/19/2022] Open
Abstract
The FMR2 gene is dysregulated by the fragile X E triplet repeat expansion in patients with FRAXE mental retardation syndrome. A CCG triplet, located in the 5' untranslated region of the FRAXE gene undergoes expansion and methylation in these patients, eliminating detectable gene transcription. FRAXE syndrome is distinct from fragile X syndrome, a more common genetic form of mental retardation caused by expansion and methylation of a similar repeat in the FMR1 gene located 600 kb proximal to FRAXE. FRAXE syndrome is rare, and patients' phenotypes are highly variable, leading to difficulties with predicting specific FMR2 functions based on the human disease. Recently, Lilliputian(Lilli), a Drosophila FMR2 orthologue, was identified; this gene has been linked with several signal transduction pathways, including the transforming growth factor-beta (TGF-beta) pathway, the Raf/MEK/MAP kinase (MAPK) pathway, and the P13K/PKB pathway. Mutation of Lilli shows defects in germinal band extension, cytoskeletal structure, cell growth, and organ development. The Lilli gene suggests possible functions for FMR2 (and related genes) in humans and mice, but cannot predict specific functions. Modeling FMR2 mutation in the mouse will be useful to understand specific functions of this gene in vertebrates. This review presents what has been learned thus far from the FMR2 knockout mouse model and suggests future studies on this model in order to compare it with the human FRAXE mental retardation disorder, Lilli mutants in Drosophila and other mouse models of genes in this family.
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Iwatate M, Gu Y, Dieterle T, Iwanaga Y, Peterson KL, Hoshijima M, Chien KR, Ross J. In vivo high-efficiency transcoronary gene delivery and Cre-LoxP gene switching in the adult mouse heart. Gene Ther 2003; 10:1814-20. [PMID: 12960971 DOI: 10.1038/sj.gt.3302077] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-efficiency somatic gene transfer in adult mouse heart has not yet been achieved in vivo. Here, we demonstrate high-efficiency in vivo transcoronary gene delivery to the adult murine myocardium using a catheter-based technique with recombinant adenovirus (AdV) and adeno-associated virus (AAV) vectors in normal and genetically engineered mice. The method involves immersion hypothermia followed by transient aortic and pulmonary artery occlusion with proximal intra-aortic segmental injection of cardioplegic solution containing substance P and viral vectors. Gene expression measured using a LacZ marker gene was observed throughout both ventricles. The expression efficiency of a cytoplasmic LacZ marker gene in the left ventricular myocardium was 56.4+/-14.5% (mean+/-s.d.) at 4 days with an AdV vector, and with an AAV vector it was 81.0+/-5.9% at 4 weeks. Following AAV gene transfer, no gene expression was found in kidney, brain, lung, and spleen, but there was slight expression in liver. In addition, we demonstrate temporally controlled genetic manipulation in the heart with an efficiency of 54.6+/-5.2%, by transferring an AdV vector carrying Cre recombinase in ROSA26 flox-LacZ reporter mice. Procedure-related mortality was 16% for AdV and zero for AAV transfer. Thus, this method provides efficient, relatively homogeneous gene expression in both ventricles of the adult mouse heart, and offers a novel approach for conditional gene rescue or ablation in genetically engineered mouse models.
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Wang Y, Zhang Y, Lewis DF, Gu Y, Li H, Granger DN, Alexander JS. Protease chymotrypsin mediates the endothelial expression of P- and E-selectin, but not ICAM and VCAM, induced by placental trophoblasts from pre-eclamptic pregnancies. Placenta 2003; 24:851-61. [PMID: 13129682 DOI: 10.1016/s0143-4004(03)00132-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
OBJECTIVES Soluble endothelial-cell adhesion molecules (ICAM, VCAM and PECAM) are markers of endothelial activation, and are elevated in the maternal circulation during pregnancy and even further increased in pregnancies complicated by pre-eclampsia (PE). To identify possible sources of endothelial activators during pregnancy, we addressed whether factors released from placental trophoblast cells (TCs) activate endothelial cells (ECs) to enhance adhesion molecule expression on ECs. We also examined whether proteases released by placental cells induce the endothelial cell surface molecule expression in PE. METHODS Confluent ECs were co-cultured with placental TCs derived from normal (n=9) or PE (n=8) pregnancies or with placental conditioned media (CM) derived from PE placental cultures (n=7). ICAM, VCAM, P-selectin and E-selectin were quantified using an enzyme-linked immunosorbent assay (ELISA). The protease inhibitors alpha(2)-macroglobulin (alpha(2)M), thrombin inhibitor (TI) and chymotrypsin inhibitor (CI) were tested in the co-culture system. mRNAs for ICAM, VCAM, P-selectin and E-selectin were determined by RNase protection assay (RPA). NF-kappaB activity in ECs was also determined. RESULTS (1) ICAM and VCAM expression was significantly increased on ECs co-cultured with both normal-TCs and PE-TCs, compared to control ECs (P<0.01). ICAM and VCAM expression in ECs co-cultured with normal-TCs did not differ from ECs co-cultured with PE-TCs. (2) E-selectin expression was increased on ECs co-cultured with normal-TCs (P<0.05) and further increased in ECs co-cultured with PE-TCs (P<0.01). (3) P-selectin expression was increased on ECs co-cultured with PE-TCs, but not ECs co-cultured with normal-TCs compared to control ECs (P<0.05). (4) alpha(2)M and TI did not alter the ICAM, VCAM, P-selectin and E-selectin expression on ECs induced by PE-CM. (5) CI blocked the upregulation of P-selectin and E-selectin (P<0.05), but not ICAM and VCAM expression, in ECs cultured with PE-CM. (6) Changes in mRNA for ICAM, VCAM, P-selectin and E-selectin paralleled the increases in protein expression on ECs cultured with PE-CM. (7) NF-kappaB activity was also increased in cells challenged with PE-CM. CONCLUSIONS (1) Factor(s) released from both normal-TCs and PE-TCs promote ICAM and VCAM expression on ECs. (2) Factor(s) released from PE-TCs significantly increase EC P-selectin and E-selectin expression. (3) CI blocks the upregulation of P-selectin and E-selectin on ECs induced by factors released from PE placental cells, suggesting that chymotrypsin is responsible for the increased endothelial expression of P-selectin and E-selectin in pre-eclampsia.
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Cenci A, Chantret N, Kong X, Gu Y, Anderson OD, Fahima T, Distelfeld A, Dubcovsky J. Construction and characterization of a half million clone BAC library of durum wheat ( Triticum turgidum ssp. durum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 107:931-9. [PMID: 12830387 DOI: 10.1007/s00122-003-1331-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2002] [Accepted: 03/14/2003] [Indexed: 05/21/2023]
Abstract
Durum wheat ( Triticum turgidum ssp. durum, 2 n = 4 x = 28, genomes AB) is an economically important cereal used as the raw material to make pasta and semolina. In this paper we present the construction and characterization of a bacterial artificial chromosome (BAC) library of tetraploid durum wheat cv. Langdon. This variety was selected because of the availability of substitution lines that facilitate the assignment of BACs to the A and B genome. The selected Langdon line has a 30-cM segment of chromosome 6BS from T. turgidum ssp. dicoccoides carrying a gene for high grain protein content, the target of a positional cloning effort in our laboratory. A total of 516,096 clones were organized in 1,344 384-well plates and blotted on 28 high-density filters. Ninety-eight percent of these clones had wheat DNA inserts (0.3% chloroplast DNA, 1.4% empty clones and 0.3% empty wells). The average insert size of 500 randomly selected BAC clones was 131 kb, resulting in a coverage of 5.1-fold genome equivalents for each of the two genomes, and a 99.4% probability of recovering any gene from each of the two genomes of durum wheat. Six known copy-number probes were used to validate this theoretical coverage and gave an estimated coverage of 5.8-fold genome equivalents. Screening of the library with 11 probes related to grain storage proteins and starch biosynthesis showed that the library contains several clones for each of these genes, confirming the value of the library in characterizing the organization of these important gene families. In addition, characterization of fingerprints from colinear BACs from the A and B genomes showed a large differentiation between the A and B genomes. This library will be a useful tool for evolutionary studies in one of the best characterized polyploid systems and a source of valuable genes for wheat. Clones and high-density filters can be requested at http://agronomy.ucdavis.edu/Dubcovsky/BAC-library/BAC_Langdon.htm
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Hu J, Pavel I, Moigno D, Wumaier M, Kiefer W, Chen Z, Ye Y, Wu Q, Huang Q, Chen S, Niu F, Gu Y. Fourier-transform Raman and infrared spectroscopic analysis of 2-nitro-tetraphenylporphyrin and metallo-2-nitro-tetraphenylporphyrins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2003; 59:1929-1935. [PMID: 12788447 DOI: 10.1016/s1386-1425(02)00279-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The Fourier-transform Raman (FT-Raman) and infrared (FT-IR) spectra of 2-nitro-tetraphenylporphyrin (2-NO(2)-TPP), nickel-2-nitro-tetraphenylporphyrin (Ni-2-NO(2)-TPP), zinc-2-nitro-tetraphenylporphyrin (Zn-2-NO(2)-TPP) and copper-2-nitro-tetraphenylporphyrin (Cu-2-NO(2)-TPP) were acquired for the first time and carefully assigned and discussed. The effects of a beta-NO(2) group and the influence of the central metal on the molecular symmetry and vibrational spectra of the porphyrin macrocycle were also examined. The bands at 1323-1339, 1516-1526 and 961-971 cm(-1) were attributed to the symmetric and asymmetric stretching vibration of the NO(2) group and to the stretching vibration of the C(beta)-N bond, respectively, which connects the NO(2) group with the beta-carbon of the porphyrin macrocycle. These bands can act as a marker to distinguish beta-NO(2) TPPs from other beta-substituent TPPs. Cu-2-NO(2)-TPP has a C(4nu) molecular symmetry, which is different from those of Ni-2-NO(2)-TPP and Zn-2-NO(2)-TPP, i.e. D(4h).
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Ferguson DO, Sekiguchi JM, Frank KM, Gao Y, Sharpless NE, Gu Y, Manis J, DePinho RA, Alt FW. The interplay between nonhomologous end-joining and cell cycle checkpoint factors in development, genomic stability, and tumorigenesis. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 65:395-403. [PMID: 12760055 DOI: 10.1101/sqb.2000.65.395] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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394
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Wang W, Gu Y, Liu Y. Applications of Weak Gel for In-Depth Profile Modification and Oil Displacement. ACTA ACUST UNITED AC 2003. [DOI: 10.2118/03-06-04] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract
Water breakthrough is a common problem when an oil field is waterflooded. Polymer solutions are widely applied to resolve the water channeling problem in deep formations. In practice, polymers are used in deep formation treatments either to block in-depth high permeability zones or to improve the mobility ratio. However, the major challenge for in-depth profile modification is how to deliver the gelling solution to the target zones. To this end, a polymer solution has to be injected at a high concentration. Thus, such a treatment sometimes becomes uneconomical. On the other hand, polymer flooding is ineffective primarily due to the viscosity loss caused by mechanical and chemical degradation. In this paper, a weak gel system is developed and used as an in-depth profile modification agent and as an oil displacement agent in a heterogeneous reservoir. The gel system has relatively low strength but can still be crosslinked in the reservoir formation. In comparison with a pure polymer solution, it suffers from less mechanical and chemical degradation because of its crosslink reaction. The EOR mechanisms of the weak gel system are described briefly. The detailed effects of polymer concentration, crosslinker concentration, temperature, and pH on gelation time are studied. Also the rheological properties, gelation range, and gel strength are examined. The coreflood results provide experimental evidence that the weak gel acts both as an in-depth profile modification agent and as an oil displacement agent. Furthermore, pilot tests have been performed in the Gudong and the Gudao oil fields of the Shengli oil field in China since 1992. The cummulative incremental oil production has been over 58,000 tonnes at the end of 2001.
Introduction
Waterflooding is the most widely used technology for improving oil recovery. However, early water breakthrough is a common problem encountered in almost every waterflooded oil field. Severe water channeling can result in low waterflooding efficiency and sometimes even make waterflooding uneconomical. There are several reasons for water breakthrough. Sometimes, it happens near the wellbore region, such as breakthrough along the casing due to poor cementing quality. In other cases, water breakthrough occurs in a deep formation because of its heterogeneity or fractures. In addition, because of the mobility difference between the displacing phase and the displaced phase, the former tends to bypass the latter in a homogeneous formation. In this case, viscous fingering is inevitable and early water breakthrough occurs in the producers(1–3). Different technologies have been implemented to reduce the high water-cut caused by water breakthrough, among which the most widely used is polymer injection. In general, polymer is increasingly used in chemical EOR in two traditional ways: either as an in-depth profile modification agent in conformance control, or as an oil displacement agent in polymer flooding.
For conformance control, polymer and crosslinker are injected into formations to reduce large channeling through fractures or high permeability zones without damaging the productivity of the hydrocarbon. However, due to the prompt crosslink reaction, gel is sometimes formed near the wellbore.
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Xu Y, Gu Y, Xu GY, Wu P, Li GW, Huang LYM. Adeno-associated viral transfer of opioid receptor gene to primary sensory neurons: a strategy to increase opioid antinociception. Proc Natl Acad Sci U S A 2003; 100:6204-9. [PMID: 12719538 PMCID: PMC156350 DOI: 10.1073/pnas.0930324100] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To develop a genetic approach for the treatment of pain, we introduced a recombinant adeno-associated viral (rAAV) vector containing the cDNA for the mu-opioid receptor (muOR) into primary afferent neurons in dorsal root ganglia (DRGs) of rats, which resulted in a long-lasting (>6 months) increase in muOR expression in DRG neurons. The increase greatly potentiated the antinociceptive effects of morphine in rAAV-muOR-infected rats with and without inflammation. Perforated patch recordings indicated that the efficacy and potency of opioid inhibition of voltage-dependent Ca(2+) channels were enhanced in infected neurons, which may underlie the increase in opiate efficacy. These data suggest that transfer of opioid receptor genes into DRG cells with rAAV vectors may offer a new therapeutic strategy for pain management.
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396
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Zask A, Gu Y, Albright JD, Du X, Hogan M, Levin JI, Chen JM, Killar LM, Sung A, DiJoseph JF, Sharr MA, Roth CE, Skala S, Jin G, Cowling R, Mohler KM, Barone D, Black R, March C, Skotnicki JS. Synthesis and SAR of bicyclic heteroaryl hydroxamic acid MMP and TACE inhibitors. Bioorg Med Chem Lett 2003; 13:1487-90. [PMID: 12668018 DOI: 10.1016/s0960-894x(03)00127-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Potent and selective bicyclic heteroaryl hydroxamic acid MMP and TACE inhibitors were synthesized by a novel convergent route. Selectivity and efficacy versus MMPs and TACE could be controlled by appropriate substitution on the scaffolds and by variation of the P1' group. Select compounds were found to be effective in in vivo models of arthritis.
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397
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Dahmen U, Gu Y, Shen K, Dirsch O, Li J, Fan L, Broelsch C. Onset of liver regeneration after subtotal resection is inhibited by the use of new immunosuppressive drugs. Transplant Proc 2003; 34:2312-3. [PMID: 12270412 DOI: 10.1016/s0041-1345(02)03249-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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398
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Dunsby C, Gu Y, French P. Single-shot phase-stepped wide-field coherencegated imaging. OPTICS EXPRESS 2003; 11:105-15. [PMID: 19461712 DOI: 10.1364/oe.11.000105] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We present a single-shot wide-field CCD based coherence-gated imaging technique that utilizes spatially separated phase-stepped images and requires only one CCD camera to achieve simultaneous acquisition of four phase-stepped images. This technique provides a relatively low cost system for depth-resolved imaging of dynamic samples. We demonstrate real-time coherence-gated imaging of a moving watch cog, 3D reconstructions of a coin, phase measurements of the surface of a test-chart and depth-resolved imaging in a weakly scattering sample of onion.
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399
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Rose WI, Gu Y, Watson IM, Yu T, Blut GJS, Prata AJ, Krueger AJ, Krotkov N, Carn S, Fromm MD, Hunton DE, Ernst GGJ, Viggiano AA, Miller TM, Ballenthin JO, Reeves JM, Wilson JC, Anderson BE, Flittner DE. The February–March 2000 eruption of Hekla, Iceland from a satellite perspective. VOLCANISM AND THE EARTH'S ATMOSPHERE 2003. [DOI: 10.1029/139gm07] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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400
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Gu Y, Ebraheim NA, Yeasting RA. Identification of the anterior and posterior portions of the lateral pedicle cortex by roentgenograms in pedicle screw fixation. Surg Radiol Anat 2002; 24:313-8. [PMID: 12497223 DOI: 10.1007/s00276-002-0049-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2001] [Accepted: 04/06/2002] [Indexed: 10/27/2022]
Abstract
Forty lumbar pedicles and pedicle screws in four cadavers were used to identify the anterior and posterior portions of the lumbar pedicle cortex by roentgenograms in order to evaluate the penetration of the pedicle cortex by pedicle screws intraoperatively. Firstly, the transverse pedicle angles were measured on roentgenograms. Three roentgenograms were taken on each pedicle in three different directions: (1). medial to the pedicle axis; (2). pedicle axis; (3). lateral to the pedicle axis. They revealed that the anterior portion of the lateral pedicle cortex was demonstrated by the pedicle lateral outline on the roentgenogram medial to the pedicle axis, and the posterior portion by the pedicle lateral outline on the roentgenogram lateral to the pedicle axis. Wire markers were used to confirm these data. Finally, anterior and/or posterior penetrations on the lateral pedicle cortex in pedicle screw fixation were studied by roentgenograms in these cadavers and showed that anterior penetration of lateral cortex was demonstrated by the view medial to the pedicle axis, and posterior penetration by the view lateral to the pedicle axis. It is concluded that projections medical and lateral to the pedicle axis are necessary to identify lateral screw penetration intraoperatively when X-ray checking is used.
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