26
|
Ling SM, Patel DD, Garnero P, Zhan M, Vaduganathan M, Muller D, Taub D, Bathon JM, Hochberg M, Abernethy DR, Metter EJ, Ferrucci L. Serum protein signatures detect early radiographic osteoarthritis. Osteoarthritis Cartilage 2009; 17:43-8. [PMID: 18571442 PMCID: PMC2667202 DOI: 10.1016/j.joca.2008.05.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Accepted: 05/04/2008] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To test the hypothesis that early knee and hand osteoarthritis (OA) development is characterized by detectable changes in serum proteins relevant to inflammation, cell growth, activation, and metabolism several years before OA becomes radiographically evident. METHODS Using microarray platforms that simultaneously test 169 proteins relevant to inflammation, cell growth, activation and metabolism, we conducted a case-control study nested within the Baltimore Longitudinal Study of Aging (BLSA). Subjects included 22 incident cases of OA and 66 age-, sex- and body mass index (BMI)-matched controls. Serum samples tested were obtained at the time of radiographic classification as either case or control, and up to 10 years earlier at a time when all participants were free of radiographic OA. Proteins with mean signal intensities fourfold higher than background were compared between cases and controls using multivariate techniques. RESULTS Sixteen proteins were different between OA cases compared to controls. Four of these proteins [matrix metalloproteinase (MMP)-7, interleukin (IL)-15, plasminogen activator inhibitor (PAI)-1 and soluble vascular adhesion protein (sVAP)-1] were already different in samples obtained 10 years before radiographic classification and remained different at the time of diagnosis. Six additional proteins were only associated with subsequent OA development and not with established OA. CONCLUSIONS Changes in serum proteins implicated in matrix degradation, cell activation, inflammation and bone collagen degradation products accompany early OA development and can precede radiographic detection by several years.
Collapse
|
27
|
Jiao X, Langenberg P, Zhan M, Perencevich E, Ioffe O, Yuan Y, Maruyama R, Krasna MJ. Clinical significance of pleural lavage cytology in non-small cell lung cancer: A meta-analysis. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.18031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
18031 Background: The clinical significance of pleural lavage cytology (PLC) in non-small-cell lung cancer (NSCLC) remains controversial. This study was performed to estimate the associations of positive PLC with the main clinicopathological characteristics, and its prognostic value. Methods: PLC studies were identified on Medline, supplemented by manual search of bibliographies and proceedings. Authors were contacted for updated information. The quality of the studies was evaluated, and the data were extracted. Pooled odds ratios (ORs) and pooled hazard ratios (HRs) with confidence intervals [95% CIs] were calculated to evaluate the association of positive PLC with clinico-pathological characteristics and survival respectively. Results: Nineteen articles assessing PLC in NSCLC were selected for this study after exclusion of repeated publications or reports with little clinical detail. Positive PLC was diagnosed in 10.2% (516) of a total of 5073 patients. Positive PLC was strongly associated with lymphatic permeation (OR 4.96 [3.29, 7.54]), pleural invasion (OR 4.38 [2.16, 8.89], and vascular involvement (OR 2.94 [1.99, 4.35]). It was also found to be associated with advanced T stage, N stage, and TNM stage. Positive PLC was more frequent in adenocarcinoma than in squamous cell carcinoma (OR 2.32, [1.51, 3.52]). It was relatively more common in moderately- and poorly-differentiated tumors than in well-differentiated tumors (OR 1.89 [0.86, 4.16]). No association was found between positive PLC and fine needle aspiration cytology (OR 1.04 [0.58, 1.81]). Positive PLC was associated with high overall recurrence (OR 2.51 [1.79, 3.53]), as well as high local recurrence (OR 3.85 [1.57, 9.44]) and distant recurrence (2.58 [1.76, 3.76]). In analysis of survival, the overall HR for mortality was 2.43 [1.87, 3.16], suggesting significantly poorer survival for patients with positive PLC. Conclusions: Positive PLC in NSCLC is strongly associated with several existing poor prognosticators including pleural invasion, lymphatic spread, and vascular involvement. It may indicate locally advanced disease with high risk of recurrence and poor survival. We recommend that the PLC test be included in future clinical trials of adjuvant therapy for patients with NSCLC. No significant financial relationships to disclose.
Collapse
|
28
|
Wang S, Zhan M, Yin J, Abraham JM, Mori Y, Sato F, Xu Y, Olaru A, Berki AT, Li H, Schulmann K, Kan T, Hamilton JP, Paun B, Yu MM, Jin Z, Cheng Y, Ito T, Mantzur C, Greenwald BD, Meltzer SJ. Transcriptional profiling suggests that Barrett's metaplasia is an early intermediate stage in esophageal adenocarcinogenesis. Oncogene 2006; 25:3346-56. [PMID: 16449976 DOI: 10.1038/sj.onc.1209357] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To investigate the relationship between Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC), we determined gene expression profiles of discrete pathological stages of esophageal neoplasia using a sequence-verified human cDNA microarray. Fifty one RNAs, comprising 24 normal esophagi (NE), 18 BEs, and nine EACs were hybridized to cDNA microarrays. Five statistical analyses were used for the data analysis. Genes showing significantly different expression levels among the three sample groups were identified. Genes were grouped into functional categories based on the Gene Ontology Consortium. Surprisingly, the expression pattern of BE was significantly more similar to EAC than to NE, notwithstanding the known histopathologic differences between BE and EAC. The pattern of NE was clearly distinct from that of EAC. Thirty-six genes were the most differentially modulated, according to these microarray data, in BE-associated neoplastic progression. Twelve genes were significantly differentially expressed in cancer-associated BE's plus EAC (as a single combined tissue group) vs noncancer-associated BE's. These genes represent potential biomarkers to diagnose EAC at its early stages. Our results demonstrate that molecular events at the transcriptional level in BE are remarkably similar to BE's-associated adenocarcinoma of the esophagus. This finding alarmingly implies that BE is biologically closer to cancer than to normal esophagus, and that the cancer risk of BE is perhaps higher than we had imagined. These findings suggest that changes modulated at the molecular biologic level supervene earlier than histologic changes, and that BE is an early intermediate stage in the process of EAC.
Collapse
|
29
|
Graber J, Zhan M, Ford D, Kursch F, Francis G, Bever C, Panitch H, Calabresi PA, Dhib-Jalbut S. Interferon-beta-1a induces increases in vascular cell adhesion molecule: implications for its mode of action in multiple sclerosis. J Neuroimmunol 2005; 161:169-76. [PMID: 15748956 DOI: 10.1016/j.jneuroim.2004.11.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2004] [Revised: 11/24/2004] [Accepted: 11/24/2004] [Indexed: 10/25/2022]
Abstract
We investigated soluble vascular cell adhesion molecule-1 (sVCAM) levels and MRI lesions over 24 weeks in 15 Relapsing Remitting MS (RRMS) patients randomized prospectively to receive once-weekly (qw) IFN-beta-1a 30 mug intramuscularly (IM) (Group I, 8 patients) or three-times-weekly (tiw) IFN-beta-1a 44 mug subcutaneously (SC) (Group II, 7 patients). Both groups demonstrated a significant increase in sVCAM during treatment when compared to pre-treatment levels. Patients on IFN-beta-1a 44 mug SC tiw had a significant (p<0.0001) mean increase in sVCAM of 321.9 ng/ml which was significantly greater (p<0.0001) than with IFN-beta-1a 30 mug IM qw (68.6 ng/ml). There was a negative correlation between combined unique (CU) MRI lesions and sVCAM levels within the IFN-beta-1a 44 mug SC tiw group (slope=-0.00106, p=0.009). We postulate that the mode of action of IFN-beta therapy in MS may involve the induction of an increase in sVCAM. sVCAM could bind VLA-4 on T-cells and intercept their adhesion to the blood brain barrier (BBB). This mechanism is consistent with the observed clinical effect of IFN-beta in reducing MRI contrast enhancing lesions.
Collapse
|
30
|
Roghmann M, Taylor KL, Gupte A, Zhan M, Johnson JA, Cross A, Edelman R, Fattom AI. Epidemiology of capsular and surface polysaccharide in Staphylococcus aureus infections complicated by bacteraemia. J Hosp Infect 2005; 59:27-32. [PMID: 15571850 DOI: 10.1016/j.jhin.2004.07.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2003] [Accepted: 07/09/2004] [Indexed: 10/26/2022]
Abstract
Staphylococcus aureus is a leading cause of serious hospital- and community-acquired infections. The discovery of serologically distinct capsular polysaccharides on the surface of clinical isolates has allowed the development of vaccines and passive protective immunity. We have studied patient characteristics, infection characteristics and the surface and capsular polysaccharide serotype distribution in patients with S. aureus infections complicated by bacteraemia admitted to VA hospitals in Maryland between 1995 and 2000. Nine hundred and ninety-three blood cultures from 331 patients were positive for S. aureus. Thirty-eight percent of patients had diabetes, 11% had end-stage renal failure, and 23% were injection drug users. Forty-two percent of infections were caused by methicillin-resistant strains (MRSA), and 60% were acquired during hospitalization. Serotyping of the first available isolate per patient (N=234 isolates) using polyclonal antibodies showed three major phenotypes--42%, type 8 (T8) capsule; 50%, type 5 (T5) capsule; and 8%, 336 polysaccharide. MRSA isolates were significantly more likely to be T5 than methicillin-susceptible isolates (66% vs. 39%, P<0.001). The proportion of T5 MRSA increased significantly (years 1-2: 41%; years 3-4: 65%; years 5-6: 90%, P<0.001). This large sample of patients with serious S. aureus infection confirms that capsular polysaccharides T5 and T8 cause most human infections, and together with serotype 336, account for nearly all those with bacteraemia.
Collapse
|
31
|
Zhan M, Han ZC. Phosphatidylinositide 3-kinase/AKT in radiation responses. Histol Histopathol 2004; 19:915-23. [PMID: 15168354 DOI: 10.14670/hh-19.915] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ionizing or ultraviolet radiation-induced cellular survival signaling pathways induce development of cancer and insensitivity of tumor cells to radiation therapy. Accumulating evidence suggests that the phosphatidylinositide 3-kinase (PI3K)/AKT signal pathway is a major contributor to radioresistance. In many cell types PI3K/AKT signaling is a key cytoprotective response downstream of the EGFR family receptors and mediated carcinogenesis. Cytokines, such as HGF, IGF-I, and IL-6 also protects cells against apoptosis induced by radiation through PI3K/AKT pathway. The mechanics by which PI3K/AKT signaling functions in radiation responses may include its regulation of mitochondrial proteins, transcription factors, translation machinery, and cell-cycle progression. In addition, cross-talk between the PI3K/AKT pathway and mitogen-activated protein kinases, protein kinase A, and protein kinase C signal pathway may also play an important role.
Collapse
|
32
|
Abstract
Apoptosis following loss of cell anchorage ('anoikis') is of relevance for development, tissue homeostasis and disease. Integrins regulate cell viability through their interaction with the extracellular matrix and they can sense mechanical forces arising from the matrix and convert these stimuli to chemical signals capable of modulating intracellular signal transduction. Recently it has been shown that protein kinase signalling pathways and apoptosis-related molecular control anoikis both positively and negatively. Focal adhesion kinase, when activated by integrins, can suppress anoikis. Phosphatidylinositol 3-kinase/Akt and mitogen-activated protein kinase may mediate the anoikis-suppressing effects of cells. Conversely, the stress-activated protein kinase/Jun amino-terminal kinase pathway promotes anoikis. In addition, certain bcl-2 and bcl-2-related proteins may also participate in the regulating of anoikis. In this review, molecular mechanisms of signal pathway inducing and perpetuating detachment-induced apoptosis will be discussed with special emphasis on the role of integrins, focal adhesion kinase, phosphatidylinositol 3-kinase/Akt, mitogen-activated protein kinase and bcl-2 family members.
Collapse
|
33
|
Zhan M, Yu D, Lang A, Li L, Pollock RE. Wild type p53 sensitizes soft tissue sarcoma cells to doxorubicin by down-regulating multidrug resistance-1 expression. Cancer 2002. [PMID: 11745235 DOI: 10.1002/1097-0142(20010915)92:6<1556::aid-cncr1482>3.0.co;2-s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND p53 mutations occur in almost half of all soft tissue sarcomas (STS) and may contribute to multidrug resistance (MDR) in patients with STS. Doxorubicin (Dox) is one of the most active single agents in STS but is less effective in STS with p53 mutations. The effect of reintroducing wild type (wt) p53 into STS cells harboring p53 mutations on the cytotoxicity of DOX in vitro and in vivo was studied. METHODS The following cell lines were used in this study: SKLMS-1 STS cells, which do not express wt p53; two wt p53 stable transfectant cells derived from SKLMS-1 cells; and SKLMS-1 transfectant cells from a p53 temperature-sensitive mutant that expresses wt p53 at 32 degrees C and mutant p53 at 38 degrees C. The cytotoxicity of Dox was examined by [3-(4,5-dimethylthiazzol-2-yl)-2,5-diphenltetrazolium] (MTT) and clonogenetic assay, and the effect of reintroducing wt p53 on tumor suppression by Dox was evaluated with a tumorigenicity assay. DNA fragmentation was used to detect apoptosis. MDR-1 P-glycoprotein (P-gp) expression was detected by Western blot and immunohistochemical analyses of protein levels and by Northern blot analysis of mRNA levels, respectively. The intracellular accumulation of Dox was detected by flow cytometric analysis. RESULTS The 50% inhibitory concentration (IC(50)) of Dox for the SKLMS-1 wt p53 transfectants decreased 16-fold compared with SKLMS-1 parental cells expressing mutant p53. Colony formation of SKLMS-1 cells after Dox treatment also was inhibited by wt p53 reintroduction. The tumorigenicity of SKLMS-1 cells was inhibited by wt p53 reintroduction alone or by Dox treatment alone and was inhibited further when p53 introduction was combined with Dox treatment in severe combined immunodeficient mice. Although no difference in DNA fragmentation, Bax expression, or Bcl-2 expression was detected among wt p53 transfectants and parental SKLMS-1 cells after Dox treatment, MDR-1 P-gp expression was decreased in wt p53 transfectants compared with parental SKLMS-1 cells. Furthermore, higher intracellular accumulations of Dox were found in wt p53 transfectants than that in SKLMS-1 cells. CONCLUSIONS Reintroduction of wt p53 into STS cells harboring p53 mutations can enhance their chemosensitivity to Dox through the inhibition of MDR-1 P-gp expression. Thus, the combination of p53 gene therapy and chemotherapy may increase the therapeutic efficacy in the treatment of patients with STS.
Collapse
|
34
|
Zhan M, Hu G, He DH, Ma WQ. Phase locking in on-off intermittency. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2001; 64:066203. [PMID: 11736264 DOI: 10.1103/physreve.64.066203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2001] [Indexed: 05/23/2023]
Abstract
Dynamical behavior of on-off intermittency around chaos synchronization-desynchronization bifurcation parameter line is investigated in coupled identical chaotic oscillators. Along this parameter line, we find that on-off intermittency can transit from phase-unlocking status to phase-locking one in the phase space of variable differences, which can be regarded as a codimension-two bifurcation, i.e., combinative bifurcations of desynchronization and phase locking. In the phase-locking case, the motions of all oscillators are chaotic and they show on-off intermittency with respect to the synchronous manifold, however, spatial phase order of variable differences is clearly established.
Collapse
|
35
|
Zhan M, Yu D, Lang A, Li L, Pollock RE. Wild type p53 sensitizes soft tissue sarcoma cells to doxorubicin by down-regulating multidrug resistance-1 expression. Cancer 2001; 92:1556-66. [PMID: 11745235 DOI: 10.1002/1097-0142(20010915)92:6<1556::aid-cncr1482>3.0.co;2-s] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND p53 mutations occur in almost half of all soft tissue sarcomas (STS) and may contribute to multidrug resistance (MDR) in patients with STS. Doxorubicin (Dox) is one of the most active single agents in STS but is less effective in STS with p53 mutations. The effect of reintroducing wild type (wt) p53 into STS cells harboring p53 mutations on the cytotoxicity of DOX in vitro and in vivo was studied. METHODS The following cell lines were used in this study: SKLMS-1 STS cells, which do not express wt p53; two wt p53 stable transfectant cells derived from SKLMS-1 cells; and SKLMS-1 transfectant cells from a p53 temperature-sensitive mutant that expresses wt p53 at 32 degrees C and mutant p53 at 38 degrees C. The cytotoxicity of Dox was examined by [3-(4,5-dimethylthiazzol-2-yl)-2,5-diphenltetrazolium] (MTT) and clonogenetic assay, and the effect of reintroducing wt p53 on tumor suppression by Dox was evaluated with a tumorigenicity assay. DNA fragmentation was used to detect apoptosis. MDR-1 P-glycoprotein (P-gp) expression was detected by Western blot and immunohistochemical analyses of protein levels and by Northern blot analysis of mRNA levels, respectively. The intracellular accumulation of Dox was detected by flow cytometric analysis. RESULTS The 50% inhibitory concentration (IC(50)) of Dox for the SKLMS-1 wt p53 transfectants decreased 16-fold compared with SKLMS-1 parental cells expressing mutant p53. Colony formation of SKLMS-1 cells after Dox treatment also was inhibited by wt p53 reintroduction. The tumorigenicity of SKLMS-1 cells was inhibited by wt p53 reintroduction alone or by Dox treatment alone and was inhibited further when p53 introduction was combined with Dox treatment in severe combined immunodeficient mice. Although no difference in DNA fragmentation, Bax expression, or Bcl-2 expression was detected among wt p53 transfectants and parental SKLMS-1 cells after Dox treatment, MDR-1 P-gp expression was decreased in wt p53 transfectants compared with parental SKLMS-1 cells. Furthermore, higher intracellular accumulations of Dox were found in wt p53 transfectants than that in SKLMS-1 cells. CONCLUSIONS Reintroduction of wt p53 into STS cells harboring p53 mutations can enhance their chemosensitivity to Dox through the inhibition of MDR-1 P-gp expression. Thus, the combination of p53 gene therapy and chemotherapy may increase the therapeutic efficacy in the treatment of patients with STS.
Collapse
|
36
|
Zhao H, Liu X, Zhan M. [Measurement of the absorption coefficient of barium using cavity ringdown spectroscopy]. GUANG PU XUE YU GUANG PU FEN XI = GUANG PU 2001; 21:284-286. [PMID: 12947646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An apparatus for cavity ringdown spectroscopy was constructed and used for atomic absorption measurement. The transition probability for 6s6p1P1<--6s6s1S0 transition of barium atoms was obtained in the self-made apparatus. The relation between atomic absorption coefficient and atomic oven temperature was also analysed.
Collapse
|
37
|
Zhan M, Hu G, Zhang Y, He D. Generalized splay state in coupled chaotic oscillators induced by weak mutual resonant interactions. PHYSICAL REVIEW LETTERS 2001; 86:1510-1513. [PMID: 11290180 DOI: 10.1103/physrevlett.86.1510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2000] [Indexed: 05/23/2023]
Abstract
Dynamic behavior of coupled chaotic oscillators is investigated. A transition from high-dimensional hyperchaos to a generalized periodic splay state is found for extremely weak coupling. Chaotic nature of a single oscillator and mutual resonant interactions are regarded to be responsible for this self-organized ordering. The functional phase distribution of the generalized splay state, which is essentially different from the equal-phase-separation distribution of the conventional splay states, can be well predicted by analyzing a single periodically forced oscillator.
Collapse
|
38
|
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Deslattes Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. The sequence of the human genome. Science 2001; 291:1304-51. [PMID: 11181995 DOI: 10.1126/science.1058040] [Citation(s) in RCA: 7685] [Impact Index Per Article: 334.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
Collapse
|
39
|
Liao S, Zhan M, Yang Z. [Preliminary study on pathogenicity of hepatitis G virus]. ZHONGHUA SHI YAN HE LIN CHUANG BING DU XUE ZA ZHI = ZHONGHUA SHIYAN HE LINCHUANG BINGDUXUE ZAZHI = CHINESE JOURNAL OF EXPERIMENTAL AND CLINICAL VIROLOGY 2000; 14:358-60. [PMID: 11471026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
OBJECTIVE To study the clinical, enzymatic and liver pathological changes in patients with hepatitis G virus (HGV) infection. METHODS RT- nested PCR was applied to detect HGV RNA in 368 patients with hepatic diseases. The liver biopsy tissue from one liver cirrhosis patient with simple HGV infection was examined. RESULTS Simple HGV RNA positive were found in 7 cases of 71 acute hepatitis jaundice, in 22 cases of 155 chronic hepatitis and in 3 cases of 51 liver cirrhosis. The immunohistochemistry of the liver biopsy tissue from a liver cirrhosis patient showed HGV NS5 antigen positive. However, HGV infection might occur simply or in combination with hepatitis B or C virus or super infected. CONCLUSIONS HGV RNA could be detected in acute hepatitis jaundice, chronic hepatitis, hepatitis B or C carriers, liver cirrhosis and hepatocellular carcinoma. HGV is proved to be a hepatotropic virus by pathological examination and immunohistochemistry, the virus located in the cytoplasm of the liver cells. It may cause chronic hepatitis and even liver cirrhosis, so HGV is pathogenic to liver tissue.
Collapse
|
40
|
Zhan M, Zheng Z, Hu G, Peng X. Nonlocal chaotic phase synchronization. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 2000; 62:3552-3557. [PMID: 11088855 DOI: 10.1103/physreve.62.3552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2000] [Revised: 05/19/2000] [Indexed: 05/23/2023]
Abstract
A novel synchronization behavior, nonlocal chaotic phase synchronization, is investigated. For two coupled Rossler oscillators with only one forced by an injected periodic signal, the phase of the unforced oscillator can be locked to the phase of the periodic signal while the forced one is well unlocked by the signal; in a chain of coupled chaotic oscillators with nearest coupling, the phase of an oscillator (or a cluster) can be locked to another nonneighbor one. Moreover, the mechanism underlying the transition to nonlocal synchronization is discussed in detail.
Collapse
|
41
|
Maddox E, Zhan M, Mundy GR, Drohan WN, Burgess WH. Optimizing human demineralized bone matrix for clinical application. TISSUE ENGINEERING 2000; 6:441-8. [PMID: 10992439 DOI: 10.1089/107632700418146] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The use of human demineralized bone matrix (DBM) powder in periodontal and orthopedic applications is limited by the variability in the osteoinductive or osteoconductive properties of the material. The goal of the present study was to establish simple in vitro and in vivo assays of DBM that would allow us to screen different lots of the material prior to testing in more rigorous animal models. The results demonstrate a wide variability in the performance of individual lots of DBM powder obtained from a single tissue bank. The studies also demonstrate that relatively simple screening can be used to establish the quality of the different lots, and that performance and ease of handling can be improved by using relatively small particle sizes delivered in a fibrin sealant matrix.
Collapse
|
42
|
Zhan M, Hu G, Yang J. Synchronization of chaos in coupled systems. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 2000; 62:2963-2966. [PMID: 11088783 DOI: 10.1103/physreve.62.2963] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2000] [Revised: 04/10/2000] [Indexed: 05/23/2023]
Abstract
The stability of synchronous chaos of coupled oscillators with diffusive and gradient couplings is investigated. The stability boundaries of all transverse modes can be simultaneously drawn by justifying the boundary of a single mode, according to a scaling relation. Therefore, the distribution of stable and unstable regions can be explicitly shown in control parameter space. Bifurcations through different unstable modes, leading to different spatial orders, are analyzed.
Collapse
|
43
|
Zhan M, Hu G. Intermingled basins and on-off intermittency in a multistate system. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 2000; 62:375-383. [PMID: 11088471 DOI: 10.1103/physreve.62.375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/1999] [Indexed: 05/23/2023]
Abstract
We consider a dynamical system containing infinite low-dimensional symmetric invariant subspaces, each of which has a chaotic state. Intermingled basins are found between these multiple chaotic states when they are stable in the subspaces. As a parameter of the system varies, the largest Lyapunov exponent transverse to the invariant subspace can change from negative to positive; then, the system dynamics changes from an intermingled basin state to a multistate on-off intermittency. The statistical behavior and physical transportation property for different dynamic states are investigated in detail.
Collapse
|
44
|
Zhao Y, Zhan M. [Coexpression of the preS1(1-42) and the Core(1-144) antigen of HBV in E. coli]. ZHONGGUO YI XUE KE XUE YUAN XUE BAO. ACTA ACADEMIAE MEDICINAE SINICAE 2000; 22:227-31. [PMID: 12903465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
OBJECTIVE To study the therapeutic T cell vaccine for the treatment of chronic hepatitis B. METHODS The genes of HBcAg (1-144) and preS1 Ag (1-42) were amplified and fused by PCR. This fusion gene was inserted in the prokaryotic expression vector pET-11d and expressed in E. coli. RESULTS It was showed by SDS-PAGE that the protein molecular weight of the coexpression product was about 20,000, twenty percent of all bacteria protein. The monoclone antibody against Core and preS1 antigen could react with this fused protein by Western-blot technique respectively. The fused gene was verified by sequencing. Under the immune electron microscopy, this fused protein is a typical particle of HBcAg but in an aggregated form. CONCLUSIONS The results may aid for studying T cell immunotherapeutic vaccine to chronic hepatitis B.
Collapse
|
45
|
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC. The genome sequence of Drosophila melanogaster. Science 2000; 287:2185-95. [PMID: 10731132 DOI: 10.1126/science.287.5461.2185] [Citation(s) in RCA: 3976] [Impact Index Per Article: 165.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.
Collapse
|
46
|
Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, Anson EL, Bolanos RA, Chou HH, Jordan CM, Halpern AL, Lonardi S, Beasley EM, Brandon RC, Chen L, Dunn PJ, Lai Z, Liang Y, Nusskern DR, Zhan M, Zhang Q, Zheng X, Rubin GM, Adams MD, Venter JC. A whole-genome assembly of Drosophila. Science 2000; 287:2196-204. [PMID: 10731133 DOI: 10.1126/science.287.5461.2196] [Citation(s) in RCA: 997] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.
Collapse
|
47
|
Moreau EJ, Langerak AW, van Gastel-Mol EJ, Wolvers-Tettero IL, Zhan M, Zhou Q, Koop BF, van Dongen JJ. Easy detection of all T cell receptor gamma (TCRG) gene rearrangements by Southern blot analysis: recommendations for optimal results. Leukemia 1999; 13:1620-6. [PMID: 10516765 DOI: 10.1038/sj.leu.2401540] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Southern blot analysis of T cell receptor (TCR) gene rearrangements has proven to be a helpful tool to establish clonality in T cell leukemias and lymphomas. To improve the detection of clonal TCR gamma (TCRG) gene rearrangements by Southern blot analysis, we designed four new Jgamma probes and determined the most optimal restriction enzymes to be used with these probes. Based on detailed analysis of the sequences as well as on hybridization experiments with the TCRGJ21 probe, the Jgamma1.2 and Jgamma2.1 downstream areas were found to be highly homologous, suggesting that during evolution the duplication of the Jgamma region was followed by deletion of the tentative Jgamma2.2 gene segment. Southern blot analysis of 51 T cell acute lymphoblastic leukemias (T-ALL) revealed that all TCRG gene rearrangements can be detected by use of the TCRGJ13 probe in EcoRI digests and the TCRGJ21 probe in PstI digests. Additional probes and digests allow a more precise identification of the exact type of TCRG gene rearrangements in the majority of cases. Almost 90% of the TCRG gene rearrangements in T-ALL involved the Jgamma2 region (16% Jgamma2.1 and 72% Jgamma2.3), whereas Jgamma1 region rearrangements were particularly found in TCRgammadelta+ T-ALL. This information has implications for design of primer sets for PCR analysis at diagnosis and for PCR target choice in detection of minimal residual disease during follow-up of T-ALL patients.
Collapse
|
48
|
Wang H, Chen H, Xia N, Tan W, Chen G, Liu Y, Cong Y, Sun J, Zeng D, Hou Y, Wang Y, Zhan M. cDNA cloning and sequence analysis of hepatitis G virus genome isolated from a Chinese blood donor. Chin Med J (Engl) 1999; 112:747-9. [PMID: 11601287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
OBJECTIVE To obtain full-length sequence of a Chinese hepatitis G virus (HGV) strain (HGVch) and investigate the genetic characteristic of HGVch and its identity to other isolates. METHODS Reverse transcription (RT) and nested-PCR were used to screen HGV RNA positive serum and amplify cDNA fragments. A positive serum without known hepatitis virus markers was selected for isolating HGV RNA template. The HGV genome was divided into 12 overlapping fragments and directly cloned into pGEM-T vector. Sequences were determined by dideoxy terminus-end method of DNA sequencing and then analyzed by computer. RESULTS The twelve fragments of HGVch cover 9213 nucleotides in length, containing a large open reading frame (ORF) encoding 2873 animo acids polyprotein that began with a methonine residue and ended at termination codon. HGVch is about 86.5%-89.5% identical to other known HGV isolates at the nucleotide level and about 93.9%-96.2% at the deduced animo acid level. CONCLUSION HGV is a non-A-E hepatitis causal agent, proved to be related with posttransfusion hepatitis in all over the world. Chinese HGV isolate has very close relationship to other isolates from Africa, Europe, Japan, without significant difference across the entire genome. It is suggested that the sequences of HGV isolates are very conservative and the evolution is very slow.
Collapse
|
49
|
Chen G, Bi S, Zhan M. [Expression of non-structural region 3 gene of the Chinese HGY and analysis of the antigenicity of the recombinant proteins]. ZHONGHUA SHI YAN HE LIN CHUANG BING DU XUE ZA ZHI = ZHONGHUA SHIYAN HE LINCHUANG BINGDUXUE ZAZHI = CHINESE JOURNAL OF EXPERIMENTAL AND CLINICAL VIROLOGY 1999; 13:117-20. [PMID: 12569774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
OBJECTIVE This study is to analyze the antigenicity of the NS3 proteins of Chinese HGV and their potential use in the serological diagnosis. METHODS All three gene fragments of NS3 region of Chinese HGV were cloned into the pRSET vectors to construct recombinant plasmids. In E. coli BL21, all three recombinant plasmids achieved a high expression level with induction of IPTG. The expressed products were analyzed with Western blot and ELISA. RESULTS The recombinant protein PA, P3 and P4 have a molecular weight of 42,000, 30,000 and 24,000, respectively. They all could react with HGV positive sera in Western blot and ELISA. Among them, the protein that covers the N terminal of NS3 region of HGV had a stronger reaction with HGV positive sera than the other two proteinsdid. CONCLUSION The N terminal in the NS3 region of Chinese HGV includes an dominant antigenic determinant, and its gene product has relatively strong antigenicity.
Collapse
|
50
|
Zhan M, Liu X. Schedule-dependent reversion of cisplatin resistance by 5-fluorouracil in a cisplatin-resistant human lung adenocarcinoma cell line A549DDP. Chin Med J (Engl) 1999; 112:336-9. [PMID: 11593534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
OBJECTIVE To study the schedule-dependent reversion of cis-diamminedichloroplatinum (CDDP) resistance by 5-fluorouracil (5-Fu) in a CDDP resistant human lung adenocarcinoma cell line A549DDP. METHODS Dimethylthiazol dipheryltetrazolium bromide (MTT) assay and immunocytochemistry were used. RESULTS After the A549DDP was treated with CDDP, followed immediately by exposure to 5-Fu, cytotoxicity of CDDP increased 1.8 fold. After pretreatment of A549DDP with 5-Fu, followed immediately by exposure to CDDP, the cytotoxicity of CDDP increased 3.9 fold. After pretreatment of A549DDP with 5-Fu, after a 24- or 48-hour drug-free interval, followed by exposure to CDDP, the cytotoxicity of CDDP increased 20 and 250 fold, respectively, and the A549DDP was rendered more sensitive than its parental cell line A549. In parallel with the increased cytotoxicity, the cellular GSH content was significantly reduced at 24 or 48-hour after 5-Fu pretreatment. However, depletion of GSH by buthionine sulfoximine (BSO) only resulted in partial reversion of CDDP resistance. 5-Fu could also inhibit the expression of MRP, but had no effect on the expression of GST pi. The effect of 5-Fu on the parental cell line A549 was much smaller than that in A549DDP. CONCLUSION Scheduled administration of 5-Fu can reverse CDDP resistance completely through reduction of GSH and inhibition of MRP expression.
Collapse
|