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Multi-objective evolutionary optimization of agent-based models: An application to emergency response planning

Chapter by: Narzisi, Giuseppe; Mysore, Venkatesh; Mishra, Bud
in: Proceedings of the 2nd IASTED International Conference on Computational Intelligence, CI 2006 by
[S.l.] : Springer Verlagservice@springer.de, 2006
pp. 224-230
ISBN: 9780889866027
CID: 2852222

Simpathica: A computational systems biology tool within the valis bioinformatics environment

Chapter by: Mishra, Bud; Antoniotti, Marco; Paxia, Salvatore; Ugel, Nadia
in: Computational Systems Biology by
[S.l.] : Elsevier Inc., 2006
pp. 79-102
ISBN: 9780120887866
CID: 2852232

Crystal structure of the agrin-responsive immunoglobulin-like domains 1 and 2 of the receptor tyrosine kinase MuSK

Stiegler, Amy L; Burden, Steven J; Hubbard, Stevan R
Muscle-specific kinase (MuSK) is a receptor tyrosine kinase expressed exclusively in skeletal muscle, where it is required for formation of the neuromuscular junction. MuSK is activated by agrin, a neuron-derived heparan sulfate proteoglycan. Here, we report the crystal structure of the agrin-responsive first and second immunoglobulin-like domains (Ig1 and Ig2) of the MuSK ectodomain at 2.2 A resolution. The structure reveals that MuSK Ig1 and Ig2 are Ig-like domains of the I-set subfamily, which are configured in a linear, semi-rigid arrangement. In addition to the canonical internal disulfide bridge, Ig1 contains a second, solvent-exposed disulfide bridge, which our biochemical data indicate is critical for proper folding of Ig1 and processing of MuSK. Two Ig1-2 molecules form a non-crystallographic dimer that is mediated by a unique hydrophobic patch on the surface of Ig1. Biochemical analyses of MuSK mutants introduced into MuSK(-/-) myotubes demonstrate that residues in this hydrophobic patch are critical for agrin-induced MuSK activation
PMCID:1752213
PMID: 17011580
ISSN: 0022-2836
CID: 70021

Effect of charge substitutions at residue his-142 on voltage gating of connexin43 channels

Shibayama, Junko; Gutierrez, Cristina; Gonzalez, Daniel; Kieken, Fabien; Seki, Akiko; Carrion, Jesus Requena; Sorgen, Paul L; Taffet, Steven M; Barrio, Luis C; Delmar, Mario
Previous studies indicate that the carboxyl terminal of connexin43 (Cx43CT) is involved in fast transjunctional voltage gating. Separate studies support the notion of an intramolecular association between Cx43CT and a region of the cytoplasmic loop (amino acids 119-144; referred to as 'L2'). Structural analysis of L2 shows two alpha-helical domains, each with a histidine residue in its sequence (H126 and H142). Here, we determined the effect of H142 replacement by lysine, alanine, and glutamate on the voltage gating of Cx43 channels. Mutation H142E led to a significant reduction in the frequency of occurrence of the residual state and a prolongation of dwell open time. Macroscopically, there was a large reduction in the fast component of voltage gating. These results resembled those observed for a mutant lacking the carboxyl terminal (CT) domain. NMR experiments showed that mutation H142E significantly decreased the Cx43CT-L2 interaction and disrupted the secondary structure of L2. Overall, our data support the hypothesis that fast voltage gating involves an intramolecular particle-receptor interaction between CT and L2. Some of the structural constrains of fast voltage gating may be shared with those involved in the chemical gating of Cx43
PMCID:1635665
PMID: 16963503
ISSN: 0006-3495
CID: 113855

ATF4 mediation of NF1 functions in osteoblast reveals a nutritional basis for congenital skeletal dysplasiae

Elefteriou, Florent; Benson, M Douglas; Sowa, Hideaki; Starbuck, Michael; Liu, Xiuyun; Ron, David; Parada, Luis F; Karsenty, Gerard
The transcription factor ATF4 enhances bone formation by favoring amino acid import and collagen synthesis in osteoblasts, a function requiring its phosphorylation by RSK2, the kinase inactivated in Coffin-Lowry Syndrome. Here, we show that in contrast, RSK2 activity, ATF4-dependent collagen synthesis, and bone formation are increased in mice lacking neurofibromin in osteoblasts (Nf1(ob)(-/-) mice). Independently of RSK2, ATF4 phosphorylation by PKA is enhanced in Nf1(ob)(-/-) mice, thereby increasing Rankl expression, osteoclast differentiation, and bone resorption. In agreement with ATF4 function in amino acid transport, a low-protein diet decreased bone protein synthesis and normalized bone formation and bone mass in Nf1(ob)(-/-) mice without affecting other organ weight, while a high-protein diet overcame Atf4(-/-) and Rsk2(-/-) mice developmental defects, perinatal lethality, and low bone mass. By showing that ATF4-dependent skeletal dysplasiae are treatable by dietary manipulations, this study reveals a molecular connection between nutrition and skeletal development
PMCID:2756713
PMID: 17141628
ISSN: 1550-4131
CID: 71593

Anatomy and histopathology of the human lacrimal gland

Obata, Hiroto
PURPOSE: To review the anatomy and histopathologic changes of the human main lacrimal gland. METHODS: Samples of lacrimal gland including palpebral lobes and orbital lobes were taken in autopsies, and the relationship between histopathologic changes and age and sex, as well as histopathologic differences between palpebral and orbital lobes of the lacrimal gland, were studied using light microscopy. RESULTS: Various histopathologic changes were observed in the human main lacrimal gland as follows: acinar atrophy; periacinar fibrosis; periductal fibrosis; interlobular ductal dilatation; interlobular ductal proliferation; lymphocytic infiltration; and fatty infiltration. Several histopathologic differences exist between the palpebral and orbital lobes. There were statistically significant correlations between age and diffuse fibrosis, diffuse atrophy, and periductal fibrosis in the orbital lobes of women. Diffuse fibrosis and diffuse atrophy in orbital lobes were more frequently observed in women than in men. CONCLUSION: It is speculated that periductal fibrosis is related to a decrease of tear flow with age and that interlobular ductal dilatation in palpebral lobes may be caused by stenosis of the excretory duct in conjunctival fornix. However, the mechanisms of these histopathologic changes in the human main lacrimal gland are not yet clear.
PMID: 17001201
ISSN: 0277-3740
CID: 2328942

Multidisciplinary management of orthopedic patients with sickle cell disease

Sathappan, Sathappan S; Ginat, Daniel; Di Cesare, Paul E
With pharmacological treatment, the lifespan of the patient with sickle cell disease can be extended to the sixth decade. Currently the only curative therapy for sickle cell disease is hemopoietic cell transplantation, which is still undergoing technical refinement. Most patients can be expected to undergo at least one orthopedic surgical procedure in their lifetime. Multidisciplinary management of orthopedic patients with sickle cell disease will decrease the overall complication rates and improve clinical outcomes
PMID: 17190168
ISSN: 0147-7447
CID: 70537

Comparison of cellular response in bovine intervertebral disc cells and articular chondrocytes: effects .of lipopolysaccharide on proteoglycan metabolism

Aota, Yoichi; An, Howard S; Imai, Yoshiyuki; Thonar, Eugene J; Muehleman, Carol; Masuda, Koichi
Lipopolysaccharide (LPS) induces matrix degradation and markedly stimulates the production of several cytokines, i.e., interleukin-1beta, -6, and -10, by disc cells and chondrocytes. We performed a series of experiments to compare cellular responses of cells from the bovine intervertebral disc (nucleus pulposus and annulus fibrosus) and from bovine articular cartilage to LPS. Alginate beads containing cells isolated from bovine intervertebral discs and articular cartilage were cultured with or without LPS in the presence of 10% fetal bovine serum. The DNA content and the rate of proteoglycan synthesis and degradation were determined. In articular chondrocytes, LPS strongly suppressed cell proliferation and proteoglycan synthesis in a dose-dependent manner and stimulated proteoglycan degradation. Compared with articular chondrocytes, nucleus pulposus cells responded in a similar, although less pronounced manner. However, treatment of annulus fibrosus cells with LPS showed no significant effects on proteoglycan synthesis or degradation. A slight, but statistically significant, inhibition of cell proliferation was observed at high concentrations of LPS in annulus fibrosus cells. Thus, LPS suppressed proteoglycan synthesis and stimulated proteoglycan degradation by articular chondrocytes and nucleus pulposus cells. The effects of LPS on annulus fibrosus cells were minor compared with those on the other two cell types. The dissimilar effects of LPS on the various cell types suggest metabolic differences between these cells and may further indicate a divergence in pathways of LPS signaling and a differential sensitivity to exogenous stimuli such as LPS.
PMID: 16788835
ISSN: 0302-766x
CID: 2164122

Perk-dependent translational regulation promotes tumor cell adaptation and angiogenesis in response to hypoxic stress

Blais, Jaime D; Addison, Christina L; Edge, Robert; Falls, Theresa; Zhao, Huijun; Wary, Kishore; Koumenis, Costas; Harding, Heather P; Ron, David; Holcik, Martin; Bell, John C
It has been well established that the tumor microenvironment can promote tumor cell adaptation and survival. However, the mechanisms that influence malignant progression have not been clearly elucidated. We have previously demonstrated that cells cultured under hypoxic/anoxic conditions and transformed cells in hypoxic areas of tumors activate a translational control program known as the integrated stress response (ISR). Here, we show that tumors derived from K-Ras-transformed Perk(-/-) mouse embryonic fibroblasts (MEFs) are smaller and exhibit less angiogenesis than tumors with an intact ISR. Furthermore, Perk promotes a tumor microenvironment that favors the formation of functional microvessels. These observations were corroborated by a microarray analysis of polysome-bound RNA in aerobic and hypoxic Perk(+/+) and Perk(-/-) MEFs. This analysis revealed that a subset of proangiogenic transcripts is preferentially translated in a Perk-dependent manner; these transcripts include VCIP, an adhesion molecule that promotes cellular adhesion, integrin binding, and capillary morphogenesis. Taken with the concomitant Perk-dependent translational induction of additional proangiogenic genes identified by our microarray analysis, this study suggests that Perk plays a role in tumor cell adaptation to hypoxic stress by regulating the translation of angiogenic factors necessary for the development of functional microvessels and further supports the contention that the Perk pathway could be an attractive target for novel antitumor modalities
PMCID:1698539
PMID: 17030613
ISSN: 0270-7306
CID: 71594

Endosome dysfunction in Alzheimer's disease: Genetic links and implications for synapse failure and neurodegeneration [Meeting Abstract]

Nixon, RA; Cataldo, A; Mathews, P; Jiang, Y; Ginsberg, SD; Peterhoff, C
ISI:000242215900084
ISSN: 0893-133x
CID: 70911