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Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J. The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci U S A 2006; 103:19581-6. [PMID: 17158798 PMCID: PMC1748268 DOI: 10.1073/pnas.0607142103] [Citation(s) in RCA: 596] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Winter wheat and barley varieties require an extended exposure to low temperatures to accelerate flowering (vernalization), whereas spring varieties do not have this requirement. In this study, we show that in these species, the vernalization gene VRN3 is linked completely to a gene similar to Arabidopsis FLOWERING LOCUS T (FT). FT induction in the leaves results in a transmissible signal that promotes flowering. Transcript levels of the barley and wheat orthologues, designated as HvFT and TaFT, respectively, are significantly higher in plants homozygous for the dominant Vrn3 alleles (early flowering) than in plants homozygous for the recessive vrn3 alleles (late flowering). In wheat, the dominant Vrn3 allele is associated with the insertion of a retroelement in the TaFT promoter, whereas in barley, mutations in the HvFT first intron differentiate plants with dominant and recessive VRN3 alleles. Winter wheat plants transformed with the TaFT allele carrying the promoter retroelement insertion flowered significantly earlier than nontransgenic plants, supporting the identity between TaFT and VRN-B3. Statistical analyses of flowering times confirmed the presence of significant interactions between vernalization and FT allelic classes in both wheat and barley (P < 0.0001). These interactions were supported further by the observed up-regulation of HvFT transcript levels by vernalization in barley winter plants (P = 0.002). These results confirmed that the wheat and barley FT genes are responsible for natural allelic variation in vernalization requirement, providing additional sources of adaptive diversity to these economically important crops.
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Fu D, Lemas V, Foss C, Fox J, Pomper M, Ambinder RF. Enzymatically-targeted 131I therapy for herpesvirus-associated malignancies. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.3010] [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
3010 Background: Epstein-Barr virus (EBV) and Kaposi’s sarcoma herpesvirus (KSHV) are associated with tumors including AIDS-related lymphoma, Burkitt’s lymphoma, Hodgkin’s lymphoma, nasopharyngeal carcinoma and Kaposi’s sarcoma. Both viruses encode kinases that selectively phosphorylate nucleoside analogs such as ganciclovir and FIAU. We hypothesized that it might be possible to use the viral enzymes to specifically concentrate 131I-FIAU in tumor cells harboring virus and thus deliver therapeutic radiation. Bortezomib is a potent stimulator of viral kinase expression in gammaherpesvirus tumor cell lines. Methods: We evaluated the effect of 131I-FIAU on human cancer xenografts in SCID mice. These included a tumor line engineered to constitutively express the EBV thymidine kinase (EBVTK), and a control engineered with a sham vector (SHAM), as well 2 EBV(+) Burkitt’s lymphoma (BL) lines, and 1 KSHV(+) primary effusion lymphoma (PEL) cell line. Mice were treated with buffer, bortezomib 2 ug/gm, or I-FIAU, or I-FIAU and bortezomib in combination. For imaging, mice, 125I -FIAU and SPECT were used. For therapy, 131I-FIAU was used and tumor dimensions were monitored with calipers. Results: Treatment with buffer had no effect on on 3 EBVTK tumors and 3 SHAM tumors all of which increased in volume. Treatment with 1.4 mCi 131I-FIAU alone led to tumor responses (>90% volume reduction at 10 days) in 3/3 mice with EBVTK tumors and 0/3 mice with SHAM tumors. Treatment with 131I-FIAU alone had no effect on BL (0/3) or PEL (0/9) xenografts and all tumors increased in volume. Treatment with bortezomib induced modest responses in all tumors but had no greater effect on EBVTK tumors than SHAM tumors. However, treatment with bortezomib and 131I-FIAU led to marked tumor regression (>95%) in each of the virus-associated tumors (3/3 BL, 9/9 PEL). SPECT imaging with 125I-FIAU showed selective concentration of radiolabel in tumor tissue in the EBVTK tumor (2/2) and in viral tumors (6/6) when bortezomib was administered. There was no selective concentration in the absence of bortezomib treatment in the viral tumors (0/8). Conclusions: Treatment with bortezomib leads to selective concentration of labeled FIAU in the herpesvirus-associated tumor xenografts evaluated and to regression of tumor when the isotope is 131I. No significant financial relationships to disclose.
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Chen J, Chong C, Hsieh W, Fu D, Lemas V, Liu JO, Ambinder RF. Screening a library of FDA-approved drugs identifies agents that induce lytic viral infection in EBV-associated tumors. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.2002] [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
2002 Background: Epstein-Barr virus (EBV) is associated with a variety of tumors including AIDS lymphoma, Burkitt’s lymphoma, nasopharyngeal carcinoma and Hodgkin’s lymphoma. We hypothesized that drugs used in practice might alter viral gene expression in tumor cells in ways that might be important to understand. For example induction of lytic viral gene expression leads to expression of immunodominant CD8 T cell antigens and expression of the viral thymidine kinase (which phosphorylates ganciclovir and other nucleotide analogues). Methods: A library of FDA-approved drugs that includes 2720 agents was screened to identify those that upregulated EBV lytic gene expression. The screen involved a Burkitt’s cell line with a recombinant GFP-EBV that assayed the impact of agents on replication of the complete viral genome, and assay of a lytic promoter reporter construct. Results: The assay identified 146 agents in the whole virus replication assay, 195 agents in the promoter assay, and 54 agents that were active in both assays. Agents with activity could be grouped into 4 families: anti-tubulin drugs, glucocorticoid and other steroid hormones, DNA damaging agents and nucleotide analogues (including cytarabine and gemcitabine), and the proteasome inhibitor bortezomib. Anti-tubulin drugs and nucleotide analogues were less active in thes whole virus assay than the promoter assay whereas bortezomib showed similar activity in both assays. Followup studies confirmed that bortezomib is a potent viral lytic activator that increases expression of the viral thymidine kinase and virion production in several different Burkitt’s lymphoma and primary effusion lymphoma cell lines. Although bortezomib decreases NFKB levels, in vitro investigations with an IKB repressor suggests that inhibition of NFKB alone does not account for lytic activation. Conclusions: Many cancer chemotherapeutic agents are upregulators of EBV lytic expression. Bortezomib is among the most potent. As strategies for using lytic induction therapeutically evolve, these agents may have an important role to play. No significant financial relationships to disclose.
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Fu D, Vissavajjhala P, Hemmings HC. Volatile anaesthetic effects on phospholipid binding to synaptotagmin 1, a presynaptic Ca2+ sensor. Br J Anaesth 2005; 95:216-21. [PMID: 15923266 DOI: 10.1093/bja/aei163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Volatile anaesthetics have important effects on synaptic transmission in the CNS. Depression of excitatory transmission involves reduced transmitter release via unidentified presynaptic mechanisms. Synaptotagmin 1 is a synaptic vesicle-associated protein that regulates Ca(2+)-evoked transmitter release involving critical Ca(2+)/phospholipid interactions within its C2 domains. METHODS We analysed the effects of halothane and isoflurane on the binding of purified recombinant rat synaptotagmin 1 C2A, C2B and C2AB domains to radiolabelled phospholipid liposomes. RESULTS Halothane and isoflurane had no significant effects on the maximal binding or Ca(2+) dependence of binding of synaptotagmin 1 C2 domains to mixed phospholipid vesicles composed of either phosphatidylserine/phosphatidylcholine or phosphatidylinositol/phosphatidylcholine. CONCLUSIONS Inhibition of synaptic vesicle exocytosis by volatile anaesthetics does not appear to involve an effect on the critical Ca(2+)/phospholipid binding properties of synaptotagmin 1, a Ca(2+) sensor involved in regulating evoked Ca(2+)-dependent neurotransmitter release.
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Qian W, Chen X, Fu D, Zou J, Meng J. Intersubgenomic heterosis in seed yield potential observed in a new type of Brassica napus introgressed with partial Brassica rapa genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 110:1187-94. [PMID: 15806350 DOI: 10.1007/s00122-005-1932-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Accepted: 01/10/2005] [Indexed: 05/09/2023]
Abstract
This paper reports the observation on the intersubgenomic heterosis for seed yield among hybrids between natural Brassica napus (A(n)A(n)C(n)C(n)) and a new type of B. napus with introgressions of genomic components of Brassica rapa (A(r)A(r)). This B. napus was selected from the progeny of B. napus x B. rapa and (B. napus x B. rapa) x B. rapa based on extensive phenotypic and cytological observation. Among the 129 studied partial intersubgenomic hybrids, which were obtained by randomly crossing 13 lines of the new type of B. napus in F(3) or BC(1)F(3) to 27 cultivars of B. napus from different regions as tester lines, about 90% of combinations exceeded the yield of their respective tester lines, whereas about 75% and 25% of combinations surpassed two elite Chinese cultivars, respectively. This strong heterosis was further confirmed by reevaluating 2 out of the 129 combinations in a successive year and by surveying hybrids between 20 lines of the new type of B. napus in BC(1)F(5) and its parental B. napus in two locations. Some DNA segments from B. rapa were identified with significant effects on seed yield and yield components of the new type of B. napus in BC(1)F(5) and intersubgenomic hybrids in positive or negative direction. It seems that the genomic components introgressed from B. rapa contributed to improvement of seed yield of rapeseed.
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Jamal S, Fu D, Singh M, Hurst P, Lewis S. Calibration of Sample-Time Error in a Two-Channel Time-Interleaved Analog-to-Digital Converter. ACTA ACUST UNITED AC 2004. [DOI: 10.1109/tcsi.2003.821302] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fu D, Ng YK, Gan P, Ling EA. Permanent occlusion of the middle cerebral artery upregulates expression of cytokines and neuronal nitric oxide synthase in the spinal cord and urinary bladder in the adult rat. Neuroscience 2004; 125:819-31. [PMID: 15120843 DOI: 10.1016/j.neuroscience.2004.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 01/18/2004] [Accepted: 02/04/2004] [Indexed: 01/16/2023]
Abstract
The expression pattern of proinflammatory cytokines, neuronal nitric oxide synthase (nNOS), substance P (SP) and calcitonin gene related peptide (CGRP) in the spinal cord and the bladder in response to permanent middle cerebral artery occlusion (MCAO) was investigated. In this connection, the gene expression of tumor necrosis factor alpha (TNF-alpha), interleukin-1 beta (IL-1beta) and interleukin-6 in the lumbosacral spinal cord and the bladder as determined by real-time polymerase chain reaction was upregulated. In the spinal cord, the immunoreactivity of TNF-alpha and IL-1beta was mainly localized in the ventral horn motoneurons contralateral to MCAO. In the bladder, TNF-alpha was mainly expressed in the inflammatory cells. The expression of nNOS immunoreactivity as well as nicotinamide adenine dinucleotide phosphate-diaphorase (NADPH-d) staining in the spinal cord and bladder was also markedly increased in response to MCAO. Furthermore, the temporal and spatial expression of nNOS paralleled that of TNF-alpha and IL-1beta in the spinal cord. On the other hand, there was no noticeable change in gene expression and immunoreactivity of SP and CGRP. The present results have shown that cytokines and nNOS expression are elevated in areas far removed from the primary site of ischemic infarct, namely, the lumbosacral spinal cord and bladder. This together with some neuronal deaths maybe linked to the dysfunction of the latter in a clinical stroke. On the other hand, the apparent lack of SP and CGRP changes following MCAO suggests that the two neurotransmitters are not directly involved.
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Li Y, Guo Q, Fu D. [Clinical observation on ondansetron in preventing nausea and vomiting after cholecystectomy under abdominoscope]. HUNAN YI KE DA XUE XUE BAO = HUNAN YIKE DAXUE XUEBAO = BULLETIN OF HUNAN MEDICAL UNIVERSITY 2002; 24:463-4. [PMID: 12080685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
OBJECTIVE To evaluate the prophylactic effect of ondansetron on postoperative nausea and vomiting (PONV) of cholecystectomy under abdominoscope. METHODS Sixty patients, scheduled for selective cholecystectomy under abdominoscope, were randomly and double-blindly allocated to receive an intravenous bolus of either 0.9% NS 10 ml(Group placebo, n = 30) or 8 mg of ondansetron in 10 ml solution(Group ondansetron, n = 30), respectively. RESULTS The incidences of nausea and vomiting in ondansetron group(33.3% and 26.7%) were significantly lower than those in placebo group(73.3% and 66.7%) (P < 0.05). Administration of ondansetron had no obvious effect on the mean arterial pressure, SpO2, and respiratory frequency. CONCLUSION Ondansetron can be used effectively and safely to prevent PONV in cholecystectomy patients under abdominoscope.
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Fu D, Benseler F, McLaughlin LW. Hammerhead Ribozymes Containing Non-Nucleoside Linkers Are Active RNA Catalysts. J Am Chem Soc 2002. [DOI: 10.1021/ja00090a007] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kamimura D, Fu D, Matsuda Y, Atsumi T, Ohtani T, Park SJ, Ishihara K, Hirano T. Tyrosine 759 of the cytokine receptor gp130 is involved in Listeria monocytogenes susceptibility. Genes Immun 2002; 3:136-43. [PMID: 12070777 DOI: 10.1038/sj.gene.6363825] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2001] [Revised: 10/16/2001] [Accepted: 10/22/2001] [Indexed: 11/08/2022]
Abstract
Interleukin-6 family cytokines have been implicated in adaptive and innate immunity, hematopoiesis, and inflammation. This cytokine family shares a signal-transducing receptor subunit called gp130. gp130(F759/F759) knockin mice carry a point mutation at the SHP2-binding site of gp130 due to the replacement of tyrosine-759 (Y759 for human gp130) with phenylalanine (F). To explore the effect of this point mutation on the host response to bacterial infection, gp130(F759/F759) knockin mice were infected with Listeria monocytogenes. gp130(F759/F759) knockin mice began to die at 3 to 4 days post infection (p.i.) and showed higher mortality than did controls. Listeria titers at 3 days p.i. in the peritoneal cavity, spleen, and liver were significantly higher in gp130(F759/F759)knockin mice than in controls. Nitric oxide production, upregulation of the mRNA levels of a variety of cytokines, and listericidal activity in gp130(F759/F759) macrophages were unchanged. However, gp130(F759/F759) knockin mice displayed significantly lower levels of interferon (IFN)gamma in serum and in the culture supernatant from peritoneal exudate cells and splenocytes, in response to Listeria infection. These results suggest that the Y759 point mutation in gp130 attenuates the early phase of defense against Listeria infection, possibly owing to insufficient elevation of IFNgamma levels, and thus gp130 is a possible candidate gene for Listeria susceptibility.
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Sun L, Liu X, Qiu L, Wang J, Liu M, Fu D, Luo Q. Administration of plasmid DNA expressing human interleukin-6 significantly improves thrombocytopoiesis in irradiated mice. Ann Hematol 2001; 80:567-72. [PMID: 11732866 DOI: 10.1007/s002770100345] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
When people are exposed to large doses of ionizing rays in a short time, hematopoiesis is impaired and hemorrhage is one of the major clinical features. Suddenly decreasing platelet counts are responsible for the life-threatening hemorrhagic complication. Therefore, some cytokines have been used to improve thrombocytopoiesis in various radiation-induced thrombocytopenia models. Current measures for this purpose involve repeated intravenous or subcutaneous injections of recombinant proteins, which are expensive and inconvenient, or gene therapy with viral vectors that could not obviate the risk of infection. We tried to determine the possibility of gene therapy with plasmid vectors for radiation-induced hematopoietic injury, which could overcome the above-mentioned problem. In this study, we describe the enhanced efficiency of radiation on gene transfer with plasmid vector in vivo and the physiological role of expressed human interleukin-6 (hIL-6) in vivo on a radiation-induced thrombocytopenia model. After a single intramuscular injection of plasmid hIL-6 DNA on 6.5-Gy-irradiated mice, the hIL-6 protein level in mouse plasma was determined with enzyme-linked immunosorbent assay (ELISA). The level of hIL-6 began to increase from the 4th day, reached the peak value on about the 11th day, and remained at a higher level on the 28th day. Meanwhile, unirradiated mice injected with the same amount of plasmid DNA showed less hIL-6 on the 11th day after administration. Further experiments demonstrated that the hIL-6 level in 7.5-Gy-irradiated mice was about three times higher than that of 5.0-Gy-irradiated mice, suggesting radiation could improve gene transfer efficiency of plasmid DNA in vivo and might be dependent on radiation doses. The expression of hIL-6 in vivo showed a significant effect on hematopoietic recovery after radiation. Not only the platelet nadir in peripheral blood, but also the number of colony-forming cells in bone marrow rose. The increased platelet counts were partially due to the increase of reticulated platelet that reflected the activity of a given population of megakaryocyte in bone marrow. We conclude that radiation could significantly enhance the gene transfer efficiency of plasmid DNA and that gene therapy with plasmid vectors for radiation-induced hematopoietic injury might be more effective than other diseases without DNA repair.
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Xiao H, Sandaltzopoulos R, Wang HM, Hamiche A, Ranallo R, Lee KM, Fu D, Wu C. Dual functions of largest NURF subunit NURF301 in nucleosome sliding and transcription factor interactions. Mol Cell 2001; 8:531-43. [PMID: 11583616 DOI: 10.1016/s1097-2765(01)00345-8] [Citation(s) in RCA: 200] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
NURF is an ISWI complex of four proteins that uses the energy of ATP hydrolysis to catalyze nucleosome sliding. Three NURF components have been identified previously. We have cloned cDNA encoding the largest NURF subunit, revealing a 301 kDa polypeptide (NURF301) that shares structural motifs with ACF1. We have reconstituted full and partial NURF complexes from recombinant proteins and show that NURF301 and the ISWI ATPase are necessary and sufficient for accurate and efficient nucleosome sliding. An HMGA/HMGI(Y)-like domain of NURF301 that facilitates nucleosome sliding indicates the importance of DNA conformational changes in the sliding mechanism. NURF301 also shows interactions with sequence-specific transcription factors, providing a basis for targeted recruitment of the NURF complex to specific genes.
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Nollert P, Harries WE, Fu D, Miercke LJ, Stroud RM. Atomic structure of a glycerol channel and implications for substrate permeation in aqua(glycero)porins. FEBS Lett 2001; 504:112-7. [PMID: 11532442 DOI: 10.1016/s0014-5793(01)02710-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of a glycerol channel from Escherichia coli at 2.2 A resolution serves as a basis for the understanding of selective transmembrane substrate permeation. In the course of permeation, glycerol molecules diffuse through a tripathic channel with their alkyl backbone wedged against a hydrophobic corner, such that OH groups become acceptors and donors of hydrogen bonds at the same time. The structure of the channel explains the preferential permeability for linear carbohydrates and absolute exclusion of ions and charged solutes. Its gene-duplicated sequence has a structural counterpart in a pseudo two-fold symmetry within the monomeric channel protein.
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Wilson J, Lin H, Fu D, Javitch JA, Strange PG. Mechanisms of inverse agonism of antipsychotic drugs at the D(2) dopamine receptor: use of a mutant D(2) dopamine receptor that adopts the activated conformation. J Neurochem 2001; 77:493-504. [PMID: 11299312 DOI: 10.1046/j.1471-4159.2001.00233.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The antipsychotic drugs have been shown to be inverse agonists at the D(2) dopamine receptor. We have examined the mechanism of this inverse agonism by making mutations in residue T343 in the base of the sixth transmembrane spanning region of the receptor. T343R, T343S and T343K mutant D(2) dopamine receptors were made and the T343R mutant characterized in detail. The T343R mutant D(2) dopamine receptor exhibits properties of a receptor that resides more in the activated state, namely increased agonist binding affinity (independent of G-protein coupling and dependent on agonist efficacy), increased agonist potency in functional tests (adenylyl cyclase inhibition) and increased inverse agonist effects. The binding of agonists to the mutant receptor also shows sensitivity to sodium ions, unlike the native receptor, so that isomerization of the receptor to its inactive state may be driven by sodium ions. The binding of inverse agonists to the receptor is, however, unaffected by the mutation. We conclude that inverse agonism at this receptor is not achieved by the inverse agonist binding preferentially to the non-activated state of the receptor over the activated state. Rather the inverse agonist appears to bind to all forms of the receptor but then renders the receptor inactive.
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Fu D, Sarker RI, Abe K, Bolton E, Maloney PC. Structure/function relationships in OxlT, the oxalate-formate transporter of oxalobacter formigenes. Assignment of transmembrane helix 11 to the translocation pathway. J Biol Chem 2001; 276:8753-60. [PMID: 11113128 DOI: 10.1074/jbc.m008417200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
OxlT, the oxalate:formate antiporter of Oxalobacter formigenes, has a lone charged residue, lysine 355 (Lys-355), at the center of transmembrane helix 11 (TM11). Because Lys-355 is the only charged residue in the hydrophobic sector, we tested the hypothesis that lysine 355 contributes to the binding site for the anionic substrate, oxalate. This idea was supported by mutational analysis, which showed that of five variants studied (Lys-355 --> Cys, Gly, Gln, Arg, or Thr), residual function was found for only the K355R derivative, in which catalytic efficiency had fallen 2,600-fold. Further insight came from a study of TM11 single-cysteine mutants, using the impermeant, thiol-specific reagents, carboxyethyl methanethiosulfonate and ethyltrimethylammonium methanethiosulfonate. Of the five reactive positions identified in TM11, four were at the cytoplasmic or periplasmic ends of TM11 (S344C and A345C, and G366C and A370C, respectively), whereas the fifth was at the center of the helix (S359C). Added study with carboxyethyl methanethiosulfonate and ethylsulfonate methylthiosulfonate showed that the attack on S359C could be blocked by the presence of the substrate, oxalate, and that protection could be predicted quantitatively by a kinetic model in which S359C is accessible only in the unliganded form of OxlT. Parallel study showed that the proteoliposomes used in such work contained OxlT of right side-out and inside-out orientations in about equal amounts. Accordingly, full inhibition of S359C by the impermeable methanethiosulfonate-linked probes must reflect an approach from both the cytosolic and periplasmic surfaces of the protein. This, coupled with the finding of substrate protection, leads us to conclude that S359C lies on the translocation pathway through OxlT. Since position 359 and 355 lie on the same helical face, we suggest that Lys-355 also lies on the translocation pathway, consistent with the idea that the essential nature of Lys-355 reflects its role in binding the anionic substrate, oxalate.
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Yang J, Moravec CS, Sussman MA, DiPaola NR, Fu D, Hawthorn L, Mitchell CA, Young JB, Francis GS, McCarthy PM, Bond M. Decreased SLIM1 expression and increased gelsolin expression in failing human hearts measured by high-density oligonucleotide arrays. Circulation 2000; 102:3046-52. [PMID: 11120693 DOI: 10.1161/01.cir.102.25.3046] [Citation(s) in RCA: 160] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Failing human hearts are characterized by altered cytoskeletal and myofibrillar organization, impaired signal transduction, abnormal protein turnover, and impaired energy metabolism. Thus, expression of multiple classes of genes is likely to be altered in human heart failure. METHODS AND RESULTS We used high-density oligonucleotide arrays to explore changes in expression of approximately 7000 genes in 2 nonfailing and 2 failing human hearts with diagnoses of end-stage ischemic and dilated cardiomyopathy, respectively. We report altered expression of (1) cytoskeletal and myofibrillar genes (striated muscle LIM protein-1 [SLIM1], myomesin, nonsarcomeric myosin regulatory light chain-2 [MLC(2)], and ss-actin); (2) genes responsible for degradation and disassembly of myocardial proteins (alpha(1)-antichymotrypsin, ubiquitin, and gelsolin); (3) genes involved in metabolism (ATP synthase alpha-subunit, succinate dehydrogenase flavoprotein [SDH Fp] subunit, aldose reductase, and TIM17 preprotein translocase); (4) genes responsible for protein synthesis (elongation factor-2 [EF-2], eukaryotic initiation factor-4AII, and transcription factor homologue-HBZ17); and (5) genes encoding stress proteins (alphaB-crystallin and mu-crystallin). In 5 additional failing hearts and 4 additional nonfailing controls, we then compared expression of proteins encoded by the differentially expressed genes, alphaB-crystallin, SLIM1, gelsolin, alpha(1)-antichymotrypsin, and ubiquitin. In each case, changes in protein expression were consistent with changes in transcript measured by microarray analysis. Gelsolin protein expression was also increased in cardiomyopathic hearts from tropomodulin-overexpressing (TOT) mice and rac1-expressing (racET) mice. CONCLUSIONS Altered expression of the genes identified in this study may contribute to development of the heart failure phenotype and/or represent compensatory mechanisms to sustain cardiac function in failing human hearts.
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Fu D, Libson A, Miercke LJ, Weitzman C, Nollert P, Krucinski J, Stroud RM. Structure of a glycerol-conducting channel and the basis for its selectivity. Science 2000; 290:481-6. [PMID: 11039922 DOI: 10.1126/science.290.5491.481] [Citation(s) in RCA: 814] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Membrane channel proteins of the aquaporin family are highly selective for permeation of specific small molecules, with absolute exclusion of ions and charged solutes and without dissipation of the electrochemical potential across the cell membrane. We report the crystal structure of the Escherichia coli glycerol facilitator (GlpF) with its primary permeant substrate glycerol at 2.2 angstrom resolution. Glycerol molecules line up in an amphipathic channel in single file. In the narrow selectivity filter of the channel the glycerol alkyl backbone is wedged against a hydrophobic corner, and successive hydroxyl groups form hydrogen bonds with a pair of acceptor, and donor atoms. Two conserved aspartic acid-proline-alanine motifs form a key interface between two gene-duplicated segments that each encode three-and-one-half membrane-spanning helices around the channel. This structure elucidates the mechanism of selective permeability for linear carbohydrates and suggests how ions and water are excluded.
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Liu B, Guan R, Zhou P, Miao Q, Wang H, Fu D, You B. A distinct mutational spectrum of p53 and K-ras genes in lung cancer of workers with silicosis. J Environ Pathol Toxicol Oncol 2000; 19:1-7. [PMID: 10905501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Crystalline silica was recently classified as a human carcinogen by the International Agency for Research on Cancer (IARC). However, the direct genotoxic effect of silica in humans remains unclear. We examined the p53 and K-ras gene mutations in lung cancer in workers with silicosis (LCWS). DNA was extracted from paraffin-embedded tissues and examined by PCR-RFLP, PCR-SSCP, and DNA sequencing. The mutation frequencies of p53 gene were high, but the mutation distributions in exons and among the histological types of LCWS differed from those of common (i.e., not silicosis-related) lung cancer. Furthermore, no mutations in codon 12 of K-ras gene (predominant in common lung cancer) were found in LCWS. These findings in the mutational spectrum support a carcinogenic effect of silica dust at the DNA molecular level.
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Payne WE, Kaiser CA, Bevis BJ, Soderholm J, Fu D, Sears IB, Glick BS. Isolation of Pichia pastoris genes involved in ER-to-Golgi transport. Yeast 2000; 16:979-93. [PMID: 10923020 DOI: 10.1002/1097-0061(200008)16:11<979::aid-yea594>3.0.co;2-c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Pichia pastoris has discrete transitional ER sites and coherent Golgi stacks, making this yeast an ideal system for studying the organization of the early secretory pathway. To provide molecular tools for this endeavour, we isolated P. pastoris homologues of the SEC12, SEC13, SEC17, SEC18 and SAR1 genes. The P. pastoris SEC12, SEC13, SEC17 and SEC18 genes were shown to complement the corresponding S. cerevisiae mutants. The SEC17 and SAR1 genes contain introns at the same relative positions in both P. pastoris and S. cerevisiae, whereas the SEC13 gene contains an intron in P. pastoris but not in S. cerevisiae. Intron structure is similar in the two yeasts, although the favoured 5' splice sequence appears to be GTAAGT in P. pastoris vs. GTATGT in S. cerevisiae. The predicted amino acid sequences of Sec13p, Sec17p, Sec18p and Sar1p show strong conservation in the two yeasts. By contrast, the predicted lumenal domain of Sec12p is much larger in P. pastoris, suggesting that this domain may help localize Sec12p to transitional ER sites. A comparison of the SEC12 loci in various budding yeasts indicates that the SEC12-related gene SED4 is probably unique to the Saccharomyces lineage.
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70
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Fu D, Levinson SF, Gracewski SM, Parker KJ. Non-invasive quantitative reconstruction of tissue elasticity using an iterative forward approach. Phys Med Biol 2000; 45:1495-509. [PMID: 10870706 DOI: 10.1088/0031-9155/45/6/307] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A novel iterative approach is presented to estimate Young's modulus in homogeneous soft tissues using vibration sonoelastography. A low-frequency (below 100 Hz) external vibration is applied and three or more consecutive frames of B-scan image data are recorded. The internal vibrational motion of the soft tissue structures is calculated from 2D displacements between pairs of consecutive frames, which are estimated using a mesh-based speckle tracking method. An iterative forward finite element approach has been developed to reconstruct Young's modulus from the measured vibrational motion. This is accomplished by subdividing the 2D image domain into sample blocks in which Young's modulus is assumed to be constant. Because the finite element equations are internally consistent, boundary values other than displacement are not required. The sensitivity of the results to Poisson's ratio and the damping coefficient (viscosity) is investigated. The approach is verified using simulated displacement data and using data from tissue-mimicking phantoms.
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71
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Liu Y, Xue J, Zhang W, Fu D, He R, Xue Z. qBrain-2, a POU domain gene expressed in quail embryos. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1491:27-36. [PMID: 10760567 DOI: 10.1016/s0167-4781(00)00011-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We isolated a quail class III POU domain gene, qBrain-2, which was cloned from a cDNA library of E5 embryos. Northern blot and in situ hybridization analyses showed that qBrain-2 was expressed in developing central nervous system and adult brain. Moreover, qBrain-2 transcripts showed a dynamic distribution in embryonic central nervous system. Its transcripts were dominantly detected in the ventricular zone of the developing brain and spinal cord, but rarely in the differentiated region of mantle zone as well as the non-neuronal roof plate and floor plate. This suggests that qBrain-2 is involved in proliferation and differentiation of the neuroepithelial cells of quail central nervous system.
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Abstract
Human milk oligosaccharides are known to play a role in protection against certain infectious diseases. Previous reports indicate that the content of human milk oligosaccharides varies widely among individuals at term but such information on preterm milk is lacking. After removal of the fat, protein and most of the lactose from non-pooled human milk samples, a total neutral oligosaccharide fraction was isolated by ion-exchange chromatography followed by gel filtration. A Dionex high-performance anion-exchange chromatography system equipped with a pulsed electrometric detector was then employed to measure the levels of ten neutral oligosaccharides in the individual milk samples. Twenty-three milk samples from thirteen mothers who delivered at a mean gestational age of 29.5 (SD 3.1) weeks were collected between days 0 and 33 of lactation, and compared with three samples of term milk from two mothers. The ranges of the total and individual levels of the ten neutral oligosaccharides in preterm milk were similar to those in term milk. Further, as previously described in term milk, preterm milk exhibited a quantitative individual variation. This variation was independent of the gestational age, day of lactation, and postconceptional age. In conclusion, levels of ten neutral oligosaccharides did not differ between preterm and term human milk.
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73
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Fu D, Shi Z, Wang Y. Bcl-2 plays a key role instead of mdr1 in the resistance to hexadecylphosphocholine in human epidermoid tumor cell line KB. Cancer Lett 1999; 142:147-53. [PMID: 10463770 DOI: 10.1016/s0304-3835(99)00146-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We induced tolerance to hexadecylphosphocholine (HePC) in the human epidermoid tumor cell line, KB. After 70 weeks of adaptation, the IC50 of HePC in the resistant cells KBr was 32-fold higher than in parental KB cells, and they were 30-fold more resistant to another ether lipid analogue, ET-18-OCH3. The KBr cells also showed cross-resistance to vincristine and colchicine while remaining sensitive to other chemotherapy agents. RT-PCR assays showed that expression of the multidrug resistance gene (MDR1) was positive in KBr cells, whereas the expression of GST-pi (glutathione S-transferase pi) and MRP (multidrug resistance protein) was undetectable in KBr cells. Both an immunocytochemistry test and Western blot analysis indicated that the expression of bcl-2 in KBr cells was strongly positive, while it was only mildly expressed in KB cells. Verapamil could not reverse the resistance of KBr to HePC although it is a well-known reversing agent against MDR1. Our results suggest that bcl-2 instead of MDR1 plays a major role in the resistance of KBr cells.
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Jung MY, Skryabin BV, Arai M, Abbondanzo S, Fu D, Brosius J, Robakis NK, Polites HG, Pintar JE, Schmauss C. Potentiation of the D2 mutant motor phenotype in mice lacking dopamine D2 and D3 receptors. Neuroscience 1999; 91:911-24. [PMID: 10391470 DOI: 10.1016/s0306-4522(98)00705-2] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Within the D2-class of dopamine receptors, the D2 and D3 subtypes share the highest degree of similarity in their primary structure. However, the extent to which these two receptor subtypes have similar or different functional properties is unclear. The present study used gene targeting to generate mice deficient for D2, D3, and D2/D3 receptors. A comparative analysis of D2 and D3 single mutants and D2/D3 double mutants revealed that D2/D3 double mutants develop motor phenotypes that, although qualitatively similar to those seen in D2 single mutants, are significantly more severe. Furthermore, increased levels of the dopamine metabolites dihydroxyphenyl acetic acid and homovanillic acid are found in the dorsal striatum of D2 single mutants. The levels of these metabolites, however, are significantly higher in mice lacking D2 and D3 receptors. In addition, results of immunoprecipitation experiments revealed that D2 single mutants express higher levels of D3 receptor proteins during later stages of their postnatal development. These results suggest that D3 receptors compensate for some of the lacking D2 receptor functions and that these functional properties of D3 receptors, detected in mice with a D2 mutant genetic background, remain masked when the abundant D2 receptor is expressed.
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Durner M, Zhou G, Fu D, Abreu P, Shinnar S, Resor SR, Moshe SL, Rosenbaum D, Cohen J, Harden C, Kang H, Wallace S, Luciano D, Ballaban-Gil K, Klotz I, Dicker E, Greenberg DA. Evidence for linkage of adolescent-onset idiopathic generalized epilepsies to chromosome 8-and genetic heterogeneity. Am J Hum Genet 1999; 64:1411-9. [PMID: 10205274 PMCID: PMC1377879 DOI: 10.1086/302371] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Several loci and candidate genes for epilepsies or epileptic syndromes map or have been suggested to map to chromosome 8. We investigated families with adolescent-onset idiopathic generalized epilepsy (IGE), for linkage to markers spanning chromosome 8. The IGEs that we studied included juvenile myoclonic epilepsy (JME), epilepsy with only generalized tonic-clonic seizures occurring either randomly during the day (random grand mal) or on awakening (awakening grand mal), and juvenile absence epilepsy (JAE). We looked for a gene common to all these IGEs, but we also investigated linkage to specific subforms of IGE. We found evidence for linkage to chromosome 8 in adolescent-onset IGE families in which JME was not present. The maximum multipoint LOD score was 3.24 when family members with IGE or generalized spike-and-waves (SW) were considered affected. The LOD score remained very similar (3.18) when clinically normal family members with SW were not considered to be affected. Families with either pure grand mal epilepsy or absence epilepsy contributed equally to the positive LOD score. The area where the LOD score reaches the maximum encompasses the location of the gene for the beta3-subunit of the nicotinic acetylcholine receptor (CHRNB3), thus making this gene a possible candidate for these specific forms of adolescent-onset IGE. The data excluded linkage of JME to this region. These results indicate genetic heterogeneity within IGE and provide no evidence, on chromosome 8, for a gene common to all IGEs.
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