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Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000; 403:503-11. [PMID: 10676951 DOI: 10.1038/35000501] [Citation(s) in RCA: 6258] [Impact Index Per Article: 250.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma, is clinically heterogeneous: 40% of patients respond well to current therapy and have prolonged survival, whereas the remainder succumb to the disease. We proposed that this variability in natural history reflects unrecognized molecular heterogeneity in the tumours. Using DNA microarrays, we have conducted a systematic characterization of gene expression in B-cell malignancies. Here we show that there is diversity in gene expression among the tumours of DLBCL patients, apparently reflecting the variation in tumour proliferation rate, host response and differentiation state of the tumour. We identified two molecularly distinct forms of DLBCL which had gene expression patterns indicative of different stages of B-cell differentiation. One type expressed genes characteristic of germinal centre B cells ('germinal centre B-like DLBCL'); the second type expressed genes normally induced during in vitro activation of peripheral blood B cells ('activated B-like DLBCL'). Patients with germinal centre B-like DLBCL had a significantly better overall survival than those with activated B-like DLBCL. The molecular classification of tumours on the basis of gene expression can thus identify previously undetected and clinically significant subtypes of cancer.
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MESH Headings
- Adult
- B-Lymphocytes/pathology
- Gene Expression Profiling
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Lymphoma, B-Cell/diagnosis
- Lymphoma, B-Cell/genetics
- Lymphoma, Large B-Cell, Diffuse/diagnosis
- Lymphoma, Large B-Cell, Diffuse/genetics
- Oligonucleotide Array Sequence Analysis
- Phenotype
- Tumor Cells, Cultured
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6258 |
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Feder JN, Gnirke A, Thomas W, Tsuchihashi Z, Ruddy DA, Basava A, Dormishian F, Domingo R, Ellis MC, Fullan A, Hinton LM, Jones NL, Kimmel BE, Kronmal GS, Lauer P, Lee VK, Loeb DB, Mapa FA, McClelland E, Meyer NC, Mintier GA, Moeller N, Moore T, Morikang E, Prass CE, Quintana L, Starnes SM, Schatzman RC, Brunke KJ, Drayna DT, Risch NJ, Bacon BR, Wolff RK. A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis. Nat Genet 1996; 13:399-408. [PMID: 8696333 DOI: 10.1038/ng0896-399] [Citation(s) in RCA: 2543] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Hereditary haemochromatosis (HH), which affects some 1 in 400 and has an estimated carrier frequency of 1 in 10 individuals of Northern European descent, results in multi-organ dysfunction caused by increased iron deposition, and is treatable if detected early. Using linkage-disequilibrium and full haplotype analysis, we have identified a 250-kilobase region more than 3 megabases telomeric of the major histocompatibility complex (MHC) that is identical-by-descent in 85% of patient chromosomes. Within this region, we have identified a gene related to the MHC class I family, termed HLA-H, containing two missense alterations. One of these is predicted to inactivate this class of proteins and was found homozygous in 83% of 178 patients. A role of this gene in haemochromatosis is supported by the frequency and nature of the major mutation and prior studies implicating MHC class I-like proteins in iron metabolism.
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Comparative Study |
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2543 |
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Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JC, Trent JM, Staudt LM, Hudson J, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO. The transcriptional program in the response of human fibroblasts to serum. Science 1999; 283:83-7. [PMID: 9872747 DOI: 10.1126/science.283.5398.83] [Citation(s) in RCA: 1311] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The temporal program of gene expression during a model physiological response of human cells, the response of fibroblasts to serum, was explored with a complementary DNA microarray representing about 8600 different human genes. Genes could be clustered into groups on the basis of their temporal patterns of expression in this program. Many features of the transcriptional program appeared to be related to the physiology of wound repair, suggesting that fibroblasts play a larger and richer role in this complex multicellular response than had previously been appreciated.
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1311 |
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Abstract
Genomic imprinting in mammals is increasingly being implicated in developmental and pathological processes, but without a clear understanding of its function in normal development. We believe that imprinting has evolved in mammals because of the conflicting interests of maternal and paternal genes in relation to the transfer of nutrients from the mother to her offspring. We present an hypothesis that accounts for many of the observed effects of imprinting in mammals and relates them to similar observations in plants. This hypothesis has implications for studies of X-chromosome inactivation and a range of human diseases.
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Review |
34 |
596 |
5
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McComas DJ, Allegrini F, Bochsler P, Bzowski M, Christian ER, Crew GB, DeMajistre R, Fahr H, Fichtner H, Frisch PC, Funsten HO, Fuselier SA, Gloeckler G, Gruntman M, Heerikhuisen J, Izmodenov V, Janzen P, Knappenberger P, Krimigis S, Kucharek H, Lee M, Livadiotis G, Livi S, MacDowall RJ, Mitchell D, Möbius E, Moore T, Pogorelov NV, Reisenfeld D, Roelof E, Saul L, Schwadron NA, Valek PW, Vanderspek R, Wurz P, Zank GP. Global observations of the interstellar interaction from the Interstellar Boundary Explorer (IBEX). Science 2009; 326:959-62. [PMID: 19833923 DOI: 10.1126/science.1180906] [Citation(s) in RCA: 390] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The Sun moves through the local interstellar medium, continuously emitting ionized, supersonic solar wind plasma and carving out a cavity in interstellar space called the heliosphere. The recently launched Interstellar Boundary Explorer (IBEX) spacecraft has completed its first all-sky maps of the interstellar interaction at the edge of the heliosphere by imaging energetic neutral atoms (ENAs) emanating from this region. We found a bright ribbon of ENA emission, unpredicted by prior models or theories, that may be ordered by the local interstellar magnetic field interacting with the heliosphere. This ribbon is superposed on globally distributed flux variations ordered by both the solar wind structure and the direction of motion through the interstellar medium. Our results indicate that the external galactic environment strongly imprints the heliosphere.
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Research Support, U.S. Gov't, Non-P.H.S. |
16 |
390 |
6
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34 |
379 |
7
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Moore T, Fallah M. Control of eye movements and spatial attention. Proc Natl Acad Sci U S A 2001; 98:1273-6. [PMID: 11158629 PMCID: PMC14744 DOI: 10.1073/pnas.98.3.1273] [Citation(s) in RCA: 349] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2000] [Accepted: 11/21/2000] [Indexed: 11/18/2022] Open
Abstract
Several lines of evidence suggest that planning eye movements and directing visuospatial attention share overlapping brain mechanisms. This study tested whether spatial attention can be enhanced by altering oculomotor signals within the brain. Monkeys performed a spatial attention task while neurons within the frontal eye field, an oculomotor area within prefrontal cortex, were electrically stimulated below the level at which eye movements are evoked. We found that we could improve the monkey's performance with microstimulation when, but only when, the object to be attended was positioned in the space represented by the cortical stimulation site.
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research-article |
24 |
349 |
8
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Dean W, Bowden L, Aitchison A, Klose J, Moore T, Meneses JJ, Reik W, Feil R. Altered imprinted gene methylation and expression in completely ES cell-derived mouse fetuses: association with aberrant phenotypes. Development 1998; 125:2273-82. [PMID: 9584126 DOI: 10.1242/dev.125.12.2273] [Citation(s) in RCA: 286] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In vitro manipulation of preimplantation mammalian embryos can influence differentiation and growth at later stages of development. In the mouse, culture of embryonic stem (ES) cells affects their totipotency and may give rise to fetal abnormalities. To investigate whether this is associated with epigenetic alterations in imprinted genes, we analysed two maternally expressed genes (Igf2r, H19) and two paternally expressed genes (Igf2, U2af1-rs1) in ES cells and in completely ES cell-derived fetuses. Altered allelic methylation patterns were detected in all four genes, and these were consistently associated with allelic changes in gene expression. All the methylation changes that had arisen in the ES cells persisted on in vivo differentiation to fetal stages. Alterations included loss of methylation with biallelic expression of U2af1-rs1, maternal methylation and predominantly maternal expression of Igf2, and biallelic methylation and expression of Igf2r. In many of the ES fetuses, the levels of H19 expression were strongly reduced, and this biallelic repression was associated with biallellic methylation of the H19 upstream region. Surprisingly, biallelic H19 repression was not associated with equal levels of Igf2 expression from both parental chromosomes, but rather with a strong activation of the maternal Igf2 allele. ES fetuses derived from two of the four ES lines appeared developmentally compromised, with polyhydramnios, poor mandible development and interstitial bleeding and, in chimeric fetuses, the degree of chimerism correlated with increased fetal mass. Our study establishes a model for how early embryonic epigenetic alterations in imprinted genes persist to later developmental stages, and are associated with aberrant phenotypes.
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27 |
286 |
9
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Hallman M, Merritt TA, Jarvenpaa AL, Boynton B, Mannino F, Gluck L, Moore T, Edwards D. Exogenous human surfactant for treatment of severe respiratory distress syndrome: a randomized prospective clinical trial. J Pediatr 1985; 106:963-9. [PMID: 3889259 DOI: 10.1016/s0022-3476(85)80253-5] [Citation(s) in RCA: 242] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We performed a randomized, prospective clinical trial comparing intratracheal administration of human surfactant with conventional treatment with intermittent mandatory mechanical ventilation alone for treatment of severe respiratory distress syndrome in preterm infants of less than 30 weeks gestation. Twenty-two infants (mean gestational age 27.0 weeks, mean birth weight 987 gm) were given surfactant, and 23 infants (mean gestational age 27.2 week, mean birth weight 1055 gm) received intermittent mandatory ventilation. Infants given surfactant required less FiO2 during the first week, had lower mean airway pressure during the first 48 hours, and had improved ventilatory index and a/A PO2 ratio. Death or the occurrence of bronchopulmonary dysplasia was significantly less among infants given surfactant (P = 0.019). Pneumothorax, pulmonary interstitial emphysema, and need for FiO2 greater than or equal to 0.3 for greater than 30 days was significantly less in the surfactant group. This trial confirms the efficacy of treatment with human surfactant in preterm infants with severe respiratory distress syndrome.
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Clinical Trial |
40 |
242 |
10
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Tolias AS, Moore T, Smirnakis SM, Tehovnik EJ, Siapas AG, Schiller PH. Eye movements modulate visual receptive fields of V4 neurons. Neuron 2001; 29:757-67. [PMID: 11301034 DOI: 10.1016/s0896-6273(01)00250-1] [Citation(s) in RCA: 219] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The receptive field, defined as the spatiotemporal selectivity of neurons to sensory stimuli, is central to our understanding of the neuronal mechanisms of perception. However, despite the fact that eye movements are critical during normal vision, the influence of eye movements on the structure of receptive fields has never been characterized. Here, we map the receptive fields of macaque area V4 neurons during saccadic eye movements and find that receptive fields are remarkably dynamic. Specifically, before the initiation of a saccadic eye movement, receptive fields shrink and shift towards the saccade target. These spatiotemporal dynamics may enhance information processing of relevant stimuli during the scanning of a visual scene, thereby assisting the selection of saccade targets and accelerating the analysis of the visual scene during free viewing.
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24 |
219 |
11
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Fideler BM, Vangsness CT, Lu B, Orlando C, Moore T. Gamma irradiation: effects on biomechanical properties of human bone-patellar tendon-bone allografts. Am J Sports Med 1995; 23:643-6. [PMID: 8526284 DOI: 10.1177/036354659502300521] [Citation(s) in RCA: 207] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Sixty 10-mm bone-patellar tendon-bone allografts from young human donors were placed into four test groups, a control fresh-frozen group and three fresh-frozen irradiated groups. The irradiated groups were exposed to 2.0, 3.0, or 4.0 Mrad of gamma irradiation. The specimens were tested to tensile failure. The initial biomechanical strength of fresh-frozen allografts was reduced up to 15% when compared with fresh-frozen controls after 2.0 Mrad of irradiation. Maximum force, strain energy, modulus, and maximum stress demonstrated a statistically significant reduction after 2.0 Mrad of irradiation (P < 0.01). Stiffness, elongation, and strain were reduced but not with statistical significance. A 10% to 24% and 19% to 46% reduction in all biomechanical properties were found after 3.0 (P < 0.005) and 4.0 (P < 0.0005) Mrad of irradiation, respectively. After irradiation with a 4.0 Mrad dose, the ultimate load was below that of reported values for the human anterior cruciate ligament. It is clinically important to observe and document changes in human ligaments that result from currently used doses of gamma irradiation. The results from this study provide important information regarding the initial biomechanical properties of fresh-frozen human bone-patellar tendon-bone allografts after bacterial sterilization with gamma irradiation. The current accepted dose for sterilization is between 1.5 and 2.5 Mrad. There appeared to be a dose-dependent effect of irradiation on all the biomechanical parameters studied. Four of seven parameters were found to be reduced after 2.0 Mrad of irradiation. Reductions were found in all parameters after 3.0 and 4.0 Mrad of irradiation.
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30 |
207 |
12
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Moore T, Constancia M, Zubair M, Bailleul B, Feil R, Sasaki H, Reik W. Multiple imprinted sense and antisense transcripts, differential methylation and tandem repeats in a putative imprinting control region upstream of mouse Igf2. Proc Natl Acad Sci U S A 1997; 94:12509-14. [PMID: 9356480 PMCID: PMC25020 DOI: 10.1073/pnas.94.23.12509] [Citation(s) in RCA: 204] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The mouse insulin-like growth factor 2 (Igf2) locus is a complex genomic region that produces multiple transcripts from alternative promoters. Expression at this locus is regulated by parental imprinting. However, despite the existence of putative imprinting control elements in the Igf2 upstream region, imprinted transcriptional repression is abolished by null mutations at the linked H19 locus. To clarify the extent to which the Igf2 upstream region contains autonomous imprinting control elements we have performed functional and comparative analyses of the region in the mouse and human. Here we report the existence of multiple, overlapping imprinted (maternally repressed) sense and antisense transcripts that are associated with a tandem repeat in the mouse Igf2 upstream region. Regions flanking the repeat exhibit tissue-specific parental allelic methylation patterns, suggesting the existence of tissue-specific control elements in the upstream region. Studies in H19 null mice indicate that both parental allelic methylation and monoallelic expression of the upstream transcripts depends on an intact H19 gene acting in cis. The homologous region in human IGF2 is structurally conserved, with the significant exception that it does not contain a tandem repeat. Our results support the proposal that tandem repeats act to target methylation to imprinted genetic loci.
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research-article |
28 |
204 |
13
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Schwadron NA, Bzowski M, Crew GB, Gruntman M, Fahr H, Fichtner H, Frisch PC, Funsten HO, Fuselier S, Heerikhuisen J, Izmodenov V, Kucharek H, Lee M, Livadiotis G, McComas DJ, Moebius E, Moore T, Mukherjee J, Pogorelov NV, Prested C, Reisenfeld D, Roelof E, Zank GP. Comparison of Interstellar Boundary Explorer observations with 3D global heliospheric models. Science 2009; 326:966-8. [PMID: 19833915 DOI: 10.1126/science.1180986] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Simulations of energetic neutral atom (ENA) maps predict flux magnitudes that are, in some cases, similar to those observed by the Interstellar Boundary Explorer (IBEX) spacecraft, but they miss the ribbon. Our model of the heliosphere indicates that the local interstellar medium (LISM) magnetic field (B(LISM)) is transverse to the line of sight (LOS) along the ribbon, suggesting that the ribbon may carry its imprint. The force-per-unit area on the heliopause from field line draping and the LISM ram pressure is comparable with the ribbon pressure if the LOS approximately 30 to 60 astronomical units and B(LISM) approximately 2.5 microgauss. Although various models have advantages in accounting for some of the observations, no model can explain all the dominant features, which probably requires a substantial change in our understanding of the processes that shape our heliosphere.
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Research Support, U.S. Gov't, Non-P.H.S. |
16 |
193 |
14
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Gault J, Robinson M, Berger R, Drebing C, Logel J, Hopkins J, Moore T, Jacobs S, Meriwether J, Choi MJ, Kim EJ, Walton K, Buiting K, Davis A, Breese C, Freedman R, Leonard S. Genomic organization and partial duplication of the human alpha7 neuronal nicotinic acetylcholine receptor gene (CHRNA7). Genomics 1998; 52:173-85. [PMID: 9782083 DOI: 10.1006/geno.1998.5363] [Citation(s) in RCA: 193] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The human alpha7 neuronal nicotinic acetylcholine receptor gene (HGMW-approved symbol CHRNA7) has been characterized from genomic clones. The gene is similar in structure to the chick alpha7 gene with 10 exons and conserved splice junction positions. The size of the human gene is estimated to be larger than 75 kb. A putative promoter 5' of the translation start in exon 1 has been cloned and sequenced. The promoter region lacks a TATA box and has a high GC content (77%). Consensus Sp1, AP-2, Egr-1, and CREB transcription factor binding sites appear to be conserved between bovine and human genes. The alpha7 nAChR gene was found to be partially duplicated, with both loci mapping to the chromosome 15q13 region. A yeast artificial chromosome contig was constructed over a genetic distance of 5 cM that includes both alpha7 loci and the region between them. Four novel exons are described, located in genomic clones containing the partially duplicated gene. The duplicated sequences, including the novel exons, are expressed in human brain.
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27 |
193 |
15
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Moore T. Vitamin A and carotene: The absence of the liver oil vitamin A from carotene. VI. The conversion of carotene to vitamin A in vivo. Biochem J 2006; 24:692-702. [PMID: 16744410 PMCID: PMC1254511 DOI: 10.1042/bj0240692] [Citation(s) in RCA: 187] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Journal Article |
19 |
187 |
16
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Rand KN, Moore T, Sriskantha A, Spring K, Tellam R, Willadsen P, Cobon GS. Cloning and expression of a protective antigen from the cattle tick Boophilus microplus. Proc Natl Acad Sci U S A 1989; 86:9657-61. [PMID: 2690068 PMCID: PMC298560 DOI: 10.1073/pnas.86.24.9657] [Citation(s) in RCA: 161] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Glycoproteins located on the luminal surface of the plasma membrane of tick gut epithelial cells, when used to vaccinate cattle, are capable of stimulating an immune response that protects cattle against subsequent tick infestation. One such tick gut glycoprotein, designated Bm86, has been purified to homogeneity and the amino acid sequences of peptide fragments generated by endoproteinase Lys-C digestion have been determined. We report here the isolation and characterization of a cDNA that encodes Bm86. The nucleotide sequence of the cDNA contains a 1982-base-pair open reading frame and predicts that Bm86 contains 650 amino acids including a 19-amino acid signal sequence and a 23-amino acid hydrophobic region adjacent to the carboxyl terminus. The main feature of the deduced protein sequence is the repeated pattern of 6 cysteine residues, suggesting the presence of several epidermal growth factor-like domains. A fusion protein consisting of 599 amino acids of Bm86 and 651 amino acids of beta-galactosidase was expressed in Escherichia coli as inclusion bodies. Ticks engorging on cattle vaccinated with these inclusion bodies were significantly damaged as a result of the immune response against the cloned antigen.
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research-article |
36 |
161 |
17
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Constância M, Dean W, Lopes S, Moore T, Kelsey G, Reik W. Deletion of a silencer element in Igf2 results in loss of imprinting independent of H19. Nat Genet 2000; 26:203-6. [PMID: 11017078 DOI: 10.1038/79930] [Citation(s) in RCA: 156] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Igf2 and H19 are closely linked, reciprocally imprinted genes on mouse distal chromosome 7. The paternally expressed Igf2 encodes a potent fetal growth factor and the maternally expressed H19 encodes a non-coding RNA (refs 1,2). Shared endoderm-specific enhancers 3' to H19 are necessary for transcription of the maternal copy of H19 and the paternal copy of Igf2 (ref. 3), a chromatin boundary upstream of H19 preventing access of the enhancers to the maternal Igf2 promoters. Mesoderm-specific control elements have not been identified, and the role of differentially methylated regions (DMRs) in Igf2 has not been addressed. Two DMRs in Igf2 are methylated on the active paternal allele, suggesting that they contain silencers. Here we have deleted the DMR1 region in Igf2. Maternal transmission of the deletion results in biallelic expression of Igf2 in most mesodermally derived tissues without altering H19 imprinting or expression. Paternal or maternal transmission leads to continued postnatal transcription of Igf2, in contrast to the wild-type allele, which is silenced soon after birth. These results reveal a mesodermal silencer, which may be regulated by methylation and which has a major role in H19-independent expression and imprinting control of Igf2. Our results establish a new mechanistic principle for imprinted genes whereby epigenetically regulated silencers interact with enhancers to control expression, and suggest a new mechanism for loss of imprinting (LOI) of Igf2, which may be important in a number of diseases.
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25 |
156 |
18
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Ganguli G, Keskinen MJ, Romero H, Heelis R, Moore T, Pollock C. Coupling of microprocesses and macroprocesses due to velocity shear: An application to the low-altitude ionosphere. ACTA ACUST UNITED AC 1994. [DOI: 10.1029/93ja03181] [Citation(s) in RCA: 151] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31 |
151 |
19
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Fideler BM, Vangsness CT, Moore T, Li Z, Rasheed S. Effects of gamma irradiation on the human immunodeficiency virus. A study in frozen human bone-patellar ligament-bone grafts obtained from infected cadavera. J Bone Joint Surg Am 1994; 76:1032-5. [PMID: 8027110 DOI: 10.2106/00004623-199407000-00011] [Citation(s) in RCA: 147] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We studied the effects of several different doses of gamma radiation, ranging from 20,000 to 40,000 gray (2.0 to 4.0 megarad), with respect to the inactivation of the human immunodeficiency virus in fresh-frozen, whole bone-patellar ligament-bone grafts. Although the International Atomic Energy Agency has recommended the use of 25,000 gray of gamma radiation for the sterilization of medical products, the dose required for the inactivation of the human immunodeficiency virus in frozen allografts has not been established. Using one of the most sensitive and specific tests for the detection of the human immunodeficiency virus, the polymerase-chain-reaction test, we found that doses of 20,000 or 25,000 gray of gamma radiation did not destroy the genes of the human immunodeficiency virus effectively; DNA of the virus was detectable in the DNA of bone-marrow tissue obtained from grafts treated with these doses. However, DNA of the human immunodeficiency virus was not detectable in the grafts treated with 30,000 or 40,000 gray of gamma radiation. We conclude that a dose of 30,000 gray of gamma radiation or more is necessary for the sterilization of a fresh-frozen bone-patellar ligament-bone allograft, so that it can be used for reconstructive procedures without the risk of transmission of the virus to the recipient.
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31 |
147 |
20
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Mendelsohn AL, Mogilner LN, Dreyer BP, Forman JA, Weinstein SC, Broderick M, Cheng KJ, Magloire T, Moore T, Napier C. The impact of a clinic-based literacy intervention on language development in inner-city preschool children. Pediatrics 2001; 107:130-4. [PMID: 11134446 DOI: 10.1542/peds.107.1.130] [Citation(s) in RCA: 142] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE To determine the effect of a clinic-based literacy intervention on the language development of preschool children. METHODS A convenience sample of families presenting to 2 urban pediatric clinics for well-child care met the following criteria: the family was Latino or black and English- or Spanish-speaking; the child was 2 to 5.9 years old, with no neurodevelopmental disability, at a gestational age of 34 weeks or more, and not attending kindergarten. Participants at the first clinic (intervention group) were exposed to a literacy support program, based on Reach Out and Read (ROR), during the previous 3 years. At the second clinic (comparison group), a similar program started 3 months before the study. Parent-child reading activities were measured using the READ Subscale of the StimQ. Language development was measured using the One-Word Expressive and Receptive Picture Vocabulary Tests, and was performed in the child's primary language. RESULTS A total of 122 study participants (49 interventions and 73 comparisons) met inclusion criteria and completed all measures. Intervention and comparison families were similar for most sociodemographic variables. Intervention families reported reading together with their children approximately 1 more day per week. Intensity of exposure to ROR (measured by total number of contacts with the program) was associated with increased parent-child reading activities, as measured by the StimQ-Read Subscale (r = 0.20). Intervention children had higher receptive language (mean: 94.5 vs 84.8) and expressive language (mean: 84.3 vs 81.6). After adjusting for potential confounders in a multiple regression analysis, intervention status was associated with an 8.6-point increase (95% confidence interval [CI]: 3.3, 14.0) in receptive language (semipartial correlation [SR]coefficient = 0.27), and a 4.3-point increase (95% CI: 0.04, 8.6) in expressive language (SR = 0.17). In a similar multiple regression, each contact with ROR was associated with an adjusted mean 0.4-point increase (95% CI: 0.1, 0.6) in receptive score, and an adjusted mean 0.21-point increase (95% CI: 0. 02, 0.4) in expressive score. CONCLUSIONS ROR is an important intervention, promoting parental literacy support and enhancing language development in impoverished preschool children. Integration of literacy promoting interventions such as these into routine pediatric health care for underserved populations can be recommended.
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24 |
142 |
21
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Mailloux LU, Bellucci AG, Mossey RT, Napolitano B, Moore T, Wilkes BM, Bluestone PA. Predictors of survival in patients undergoing dialysis. Am J Med 1988; 84:855-62. [PMID: 3364444 DOI: 10.1016/0002-9343(88)90063-0] [Citation(s) in RCA: 134] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Survival and risk analyses were performed on all 532 patients in whom long-term dialysis was started from 1970 through 1985. During this 16-year period, starting age increased from 47 to 60 years (p less than 0.001), and the incidence of diabetes mellitus and renal vascular disease increased. Survival analysis showed age, renal diagnosis, type of dialysis, and year starting dialysis to be important predictors of survival. There was a fourfold rise in the risk ratio as starting age increased from 25 to 65 years. The risk was 1.5 times higher for those patients who did not start dialysis in 1978 through 1981 than for those who did. Risk decreased fivefold for patients choosing home hemodialysis. Home hemodialysis patients survived longer compared with patients utilizing other dialysis modalities, possibly because of a younger average age and a lower incidence of diabetes mellitus and renal vascular disease. There was greater than a threefold rise in risk ratio with the diagnosis of diabetes mellitus compared with either chronic glomerulonephritis or polycystic kidney disease. Older patients and those with diabetes mellitus formed the high-risk group; these two characteristics have been increasing during the last eight years of the study. It is concluded that although patients with high risk have an increased and a high mortality, overall survival has improved.
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Shingler V, Moore T. Sensing of aromatic compounds by the DmpR transcriptional activator of phenol-catabolizing Pseudomonas sp. strain CF600. J Bacteriol 1994; 176:1555-60. [PMID: 8132448 PMCID: PMC205239 DOI: 10.1128/jb.176.6.1555-1560.1994] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The dmp operon of the pVI150 catabolic plasmid of Pseudomonas sp. strain CF600 encodes the enzymes involved in the catabolism of phenol and methylphenols. The regulator of this dmp pathway, DmpR, is a member of the NtrC family of transcriptional activators and controls transcription of the dmp operon in response to aromatic effector compounds (V. Shingler, M. Bartilson, and T. Moore, J. Bacteriol. 175:1596-1604, 1993). Using a lux gene fusion reporter system, in which the DmpR-regulated operon promoter controls the expression of luciferase activity, we have shown in the study reported here that DmpR is activated by, but responds differentially to, the presence of a wide range of aromatic compounds. In many microbial regulatory systems, including some members of the NtrC family, the response to environmental fluctuations involves information transfer from surface sensory proteins to transcriptional regulators. However, DmpR-mediated activation of phenol metabolism in response to aromatic compounds occurs in the absence of a specific sensory protein. We used hybrids between DmpR and XylR, a structurally related regulator of toluene and xylene metabolism, to demonstrate that it is the amino-terminal domains of these regulators that determine the specificity of transcriptional activation. The results suggest that it is the direct interaction of aromatic compounds with the DmpR and XylR proteins that regulates their transcriptional promoting activity.
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Reboul J, Vaglio P, Tzellas N, Thierry-Mieg N, Moore T, Jackson C, Shin-i T, Kohara Y, Thierry-Mieg D, Thierry-Mieg J, Lee H, Hitti J, Doucette-Stamm L, Hartley JL, Temple GF, Brasch MA, Vandenhaute J, Lamesch PE, Hill DE, Vidal M. Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat Genet 2001; 27:332-6. [PMID: 11242119 DOI: 10.1038/85913] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genome sequences of Caenorhabditis elegans, Drosophila melanogaster and Arabidopsis thaliana have been predicted to contain 19,000, 13,600 and 25,500 genes, respectively. Before this information can be fully used for evolutionary and functional studies, several issues need to be addressed. First, the gene number estimates obtained in silico and not yet supported by any experimental data need to be verified. For example, it seems biologically paradoxical that C. elegans would have 50% more genes than Drosophilia. Second, intron/exon predictions need to be tested experimentally. Third, complete sets of open reading frames (ORFs), or "ORFeomes," need to be cloned into various expression vectors. To address these issues simultaneously, we have designed and applied to C. elegans the following strategy. Predicted ORFs are amplified by PCR from a highly representative cDNA library using ORF-specific primers, cloned by Gateway recombination cloning and then sequenced to generate ORF sequence tags (OSTs) as a way to verify identity and splicing. In a sample (n=1,222) of the nearly 10,000 genes predicted ab initio (that is, for which no expressed sequence tag (EST) is available so far), at least 70% were verified by OSTs. We also observed that 27% of these experimentally confirmed genes have a structure different from that predicted by GeneFinder. We now have experimental evidence that supports the existence of at least 17,300 genes in C. elegans. Hence we suggest that gene counts based primarily on ESTs may underestimate the number of genes in human and in other organisms.
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Shingler V, Bartilson M, Moore T. Cloning and nucleotide sequence of the gene encoding the positive regulator (DmpR) of the phenol catabolic pathway encoded by pVI150 and identification of DmpR as a member of the NtrC family of transcriptional activators. J Bacteriol 1993; 175:1596-604. [PMID: 8449869 PMCID: PMC203952 DOI: 10.1128/jb.175.6.1596-1604.1993] [Citation(s) in RCA: 123] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The catabolic plasmid pVI150 of Pseudomonas sp. strain CF600 encodes all the genetic information required for the regulated metabolism of phenol and some of its methyl-substituted derivatives. The structural dmp genes of the pathway are clustered in a single operon that lies just downstream of a -24 TGGC, -12 TTGC nif/ntr-like promoter sequence. Promoters of this class are recognized by a minor form of RNA polymerase utilizing sigma 54 (NtrA, RpoN). Primer extension analysis demonstrated that the dmp operon transcript initiates downstream of the -24, -12 promoter. Transposon insertion mutants, specifically defective in the regulation of the dmp operon, were isolated, and complementation of a phenol-utilization regulatory mutant was used to identify the regulatory locus, dmpR. The 67-kDa dmpR gene product alone was shown to be sufficient for activation of transcription from the dmp operon promoter. Nucleotide sequence determination revealed that DmpR belongs to the NtrC family of transcriptional activators that regulate transcription from -24, -12 promoters. The deduced amino acid sequence of DmpR has high homology (40 to 67% identity) with the central and carboxy-terminal regions of these activators, which are believed to be involved in the interaction with the sigma 54 RNA polymerase and in DNA binding, respectively. The amino-terminal region of DmpR was found to share 64% identity with the amino-terminal region of XylR, which is also a member of this family of activators. This region has been implicated in effector recognition of aromatic compounds that is required for the regulatory activity of XylR.
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Yip WK, Moore T, Yang SF. Differential accumulation of transcripts for four tomato 1-aminocyclopropane-1-carboxylate synthase homologs under various conditions. Proc Natl Acad Sci U S A 1992; 89:2475-9. [PMID: 1549612 PMCID: PMC48681 DOI: 10.1073/pnas.89.6.2475] [Citation(s) in RCA: 120] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Degenerate oligonucleotide primers corresponding to conserved regions flanking the active-site domain of 1-aminocyclopropane-1-carboxylate (ACC) synthase (EC 4.4.1.14) were used for the polymerase chain reaction (PCR) to amplify DNA fragments from mRNA isolated from tomato fruit and tomato suspension cell culture. Antibodies raised against two conserved peptide sequences (TNPSNPLGTT and SLSKDLGLPGFRVG) were used to screen for positive colonies, after the PCR products were cloned into a Bluescript plasmid and expressed in Escherichia coli. Four distinct cDNA fragments encoding ACC synthase homologs were isolated. While pBTAS1 and pBTAS4 were obtained from fruit mRNA, cell culture mRNA yielded three sequences, pBTAS1, pBTAS2, and pBTAS3. Sequencing of these gene fragments revealed that pBTAS1 and pBTAS4 were identical to those full-length sequences previously reported by Van Der Straeten et al. [Van Der Straeten, D., Van Wiemeersch, L., Goodman, H. & Van Montague, M. (1990) Proc. Natl. Acad. Sci. USA 87, 4859-4863] and Olson et al. [Olson, D. C., White, J. A., Edelman, J., Harkin, R. N. & Kende, H. (1991) Proc. Natl. Acad. Sci. USA 88, 5340-5344] from tomato fruit, whereas pBTAS2 and pBTAS3 represent new sequences. Ribonuclease protection assays were used to examine the expression of these transcripts under three different conditions of enhanced ethylene production--namely, during fruit ripening, in response to mechanical wounding in fruit tissue, and auxin stimulation in vegetative tissue. Transcripts of pBTAS1 accumulated massively during ripening and wounding but only slightly in response to auxin treatment. Although pBTAS4 was associated with fruit ripening, it was unresponsive to auxin treatment in vegetative tissue. In contrast, the expression of pBTAS2 and pBTAS3 was greatly promoted in auxin-treated vegetative tissue but was absent from fruit tissue. While the expression of pBTAS2 was moderately dependent on wounding, pBTAS3 was unresponsive to wounding. These data support the view that ACC synthase is encoded by a multigene family and that the members are differentially expressed in response to developmental, environmental, and hormonal factors.
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