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Nagase T, Ishikawa K, Nakajima D, Ohira M, Seki N, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. DNA Res 1997; 4:141-50. [PMID: 9205841 DOI: 10.1093/dnares/4.2.141] [Citation(s) in RCA: 190] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In this series of projects of sequencing human cDNA clones which correspond to relatively long transcripts, we newly determined the entire sequences of 100 cDNA clones which were screened on the basis of the potentiality of coding for large proteins in vitro. The cDNA libraries used were the fractions with average insert sizes from 5.3 to 7.0 kb of the size-fractionated cDNA libraries from human brain. The randomly sampled clones were single-pass sequenced from both the ends to select clones that are not registered in the public database. Then their protein-coding potentialities were examined by an in vitro transcription/translation system, and the clones that generated proteins larger than 60 kDa were entirely sequenced. Each clone gave a distinct open reading frame (ORF), and the length of the ORF was roughly coincident with the approximate molecular mass of the in vitro product estimated from its mobility on SDS-polyacrylamide gel electrophoresis. The average size of the cDNA clones sequenced was 6.1 kb, and that of the ORFs corresponded to 1200 amino acid residues. By computer-assisted analysis of the sequences with DNA and protein-motif databases (GenBank and PROSITE databases), the functions of at least 73% of the gene products could be anticipated, and 88% of them (the products of 64 clones) were assigned to the functional categories of proteins relating to cell signaling/communication, nucleic acid managing, and cell structure/motility. The expression profiles in a variety of tissues and chromosomal locations of the sequenced clones have been determined. According to the expression spectra, approximately 11 genes appeared to be predominantly expressed in brain. Most of the remaining genes were categorized into one of the following classes: either the expression occurs in a limited number of tissues (31 genes) or the expression occurs ubiquitously in all but a few tissues (47 genes).
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Nakayama M, Nakajima D, Nagase T, Nomura N, Seki N, Ohara O. Identification of high-molecular-weight proteins with multiple EGF-like motifs by motif-trap screening. Genomics 1998; 51:27-34. [PMID: 9693030 DOI: 10.1006/geno.1998.5341] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To identify large proteins with an EGF-like-motif in a systematic manner, we developed a computer-assisted method called motif-trap screening. The method exploits 5'-end single-pass sequence data obtained from a pool of cDNAs whose sizes exceed 5 kb. Using this screening procedure, we were able to identify five known and nine new genes for proteins with multiple EGF-like-motifs from 8000 redundant human brain cDNA clones. These new genes were found to encode a novel mammalian homologue of Drosophila fat protein, two seven-transmembrane proteins containing multiple cadherin and EGF-like motifs, two mammalian homologues of Drosophila slit protein, an unidentified LDL receptor-like protein, and three totally uncharacterized proteins. The organization of the domains in the proteins, together with their expression profiles and fine chromosomal locations, has indicated their biological significance, demonstrating that motif-trap screening is a powerful tool for the discovery of new genes that have been difficult to identify by conventional methods.
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Nakajima D, Cypel M, Bonato R, Machuca TN, Iskender I, Hashimoto K, Linacre V, Chen M, Coutinho R, Azad S, Martinu T, Waddell TK, Hwang DM, Husain S, Liu M, Keshavjee S. Ex Vivo Perfusion Treatment of Infection in Human Donor Lungs. Am J Transplant 2016; 16:1229-37. [PMID: 26730551 DOI: 10.1111/ajt.13562] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/17/2015] [Accepted: 10/04/2015] [Indexed: 01/25/2023]
Abstract
Ex vivo lung perfusion (EVLP) is a platform to treat infected donor lungs with antibiotic therapy before lung transplantation. Human donor lungs that were rejected for transplantation because of clinical concern regarding infection were randomly assigned to two groups. In the antibiotic group (n = 8), lungs underwent EVLP for 12 h with high-dose antibiotics (ciprofloxacin 400 mg or azithromycin 500 mg, vancomycin 15 mg/kg, and meropenem 2 g). In the control group (n = 7), lungs underwent EVLP for 12 h without antibiotics. A quantitative decrease in bacterial counts in bronchoalveolar lavage (BAL) was found in all antibiotic-treated cases but in only two control cases. Perfusate endotoxin levels at 12 h were significantly lower in the antibiotic group compared with the control group. EVLP with broad-spectrum antibiotic therapy significantly improved pulmonary oxygenation and compliance and reduced pulmonary vascular resistance. Perfusate endotoxin levels at 12 h were strongly correlated with levels of perfusates tumor necrosis factor α, IL-1β and macrophage inflammatory proteins 1α and 1β at 12 h. In conclusion, EVLP treatment of infected donor lungs with broad-spectrum antibiotics significantly reduced BAL bacterial counts and endotoxin levels and improved donor lung function.
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Nagase T, Nakayama M, Nakajima D, Kikuno R, Ohara O. Prediction of the Coding Sequences of Unidentified Human Genes. XX. The Complete Sequences of 100 New cDNA Clones from Brain Which Code for Large Proteins in vitro. DNA Res 2001; 8:85-95. [PMID: 11347906 DOI: 10.1093/dnares/8.2.85] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
To accumulate information on the coding sequences of unidentified genes, we have carried out a sequencing project of human cDNA clones which encode large proteins. We herein present the entire sequences of 100 cDNA clones of unidentified human genes, named KIAA1776 and KIAA1780-KIAA1878, from size-fractionated cDNA libraries derived from human fetal brain, adult whole brain, hippocampus and amygdala. Most of the cDNA clones to be entirely sequenced were selected as cDNAs which were shown to have coding potentiality by in vitro transcription/translation experiments, and some clones were chosen by using computer-assisted analysis of terminal sequences of cDNAs. Three of these clones (fibrillin2/KIAA1776, MEGF10/KIAA1780 and MEGF11/KIAA1781) were isolated as genes encoding proteins with multiple EGF-like domains by motif-trap screening. The average sizes of the inserts and corresponding open reading frames of eDNA clones analyzed here reached 4.7 kb and 2.4 kb (785 amino acid residues), respectively. From the results of homology and motif searches against the public databases, the functional categories of the predicted gene products of 54 genes were determined; 93% of these predicted gene products (50 gene products) were classified as proteins related to cell signaling/communication, nucleic acid management, or cell structure/motility. To collect additional information on these genes, their expression profiles were also studied in 10 human tissues, 8 brain regions, spinal cord, fetal brain and fetal liver by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.
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Aleksić J, Ansoldi S, Antonelli LA, Antoranz P, Babic A, Bangale P, Barrio JA, González JB, Bednarek W, Bernardini E, Biasuzzi B, Biland A, Blanch O, Bonnefoy S, Bonnoli G, Borracci F, Bretz T, Carmona E, Carosi A, Colin P, Colombo E, Contreras JL, Cortina J, Covino S, Da Vela P, Dazzi F, De Angelis A, De Caneva G, De Lotto B, Wilhelmi EDO, Mendez CD, Prester DD, Dorner D, Doro M, Einecke S, Eisenacher D, Elsaesser D, Fonseca MV, Font L, Frantzen K, Fruck C, Galindo D, López RJG, Garczarczyk M, Terrats DG, Gaug M, Godinović N, Muñoz AG, Gozzini SR, Hadasch D, Hanabata Y, Hayashida M, Herrera J, Hildebrand D, Hose J, Hrupec D, Idec W, Kadenius V, Kellermann H, Kodani K, Konno Y, Krause J, Kubo H, Kushida J, La Barbera A, Lelas D, Lewandowska N, Lindfors E, Lombardi S, Longo F, López M, López-Coto R, López-Oramas A, Lorenz E, Lozano I, Makariev M, Mallot K, Maneva G, Mankuzhiyil N, Mannheim K, Maraschi L, Marcote B, Mariotti M, Martínez M, Mazin D, Menzel U, Miranda JM, Mirzoyan R, Moralejo A, Munar-Adrover P, Nakajima D, Niedzwiecki A, Nilsson K, Nishijima K, Noda K, Orito R, Overkemping A, Paiano S, Palatiello M, Paneque D, et alAleksić J, Ansoldi S, Antonelli LA, Antoranz P, Babic A, Bangale P, Barrio JA, González JB, Bednarek W, Bernardini E, Biasuzzi B, Biland A, Blanch O, Bonnefoy S, Bonnoli G, Borracci F, Bretz T, Carmona E, Carosi A, Colin P, Colombo E, Contreras JL, Cortina J, Covino S, Da Vela P, Dazzi F, De Angelis A, De Caneva G, De Lotto B, Wilhelmi EDO, Mendez CD, Prester DD, Dorner D, Doro M, Einecke S, Eisenacher D, Elsaesser D, Fonseca MV, Font L, Frantzen K, Fruck C, Galindo D, López RJG, Garczarczyk M, Terrats DG, Gaug M, Godinović N, Muñoz AG, Gozzini SR, Hadasch D, Hanabata Y, Hayashida M, Herrera J, Hildebrand D, Hose J, Hrupec D, Idec W, Kadenius V, Kellermann H, Kodani K, Konno Y, Krause J, Kubo H, Kushida J, La Barbera A, Lelas D, Lewandowska N, Lindfors E, Lombardi S, Longo F, López M, López-Coto R, López-Oramas A, Lorenz E, Lozano I, Makariev M, Mallot K, Maneva G, Mankuzhiyil N, Mannheim K, Maraschi L, Marcote B, Mariotti M, Martínez M, Mazin D, Menzel U, Miranda JM, Mirzoyan R, Moralejo A, Munar-Adrover P, Nakajima D, Niedzwiecki A, Nilsson K, Nishijima K, Noda K, Orito R, Overkemping A, Paiano S, Palatiello M, Paneque D, Paoletti R, Paredes JM, Paredes-Fortuny X, Persic M, Poutanen J, Moroni PGP, Prandini E, Puljak I, Reinthal R, Rhode W, Ribó M, Rico J, Garcia JR, Rügamer S, Saito T, Saito K, Satalecka K, Scalzotto V, Scapin V, Schultz C, Schweizer T, Shore SN, Sillanpää A, Sitarek J, Snidaric I, Sobczynska D, Spanier F, Stamatescu V, Stamerra A, Steinbring T, Storz J, Strzys M, Takalo L, Takami H, Tavecchio F, Temnikov P, Terzić T, Tescaro D, Teshima M, Thaele J, Tibolla O, Torres DF, Toyama T, Treves A, Uellenbeck M, Vogler P, Zanin R, Kadler M, Schulz R, Ros E, Bach U, Krauß F, Wilms J. Black hole lightning due to particle acceleration at subhorizon scales. Science 2014; 346:1080-4. [DOI: 10.1126/science.1256183] [Show More Authors] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Ohara O, Nagase T, Ishikawa K, Nakajima D, Ohira M, Seki N, Nomura N. Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins. DNA Res 1997; 4:53-9. [PMID: 9179496 DOI: 10.1093/dnares/4.1.53] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Analysis of proteins registered in the PIR protein database implied that most of relatively large proteins are related to important functions in higher multicellular organisms, but not many large proteins have been registered to date. To establish a protocol for efficient analysis of cDNA clones coding for large proteins, we constructed a series of strictly size-fractionated cDNA libraries of human brain, where the average insert sizes of cDNA clones ranged from 3.3 kb to 10 kb. As judged by hybridization analysis with probes derived from mRNAs of known sizes, the libraries with insert sizes up to 7 kb, at least, contained the clones corresponding to full-length transcripts in addition to truncated products of longer transcripts, but few chimeric clones. Using one of the fractionated libraries with an average insert size of 7 kb, the single-pass sequences from both the ends of randomly sampled clones were determined and sarched against DNA databases. Approximately 90% of the clones were found to be new with respect to their 5'-sequences while their 3'-sequences were frequently similar to the registered expression sequence tags. Examination of the protein-coding capacity in an in vitro transcription/translation system showed that about 20% of the clones direct the synthesis of proteins with apparent molecular masses larger than 50 kDa. The set of libraries constructed here should be very useful for the accumulation of sequence data on large proteins in the human brain.
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Ishikawa K, Nagase T, Nakajima D, Seki N, Ohira M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O. Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro. DNA Res 1997; 4:307-13. [PMID: 9455477 DOI: 10.1093/dnares/4.5.307] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
As a part of our project for accumulating sequence information of the coding regions of unidentified human genes, we herein report the sequence features of 78 new cDNA clones isolated from human brain cDNA libraries as those which may code for large proteins. The sequence data showed that the average size of the cDNA inserts and their open reading frames was 6.0 kb and 2.8 kb (925 amino acid residues), respectively, and these clones produced the corresponding sizes of protein products in an in vitro transcription/translation system. Homology search against the public databases indicated that the predicted coding sequences of 68 genes contained sequences similar to known genes, 69% of which (47 genes) were related to cell signaling/communication, nucleic acid management, and cell structure/motility. The expression profiles of these genes in 14 different tissues have been analyzed by the reverse transcription-coupled polymerase chain reaction method, and 8 genes were found to be predominantly expressed in the brain.
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Ohara O, Ohara R, Yamakawa H, Nakajima D, Nakayama M. Characterization of a new beta-spectrin gene which is predominantly expressed in brain. BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 1998; 57:181-92. [PMID: 9675416 DOI: 10.1016/s0169-328x(98)00068-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We recently identified a gene which shows high similarity to the beta-spectrin gene but with a different chromosomal location from either of the two known beta-spectrin genes [T. Nagase, K.-I. Ishikawa, D. Nakajima, M. Ohira, N. Seki, N. Miyajima, A. Tanaka, H. Kotani, N. Nomura, O. Ohara, Prediction of the coding sequences of unidentified human genes: VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro, DNA Res. 4 (1997) 141-150]. In order to further characterize this new spectrin gene and its product, we isolated the rat counterpart of this gene and analyzed it in terms of its protein coding sequence, the tissue distribution of its mRNA and the product, and the regional distribution of the mRNA and the product in the brain. The results indicated that this gene was most abundantly transcribed in the brain and neurons were the predominant cell-type to express this gene. In particular, Purkinje cells were the richest in this gene product, and this new form of beta-spectrin was found more prominently in the dendrites than in the cell bodies. Since the expression pattern and the subcellular localization of this gene product were quiet distinct from those of the two beta-spectrin isoforms already characterized, this beta-spectrin gene would play an important role in neuronal membrane skeleton although it has been overlooked to date.
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Nakajima D, Nakayama M, Kikuno R, Hirosawa M, Nagase T, Ohara O. Identification of three novel non-classical cadherin genes through comprehensive analysis of large cDNAs. BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 2001; 94:85-95. [PMID: 11597768 DOI: 10.1016/s0169-328x(01)00218-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The terminal sequences of long cDNAs from human brains were subjected to an improved method of motif-trap screening. This process resulted in the identification of three novel genes that encode proteins with 27, 27, and six cadherin domains that we denoted as KIAA1773, KIAA1774 and KIAA1775, respectively. Sequence analysis indicated that the products of these genes were non-classical cadherins. KIAA1773 was found to be a mammalian homologue of the Drosophila dachsous gene but the remaining two genes did not have any likely homologues in public databases. Assessment of their expression in rat tissues indicated that these genes are expressed in highly distinct and tissue-specific patterns. Notably, KIAA1775 is expressed almost exclusively in the olfactory bulb in the rat brain. In situ hybridization further showed that KIAA1775 is strongly expressed by the mitral and tufted cells in the main and accessory olfactory bulbs, suggesting that KIAA1775 may be important in the formation and maintenance of neuronal networks, particularly those in the olfactory bulb. This study clearly shows the importance and usefulness of our cDNA project in search for genes encoding large proteins, as this project has allowed us to identify several novel non-classical cadherin genes that have thus far not been detected by conventional methods.
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Win-Shwe TT, Mitsushima D, Nakajima D, Ahmed S, Yamamoto S, Tsukahara S, Kakeyama M, Goto S, Fujimaki H. Toluene induces rapid and reversible rise of hippocampal glutamate and taurine neurotransmitter levels in mice. Toxicol Lett 2007; 168:75-82. [PMID: 17145141 DOI: 10.1016/j.toxlet.2006.10.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Revised: 10/27/2006] [Accepted: 10/27/2006] [Indexed: 11/30/2022]
Abstract
Toluene, a widely used aromatic organic solvent, has been well characterized as a neurotoxic chemical. Although the neurobehavioral effects of toluene have been studied substantially, the mechanisms involved are not clearly understood. Hippocampus, which is one of the limbic areas of brain associated with neuronal plasticity, and learning and memory functions, may be a principal target of toluene. In the present study, to establish a mouse model for investigating the effects of acute toluene exposure on the amino acid neurotransmitter levels in the hippocampus, in vivo microdialysis study was performed in freely moving mice after a single intraperitoneal administration of toluene (150 and 300 mg/kg). Amino acid neurotransmitters in microdialysates were measured by a high performance liquid chromatography system. The extracellular levels of glutamate and taurine were rapidly and reversibly increased within 30 min after the toluene administration in a dose-dependent manner and returned to the basal level by 1h. Conversely, the extracellular level of glycine and GABA were stable, and no significant change was observed after the toluene administration. To further investigate the brain toluene level in the hippocampus of toluene-administered mice, we used a solid-phase microextraction (SPME) method and examined the time course changes of toluene in the hippocampus of living mice. The brain toluene level reached the peak at 30 min after injection and returned to the basal level after 2h. In the present study, we observed the relationship between brain toluene levels and amino acid neurotransmitter glutamate and taurine levels in the hippocampus. Therefore, we suggest that toluene may mediate its action through the glutamatergic and taurinergic neurotransmission in the hippocampus of freely moving mice.
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Nakajima D, Kim CS, Oh TW, Yang CY, Naka T, Igawa S, Ohta F. Suppressive effects of genistein dosage and resistance exercise on bone loss in ovariectomized rats. JOURNAL OF PHYSIOLOGICAL ANTHROPOLOGY AND APPLIED HUMAN SCIENCE 2001; 20:285-91. [PMID: 11759267 DOI: 10.2114/jpa.20.285] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
This study was designed to determine whether combined treatments with genistein dosage and moderate resistance exercise would exhibit synergistically preventive effects on bone loss following the onset of menopause. Forty-one 12 wk-old female SD rats were assigned to five groups: 1) Sham operated (Sham); 2) ovariectomized (OVX-Cont); 3) OVX received genistein (OVX-GEN); 4) OVX exercised (OVX-EXE); and 5) OVX treated with both genistein and exercise (OVX-GEN-EXE). All rats were fed a low Ca (0.1%) diet ad libitum. Daily genistein dosage was 12 mg/kg body weight. Exercising rats took 40 sets of 1-min run interspersed with 1-min rest with a 100 g weight on the back on an uphill treadmill at 20 m/min. The experimental duration consisted of the adaptation and treatment periods of 4 weeks each. Uterine weight in OVX-Cont, OVX-GEN, OVX-EXE and OVX-GEN-EXE decreased to about 15% of that in Sham (p < 0.001). The femoral BMD (mg/cm2; mean +/- SE), assessed by DEXA (Lunar), of OVX-Cont was significantly lowered to 206 +/- 5 by -9%, as compared to 226 +/- 2 of Sham (p < 0.001). The BMD of OVX-GEN, OVX-EXE and OVX-GEN-EXE were 217 +/- 2, 217 +/- 2 and 222 +/- 2, respectively, and genistein dosage and resistance exercise equally increased the BMD of OVX rats by 5% (p < 0.01). Combined treatment of genistein and exercise more successfully recovered their decreased BMD by 8% (p < 0.001). BMD of the fourth lumbar vertebrae in OVX-Cont was declined to 191 +/- 7 by -15%, as compared to 225 +/- 4 in Sham (p < 0.001). OVX-EXE and OVX-GEN-EXE gained the BMD by 6% to 205 +/- 4 and 203 +/- 3, respectively, as compared to that of OVX-Cont (p < 0.01). These results suggest the possibility that the combined treatment of genistein dosage and resistance exercise have more beneficial effects by acting rather independently than their separate trials on the prevention of ovx-induced bone loss in femurs.
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Arisaka O, Hoshi M, Kanazawa S, Numata M, Nakajima D, Kanno S, Negishi M, Nishikura K, Nitta A, Imataka M, Kuribayashi T, Kano K. Preliminary report: effect of adrenal androgen and estrogen on bone maturation and bone mineral density. Metabolism 2001; 50:377-9. [PMID: 11288028 DOI: 10.1053/meta.2001.21678] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To clarify the independent physiological roles of adrenal androgen and estrogen on bone growth, we compared the lumbar spine bone mineral density (BMD) in prepubertal girls with virilizing congenital adrenal hyperplasia (CAH) (n = 17) and girls with central precocious puberty (CPP) (n = 18). When BMD was analyzed according to chronologic age, no significant differences were found between CPP and CAH patients. However, when adjusted to bone age, BMD was statistically higher in CAH than in CPP subjects. This finding suggests that adrenal androgen, as well as estrogen, plays an important role in increasing BMD. Adrenal androgen may act on bone not only as androgen, but as estrogen after having been metabolized into an aromatized bone-active compound in peripheral tissues, such as bone and fat. Therefore, adrenal androgen may have a more important role in increasing BMD than previously realized.
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Hashimoto K, Cypel M, Kim H, Machuca TN, Nakajima D, Chen M, Hsin MK, Zamel R, Azad S, Waddell TK, Liu M, Keshavjee S. Soluble Adhesion Molecules During Ex Vivo Lung Perfusion Are Associated With Posttransplant Primary Graft Dysfunction. Am J Transplant 2017; 17:1396-1404. [PMID: 27977885 DOI: 10.1111/ajt.14160] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 10/30/2016] [Accepted: 11/28/2016] [Indexed: 01/25/2023]
Abstract
Ex vivo lung perfusion (EVLP) enables assessment of marginal donor lungs for transplantation. We aimed to discover biomarkers in EVLP perfusate that could predict development of primary graft dysfunction (PGD). From September 2008 to August 2013, 100 clinical EVLPs were performed. Eleven patients developed PGD grade 3 within 72 h after transplant. The non-PGD group consisted of 34 patients without PGD grade 3. Nonbilateral lung transplants or transplant after extracorporeal life support were excluded from analyses. Soluble intercellular adhesion molecule 1 (sICAM-1), soluble VCAM-1 (sVCAM-1), and soluble E selectin (sE-selectin) levels, as markers of endothelial activation, were measured in the perfusate of EVLP by enzyme-linked immunosorbent assay and were correlated with clinical outcome. Levels of sICAM-1 at 1 h and sVCAM-1 at 1 and 4 h were significantly higher in the PGD group compared with the non-PGD group. The sE selectin levels were not statistically different between the study groups. Higher levels of sVCAM-1 at 1 and 4 h were statistically significantly associated with PGD either alone or after adjustment for other PGD risk factors. These adhesion molecules may help identify donor lungs at higher risk of PGD during EVLP.
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Seki N, Ohira M, Nagase T, Ishikawa K, Miyajima N, Nakajima D, Nomura N, Ohara O. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. DNA Res 1997; 4:345-9. [PMID: 9455484 DOI: 10.1093/dnares/4.5.345] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
To evaluate the size-fractionated cDNA libraries of human brain previously constructed (O. O'hara et al. DNA Research, 4, 53-59, 1997), the occurrence of chimeric clones and the content of clones with coding potentiality were analyzed using the randomly sampled clones with insert sizes of 5 to 7 kb. When the chromosomal location of 30 clones was determined by the radiation-hybrid mapping method, the map positions assigned from the 3'- and 5'-end sequences separately were coincident for 29 clones, suggesting that the occurrence of chimeric clones is at most 1/30. Using 91 clones mapped to chromosome 1, the content of clones that have the potentiality coding for proteins larger than 100 amino acid residues was estimated to be approximately 50% (46 out of 91 clones) on the basis of nucleotide sequence analysis and coding potentiality assay in vitro. No significant open reading frames were detected in the remaining clones. Although the clones coding for short peptides may not have been included in the above estimation, the libraries constructed from the whole brain mRNA fraction appear to contain a considerable amount of clones corresponding to the 5'-truncated transcripts in an unprocessed form and/or those with long 3'-untranslated regions.
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MESH Headings
- Animals
- Brain Chemistry/genetics
- Chimera
- Chromosome Mapping
- Chromosomes, Human, Pair 1
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Electrophoresis, Polyacrylamide Gel
- Gene Library
- HSP40 Heat-Shock Proteins
- Humans
- Open Reading Frames
- Polymerase Chain Reaction
- RNA, Messenger/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Homology, Nucleic Acid
- Sequence Tagged Sites
- Transcription, Genetic
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Yamakawa H, Ohara R, Nakajima D, Nakayama M, Ohara O. Molecular characterization of a new member of the protein 4.1 family (brain 4.1) in rat brain. BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 1999; 70:197-209. [PMID: 10407168 DOI: 10.1016/s0169-328x(99)00139-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In addition to the well-known erythroid 4.1 gene, two human genes (KIAA0338 and 4.1G) have recently been identified as members of the protein 4.1 family of genes. We compared the expression levels of these three genes and found that the KIAA0338 gene was predominantly expressed in human brain. To further characterize this novel protein 4.1, called brain 4.1, we isolated rat brain 4.1 cDNA and analyzed its gene products in rat brain. The results indicated that the mRNA and protein products of the brain 4.1 gene were more abundant in brain compared to any other tissues examined. The brain 4.1 mRNA appeared as multiple bands with estimated sizes of 3.9 kb, 6.2 kb and 8.7 kb on RNA blotting analysis, and was found to consist of various alternative forms as reported previously for the erythroid 4. 1 gene. As for the brain 4.1 gene product, many isoforms discernible by immunoblotting analysis were also observed depending on the tissue type and the brain region. The existence of multiple forms of the brain 4.1 implies that it has multiple and diverse functions like the erythroid 4.1 gene product.
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Comparative Study |
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Yamakawa H, Nakajima D, Ohara O. Identification of sequence motifs causing band compressions on human cDNA sequencing. DNA Res 1996; 3:81-6. [PMID: 8804859 DOI: 10.1093/dnares/3.2.81] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In order to characterize DNA sequences leading to band compressions in an automated dideoxy-DNA sequencing system which uses fluorescent dye primers, we compiled DNA sequences at compression sites from accumulated sequence data of human cDNAs (about 205 kb in total length). The results clearly showed that almost all the 3'-end regions at the compression sites (> 98%) carried two types of common sequence motifs. The predominant one (about 68%) contained a sequence of 5'-Y'GN1-2AR'-3' (Y' and R': pyrimidine and purine residues capable of base pairing). The remainder (about 32%) carried a hairpin motif with a relatively stable GC-rich stem (> or = 3 bp) connected by a loop consisting of 3 or 4 nucleotides. The occurrence of compressions at these motif sites was further confirmed by using synthetic DNAs with random sequences (about 58 kb in total length). Since DNA sequences at compression sites analyzed so far shared either of the type of motifs in the sequencing system employed here, it was possible to predict the nucleotide residue to be located at a compression site by carefully checking the sequence preceding the site.
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Arisaka O, Hoshi M, Kanazawa S, Nakajima D, Numata M, Nishikura K, Oyama M, Nitta A, Kuribayashi T, Kano K, Nakayama Y, Yamashiro Y. Systemic effects of transdermal testosterone for the treatment of microphallus in children. Pediatr Int 2001; 43:134-6. [PMID: 11285063 DOI: 10.1046/j.1442-200x.2001.01353.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVES To elucidate the metabolic effects of topical testosterone for the treatment of microphallus in children. METHODS We administered 5% testosterone ointment to 50 prepubertal boys for the treatment of microphallus, allowing us to observe its metabolic effect on plasma concentrations of testosterone as a marker of transdermally absorbed testosterone, insulin-like growth factor (IGF)-I as a marker of growth hormone secretion status, and osteocalcin as a marker of bone metabolic turnover. RESULTS Transdermal application of testosterone for 30 days at a dose that affects penile growth increased mean (+/-SD) plasma testosterone concentrations from 7.5+/-5.1 to 31.0+/-8.2 ng/dL (pre- vs. post-treatment, respectively; P<0.01). This was associated with a slight but statistically significant elevation of IGF-I concentrations (117.2+/-76.9 vs. 154.4+/-81.5 ng/mL; P<0.05). No significant change in osteocalcin levels was found. CONCLUSIONS When using testosterone ointment as a treatment for microphallus, it should be borne in mind that this application has systemic effects.
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Allinson M, Kadokami K, Shiraishi F, Nakajima D, Zhang J, Knight A, Gray SR, Scales PJ, Allinson G. Wastewater recycling in Antarctica: Performance assessment of an advanced water treatment plant in removing trace organic chemicals. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 224:122-129. [PMID: 30036806 DOI: 10.1016/j.jenvman.2018.07.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/01/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
The Australian Antarctic Division (AAD) operates Australia's Davis Station in the Antarctic. In 2005, Davis Station's wastewater treatment plant failed and since then untreated, macerated effluent has been discharged to the ocean. The objectives of this study were to determine whether an advanced water treatment plant (AWTP) commissioned by the AAD and featuring a multi-barrier process involving ozonation, ceramic microfiltration, biologically activated carbon filtration, reverse osmosis, ultraviolet disinfection and chlorination was capable of producing potable water and a non-toxic brine concentrate that can be discharged with minimal environmental impact. The AWTP was tested using water from a municipal wastewater treatment plant in Tasmania, Australia. We used spot water and passive sampling combined with two multi-residue chromatographic-mass spectrometric methods and a range of recombinant receptor-reporter gene bioassays to screen trace organic chemicals (TrOCs), toxicity and receptor activity in the Feed water, in the environmental discharge (reject water), and product water from the AWTP for six months during 2014-15, and then again for three months in 2016. Across the two surveys we unambiguously detected 109 different TrOCs in the feed water, 39 chemicals in the reject water, and 34 chemicals in the product water. Sample toxicity and receptor activity in the feed water samples was almost totally removed in both testing periods, confirming that the vast majority of the receptor active TrOCs were removed by the treatment process. All the NDMA entering the AWTP in the feed and/or produced in the plant (typically < 50 ng/L), was retained into the reject water with no NDMA observed in the product water. In conclusion, the AWTP was working to design, and releases of TrOCs at the concentrations observed in this study would be unlikely cause adverse effects on populations of aquatic organisms in the receiving environment or users of the potable product water.
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Kim CS, Nakajima D, Yang CY, Oh TW, Igawa S, Miyazaki M, Fukuoka H, Ohta F. Prolonged swimming exercise training induce hypophosphatemic osteopenia in stroke-prone spontaneously hypertensive rats (SHRSP). JOURNAL OF PHYSIOLOGICAL ANTHROPOLOGY AND APPLIED HUMAN SCIENCE 2000; 19:271-7. [PMID: 11204874 DOI: 10.2114/jpa.19.271] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Stroke-prone spontaneously hypertensive rats (SHRSP) induce spontaneous osteoporosis. To elucidate the specific characteristics of bone metabolism, the SHRSP was compared with age matched Wistar-Kyoto (WKY) rats. We investigated the effects of prolonged swimming exercise training on bone mineral density (BMD) and metabolism in the SHRSP. Seven-week-old male SHRSP and WKY were divided into three groups; the sedentary control WKY group (n = 6, WKY), the sedentary control SHRSP group (n = 6, SP) and the swimming exercise training SHRSP group (n = 6, SWIM) (in pool with 60 min./day, 5 days/week for 12 weeks). The femoral BMD, bone mineral content (BMC), strength, Ca and P contents (%) of SHRSP were approximately 17, 27, 25, 20 and 9%, respectively, lower than that of WKY (p < 0.001). Serum alkaline phosphatase (AlP) had not changed between both of SP and WKY, but tartrate-resistant acid phosphatase (TrAcP) of SP approximately 3-fold higher than that of WKY (p < 0.05). Both serum calcium (Ca) and intact parathyroid hormone (i-PTH) were similar between SP and WKY. However, serum phosphate (P) of SP was approximately 18% lower than that of WKY (N.S.). These results suggested that SHRSP induces osteopenia by the bone turnover of the promoted osteoclast activity with disturbed phosphate homeostasis. On the other hand, the femoral BMD and strength were approximately 7% and 20%, respectively, decreased in the SWIM (p < 0.001), and femoral bone Ca and P contents (%) were also approximately 11% and 14%, respectively, lower than that of SP (p < 0.001). There were no significant difference between SWIM and SP on serum Ca, but serum P of SWIM was significantly lower than that of SP (p < 0.05). These results suggested that the prolonged swimming exercise training in the SHRSP induces more cruelly hypophosphatemia, and leading to osteopenia eventually. We conclude that SHRSP induces osteopenia with disturbance of phosphate homeostasis, and the prolonged swimming exercise in the SHRSP might deteriorate hypophosphatemia and osteopenia.
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Nakajima D, Nagame S, Kuramochi H, Sugita K, Kageyama S, Shiozaki T, Takemura T, Shiraishi F, Goto S. Polycyclic aromatic hydrocarbon generation behavior in the process of carbonization of wood. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2007; 79:221-5. [PMID: 17639321 DOI: 10.1007/s00128-007-9177-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 06/01/2007] [Indexed: 05/16/2023]
Abstract
PAH generation behaviors in carbonization were compared, using cypress, chestnut, and bamboo as samples. Generation of tarry matter was almost completed by the time the temperature reached 400 degrees C, while generation of PAHs continued until the temperature reached 1,000 degrees C. The weight of tarry matter per unit sample weight was large with bamboo, while the amount of PAHs was large with cypress. Of the 15 types of PAHs measured this time, the largest amount collected was fluorene, followed by phenanthrene and anthracene. The amount of PAHs generated accounted for 6 x 10(-6) to 16 x 10(-6) of the weight of the wood samples.
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Nakajima D, Kamakura S, Nakamura M, Suzuki O, Echigo S, Sasano Y. Analysis of appositional bone formation using a novel rat experimental model. Oral Dis 2008; 14:308-13. [PMID: 18410575 DOI: 10.1111/j.1601-0825.2007.01377.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIM To analyze the process of appositional bone formation using our original rat experimental model. MATERIALS AND METHODS Rats were anesthetized and a ring made of polytetrafluorethylene was placed on the parietal bone surface in the surgical procedure. The time course of appositional bone formation was analyzed with histomorphometry and in situ hybridization for type I collagen and bone sialoprotein. RESULTS The rat experimental model allowed new bone to be formed on the pre-existing bone surface and persist for 12 weeks. We demonstrated that bone is apposed actively for the first 4 weeks and less actively thereafter. CONCLUSIONS The experimental model may contribute to biological analysis for appositional bone formation expected to occur in clinical procedures such as alveolar bone augmentation and sinus lifting.
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Research Support, Non-U.S. Gov't |
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Wang Q, Nakamura S, Gong S, Suzuki M, Nakajima D, Takai Y, Lu S, Sekiguchi K, Miwa M. Release behaviour of cryptomeria japonica pollen allergenic cry J 1 and cry J 2 in rainwater containing air pollutants. ACTA ACUST UNITED AC 2014. [DOI: 10.2495/sdp-v9-n1-42-53] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Yamada T, Nakajima D, Sakamoto J, Chen F, Okamoto T, Ohsumi A, Fujinaga T, Shoji T, Sakai H, Bando T, Date H. 422 Reconditioning of Lungs with Pulmonary Edema in Ex Vivo Lung Perfusion Circuit. J Heart Lung Transplant 2011. [DOI: 10.1016/j.healun.2011.01.431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Linacre V, Cypel M, Machuca T, Nakajima D, Hashimoto K, Zamel R, Chun Y, Waddell T, Liu M, Keshavjee S. Extravascular Lung Water Measurement During Ex Vivo Lung Perfusion. J Heart Lung Transplant 2014. [DOI: 10.1016/j.healun.2014.01.452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Kalaf-Mussi R, Lee J, Nakajima D, Chen M, Maahs L, Coutinho R, Liu M, Keshavjee S, Cypel M. Ex-Vivo Therapeutic Use of Carbon Monoxide (CO) to Improve Donor Lungs for Transplantation. J Heart Lung Transplant 2015. [DOI: 10.1016/j.healun.2015.01.246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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