Sasaki T

References (25)

Title : Associations of cardiovascular biomarkers and plasma albumin with exceptional survival to the highest ages - Hirata_2020_Nat.Commun_11_3820
Author(s) : Hirata T , Arai Y , Yuasa S , Abe Y , Takayama M , Sasaki T , Kunitomi A , Inagaki H , Endo M , Morinaga J , Yoshimura K , Adachi T , Oike Y , Takebayashi T , Okano H , Hirose N
Ref : Nat Commun , 11 :3820 , 2020
Abstract : Supercentenarians (those aged >=110 years) are approaching the current human longevity limit by preventing or surviving major illness. Identifying specific biomarkers conducive to exceptional survival might provide insights into counter-regulatory mechanisms against aging-related disease. Here, we report associations between cardiovascular disease-related biomarkers and survival to the highest ages using a unique dataset of 1,427 oldest individuals from three longitudinal cohort studies, including 36 supercentenarians, 572 semi-supercentenarians (105-109 years), 288 centenarians (100-104 years), and 531 very old people (85-99 years). During follow-up, 1,000 participants (70.1%) died. Overall, N-terminal pro-B-type natriuretic peptide (NT-proBNP), interleukin-6, cystatin C and cholinesterase are associated with all-cause mortality independent of traditional cardiovascular risk factors and plasma albumin. Of these, low NT-proBNP levels are statistically associated with a survival advantage to supercentenarian age. Only low albumin is associated with high mortality across age groups. These findings expand our knowledge on the biology of human longevity.
ESTHER : Hirata_2020_Nat.Commun_11_3820
PubMedSearch : Hirata_2020_Nat.Commun_11_3820
PubMedID: 32732919

Title : Identification of factors contributing to phenotypic divergence via quantitative image analyses of autosomal recessive woolly hair\/hypotrichosis with homozygous c.736T>A LIPH mutation - Kinoshita-Ise_2017_Br.J.Dermatol_176_138
Author(s) : Kinoshita-Ise M , Kubo A , Sasaki T , Umegaki-Arao N , Amagai M , Ohyama M
Ref : Br J Dermatol , 176 :138 , 2017
Abstract : BACKGROUND: Autosomal recessive woolly hair/hypotrichosis (ARWH/H) is caused by mutations in LIPH. Homozygotes for the LIPH c.736T>A (p.C246S) mutation, the most prevalent genotype in Japanese patients, present varying degrees of hair loss; however, determinants of this phenotypic diversity remain elusive. OBJECTIVES: To establish methodologies for quantitative assessment of clinical severity and provide a detailed characterization to elucidate the factors contributing to phenotypic divergence. METHODS: Digital image analyses were conducted to convert clinical severities into numerical values. Eight patients with ARWH/H were classified into three groups (mild, severe, very severe), based on severity scores. Dermoscopic images were collected and assessed for total hair numbers and hair thickness for intergroup comparisons. RESULTS: The image analysis detected a difference in hair thickness but not in total hair numbers, between mild and severe cases. A marked decrease in total hair number was noted in an atypical very severe case. Histopathologically, a patient with a mild case demonstrated hair miniaturization and a high telogen/anagen ratio without a decrease in total hair count, endorsing dermoscopic observations. Two children demonstrated spontaneous improvement without an increase in total hair numbers, and two adults responded well to topical minoxidil with increased total hair numbers and hair thickness. CONCLUSIONS: The difference in the frequency of underdeveloped hairs may be a major factor contributing to the clinical diversity of hair sparseness in LIPH c.736T>A homozygotes with ARWH/H. Hence, pharmacological modification to thicken existing fine hairs may provide a therapeutic strategy.
ESTHER : Kinoshita-Ise_2017_Br.J.Dermatol_176_138
PubMedSearch : Kinoshita-Ise_2017_Br.J.Dermatol_176_138
PubMedID: 27375176
Gene_locus related to this paper: human-LIPH

Title : Total cholesterol level for assessing pancreatic insufficiency due to chronic pancreatitis - Hirano_2014_Gut.Liver_8_563
Author(s) : Hirano K , Saito T , Mizuno S , Tada M , Sasahira N , Isayama H , Matsukawa M , Umefune G , Akiyama D , Saito K , Kawahata S , Takahara N , Uchino R , Hamada T , Miyabayashi K , Mohri D , Sasaki T , Kogure H , Yamamoto N , Nakai Y , Koike K
Ref : Gut Liver , 8 :563 , 2014
Abstract : BACKGROUND/AIMS: To determine the nutritional markers important for assessing the degree of pancreatic insufficiency due to chronic pancreatitis in routine clinical practice.
METHODS: A total of 137 patients with chronic pancreatitis were followed up for more than 1 year. They were divided into two groups: a pancreatic diabetes mellitus (DM) group, consisting of 47 patients undergoing medical treatment for DM of pancreatic origin, and a nonpancreatic DM group, consisting of 90 other patients (including 86 patients without DM). Serum albumin, prealbumin, total cholesterol, cholinesterase, magnesium, and hemoglobin were compared between the two groups.
RESULTS: The total cholesterol was significantly lower in the pancreatic than the nonpancreatic DM group (164 mg/dL vs 183 mg/dL, respectively; p=0.0028). Cholinesterase was significantly lower in the former group (263 U/L vs 291 U/L, respectively; p=0.016). Among the 37 patients with nonalcoholic pancreatitis, there was no difference in the cholinesterase levels between the pancreatic and nonpancreatic (296 U/L vs 304 U/L, respectively; p=0.752) DM groups, although cholesterol levels remained lower in the former (165 mg/dL vs 187 mg/dL, respectively; p=0.052).
CONCLUSIONS: Cholinesterase levels are possibly affected by concomitant alcoholic liver injury. The total cholesterol level should be considered when assessing pancreatic insufficiency due to chronic pancreatitis.
ESTHER : Hirano_2014_Gut.Liver_8_563
PubMedSearch : Hirano_2014_Gut.Liver_8_563
PubMedID: 25228979

Title : Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics - Sakai_2013_Plant.Cell.Physiol_54_e6
Author(s) : Sakai H , Lee SS , Tanaka T , Numa H , Kim J , Kawahara Y , Wakimoto H , Yang CC , Iwamoto M , Abe T , Yamada Y , Muto A , Inokuchi H , Ikemura T , Matsumoto T , Sasaki T , Itoh T
Ref : Plant Cell Physiol , 54 :e6 , 2013
Abstract : The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.
ESTHER : Sakai_2013_Plant.Cell.Physiol_54_e6
PubMedSearch : Sakai_2013_Plant.Cell.Physiol_54_e6
PubMedID: 23299411
Gene_locus related to this paper: orysa-Q0JK71 , orysj-q6yse8 , orysa-q6yzk1 , orysj-q2r2z8

Title : The genome of a lepidopteran model insect, the silkworm Bombyx mori - Xia_2008_Insect.Biochem.Mol.Biol_38_1036
Author(s) : Xia Q , Wang J , Zhou Z , Li R , Fan W , Cheng D , Cheng T , Qin J , Duana J , Xu H , Li Q , Li N , Wang M , Dai F , Liu C , Lin Y , Zhao P , Zhang H , Liu S , Zha X , Li C , Zhao A , Pan M , Pan G , Shen Y , Gao Z , Wang Z , Wang G , Wu Z , Hou Y , Chai C , Yu Q , He N , Zhang Z , Li S , Yang H , Lu C , Xiang Z , Mita K , Kasahara M , Nakatani Y , Yamamoto K , Abe H , Ahsan B , Daimoni T , Doi K , Fujii T , Fujiwara H , Fujiyama A , Futahashi R , Hashimotol S , Ishibashi J , Iwami M , Kadono-Okuda K , Kanamori H , Kataoka H , Katsuma S , Kawaoka S , Kawasaki H , Kohara Y , Kozaki T , Kuroshu RM , Kuwazaki S , Matsushima K , Minami H , Nagayasu Y , Nakagawa T , Narukawa J , Nohata J , Ohishi K , Ono Y , Osanai-Futahashi M , Ozaki K , Qu W , Roller L , Sasaki S , Sasaki T , Seino A , Shimomura M , Shin-I T , Shinoda T , Shiotsuki T , Suetsugu Y , Sugano S , Suwa M , Suzuki Y , Takiya S , Tamura T , Tanaka H , Tanaka Y , Touhara K , Yamada T , Yamakawa M , Yamanaka N , Yoshikawa H , Zhong YS , Shimada T , Morishita S
Ref : Insect Biochemistry & Molecular Biology , 38 :1036 , 2008
Abstract : Bombyx mori, the domesticated silkworm, is a major insect model for research, and the first lepidopteran for which draft genome sequences became available in 2004. Two independent data sets from whole-genome shotgun sequencing were merged and assembled together with newly obtained fosmid- and BAC-end sequences. The remarkably improved new assembly is presented here. The 8.5-fold sequence coverage of an estimated 432 Mb genome was assembled into scaffolds with an N50 size of approximately 3.7 Mb; the largest scaffold was 14.5 million base pairs. With help of a high-density SNP linkage map, we anchored 87% of the scaffold sequences to all 28 chromosomes. A particular feature was the high repetitive sequence content estimated to be 43.6% and that consisted mainly of transposable elements. We predicted 14,623 gene models based on a GLEAN-based algorithm, a more accurate prediction than the previous gene models for this species. Over three thousand silkworm genes have no homologs in other insect or vertebrate genomes. Some insights into gene evolution and into characteristic biological processes are presented here and in other papers in this issue. The massive silk production correlates with the existence of specific tRNA clusters, and of several sericin genes assembled in a cluster. The silkworm's adaptation to feeding on mulberry leaves, which contain toxic alkaloids, is likely linked to the presence of new-type sucrase genes, apparently acquired from bacteria. The silkworm genome also revealed the cascade of genes involved in the juvenile hormone biosynthesis pathway, and a large number of cuticular protein genes.
ESTHER : Xia_2008_Insect.Biochem.Mol.Biol_38_1036
PubMedSearch : Xia_2008_Insect.Biochem.Mol.Biol_38_1036
PubMedID: 19121390
Gene_locus related to this paper: bommo-a0mnw6 , bommo-a1yw85 , bommo-a9ls22 , bommo-ACHE1 , bommo-ACHE2 , bommo-b0fgv8 , bommo-b1q137 , bommo-b1q139 , bommo-b1q140 , bommo-b1q141 , bommo-b2zdz0 , bommo-b3gef6 , bommo-b3gef7 , bommo-b3gs55 , bommo-b3gs56 , bommo-d2ktu3 , bommo-d2ktu5 , bommo-d9ile0 , bommo-e1cga5 , bommo-e1cga6 , bommo-g8fpz6 , bommo-h9iu43 , bommo-h9iu46 , bommo-h9iu47.1 , bommo-h9iu47.2 , bommo-h9iue5 , bommo-h9ivg2 , bommo-h9iwj7 , bommo-h9iwj8 , bommo-h9ix58 , bommo-h9ixi1.1 , bommo-h9ixi1.2 , bommo-h9iy47 , bommo-h9izw1 , bommo-h9j0s4 , bommo-h9j1y0 , bommo-h9j3r0 , bommo-h9j3w6 , bommo-h9j3w7 , bommo-h9j5t0 , bommo-h9j8g3 , bommo-h9j9k9 , bommo-h9j066 , bommo-h9j067 , bommo-h9j593 , bommo-h9j594 , bommo-h9j990 , bommo-h9jde8 , bommo-h9jde9 , bommo-h9jdf0 , bommo-h9jds4 , bommo-h9jle7 , bommo-h9jn83 , bommo-h9jn85 , bommo-h9jrg2 , bommo-h9jyh9 , bommo-JHE , bommo-m1rmh6 , bommo-q1hq05 , bommo-q4tte1 , bommo-h9j592 , bommo-h9j604 , bommo-h9jpm8 , bommo-h9iss4 , bommo-h9j2c7

Title : The Rice Annotation Project Database (RAP-DB): 2008 update - Tanaka_2008_Nucleic.Acids.Res_36_D1028
Author(s) : Tanaka T , Antonio BA , Kikuchi S , Matsumoto T , Nagamura Y , Numa H , Sakai H , Wu J , Itoh T , Sasaki T , Aono R , Fujii Y , Habara T , Harada E , Kanno M , Kawahara Y , Kawashima H , Kubooka H , Matsuya A , Nakaoka H , Saichi N , Sanbonmatsu R , Sato Y , Shinso Y , Suzuki M , Takeda J , Tanino M , Todokoro F , Yamaguchi K , Yamamoto N , Yamasaki C , Imanishi T , Okido T , Tada M , Ikeo K , Tateno Y , Gojobori T , Lin YC , Wei FJ , Hsing YI , Zhao Q , Han B , Kramer MR , McCombie RW , Lonsdale D , O'Donovan CC , Whitfield EJ , Apweiler R , Koyanagi KO , Khurana JP , Raghuvanshi S , Singh NK , Tyagi AK , Haberer G , Fujisawa M , Hosokawa S , Ito Y , Ikawa H , Shibata M , Yamamoto M , Bruskiewich RM , Hoen DR , Bureau TE , Namiki N , Ohyanagi H , Sakai Y , Nobushima S , Sakata K , Barrero RA , Souvorov A , Smith-White B , Tatusova T , An S , An G , S OO , Fuks G , Messing J , Christie KR , Lieberherr D , Kim H , Zuccolo A , Wing RA , Nobuta K , Green PJ , Lu C , Meyers BC , Chaparro C , Piegu B , Panaud O , Echeverria M
Ref : Nucleic Acids Research , 36 :D1028 , 2008
Abstract : The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.
ESTHER : Tanaka_2008_Nucleic.Acids.Res_36_D1028
PubMedSearch : Tanaka_2008_Nucleic.Acids.Res_36_D1028
PubMedID: 18089549
Gene_locus related to this paper: orysa-Q9FW17 , orysa-Q0JK71 , orysa-B9EWJ8 , orysa-Q5N7L1 , orysa-pir7a , orysa-q2qyj1 , orysj-q6yse8 , orysa-q6yzk1 , orysa-Q8S0U8 , orysa-q33aq0 , orysa-Q0J0A4 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-b9fi05 , orysj-b9fkb0 , orysj-cgep , orysj-q0djj0 , orysj-q0dud7 , orysj-q0jaf0 , orysj-q0jga1 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q7xcx3 , orysj-q9fwm6 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6 , orysj-q94d71 , orysj-q0iq98 , orysj-b9gbs4 , orysj-b9gbs1 , orysj-pla4 , orysj-pla1

Title : Human brain structural change related to acute single exposure to sarin - Yamasue_2007_Ann.Neurol_61_37
Author(s) : Yamasue H , Abe O , Kasai K , Suga M , Iwanami A , Yamada H , Tochigi M , Ohtani T , Rogers MA , Sasaki T , Aoki S , Kato T , Kato N
Ref : Annals of Neurology , 61 :37 , 2007
Abstract : OBJECTIVE: This study aimed to identify persistent morphological changes subsequent to an acute single-time exposure to sarin, a highly poisonous organophosphate, and the neurobiological basis of long-lasting somatic and cognitive symptoms in victims exposed to sarin. METHODS: Thirty-eight victims of the 1995 Tokyo subway sarin attack, all of whom had been treated in an emergency department for sarin intoxication, and 76 matched healthy control subjects underwent T1-weighted and diffusion tensor magnetic resonance imaging (DTI) in 2000 to 2001. Serum cholinesterase (ChE) levels measured immediately and longitudinally after the exposure and the current severity of chronic reports in the victims were also evaluated. RESULTS: The voxel-based morphometry exhibited smaller than normal regional brain volumes in the insular cortex and neighboring white matter, as well as in the hippocampus in the victims. The reduced regional white matter volume correlated with decreased serum cholinesterase levels and with the severity of chronic somatic complaints related to interoceptive awareness. Voxel-based analysis of diffusion tensor magnetic resonance imaging further demonstrated an extensively lower than normal fractional anisotropy in the victims. All these findings were statistically significant (corrected p < 0.05). INTERPRETATION: Sarin intoxication might be associated with structural changes in specific regions of the human brain, including those surrounding the insular cortex, which might be related to elevated subjective awareness of internal bodily status in exposed individuals.
ESTHER : Yamasue_2007_Ann.Neurol_61_37
PubMedSearch : Yamasue_2007_Ann.Neurol_61_37
PubMedID: 17187377

Title : Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana - Itoh_2007_Genome.Res_17_175
Author(s) : Itoh T , Tanaka T , Barrero RA , Yamasaki C , Fujii Y , Hilton PB , Antonio BA , Aono H , Apweiler R , Bruskiewich R , Bureau T , Burr F , Costa de Oliveira A , Fuks G , Habara T , Haberer G , Han B , Harada E , Hiraki AT , Hirochika H , Hoen D , Hokari H , Hosokawa S , Hsing YI , Ikawa H , Ikeo K , Imanishi T , Ito Y , Jaiswal P , Kanno M , Kawahara Y , Kawamura T , Kawashima H , Khurana JP , Kikuchi S , Komatsu S , Koyanagi KO , Kubooka H , Lieberherr D , Lin YC , Lonsdale D , Matsumoto T , Matsuya A , McCombie WR , Messing J , Miyao A , Mulder N , Nagamura Y , Nam J , Namiki N , Numa H , Nurimoto S , O'Donovan C , Ohyanagi H , Okido T , Oota S , Osato N , Palmer LE , Quetier F , Raghuvanshi S , Saichi N , Sakai H , Sakai Y , Sakata K , Sakurai T , Sato F , Sato Y , Schoof H , Seki M , Shibata M , Shimizu Y , Shinozaki K , Shinso Y , Singh NK , Smith-White B , Takeda J , Tanino M , Tatusova T , Thongjuea S , Todokoro F , Tsugane M , Tyagi AK , Vanavichit A , Wang A , Wing RA , Yamaguchi K , Yamamoto M , Yamamoto N , Yu Y , Zhang H , Zhao Q , Higo K , Burr B , Gojobori T , Sasaki T
Ref : Genome Res , 17 :175 , 2007
Abstract : We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.
ESTHER : Itoh_2007_Genome.Res_17_175
PubMedSearch : Itoh_2007_Genome.Res_17_175
PubMedID: 17210932
Gene_locus related to this paper: orysa-Q7XTC5 , orysa-Q852M6 , orysa-Q8GSE8 , orysa-Q9FYP7 , orysa-Q5ZA26 , orysa-Q5JLP6 , orysa-Q8H5P5 , orysa-Q7F1Y5 , orysa-cbp3 , orysa-cbpx , orysa-Q6YSZ8 , orysa-Q9FW17 , orysa-Q84QZ6 , orysa-Q0JK71 , orysa-B9EWJ8 , orysa-Q6ZDG6 , orysa-Q6ZDG5 , orysa-Q658B2 , orysa-Q5N7L1 , orysa-Q8RYV9 , orysa-Q8H3R3 , orysa-Q5SNH3 , orysa-pir7a , orysa-q2qnj4 , orysa-q2qyj1 , orysa-q2r077 , orysa-Q4VWY7 , orysa-q5smv5 , orysa-q5z901 , orysa-Q5ZBI5 , orysa-q6atz0 , orysa-q6i5q3 , orysa-q6j657 , orysa-q6k4q2 , orysj-q6yse8 , orysa-q6yy42 , orysa-q6yzk1 , orysa-q6z8b1 , orysa-q6z995 , orysa-q6zjq6 , orysa-q7x7y5 , orysa-Q7XC50 , orysa-q7xr62 , orysa-q7xr63 , orysa-q7xsg1 , orysa-q7xsq2 , orysa-q7xts6 , orysa-q7xv53 , orysa-Q8LQS5 , orysa-Q8RZ79 , orysa-Q8S0U8 , orysa-Q8W3C6 , orysa-Q9LHX5 , orysa-q53m20 , orysa-q53nd8 , orysa-q60e79 , orysa-q67iz2 , orysa-q67iz3 , orysa-q67iz7 , orysa-q67iz8 , orysa-q67j02 , orysa-q67j05 , orysa-q67j09 , orysa-q67j10 , orysa-q67tr6 , orysa-q67tv0 , orysa-q69j38 , orysa-q69y21 , orysa-q75hy1 , orysa-q75hy2 , orysa-Q0J0A4 , orysa-q651a8 , orysa-q652g4 , orysa-q688m8 , orysa-Q6H8G1 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-b9fi05 , orysj-q0djj0 , orysj-q0jaf0 , orysj-q0jga1 , orysj-q0jhi5 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q7xcx3 , orysj-q9fwm6 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6 , orysj-q94d71 , orysj-q0iq98 , orysj-b9gbs4 , orysj-b9gbs1

Title : The medaka draft genome and insights into vertebrate genome evolution - Kasahara_2007_Nature_447_714
Author(s) : Kasahara M , Naruse K , Sasaki S , Nakatani Y , Qu W , Ahsan B , Yamada T , Nagayasu Y , Doi K , Kasai Y , Jindo T , Kobayashi D , Shimada A , Toyoda A , Kuroki Y , Fujiyama A , Sasaki T , Shimizu A , Asakawa S , Shimizu N , Hashimoto S , Yang J , Lee Y , Matsushima K , Sugano S , Sakaizumi M , Narita T , Ohishi K , Haga S , Ohta F , Nomoto H , Nogata K , Morishita T , Endo T , Shin IT , Takeda H , Morishita S , Kohara Y
Ref : Nature , 447 :714 , 2007
Abstract : Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.
ESTHER : Kasahara_2007_Nature_447_714
PubMedSearch : Kasahara_2007_Nature_447_714
PubMedID: 17554307
Gene_locus related to this paper: fugru-3cxest , fugru-4cxest , fugru-4neur , fugru-ACHE , fugru-ACHEE , fugru-balip , fugru-BCHE , fugru-BCHEB , fugru-cxest , oryla-ACHE , oryla-BCHE , oryla-d2x2i4 , oryla-h2m6h1 , oryla-h2m7w4 , oryla-h2m361 , oryla-h2mbn6 , oryla-h2mfw1 , oryla-h2mhi0 , oryla-h2mhl7 , oryla-h2mpb5 , oryla-h2mqz5 , oryla-h2mvs7 , oryla-h2mz49 , oryla-h2n1l9 , oryla-nlgn2 , takru-1neur , takru-2bneur , takru-3bneur , takru-h2rke7 , takru-h2rmg3 , takru-h2rsj9 , takru-h2rw77 , takru-h2ryq0 , takru-h2sci9 , takru-h2se90 , takru-h2spg7 , takru-h2sxi1 , takru-h2ts55 , takru-h2ts56 , takru-h2uxa9 , takru-h2vaf1 , takru-nlgn2a , takru-nlgn3a , takru-nlgn4a , oryla-h2mff8 , oryla-h2m2f0 , oryla-h2ler5 , takru-h2tsm6 , takru-h2tq49 , takru-h2tq47 , takru-h2s286 , takru-h2tng4 , takru-h2tq50 , takru-h2tng3 , takru-h2tng2 , oryla-h2lj38 , oryla-h2mxe6 , takru-h2tq48 , oryla-h2lf11 , takru-h2u5j0 , takru-h2rpm8 , oryla-h2n273 , oryla-h2n271 , oryla-h2lum7 , takru-h2tpz2 , takru-h2u3j1 , oryla-h2mdv3 , takru-h2tzm9 , takru-h2u8u6 , oryla-h2lcw8 , oryla-h2lc35 , oryla-h2ln66 , oryla-h2m8k0 , oryla-h2mdj7 , oryla-h2lw61 , oryla-h2lxe3 , oryla-h2l8y7 , oryla-h2mr84 , oryla-h2mr95 , oryla-h2mcz6 , oryla-h2lxr5 , oryla-h2ly57 , oryla-a0a3p9kz03 , oryla-a0a3p9hfu1 , oryla-h2m307 , oryla-h2lch5 , oryla-h2ldw9 , oryla-a0a3b3ic40 , oryla-h2ldi5 , oryla-h2mun1 , oryla-a0a3p9jla3

Title : DNA sequence and analysis of human chromosome 8 - Nusbaum_2006_Nature_439_331
Author(s) : Nusbaum C , Mikkelsen TS , Zody MC , Asakawa S , Taudien S , Garber M , Kodira CD , Schueler MG , Shimizu A , Whittaker CA , Chang JL , Cuomo CA , Dewar K , Fitzgerald MG , Yang X , Allen NR , Anderson S , Asakawa T , Blechschmidt K , Bloom T , Borowsky ML , Butler J , Cook A , Corum B , DeArellano K , Decaprio D , Dooley KT , Dorris L, 3rd , Engels R , Glockner G , Hafez N , Hagopian DS , Hall JL , Ishikawa SK , Jaffe DB , Kamat A , Kudoh J , Lehmann R , Lokitsang T , Macdonald P , Major JE , Matthews CD , Mauceli E , Menzel U , Mihalev AH , Minoshima S , Murayama Y , Naylor JW , Nicol R , Nguyen C , O'Leary SB , O'Neill K , Parker SC , Polley A , Raymond CK , Reichwald K , Rodriguez J , Sasaki T , Schilhabel M , Siddiqui R , Smith CL , Sneddon TP , Talamas JA , Tenzin P , Topham K , Venkataraman V , Wen G , Yamazaki S , Young SK , Zeng Q , Zimmer AR , Rosenthal A , Birren BW , Platzer M , Shimizu N , Lander ES
Ref : Nature , 439 :331 , 2006
Abstract : The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.
ESTHER : Nusbaum_2006_Nature_439_331
PubMedSearch : Nusbaum_2006_Nature_439_331
PubMedID: 16421571
Gene_locus related to this paper: human-TG

Title : The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information - Ohyanagi_2006_Nucleic.Acids.Res_34_D741
Author(s) : Ohyanagi H , Tanaka T , Sakai H , Shigemoto Y , Yamaguchi K , Habara T , Fujii Y , Antonio BA , Nagamura Y , Imanishi T , Ikeo K , Itoh T , Gojobori T , Sasaki T
Ref : Nucleic Acids Research , 34 :D741 , 2006
Abstract : With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through http://rapdb.lab.nig.ac.jp/.
ESTHER : Ohyanagi_2006_Nucleic.Acids.Res_34_D741
PubMedSearch : Ohyanagi_2006_Nucleic.Acids.Res_34_D741
PubMedID: 16381971
Gene_locus related to this paper: orysa-Q9FW17 , orysa-Q0JK71 , orysa-B9EWJ8 , orysa-Q5N7L1 , orysa-Q5N7J6 , orysa-pir7a , orysa-q2qyi1 , orysa-q2qyj1 , orysa-q2rbb3 , orysj-q6yse8 , orysa-q6yzk1 , orysa-Q8S0U8 , orysa-Q84ZY8 , orysa-Q0J0A4 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-b9fi05 , orysj-q0d4u5 , orysj-q0djj0 , orysj-q0jaf0 , orysj-q0jga1 , orysj-q0jhi5 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q7xcx3 , orysj-q9fwm6 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6 , orysj-q94d71 , orysj-q0iq98 , orysj-b9gbs4 , orysj-b9gbs1

Title : Support for relationship between serum cholinesterase and post-traumatic stress disorder\; 5-year follow-ups of victims of the Tokyo subway sarin poisoning -
Author(s) : Tochigi M , Otani T , Yamasue H , Kasai K , Kato T , Iwanami A , Kato N , Sasaki T
Ref : Neurosci Res , 52 :129 , 2005
PubMedID: 15876465

Title : The map-based sequence of the rice genome. -
Author(s) : Matsumo T , Sasaki T
Ref : Nature , 436 :793 , 2005
PubMedID: 16100779
Gene_locus related to this paper: orysa-Q9FRJ0 , orysa-Q7XTC5 , orysa-Q852M6 , orysa-Q8GSE8 , orysa-Q9FYP7 , orysa-Q5ZBH3 , orysa-Q5ZA26 , orysa-Q5JLP6 , orysa-Q8H5P5 , orysa-Q7F1Y5 , orysa-Q949C9 , orysa-cbp3 , orysa-cbpx , orysa-Q6YSZ8 , orysa-Q8S5X5 , orysa-Q8LIG3 , orysa-Q6K7F5 , orysa-Q69UB1 , orysa-Q9FW17 , orysa-Q337C3 , orysa-Q84QZ6 , orysa-Q84QY7 , orysa-Q851E7 , orysa-Q851E3 , orysa-Q0JK71 , orysa-Q8S1D9 , orysa-Q5N8V4 , orysa-Q8GTK2 , orysa-B9EWJ8 , orysa-Q8H3K6 , orysa-Q6ZDG8 , orysa-Q6ZDG6 , orysa-Q6ZDG5 , orysa-Q658B2 , orysa-Q5N7L1 , orysa-Q8RYV9 , orysa-Q8H3R3 , orysa-Q5SNH3 , orysa-Q8W0F0 , orysa-pir7a , orysa-q2qnj4 , orysa-q2qnt9 , orysa-q2qx94 , orysa-q2qyj1 , orysa-q2r051 , orysa-q2r077 , orysa-Q4VWY7 , orysa-q5nbu1 , orysa-q5smv5 , orysa-q5vnp5 , orysa-q5vrt2 , orysa-q5w6c5 , orysa-q5z5a3 , orysa-q5z901 , orysa-Q5ZBI5 , orysa-q6atz0 , orysa-q6ave2 , orysa-q6h7i6 , orysa-q6i5q3 , orysa-q6j657 , orysa-q6k3d9 , orysa-q6k4q2 , orysa-q6l5b6 , orysj-q6yse8 , orysa-q6yy42 , orysa-q6yzk1 , orysa-q6z8b1 , orysa-q6z995 , orysa-q6zjq6 , orysa-q7x7y5 , orysa-Q7XC50 , orysa-q7xkj9 , orysa-q7xr62 , orysa-q7xr63 , orysa-q7xsg1 , orysa-q7xsq2 , orysa-q7xts6 , orysa-q7xv53 , orysa-Q8LQS5 , orysa-Q8RZ79 , orysa-Q8S0U8 , orysa-Q8W3C6 , orysa-Q9LHX5 , orysa-q33aq0 , orysa-q53lh1 , orysa-q53m20 , orysa-q53nd8 , orysa-q60e79 , orysa-q67iz2 , orysa-q67iz3 , orysa-q67iz7 , orysa-q67iz8 , orysa-q67j02 , orysa-q67j05 , orysa-q67j09 , orysa-q67j10 , orysa-q67tr6 , orysa-q67tv0 , orysa-q69j38 , orysa-q69k08 , orysa-q69md7 , orysa-q69me0 , orysa-q69pf3 , orysa-q69xr2 , orysa-q69y17 , orysa-q69y21 , orysa-q75hy1 , orysa-q75hy2 , orysa-q75i01 , orysa-Q94JD7 , orysa-Q0J0A4 , orysa-q651a8 , orysa-q652g4 , orysa-q688m0 , orysa-q688m8 , orysa-q688m9 , orysa-Q6H8G1 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-b9fi05 , orysj-b9fkb0 , orysj-cgep , orysj-q0djj0 , orysj-q0dud7 , orysj-q0jaf0 , orysj-q0jga1 , orysj-q0jhi5 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q7xcx3 , orysj-q9fwm6 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6 , orysj-q94d71 , orysj-q338c0 , orysj-b9gbs1 , orysj-a0a0p0y6l9 , orysj-pla4 , orysj-pla1 , orysj-q2r2z8

Title : A fine physical map of the rice chromosome 5 - Cheng_2005_Mol.Genet.Genomics_274_337
Author(s) : Cheng CH , Chung MC , Liu SM , Chen SK , Kao FY , Lin SJ , Hsiao SH , Tseng IC , Hsing YI , Wu HP , Chen CS , Shaw JF , Wu J , Matsumoto T , Sasaki T , Chen HH , Chow TY
Ref : Mol Genet Genomics , 274 :337 , 2005
Abstract : A fine physical map of the rice (Oryza sativa spp. Japonica var. Nipponbare) chromosome 5 with bacterial artificial chromosome (BAC) and PI-derived artificial chromosome (PAC) clones was constructed through integration of 280 sequenced BAC/PAC clones and 232 sequence tagged site/expressed sequence tag markers with the use of fingerprinted contig data of the Nipponbare genome. This map consists of five contigs covering 99% of the estimated chromosome size (30.08 Mb). The four physical gaps were estimated at 30 and 20 kb for gaps 1-3 and gap 4, respectively. We have submitted 42.2-Mb sequences with 29.8 Mb of nonoverlapping sequences to public databases. BAC clones corresponding to telomere and centromere regions were confirmed by BAC-fluorescence in situ hybridization (FISH) on a pachytene chromosome. The genetically centromeric region at 54.6 cM was covered by a minimum tiling path spanning 2.1 Mb with no physical gaps. The precise position of the centromere was revealed by using three overlapping BAC/PACs for approximately 150 kb. In addition, FISH results revealed uneven chromatin condensation around the centromeric region at the pachytene stage. This map is of use for positional cloning and further characterization of the rice functional genomics.
ESTHER : Cheng_2005_Mol.Genet.Genomics_274_337
PubMedSearch : Cheng_2005_Mol.Genet.Genomics_274_337
PubMedID: 16261349
Gene_locus related to this paper: orysa-gid1 , orysa-q6f358 , orysj-PLA7

Title : Portal hypertensive gastropathy after surgery for biliary atresia - Sasaki_2005_Surg.Today_35_385
Author(s) : Sasaki T , Hasegawa T , Shimizu Y , Kimura T , Soh H , Fukuzawa M
Ref : Surg Today , 35 :385 , 2005
Abstract : PURPOSE: To clarify the correlation between portal hypertensive gastropathy (PHG) and clinical features after surgery for biliary atresia (BA).
METHODS: Routine upper gastrointestinal endoscopies were done over 3 years in 27 children who underwent surgery for BA. We reviewed the recorded endoscopic findings, and retrospectively diagnosed PHG according to McCormack's criteria. The differences in clinical features, such as endoscopically treated gastroesophageal varices and the results of routine laboratory tests, were compared between the children with PHG (PHG group) and those without PHG (non-PHG group).
RESULTS: Nine (33%) of the 27 children had PHG. Although there was no significant difference in age between the PHG and non-PHG groups, the frequency of past endoscopic variceal treatments was significantly higher in the PHG group (3.0 +/- 3.0 vs 0.6 +/- 1.5 times, P = 0.01). The PHG group also had lower white blood cell and platelet counts, at 3008 +/- 2411 vs 5527 +/- 2938/mm3 (P < 0.05) and 6.0 +/- 3.4 vs 13.9 +/- 4.7 x 10(4)/mm3 (P = 0.0001), respectively; higher serum aspartate aminotransferase, total bile acid, and total bilirubin levels at 80 +/- 31 vs 46 +/- 29 U/l (P < 0.05), 161 +/- 93 vs 64 +/- 88 U/l (P < 0.05), and 4.8 +/- 5.6 vs 1.0 +/- 0.8 mg/dl (P < 0.01), respectively; and lower prothrombin time, albumin, and cholinesterase levels, at 66 +/- 16 vs 79% +/- 14% (P < 0.05), 3.6 +/- 0.8 vs 4.1 +/- 0.5 g/dl (P < 0.05), and 2158 +/- 925 vs 3376 +/- 700 U/l (P < 0.001), respectively. CONCLUSION: Portal hypertensive gastropathy was found in 33% of children after surgery for BA. The factors contributing to the development of PHG were frequent endoscopic treatments of gastroesophageal varices, liver dysfunction, and hypersplenism.
ESTHER : Sasaki_2005_Surg.Today_35_385
PubMedSearch : Sasaki_2005_Surg.Today_35_385
PubMedID: 15864420

Title : Proposal of fibrosis index using image analyzer as a quantitative histological evaluation of liver fibrosis in biliary atresia - Tanano_2003_Pediatr.Surg.Int_19_52
Author(s) : Tanano H , Hasegawa T , Kimura T , Sasaki T , Kawahara H , Kubota A , Okada A
Ref : Pediatr Surg Int , 19 :52 , 2003
Abstract : This study was designed to elucidate whether the fibrosis index (FI), which was measured as a ratio of histological fibrotic tissue area to the whole area using an image analyzer, could reflect liver function and long-term prognosis in biliary atresia (BA). Liver biopsies were performed in 46 BA patients at hepatic portoenterostomy (HPE) and stoma closure. The chronological difference rate of FI (FIDR) was the monthly FI difference between HPE and stoma closure. FI at HPE and stoma closure was significantly higher than in the control. FI at HPE and at stoma closure significantly correlated with gammaGTP or T.Bil, D.Bil, cholinesterase and total bile acid, respectively. FIDR in jaundice-free group was significantly lower than in jaundiced group at 5 years after HPE. FIDR in V-2 (varices with red-color sign) was significantly higher than in V-0 (no varices) or V-1 (varices without red-color sign). ICG-K value significantly correlated with FIDR. FI at stoma closure or FIDR was significantly lower in living patients than in patients who eventually died or underwent liver transplantation. In conclusion, FI can reflect the degree of cholestasis in BA. FIDR would be useful for predicting long-term outcome in BA.
ESTHER : Tanano_2003_Pediatr.Surg.Int_19_52
PubMedSearch : Tanano_2003_Pediatr.Surg.Int_19_52
PubMedID: 12721724

Title : Indication for redo hepatic portoenterostomy for insufficient bile drainage in biliary atresia: re-evaluation in the era of liver transplantation - Hasegawa_2003_Pediatr.Surg.Int_19_256
Author(s) : Hasegawa T , Kimura T , Sasaki T , Okada A , Mushiake S
Ref : Pediatr Surg Int , 19 :256 , 2003
Abstract : To determine the role of redo hepatic portoenterostomy (HPE) in biliary atresia (BA) patients with insufficient bile excretion after the initial HPE, 25 patients (type I, correctable: 2; type III, uncorrectable: 23) undergoing the initial HPE at 25 to 119 days of age were studied. Four patients achieved disappearance of jaundice (total bilirubin [T.Bil] < 2 mg/dl) postoperatively. A redo HPE was performed at 2 to 8 months of age with sufficient and extensive removal of granulation and scar tissue at the hepatic hilum. Five patients became free of jaundice in 3 to 6 months (group 1), while the remaining 20 did not (group 2). Disappearance of jaundice after the initial HPE had been achieved in 2 of 5 patients (40%) in group 1 and 2 of 20 (10%) in group 2 ( P < 0.05). Age, serum T.Bil, aspartate aminotransferase albumin, prothrombin time, cholinesterase, total cholesterol, and Fischer's ratio at redo HPE showed no significant differences between the two groups. On liver histology obtained at redo HPE, cirrhosis and hepatocyte degeneration were seen in 1 of 5 cases (20%) in group 1 and 12 of 20 (60%) in group 2 ( P < 0.05). Redo HPE may thus be effective in BA patients with insufficient bile drainage who achieved disappearance of jaundice after the initial HPE and have not developed cirrhosis.
ESTHER : Hasegawa_2003_Pediatr.Surg.Int_19_256
PubMedSearch : Hasegawa_2003_Pediatr.Surg.Int_19_256
PubMedID: 12682751

Title : Serum cholesterol, uric acid and cholinesterase in victims of the Tokyo subway sarin poisoning: a relation with post-traumatic stress disorder - Tochigi_2002_Neurosci.Res_44_267
Author(s) : Tochigi M , Umekage T , Otani T , Kato T , Iwanami A , Asukai N , Sasaki T , Kato N
Ref : Neurosci Res , 44 :267 , 2002
Abstract : Cholesterol and uric acid, which might correlate with steroidogenesis and monoamine functions, may change under emotionally stressful conditions and in mental disturbances. Among anxiety disorders, an increase of serum cholesterol has been observed in panic disorder. However, the issue has not been adequately investigated in other anxiety disorders, including post-traumatic stress disorder (PTSD). The present study investigated serum cholesterols, uric acid and cholinesterase in victims of the Tokyo subway sarin poisoning, 1995, in a series of 5-year follow-ups. Cholinesterase was studied, in relevance with serum lipid changes and symptoms of PTSD, and also in light of a biological effect of sarin. Out of 34 victims, eight developed PTSD and two were currently diagnosed with PTSD using the Clinician-Administered PTSD Scale (CAPS). No significant relationship was observed between PTSD and serum cholesterols or uric acid. Several factors including co-occurrence of other mental disturbances with PTSD, in addition to the limited sample size, might have affected the result. In contrast, serum cholinesterase level was significantly reduced in the victims with the development of PTSD, compared with the matched controls (P<0.02, t-test). This might partly reflect a long-term remnant effect of sarin intoxication, although an effect of the psychological experience could not be totally excluded.
ESTHER : Tochigi_2002_Neurosci.Res_44_267
PubMedSearch : Tochigi_2002_Neurosci.Res_44_267
PubMedID: 12413655

Title : Role of plasma thrombopoietin level in thrombocytopenia of postoperative biliary atresia patients - Hasegawa_2002_J.Pediatr.Surg_37_1195
Author(s) : Hasegawa T , Sasaki T , Kimura T , Okada A
Ref : J Pediatr Surg , 37 :1195 , 2002
Abstract : BACKGROUND/PURPOSE: To evaluate if thrombocytopenia may be related to plasma thrombopoietin level (P-TPO) in postoperative biliary atresia (BA). METHODS: Forty-three postoperative BA patients aged 1 to 20 years were included. P-TPO was measured by enzyme immunoassay. P-TPO was compared with platelet counts (Plt), Child's classification, presence of splenomegaly, and liver function tests. RESULTS: P-TPO significantly correlated with Plt, child's classification, serum albumin, and cholinesterase level, respectively. In 4 patients undergoing portal decompression procedure, preoperative and postoperative Plt and P-TPO were 87.5 +/- 69.1 x 10(3) and 50.3 +/- 28.0, 118.8 +/- 62.3 x 10(3)/mm3, and 53.0 +/- 55.0 pg/mL, respectively, without significant difference. In 6 patients undergoing liver transplantation (LTx), Plt and P-TPO after LTx was 157.5 +/- 83.5 x 10(3) and 143.5 +/- 75.2, respectively, which were significantly higher than those before LTx (55.0 +/- 15.6 x 10(3)/mm3 and 53.2 +/- 32.9 pg/mL). CONCLUSION: Thrombocytopenia in postoperative BA may be caused by decreased plasma TPO level in accordance with the severity of liver dysfunction rather than hypersplenism.
ESTHER : Hasegawa_2002_J.Pediatr.Surg_37_1195
PubMedSearch : Hasegawa_2002_J.Pediatr.Surg_37_1195
PubMedID: 12149701

Title : The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans - Sasaki_2002_Nucleic.Acids.Res_30_5293
Author(s) : Sasaki Y , Ishikawa J , Yamashita A , Oshima K , Kenri T , Furuya K , Yoshino C , Horino A , Shiba T , Sasaki T , Hattori M
Ref : Nucleic Acids Research , 30 :5293 , 2002
Abstract : The complete genomic sequence of an intracellular bacterial pathogen, Mycoplasma penetrans HF-2 strain, was determined. The HF-2 genome consists of a 1 358 633 bp single circular chromosome containing 1038 predicted coding sequences (CDSs), one set of rRNA genes and 30 tRNA genes. Among the 1038 CDSs, 264 predicted proteins are common to the Mycoplasmataceae sequenced thus far and 463 are M.penetrans specific. The genome contains the two-component system but lacks the essential cellular gene, uridine kinase. The relatively large genome of M.penetrans HF-2 among mycoplasma species may be accounted for by both its rich core proteome and the presence of a number of paralog families corresponding to 25.4% of all CDSs. The largest paralog family is the p35 family, which encodes surface lipoproteins including the major antigen, P35. A total of 44 genes for p35 and p35 homologs were identified and 30 of them form one large cluster in the chromosome. The genetic tree of p35 paralogs suggests the occurrence of dynamic chromosomal rearrangement in paralog formation during evolution. Thus, M.penetrans HF-2 may have acquired diverse repertoires of antigenic variation-related genes to allow its persistent infection in humans.
ESTHER : Sasaki_2002_Nucleic.Acids.Res_30_5293
PubMedSearch : Sasaki_2002_Nucleic.Acids.Res_30_5293
PubMedID: 12466555
Gene_locus related to this paper: mycpe-MYPE3930 , mycpe-MYPE5460 , mycpe-MYPE8330 , mycpe-MYPE9300 , mycpe-q8eve6

Title : The genome sequence and structure of rice chromosome 1 - Sasaki_2002_Nature_420_312
Author(s) : Sasaki T , Matsumoto T , Yamamoto K , Sakata K , Baba T , Katayose Y , Wu J , Niimura Y , Cheng Z , Nagamura Y , Antonio BA , Kanamori H , Hosokawa S , Masukawa M , Arikawa K , Chiden Y , Hayashi M , Okamoto M , Ando T , Aoki H , Arita K , Hamada M , Harada C , Hijishita S , Honda M , Ichikawa Y , Idonuma A , Iijima M , Ikeda M , Ikeno M , Ito S , Ito T , Ito Y , Iwabuchi A , Kamiya K , Karasawa W , Katagiri S , Kikuta A , Kobayashi N , Kono I , Machita K , Maehara T , Mizuno H , Mizubayashi T , Mukai Y , Nagasaki H , Nakashima M , Nakama Y , Nakamichi Y , Nakamura M , Namiki N , Negishi M , Ohta I , Ono N , Saji S , Sakai K , Shibata M , Shimokawa T , Shomura A , Song J , Takazaki Y , Terasawa K , Tsuji K , Waki K , Yamagata H , Yamane H , Yoshiki S , Yoshihara R , Yukawa K , Zhong H , Iwama H , Endo T , Ito H , Hahn JH , Kim HI , Eun MY , Yano M , Jiang J , Gojobori T
Ref : Nature , 420 :312 , 2002
Abstract : The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence indicates the importance of a high-quality finished sequence.
ESTHER : Sasaki_2002_Nature_420_312
PubMedSearch : Sasaki_2002_Nature_420_312
PubMedID: 12447438
Gene_locus related to this paper: orysa-Q9S7P1 , orysa-Q9FYP7 , orysa-Q5ZBH3 , orysa-Q5NA74 , orysa-Q5ZA26 , orysa-Q5JLP6 , orysa-Q94D81 , orysa-cbp , orysa-Q5VQE5 , orysa-Q8RZ95 , orysa-Q9AWW1 , orysa-Q9AS70 , orysa-Q0JK71 , orysa-Q8S1D9 , orysa-Q5N8V4 , orysa-Q943F9 , orysa-B9EWJ8 , orysa-Q5N8H1 , orysa-Q5NAI4 , orysa-Q94DP8 , orysa-Q658B2 , orysa-Q5JMQ8 , orysa-Q5QMD9 , orysa-Q5N7L1 , orysa-Q5N7J6 , orysa-Q8RYV9 , orysa-Q5SNH3 , orysa-Q94DD0 , orysa-Q8W0F0 , orysa-pir7a , orysa-pir7b , orysa-Q4VWY7 , orysa-q5jlm9 , orysa-q5na00 , orysa-q5nbu1 , orysa-Q5QLC0 , orysa-q5vnp5 , orysa-Q5VP27 , orysa-Q5ZAM8 , orysa-Q5ZBI5 , orysa-q5zc23 , orysa-Q5ZCR3 , orysa-Q8L562 , orysa-Q8L570 , orysa-Q8LQS5 , orysa-Q8RZ40 , orysa-Q8RZ79 , orysa-Q8S0U8 , orysa-Q8S0V0 , orysa-Q8S125 , orysa-Q9LHX5 , orysa-Q94E46 , orysa-Q656F2 , orysi-a2wn01 , orysi-b8a7e6 , orysi-b8a7e7 , orysj-b9eya5 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q94d71

Title : Plasma endothelin-1 level as a marker reflecting the severity of portal hypertension in biliary atresia - Hasegawa_2001_J.Pediatr.Surg_36_1609
Author(s) : Hasegawa T , Kimura T , Sasaki T , Okada A
Ref : J Pediatr Surg , 36 :1609 , 2001
Abstract : BACKGROUND/PURPOSE: The aim of this study was to examine if the plasma endothelin-1 (ET-1), a potent vasoconstrictor, level may reflect the severity of portal hypertension associated with liver cirrhosis in biliary atresia (BA). METHODS: Forty-eight postoperative BA patients aged 6 months to 20 years were studied. Plasma ET-1 was measured by a sandwich method of enzyme immunoassay. ET-1 was compared with Child's score and laboratory data. ET-1 levels were compared among groups of patients with various degrees of histologic fibrosis and portal hypertension. RESULTS: Plasma ET-1 was 5.3 +/- 3.5 pg/mL in BA, higher than in controls (3.1 +/- 0.8, n = 27; P <.05). ET-1 correlated with Child's score, serum total bilirubin, direct bilirubin, aspartate aminotransferase, albumin, prothrombin time, hepaplastin test, fibrinogen, cholinesterase, total cholesterol, Fischer's molar ratio, prealubumin, and hyaluronic acid, respectively (P <.05). ET-1 also correlated with the severity of histologic fibrosis, gastroesophageal varices, the presence of splenomegaly, ascites, venous dilatation on the abdominal wall, or pulmonary vascular abnormalities. In 4 patients undergoing liver transplantation (LTx), ET-1 after LTx was lower than that before LTx (P <.05).
ESTHER : Hasegawa_2001_J.Pediatr.Surg_36_1609
PubMedSearch : Hasegawa_2001_J.Pediatr.Surg_36_1609
PubMedID: 11685683

Title : The DNA sequence of human chromosome 21 - Hattori_2000_Nature_405_311
Author(s) : Hattori M , Fujiyama A , Taylor TD , Watanabe H , Yada T , Park HS , Toyoda A , Ishii K , Totoki Y , Choi DK , Groner Y , Soeda E , Ohki M , Takagi T , Sakaki Y , Taudien S , Blechschmidt K , Polley A , Menzel U , Delabar J , Kumpf K , Lehmann R , Patterson D , Reichwald K , Rump A , Schillhabel M , Schudy A , Zimmermann W , Rosenthal A , Kudoh J , Schibuya K , Kawasaki K , Asakawa S , Shintani A , Sasaki T , Nagamine K , Mitsuyama S , Antonarakis SE , Minoshima S , Shimizu N , Nordsiek G , Hornischer K , Brant P , Scharfe M , Schon O , Desario A , Reichelt J , Kauer G , Blocker H , Ramser J , Beck A , Klages S , Hennig S , Riesselmann L , Dagand E , Haaf T , Wehrmeyer S , Borzym K , Gardiner K , Nizetic D , Francis F , Lehrach H , Reinhardt R , Yaspo ML
Ref : Nature , 405 :311 , 2000
Abstract : Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down syndrome, the most frequent genetic cause of significant mental retardation, which affects up to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions for common complex disorders have also been mapped to this chromosome, and loss of heterozygosity has been observed in regions associated with solid tumours. Here we report the sequence and gene catalogue of the long arm of chromosome 21. We have sequenced 33,546,361 base pairs (bp) of DNA with very high accuracy, the largest contig being 25,491,867 bp. Only three small clone gaps and seven sequencing gaps remain, comprising about 100 kilobases. Thus, we achieved 99.7% coverage of 21q. We also sequenced 281,116 bp from the short arm. The structural features identified include duplications that are probably involved in chromosomal abnormalities and repeat structures in the telomeric and pericentromeric regions. Analysis of the chromosome revealed 127 known genes, 98 predicted genes and 59 pseudogenes.
ESTHER : Hattori_2000_Nature_405_311
PubMedSearch : Hattori_2000_Nature_405_311
PubMedID: 10830953
Gene_locus related to this paper: human-LIPI

Title : The DNA sequence of human chromosome 22 - Dunham_1999_Nature_402_489
Author(s) : Dunham I , Hunt AR , Collins JE , Bruskiewich R , Beare DM , Clamp M , Smink LJ , Ainscough R , Almeida JP , Babbage AK , Bagguley C , Bailey J , Barlow KF , Bates KN , Beasley OP , Bird CP , Blakey SE , Bridgeman AM , Buck D , Burgess J , Burrill WD , Burton J , Carder C , Carter NP , Chen Y , Clark G , Clegg SM , Cobley VE , Cole CG , Collier RE , Connor R , Conroy D , Corby NR , Coville GJ , Cox AV , Davis J , Dawson E , Dhami PD , Dockree C , Dodsworth SJ , Durbin RM , Ellington AG , Evans KL , Fey JM , Fleming K , French L , Garner AA , Gilbert JGR , Goward ME , Grafham DV , Griffiths MND , Hall C , Hall RE , Hall-Tamlyn G , Heathcott RW , Ho S , Holmes S , Hunt SE , Jones MC , Kershaw J , Kimberley AM , King A , Laird GK , Langford CF , Leversha MA , Lloyd C , Lloyd DM , Martyn ID , Mashreghi-Mohammadi M , Matthews LH , Mccann OT , Mcclay J , Mclaren S , McMurray AA , Milne SA , Mortimore BJ , Odell CN , Pavitt R , Pearce AV , Pearson D , Phillimore BJCT , Phillips SH , Plumb RW , Ramsay H , Ramsey Y , Rogers L , Ross MT , Scott CE , Sehra HK , Skuce CD , Smalley S , Smith ML , Soderlund C , Spragon L , Steward CA , Sulston JE , Swann RM , Vaudin M , Wall M , Wallis JM , Whiteley MN , Willey DL , Williams L , Williams SA , Williamson H , Wilmer TE , Wilming L , Wright CL , Hubbard T , Bentley DR , Beck S , Rogers J , Shimizu N , Minoshima S , Kawasaki K , Sasaki T , Asakawa S , Kudoh J , Shintani A , Shibuya K , Yoshizaki Y , Aoki N , Mitsuyama S , Roe BA , Chen F , Chu L , Crabtree J , Deschamps S , Do A , Do T , Dorman A , Fang F , Fu Y , Hu P , Hua A , Kenton S , Lai H , Lao HI , Lewis J , Lewis S , Lin S-P , Loh P , Malaj E , Nguyen T , Pan H , Phan S , Qi S , Qian Y , Ray L , Ren Q , Shaull S , Sloan D , Song L , Wang Q , Wang Y , Wang Z , White J , Willingham D , Wu H , Yao Z , Zhan M , Zhang G , Chissoe S , Murray J , Miller N , Minx P , Fulton R , Johnson D , Bemis G , Bentley D , Bradshaw H , Bourne S , Cordes M , Du Z , Fulton L , Goela D , Graves T , Hawkins J , Hinds K , Kemp K , Latreille P , Layman D , Ozersky P , Rohlfing T , Scheet P , Walker C , Wamsley A , Wohldmann P , Pepin K , Nelson J , Korf I , Bedell JA , Hillier L , Mardis E , Waterston R , Wilson R , Emanuel BS , Shaikh T , Kurahashi H , Saitta S , Budarf ML , McDermid HE , Johnson A , Wong ACC , Morrow BE , Edelmann L , Kim UJ , Shizuya H , Simon MI , Dumanski JP , Peyrard M , Kedra D , Seroussi E , Fransson I , Tapia I , Bruder CE , O'Brien KP
Ref : Nature , 402 :489 , 1999
Abstract : Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.
ESTHER : Dunham_1999_Nature_402_489
PubMedSearch : Dunham_1999_Nature_402_489
PubMedID: 10591208
Gene_locus related to this paper: human-CES5A , human-SERHL2

Title : A unique protease responsible for selective degradation of a yolk protein in Bombyx mori. Purification, characterization, and cleavage profile - Indrasith_1988_J.Biol.Chem_263_1045
Author(s) : Indrasith LS , Sasaki T , Yamashita O
Ref : Journal of Biological Chemistry , 263 :1045 , 1988
Abstract : A yolk protein, egg-specific protein, synthesized and accumulated in the developing ovaries of Bombyx mori serves not only as the nutritive source for embryogenesis but also for the reorganization of the yolk system through limited degradation. Using the purified egg-specific protein as a substrate, a protease responsible for its limited hydrolysis was identified in embryonating eggs and purified to homogeneity. The protease had an apparent molecular mass of 30,500 with one subunit of 29,000 daltons. It hydrolyzes synthetic substrates at carbonyl bonds of Arg or Lys residues, and the hydrolysis is strongly inhibited by diisopropylfluorophosphate, phenylmethanesulfonyl fluoride, and leupeptin, suggesting that it is a trypsin-like protease. The protease shows an extremely high degree (over 2,000-fold) of specificity for egg-specific protein compared to other yolk proteins. Intact egg-specific protein is cleaved into three fragments in two steps; the first releases a 8.7-kDa peptide as an end product and a 55-kDa peptide intermediate, and in the second the intermediate is cleaved into 36- and 17.2-kDa peptides. By relating the NH2-terminal amino acid sequences of these peptides to the sequence of the intact egg-specific protein, the protease was shown to cleave first at a Lys-Asn site and secondly at Arg-Asp. Proteolytic activity abruptly appears mid-way in embryogenesis and increases steeply during completion of larval differentiation.
ESTHER : Indrasith_1988_J.Biol.Chem_263_1045
PubMedSearch : Indrasith_1988_J.Biol.Chem_263_1045
PubMedID: 3275655