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[慶賀]恭喜張清貿醫師升任北榮傳醫科主治醫師-20170201

  列出文章 - 96443064
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1  97學年(下)課程2009Spring / 基礎生物資訊學 / 回覆: [公告]980615 期末專題說明-20080608 於: 六月 18, 2009, 11:46:59 pm
96443064  http://96443064.5d6d.com/bbs.php
2  97學年(下)課程2009Spring / 基礎生物資訊學 / [作業三]-primer-96443064 於: 五月 11, 2009, 09:27:45 am
Primer pair 1
 Sequence (5'->3') Strand on template Length Start Stop Tm GC%
Forward primer CTGCAATCGTCACTCCAGAA Plus 20 665 684 59.98 50.00%
Reverse primer GGTTTTGCCCATGTTGTACC Minus 20 1013 994 60.10 50.00%
Internal oligo  Plus     
Product length 349
Product Tm 
Product Tm - min(OLIGO Tm) 

Products on intended target

--------------------------------------------------------------------------------

>XM_640364.1 Dictyostelium discoideum AX4 Ras GTPase activation domain-containing protein (DDB_0233763) partial mRNA

product length = 349
Forward primer  1    CTGCAATCGTCACTCCAGAA  20
Template        665  ....................  684

Reverse primer  1     GGTTTTGCCCATGTTGTACC  20
Template        1013  ....................  994

Products on allowed transcript variants

--------------------------------------------------------------------------------

Products on potentially unintended templates

--------------------------------------------------------------------------------

Products on target templates
3  97學年(下)課程2009Spring / 基礎生物資訊學 / [作業九]-Docking-96443064 於: 五月 11, 2009, 09:26:45 am
參數
--------------------------------
(1)Search Algorithm: MolDock SE
 Number of runs: 1


(2)Parameter Settings
 Max iterations: 500
 Max Population: 50
 Energy threshold: 50

(3)Simplex Evolution
 Max steps: 150
 Neighbour distance factor: 1.0
========================
結果
---------------------------------
MolDockScore = -152.891
4  97學年(下)課程2009Spring / 基礎生物資訊學 / [作業十]-Microarray-96443064 於: 五月 11, 2009, 09:25:38 am
Spot   Clone ID   Gene SySpot   Clone ID   Gene Symbol   Gene Name
1   IMAGE:342721   ITGB2   integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)
2   IMAGE:233721   IGFBP2   insulin-like growth factor binding protein 2, 36kDa
3   IMAGE:50754   MTIF2   mitochondrial translational initiation factor 2
4   IMAGE:126243   HMBS   hydroxymethylbilane synthase
5   IMAGE:234736   GATA6   GATA binding protein 6
5  97學年(下)課程2009Spring / 基礎生物資訊學 / [作業一]-Pubmed-96443064 於: 四月 20, 2009, 09:27:22 am
期刊:
Exp Hematol. 2008 Oct;36(10):1377-89.
標題:
Molecular profiling reveals similarities and differences between primitive subsets of hematopoietic cells generated in vitro from human embryonic stem cells and in vivo during embryogenesis.
作者:Salvagiotto G, Zhao Y, Vodyanik M, Ruotti V, Stewart R, Marra M, Thomson J, Eaves C, Slukvin I.
PMID:18922365

摘要(英): Cellular and molecular changes that occur during the genesis of the hematopoietic system and hematopoietic stem cells in the human embryo are mostly inaccessible to study and remain poorly understood. To address this gap we have exploited the human embryonic stem cell (hESC) system to molecularly characterize the global transcriptomes of the two functionally discreet and phenotypically separable populations of multipotent hematopoietic cells that first appear when hESCs are induced to differentiate on OP9 cells. MATERIALS AND METHODS: We prepared long serial analysis of gene expression libraries from lin-CD34+CD43+CD45- and lin-CD34+CD43+CD45+ subsets of primitive hematopoietic cells derived in vitro from hESCs, sequenced them to a depth of 200,000 tags and compared their content with similar libraries prepared from highly purified populations of very primitive human fetal liver and cord blood hematopoietic cells. RESULTS: Comparison of libraries obtained from hESC-derived lin-CD34+CD43+CD45- and lin-CD34+CD43+CD45+ revealed differences in their expression of genes associated with myeloid development, cellular biosynthetic processes, and cell-cycle regulation. Further comparisons with analogous data for primitive hematopoietic cells isolated from first-trimester human fetal liver and newborn cord blood showed an apparent similarity between the transcriptomes of the most primitive hESC- and in vivo-derived populations, with the main differences involving genes that regulate HSC self-renewal and homing, chromatin remodeling, AP1 transcription complex genes, and noncoding RNAs. CONCLUSION: These data suggest that primitive hematopoietic cells are generated from hESCs in vitro by processes similar to those operative during human embryogenesis in vivo, although some differences were also detected.


摘要(中):
細胞和分子的變化發生在起源的造血系統和造血幹細胞的人類胚胎大多無法繼續學習和了解甚少。為了解決這一差距,我們必須利用人類胚胎幹細胞( hESC )系統分子特徵的全球transcriptomes兩個功能審慎和表型可分多人口的造血細胞,首先出現的hESCs是誘導分化細胞的執行部分第9段。材料與方法:我們準備長期基因表達系列分析庫林臍血CD34 + CD43 + CD45 -和林臍血CD34 + CD43 + CD45 +亞群的原始造血細胞的體外的hESCs ,測序,他們的深度200000標籤和相比,其內容類似圖書館準備從高純度人口非常原始人胎肝和臍血造血細胞。結果:比較圖書館獲得hESC源性林臍血CD34 + CD43 + CD45 -和林臍血CD34 + CD43 + CD45 +顯示差異表達相關基因骨髓發展,蜂窩生物合成過程,以及細胞週期調控。進一步的比較類似的數據,原始造血幹細胞分離的早期人胎肝和新生兒臍血顯示明顯相似之處transcriptomes的最原始的hESC和在體內源性人口,主要分歧涉及基因調控造血幹細胞自我更新和歸巢,染色質重塑,複雜的第一附加議定書轉錄基因,非編碼RNA的。結論:這些數據表明,原始造血細胞的生成的hESCs在體外的過程類似手術在人類胚胎的研究,但也有一些差異,也發現。
6  97學年(下)課程2009Spring / 基礎生物資訊學 / [作業八]-Uniprot-96443064 於: 四月 20, 2009, 09:25:44 am
Protein names:HLA class I histocompatibility antigen, B-27 alpha chain
Sequence:P03989-1
       
MRVTAPRTLL LLLWGAVALT ETWAGSHSMR YFHTSVSRPG RGEPRFITVG YVDDTLFVRF

       
DSDAASPREE PRAPWIEQEG PEYWDRETQI CKAKAQTDRE DLRTLLRYYN QSEAGSHTLQ


NMYGCDVGPD GRLLRGYHQD AYDGKDYIAL NEDLSSWTAA DTAAQITQRK WEAARVAEQL


RAYLEGECVE WLRRYLENGK ETLQRADPPK THVTHHPISD HEATLRCWAL GFYPAEITLT


WQRDGEDQTQ DTELVETRPA GDRTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEP


SSQSTVPIVG IVAGLAVLAV VVIGAVVAAV MCRRKSSGGK GGSYSQAACS DSAQGSDVSL


TA

PDB:1HSA http://www.pdb.org/pdb/files/1hsa.pdb
7  97學年(下)課程2009Spring / 基礎生物資訊學 / [作業七]-QSAR-96443064 於: 四月 20, 2009, 09:21:37 am
Name   (Eng)CBG  Predicted
ster7    7.881       6.892
8  97學年(下)課程2009Spring / 基礎生物資訊學 / [作業六]-Protein-96443064 於: 三月 30, 2009, 09:18:20 am
Ragweed Pollen Allergen From Ambrosia Trifida V, Nmr, 30 Structures

2BBG_A                    40 aa            linear
9  97學年(下)課程2009Spring / 基礎生物資訊學 / [作業五]-ClustalW-96443064 於: 三月 23, 2009, 09:50:13 am
GeneID: 947     -CD34 molecule [Homo sapiens]     -NM_001025109
GeneID: 305081-CD34 molecule [Rattus norvegicus]-NM_001107202
GeneID: 397160-CD34 molecule [Sus scrofa]          -NM_214086
GeneID: 419856-CD34 molecule [Gallus gallus]       -XM_417984


 
                   

(
(
gi|68342037|ref|NM_001025109.1:0.09557,
gi|47522983|ref|NM_214086.1|:0.15815)
:0.06192,
gi|169790781|ref|NM_001107202.:0.10537,
gi|118102442|ref|XM_417984.2|:0.68878);
 













http://www.ebi.ac.uk/Tools/es/cgi-bin/clustalw2/result.cgi?tool=clustalw2&jobid=clustalw2-20090323-01451181&poll=yes
10  97學年(下)課程2009Spring / 基礎生物資訊學 / [作業四]-Blast-96443064 於: 三月 16, 2009, 09:13:09 am
Query  75   CTTCCAAAATCAGAGTCAGACTGCTCCCGGTGCCATGAACGGAGACGACGCCTTTGCAAG  134
            |||||||||||||||||||||| ||||| |||||||||||||||| ||| ||||||||||
Sbjct  61   CTTCCAAAATCAGAGTCAGACTACTCCCTGTGCCATGAACGGAGATGACACCTTTGCAAG  120

Query  135  GAGACCCACGGTTGGTGCTCAAATACCAGAGAAGATCCAAAAGGCCTTCGATGATATTGC  194
            |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct  121  GAGACCCACGGTTGGTGCTCAAATACCAGAGAAGATACAAAAGGCCTTCGATGATATTGC  180

Query  195  CAAATACTTCTCTAAGGAAGAGTGGGAAAAGATGAAAGCCTCGGAGAAAATCTTCTATGT  254
            |||||||||||||||||||||||||||||||||||||| ||||||||||||| |||||||
Sbjct  181  CAAATACTTCTCTAAGGAAGAGTGGGAAAAGATGAAAGTCTCGGAGAAAATCGTCTATGT  240

11  97學年(下)課程2009Spring / 基礎生物資訊學 / [作業二]-Gene-96443064 於: 三月 02, 2009, 09:55:04 am
基因名:Nf1
基因描述:無
基因型別:protein coding
所在地標籤:無
生物:Escherichia coli CFT073 (strain: CFT073)
基因世系:
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia
別名:nfi
染色體別:無
UGID:無
基因序列:ORIGIN     
        1 mdlaslraqq ielassvire drldkdppdl iagadvgfeq ggevtraamv llkypslelv
       61 eykvariatt mpyipgflsf reypallaaw emlsqkpdlv fvdghgishp rrlgvashfg
      121 llvdvptigv akkrlcgkfe plssepgala plmdkgeqla wvwrskarcn plfiatghrv
      181 svdsalawvq rcmkgyrlpe ptrwadavas erpafvryta nqp
//
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