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Joachim Frank HHMI, Wadsworth CentertRNA A/T site A site P site
/ tRNA tRNA EF-Tu GTP tRNA Joachim Frank
GTPase-associated center (GAC) action brings codon and anticodon together.Codon-anticodon interaction stabilizes the twisted anticodon conformation. Cognate binding leads to accommodation.
Bob Grassucci tRNA Michael Watters Joachim Frank
the decoding process is facilitated by a dynamic interply between the ribosome and the tRNA in which the tRNA acts like a molecular spring .(nature structural biology 10: 899-906, 2003)
Marianne Grunberg-Manago PNPase
RNA
RNA RNA
ncRNA/ncDNA
PUS
FASEB
Mechanisms of mRNA decay
mRNA
mRNA
NMD nonstop decay, tmRNA
mRNA decay
decay degra-
dosome
PNPase
PNPase Marianne Grunberg-Manago
Marianne Severo Ochoa
PNPase
RNA
Ochoa RNA
PNPase
Marianne
Marianne
PNPase
NusA
Marianne
Marianne
Marianne "Enjoy Paris. Continue in Tokyo"
Marianne
Marianne
Marianne
Marianne
Institut de Biologie
Physico-Chimique (CNRS)
IUB
Marianne
Marianne
Marianne Grunberg-Manago PNPase
Marianne
EMBO
Marianne
Marianne
Marianne
PNPase RNA
PNPase
PNPase mRNA decay
PNPase
Yoshikazu NAKAMURA
Marianne
DNA
RNA non-coding
RNA
RNA
RNA
RNA
RNA
RNA
RNA
RNA
RNA
Kimitsuna WATANABE
RNA
RNA
RNA
RNA
RNA
RNA
Non-coding RNA
RNA snRNA snoRNA
RNA
RNA
RNomics
RNA
cDNA
Non-coding RNA
RNomics
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Non-coding RNA
boxC/D snoRNA
Non-coding RNA
Non-coding RNA
Non-coding RNA
SRP RNA
Non-
coding RNA
Non-coding RNA
Non-coding RNA
Non-coding RNA
Non-coding RNA
transcriptome
RNA
Non-coding RNA
Non-coding RNA
JICA
EU
RNA
RNA
Non-coding RNA
Non-coding RNA
Kouji NAKAMURA
RNA
Non-coding RNA
non-coding RNA
RNA
non-coding RNA
non-coding RNA
non-coding RNA
snoRNA, Xist
non-coding RNA RNA RNAi/miRNA
mRNA non-coding RNA
RNA
non-coding
RNA
RNA
non-
coding RNA
Xist RNA
snoRNA
RNA
non-coding RNA
non-coding RNA
RNA
non-coding RNA RNA
RNA
RNA
omt1,2,3
RNA
non-coding RNA
BS190RNA mRNA 5
non-
coding RNA
OK
non-coding RNA
non-coding RNA
RNA
non-coding RNA
non-coding RNA
Hitoshi ONOUCHI
RNA
RNA
RNA
RNA
RNA
RNA
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RNA Network
Newsletter volume 2 number 2
CDB
RNA
RNA
RNA
RNA
RNA
Akira NAKAMURA
McGillMedical Research Council
Yuji KAGEYAMA
Howard Hughes Medical Institute
Baylor
EMBL Anne
Ephrussi
RNA
RNA
RNA
RNA
UP RNA
RNA
RNA
RNA
RNA
RNA
RNA
RNA
RNA
RNA
RNA
non-cording RNA RNAi
RNA
RNA
RNA
RNA
RNA RNA
non-cording
RNA RNAi RNA
RNA RNAi
CDB
RNA
RNA
CDB
Tamaki YANO
European Molecular Biology Laboratory (EMBL)
RNA
RNA
RNA
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non-coding RNA
RNA
RNA
RNA mRNA
RNA interference
Cell Dicer
RNAi
RNA RNAi /
PTGS DNA
RdDM
TGS nt
RNA
Yusuke Hokii
RNA
M
RNA
RNA
RNA
A
T G C
RNA
RNA
M
RNA
mRNA tRNA rRNA
RNA
RNA
RNA
RNA
HeLa
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.
HeLa
Hisashi KIRIU
RNA
RNA
HOTRNA
RNA
RNA
CDB
RNA
RNA
Kiyokazu AGATA
CDB
Group Director
URLhttp://www.cdb.riken.go.jp/erb/
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James McCloskey Univ. of Utah
rRNA
2 0
tRNA tRNA
SINE LINE SINE
Mathias Sprinzl Univ. of
Bayreuth
RF
DNA Hef
Hef dicer
Jens Nyborg Univ.
of Aarhus EF
T RNA
RRF tRNA
tmRNA GTPase,YjeQ
50S GTPase center
GTPase 30S
30S GTPase center
Linda L. Spremulli
Univ. of North Carolina IF2
McCloskey Spremulli
tRNA
s2T tRNA
tRNA
in vitro
RNA
SerRS tRNASer
Spremulli
Closing remarks
Sprinzl
McCloskey
McCloskey
Sprinzl
Spremulli Nyborg
RNA
Taeko KOMODA
McCloskeyMcCloskey
JSPS
RNA biology
OK
Hooray
JSPS
KLM
CDB
Uppsala
Gustav Vasa
SEK
Eklundshof
reception
reception
OK. I
will let you in!
pick up
information
Greek Italian Restaurant Alexandria
Greek Italian
Where is our beer?
Swedish Greek
RNA Biology
Chinese Thai
Thai
Lunch menu
SEK
It does not happen so often
SEK
sport pub restaurant
Sweden vs. Bulgaria
Sweden
receipt
receipt
receipt
JSPS
JSPS
Prof. Leif Kirsebom
Dept. of Cell and Molecular Biology, Uppsala Univ.
Versatility of RNA
Dr. Kunio Inoue Faculty of Science, Kobe Univ.
Mechanisms of alternative RNA splicing
Dr. Marie Ohman
Dept. of Molecular Biology & Functional Genomics, Stockholm Univ.
RNA editing by adenosine deamination in the mammalian brain
Dr. Naoyuki Kataoka
Institute for Virus research, Kyoto Univ.
Analysis of the post-splicing recycling pathway in the nucleus
dinner time JSPS
Dr. Anders Virtanen
Dept. of Cell and Molecular Biology, Uppsala Univ.
Poly(A)-specific ribinuclease (PARN):Connecting mRNA
poly(A) tail degradation to the 5 end located cap structure
Dr. Hitoshi Onouchi
Graduate School of Agriculture, Hokkaido Univ.
Nascent polypeptide-mediated posttranscriptional regulation
of the cystathione gamma-synthase gene in Arabidopsis
Dr. Mikiko Siomi
Institute for Genome Research, Univ. of Tokushima
Distinct roles for Argonaute proteins in small RNA-directed
RNA cleavage pathways in Drosophila
Dr. Gerhart Wagner
Dept. of Cell and Molecular Biology, Uppsala Univ.
Small RNA encoded by the E. coli chromosome
Dr. Fredrik Soderbom
Dept. of Molecular Biology, Swedish Agricultural Univ.
Non-coding RNAs in Dictyostelium discoideum
Dr. Akira Nakamura
Center for Developmental Biology, RIKEN
Spatio-temporal regulation of maternal RNA localization and
translation in Drosophila
Dr. Mikael Wikstrom Dept. of Molecular Biology, Umea Univ.
Role of ribosome-associated proteins in S rRNA
processing and ribosome maturation
Dr. Tsutomu Suzuki
Graduate School of Engineering, The Univ. of Tokyo
Biosynthesis and function of tRNA wobble modification
pick up
abstract
UCSF
Concluding remark
Prof. Leif Isaksson JSPS
cocktail time champagne
dinner time
dinner time
dinner
check out JSPS
Blue Hall
RNA Society meeting
role
RISC siRNA
souvenir shop
Nobel Museum
Nobel laureates
open theater
Watson Click
Nobel Museum
beer
jet lag
non-alcohol
lady
Stadshuset
tour
tour
Blue Hall Nobel
laureates
tour
,
tour
Golden Hall Blue Hall blue
Golden Hall
Nobel laureates dance
Hall
Golden Hall Blue Hall
Hotel Sheraton JSPS
party
JSPSJSPS JSPS
JSPSMs.
Lonn
JSPS
serve
coffee shop Sushi Caf�
coffee shop
coffee table
mismatch
beer
JSPS
RNAi miRNA
Dr.
Gerhart Wagner
small RNA
Dr. Fredrik Soderbom Dic-
tyostelium discoideum non-coding RNA
collaboration
JSPS
RiddarfjardenMikiko C. SIOMI
Howerd Hughes Medical Institute
RNA
P.Sharp R.Roberts
PNAS Cell
Abelson tRNA
RNA
RNA
cDNA
cDNA
HeLa in vitro
RNA
in vitro
mRNA
RNA
RNA
ApppG 5
RNA in
vivo
kd
Mattaj kd kd
RNA transport
RNA
RNA
RNA
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cDNA
RNA
Sexlethal (Sxl) tansformer (tra) transformer (tra)
doublesex (dsx)
Sxl tra RNA
tra-mRNA
tra tra2 dsx-mRNA
Sxl pre-mRNA
Sxl mRNA
mRNA
Maniatis
Baker McKeown
McKeown Your people are too fast
RNA closed meeting
5
5
Genes and Development Molecular and Cellular
Biology
Genes & Development
Exon Recognition Sequence
Exonic Splicing Enhancer
RNA
RNA
Yoshiro SHIMURA
RNA
SARS
SARS
RNA RNA
RNA
RNA
RNA
RNA
RNA RNA
Hsp90
V STAT1 STAT2
RNA
cDNA
cDNA
ATP, dNTP cDNA 32P
RI
DNA
RNA
RNA RNA
RNA
DNA DNA
RNA
Kaoru TAKEUCHI
Newsletter
RNA
Newsletter
RNA RNA
RNA
RNA
RNA
RNA
RNA
RNA
RNA
small RNA world tRNA world
RNA
tRNA The tRNA
World
RNA
RNA
Orgel Crick
JMB JMB
Cech Cell
RNA
Gilbert RNA
RNA RNA
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The tRNA World 2003 Kloster BanzProf. Hildburg Beier
Nature
RNA
RNA
RNA RNA
RNA
RNA
RNA
RNA DNA
RNA
RNA
RNA
RNA
RNA
RNA
RNA
RNA
,
RNA
RNA RNA
RNA
SELEX
RNA
RNA
JB
RNA
RNA
RNA
SELEX
RNA
RNA
RNA
RNA RNA
RNA RNA
RNA
RNA Rhodovulum
NAR Supplement
RNA
RNA
RNA RNA
RNA
RNA
SELEX
RNA
RNA
RNA
RNA RNA
RNA
mRNA
mRNA
transformer (tra)
Sex-lethal (Sxl)
Sxl
msl-2
msl-2
Sxl
in vitro selection RNA
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Sxl
Sxl
Sxl tra
in vitro
in vitro
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H. J. Gross
Sxl
msl-2 Sxl msl-2
Cell
Sxl
Sxl
in vitro
Cold Spring Harbor
in vitro
RNPS1
in
vitro
RNPS1
nonsense-mediated decay
two-hybrid RNPS1
RNPS1
ATP
F1
ATP
ATP
F1
F1
F1
in vitro
Fox-1 F1
Fox-1
F1
Eiji SAKASHITA
RNA
RNA
RNA
RNA
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Halo-
cynthia roretzi EST
Ciona intestinalis
Ciona savignyi EST
EST
Phallusia mammillata
Kovelevski
RNA RNA
settle down
settle down
Kazuhiro W. MAKABE
RNA Network
Newsletter
RNA
cDNA
RNA Network Newsletter
EST
http://www.ra-bio.or.jp/
EST EST
mRNA
SNPs
alternaive splicing
dbProP
http://dbprop.nirs.go.jp/ SNP
NCBI dbSNP
SNP
AMSTL/CRIP dbSNP
dbProP AMSTL/CRIPSNP
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alternative
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ASV
alternative splicing
ASV
ASV
dbProP
alternative micro exon mRNA EST
ag gt -
mRNA surveillance nonsense mutation-
mediated mRNA decay; NMD
mRNA
RNA
NCBI RefSeq
NMD
RefSeq
NMD cDNA
NMD
mRNA
NMD
mRNA
cDNA
artifact
EST
cDNA
mRNA mRNA
mRNA
head-to-head tail-to-tail
head-to-head -RACE tail-
to-tail -RACE
head-to-
head tail-to-tail
mRNA
mRNA
mRNA surveillance
mRNA
CARD SGSH mRNACARD SGSH
RACE SGSHmRNA '-UTR CARD mRNA
FTSJ PSMC mRNAFTSJ PSMC
RACEFTSJ mRNA '-UTR PSMC mRNA '-UTR
head-to-head
mRNA tail-to-tail
mRNA RACE
miRNA siRNA
RNA
mRNA
RNA
mRNA
non-coding RNA
mRNA
mRNA
RNA Network
Newsletter
mRNA
RNA
poly-cistronic
mRNA trans-splicing
non-coding RNA
mRNA mRNA
pre-
mRNA
RNA
RNA
Toshiyuki SAITO
RNA
SV T
NLS
Fish
is downstairs
SDSPAGE
cDNA
RNA
RNA
RNA
RNA
RNA UTP
RNA
RNA
RNA
RNA
RNA
CSHL RNA processing
meeting
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mRNA
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CSHL
DNA
Southern blot
mRNA
Oh! You
are the Bottleman Nice
to meet you
hnRNP A
Cell hnRNP
mRNA
RNA
mRNA
CWRU
mRNA
Mutsuhito OHNO
~EMBL
J. D. Watson
The Double Helix
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Science
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Advances in Biophysics, Vol. ,
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T. Steitz tRNAGln Gln-RS
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Tom
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RNA DNA
ncRNA/ncDNA
ncRNA/ncDNA
LINE/SINE
LINE/SINE
segmental A PABP
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ccGA[G]4Agg 8
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mRNA
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Noriko HARAGUCHI
NASA
Water Bears
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mRNA
RNA
Department of Biochemistry
Brandeis University
RNA
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Melissa
EJC
pre-mRNA
Exon Junction Complex (EJC)
EJC mRNA
mRNA
EJC Exon Junction Complex
pre-mRNA mRNAEJC
eIF AIII EJC mRNAEJC mRNA
mRNA EJC
exon-exon junction
mRNA EJC
NMD (nonsense mediated mRNA decay)
mRNA
Moore
EJC
C-
complex Accession
number
EJC
EJC
EJC EJC
RNA
Toshiharu SHIBUYA
Department of BiochemistryBrandeis University
Brandeis University, Melissa Moore HHMI
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Public
Understanding of Science, No.1, p45-68
PUS
Scientific
truth is contingent with conditions.
Jasanoff
X
Y
operationali-
zation
over-generalization
operationalization
publicYuko FUJIGAKI
Proposals
Relating to the Education of Youth in Pensilvania (1749)
one that would offer practical as well as
classical instruction in order to prepare youth for real-world
pursuits
RNA
CPEB
Stanford
Department of Biological Sciences
NIH
NIH
Stanford
Stanford
Stanford
http://www.stanford.edu/class/biosci158/
Yasuyuki KURIHARA
RNA
RNA
2004
....the basic idea is how you think, at some point the student,
in close collaboration with the advisor, has formed a clear and
presentable thesis project, and has demonstrated competence in
completing it, usually by experimental and written progress. At
a minimum, the student should be able to present orally and in
writing a project that will lead to several quality publications.
qualifying exam
Colin A. Smith
Qualifying exam
UCSF
Stipend
Washington University in St. Louis WUSTL
UCSF
Colin A. Smith
American University of Beirut Assistant Professor
Colin
UCSF Program
in Biological Sciences (PIBS)
Teaching Assistant
(TA)
Colin WUSTL
Chemistry Department TA
UCSF
TA TA
PIBS
rotations
TA
entrance examinations cumulative exami-
nations for advancements Colin
WUSTL In my program, the first
week we arrived were used to give us entrance exams, to see if
we had any deficiencies, and to make sure we remembered
enough basic chemistry to be Teaching assistants in the
undergraduate lab courses. Out of 15-20 of us, I think three or
so had to do all the freshman lab experiments before they could
be Teaching assistants. Then we had a series of cumulative
exams, offered 3 times a semester, sometimes related to a
course, sometimes not, each time given by a different professor
in the program, and we were strongly encouraged to take every
one until we passed four. We had to pass two exams in the first
four semesters (2/12) and four by the end of the sixth semester
(4/18). The best students passed the first four they took, most
students finished in the second year, and the weaker students
just made it.
with the help of
Colin A. Smith
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Qualifying Exam
Qualifying Exam UCSF PIBS Orals proposal
thesis
committee
defense Colin
UCSF PIBS Qualifying Exam
Qualifying exam
Research
proposal
UCSF PIBS Secondary orals
proposal
Qualifying exam
Research proposal written proposal
NIH
Qualifying exam
Qualifying exam
NIH web site
Significance; Approach; Innovation; Investi-
gator Environment (http://www.niaid.nih.gov/ncn/grants/basics/)
NIH
NIH
defend
Colin ......in US academics, whether
one is submitting a proposal or a publication, great weight is put
on being able to defend the importance and conclusions of the
work. I think the guiding principle in all these evaluations is to
set up a somewhat adversarial process, where the proponent
tries to convince others that the work is interesting and good,
and the evaluators question the arguments. In this way, whether
the scientist is trying to pass a qualifying exam, or thesis
defense, or get a paper published, or present a talk at a
professional conference, or even RNA club, this aspect is the
same.
Stipend
Stipend
Colin Stipend
A stipend is a salary, but it
has the sense of a salary for a specific
purpose, pay that is sufficient for living expenses, but not
competitive with an open market. The original use was to
describe soldier' s pay, but is most often used to describe the
compensation for students or fellows. You will also often see it
used for short-term purposes, such as a stipend for daily
expenses while traveling.
Biomedicine
Colin
WUSTL
NIH NSF
WUSTL Biomedical Department Colin
Ingrid Ghattas NIH training grant
NIH training grant
NSF Howard Hughes
External funding
UCSF UCSF PIBS
in US academics, whether one
is submitting a proposal or a
publication, great weight is put
on being able to defend the
importance and conclusions of
the work
TA
Colin In the US, the stipend is meant to be
enough to live on, and depending on how expensive the city, to
live alone, eat well, travel, and save money (not in San
Francisco). UCSF Web site
Biophysics
,
San Francisco
stipend
http://www.nigms.nih.gov/funding/trngmech.html#b/
http://www.ehr.nsf.gov/dge/programs/
http://www.hhmi.org/grants/funding/indiv/precomp.html/
http://biophysics.ucsf.edu/bp_adm.html#financial/
Colin
.....it
was typical, the student designs the experiments, orders the
materials, carries out the experiment, analyses the results, and is
responsible for writing the first draft of the publication. The
advisor provides the laboratory and funds, and discusses
everything else as much as the student requests or need (judged
by the advisor), which means a substantial contribution to the
research questions, the experimental strategy, interpretation, and
almost always, great scientific and editorial contributions to the
final published work.
UCSF Ira
Herskowitz UCSF
Cell
ColinIngrid Celine Colin
Salk
Kazuo HARADA����
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WashingtonUniversity, Ph.D
MologenAG, Berlin, Leader of Basic Research
Assistant Professor
Colin A. SmithAmerican Universityof Beirut, Lebanon
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RNA
Ph.D.
RNA
Molecular Biology
of the Gene
maturase
Ph.D.
RNA
MS2 RNA
RNA
RNA
tRNA
RNA
tRNA
RNA
tRNA
tRNA
RNase P RNA
RNase P
RNA
RNA
mRNA
ATP U snRNA
Naoyuki KATAOKA
Dreyfuss
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non-coding RNA
prototype neotype
prototype general basic
neotype specific individualized
RNA
non-coding RNA
non-coding RNA
transcriptional interference
mRNA RNAi
(gene silencing) non-coding RNA
off-switch
RNA
770-8503 3-18-15Tel: 088-633-9450 Fax: 088-633-9451e-mail: [email protected]
RNA
http://db.shichiou-net.jp/rna/
