A Scientist's Career: Jonathan S. Weissman

Mondays 17:45-19:45 in room C00.013 (unless noted otherwise); in English; 9 participants

The seminar aims for several goals. On the science side, we will follow the scientific work of Jonathan S. Weissman over a period of more than 20 years. The Weissman lab has made important contributions in a wide variety of biological topics. Each seminar day is centered on the discussion of a specific publication and the respectice general topic. This will also provide a good introduction into various methods used in molecular biology. In addition to this, the seminar offers the opportunity to improve your presentation as well as your discussion skills, both of which are crucial abilities in research.

Each seminar consists of two parts:
1. Introduction into the topic of the seminar day

In the beginning of each seminar day the speaker introduces the topic of the day's publication. For this, the speaker familiarizes her/himself with the publication and asks her/himself the important questions: "What is interesting about this?" "What could I present that will help and interest my fellow participants?" From the (very individual) answers to these questions the speaker compiles a list of "Take-Home-Messages" (max. 5) which she/he hands in at least 2 weeks before the seminar day for review. At least 1 week before the seminar date the speaker hands in the final presentation (max. 12 min) for feedback on content and design. Remember: the presentation should benefit all members of the group! A handout with the central Take-Home-Messages and important background information is handed out to each participant.
After this presentation there is time for questions and also evaluation and feedback on the performance, using our seminar talk evaluation sheet.
2. The original publication
All participants have read the publication of the day and hand in a list of the main messages of the paper at the beginning of the seminar day. The speaker has prepared a PowerPoint presentation containing all the figures and tables (including supplementary data) in locigal order and in sufficient quality. Using this presentation a randomly chosen moderator first compiles the consensus of main messages. She/he afterwords moderates the figure-by-figure discussion within the group.

IMPORTANT: In order to enable a fruitful discussion, thorough reading of the original publications is mandatory for all participants. Articles under the heading 'background information' are for further reading and as a starting point for the speaker of that day. It is essential to contact the lecturer during preparation of your presentation for help and support. At least 2 weeks before the seminar date every speaker has to hand in the list of "Take-Home-Messages" (ca. 5) that will be covered in the talk. At least 1 week before the seminar date every speaker has to hand in the presentation for feedback on content and design.

DateTopicOriginal publicationBackground informationPresented by
18.04.16 How to read a scientific article
Gracheva EO et al. (2010)
Molecular basis of infrared detection by snakes.
Nature 464: 1006-1011
Hilton JK et al. (2015)
Understanding thermosensitive transient receptor potential channels as versatile polymodal cellular sensors.
Biochemistry 54: 2401-2413

Saito S & Tominaga M (2015)
Functional diversity and evolutionary dynamics of thermoTRP channels.
Cell Calcium 57: 214-221
Andreas Brachmann
25.04.16 No seminar
02.05.16 How to make a good presentation
Material from the seminar day
same as day one
Andreas Brachmann
09.05.16 Protein folding
Weissman JS & Kim PS (1992)
The pro region of BPTI facilitates folding.
Cell 71: 841-851
Chang J-Y (2011)
Diverse pathways of oxidative folding of disulfide proteins: underlying causes and folding models.
Biochemistry 50: 3414-3431
Maximilian Höselbarth
16.05.16 No seminar (Whit Monday)
23.05.16 Molecular chaperones
Weissman JS et al. (1995)
Mechanism of GroEL action: productive release of polypeptide from a sequestered position under GroES.
Cell 83: 577-587
Hayer-Hartl M et al. (2016)
The GroEL-GroES chaperonin machine: a nano-cage for protein folding.
Trends in Biochemical Sciences 41: 62-76
Iris Stockmar
30.05.16 Yeast prions
Sparrer HE et al. (2000)
Evidence for the prion hypothesis: induction of the yeast [PSI+] factor by in vitro-converted Sup35 protein.
Science 289: 595-599
Wickner RB et al. (2015)
Yeast prions: structure, biology and prion-handling systems.
Microbiology and Molecular Biology Reviews 79: 1-17
Sonja Glauß
06.06.16 Lipid biosynthesis
Denic V & Weissman JS (2007)
A molecular caliper mechanism for determining very long-chain fatty acid length.
Cell 130: 663-677
Kihara A (2012)
Very long-chain fatty acids: elongation, physiology and related disorders.
Journal of Biochemistry 152: 387-395
Tommy Karlsson
13.06.16 Transcription
Larson MH et al. (2014)
A pause sequence enriched at translation start sites drives transcription dynamics in vivo.
Science 344: 1042-1047
Churchman LS & Weissman JS (2011)
Nascent transcript sequencing vizualizes transcription at nucleotide resolution.
Nature 469: 368-373

Gordon AJE et al. (2015)
Lost in transcription: transient errors in information transfer.
Current Opinion in Microbiology 24: 80-87
Aykut Turan
20.06.16 RNA structure
Rouskin S et al. (2014)
Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.
Nature 505: 701-705
Kwok CK et al. (2015)
The RNA structurome: transcriptome-wide structure probing with next-generation sequencing.
Trends in Biochemical Sciences 40: 221-232
Felix Schneider
27.06.16 Translation
Jan CH et al. (2014)
Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling.
Science 346: 716
Comment by Reid DW & Nicchitta CV; response by Jan CH et al.

Williams CC et al. (2014)
Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling.
Science 346: 748-751
Shao S & Hedge RS (2014)
Local synthesis and disposal.
Science 346: 701-702

Ingolia NT et al. (2009)
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
Science 324: 218-223

Ingolia NT (2016)
Ribosome footprint profiling of translation throughout the genome.
Cell 165: 22-33
Kaoutar Adjabi
04.07.16 Regulation of protein synthesis
Li G-W et al. (2014)
Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources.
Cell 157: 624-635
Vásquez-Laslop N & Mankin AS (2014)
Protein accounting in the cellular economy.
Cell 157: 529-531

Huh W-K et al. (2003)
Global analysis of protein localization in budding yeast.
Nature 425: 686-691

Gheammaghami S et al. (2003)
Global analysis of protein expression in yeast.
Nature 425: 737-741

Newman JRS et al. (2006)
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.
Nature 441: 840-846
Domagoj Vugic
14.07.16 No seminar
18.07.16 Genome-scale gene regulation
Gilbert LA et al. (2014)
Genome-scale CRISPR-mediated control of gene repression and activation.
Cell 159: 647-661
Barrangou R & Marraffini LA (2014)
CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity.
Molecular Cell 54: 234-244

Bassik MC et al. (2013)
A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility.
Cell 152: 909-922
Tim Kratz