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A lab reading list will be curated for our journal clubs. We will likely use zotero. This list is for books, blogs, articles of a more general nature. Please edit as you find interesting and valuable resources.

General C. elegans maintenance

Wormbook has everything from protocols to review articles. it's a great starting point to get familiar with the organism.

wormBase is the resource for genetics and cloning. It has the sequenced reference genome, functional annotations for mutants, protein homologies etc.

Wormatlas is the original resource for anatomical information about the Worm. A copy of the original Atlas (prints of the EM scans with annotations) can be borrowed from Monika.

Strain name conventions Beginner’s guide of C. elegans basic genetics

Useful online tools

https://cgc.umn.edu/ is the strain repository for worms. We depositi published strains there and order worms off this website.

http://www.wormweb.org/ a nice visualization tool for the connectome. the left sidebar has supporting information on expression, and function with citations. Unfortunately this is not updated anymore.

Science and Lab conduct

At the bench (Kathy Barker) : A general introduction into conduct, lab procedures and how labs work. It's great if you come from a computational or Physics background or if you want to refresh your knowledge on wet-lab howtos. A copy can be borrowed from Monika.

Science as a career

Since we are a worm lab, Sidney Brenner is our scientific great-grandfather. He used to write a column about science which is both excellent and relevant to this day. I recommend browsing through it.

Loose Ends and False Starts by Sidney Brenner

Introductory reading for our lab

How to plan a behavior experiment

These papers are an ideal start. Powerpoint presentations can be found on our dropbox.

Template for paper summary: paper_summaries

Reading Suggestions

Title Link Summary Topic Presenter
1 Methods
An Hourglass Circuit Motif Transforms a Motor Program via Subcellularly Localized Muscle Calcium Signaling and Contraction https://www.biorxiv.org/content/10.1101/2020.06.02.129825v2.full motor program allowing spitting or pumping Monika (?)
Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy https://www.nature.com/articles/nmeth.2964 Using micro-array lens system to image in 3D 3D brain imaging Luis
2 Behavior
Natural sensory context drives diverse brain-wide activity during C. elegans mating https://www.biorxiv.org/content/10.1101/2020.09.09.289454v1 male tail whole-brain imaging with ID, predictive models
Global Brain Dynamics Embed the Motor Command Sequence of Caenorhabditis elegans https://www.cell.com/fulltext/S0092-8674(15)01196-4 Whole-brain imaging unveils dynamic activity patterns on C. elegans that underlie behaviors. Whole-brain imaging and behavior Luis
3 Neuroscience
Connectomes across development reveal principles of brain maturation in C. elegans https://www.biorxiv.org/content/10.1101/2020.04.30.066209v2 paper_summaries_wietlievet2020 Connectomics, elegans
Decoding the intensity of sensory input by two glutamate receptors in one C. elegans interneuron https://doi.org/10.1038/s41467-018-06819-5 Calcium imaging, feeding, locomotion Elsa
The computational worm: spatial orientation and its neuronal basis in C. elegans https://www.sciencedirect.com/science/article/abs/pii/S0959438811001085?via%3Dihub Overview of how spatial orientation might be accomplished in the worm Taxis in C. elegans Luis
EGL-19 AND EXP-2 ION CHANNELS MODELLING WITHIN C. ELEGANS PHARYNGEAL MUSCLE CELL ALLOWS REPRODUCTION OF CA2+ DRIVEN ACTION POTENTIALS, BOTH SINGLE EVENTS AND TRAINS https://www.biorxiv.org/content/biorxiv/early/2017/12/20/228650.full.pdf Barbara
Arrhythmogenic effects of mutated L-type Ca2+-channels on an optogenetically paced muscular pump in Caenorhabditis elegans https://www.nature.com/articles/srep14427 Barbara
The enteric nervous system of C. elegans is specified by the Sine Oculis-like homeobox gene ceh-34 https://www.biorxiv.org/content/10.1101/2021.11.30.470650v1.full.pdf characterization of ceh-34 in specifying the pharynx, and its potential role in combination with other TF The role of ceh-34 as a master transcription factor for specifying the pharynx Jun
4 Miscellaneous Neuroscience
An Algorithmic Approach to Natural Behavior Monika

Introduction to version control (git)

wiki/join/read.txt · Last modified: 2022/01/18 00:25 by jliu

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