Monthly Archives: October 2016

Paper #20 - Specific roles for DEG/ENaC and TRP channels in touch and thermosensation in C. elegans nociceptors

Title: Specific roles for DEG/ENaC and TRP channels in touch and thermosensation in C. elegans nociceptors

Year: 2010

Summary:

Here they were interested in discovering which proteins mediate nociception - the sensation of pain. Neurons that detect pain are referred to as nociceptors, and are thought to be multimodal - that is, they respond to many kinds of sensory inputs that generate pain, like heat, cold, harsh touch, extreme pH, or noxious chemicals. This paper seeks to answer the question of how nociceptors obtain their multimodality. Do they have single receptors that respond to all these inputs? Or do they have many receptors? At which point do these sensory inputs converge onto the same signal transduction path?

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Top 47 functions to know when using R

I was trying to figure out what I'd want to know if I were just learning R, and I think these might be my favorites. The list is not complete, and I welcome suggestions! I will also try to add some documentation to this so that it could be printed out and used for reference.

  1. ls
  2. rm
  3. library
  4. install.packages
  5. list.files
  6. getwd, setwd
  7.  apply
    • mapply
    • sapply
    • lapply
  8. str
  9. dim
  10. colnames
  11. rownames
  12. names
  13. summary
  14. %in%
  15. which
  16. c
  17.  plot
    • points
    • lines
  18. hist
  19. heatmap
  20. density
  21. par
  22. layout
  23. legend
  24. text
  25. mtext
  26. colorRampPalette
  27. read.table
  28. write.table
  29. as. (as.character, as.numeric, as.matrix...)
  30. data.frame
  31. aggregate
  32. merge
  33. reshape
  34. order
  35. sort
  36. cbind/rbind
  37. lm
  38. nls
  39. optim
  40. unique
  41. sum
  42. cumsum
  43. diff
  44. setdiff
  45. intersect
  46. rnorm
  47. sample

Paper #19 - Natural light-gated anion channels: a family of microbial rhodopsins for advanced optogenetics

TitleNatural light-gated anion channels: a family of microbial rhodopsins for advanced optogenetics

Year: 2015

SummaryIn this paper, they're interested in finding new optical actuators for controlling the membrane polarization of the cell (and particularly neurons). they begin by investigated a class of class of rhodopsins from cryptophytes, as opposed to previous channelrhodopsins which have been obtained for chlorophytes (green algae). Cryptophytes are also algae, but in a different kingdom (chromalveolata) than green algae (archaeplastida), thus they're probably quite significantly diverged.

They focus very quickly and with little justification (probably not their fault, Science doesn't provide much space) on  Guillardia theta, a cryptophyte alga with a fully-sequenced genome. In this genome, there are 53 proteins sharing similiarity to microbial rhodopsins.

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Paper #18 - A neuropeptide-mediate stretch response links muscle contraction to changes in neurotransmitter release

TitleA neuropeptide-mediate stretch response links muscle contraction to changes in neurotransmitter release

Year: 2011

SummaryC. elegans has a ton of neuropeptides (apparently 115 proneuropeptide genes for up to 250 mature peptides, many of which have been observed experimentally by mass spec). These neuropeptides are generally secreted extrasynaptically, and have been shown to modulate choline/acetylcholine release at neuromuscular junctions in C. elegans. In this paper, they want to know how neuropeptides can control synaptic plasticity.

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Paper #17 - Caenorhabditis elegans exhibit a coupling between the defecation motor program and directed locomotion

TitleCaenorhabditis elegans exhibit a coupling between the defecation motor program and directed locomotion

Year: 2015

Summary: This will be my second post I think that actually has nothing to do with neurons.

When worms defecate, they apparently have a very characteristic body pattern consisting first of posterior contraction (both dorsal and ventral), followed by anterior contraction (again, both dorsal and ventral) followed by expulsion. Subdividing this process into these three steps (called pBoc, aBoc and Exp) goes back to at least (Thomas, Genetics, 1990). In this paper, they refer to this as the defecation motor program (DMP).

This process occurs via a calcium wave that starts in the posterior intestinal cells and propagates via innexins to the anterior intestinal cells. I have some questions about this* but I'll hold off on them for now.  The calcium influx into these intestinal cells induces pumping protons from the intestinal cells into the pseucoelomic space and acidifying it. Body wall muscles then respond to this acidication via proton-gated ion channels (PBO-5/6) and contract.

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My rules for good figures

Abstractly:

  • Put the labels as close to the data as possible.
  • When possible, reuse as much of the plot format as possible

More concretely:

  • For scale bars on images, it doesn't hurt to put text right next to the bar, telling your readers what the scale bar actually means (so that they don't have to go to the legend to find out that bar is 100um).
  • Putting the sample size directly on your plots is helpful (rather than in legends).
  • Bar plots with numeric values on the x-axis are almost never the best way to show the information - numeric variables demand quantitative plotting!
  • Axis labels are essential, and they need to be be as clear as possible about two things: 1) what was measured, and b) what that measurement should be interpreted as.
    • labels like 'Fraction' or 'Count' are generally not very helpful.

As always, suggestions welcome! I will update this list as I think of more things (and read more papers!).

Paper #16 - Dissecting a central flip-flop circuit that integrates contradictory sensory cues in C. elegans feeding regulation

TitleDissecting a central flip-flop circuit that integrates contradictory sensory cues in C. elegans feeding regulation

Year: 2012

Summary:

In this paper, they sought to understand how C. elegans controls its pharyngeal pumping ('feeding') behavior in response to attractive and repulsive chemical stimuli. They use diacetyl as an attractive stimulus, and quinine or high concentrations of isoamyl alcohol as repulsive stimuli.

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