Kopp Lab

An evolutionary & developmental biology lab

Month: April 2012 (Page 1 of 2)

Cell type–specific chromatin immunoprecipitation

Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

This is based on FACS sorting of cells from formaldehyde-fixed tissues.  Not easily applicable to a lot of our questions, but there are cases where it may be useful.

Single-cell RNA sequencing protocol

Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing


Sex determination

Tony Gamble and David Zarkower have a nice primer on sex determination in Current Biology.

A program for picking probes for RNA in situs

As you all know, getting good in situs is a pain in the butt.  One problem is the difficulty in finding the optimal probe.  Here is a paper from Bill McGinnis’ lab that looks at some of the issues affecting probe quality, and a program that helps you pick the best in situ probes.


Fluorescent in situ hybridization (FISH) techniques are becoming extremely sensitive, to the point where individual RNA or DNA molecules can be detected with small probes. At this level of sensitivity, the elimination of ‘off-target’ hybridization is of crucial importance, but typical probes used for RNA and DNA FISH contain sequences repeated elsewhere in the genome. We find that very short (e.g. 20 nt) perfect repeated sequences within much longer probes (e.g. 350-1500 nt) can produce significant off-target signals. The extent of noise is surprising given the long length of the probes and the short length of non-specific regions. When we removed the small regions of repeated sequence from either short or long probes, we find that the signal-to-noise ratio is increased by orders of magnitude, putting us in a regime where fluorescent signals can be considered to be a quantitative measure of target transcript numbers. As the majority of genes in complex organisms contain repeated k-mers, we provide genome-wide annotations of k-mer-uniqueness at http://cbio.mskcc.org/ approximately aarvey/repeatmap.

Optimized transgenic constructs for ectopic protein expression

Here’s a recent paper in PNAS that looks at the use of viral 5′ and 3′ UTRs to enhance gene expression from UAS trangenes.  They show that using particular viral and other heterospecific UTRs can seriously increase protein abundance, and thus give stronger phenotypes.

These tricks are worth considering if you are making UAS or Lex constructs for ectopic geen expression.  More immediately, the enhanced UAS-shi[ts] construct they made can be useful for some of your neuronal silencing experiments.

Quote: “In this report, we demonstrate that sequences derived from the 5′-UTR and 3′-UTR of viral mRNAs, as well as from the abundantly expressed lobster tropomyosin gene (35), are able to function in Drosophila to enhance protein production. By using 5′- and 3′-UTR elements in combination, increases of >20-fold have been achieved, allowing single transgenes to achieve protein expression levels that previously required multiple transgenes, thereby greatly facilitating genetic strain construction. We also show that the 3′-UTR from the Autographa californica nuclear polyhedrosis virus (AcNPV) p10 gene functions efficiently in the female germline. “

Pam receives college Citation for Outstanding Performance in Genetics

Hey everybody – Pam has just received the College of Biological Sciences Citation for Outstanding Performance in Genetics.  These citations “are awarded to students who have achieved academic excellence in their majors and who have participated in an independent research project”.

The CBS annual Honors and Citation Awards Ceremony will be held in the Ballroom in the UC Davis Conference Center on Friday, June 1st, 2012.

Evolution of pigmentation in beach mice

There’s a paper from Hopi Hoekstra’s lab coming out in Evolution, where they look at the genetics of pigmentation in their favorite oldfield/beach mouse populations. The main point of the paper is a comparison between population history estimated from multi-locus data and the phylogeny of the causative gene that causes color variation.  In addition, take a look at the methods – see how they used a combination of sequence capture and barcoding to sequence several thousand random loci as well as a very large region surrounding Mc1R.

Performance comparison of benchtop high-throughput sequencing platforms

A recent paper in Nature Biotechnology has a performance comparison of benchtop high-throughput sequencing platforms.  These “small-scale” (hundreds of megabases to a few gigabases) machines will probably be increasingly prevalent, and useful for our kind of work, so check it out.

Undergraduate research conference

This year, Daniel and Nancy are giving talks, and Emmanuel, George, Lisa, and Margaret are presenting posters at the UC-Davis Undergraduate Research Conference.  They will be describing their recent work on subjects that include sex-specific neural circuits, cell motility, evolution of alternative splicing, tissue-specific transcriptome analysis, and ecological innovations.  Here is the time and place:

Poster Presentations • Friday, April 27, 2012 • Freeborn Hall • 3 – 5:30 p.m.
Oral Presentations • Saturday, April 28, 2012 • Wellman Hall • 9:00 a.m. – 12:30 p.m.

See here for more details

Happy DNA Day!

Everyone! Today April 20, 2012 is national DNA day!

Read more about its history on Wikipedia.

See the cool activities held today to promote education.

Celebrate well (like, by making some themed jewelry or something)!

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