Category: Research Blog Page 6 of 7

Here is the story that Felicity Jones talked about last year:

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

Most of it is probably not “real” convergence from the genetic point of view, but the result of parallel selective sweeps acting on the same standing variation.  It’s a really nice systematic analysis.

This might be useful for enhancer analysis, if our current vectors misbehave for some reason:

Drosophila Reporter Vectors Compatible with ΦC31 Integrase Transgenesis Techniques and Their Use to Generate New Notch Reporter Fly Lines

They have GFP, mCherry, and YFP versions.  The polylinker is smallish though – a common problem.  The promoter is hsp70.

If you are thinking of doing a comparative ChIP study in different species, genotypes, or cell types, take a look at this paper:

A computational pipeline for comparative ChIP-seq analyses

It deals specifically with the issues and solutions for comparative analysis, which most ChIP papers do not address.

Here is a nice review paper in the last issue of Nature Methods:

Power tools for gene expression and clonal analysis in Drosophila

It will give you a good introduction to the recent developments in Drosophila transgenic techniques, but the main emphasis is on clonal analysis techniques.

Lots of other good stuff in this issue of Nature Methods, including several papers on the use of gene-editing nucleases.

Gene-editing nucleases

Here is a couple of recent papers on transposome-mediated construction of sequencing libraries:

Transposase mediated construction of RNA-seq libraries

Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA

Transposase-based methods are much more efficient than the traditional fragmentation/end-repair/tailing/ligation approach.  With fewer enzymatic and purification steps, template losses are greatly reduced and small-volume handling is easier, allowing you to use a lot less template.  I think there is already at least one transposome-based kit for making sequencing libraries, and I am sure more are coming in the near future.

Evolution of Insect Olfaction

Neuroethology utilizes a wide range of multidisciplinary approaches to decipher neural correlates of natural behaviors associated with an animal’s ecological niche. By placing emphasis on comparative analyses of adaptive and evolutionary trends across species, a neuroethological perspective is uniquely suited to uncovering general organizational and biological principles that shape the function and anatomy of the nervous system. In this review, we focus on the application of neuroethological principles in the study of insect olfaction and discuss how ecological environment and other selective pressures influence the development of insect olfactory neurobiology, not only informing our understanding of olfactory evolution but also providing broader insights into sensory processing.

Here’s a very interesting butterfly paper where they leveraged evolutionary genetic and evo-devo data to look at the history of phenotypes and populations:

Wing patterning gene redefines the mimetic history of Heliconius butterflies

Population phylogeny based on neutral markers is a mess and reflects geography more than history due to episodes of hybridization.  On the other, phylogeny based on the gene responsible for part of the wing color pattern reveals the evolutionary history of that phenotype.  This should be true in a lot of cases – the best way to understand the evolution of phenotypes is to identify the genetic changes responsible for those phenotypes.  Mapping phenotypic characters on trees constructed from random loci will not always give you the true answer.  All the more reason to go after the causative genes!

This sounds great – will make it much easier to select the right pupae for dissection.  Here is the paper:

Tubby-tagged balancers for the Drosophila X and second chromosomes

We generated FM7a and CyO balancer chromosomes bearing a Tubby1 (Tb1) dominant transgene. Flies heterozygous for these FM7a and CyO derivatives exhibit a phenotype undistinguishable from that elicited by the Tb1 mutation associated with the TM6B balancer. We tested two of these Tb-bearing balancers (FM7-TbA and CyO-TbA) for more than 30 generations and found that the Tb1 transgene they carry is stable. Thus, these new Tb-tagged balancers are particularly useful for balancing lethal mutations and distinguish homozygous mutant larvae from their heterozygous siblings.

Several papers in Nature Methods describe high-throughput yeast one-hybrid screens and their integration with ChIP to characterize transcriptional networks:

Exciting times: bountiful data to facilitate studies of cis-regulatory control

Automated protein-DNA interaction screening of Drosophila regulatory elements

Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping

Yeast one-hybrid assays for gene-centered human gene regulatory network mapping

Here’s a perspective on the use of kits in molecular biology that I agree wholeheartedly with:

Training the kit generation

You guys know my anti-kit bias. They are great, and they save a lot of time and troubleshooting, but you REALLY have to understand how they work!