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.
Here is a couple of recent papers on transposome-mediated construction of sequencing libraries:
Transposase mediated construction of RNA-seq libraries
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.
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:
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!
It always bugged me that so little was known about the evolutionary and ecological context of the C. elegans model system. Why haven’t these worms become a model of speciation or ecological adaptation? Compared to Drosophila, evolutionary biologists were slow to take them up. The situation has been getting much better recently, with some really good evo-devo and evolutionary genetics studies coming out in the last few year. Now, this paper should really expand the scope and power of comparative studies:
A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits
It describes a field survey of Caenorhabditis population and characterization of lots of new species – their phylogeny, reproductive isolation, phenotypic differences, etc. This should be really exciting for worm people and even, vicariously, for me.
The genome of the spider mite, Tetranychus, is finally published:
The genome of Tetranychus urticae reveals herbivorous pest adaptations
We now have three complete mite genomes. With these plus Daphnia (and more chelicerates, crustaceans, and myriapods on the way), it will be easier to look at the evolution of insect-specific features. Have fun!
As we think about the evolution of enhancers that their role in the evolution of phenotypes, defining the boundaries of the functionally and evolutionarily relevant CREs is one important question (see previous post). Another question/danger/caveat is the potential presence of redundant enhancers contributing to gene expression in the same tissue or organ – the so-called shadow enhancers. In such cases, evolution can modify any or all of these enhancers to change the phenotype. The danger is that any enhancer you identify, even if it is behaving as you expect, may only be telling you part of the story.
In this paper, Scott Barolo, an enhancer-bashing enthusiast and guru, gives a nice overview of shadow enhancers:
Check it out.
Powered by WordPress & Theme by Anders Norén