Kismeth: Analyzer of plant methylation states through bisulfite sequencing

<p>Abstract</p> <p>Background</p> <p>There is great interest in probing the temporal and spatial patterns of cytosine methylation states in genomes of a variety of organisms. It is hoped that this will shed light on the biological roles of DNA methylation in the epigenetic control of gene expression. Bisulfite sequencing refers to the treatment of isolated DNA with sodium bisulfite to convert unmethylated cytosine to uracil, with PCR converting the uracil to thymidine followed by sequencing of the resultant DNA to detect DNA methylation. For the study of DNA methylation, plants provide an excellent model system, since they can tolerate major changes in their DNA methylation patterns and have long been studied for the effects of DNA methylation on transposons and epimutations. However, in contrast to the situation in animals, there aren't many tools that analyze bisulfite data in plants, which can exhibit methylation of cytosines in a variety of sequence contexts (CG, CHG, and CHH).</p> <p>Results</p> <p>Kismeth <url>http://katahdin.mssm.edu/kismeth</url> is a web-based tool for bisulfite sequencing analysis. Kismeth was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species.</p> <p>Conclusion</p> <p>Kismeth simplifies bisulfite sequencing analysis. It is the only publicly available tool for the design of bisulfite primers for plants, and one of the few tools for the analysis of methylation patterns in plants. It facilitates analysis at both global and local scales, demonstrated in the examples cited in the text, allowing dissection of the genetic pathways involved in DNA methylation. Kismeth can also be used to study methylation states in different tissues and disease cells compared to a reference sequence.</p

Integration of the olfactory code across dendritic claws of single mushroom body neurons. Nature Neuroscience 16:1821–1829. doi: 10.1038/nn.3547

nature neurOSCIenCe advance online publication a r t I C l e S The olfactory system of Drosophila is an excellent platform for studying how sensory information is transformed as it passes through the successive layers of a neural circuit. Although the fly olfactory circuit is organized similarly to more complex organisms, it is numerically simpler and has been mapped with cellular resolution. Sensory input comes in from a large set of olfactory receptor neurons (ORNs), each of which has a particular chemical sensitivity 1,2 . These inputs are organized into distinct channels in the antennal lobe, as ORNs that express the same type of olfactory receptor converge to form synapses with a cognate set of projection neurons in structures termed glomeruli 3 . There are 54 different glomerular channels that have been identified in Drosophila 4 , and the constellation of different physiochemical features in an odor evokes widely distributed patterns of activity across these channels. In Drosophila, the main transformations at the first synapse in the circuit are noise reduction and gain control The transformation from the projection neurons to the mushroom body is of particular interest, as the mushroom body is essential for olfactory learning and memory Projection neuron-Kenyon cell synapses are remarkable structures. They are among the largest synapses in the Drosophila brain and have a striking morphology The unusual morphology of projection neuron-Kenyon cell connections presents us with the opportunity to investigate the response properties of individual synaptic sites from a functional perspective. First, using in vivo dendritic imaging, we directly examined the odor response properties of individual synaptic sites. This approach enabled us to determine whether functionally distinct inputs converge onto individual Kenyon cells. Second, to understand how Kenyon cells integrate synaptic input, we used optogenetic methods to provide precisely controlled input to the claws and intracellular recordings to examine the postsynaptic response. The large size of projection In the olfactory system, sensory inputs are arranged in different glomerular channels, which respond in combinatorial ensembles to the various chemical features of an odor. We investigated where and how this combinatorial code is read out deeper in the brain. We exploited the unique morphology of neurons in the Drosophila mushroom body, which receive input on large dendritic claws. Imaging odor responses of these dendritic claws revealed that input channels with distinct odor tuning converge on individual mushroom body neurons. We determined how these inputs interact to drive the cell to spike threshold using intracellular recordings to examine mushroom body responses to optogenetically controlled input. Our results provide an elegant explanation for the characteristic selectivity of mushroom body neurons: these cells receive different types of input and require those inputs to be coactive to spike. These results establish the mushroom body as an important site of integration in the fly olfactory system

Integration of the olfactory code across dendritic claws of single mushroom body neurons

In the olfactory system, sensory inputs are arranged in different glomerular channels, which respond in combinatorial ensembles to the various chemical features of an odor. We investigated where and how this combinatorial code is read out deeper in the brain. We exploited the unique morphology of neurons in the Drosophila mushroom body, which receive input on large dendritic claws. Imaging odor responses of these dendritic claws revealed that input channels with distinct odor tuning converge on individual mushroom body neurons. We determined how these inputs interact to drive the cell to spike threshold using intracellular recordings to examine mushroom body responses to optogenetically controlled input. Our results provide an elegant explanation for the characteristic selectivity of mushroom body neurons: these cells receive different types of input and require those inputs to be coactive to spike. These results establish the mushroom body as an important site of integration in the fly olfactory system