Biology subjects

Song, Y.

Publications and source records attributed to Song, Y..

24 records · Page 2Linked to original sources

bioRxiv2017

Collaborations between CpG sites in DNA methylation

DNA methylation patterns have profound impacts on genome stability, gene expression, and development. The molecular base of DNA methylation patterns has long been focused at single CpG sites level. Here, we construct a kinetic model of DNA methylation with collaborations between CpG sites, from which a correlation function was established based on experimental data. The function consists of three parts that suggest three possible sources of the correlation: movement of enzymes along DNA, collaboration between DNA methylation and nucleosome modification, and global enzyme concentrations within a cell. Moreover, the collaboration strength between DNA methylation and nucleosome modification is universal for mouse early embryo cells. The obtained correlation function provide insightful understanding for the mechanisms of inheritance of DNA methylation patterns.

genetics↗

bioRxiv2017

Natural Chromatin Is Heterogeneous And Self Associates In Vitro

The 30-nm fiber is commonly found in oligonucleosome arrays in vitro but rarely found in chromatin within nuclei. To determine how chromatin high-order structure is controlled, we used cryo-ET to study the undigested natural chromatin released from cells that do not have evidence of 30-nm fibers in vivo: picoplankton and yeast. In the presence of divalent cations, most of the chromatin from both organisms is compacted into a large mass. Rare irregular 30-nm fibers do form at the periphery of this mass, some of which include face-to-face interactions. In the absence of divalent cations, picoplankton chromatin decondenses into open zigzags. By contrast, yeast chromatin mostly remains compact with looser nucleosome packing, even after treatment with histone-deacetylase inhibitor. The 3-D configuration of natural chromatin is therefore sensitive to the local environment, but generally nonpermissive of regular motifs, even at the level of oligonucleosomes.

cell biology↗

bioRxiv2017

Fundamental Constraints In Synchronous Muscle Limit Superfast Motor Control In Vertebrates

Superfast muscles (SFM) are extremely fast synchronous muscles capable of contraction rates up to 250 Hz, enabling precise motor execution at the millisecond time scale. To allow such speed, the archetypal SFM, found in the toadfish swimbladder, has hallmark structural and kinetic adaptations at each step of the conserved excitation-contraction coupling (ECC) pathway. More recently SFM phenotypes have been discovered in most major vertebrate lineages, but it remains unknown whether all SFM share ECC adaptations for speed, and if SFM arose once, or from independent evolutionary events. Here we use genomic analysis to identify the myosin heavy chain genes expressed in bat and songbird SFM to achieve rapid actomyosin crossbridge kinetics and demonstrate that these are evolutionarily and ontologically distinct. Furthermore, by quantifying cellular morphometry and calcium signal transduction combined with force measurements we show that all known SFM share multiple functional adaptations that minimize ECC transduction times. Our results suggest that SFM evolved independently in sound producing organs in ray-finned fish, birds, and mammals, and that SFM phenotypes operate at a maximum operational speed set by fundamental constraints in synchronous muscle. Consequentially, these constraints set a fundamental limit to the maximum speed of fine motor control.

physiology↗

bioRxiv2017

Automated 3D Neuron Tracing with Precise Branch Erasing and Confidence Controlled Back-Tracking

The automatic reconstruction of single neuron cells from microscopic images is essential to enabling large-scale data-driven investigations in neuron morphology research. However, few previous methods were able to generate satisfactory results automatically from 3D microscopic images without human intervention. In this study, we developed a new algorithm for automatic 3D neuron reconstruction. The main idea of the proposed algorithm is to iteratively track backwards from the potential neuronal termini to the soma centre. An online confidence score is computed to decide if a tracing iteration should be stopped and discarded from the final reconstruction. The performance improvements comparing to the previous methods are mainly introduced by a more accurate estimation of the traced area and the confidence controlled back-tracking algorithm. The proposed algorithm supports large-scale batch-processing by requiring only one hyper-parameter for background segmentation. We bench-tested the proposed algorithm on the images obtained from both the DIADEM challenge and the BigNeuron challenge. Our proposed algorithm achieved the state-of-the-art results.

neuroscience↗

bioRxiv2017

Tomato immune receptor Ve1 recognizes surface-exposed co-localized N- and C-termini of Verticillium dahliae effector Ave1

Effectors are secreted by plant pathogens to facilitate infection, often through deregulation of host immune responses. During host colonization, race 1 strains of the soil-borne vascular wilt fungus Verticillium dahliae secrete the effector protein Ave1 that triggers immunity in tomato genotypes that encode the Ve1 immune receptor. Homologs of V. dahliae Ave1 (VdAve1) are found in plants and in few plant pathogenic microbes, and are differentially recognized by Ve1. However, how VdAve1 is recognized by Ve1 remained unknown. Interestingly, C-terminally affinity-tagged versions of VdAve1 failed to activate Ve1-mediated immunity, suggesting that exposure of the C-terminus of VdAve1 is required for Ve1-mediated recognition. This was confirmed by subsequent analysis of C-terminal deletion mutants, and by domain swap experiments. Although required, only the C-terminus of VdAve1 is not sufficient to activate Ve1-mediated immunity. Intriguingly, a three-dimensional structural model of VdAve1 revealed that the N- and C-termini co-localize on a surface-exposed patch of the VdAve1 protein. Indeed, subsequent analyses of N-terminal deletion mutants confirmed that also the N-terminus of VdAve1 is required to activate Ve1-mediated immunity. Thus, we conclude that a surface-exposed patch of the VdAve1 protein that is composed by co-localized N- and C-termini is recognized by the tomato immune receptor Ve1.

plant biology↗

bioRxiv2016

Evolutionary history of the brown rat: out of southern East Asia and selection

The brown rat (Rattus norvegicus) is found wherever humans live and transmits many diseases, and its breeding produced the laboratory rat used widely in medical research. Here, we sequenced whole genomes from 118 rats to explore the origin and dispersal routes of the brown rat and the domestication of the laboratory rat. We showed that brown rats migrated about 3600 years ago from southern East Asia, rather than Northern Asia as formerly suggested, to the Middle East and then to Europe and Africa. Many genes involved in the immune system experienced positive selection in the wild brown rat, while genes involved in the nervous system and energy metabolism showed evidence of artificial selection during the domestication of laboratory strains. Our findings demystify the puzzling origin and migration of brown rats and reveal the impact of evolution and domestication on this animal.

evolutionary biology↗