Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing

<p>Abstract</p> <p>Background</p> <p>Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.</p> <p>Results</p> <p>Pash 3.0 generally matches the accuracy and speed of niche programs for fast mapping of short reads, and exceeds their performance on longer reads generated by a new generation of massively parallel sequencing technologies. By exploiting longer read lengths, Pash 3.0 maps reads onto the large fraction of genomic DNA that contains repetitive elements and polymorphic sites, including indel polymorphisms.</p> <p>Conclusions</p> <p>We demonstrate the versatility of Pash 3.0 by analyzing the interaction between CpG methylation, CpG SNPs, and imprinting based on publicly available whole-genome shotgun bisulfite sequencing data. Pash 3.0 makes use of gapped k-mer alignment, a non-seed based comparison method, which is implemented using multi-positional hash tables. This allows Pash 3.0 to run on diverse hardware platforms, including individual computers with standard RAM capacity, multi-core hardware architectures and large clusters.</p

VaBUS: Edge-Cloud Real-Time Video Analytics via Background Understanding and Subtraction

Edge-cloud collaborative video analytics is transforming the way data is being handled, processed, and transmitted from the ever-growing number of surveillance cameras around the world. To avoid wasting limited bandwidth on unrelated content transmission, existing video analytics solutions usually perform temporal or spatial filtering to realize aggressive compression of irrelevant pixels. However, most of them work in a context-agnostic way while being oblivious to the circumstances where the video content is happening and the context-dependent characteristics under the hood. In this work, we propose VaBUS, a real-time video analytics system that leverages the rich contextual information of surveillance cameras to reduce bandwidth consumption for semantic compression. As a task-oriented communication system, VaBUS dynamically maintains the background image of the video on the edge with minimal system overhead and sends only highly confident Region of Interests (RoIs) to the cloud through adaptive weighting and encoding. With a lightweight experience-driven learning module, VaBUS is able to achieve high offline inference accuracy even when network congestion occurs. Experimental results show that VaBUS reduces bandwidth consumption by 25.0%-76.9% while achieving 90.7% accuracy for both the object detection and human keypoint detection tasks

Data from: Evolutionary suppression of erythropoiesis via the modulation of TGF-β signaling in an Antarctic icefish

The Antarctic icefish, a family (Channichthyidae) of teleosts within the perciform suborder Notothenioidei, are the only known vertebrates without oxygen-transporting haemoglobins and that are largely devoid of circulating erythrocytes. To elucidate the evo-devo mechanisms underpinning the suppressed erythropoiesis in the icefish, we conducted comparative studies on the transcriptomes and microRNAomes of the primary haematopoietic tissues between an icefish (Chionodraco hamatus) and two red-blooded notothenioids (Trematomus bernacchii and Gymnodraco acuticeps). We identified substantial remodelling of the haematopoietic programs in the icefish through which erythropoiesis is selectively suppressed. Experimental verification showed that erythropoietic suppression in the icefish may be attributable to the upregulation of TGF-β signalling, which coincides with reductions in multiple transcription factors essential for erythropoiesis and the upregulation of hundreds of microRNAs, the majority (> 80%) of which potentially target erythropoiesis regulating factors. Of the six microRNAs selected for verification, three miRNAs (miR-152, miR-1388 and miR-16b) demonstrated suppressive functions on GATA1 and ALAS2, which are two factors important for erythroid differentiation, resulting in reduced numbers of erythroids in microinjected zebra fish embryos. Codon substitution analyses of the genes of the TGF-β superfamily revealed signs of positive selection in TGF-β1 and endoglin in the lineages leading to Antarctic notothenioids. Both genes are previously known to function in erythropoietic suppression. These findings implied a general trend of erythropoietic suppression in the cold-adapted notothenioid lineages through evolutionary modulation of the multi-functional TGF-β signalling pathway. This trend is more pronounced in the haemoglobin-less icefish, which may pre-emptively hinder the otherwise defective erythroids from production

Variation of DNA Methylome of Zebrafish Cells under Cold Pressure

<div><p>DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure.</p></div

DNA methylation levels of different genomic regions under cold pressure.

<p>DNA methylation level of each genomic region from three samples (28°C, 18°C /5d, 18°C /30d) was shown as log2(RPKM+1). The RPKM value of each genomic region was compared as 18°C /5d vs 28°C, 18°C /30d vs 28°C and 18°C /30d vs 18°C /5d using T test. The corrected P values of FDR are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160358#pone.0160358.t001" target="_blank">Table 1</a>. CpG: CpG island; codexon: coding regions of exon; UP3k: regions within 3 kbs upstream gene; Down5k: regions within 5 kbs downstream gene; TSS 1k: regions within ±1 kb around transcription start site; LINE: long interspersed nuclear element; SINE: short interspersed nuclear element; Low complexity: low complexity DNA; Satellite: Satellite DNA; LTR: long terminal repeat.</p