Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis

Background\ud DNA methylation is an epigenetic mechanism associated with regulation of gene expression and it is modulated during chemical carcinogenesis. The zebrafish is increasingly employed as a human disease model; however there is a lack of information on DNA methylation in zebrafish and during fish tumorigenesis. \ud \ud Results\ud A novel CpG island tiling array containing 44,000 probes, in combination with immunoprecipitation of methylated DNA, was used to achieve the first comprehensive methylation profiling of normal adult zebrafish liver. DNA methylation alterations were detected in zebrafish liver tumors induced by the environmental carcinogen 7, 12-dimethylbenz(a)anthracene. Genes significantly hypomethylated in tumors were associated particularly with proliferation, glycolysis, transcription, cell cycle, apoptosis, growth and metastasis. Hypermethylated genes included those associated with anti-angiogenesis and cellular adhesion. Of 49 genes that were altered in expression within tumors, and which also had appropriate CpG islands and were co-represented on the tiling array, approximately 45% showed significant changes in both gene expression and methylation. \ud \ud Conclusion\ud The functional pathways containing differentially methylated genes in zebrafish hepatocellular carcinoma have also been reported to be aberrantly methylated during tumorigenesis in humans. These findings increase the confidence in the use of zebrafish as a model for human cancer in addition to providing the first comprehensive mapping of DNA methylation in the normal adult zebrafish liver. \ud \u

Probing the connectivity of neural circuits at single-neuron resolution using high-throughput DNA sequencing

There is growing excitement in determining the complete connectivity diagram of the brain—the "connectome". So far, the complete connectome has been established for only one organism, C. elegans, with 302 neurons connected by about 7000 synapses—and even this was a heroic task, requiring over 50 person-years of labor. Like all current approaches, this reconstruction was based on microscopy. Unfortunately, microscopy is poorly suited to the study of neural connectivity because brains are macroscopic structures, whereas synapses are microscopic. Nevertheless, there are several large-scale projects underway to scale up high-throughput microscopic approaches to the connectome.
Here we present a completely novel method for determining the brain's wiring diagram based on high-throughput DNA sequencing technology, which has not previously been applied in the context of neural connectivity. The appeal of using sequencing is that it is getting faster and cheaper exponentially: it will soon be routine to sequence an entire human genome (~3B nucleotides) within one day for $1000.
Our approach has three main components. First, we express a unique sequence of nucleotides—a DNA "barcode"—in individual neurons. A barcode consisting of a random string of even 30 nucleotides can uniquely label 10^{18} neurons, far more than the number of neurons in a mouse brain (fewer than 100 million). Second, we use a specially engineered transsynaptic virus to transport “host” barcodes from one neuron to synaptically coupled partners; after transsynaptic spread, each neuron contains copies of "invader" barcodes from other synaptically coupled neurons, as well its own "host" barcode. Third, we join pairs of host and invader barcodes into single pieces of DNA suitable for high-throughput sequencing. 
Modern sequencing technology could in principle yield the connectivity diagram of the entire mouse brain. Similar approaches can be applied to Drosophila and C. elegans. 
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Microstructural and functional impairment of the basal ganglia in Wilson’s disease: a multimodal neuroimaging study

ObjectivesMagnetic susceptibility changes in brain MRI of Wilson’s disease (WD) patients have been described in subcortical nuclei especially the basal ganglia. The objectives of this study were to investigate its relationship with other microstructural and functional alterations of the subcortical nuclei and the diagnostic utility of these MRI-related metrics.MethodsA total of 22 WD patients and 20 healthy controls (HCs) underwent 3.0T multimodal MRI scanning. Susceptibility, volume, diffusion microstructural indices and whole-brain functional connectivity of the putamen (PU), globus pallidus (GP), caudate nucleus (CN), and thalamus (TH) were analyzed. Receiver operating curve (ROC) was applied to evaluate the diagnostic value of the imaging data. Correlation analysis was performed to explore the connection between susceptibility change and microstructure and functional impairment of WD and screen for neuroimaging biomarkers of disease severity.ResultsWilson’s disease patients demonstrated increased susceptibility in the PU, GP, and TH, and widespread atrophy and microstructural impairments in the PU, GP, CN, and TH. Functional connectivity decreased within the basal ganglia and increased between the PU and cortex. The ROC model showed higher diagnostic value of isotropic volume fraction (ISOVF, in the neurite orientation dispersion and density imaging model) compared with susceptibility. Severity of neurological symptoms was correlated with volume and ISOVF. Susceptibility was positively correlated with ISOVF in GP.ConclusionMicrostructural impairment of the basal ganglia is related to excessive metal accumulation in WD. Brain atrophy and microstructural impairments are useful neuroimaging biomarkers for the neurological impairment of WD

Cellular anatomy of the mouse primary motor cortex.

An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input-output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture

Establishment of transgenic zebrafish model for liver cancer studies

Ph.DDOCTOR OF PHILOSOPH

Puerarin protects renal ischemia-reperfusion injury in rats through NLRP3/Caspase-1/GSDMD pathway

ABSTRACT Purpose: To observe the effect of puerarin on renal ischemia-reperfusion (I/R) injury in rats, and to explore its mechanism based on NLRP3/Caspase-1/GSDMD pathway. Methods: Twenty-one Sprague-Dawley rats were divided into three groups: sham-operated group (sham), model group (RIRI), and puerarin treatment group (RIRI + Pue). The model of acute renal I/R injury was established by cutting the right kidney and clamping the left renal pedicle for 45 min. Results: Renal function parameters were statistically significant in group comparisons. The renal tissue structure of rats in sham group was basically normal. Pathological changes were observed in the RIRI group. The renal pathological damage score and apoptosis rate in the RIRI group were higher than those in the sham group, and significantly lower in the RIRI + Pue group than in the RIRI group. Indicators of oxidative stress–superoxide dismutase, malondialdehyde, and glutathione peroxidase–were statistically significant in group comparisons. Compared with the sham group, the relative expressions of NLRP3, Caspase-1 and GSDMD proteins in the RIRI group were increased. Compared with the RIRI group, the RIRI + Pue group had significant reductions. Conclusions: Puerarin can inhibit the activation of NLRP3/Caspase-1/GSDMD pathway, inhibit inflammatory response and pyroptosis, and enhance the antioxidant capacity of kidney, thereby protecting renal I/R injury in rats

A comparative study between AI-HM and SPD-HM for railway auxiliary inverter with pulsating DC-Link

High frequency isolated dc–ac converters are becoming popular in on-board auxiliary inverters for railway applications. Compared to conventional fixed dc-link inverter (FDCLI), pulse dc-link inverter (PDCLI) has simpler circuit topology and higher power density, but greatly different control algorithm. This paper is going to study the application possibility of PDCLI for railway auxiliary inverter, and will be concerned with algorithm and their performance comparison between approximately independent hybrid modulation (AI-HM) and six-pulse demodulation hybrid modulation for PDCLIs, including fundamental principle and harmonic performance of output voltage under zero portion effect. Then a piecewise compensation of modulation wave and a carrier phase-shift strategy are proposed to improve the output voltage quality of AI-HM under zero portion effect. The simulation and experimental results, as well as the output filter parameter comparison are provided to verify the theoretical analysis and the feasibility of the proposed strategies