Comprehensive characterization of a time-course transcriptional response induced by autotoxins in Panax ginseng using RNA-Seq

The lists for all the differentially expressed genes. (XLS 1362 kb

The genetic architecture of DNA replication timing in human pluripotent stem cells.

DNA replication follows a strict spatiotemporal program that intersects with chromatin structure but has a poorly understood genetic basis. To systematically identify genetic regulators of replication timing, we exploited inter-individual variation in human pluripotent stem cells from 349 individuals. We show that the human genome's replication program is broadly encoded in DNA and identify 1,617 cis-acting replication timing quantitative trait loci (rtQTLs) - sequence determinants of replication initiation. rtQTLs function individually, or in combinations of proximal and distal regulators, and are enriched at sites of histone H3 trimethylation of lysines 4, 9, and 36 together with histone hyperacetylation. H3 trimethylation marks are individually repressive yet synergistically associate with early replication. We identify pluripotency-related transcription factors and boundary elements as positive and negative regulators of replication timing, respectively. Taken together, human replication timing is controlled by a multi-layered mechanism with dozens of effectors working combinatorially and following principles analogous to transcription regulation

THE GENETIC ARCHITECTURE OF HUMAN DNA REPLICATION TIMING

187 pagesEukaryotic DNA replication follows a strict spatiotemporal program, which intersects with gene regulation and shapes the mutational landscape. However, the genetic basis of the mammalian DNA replication timing program is poorly understood. In Chapter 2, I present an approach based on population genetics to study DNA replication timing in human cells. Specifically, I identify more than 1,500 replication timing quantitative trait loci (rtQTLs), i.e., genetic variants associated with inter-individual variation in DNA replication timing, in hundreds of human pluripotent stem cell lines. I reveal that a unique combination of histone modifications, composed of trimethylation on histone H3 lysines 4, 9 and 36, acetylation on H3 lysine 56, and histone hyperacetylation, shows enrichment at rtQTL locations. I further find that this unique “histone code” could predict locations of replication initiation in multiple human cell types, even for origins that are cell-type-specific. In addition, based on inter-individual variation in chromatin state, histone modification, and predicted transcription factor (TF) binding at rtQTLs in human embryonic stem cell lines, I identify positive (e.g., pluripotency-related TFs) and negative regulators (e.g., boundary elements) of DNA replication timing. I conclude that human DNA replication timing is controlled by a multi-layered mechanism that operates on target DNA sequences, is composed of dozens of effectors working combinatorially, and follows principles analogous to transcription regulation: a histone code, activators and repressors, and a promoter-enhancer logic. In Chapter 4, I present the first characterization of replication timing of the human Y chromosome and reveal a negative relationship between replication timing and mutation (both germline and within-cell-line, i.e., those mutations that arose somatically or during cell culture). Using within-cell-line mutation data from more than > 1,700 males, I uncover that mutation rate of the Y chromosome likely varies among human Y-chromosome haplogroups. Taken together, the findings presented in this thesis substantially improve our understanding into the causes and consequences of human DNA replication timing.2023-01-1

Growth Performance and Stress Responses of Larval Mississippi Paddlefish Polyodon spathula to Hypoxia under Different Diet Treatments

A growth trial was conducted to detect the effects of different diets on the growth performance and hypoxia adaptation capacity of Mississippi Paddlefish (Polyodon spathula) larvae. The larvae were fed with live food, formulated diets, and 1/2 live food with 1/2 formulated diets. After a 15-d growth trial, final body weight and total body length were measured, and five larvae from each dietary group were subjected to 1 h of hypoxia treatment. Serum total antioxidant capacity (T-AOC), serum superoxide dismutase (SOD), and liver malondialdehyde (MDA) were measured. Final body weight and weight gain of the fish fed live food were significantly higher than the values for the other two groups. Total body length of the fish fed live food and 1/2 live food with 1/2 formulated diets exhibited no significant difference. After hypoxia treatment, serum T-AOC and SOD activities of the fish fed formulated diets were significantly lower than those of the other two groups. Liver MDA content of the fish fed with live food was significantly higher than that of the other two groups. In conclusion, larval paddlefish fed with an appropriate proportion of live food and formulated diets exhibit improved adaptive capacity to hypoxia

Mechanical Properties of 6061 Aluminum Alloy under Cyclic Tensile Loading

During the service process of an aluminum alloy structure, its complex deformation zone experiences repeated loading problems such as repeated tension, compression, bending and reverse bending. At the same time, the cyclic loading and heat treatment process also have a certain impact on the mechanical properties of aluminum alloy extruded tubes. Therefore, the study of heat treatment process parameters has important engineering and practical value for the mechanical properties of aluminum alloy extrusion tubes under cyclic loading conditions. The experiment takes 6061-T6 aluminum alloy extruded tubes as the research objects. In the study, heat treatment and cyclic tensile tests were carried out on 26 aluminum alloy specimens to study the effects of different heat treatment parameters (such as heating temperature, holding time, and cooling method) on the stress–strain hysteresis curves, stress characteristics, hysteretic energy, skeleton curves and failure characteristics of the alloy under the same loading system. In addition, different cyclic tensile tests were carried out on 20 aluminum alloy samples without secondary heat treatment to discuss the effects of different cyclic loading regimes on the mechanical properties of the alloy. The research results indicate that the effect of heating temperature on the cyclic loading performance of the alloy is greater than that of the holding time, and the effect of the cooling method on the cyclic loading performance of the alloy is not obvious. A cyclic tensile loading regime has a significant impact on the strength, elongation and hysteresis energy of the alloy. The hysteretic behavior of the alloy during cyclic tensile loading depends on the applied stress level and loading history. As the number of cycles increases, the shape of the hysteresis curve tends to be stable, but there is no monotonic relationship between the number of cycles loaded and the hysteresis energy

Synthesis of Flexible Aerogel Composites Reinforced with Electrospun Nanofibers and Microparticles for Thermal Insulation

Flexible silica aerogel composites in intact monolith of 12 cm were successfully fabricated by reinforcing SiO2 aerogel with electrospun polyvinylidene fluoride (PVDF) webs via electrospinning and sol-gel processing. Three electrospun PVDF webs with different microstructures (e.g., nanofibers, microparticles, and combined nanofibers and microparticles) were fabricated by regulating electrospinning parameters. The as-electrospun PVDF webs with various microstructures were impregnated into the silica sol to synthesize the PVDF/SiO2 composites followed by solvent exchange, surface modification, and drying at ambient atmosphere. The morphologies of the PVDF/SiO2 aerogel composites were characterized and the thermal and mechanical properties were measured. The effects of electrospun PVDF on the thermal and mechanical properties of the aerogel composites were evaluated. The aerogel composites reinforced with electrospun PVDF nanofibers showed intact monolith, improved strength, and perfect flexibility and hydrophobicity. Moreover, the aerogel composites reinforced with the electrospun PVDF nanofibers had the lowest thermal conductivity (0.028 W·m−1·K−1). It indicates that the electrospun PVDF nanofibers could greatly improve the mechanical strength and flexibility of the SiO2 aerogels while maintaining a lower thermal conductivity, which provides increasing potential for thermal insulation applications

Flammeovirga pacifica sp nov, isolated from deep-sea sediment

China Ocean Mineral Resources R D Association [DY115-02-2-04]; Hi-Tech Research and Development of China [2007AA091407]; Marine Scientific Research Special Foundation [200805050]Strain WPAGA1(T) was isolated from marine sediment of the west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Flammeovirga. Strain WPAGA1(T) exhibited highest 16S rRNA gene sequence similarity with Flammeovirga yaeyamensis NBRC 100898(T) (98.1%) and lower sequence similarity with Flammeovirga arenaria IFO 15982(T) (94.6%) and other members of the genus Flammeovirga (<94.2%). DNA DNA relatedness studies showed that strain WPAGA1(T) was distinct from F. yaeyamensis NBRC 100898(T) and F. arenaria NBRC 15982(T) (43 +/- 4% and 32 +/- 2% relatedness values, respectively). Strain WPAGA1(T) could be distinguished from all known members of the genus Flammeovirga by a number of phenotypic features. However, the dominant fatty acids of strain WPAGA1(T) (iso-C-15:0, C-16:0 and C-20:4 omega 6,9,12,15c), the major polyamine (cadaverine) and the G+C content of the chromosomal DNA (32.9 mol%) were consistent with those of members of the genus Flammeovirga. Based on phenotypic and chemotaxonomic features and 16S rRNA gene sequences, strain WPAGA1(T) can be assigned to the genus Flammeovirga as a representative of a novel species, for which the name Flammeovirga pacifica sp. nov. is proposed; the type strain is WPAGA1(T) (=CCTCC AB 2010364(T)=LMG 26175(T)=DSM 24597(T)=MCCC 1A06425(T))

Illuminating the Live-Cell Dynamics of Hepatitis B Virus Covalently Closed Circular DNA Using the CRISPR-Tag System

ABSTRACT The covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) is the major obstacle to curing chronic hepatitis B (CHB). Current cccDNA detection methods are mostly based on biochemical extraction and bulk measurements. They nevertheless generated a general sketch of its biological features. However, an understanding of the spatiotemporal features of cccDNA is still lacking. To achieve this, we established a system combining CRISPR-Tag and recombinant HBV minicircle technology to visualize cccDNA at single-cell level in real time. Using this system, we found that the observed recombinant cccDNA (rcccDNA) correlated quantitatively with its active transcripts when a low to medium number of foci (<20) are present, but this correlation was lost in cells harboring high copy numbers (≥20) of rcccDNA. The disruption of HBx expression seems to displace cccDNA from the dCas9-accessible region, while HBx complementation restored the number of observable cccDNA foci. This indicated regulation of cccDNA accessibility by HBx. Second, observable HBV and duck HBV (DHBV) cccDNA molecules are substantially lost during cell division, and the remaining ones were distributed randomly to daughter cells. In contrast, Kaposi's sarcoma-associated herpesvirus (KSHV)-derived episomes can be retained in a LANA (latency-associated nuclear antigen)-dependent manner. Last, the dynamics of rcccDNA episomes in nuclei displayed confined diffusion at short time scales, with directional transport over longer time scales. In conclusion, this system enables the study of physiological kinetics of cccDNA at the single-cell level. The differential accessibility of rcccDNA to dCas9 under various physiological conditions may be exploited to elucidate the complex transcriptional and epigenetic regulation of the HBV minichromosome. IMPORTANCE Understanding the formation and maintenance of HBV cccDNA has always been a central issue in the study of HBV pathobiology. However, little progress has been made due to the lack of robust assay systems and its resistance to genetic modification. Here, a live-cell imaging system by grafting CRISPR-Tag into the recombinant cccDNA was established to visualize its molecular behavior in real time. We found that the accessibility of rcccDNA to dCas9-based imaging is related to HBx-regulated mechanisms. We also confirmed the substantial loss of observable rcccDNA in one-round cell division and random distribution of the remaining molecules. Molecular dynamics analysis revealed the confined movement of the rcccDNA episome, suggesting its juxtaposition to chromatin domains. Overall, this novel system offers a unique platform to investigate the intranuclear dynamics of cccDNA within live cells