Differential Expression Analysis of Olfactory Genes Based on a Combination of Sequencing Platforms and Behavioral Investigations in Aphidius gifuensis

Aphidius gifuensis Ashmead is a dominant endoparasitoid of aphids, such as Myzus persicae and Sitobion avenae, and plays an important role in controlling aphids in various habitats, including tobacco plants and wheat in China. A. gifuensis has been successfully applied for the biological control of aphids, especially M. persicae, in green houses and fields in China. The corresponding parasites, as well as its mate-searching behaviors, are subjects of considerable interest. Previous A. gifuensis transcriptome studies have relied on short-read next-generation sequencing (NGS), and the vast majority of the resulting isotigs do not represent full-length cDNA. Here, we employed a combination of NGS and single-molecule real-time (SMRT) sequencing of virgin females (VFs), mated females (MFs), virgin males (VMs), and mated males (MMs) to comprehensively study the A. gifuensis transcriptome. Behavioral responses to the aphid alarm pheromone (E-β-farnesene, EBF) as well as to A. gifuensis of the opposite sex were also studied. VMs were found to be attracted by female wasps and MFs were repelled by male wasps, whereas MMs and VFs did not respond to the opposite sex. In addition, VFs, MFs, and MMs were attracted by EBF, while VMs did not respond. According to these results, we performed a personalized differential gene expression analysis of olfactory gene sets (66 odorant receptors, 25 inotropic receptors, 16 odorant-binding proteins, and 12 chemosensory proteins) in virgin and mated A. gifuensis of both sexes, and identified 13 candidate genes whose expression levels were highly consistent with behavioral test results, suggesting potential functions for these genes in pheromone perception

Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer Progression

DNA methylation plays a critical role in tumorigenesis through regulating oncogene activation and tumor suppressor gene silencing. Although extensively analyzed, the implication of DNA methylation in gene regulatory network is less characterized. To address this issue, in this study we performed an integrative analysis on the alteration of DNA methylation patterns and the dynamics of gene regulatory network topology across distinct stages of stomach cancer. We found the global DNA methylation patterns in different stages are generally conserved, whereas some significantly differentially methylated genes were exclusively observed in the early stage of stomach cancer. Integrative analysis of DNA methylation and network topology alteration yielded several genes which have been reported to be involved in the progression of stomach cancer, such as IGF2, ERBB2, GSTP1, MYH11, TMEM59, and SST. Finally, we demonstrated that inhibition of SST promotes cell proliferation, suggesting that DNA methylation-associated SST suppression possibly contributes to the gastric cancer progression. Taken together, our study suggests the DNA methylation-associated regulatory network analysis could be used for identifying cancer-related genes. This strategy can facilitate the understanding of gene regulatory network in cancer biology and provide a new insight into the study of DNA methylation at system level

A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.

We conducted a multi-stage, genome-wide association study of bladder cancer with a primary scan of 591,637 SNPs in 3,532 affected individuals (cases) and 5,120 controls of European descent from five studies followed by a replication strategy, which included 8,382 cases and 48,275 controls from 16 studies. In a combined analysis, we identified three new regions associated with bladder cancer on chromosomes 22q13.1, 19q12 and 2q37.1: rs1014971, (P = 8 × 10⁻¹²) maps to a non-genic region of chromosome 22q13.1, rs8102137 (P = 2 × 10⁻¹¹) on 19q12 maps to CCNE1 and rs11892031 (P = 1 × 10⁻⁷) maps to the UGT1A cluster on 2q37.1. We confirmed four previously identified genome-wide associations on chromosomes 3q28, 4p16.3, 8q24.21 and 8q24.3, validated previous candidate associations for the GSTM1 deletion (P = 4 × 10⁻¹¹) and a tag SNP for NAT2 acetylation status (P = 4 × 10⁻¹¹), and found interactions with smoking in both regions. Our findings on common variants associated with bladder cancer risk should provide new insights into the mechanisms of carcinogenesis

Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging

Background Biological aging estimators derived from DNA methylation data are heritable and correlate with morbidity and mortality. Consequently, identification of genetic and environmental contributors to the variation in these measures in populations has become a major goal in the field. Results Leveraging DNA methylation and SNP data from more than 40,000 individuals, we identify 137 genome-wide significant loci, of which 113 are novel, from genome-wide association study (GWAS) meta-analyses of four epigenetic clocks and epigenetic surrogate markers for granulocyte proportions and plasminogen activator inhibitor 1 levels, respectively. We find evidence for shared genetic loci associated with the Horvath clock and expression of transcripts encoding genes linked to lipid metabolism and immune function. Notably, these loci are independent of those reported to regulate DNA methylation levels at constituent clock CpGs. A polygenic score for GrimAge acceleration showed strong associations with adiposity-related traits, educational attainment, parental longevity, and C-reactive protein levels. Conclusion This study illuminates the genetic architecture underlying epigenetic aging and its shared genetic contributions with lifestyle factors and longevity.Peer reviewe

Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging

Background Biological aging estimators derived from DNA methylation data are heritable and correlate with morbidity and mortality. Consequently, identification of genetic and environmental contributors to the variation in these measures in populations has become a major goal in the field. Results Leveraging DNA methylation and SNP data from more than 40,000 individuals, we identify 137 genome-wide significant loci, of which 113 are novel, from genome-wide association study (GWAS) meta-analyses of four epigenetic clocks and epigenetic surrogate markers for granulocyte proportions and plasminogen activator inhibitor 1 levels, respectively. We find evidence for shared genetic loci associated with the Horvath clock and expression of transcripts encoding genes linked to lipid metabolism and immune function. Notably, these loci are independent of those reported to regulate DNA methylation levels at constituent clock CpGs. A polygenic score for GrimAge acceleration showed strong associations with adiposity-related traits, educational attainment, parental longevity, and C-reactive protein levels. Conclusion This study illuminates the genetic architecture underlying epigenetic aging and its shared genetic contributions with lifestyle factors and longevity.</p

Itinerant ferromagnetism of repulsive two-component Fermi gas in the triple-well traps

Based on Thomas-Fermi density functional theory, itinerant ferromagnetism of repulsive two-component Fermi gas trapped in a triple-well is studied. The density profiles of the two components are calculated in three types of triple-well trapping potential. The conclusion is drawn that phase separation relates closely not only to the interaction strength, but also to the shape of the trapping potential, which plays a critical role in determining the density profile of the gas. The separation in each type of trapping potential is a result of the competition between repulsive interaction energy and the kinetic energy. Numerical results show that phase separation occurs once the coupling constant reaches a critical value. With further increase in the coupling constant, the interplay between wells is enhanced, which may cause complex separation. Despite our crude treatment in the Thomas-Fermi approximation, the results may help to explore and understand the nature of itinerant ferromagnetism of trapped Fermi mixtures in both theoretical and experimental research in the future

Contrasting Strategies of Alfalfa Stem Elongation in Response to Fall Dormancy in Early Growth Stage: The Tradeoff between Internode Length and Internode Number.

Fall dormancy (FD) in alfalfa (Medicago sativa L.) can be described using 11 FD ratings, is widely used as an important indicator of stress resistance, productive performance and spring growth. However, the contrasting growth strategies in internode length and internode number in alfalfa cultivars with different FD rating are poorly understood. Here, a growth chamber study was conducted to investigate the effect of FD on plant height, aboveground biomass, internode length, and internode number in alfalfa individuals in the early growth stages. In order to simulate the alfalfa growth environment in the early stage, 11 alfalfa cultivars with FD ratings from one to 11 were chosen and seeded at the greenhouse, and then were transplanted into an artificial growth chamber. The experimental design was a randomized complete block in a split-plot arrangement with three replicates. Plant height, above-ground biomass, internode length, and internode number were measured in early growth stage in all individuals. Our findings showed that plant height and the aboveground biomass of alfalfa did not significantly differ among 11 different FD rated cultivars. Also, internode length and internode number positively affected plant height and the aboveground biomass of alfalfa individuals and the average internode length significantly increased with increasing FD rating. However, internode number tended to sharply decline when the FD rating increased. Moreover, there were no correlations, slightly negative correlations, and strongly negative correlations between internode length and internode number in alfalfa individuals among the three scales, including within-FD ratings, within-FD categories and inter-FD ratings, respectively. Therefore, our results highlighted that contrasting growth strategies in stem elongation were adopted by alfalfa with different FD ratings in the early growth stage. Alfalfa cultivars with a high FD rating have longer internodes, whereas more dormant alfalfa cultivars have a larger number of internodes. There were tradeoffs between internode length and internode number in response to FD in alfalfa, which reflected certain scale-dependence

Inhomogeneous elastic moduli of the Weeks-Chandler-Andersen fluids close to a sphere

Based on the classical elastic theory, expressions for the shear and bulk moduli of the inhomogeneous fluids are derived. Both moduli are expressed as functionals of the density function of the particles. The theoretical derivations are firstly applied to the homogeneous Weeks-Chandler-Andersen fluids. Agreement between our results and those from the molecular-dynamics simulations is observed. In their application to the inhomogeneous fluids close to a large sphere, influences of the volume fraction, temperature and the external potential on their values are calculated and analyzed. The satisfactory performance achieved in this work suggests that our results may be applicative and effective in even wider areas of fluid of the micro- or nano-scale, including the mechanical behavior and hydrodynamical properties

Structural Properties of the Fluid Mixture Confined by a Semipermeable Membrane: A Density Functional Study

Classical density functional theory (DFT) is employed to study the structural properties of a binary fluid mixture confined by a semipermeable membrane. The influences of volume fraction and size asymmetry on three characteristic densities and excess adsorption are investigated in detail. In addition, some of our results are calculated by the analytical method, which agree well with those from the DFT calculations. These results may provide helpful clues to understand the structural properties of other complex fluids or mixture confined by semipermeable membrane

The Relationship between Anterior Chamber Angle and Intraocular Pressure Early after V4c Implantable Collamer Lens Implantation

Purpose. To confirm the relationship between anterior chamber angle (ACA) and intraocular pressure (IOP) early after V4c implantable collamer lens (ICL) implantation. Methods. Patients were assigned to two groups: (1) right eyes (control group) and (2) left eyes (experimental group), with miosis conducted immediately after ICL implantation in the left eyes. IOP, angle opening distance (AOD), trabecular-iris angle (TIA), and pupil diameter (PD) were compared between two groups at postoperative hours 1, 2, and 24. The relationship between ACA, PD, and IOP was analyzed by multiple linear regression. Result. Thirty-six eyes of 18 patients were enrolled. The prevalence of ocular hypertension (OHT, defined as IOP ≥ 21 mmHg) was 61.11% and 16.67% in the right and left eyes, respectively, (χ2 = 7.481, p=0.006). At postoperative hours 1 and 2, IOP and PD were significantly higher p<0.001 in the right eyes, and TIA and AOD were significantly lower p<0.05 in the right eyes than in the left eyes. There was no significant difference at 24 h postoperative in these parameters. After the right eye ICL implantation, the changes of AOD 500 and PD were both linearly correlated with postoperative IOP change (β = −23.707 and 1.731, respectively; p = 0.013 and 0.002, respectively). Conclusion. The ACA was significantly narrowed immediately after V4c ICL implantation. There was a negative linear correlation between ACA and early IOP and a positive linear correlation between PD and early IOP. We recommend the use of intracameral miotics immediately after V4c ICL implantation to reduce the incidence of IOP spikes