Analysis of polymorphism in human cytomegalovirus (HCMV) chemokine, vCXCL-1, and its role in cellular activation

The human cytomegalovirus (HCMV) viral chemokine gene, UL146, shows a high degree of variability in clinical isolates. The UL146-produced viral chemokine, vCXCL-1, has homology to CXC chemokines and is predicted to be an immune modulator that may contribute to the pathogenesis of HCMV infections. In the analysis of clinical isolates from congenitally infected infants, we found 11 distinct vCXCL-1 clades. Although the four cysteine residues that create two disulfide bonds providing the essential structure for CXC chemokines,are conserved, the N-loop region, which is important for receptor binding and activation, was hypervariable. One clade also contained a modified glutamic acid-leucine-arginine (ELR) motif (asparagine-glycine-arginine / NGR), which regulates binding to CXCR1 and CXCR2 receptors. Based on this sequence information, we hypothesize that these proteins differentially activate neutrophils, which may have a role in HCMV pathogenesis. To address these functional differences, we produced representative vCXCL-1 proteins from each of the 11 clades using a baculovirus protein expression system. Using competition binding assays, we have examined their binding affinities to either CXCR1 or CXCR2 expressed on HEK293 cells. All vCXCL-1s bound to CXCR2 with different binding affinities. Interestingly, only three vCXCL-1s bound to CXCR1 while the others demonstrated did not. We analyzed functional differences between the vCXCL-1s in calcium mobilization, adhesion molecule induction, and chemotaxis on human peripheral blood neutrophils (PBNs). Although the binding affinities to CXCR2 and/or CXCR1 were variable, all vCXCL-1s were capable of inducing intracellular calcium mobilization in PBNs and upregulating adhesion molecules on the surface of PBNs to similar levels as human CXCL1. However, the potency of the vCXCL-1s in the chemotaxis of neutrophils varied and was affinity independent. We also examined secondary chemokine production upon vCXCL-1 treatment on neutrophil-like HL60 T2 cells using real-time PCR. The results showed CCL22 induction was affinity dependent. Taken together, these results provide insights into the potential role of vCXCL-1 in HCMV pathogenesis and how the variability in these chemokines can affect neutrophil function

Treatment strategy for papillary renal cell carcinoma type 2: a case series of seven patients treated based on next generation sequencing data

Background: Papillary renal cell carcinoma type 2 (PRCC2) is refractory to systemic treatment and has a dismal prognosis. Previous studies showed that genetic alterations in PRCC2 were heterogeneous regardless of germline or somatic mutations. In this study, we aimed to perform precision treatment of PRCC2 based on genetic information. Methods: We performed exome and genome sequencing of tumor tissues and matched normal samples. Based on sequencing data, we treated patients with metastatic PRCC2 using precision oncology. Results: Four patients underwent curative surgery of PRCC2 and three patients had metastatic PRCC2. All PRCC2 heterogeneously harbored own driver mutations. Two out of the three patients with metastatic disease had fumarate hydratase (FH) germline mutations. One patient with a germline FH mutation was diagnosed with hereditary leiomyomatosis RCC. He was treated with bevacizumab and erlotinib combination and showed a durable response. The other metastatic PRCC2 patient harboring a germline FH mutation had an additional somatic FH mutation and was durably controlled with pazopanib. Other metastatic PRCC2 patient with somatic PBRM1 and SETD2 mutations had over 5 years of overall survival with axitinib treatment. Conclusions: We performed precision systemic treatment based on genetic information. Genome sequencing could help identify candidates for targeted therapy in PRCC2, a genetically heterogeneous disease

Transcriptome-wide association study and eQTL colocalization identify potentially causal genes responsible for bone mineral density GWAS associations

Genome-wide association studies (GWASs) for bone mineral density (BMD) have identified over 1,100 associations to date. However, identifying causal genes implicated by such studies has been challenging. Recent advances in the development of transcriptome reference datasets and computational approaches such as transcriptome-wide association studies (TWASs) and expression quantitative trait loci (eQTL) colocalization have proven to be informative in identifying putatively causal genes underlying GWAS associations. Here, we used TWAS/eQTL colocalization in conjunction with transcriptomic data from the Genotype-Tissue Expression (GTEx) project to identify potentially causal genes for the largest BMD GWAS performed to date. Using this approach, we identified 512 genes as significant (Bonferroni <= 0.05) using both TWAS and eQTL colocalization. This set of genes was enriched for regulators of BMD and members of bone relevant biological processes. To investigate the significance of our findings, we selected PPP6R3, the gene with the strongest support from our analysis which was not previously implicated in the regulation of BMD, for further investigation. We observed that Ppp6r3 deletion in mice decreased BMD. In this work, we provide an updated resource of putatively causal BMD genes and demonstrate that PPP6R3 is a putatively causal BMD GWAS gene. These data increase our understanding of the genetics of BMD and provide further evidence for the utility of combined TWAS/colocalization approaches in untangling the genetics of complex traits.First author draf

A Decision-Making Model for Optimized Energy Plans for Buildings Considering Peak Demand Charge&mdash;A South Korea Case Study

The energy industry has been trying to reduce the use of fossil fuels that emit carbon and to proliferate renewable energy as a way to respond to climate change. The attempts to reduce carbon emissions resulting from the process of generating the electric and thermal energy needed by a building were bolstered with the introduction of the concept of nZEB (nearly zero-energy building). In line with such initiatives, the South Korean government made it mandatory for new buildings to have an nZEB certificate as a way to promote the supply of renewable energy. The criteria for Energy Independence Rate, which is one of the nZEB certification criteria in South Korea, is to maintain the share of renewable energy as at least 20% of the primary energy sources for the building. For a new building in South Korea to have an nZEB certificate, it is required to establish an energy plan that would allow the building to meet the Energy Independence requirement. This optimally reflects the cost of installation for renewable energy facilities and the cost of purchasing energy from external sources, such as the national grid or district heating companies. In South Korea, the base retail rate of energy is calculated based on the peak demand per hour over the year, rather than the contracted energy. This has produced difficulties in standardizing the process with a mathematical model; in addition, there have not been many preceding studies that could be used as a reference. In this regard, this paper analyzed a modeling strategy for developing a realistic yet optimized energy plan in consideration of the unique conditions of the retail energy rates of South Korea, and analyzed the impact of the rates based on peak demands upon the total energy plan. In this study, our research team analyzed the electric billing system, conducted a case study, and analyzed the impact of the billing system that is based on the peak demand upon the optimal cost. By utilizing the restrictions for reaching the 20% Energy Independence goal, this paper calculated the proper energy supply facility capacity for renewable energy. Then, the cases in which the maximum demand modeling was used and the cases without one were compared to confirm the cost benefits observable when the suggested model is added or implemented

Tour into the Picture with Water Surface Reflection and Object Movements

Given a still picture, tour into the picture (TIP) generates a walk-through animation of a 3D scene constructed from the picture. In this paper, we generalize TIP to deal with water surface reflection while allowing foreground objects to move. We formu-late a non-linear optimization problem to find the 3D scene parameters with respect to the camera position, to automatically construct a reasonable 3D scene model, provided with a set of points and their corresponding points on the water surface. To synthesize a stream of reflected images on the water surface in accordance with the camera move-ment, we propose a novel image-based approach, which makes the best of the limited information available in the input picture. Furthermore, we incorporate water surface movement data acquired from water simulation on top of stochastic motion textures for objects such as trees and plants, to create a dynamic scene

Proteomic Investigation to Identify Anticancer Targets of Nemopilema nomurai Jellyfish Venom in Human Hepatocarcinoma HepG2 Cells

Nemopilema nomurai is a giant jellyfish that blooms in East Asian seas. Recently, N. nomurai venom (NnV) was characterized from a toxicological and pharmacological point of view. A mild dose of NnV inhibits the growth of various kinds of cancer cells, mainly hepatic cancer cells. The present study aims to identify the potential therapeutic targets and mechanism of NnV in the growth inhibition of cancer cells. Human hepatocellular carcinoma (HepG2) cells were treated with NnV, and its proteome was analyzed using two-dimensional gel electrophoresis, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI/TOF/MS). The quantity of twenty four proteins in NnV-treated HepG2 cells varied compared to non-treated control cells. Among them, the amounts of fourteen proteins decreased and ten proteins showed elevated levels. We also found that the amounts of several cancer biomarkers and oncoproteins, which usually increase in various types of cancer cells, decreased after NnV treatment. The representative proteins included proliferating cell nuclear antigen (PCNA), glucose-regulated protein 78 (GRP78), glucose-6-phosphate dehydrogenase (G6PD), elongation factor 1&gamma; (EF1&gamma;), nucleolar and spindle-associated protein (NuSAP), and activator of 90 kDa heat shock protein ATPase homolog 1 (AHSA1). Western blotting also confirmed altered levels of PCNA, GRP78, and G6PD in NnV-treated HepG2 cells. In summary, the proteomic approach explains the mode of action of NnV as an anticancer agent. Further characterization of NnV may help to unveil novel therapeutic agents in cancer treatment

Charge breeding experiment of stable ion beams in EBIS charge breeder for RAON facility

The Electron Beam Ion Source (EBIS) charge breeder is used to produce highly charged ions in the Isotope Separation On-Line (ISOL) system of the Rare isotope Accelerator complex for ON-line experiments (RAON). Beam tests of the EBIS are performed using stable Cs and Sn ion beams. Cs-133(1+) ions from a test ion source were injected into the EBIS to measure the breeding effect with the electron beam. The resulting relative abundance of Cs-133(27+) was 25.0%, and the extraction energy was 49.3 keV/q. A charge breeding test of the Sn-120 ions from the Target Ion Source (TIS) of the ISOL system was also carried out. The charge fraction of Sn-120(24+) was 23.0%, and the energy was 50 keV/q. These results fulfilled the input beam condition of the RFQ accelerator (A/q &lt; 6 and 10 keV/u). Additionally, Cs-133(27+) ions were extracted with a pulse length up to 10 ms (FWHM) by the preliminary pulse-stretching experiment

Novel Human Cytomegalovirus Viral Chemokines, vCXCL-1s, Display Functional Selectivity for Neutrophil Signaling and Function

Human CMV (HCMV) uses members of the hematopoietic system including neutrophils for dissemination throughout the body. HCMV encodes a viral chemokine, vCXCL-1, that is postulated to attract neutrophils for dissemination within the host. The gene encoding vCXCL-1, UL146, is one of the most variable genes in the HCMV genome. Why HCMV has evolved this hypervariability and how this affects the virus' dissemination and pathogenesis is unknown. Because the vCXCL-1 hypervariability maps to important binding and activation domains, we hypothesized that vCXCL-1s differentially activate neutrophils, which could contribute to HCMV dissemination, pathogenesis, or both. To test whether these viral chemokines affect neutrophil function, we generated vCXCL-1 proteins from 11 different clades from clinical isolates from infants infected congenitally with HCMV. All vCXCL-1s were able to induce calcium flux at a concentration of 100 nM and integrin expression on human peripheral blood neutrophils, despite differences in affinity for the CXCR1 and CXCR2 receptors. In fact, their affinity for CXCR1 or CXCR2 did not correlate directly with chemotaxis, G protein-dependent and independent (β-arrestin-2) activation, or secondary chemokine (CCL22) expression. Our data suggest that vCXCL-1 polymorphisms affect the binding affinity, receptor usage, and differential peripheral blood neutrophil activation that could contribute to HCMV dissemination and pathogenesis

Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (<i>Glycine max</i> L.)

The depletion of the stratospheric ozone layer is a major environmental issue and has increased the dosage of ultraviolet-B (UV-B) radiation reaching the Earth’s surface. Organisms are negatively affected by enhanced UV-B radiation, and especially in crop plants this may lead to severe yield losses. Soybean (Glycine max L.), a major legume crop, is sensitive to UV-B radiation, and therefore, it is required to breed the UV-B-resistant soybean cultivar. In this study, 688 soybean germplasms were phenotyped for two categories, Damage of Leaf Chlorosis (DLC) and Damage of Leaf Shape (DLS), after supplementary UV-B irradiation for 14 days. About 5% of the germplasms showed strong UV-B resistance, and GCS731 was the most resistant genotype. Their phenotypic distributions showed similar patterns to the normal, suggesting UV-B resistance as a quantitative trait governed by polygenes. A total of 688 soybean germplasms were genotyped using the Axiom® Soya 180K SNP array, and a genome-wide association study (GWAS) was conducted to identify SNPs significantly associated with the two traits, DLC and DLS. Five peaks on chromosomes 2, 6, 10, and 11 were significantly associated with either DLC or DLS, and the five adjacent genes were selected as candidate genes responsible for UV-B resistance. Among those candidate genes, Glyma.02g017500 and Glyma.06g103200 encode cryptochrome (CRY) and cryptochrome 1 (CRY1), respectively, and are known to play a role in DNA repair during photoreactivation. Real-time quantitative RT-PCR (qRT-PCR) results revealed that CRY1 was expressed significantly higher in the UV-B-resistant soybean compared to the susceptible soybean after 6 h of UV-B irradiation. This study is the first GWAS report on UV-B resistance in soybean, and the results will provide valuable information for breeding UV-B-resistant soybeans in preparation for climate change