Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen

Replication protein A (RPA) is a three-subunit complex with multiple roles in DNA metabolism. DNA-binding domain A in the large subunit of human RPA (hRPA70A) binds to single-stranded DNA (ssDNA) and is responsible for the species-specific RPA–T antigen (T-ag) interaction required for Simian virus 40 replication. Although Saccharomyces cerevisiae RPA70A (scRPA70A) shares high sequence homology with hRPA70A, the two are not functionally equivalent. To elucidate the similarities and differences between these two homologous proteins, we determined the solution structure of scRPA70A, which closely resembled the structure of hRPA70A. The structure of ssDNA-bound scRPA70A, as simulated by residual dipolar coupling-based homology modeling, suggested that the positioning of the ssDNA is the same for scRPA70A and hRPA70A, although the conformational changes that occur in the two proteins upon ssDNA binding are not identical. NMR titrations of hRPA70A with T-ag showed that the T-ag binding surface is separate from the ssDNA-binding region and is more neutral than the corresponding part of scRPA70A. These differences might account for the species-specific nature of the hRPA70A–T-ag interaction. Our results provide insight into how these two homologous RPA proteins can exhibit functional differences, but still both retain their ability to bind ssDNA

A Study on the Manufacturing of Large Size Hollow Shape Parts for Prototype-Car Using Rapid Prototyping Technology and Vacuum Molding

Rapid Prototyping(RP) techniques have revolutionized traditional manufacturing methods. These techniques allow the user to fabricate a part directly from a conceptual model before investing in production tooling and help develop new models with significant short time. This paper suggests the new process to manufacture large size hollow shape parts for prototype-car using Rapid Prototyping technology and Vacuum Molding with the reduction of delivery time. In addition, this paper introduces the dividing and combining method to make large size RP master model in spite of the limit of the build chamber dimensions of commercialized RP systems and post-processing method to achieve sufficient surface quality.Mechanical Engineerin

Distribution and Conservation of Long-billed Plovers Charadrius placidus in Korea

AbstractThe Long-billed Plover Charadrius placidus of distribution was surveyed from 2002 to 2005, on rivers, streams and coasts of 38 areas within Korea. The Sum of highest numbers (sum of peak counts) of Long-billed Plovers at 24 sites was 198 individuals. Number of observed individuals during breeding period was 88 individuals, 129 individuals during the migration period, and 56 individuals during the wintering period. The Long-billed Plover breeds and migrates throughout Korea. They spend winter south of 37° latitude. Highest numbers (73 individuals) were observed at Daejeon. Therefore, streams and rivers of Korea are considered as an important habitat for the Long-billed Plover

Fibroblast growth factor-2, derived from cancer-associated fibroblasts, stimulates growth and progression of human breast cancer cells via FGFR1 signaling

Cancer-associated fibroblasts (CAFs) constitute a major compartment of the tumor microenvironment. In the present study, we investigated the role for CAFs in breast cancer progression and underlying molecular mechanisms. Human breast cancer MDA-MB-231 cells treated with the CAF-conditioned media manifested a more proliferative phenotype, as evidenced by enhanced messenger RNA (mRNA) expression of Cyclin D1, c-Myc, and proliferating cell nuclear antigen. Analysis of data from The Cancer Genome Atlas revealed that fibroblast growth factor-2 (FGF2) expression was well correlated with the presence of CAFs. We noticed that the mRNA level of FGF2 in CAFs was higher than that in normal fibroblasts. FGF2 exerts its biological effects through interaction with FGF receptor 1 (FGFR1). In the breast cancer tissue array, 42% estrogen receptor-negative patients coexpressed FGF2 and FGFR1, whereas only 19% estrogen receptor-positive patients exhibited coexpression. CAF-stimulated MDA-MB-231 cell migration and invasiveness were abolished when FGF2-neutralizing antibody was added to the conditioned media of CAFs. In a xenograft mouse model, coinjection of MDA-MB-231 cells with activated fibroblasts expressing FGF2 dramatically enhanced tumor growth, and this was abrogated by silencing of FGFR1 in cancer cells. In addition, treatment of MDA-MB-231 cells with FGF2 enhanced expression of Cyclin D1, a key molecule involved in cell cycle progression. FGF2-induced cell migration and upregulation of Cyclin D1 were abolished by siRNA-mediated FGFR1 silencing. Taken together, the above findings suggest that CAFs promote growth, migration and invasion of MDA-MB-231 cells via the paracrine FGF2-FGFR1 loop in the breast tumor microenvironment.

Inhibition of poly(ADP-ribose)polymerase binding to DNA by thymidine dimer

AbstractThe ability of poly(ADP-ribose)polymerase to bind damaged DNA was assessed by electrophoretic mobility shift assay. DNA binding domain of poly(ADP-ribose)polymerase (PARPDBD) binds to synthetic deoxyribonucleotide duplex 10-mer. However, the synthetic deoxyribonucleotide duplex containing cys-syn thymidine dimer which produces the unwinding of DNA helix structure lost its affinity to PARPDBD. It was shown that the binding of PARPDBD to the synthetic deoxyribonucleotide duplex was not affected by O6-Me-dG which causes only minor distortion of DNA helix structure. This study suggests that the stabilized DNA helix structure is important for poly(ADP-ribose)polymerase binding to DNA breaks, which are known to stimulate catalytic activity of poly(ADP-ribose)polymerase

X-ray crystal structure of endosulfan sulfate

X-ray crystallography is an important method used to confirm the three-dimensional structure of a chemical compound. In this study, the crystal structure of endosulfan sulfate was investigated. Endosulfan sulfate is the major metabolite of the insecticide endosulfan, which is composed of two stereoisomers (α and β). From GC–MS analysis, α- and β-endosulfan each gave a single peak in the endosulfan sample, but only one peak was observed for endosulfan sulfate. Interestingly, in X-ray crystallography, two conformers of endosulfan sulfate (A and B) were observed at a ratio of 2(A):1(B). A heterocyclic seven-membered ring of conformer B assumed a horizontal-chair form, differing from two twisted forms of α-endosulfan while a vertical-chair form was observed for conformer A, showing the very similar structure to β-endosulfan; this difference in conformation is caused by differing bond angles at O(1)–C(8)–C(3) and O(2)–C(9)–C(4). In space packing, two asymmetric units were obtained, and three molecules were aligned in the order of A–A–B conformers in each unit. The total potential energy of A was slightly lower (approximately 4 kcal/mol) than B, possibly resulting in the two molecules of A that exist in a rigid crystal state. However, A and B conformers should not exist at room temperature in a solution state for GC–MS analysis, likely due to the small energy difference.The authors research was supported by contract research funds (Grant no. 550–20170104) of the Research Institute for Veterinary Science (RIVS) from the College of Veterinary Medicine and by the BK 21 Plus Program (Grant no. 5260–20150100) for Creative Veterinary Science Research. The funders had no role in study design, data collection, analysis and interpretation, decision to publish, or preparation of the manuscript

SelecMix: Debiased Learning by Contradicting-pair Sampling

Neural networks trained with ERM (empirical risk minimization) sometimes learn unintended decision rules, in particular when their training data is biased, i.e., when training labels are strongly correlated with undesirable features. To prevent a network from learning such features, recent methods augment training data such that examples displaying spurious correlations (i.e., bias-aligned examples) become a minority, whereas the other, bias-conflicting examples become prevalent. However, these approaches are sometimes difficult to train and scale to real-world data because they rely on generative models or disentangled representations. We propose an alternative based on mixup, a popular augmentation that creates convex combinations of training examples. Our method, coined SelecMix, applies mixup to contradicting pairs of examples, defined as showing either (i) the same label but dissimilar biased features, or (ii) different labels but similar biased features. Identifying such pairs requires comparing examples with respect to unknown biased features. For this, we utilize an auxiliary contrastive model with the popular heuristic that biased features are learned preferentially during training. Experiments on standard benchmarks demonstrate the effectiveness of the method, in particular when label noise complicates the identification of bias-conflicting examples.Comment: NeurIPS 202