Recruitment of DNA repair synthesis machinery to sites of DNA damage/repair in living human cells

The eukaryotic sliding DNA clamp, proliferating cell nuclear antigen (PCNA), is essential for DNA replication and repair synthesis. In order to load the ring-shaped, homotrimeric PCNA onto the DNA double helix, the ATPase activity of the replication factor C (RFC) clamp loader complex is required. Although the recruitment of PCNA by RFC to DNA replication sites has well been documented, our understanding of its recruitment during DNA repair synthesis is limited. In this study, we analyzed the accumulation of endogenous and fluorescent-tagged proteins for DNA repair synthesis at the sites of DNA damage produced locally by UVA-laser micro-irradiation in HeLa cells. Accumulation kinetics and in vitro pull-down assays of the large subunit of RFC (RFC140) revealed that there are two distinct modes of recruitment of RFC to DNA damage, a simultaneous accumulation of RFC140 and PCNA caused by interaction between PCNA and the extreme N-terminus of RFC140 and a much faster accumulation of RFC140 than PCNA at the damaged site. Furthermore, RFC140 knock-down experiments showed that PCNA can accumulate at DNA damage independently of RFC. These results suggest that immediate accumulation of RFC and PCNA at DNA damage is only partly interdependent

Impactos da pandemia de covid-19 no setor econômico da construção civil : estudo de caso

A pandemia de Covid-19 afetou de forma significativa a rotina das pessoas e a economia como um todo. Na construção civil, as obras sofreram paralisações e aumento nos preços dos materiais. Assim, o presente artigo buscou entender os principais impactos causados pela pandemia em uma construtora de grande porte no Rio Grande do Sul, a Melnick. Os dados analisados foram obtidos através da seção de relacionamento com investidores, utilizando-se a apresentação de resultados e os demonstrativos financeiros padronizados (DFP), além de entrevistas realizadas com colaboradores da empresa. A análise permitiu observar significativa redução de despesas devido ao trabalho remoto, além de uma queda no volume de vendas e lançamentos no período de pandemia, em conjunto com uma procura maior por imóveis mais arejados, com melhor ventilação e iluminação, em uma localização mais afastada dos grandes centros urbanos.The Covid-19 pandemic significantly affected people's lives and the economy as a whole. In civil construction, the works suffered stoppages and an increase in the prices of materials. Thus, this article sought to understand the main impacts caused by the pandemic on a major construction company in Rio Grande do Sul, Melnick. The data analyzed were obtained through the investor relations section, using the presentation of results and standard financial statement (DFP), in addition to interviews conducted with company employees. The analysis allowed us to observe a significant reduction in expenses due to remote work, in addition to a drop in the volume of sales and launches during the pandemic period, together with a greater demand for more airy properties, with better ventilation and lighting, in a more remote location of large urban centers

Biomechanical Study of Cervical Posterior Decompression

Study Design Biomechanical study. Purpose We examined the dynamic characteristics of different operative procedures using three-dimensional finite-element models. Overview of Literature Cervical laminoplasty is often selected for patients requiring multilevel spinal decompression. Many laminoplasty techniques have been developed and are continually being improved. Methods Images were extracted for the two intervertebral joints between C3 and C5 in domestic rabbits. The following models were created: preoperative, laminectomy, Z-plasty, open door laminoplasty, French open door laminoplasty, en-bloc laminoplasty, and double-door laminoplasty. The loads required for sagittal rotation of 2.5°, 5°, and 7.5° were measured in vitro and respectively placed at the bottom of the C5 model. Displacement of the plate in the X, Y, and Z coordinates was measured and the rotational angles of the plate were determined. Results The sagittal rotation angle was greater in the laminectomy model than in the preoperative model, but was almost the same in the preoperative and Z-plasty models. Compared with the preoperative model, sagittal rotation angles were smaller in the French open door, open door, en-bloc, and double-door laminoplasty models. Conclusions Laminectomy and various types of laminoplasty are associated with different mechanical features, such as stability and mobility, allowing for selection of the most appropriate surgical procedure for each case

Formation of an Ultracarbonaceous Antarctic Micrometeorite through Minimum Aqueous Alteration in a Small Porous Icy Body

A comprehensive study of the organic chemistry and mineralogy of an ultracarbonaceous micrometeorite (UCAMM D05IB80) collected from near the Dome Fuji Station, Antarctica, was carried out to understand the genetic relationship among organic materials, silicates, and water. The micrometeorite is composed of a dense aggregate of ∼5 µm-sized hollow ellipsoidal organic material containing submicrometer-sized phases such as glass with embedded metal and sulfides (GEMS) and mineral grains. There is a wide area of organic material (∼15 × 15 μm) in its interior. Low-Ca pyroxene is much more abundant than olivine and shows various Mg/(Mg + Fe) ratios ranging from ∼1.0 to 0.78, which is common to previous works on UCAMMs. By contrast, GEMS grains in this UCAMM have unusual chemical compositions. They are depleted in both Mg and S, which suggests that these elements were leached out from the GEMS grains during very weak aqueous alteration, without the formation of phyllosilicates. The organic materials have two textures—smooth and globular with an irregular outline—and these are composed of imine, nitrile and/or aromatic nitrogen heterocycles, and amide. The ratio of nitrogen to carbon (N/C) in the smooth region of the organics is ∼0.15, which is five times higher than that of insoluble organic macromolecules in types 1 and 2 carbonaceous chondritic meteorites. In addition, the UCAMM organic materials are soluble in epoxy and are thus hydrophilic; this polar nature indicates that they are very primitive. The surface of the material is coated with an inorganic layer, a few nanometers thick, that consists of C, O, Si, S, and Fe. Sulfur is also contained in the interior, implying the presence of organosulfur moieties. There are no isotopic anomalies of D, 13C, or 15N in the organic material. Interstellar photochemistry alone would not be sufficient to explain the N/C ratio of the UCAMM organics; therefore, we suggest that a very small amount of fluid on a comet must have been necessary for the formation of the UCAMM. The GEMS grains depleted in Mg and S in the UCAMM prove a very weak degree of aqueous alteration; weaker than that of carbonaceous chondrites. Short-duration weak alteration probably caused by planetesimal shock locally melted cometary ice grains and released water that dissolved the organics; the fluid would likely have not mobilized because of the very low thermal conductivity of the porous icy body. This event allowed the formation of the large organic puddle of the UCAMM, as well as organic matter sulfurization, formation of thin membrane-like layers of minerals, and deformation of organic nanoglobules.アクセプト後にタイトル・アブストラクト等変更あり、著者最終稿は変更前のタイトル"Formation of an Ultracarbonaceous Antarctic Micrometeorite through Minimum Aqueous Alteration in a Small Porous Icy Body"This work was supported by a Grant-in-Aid for Scientific Research from the Japanese Ministry of Education, Culture, Sports, Science and Technology (No. 22224010, PI: H. Nagahara). The STXM facility at the beamline 5.3.2.2, ALS, is supported by the Department of Energy, Basic Energy Sciences Program

Meeting Abstract Enhancing Automatic Classification of Hepatocellular Carcinoma Images through Image Masking, Tissue Changes, and Trabecular Features

Background Hepatocellular carcinoma (HCC) is a malignant tumor with hepatocellular differentiation and one of the most common cancers in the world. This type of cancer is often diagnosed when the survival time is measured in months causing high death rates Method We enhanced the classification process presented in [3] by including 11 features of tissue changes (i.e., features related to fatty change, cytoplasm colors, cell clearness index, and stroma) and 10 features of trabecular (e.g., nuclei-cytoplasmic ratio, irregularity of sinusoid, and trabecular arrangements). Furthermore, we apply a mask obtained by the stroma segmentation before calculating the 13 types of nuclear and structural features such that those features are derived from hepatocytes only, thus generating in total 177 features. The experiments were performed on a collection of region-ofinterest (ROI) images extracted from HE stained whole slide images (WSI), consisting of 1054 ROIs of HCC biopsy samples (504 negatives and 550 positives) and 1076 ROIs of HCC surgically resected samples (533 negatives and 543 positives). In the process, we made some combinations on the sets of features and sets of training data from both biopsy and surgery samples. As for the classification, we used 5-fold cross validation support vector machine (SVM) with LibSVM as our library. Results The results of classification experiment are summarized in Conclusion The combination of nuclear, trabecular, and other tissue features enables improved classification rate in HCC detection using SVM. Even though the image characteristics are different in biopsy and surgically resected samples, the same classification system gives good performance in both samples. The HCC classification scheme introduced in this paper is implemented in the prototype "feature measurement software for liver biopsy, " and the probability of HCC is visualized for every ROI in the WSI. It will support pathologists in the HCC diagnosis along with the quantitative measurements of tissue morphology

Comparison of rapid immunochromatographic assays using sputum and urine for Streptococcus pneumoniae detection in adult patients with respiratory tract infection

Aim: Streptococcus pneumoniae is the most frequently detected bacterium in pneumonia. RAPIRUN Streptococcus pneumoniae (RAPIRUN) using sputum and BinaxNow Streptococcus pneumoniae (BinaxNow) using urine have been used as rapid diagnostic methods for S. pneumoniae detection in Japan; however, their correlation with quantitative culture tests has not been well evaluated.Methods: A prospective study was conducted on adult patients with respiratory tract infections whose sputum and urine samples were available in six hospitals. Sputum and urine samples were tested at each site, and quantitative sputum cultures were performed. The performance of RAPIRUN and BinaxNow was compared in cases in which quantitative culture showed S. pneumoniae.Results: A total of 192 patients were analyzed. Of these, 167 were diagnosed with pneumonia (87.0%) including 161 of community-acquired pneumonia. Of the 192 cases, 86 (44.8%) were culture-proven for S. pneumoniae. There were 83 and 57 RAPIRUN- and BinaxNow-positive cases, respectively. The sensitivity and specificity of RAPIRUN were 84.9% and 90.6%, respectively, and those of BinaxNOW were 55.8% and 91.5%, respectively, indicating that RAPIRUN was significantly superior in sensitivity (p < 0.0001) with almost equal specificity (p = 0.317). Positive and negative percent agreements of both tests were 59.3% (κ, 0.114 [95% CI, 0.053–0.281]) and 99.1% (κ, 0.942 [95% CI, 0.830–1]), respectively, indicating they were well matched in specificity but not in sensitivity. The positivity rate of RAPIRUN increased with an increase in the number of bacteria (p< 0.0001) but not BinaxNow (p = 0.275).Conclusion: In adult patients with respiratory tract infections in whom sputum collection is feasible, RAPIRUN will increase the diagnostic efficacy of S. pneumoniae infection

A polycomb group protein, PHF1, is involved in the response to DNA double-strand breaks in human cell

DNA double-strand breaks (DSBs) represent the most toxic DNA damage arisen from endogenous and exogenous genotoxic stresses and are known to be repaired by either homologous recombination or nonhomologous end-joining processes. Although many proteins have been identified to participate in either of the processes, the whole processes still remain elusive. Polycomb group (PcG) proteins are epigenetic chromatin modifiers involved in gene silencing, cancer development and the maintenance of embryonic and adult stem cells. By screening proteins responding to DNA damage using laser micro-irradiation, we found that PHF1, a human homolog of Drosophila polycomb-like, Pcl, protein, was recruited to DSBs immediately after irradiation and dissociated within 10 min. The accumulation at DSBs is Ku70/Ku80-dependent, and knockdown of PHF1 leads to X-ray sensitivity and increases the frequency of homologous recombination in HeLa cell. We found that PHF1 interacts physically with Ku70/Ku80, suggesting that PHF1 promotes nonhomologous end-joining processes. Furthermore, we found that PHF1 interacts with a number of proteins involved in DNA damage responses, RAD50, SMC1, DHX9 and p53, further suggesting that PHF1, besides the function in PcG, is involved in genome maintenance processes

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Atrasentan and renal events in patients with type 2 diabetes and chronic kidney disease (SONAR): a double-blind, randomised, placebo-controlled trial

Background: Short-term treatment for people with type 2 diabetes using a low dose of the selective endothelin A receptor antagonist atrasentan reduces albuminuria without causing significant sodium retention. We report the long-term effects of treatment with atrasentan on major renal outcomes. Methods: We did this double-blind, randomised, placebo-controlled trial at 689 sites in 41 countries. We enrolled adults aged 18–85 years with type 2 diabetes, estimated glomerular filtration rate (eGFR)25–75 mL/min per 1·73 m 2 of body surface area, and a urine albumin-to-creatinine ratio (UACR)of 300–5000 mg/g who had received maximum labelled or tolerated renin–angiotensin system inhibition for at least 4 weeks. Participants were given atrasentan 0·75 mg orally daily during an enrichment period before random group assignment. Those with a UACR decrease of at least 30% with no substantial fluid retention during the enrichment period (responders)were included in the double-blind treatment period. Responders were randomly assigned to receive either atrasentan 0·75 mg orally daily or placebo. All patients and investigators were masked to treatment assignment. The primary endpoint was a composite of doubling of serum creatinine (sustained for ≥30 days)or end-stage kidney disease (eGFR <15 mL/min per 1·73 m 2 sustained for ≥90 days, chronic dialysis for ≥90 days, kidney transplantation, or death from kidney failure)in the intention-to-treat population of all responders. Safety was assessed in all patients who received at least one dose of their assigned study treatment. The study is registered with ClinicalTrials.gov, number NCT01858532. Findings: Between May 17, 2013, and July 13, 2017, 11 087 patients were screened; 5117 entered the enrichment period, and 4711 completed the enrichment period. Of these, 2648 patients were responders and were randomly assigned to the atrasentan group (n=1325)or placebo group (n=1323). Median follow-up was 2·2 years (IQR 1·4–2·9). 79 (6·0%)of 1325 patients in the atrasentan group and 105 (7·9%)of 1323 in the placebo group had a primary composite renal endpoint event (hazard ratio [HR]0·65 [95% CI 0·49–0·88]; p=0·0047). Fluid retention and anaemia adverse events, which have been previously attributed to endothelin receptor antagonists, were more frequent in the atrasentan group than in the placebo group. Hospital admission for heart failure occurred in 47 (3·5%)of 1325 patients in the atrasentan group and 34 (2·6%)of 1323 patients in the placebo group (HR 1·33 [95% CI 0·85–2·07]; p=0·208). 58 (4·4%)patients in the atrasentan group and 52 (3·9%)in the placebo group died (HR 1·09 [95% CI 0·75–1·59]; p=0·65). Interpretation: Atrasentan reduced the risk of renal events in patients with diabetes and chronic kidney disease who were selected to optimise efficacy and safety. These data support a potential role for selective endothelin receptor antagonists in protecting renal function in patients with type 2 diabetes at high risk of developing end-stage kidney disease. Funding: AbbVie