Influence of DNA extraction kits on freshwater fungal DNA metabarcoding

[Background] Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. [Methods] DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples. [Results] No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals

Inner Magnetospheric Response to the Interplanetary Magnetic Field By Component:Van Allen Probes and Arase Observations

We utilise 17 years of combined Van Allen Probes and Arase data to statistically analyse the response of the inner magnetosphere to the orientation of the IMF By component. Past studies have demonstrated that the IMF By component introduces a similarly oriented By component into the magnetosphere. However, these studies have tended to focus on field lines in the magnetotail only reaching as close to Earth as geosynchronous orbit. By exploiting data from these inner magnetospheric spacecraft, we have been able to investigate the response at radial distances of < 7 RE. When subtracting the background magnetic field values, provided by the T01 and IGRF magnetic field models, we find that the IMF By component does affect the configuration of the magnetic field lines in the inner magnetosphere. This control is observed throughout the inner magnetosphere, across both hemispheres, all radial distances, and all MLT sectors. The ratio of IMF By to observed By residual, also known as the "penetration efficiency", is found to be ~0.33. The IMF Bz component is found to increase, or inhibit, this control depending upon its orientation

A Solution for Universal Classification of Species Based on Genomic DNA

Traditionally, organisms have been classified on the basis of their phenotype. Recently, genotype-based classification has become possible through the development of sequencing technology. However, it is still difficult to apply sequencing approaches to the analysis of a large number of species due to the cost and labor. In most biological fields, the analysis of complex systems comprising various species has become an important theme, demanding an effective method for handling a vast number of species. In this paper, we have demonstrated, using plants, fish, and insects, that genome profiling, a compact technology for genome analysis, can classify organisms universally. Surprisingly, in all three of the domains of organisms tested, the phylogenetic trees generated from the phenotype topologically matched completely those generated from the genotype. Furthermore, a single probe was sufficient for the genome profiling, thereby demonstrating that this methodology is universal and compact

Determination of natural estrogens in the sediment of coastal area in Japan

The concentration of natural estrogens such as 17β-estradiol (E2) and estrone (E1) in the sediment of coastal areas in Japan was determined using an enzyme-1inked immunosorbent assay (ELISA). The samples of sediment were collected in Osaka Bay and Otsuchi Bay, Yamada Bay and Ofunato Bay, in Iwate Prefecture, Japan. In addition, core samples were taken in Otsuchi Bay and Yamada Bay, Estrogens in sediments were extracted by sonication in acetone followed by liquid-1iquid extraction with dichloromethane. The levels of E1 were generally higher than those of E2 in sediments, whereas the concentrations of E2 were higher than E1 at some sampling sites. The levels of estrogens in the sites located near estuaries tended to be higher, and levels decreased at the sampling stations nearer to the mouth of the bay However, the estrogen concentration in the sediment collected from near the mouth of bay was highest of all samples in Osaka Bay, both in summer and winter. Core samples were sliced every 2cm from the surface to 20cm deep for the measurement of estrogen. Although the concentrations of estrogens decreased with the depth of core samples, fairly high levels of estrogens were again noticed at the layer deeper than 16cm

Evaluation of Therapeutic Target Gene Expression Based on Residual Cancer Burden Classification After Neoadjuvant Chemotherapy for HER2-Negative Breast Cancer

Introduction Patients with residual disease usually have a poor prognosis after neoadjuvant chemotherapy for breast cancer. The aim of this study was to explore therapeutic targets and potential additional adjuvant treatments for patients with residual disease after standard neoadjuvant chemotherapy. Patients and Methods We retrieved publicly available complementary DNA microarray data from 399 human epidermal growth factor receptor 2 (HER2)-negative primary breast cancer samples from patients who underwent standard neoadjuvant chemotherapy. We analyzed the messenger RNA (mRNA) expression levels of key breast cancer markers and therapeutic target genes according to residual cancer burden (RCB) classification: RCB-0/I, RCB-II, and RCB-III. Results Among hormone receptor–positive samples, there were more luminal A tumors by PAM50 (Prediction Analysis of Microarray 50 [Prosigna], aka Prosigna Breast Cancer Prognostic Gene Signature Assay) in RCB-III than in RCB-0/I and RCB-II (P Conclusion In hormone receptor–positive breast cancer, biological features such as luminal A were associated with RCB; this trend was not observed in TN breast cancer. Further, some targeted therapies should be tested as new strategies after standard neoadjuvant chemotherapy in future clinical trials

Current Multidisciplinary Approach to Fertility Preservation for Breast Cancer Patients

Adverse effects on fertility are a significant problem for premenopausal breast cancer patients. Since April 2009, we have been referring young patients for fertility counseling provided by a multidisciplinary team. Here we evaluated the efficacy and safety of our current fertility preservation approach. We retrospectively analyzed the cases of 277 patients < 45 years old at diagnosis, which was made between 2009 and 2016. Seventy-two (26%) patients received fertility counseling. Seventeen (6%) of the 277 patients decided to preserve their fertility before starting adjuvant systemic therapy. Six (35%) patients underwent oocyte cryopreservation, and 11 (65%) married patients opted for embryo cryopreservation. There were no pregnancies among the patients undergoing oocyte cryopreservation, whereas 3 (27%) of the patients who opted for embryo cryopreservation became pregnant. Two (12%) patients stopped endocrine therapy after 2 years in an effort to become pregnant, but their breast cancers recurred. Though the problem of fertility loss for breast cancer patients is important and we should assess the infertility risk for all patients, we should also consider the prognosis. In June 2016, we launched a prospective multicenter cohort study to evaluate the efficacy and safety of fertility preservation in greater detail

A Wide and Deep Exploration of Radio Galaxies with Subaru HSC (WERGS). IX. The most overdense region at z ∼ 5 inhabited by a massive radio galaxy

We report on the galaxy density environment around a high-z radio galaxy (HzRG) at z = 4.72, HSC J083913.17+011308.1 (HSC J0839+0113), probed using an r-dropout Lyman break galaxy (LBG) sample from the Hyper Suprime-Cam Subaru Strategic Program data. We find that HSC J0839+0113 resides in the outskirts of an overdense region identified by the r-dropout galaxies at a 4.7σ significance level. The projected distance between HSC J0839+0113 and the peak position of the overdense region is 0.4 physical Mpc, which is shorter than the typical protocluster radius in this epoch. According to the extended Press–Schechter and the light cone models, the HSC J0839+0113-hosted overdense region is expected to evolve into a halo &gt;1014 M⊙ at z = 0 with a high probability of &gt;80%⁠. These findings suggest that HSC J0839+0113 is associated with a protocluster. The HSC J0839+0113 rich-system is the most overdense region of LBGs among the known protoclusters with LBGs in the same cosmic epoch

Efficacy and safety of olaparib, olaparib plus bevacizumab and niraparib maintenance treatment in Japanese patients with platinum-sensitive advanced ovarian cancer

Objective: To investigate whether maintenance treatment could be safely and effectively performed with olaparib, olaparib plus bevacizumab and niraparib in platinum-sensitive advanced ovarian cancer at multiple institutions in Japan. Methods: We investigated progression-free survival and adverse events in 117 patients with platinum-sensitive advanced ovarian cancer treated with maintenance therapy. Results: The median progression-free survival of 117 patients was 20.1 months. Patients with germline BRCA pathogenic variants had a significantly better prognosis than the other groups (P Conclusion: Maintenance treatment was performed effectively and safely. Renal function deterioration is likely to occur during maintenance treatment, and careful administration is important in platinum-sensitive advanced ovarian cancer

The Association of Postprandial Triglyceride Variability with Renal Dysfunction and Microalbuminuria in Patients with Type 2 Diabetic Mellitus: A Retrospective and Observational Study

Objective. We examined whether or not day-to-day variations in lipid profiles, especially triglyceride (TG) variability, were associated with the exacerbation of diabetic kidney disease. Methods. We conducted a retrospective and observational study. First, 527 patients with type 2 diabetes mellitus (DM) who had had their estimated glomerular filtration rate (eGFR) checked every 6 months since 2012 for over 5 years were registered. Variability in postprandial TG was determined using the standard deviation (SD), SD adjusted (Adj-SD) for the number of measurements, and maximum minus minimum difference (MMD) during the first three years of follow-up. The endpoint was a & GE;40% decline from baseline in the eGFR, initiation of dialysis or death. Next, 181 patients who had no micro- or macroalbuminuria in February 2013 were selected from among the 527 patients for an analysis. The endpoint was the incidence of microalbuminuria, initiation of dialysis, or death. Results. Among the 527 participants, 110 reached a & GE;40% decline from baseline in the eGFR or death. The renal survival was lower in the higher-SD, higher-Adj-SD, and higher-MMD groups than in the lower-SD, lower-Adj-SD, and lower-MMD groups, respectively (log-rank test p=0.0073, 0.0059, and 0.0195, respectively). A lower SD, lower Adj-SD, and lower MMD were significantly associated with the renal survival in the adjusted model (hazard ratio, 1.62, 1.66, 1.59; 95% confidence intervals, 1.05-2.53, 1.08-2.58, 1.04-2.47, respectively). Next, among 181 participants, 108 developed microalbuminuria or death. The nonincidence of microalbuminuria was lower in the higher-SD, higher-Adj-SD, and higher-MMD groups than in the lower-SD, lower-Adj-SD, and lower-MMD groups, respectively (log-rank test p=0.0241, 0.0352, and 0.0474, respectively). Conclusions. Postprandial TG variability is a novel risk factor for eGFR decline and the incidence of microalbuminuria in patients with type 2 DM