Aberrant proximal tubule DNA methylation underlies phenotypic changes related to kidney dysfunction in patients with diabetes.

Epigenetic mechanisms are considered to contribute to diabetic nephropathy by maintaining memory of poor glycemic control during the early stages of diabetes. However, DNA methylation changes in the human kidney are poorly characterized, because of the lack of cell type-specific analysis. We examined DNA methylation in proximal tubules purified from diabetic nephropathy patients and identified differentially methylated CpG sites, given the critical role of proximal tubules in the kidney injury. Hypermethylation was observed at CpG sites annotated to genes responsible for proximal tubule functions, including gluconeogenesis, nicotinamide adenine dinucleotide synthesis, transporters of glucose, water, phosphate, and drugs, in diabetic kidneys, while genes involved in oxidative stress and the cytoskeleton exhibited demethylation. Methylation levels of CpG sites annotated to ACTN1, BCAR1, MYH9, UBE4B, AFMID, TRAF2, TXNIP, FOXO3, and HNF4A were correlated with the estimated glomerular filtration rate, while methylation of the CpG site in RUNX1 was associated with interstitial fibrosis and tubular atrophy. Hypermethylation of G6PC and HNF4A was accompanied by decreased expression in diabetic kidneys. Proximal tubule-specific hypomethylation of metabolic genes related to HNF4A observed in control kidneys was compromised in diabetic kidneys, suggesting a role for aberrant DNA methylation in the dedifferentiation process. Multiple genes with aberrant DNA methylation in diabetes overlapped genes with altered expressions in maladaptive proximal tubule cells, including transcription factors PPARA and RREB1. In conclusion, DNA methylation derangement in the proximal tubules of patients with diabetes may drive phenotypic changes, characterized by inflammatory and fibrotic features, along with impaired function in metabolism and transport.

Emergence of integrated behaviors through direct optimization for homeostasis.

Homeostasis is a self-regulatory process, wherein an organism maintains a specific internal physiological state. Homeostatic reinforcement learning (RL) is a framework recently proposed in computational neuroscience to explain animal behavior. Homeostatic RL organizes the behaviors of autonomous embodied agents according to the demands of the internal dynamics of their bodies, coupled with the external environment. Thus, it provides a basis for real-world autonomous agents, such as robots, to continually acquire and learn integrated behaviors for survival. However, prior studies have generally explored problems pertaining to limited size, as the agent must handle observations of such coupled dynamics. To overcome this restriction, we developed an advanced method to realize scaled-up homeostatic RL using deep RL. Furthermore, several rewards for homeostasis have been proposed in the literature. We identified that the reward definition that uses the difference in drive function yields the best results. We created two benchmark environments for homeostasis and performed a behavioral analysis. The analysis showed that the trained agents in each environment changed their behavior based on their internal physiological states. Finally, we extended our method to address vision using deep convolutional neural networks. The analysis of a trained agent revealed that it has visual saliency rooted in the survival environment and internal representations resulting from multimodal input.

Highly Efficient Blue Fluorescent Organic Light-Emitting Devices Based on λ5-Phosphinine Derivatives.

Although λ5-phosphinine derivatives are known as a promising class of blue fluorescent emitters, those photoluminescent quantum yield (PLQY) values have been reached up to 92 %, however, only a few examples have been explored as an emitter for blue organic light-emitting device (OLED), and the external quantum efficiency (EQE) has been below 2.4 % so far. In this study, we newly developed two types of blue λ5-phosphinine derivatives namely CN-COCF3 and CO2Me-CHO, and investigated the photophysical properties in the solid states. The photophysical analyses in solid state films suggested that the strong electron-accepting nature of these λ5-phosphinine derivatives caused the inferior PLQY values, and the exciplex formation with the host and neighboring materials should be avoided to improve the device efficiency. By choosing suitable host and neighboring materials with deep ionization potentials, we successfully realized efficient blue fluorescent OLEDs with EQE of over 4 % and CIE (0.14, 0.18). This is among the best in λ5-phosphinine-based blue OLEDs so far.

Effect of spo0A, sigE, sigG, and sigK disruption on butanol production and spore formation in Clostridium saccharoperbutylacetonicum strain N1-4 (ATCC13564).

Clostridium saccharoperbutylacetonicum strain N1-4 (ATCC13564) is a butanol-producing strain suitable for application to butanol production from cellulosic materials by co-culture with cellulolytic and thermophilic species, such as Hungateiclostridium thermocellum (synonym: Clostridium thermocellum). The optimal temperature for butanol production by strain N1-4 is 30 °C, and the strain is sensitive to a high culture temperature of 37 °C. Given that spore formation is observed at high frequency when strain N1-4 is cultivated at 37 °C, we assumed in a previous study that the initiation of sporulation is related to a decrease in butanol production. Therefore, to investigate the relationship between butanol production and spore formation, we generated strain N1-4 isolates in which genes related to spore formation were disrupted. The sporulation-related gene disruptants of spo0A, sigE, sigG, and sigK lost the ability to produce heat-resistant spores, irrespective of the culture temperature. Among the gene disruptants produced, only the spo0A disruptant lost butanol-producing ability when cultivated at 30 °C. Interestingly, the sigE disruptant maintained butanol productivity similar to that observed at 30 °C, even when cultivated at 37 °C. In addition, the sigE disruptant successfully produced butanol from Avicel cellulose by co-culture with H. thermocellum at a fermentation temperature of 37 °C.

Identification of a Novel Quinvirus in the Family Betaflexiviridae That Infects Winter Wheat.

Yellow mosaic disease in winter wheat is usually attributed to the infection by bymoviruses or furoviruses; however, there is still limited information on whether other viral agents are also associated with this disease. To investigate the wheat viromes associated with yellow mosaic disease, we carried out de novo RNA sequencing (RNA-seq) analyses of symptomatic and asymptomatic wheat-leaf samples obtained from a field in Hokkaido, Japan, in 2018 and 2019. The analyses revealed the infection by a novel betaflexivirus, which tentatively named wheat virus Q (WVQ), together with wheat yellow mosaic virus (WYMV, a bymovirus) and northern cereal mosaic virus (a cytorhabdovirus). Basic local alignment search tool (BLAST) analyses showed that the WVQ strains (of which there are at least three) were related to the members of the genus Foveavirus in the subfamily Quinvirinae (family Betaflexiviridae). In the phylogenetic tree, they form a clade distant from that of the foveaviruses, suggesting that WVQ is a member of a novel genus in the Quinvirinae. Laboratory tests confirmed that WVQ, like WYMV, is potentially transmitted through the soil to wheat plants. WVQ was also found to infect rye plants grown in the same field. Moreover, WVQ-derived small interfering RNAs accumulated in the infected wheat plants, indicating that WVQ infection induces antiviral RNA silencing responses. Given its common coexistence with WYMV, the impact of WVQ infection on yellow mosaic disease in the field warrants detailed investigation.

Isolation of ammonia gas-tolerant extremophilic bacteria and their application to the elimination of malodorous gas emitted from outdoor heat-treated toilets.

Ammonia gas-tolerant extremophilic bacteria capable of growing in atmospheres containing up to 4000 ppm of gaseous ammonia were isolated. These bacteria were capable of growing in nutrient broth containing high concentrations of ammonia water, with growth in medium augmented with 0.1-0.2% ammonia exceeding that in medium without ammonia. The minimal inhibitory concentration of ammonia in the medium was 0.5%. The isolated ammonia gas-tolerant bacterium was moderately alkaliphilic, with optimum growth was observed at pH 9. DNA sequence analysis of the 16SrRNA gene revealed that the isolated bacterium was Bacillus lentus. Furthermore, extremophilic bacteria cultured in a 1300 ppm ammonia gas atmosphere on agar medium containing no nitrogen sources were observed to use ammonia gas for growth. These bacteria were identified as Paenibacillus lentus and Bacillus altitudinis based on 16SrRNA gene sequence analysis. The deodorizing effect of ammonia odor by the isolated bacteria immobilized on sawdust was evaluated. The findings showed that forcing ammonia gas through a column containing B. altitudinis immobilized on sawdust reduced the concentration of ammonia gas by 30% compared to columns containing sawdust only. The isolated bacteria immobilized on wood sawdust lost the capacity deodorization after drying, but this function could be restored with increased moisture. The ammonia gas-tolerant extremophilic bacteria immobilized on sawdust show considerable potential for use in ameliorating malodors associated with outdoor heat-treated toilets.

Loop-Mediated Isothermal Amplification Screening for COVID-19 in Asymptomatic Preoperative Orthopedic Patients in a General Hospital in Kanagawa, Japan.

The global coronavirus disease 2019 (COVID-19) pandemic has caused several million infections and hundreds of thousands of deaths. A large number of healthcare workers have died as a result of infection with this virus. Therefore, elective surgery was markedly reduced or stopped in our hospital's orthopedic department. The detection of asymptomatic COVID-19-positive patients became key to reducing the infection risk to physicians and staff to allow orthopedic surgery to be performed. A total of 21 patients were scheduled to undergo orthopedic surgery, including elective surgery, in Shonantobu General Hospital, Chigasaki City, Kanagawa, Japan. All 21 patients gave permission to undergo loop-mediated isothermal amplification (LAMP) screening the day before surgery. None of the 21 patients we tested was positive for COVID-19. All patients remained asymptomatic during the two to four weeks of postoperative follow-up. No physicians or medical staff developed COVID-19 symptoms. This was a very small study in a city with a relatively low incidence of COVID-19. We found that LAMP screening was accurate, in terms of its negative predictive value. Larger studies are needed.

Tylosin degradation during manure composting and the effect of the degradation byproducts on the growth of green algae.

In this study, we investigate the tylosin degradation in sheep feces during composting. The sheep feces containing tylosin were composted using the laboratory-scale composting units. Tylosin was degraded during composting, and the half-life of tylosin degradation decreased with increasing temperature from 40 °C to 65 °C. The tylosin degradation in sheep feces can be attributed to the microorganisms in the feces and not to heating because tylosin did not degrade over a period of 48 h at temperatures of 0 °C-65 °C in sterilized water. The artificial rainwater solution extracted from the composted sample did not inhibit the growth of Raphidocelis subcapitata, a type of green alga. Our results indicate that composting the feces containing tylosin is effective in degrading tylosin, which may result in the preservation of agricultural fields as well as nearby aquatic environments.

Electrically Conductive Gels Prepared from Syndiotactic Polystyrene and an Ionic Liquid.

Syndiotactic polystyrene (SPS) physical gels containing a large amount of the ionic liquid 1-butylpyridinium bromide ([C4py]Br) were systematically prepared and their physical properties were examined in detail. The gels had stable forms for a long time, having storage elastic modulus values of normal gels. They showed nearly the same values of the electrical conductivity (∼7 mS/cm) as those of the mixed solutions of [C4py]Br, suggesting that the distribution of [C4py]Br was uniform in these gels and that the charge transportation in these SPS gels was not interrupted by a three-dimensional network of SPS fibrils consisting of the SPS δ crystalline phases.

Diastereodivergent and Regiodivergent Total Synthesis of Princepin and Isoprincepin in Both (7″R,8″R) and (7″S,8″S) Isomers.

The first total synthesis of (7″R,8″R)-, (7″S,8″S)-isomers of princepin (1) and (7″R,8″R)-, (7″S,8″S)-isomers of isoprincepin (2) was accomplished in a highly stereoselective manner via para quinomethide-mediated construction of the furofuran and 1,4-benzodioxane rings. Structural confirmation methods of 1 and 2 were established by CD and HPLC analysis of each diastereomers with natural products.

Effect of Target Gene Silencing on Calcite Single Crystal Formation by Thermophilic Bacterium Geobacillus thermoglucosidasius NY05.

Geobacillus thermoglucosidasius NY05 catalyzes calcite single crystal formation at 60 °C by using acetate and calcium. Endospores are embedded at the central part of the calcite single crystal and carbon atoms in the calcite lattice are derived from acetate carbon. Here, we synthesized 21-mer antisense DNA oligonucleotides targeting sporulation transcription factor, acetate-CoA ligase, isocitrate lyase, and malate synthase G mRNAs and evaluated the effect of these oligonucleotides on calcite formation in G. thermoglucosidasius NY05. G. thermoglucosidasius NY05 cells containing antisense DNA oligonucleotides targeting sporulation transcription factor, acetate-CoA ligase, isocitrate lyase, and malate synthase G mRNAs had reduced calcite single crystal formation by 18.7, 50.6, 55.7, and 82.3%, respectively, compared with cells without antisense DNA oligonucleotides. These results support that calcite formation needs endospores as the nucleus to grow, and carbon dioxide generated from acetate, which is metabolized via the glyoxylate pathway and glucogenesis, is supplied to the crystal lattice.

Long-term vulnerability of access to hemodialysis facilities in repopulated areas after the Fukushima Nuclear Disaster: a case report.

In 2011, an earthquake and tsunami struck Japan, and these were followed by the Fukushima Daiichi nuclear power plant accident. The long-term impact on hemodialysis care access in rural areas after the disaster is unknown. Here we report on a 66-year-old male hemodialysis patient who was forced to evacuate and relocate multiple times to receive hemodialysis after the accident. While he returned to his hometown in 2012, all the available hemodialysis facilities had been placed in different districts. Therefore, the patient needed to cross a mountain to visit the hemodialysis facility. On a snowy day, the patient was unable to reach hemodialysis care in a timely manner. With community cooperation, a public ambulance successfully transferred the patient via a detour, taking 4 h to reach the hemodialysis facility. This case demonstrates that access to hemodialysis care in rural areas remains vulnerable even in the long term after a nuclear disaster.

Determination of tylosin excretion from sheep to assess tylosin spread to agricultural fields by manure application.

Antibiotics administered to livestock are partly excreted with urine and feces. As livestock excrement is used as manure on agricultural fields, soil may be contaminated by excreted antibiotics, potentially resulting in the development of antibiotic-resistant bacteria. Therefore, it is necessary to determine the amount of antibiotic administered to livestock that could spread to agricultural fields through manure application. This study reveals the excretion ratio of tylosin from sheep. After developing an analysis procedure for tylosin in urine and feces from sheep, a tylosin excretion study was performed with two sheep. Tylosin was excreted in urine and feces for four days, after which its concentrations dropped below the limits of quantification (urine: 0.5µg/kg, feces: 2.4µg/kg). The total excretion ratio was 11% on average. The results of our study can provide useful knowledge for treating excrement in order to prevent the spread of antibiotics to agricultural fields through manure application.

Suvorexant is associated with a low incidence of delirium in critically ill patients: a retrospective cohort study.

BACKGROUND: Benzodiazepine use is a risk factor for the development of delirium in adult intensive care unit (ICU) patients. Suvorexant is an alternative to benzodiazepines to induce sleep, but the incidence of delirium in critically ill patients is unknown. We undertook this retrospective study to investigate the incidence of delirium in patients who receive suvorexant in the ICU. METHODS: This retrospective cohort study was conducted in a closed 12-bed ICU at a tertiary teaching hospital. Patients admitted to the ICU for 72 h or longer between January and June 2015 were evaluated for delirium using the Confusion Assessment Method for the Intensive Care Unit tool. We evaluated the incidence of delirium in patients who received suvorexant and those who did not. To adjust for confounding factors, multivariable logistic regression analysis was conducted. RESULTS: Study subjects included 118 patients, with a median age of 72 years and a median Acute Physiology and Chronic Health Evaluation II score of 18 points. Eighty-two patients (69.5%) were admitted after cardiovascular surgery. In the suvorexant group, there were fewer post-cardiovascular surgical patients and more medical patients. The duration of mechanical ventilation during ICU stay was longer in the suvorexant group, and sedatives and sleep inducers other than suvorexant were used more frequently in the suvorexant group. The incidence of delirium was 43.8% in the suvorexant group and 58.8% in the non-suvorexant group (P = 0.149). After adjustment for risk factors using multivariable logistic regression analysis, suvorexant was associated with a lower incidence of delirium (odds ratio = 0.23, 95% confidence interval: 0.07-0.73; P = 0.012). CONCLUSIONS: Suvorexant was associated with decreased odds of transitioning to delirium in critically ill patients. The use of suvorexant may lower the incidence of delirium in ICU patients. Future prospective studies are warranted.

Allexiviruses may have acquired inserted sequences between the CP and CRP genes to change the translation reinitiation strategy of CRP.

Allexiviruses are economically important garlic viruses that are involved in garlic mosaic diseases. In this study, we characterized the allexivirus cysteine-rich protein (CRP) gene located just downstream of the coat protein (CP) gene in the viral genome. We determined the nucleotide sequences of the CP and CRP genes from numerous allexivirus isolates and performed a phylogenetic analysis. According to the resulting phylogenetic tree, we found that allexiviruses were clearly divided into two major groups (group I and group II) based on the sequences of the CP and CRP genes. In addition, the allexiviruses in group II had distinct sequences just before the CRP gene, while group I isolates did not. The inserted sequence between the CP and CRP genes was partially complementary to garlic 18S rRNA. Using a potato virus X vector, we showed that the CRPs affected viral accumulation and symptom induction in Nicotiana benthamiana, suggesting that the allexivirus CRP is a pathogenicity determinant. We assume that the inserted sequences before the CRP gene may have been generated during viral evolution to alter the termination-reinitiation mechanism for coupled translation of CP and CRP.

Degarelix treatment is compatible with diabetes and antithrombotic therapy in patients with prostate cancer.

INTRODUCTION: Therapeutically induced androgen deficiency (AD) is a standard treatment for patients with prostate cancer, but it is often associated with various adverse effects (AEs) that may lead to discontinuation. Some AEs may depend on the patient's health condition, while others may be due to complications of the drug delivery method. Degarelix is a gonadotropin-releasing hormone (GnRH) antagonist widely used for the treatment of androgen-dependent prostate cancer. This study aimed to ascertain the following: 1) the compatibility of degarelix treatment with diabetes and 2) any specific causal associations of degarelix injections with increased blood clotting and antithrombotic therapy requirements. PATIENTS AND METHODS: The medical records of 162 patients with prostate cancer who had undergone degarelix treatment were retrospectively examined. The association of a medical history of diabetes and anticoagulant co-treatment with degarelix treatment discontinuation was analyzed statistically. RESULTS: Rapid and significant decreases in prostate-specific antigen (PSA) levels during the course of degarelix treatment were detected for patients with prostate cancer regardless of clinical state. During the 27 months of treatment, 68 subjects (48%) ceased degarelix treatment, owing to several reasons, mainly financial issues. Among these subjects, 19 had diabetes, while 35 were treated with antithrombotics. Extensive statistical analysis indicated that there were no causal associations between degarelix treatment discontinuation and preexisting diabetes or antithrombotic therapy. CONCLUSION: Our study suggests that preexisting diabetes and antithrombotic therapy were not significant factors for the discontinuation of degarelix treatment in patients with prostate cancer.

Magnesium-Calcite Crystal Formation Mediated by the Thermophilic Bacterium Geobacillus thermoglucosidasius Requires Calcium and Endospores.

Fresh Geobacillus thermoglucosidasius cells grown on soybean-casein digest nutrient agar were inoculated as a parent colony 1 cm in diameter on the surface of an agar gel containing acetate and calcium ions (calcite-promoting hydrogel) and incubated at 60 °C for 4 days, after which magnesium-calcite single crystals of 50-130 µm in size formed within the parent colony. Addition of EDTA, polyacrylic acid or N,N-dicyclohexylcarbodiimide to the calcite-forming hydrogel inhibited the parent colony from forming magnesium-calcite crystals. Inoculation of G. thermoglucosidasius on calcite-forming hydrogel containing 5 µM cadmium and 20 µM zinc resulted in a decrease in the sporulation rate from 55 to 7-8 %. Magnesium-calcite synthesis decreased relative to the sporulation rate. G. thermoglucosidasius exhibited higher adsorption/absorbance of calcium than other Geobacillus sp. that do not mediate calcite formation and higher levels of magnesium accumulation. Calcium ions contained in the calcite-promoting hydrogel and magnesium ions concentrated in G. thermoglucosidasius cells serve as the elements for magnesium-calcite synthesis. The observed decreases in sporulation rate and magnesium-calcite formation support the hypothesis that endospores act as nuclei for the synthesis of magnesium-calcite single crystals.

The use of nano-sized acicular material, sliding friction, and antisense DNA oligonucleotides to silence bacterial genes.

Viable bacterial cells impaled with a single particle of a nano-sized acicular material formed when a mixture containing the cells and the material was exposed to a sliding friction field between polystyrene and agar gel; hereafter, we refer to these impaled cells as penetrons. We have used nano-sized acicular material to establish a novel method for bacterial transformation. Here, we generated penetrons that carried antisense DNA adsorbed on nano-sized acicular material (α-sepiolite) by providing sliding friction onto the surface of agar gel; we then investigated whether penetron formation was applicable to gene silencing techniques. Antisense DNA was artificially synthesized as 15 or 90mer DNA oligonucleotides based on the sequences around the translation start codon of target mRNAs. Mixtures of bacterial cells with antisense DNA adsorbed on α-sepiolite were stimulated by sliding friction on the surface of agar gel for 60 s. Upon formation of Escherichia coli penetrons, ß-lactamase and ß-galactosidase expression was evaluated by counting the numbers of colonies formed on LB agar containing ampicillin and by measuring ß-galactosidase activity respectively. The numbers of ampicillin resistant colonies and the ß-galactosidase activity derived from penetrons bearing antisense DNA (90mer) was repressed to 15% and 25%, respectively, of that of control penetrons which lacked antisense DNA. Biphenyl metabolite, ring cleavage yellow compound produced by Pseudomonas pseudoalcaligenes penetron treated with antisense oligonucleotide DNA targeted to bphD increased higher than that lacking antisense DNA. This result indicated that expression of bphD in P. pseudoalcaligenes penetrons was repressed by antisense DNA that targeted bphD mRNA. Sporulation rates of Bacillus subtilis penetrons treated with antisense DNA (15mer) targeted to spo0A decreased to 24.4% relative to penetrons lacking antisense DNA. This novel method of gene silencing has substantial promise for elucidation of gene function in bacterial species that have been refractory to experimental introduction of exogenous DNA.

The 2b protein of Asparagus virus 2 functions as an RNA silencing suppressor against systemic silencing to prove functional synteny with related cucumoviruses.

Asparagus virus 2 (AV-2) is a member of the genus Ilarvirus in the family Bromoviridae. We cloned the coat protein (CP) and the 2b protein (2b) genes of AV-2 isolates from asparagus plants from various regions and found that the sequence for CP and for 2b was highly conserved among the isolates, suggesting that AV-2 from around the world is almost identical. We then made an AV-2 infectious clone by simultaneous inoculation with in vitro transcripts of RNAs 1-3 of AV-2 and in vitro-synthesized CP, which is necessary for initial infection. Because 2b of cucumoviruses in Bromoviridae can suppress systemic silencing as well as local silencing, we analyzed whether there is functional synteny of 2b between AV-2 and cucumovirus. Using the AV-2 infectious clone, we here provided first evidence that Ilarvirus 2b functions as an RNA silencing suppressor; AV-2 2b has suppressor activity against systemic silencing but not local silencing.