DeLTa-Seq: High-Throughput Targeted RNA-Seq of Rice Leaves Without RNA Purification.

DeLTa-seq is a high-throughput RNA-seq library preparation method that enables quantification of the expression of hundreds of arbitrarily selected genes without RNA purification. This method involves direct reverse transcription using rice leaf lysate and targeted RNA-seq library preparation. DeLTa-seq enables the precise quantification of gene expression with a small number of sequencing reads. This chapter provides detailed information on the design of gene-specific primers, sampling of rice leaves, preparation of lysates, direct-lysate reverse transcription, targeted RNA-seq library preparation, and bioinformatic analysis of DeLTa-seq data.

Premature senescence is regulated by crosstalk among TFEB, the autophagy lysosomal pathway and ROS derived from damaged mitochondria in NaAsO2-exposed auditory cells.

Age-related hearing loss (ARHL) is one of the most prevalent types of sensory decline in a superaging society. Although various studies have focused on the effect of oxidative stress on the inner ear as an inducer of ARHL, there are no effective preventive approaches for ARHL. Recent studies have suggested that oxidative stress-induced DNA damage responses (oxidative DDRs) drive cochlear cell senescence and contribute to accelerated ARHL, and autophagy could function as a defense mechanism against cellular senescence in auditory cells. However, the underlying mechanism remains unclear. Sodium arsenite (NaAsO2) is a unique oxidative stress inducer associated with reactive oxygen species (ROS) that causes high-tone hearing loss similar to ARHL. Transcription factor EB (TFEB) functions as a master regulator of the autophagy‒lysosome pathway (ALP), which is a potential target during aging and the pathogenesis of various age-related diseases. Here, we focused on the function of TFEB and the impact of intracellular ROS as a potential target for ARHL treatment in a NaAsO2-induced auditory premature senescence model. Our results suggested that short exposure to NaAsO2 leads to DNA damage, lysosomal damage and mitochondrial damage in auditory cells, triggering temporary signals for TFEB transport into the nucleus and, as a result, causing insufficient autophagic flux and declines in lysosomal function and biogenesis and mitochondrial quality. Then, intracellular ROS derived from damaged mitochondria play a role as a second messenger to induce premature senescence in auditory cells. These findings suggest that TFEB activation via transport into the nucleus contributes to anti-senescence activity in auditory cells and represents a new therapeutic target for ARHL. We have revealed the potential function of TFEB as a master regulator of the induction of oxidative stress-induced premature senescence and the senescence-associated secretion phenotype (SASP) in auditory cells, which regulates ALP and controls mitochondrial quality through ROS production.

Root anatomical plasticity contributes to the different adaptive responses of two Phragmites species to water-deficit and low-oxygen conditions.

The runner reed (Phragmites japonica ) is the dominant species on riverbanks, whereas the common reed (Phragmites australis ) thrives in continuously flooded areas. Here, we aimed to identify the key root anatomical traits that determine the different adaptative responses of the two Phragmites species to water-deficit and low-oxygen conditions. Growth measurements revealed that P . japonica tolerated high osmotic conditions, whereas P . australis preferred low-oxygen conditions. Root anatomical analysis revealed that the ratios of the cortex to stele area and aerenchyma (gas space) to cortex area in both species increased under low-oxygen conditions. However, a higher ratio of cortex to stele area in P . australis resulted in a higher ratio of aerenchyma to stele, which includes xylem vessels that are essential for water and nutrient uptakes. In contrast, a lower ratio of cortex to stele area in P . japonica could be advantageous for efficient water uptake under high-osmotic conditions. In addition to the ratio of root tissue areas, rigid outer apoplastic barriers composed of a suberised exodermis may contribute to the adaptation of P . japonica and P . australis to water-deficit and low-oxygen conditions, respectively. Our results suggested that root anatomical plasticity is essential for plants to adapt and respond to different soil moisture levels.

Alkannin Attenuates Amyloid ß Aggregation and Alzheimer's Disease Pathology.

Alzheimer's disease (AD) is a neurodegenerative disease that is accompanied by memory decline and cognitive dysfunction. Aggregated amyloid ß formation and accumulation may be one of the underlying mechanisms of the pathophysiology of AD. Therefore, compounds that can inhibit amyloid ß aggregation may be useful for treatment. Based on this hypothesis, we screened plant compounds used in Kampo medicine for chemical chaperone activity and identified that alkannin had this property. Further analysis indicated that alkannin could inhibit amyloid ß aggregation. Importantly, we also found that alkannin inhibited amyloid ß aggregation after aggregates had already formed. Through the analysis of circular dichroism spectra, alkannin was found to inhibit ß-sheet structure formation, which is an aggregation-prone toxic structure. Furthermore, alkannin attenuated amyloid ß-induced neuronal cell death in PC12 cells, ameliorated amyloid ß aggregation in the AD model of Caenorhabditis elegans (C. elegans), and inhibited chemotaxis observed in AD C. elegans, suggesting that alkannin could potentially inhibit neurodegeneration in vivo. Overall, these results suggest that alkannin may have novel pharmacological properties for inhibiting amyloid ß aggregation and neuronal cell death in AD. SIGNIFICANCE STATEMENT: Aggregated amyloid ß formation and accumulation is one of the underlying mechanisms of the pathophysiology of Alzheimer's disease. We found that alkannin had chemical chaperone activity, which can inhibit ß-sheet structure formation of amyloid ß and its aggregation, neuronal cell death, and Alzheimer's disease phenotype in C. elegans. Overall, alkannin may have novel pharmacological properties for inhibiting amyloid ß aggregation and neuronal cell death in Alzheimer's disease.

COOH-terminal fragment of APP interacts with p62, forms an aggregate, and induces autophagic degradation in Alzheimer's cell model.

Alzheimer's disease is an intractable disease, and the accumulation of amyloid ß in the brain is thought to be involved in the onset of the disease. Additionally, abnormal protein accumulation due to autophagic deficiency may also be involved in disease progression. Autophagy involves a mechanism called selective autophagy. However, the relationship between selective autophagy and the amyloid precursor protein (APP) remains unclear. In the present study, we analyzed the interaction between p62, an adapter protein, and an APP-related molecule and found that p62 interacted with the COOH-terminal fragment of APP (C60). When C60 and p62 are overexpressed, aggregates are formed and C60 is degraded by autophagy. These aggregates cannot be easily degraded, even with a reducing agent. We also found that autophagosome- and lysosome marker-positive vesicles were formed in the C60- and p62-expressing cells. Superresolution technology also revealed that p62-C60-positive autophagosomes were formed in the cells. Overall, these results suggest that p62 may bind with C60 to form aggregates and induce autophagy in autophagosomes. These results reveal one of the mechanisms underlying the progression of Alzheimer's disease, in which selective autophagy may be involved.

DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate.

BACKGROUND: Quantification of gene expression such as RNA-Seq is a popular approach to study various biological phenomena. Despite the development of RNA-Seq library preparation methods and sequencing platforms in the last decade, RNA extraction remains the most laborious and costly step in RNA-Seq of tissue samples of various organisms. Thus, it is still difficult to examine gene expression in thousands of samples. RESULTS: Here, we developed Direct-RT buffer in which homogenization of tissue samples and direct-lysate reverse transcription can be conducted without RNA purification. The DTT concentration in Direct-RT buffer prevented RNA degradation but not RT in the lysates of several plant tissues, yeast, and zebrafish larvae. Direct reverse transcription on these lysates in Direct-RT buffer produced comparable amounts of cDNA to those synthesized from purified RNA. To maximize the advantage of the Direct-RT buffer, we integrated Direct-RT and targeted RNA-Seq to develop a cost-effective, high-throughput quantification method for the expressions of hundreds of genes: DeLTa-Seq (Direct-Lysate reverse transcription and Targeted RNA-Seq). The DeLTa-Seq method could drastically improve the efficiency and accuracy of gene expression analysis. DeLTa-Seq analysis of 1056 samples revealed the temperature-dependent effects of jasmonic acid and salicylic acid in Arabidopsis thaliana. CONCLUSIONS: The DeLTa-Seq method can realize large-scale studies using thousands of animal, plant, and microorganism samples, such as chemical screening, field experiments, and studies focusing on individual variability. In addition, Direct-RT is also beneficial for gene expression analysis in small tissues from which it is difficult to purify enough RNA for the experiments.

Fillable and unfillable gaps in plant transcriptome under field and controlled environments.

The differences between plants grown in field and in controlled environments have long been recognized. However, few studies have addressed the underlying molecular mechanisms. To evaluate plant responses to fluctuating environments using laboratory equipment, we developed SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature and humidity of field environments. We analysed massive transcriptome data of rice plants grown under field and SmartGC conditions to clarify the differences in plant responses to field and controlled environments. Rice transcriptome dynamics in SmartGC mimicked those in the field, particularly during the morning and evening but those in conventional growth chamber conditions did not. Further analysis revealed that fluctuation of irradiance affects transcriptome dynamics in the morning and evening, while fluctuation of temperature affects transcriptome dynamics only in the morning. We found upregulation of genes related to biotic and abiotic stress, and their expression was affected by environmental factors that cannot be mimicked by SmartGC. Our results reveal fillable and unfillable gaps in the transcriptomes of rice grown in field and controlled environments and can accelerate the understanding of plant responses to field environments for both basic biology and agricultural applications.

Early introduction of very small amounts of multiple foods to infants: A randomized trial.

BACKGROUND: We investigated whether multiple food allergies could be safely prevented by simultaneously administering very small amounts of multiple foods. METHODS: Infants 3-4 months old with atopic dermatitis from 14 primary care pediatric clinics in Japan were enrolled in this randomized, placebo-controlled trial. The infants were administered either mixed allergenic food powder (MP) containing egg, milk, wheat, soybean, buckwheat, and peanuts, or placebo powder (PP). The amount of powder was increased in a stepwise manner on weeks 2 and 4, and continued until week 12. The occurrence of food allergy episodes after powder intervention was assessed at 18 months old. This trial was registered with the University Hospital Medical Information Network Clinical Trials Registry (number UMIN000027837). RESULTS: A total of 163 participants were randomly allocated to either the MP group (n = 83) or the PP group (n = 80). The incidence of food allergy episodes by 18 months was significantly different between the MP and PP groups (7/83 vs. 19/80, respectively; risk ratio 0.301 [95% CI 0.116-0.784]; P = 0.0066). Egg allergies were reduced in the MP group. In addition, food allergy episodes from any of the other five foods were significantly reduced, although the reductions in those due to individual foods were not significant. CONCLUSIONS: Gradually increasing the intake of very small amounts of multiple foods in early infancy can safely reduce the incidence of egg allergies. Other foods may also suppress food allergies, but no definitive conclusions could be reached.

Post-earthquake dizziness syndrome following the 2016 Kumamoto earthquakes, Japan.

This study aimed to examine the types and causes of dizziness experienced by individuals after a major earthquake. This cross-sectional study enrolled healthy participants who experienced the 2016 Kumamoto earthquakes and their aftershocks. Participants completed a questionnaire survey on their symptoms and experiences after the earthquakes. The primary outcome was the occurrence of dizziness and the secondary outcome was the presence of autonomic dysfunction and anxiety. Among 4,231 eligible participants, 1,543 experienced post-earthquake dizziness. Multivariate logistic regression analysis revealed that age (≥21, P < .001), female sex (P < .001), floor on which the individual was at the time (≥3, P = .007), tinnitus/ear fullness (P < .001), anxiety (P < .001), symptoms related to autonomic dysfunction (P = .04), and prior history of motion sickness (P = .002) were significantly associated with the onset of post-earthquake dizziness. Thus suggesting that earthquake-related effects significantly affect inner ear symptoms, autonomic function, and psychological factors. Earthquake-induced disequilibrium may be further influenced by physical stressors, including sensory disruptions induced by earthquake vibrations, changes in living conditions, and autonomic stress. This study increases our understanding of human equilibrium in response to natural disasters.

H3K27me3 demethylases alter HSP22 and HSP17.6C expression in response to recurring heat in Arabidopsis.

Acclimation to high temperature increases plants' tolerance of subsequent lethal high temperatures. Although epigenetic regulation of plant gene expression is well studied, how plants maintain a memory of environmental changes over time remains unclear. Here, we show that JUMONJI (JMJ) proteins, demethylases involved in histone H3 lysine 27 trimethylation (H3K27me3), are necessary for Arabidopsis thaliana heat acclimation. Acclimation induces sustained H3K27me3 demethylation at HEAT SHOCK PROTEIN22 (HSP22) and HSP17.6C loci by JMJs, poising the HSP genes for subsequent activation. Upon sensing heat after a 3-day interval, JMJs directly reactivate these HSP genes. Finally, jmj mutants fail to maintain heat memory under fluctuating field temperature conditions. Our findings of an epigenetic memory mechanism involving histone demethylases may have implications for environmental adaptation of field plants.

Polymorphic SERPINA3 prolongs oligomeric state of amyloid beta.

Molecular chaperon SERPINA3 colocalizes with accumulated amyloid peptide in Alzheimer's disease (AD) patient's brain. From the QTL analysis, we narrowed down Serpina3 with two SNPs in senescence-accelerated mouse prone (SAMP) 8 strain. Our study showed SAMP8 type Serpina3 prolonged retention of oligomeric Aß 42 for longer duration (72 hr) while observing under transmission electron microscope (TEM). From Western blot results, we confirmed presence of Aß 42 oligomeric forms (trimers, tetramers) were maintained for longer duration only in the presences of SAMP8 type Serpina3. Using SH-SY5Y neuroblastoma cell line, we observed until 36 hr preincubated Aß 42 with SAMP8 type Serpina3 caused neuronal cell death compared to 12 hr preincubated Aß 42 with SAMR1 or JF1 type Serpina3 proteins. Similar results were found by extending this study to analyze the effect of polymorphism of SERPINA3 gene of the Japanese SNP database for geriatric research (JG-SNP). We observed that polymorphic SERPINA3 I308T (rs142398813) prolonged toxic oligomeric Aß 42 forms till 48 hr in comparison to the presence wild type SERPINA3 protein, resulting neuronal cell death. From this study, we first clarified pathogenic regulatory role of polymorphic SERPINA3 in neurodegeneration.

Comparison between MB11 BERAphone® and ALGO2e color for hearing screening in Japanese healthy newborns.

BACKGROUND: Since 2001, newborn hearing screening has been performed in Japan. OBJECTIVE: This study compared newborn hearing screening results between the MAICO MB11 BERAphone (MB11) and the Natus ALGO2e color (ALGO) Automated Auditory Brainstem Response (AABR) devices among healthy Japanese newborns. MATERIALS AND METHODS: From December 2014 to April 2018, 1477 healthy newborns were screened by MB11 and 267 by ALGO. Data from at-risk newborns were not included. Outcomes were 'Pass' and 'Refer' rates, specificity, false-positive rates, and assessment duration. Infants with a Refer result were examined using Interacoustics Eclipse. RESULTS: MB11 identified 1425 (96.5%) as Pass and 52 (3.5%) as Refer. ALGO identified 263 (98.5%) as Pass and four (1.5%) as Refer. Specificity and false-positive rates were 97.7% and 2.3% for MB11 and 98.5% and 1.5% for ALGO, respectively. Using MB11, the total mean assessment time was 320.2 ± 220.7 s, with 315.6 ± 214.2 s for Pass and 628.6 ± 288.8 s for Refer. CONCLUSIONS: MB11 is useful for hearing screening in healthy Japanese newborns and is fast and easy to operate. MB11 showed high specificity equivalent to ALGO.

Long-term treatment of Japanese cedar pollinosis with Japanese cedar pollen SLIT drops and persistence of treatment effect: A post-marketing clinical trial.

BACKGROUND: There have been no reports of treatment effect persistence after long-term sublingual immunotherapy (SLIT) in patients with Japanese cedar (JC) pollinosis. Therefore, we conducted a post-marketing clinical trial to investigate the efficacy, safety, and effect persistence of JC pollen SLIT drops after approximately 3 years of treatment. METHODS: This was an open-label trial of 233 patients with JC pollinosis who were treated with JC pollen SLIT drops for approximately 3 years (2015-2017) and followed-up for an additional 2 years (2018-2019). Efficacy and effect persistence were evaluated using nasal and ocular symptom scores, daily use of rescue medication, and Japanese Rhinoconjunctivitis Quality of Life Questionnaire scores recorded during the JC pollen dispersal season of each year. Safety was evaluated by monitoring adverse events and adverse drug reactions. RESULTS: The mean combined total nasal symptom and medication score (range 0-18) during the peak symptom periods of 2015 through 2019 were 5.47 ± 3.38, 4.52 ± 3.13, 3.58 ± 2.63, 5.28 ± 4.01, and 6.83 ± 4.65, respectively. The percentage of patients who used no rescue medications during the same periods was 64.8%, 75.2%, 80.3%, 63.7%, and 50.3%, respectively. A total of 138 adverse drug reaction incidents were recorded in 73 of the 233 patients (31.3%), of which 134 incidents (97.1%) were mild in severity. CONCLUSIONS: JC pollen SLIT drops demonstrated treatment duration-dependent efficacy with effects that persisted for 2 years after cessation of treatment. The drug had a favorable safety profile over the 5-year study period.

Transitional nystagmus in a Bow Hunter's Syndrome case report.

BACKGROUND: Bow Hunter's Syndrome (BHS) is known as one of cervical diseases which causes vertigo, but the details of its vertigo, especially nystagmus and eye movement, are still incompletely understood. This time, we reported the first case of BHS with a nystagmus chart with video record of transitional nystagmus. CASE PRESENTATION: The patient, a 47-year-old female, complained of vertigo caused by head rotation. When she turned her head leftward, leftward nystagmus appeared, and this was followed by dullness of the right arm. After her head was returned to the central position, downbeat nystagmus appeared, which changed to rightward nystagmus. She was diagnosed with BHS by her symptoms and images. We recorded a nystagmus video and nystagmus chart of this transitional nystagmus including downbeat nystagmus. Her vertigo was cured by the modification of a prescription for her past medical history: hypertension. CONCLUSION: The vertigo of BHS accompanies nystagmus. In this present case, the transitional nystagmus was observed, and it occurred toward the healthy side. Then the nystagmus direction was changed to the affected side via downbeat nystagmus. This is the first report with both a nystagmus chart with video of BHS. Nowadays, various kinds of vertigo induced by neck movement are known. BHS is a rare disease among vertigo diseases, but we should consider it as a different diagnosis of vertigo patients. A precise interview and proper examination are required to make the final diagnosis.

Prognostic factors of recovery with medication in patients with taste disorders.

OBJECTIVES: We aimed to elucidate the prognostic factors of the patients with taste disorders who were treated with popular and common medication in Japan. MATERIALS AND METHODS: A retrospective study on the medical charts of a total of 255 patients with taste disorders who were treated primarily with oral medication including a zinc agent. RESULTS: The factors below were significantly linked with poor prognosis: 1) male gender, 2) taste disorders that began 3 months before starting treatment and 3) a severe taste disorder grade at the initial visit. CONCLUSIONS: We have concluded that the prognosis for the patients with taste disorders who were treated by popular and standard medication therapy in Japan recently was significantly linked to gender, the period of 3 months before starting the treatment and the severity of the disorder at the time of diagnosis. In addition, we recognized some limitations we should resolve in further research including a method of measuring "umami" and so on. CLINICAL RELEVANCE: Better awareness of these factors should be clinically useful when we manage patients with taste disorders. Earlier treatment should be started to cure the symptoms.

Uptake of further investigations following universal urinary screening among elementary and junior high school students in Shiga Prefecture, Japan: A retrospective cohort study.

AIM: This study aimed to investigate the current progression status from screening phase to further investigation phase in the Japanese school urine mass screening (SUS) project. METHODS: This retrospective cohort study on the SUS project across the Shiga Prefecture during 2012 to 2017 analysed data from school life instruction sheets, which are principal documents in the SUS project, regarding urinalysis, attendance at follow-up and diagnoses. RESULTS: Between the years 2012 to 2017, a median of 107 out of 83 749 elementary school students (aged 6-11 years) and 215 out of 42 870 junior high students (aged 12-14 years) had urine abnormalities identified for the first time in the SUS project. Among those with urine abnormalities, a mean of 4.2% of elementary school and 1.8% of junior high school students, respectively, were diagnosed with suspected glomerulonephritis for the first time. Overall, 5.9% (95% confidence interval [CI] 4.1, 7.7) and 23.6% (95% CI 21.3, 25.9) of proteinuria-positive elementary and junior high school students, respectively, did not undergo further investigations. The probability of a student undergoing further investigations was not affected by the local availability of medical care benefits. CONCLUSION: In the current SUS project, screening frequently does not lead to further investigation, especially among junior high school students. To maintain the integrity of the SUS project and to prevent the progression of renal disease in young students, efforts including elucidation of barriers to further investigations should be made to reduce the proportions of students not undergoing further investigations for abnormal urinalysis findings.

Caspase-8 Regulates Endoplasmic Reticulum Stress-Induced Necroptosis Independent of the Apoptosis Pathway in Auditory Cells.

The aim of this study is to elucidate the detailed mechanism of endoplasmic reticulum (ER) stress-induced auditory cell death based on the function of the initiator caspases and molecular complex of necroptosis. Here, we demonstrated that ER stress initiates not only caspase-9-dependent intrinsic apoptosis along with caspase-3, but also receptor-interacting serine/threonine kinase (RIPK)1-dependent necroptosis in auditory cells. We observed the ultrastructural characteristics of both apoptosis and necroptosis in tunicamycin-treated cells under transmission electron microscopy (TEM). We demonstrated that ER stress-induced necroptosis was dependent on the induction of RIPK1, negatively regulated by caspase-8 in auditory cells. Our data suggested that ER stress-induced intrinsic apoptosis depends on the induction of caspase-9 along with caspase-3 in auditory cells. The results of this study reveal that necroptosis could exist for the alternative backup cell death route of apoptosis in auditory cells under ER stress. Interestingly, our data results in a surge in the recognition that therapies aimed at the inner ear protection effect by caspase inhibitors like zVAD-fmk might arrest apoptosis but can also have the unanticipated effect of promoting necroptosis. Thus, RIPK1-dependent necroptosis would be a new therapeutic target for the treatment of sensorineural hearing loss due to ER stress.

Otorhinolaryngology surgery analysis in Japan and Thailand: Comparing Nihon University School of Medicine with Thammasat University Faculty of Medicine.

BACKGROUND/OBJECTIVE: We compared the surgery data of the department of otorhinolaryngology of the university hospitals in Japan and Thailand to make each feature and the differences of both otorhinolaryngology surgeries clear. There are some medical meetings and congresses between Japan and Thailand, but so far it has not reported about the comparison of surgery data. METHODS: Retrospectively, we analyzed the surgical statistics of department of otorhinolaryngology of Nihon University Itabashi Hospital (Japan) and Thammasat University Hospital (Thailand) between 2013 and 2014. RESULTS: In Japan, there were many surgeries involving the middle ear and paranasal sinuses whereas in Thailand, tracheotomy and tonsillectomy were more frequently performed. Statistical analysis of the surgical data revealed specific tendencies in the nature of the operations performed at each university. CONCLUSION: This study revealed that there are rather differences between two hospitals' surgeries features. It was thought that it would be beneficial to both institutions to gain a deeper understanding of the areas of expertise of each university in order to foster an environment conducive to increasing future international collaborations.