Neuronal subtype-specific transcriptomic changes in the cerebral neocortex associated with sleep pressure

Sleep is homeostatically regulated by sleep pressure, which increases during wakefulness and dissipates during sleep. Recent studies have suggested that the cerebral neocortex, a six-layered structure composed of various layer- and projection-specific neuronal subtypes, is involved in the representation of sleep pressure governed by transcriptional regulation. Here, we examined the transcriptomic changes in neuronal subtypes in the neocortex upon increased sleep pressure using single-nucleus RNA sequencing datasets and predicted the putative intracellular and intercellular molecules involved in transcriptome alterations. We revealed that sleep deprivation (SD) had the greatest effect on the transcriptome of layer 2 and 3 intratelencephalic (L2/3 IT) neurons among the neocortical glutamatergic neuronal subtypes. The expression of mutant SIK3 (SLP), which is known to increase sleep pressure, also induced profound changes in the transcriptome of L2/3 IT neurons. We identified Junb as a candidate transcription factor involved in the alteration of the L2/3 IT neuronal transcriptome by SD and SIK3 (SLP) expression. Finally, we inferred putative intercellular ligands, including BDNF, LSAMP, and PRNP, which may be involved in SD-induced alteration of the transcriptome of L2/3 IT neurons. We suggest that the transcriptome of L2/3 IT neurons is most impacted by increased sleep pressure among neocortical glutamatergic neuronal subtypes and identify putative molecules involved in such transcriptional alterations.

DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle

Each tissue has a dominant set of functional proteins required to mediate tissue-specific functions. Epigenetic modifications, transcription, and translational efficiency control tissue-dominant protein production. However, the coordination of these regulatory mechanisms to achieve such tissue-specific protein production remains unclear. Here, we analyzed the DNA methylome, transcriptome, and proteome in mouse liver and skeletal muscle. We found that DNA hypomethylation at promoter regions is globally associated with liver-dominant or skeletal muscle-dominant functional protein production within each tissue, as well as with genes encoding proteins involved in ubiquitous functions in both tissues. Thus, genes encoding liver-dominant proteins, such as those involved in glycolysis or gluconeogenesis, the urea cycle, complement and coagulation systems, enzymes of tryptophan metabolism, and cytochrome P450-related metabolism, were hypomethylated in the liver, whereas those encoding-skeletal muscle-dominant proteins, such as those involved in sarcomere organization, were hypomethylated in the skeletal muscle. Thus, DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins.

Granulocyte Colony-stimulating Factor-associated Aortitis on Gallium Scintigraphy

Aortitis is a rare adverse event associated with granulocyte colony-stimulating factor (G-CSF). Contrast-enhanced computed tomography (CECT) is widely used to diagnose G-CSF-associated aortitis. However, the usefulness of gallium scintigraphy for the diagnosis of G-CSF-associated aortitis is unknown. We herein report a set of pre- and post-treatment gallium scintigrams of a patient with G-CSF-associated aortitis. During the diagnosis, gallium scintigraphy revealed hot spots on the arterial walls that appeared inflamed on CECT. Both the CECT and gallium scintigraphy findings disappeared. Gallium scintigraphy can be a supportive diagnostic tool for G-CSF-associated aortitis, especially in patients with an impaired renal function or allergy to iodine contrast.

Erratum: Search for Cosmic-Ray Boosted Sub-GeV Dark Matter Using Recoil Protons at Super-Kamiokande [Phys. Rev. Lett. 130, 031802 (2023)]

This corrects the article DOI: 10.1103/PhysRevLett.130.031802.

Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans

BACKGROUND

Transcription factors (TFs) exhibit heterogeneous DNA-binding specificities in individual cells and whole organisms under natural conditions, and de novo motif discovery usually provides multiple motifs, even from a single chromatin immunoprecipitation-sequencing (ChIP-seq) sample. Despite the accumulation of ChIP-seq data and ChIP-seq-derived motifs, the diversity of DNA-binding specificities across different TFs and cell types remains largely unexplored.

RESULTS

Here, we applied MOCCS2, our k-mer-based motif discovery method, to a collection of human TF ChIP-seq samples across diverse TFs and cell types, and systematically computed profiles of TF-binding specificity scores for all k-mers. After quality control, we compiled a set of TF-binding specificity score profiles for 2,976 high-quality ChIP-seq samples, comprising 473 TFs and 398 cell types. Using these high-quality samples, we confirmed that the k-mer-based TF-binding specificity profiles reflected TF- or TF-family dependent DNA-binding specificities. We then compared the binding specificity scores of ChIP-seq samples with the same TFs but with different cell type classes and found that half of the analyzed TFs exhibited differences in DNA-binding specificities across cell type classes. Additionally, we devised a method to detect differentially bound k-mers between two ChIP-seq samples and detected k-mers exhibiting statistically significant differences in binding specificity scores. Moreover, we demonstrated that differences in the binding specificity scores between k-mers on the reference and alternative alleles could be used to predict the effect of variants on TF binding, as validated by in vitro and in vivo assay datasets. Finally, we demonstrated that binding specificity score differences can be used to interpret disease-associated non-coding single-nucleotide polymorphisms (SNPs) as TF-affecting SNPs and provide candidates responsible for TFs and cell types.

CONCLUSIONS

Our study provides a basis for investigating the regulation of gene expression in a TF-, TF family-, or cell-type-dependent manner. Furthermore, our differential analysis of binding-specificity scores highlights noncoding disease-associated variants in humans.

SAGAS: Simulated annealing and greedy algorithm scheduler for laboratory automation

During laboratory automation of life science experiments, coordinating specialized instruments and human experimenters for various experimental procedures is important to minimize the execution time. In particular, the scheduling of life science experiments requires the consideration of time constraints by mutual boundaries (TCMB) and can be formulated as the "scheduling for laboratory automation in biology" (S-LAB) problem. However, existing scheduling methods for the S-LAB problems have difficulties in obtaining a feasible solution for large-size scheduling problems at a time sufficient for real-time use. In this study, we proposed a fast schedule-finding method for S-LAB problems, SAGAS (Simulated annealing and greedy algorithm scheduler). SAGAS combines simulated annealing and the greedy algorithm to find a scheduling solution with the shortest possible execution time. We have performed scheduling on real experimental protocols and shown that SAGAS can search for feasible or optimal solutions in practicable computation time for various S-LAB problems. Furthermore, the reduced computation time by SAGAS enables us to systematically search for laboratory automation with minimum execution time by simulating scheduling for various laboratory configurations. This study provides a convenient scheduling method for life science automation laboratories and presents a new possibility for designing laboratory configurations.

Association of B7H3 and B7H4 gene polymorphisms and protein expression with the development and prognosis of autoimmune thyroid diseases

BACKGROUND

The prognosis of autoimmune thyroid diseases (AITDs), including Graves' disease (GD) and Hashimoto's disease (HD), varies among patients. B7-H3 and B7-H4, members of the B7 family of proteins, regulate immune response. To clarify the association of B7-H3 and B7-H4 with the pathogenesis and prognosis of AITDs, we examined the expression of the soluble and membrane form of B7-H3 and B7-H4 and genotyped single nucleotide polymorphisms (SNPs) in the B7H3 and B7H4 genes.

METHODS

We examined the expression of the membrane form of B7-H3 and B7-H4 by flow cytometry and their soluble forms by ELISA. We genotyped SNPs in B7H3 and B7H4 in 187 GD patients, 217 HD patients, and 110 healthy volunteers using the PCR-RFLP method.

RESULTS

The frequency of the B7H3 rs3816661 CC genotype was higher in patients with severe HD. G carriers of B7H4 rs10754339 A/G and B7H4 rs13505 T/G were more frequent in patients with AITD. A carrier of B7H4 rs10158166 A/G and C carriers of B7H4 rs3806373 C/T were more frequent in patients with intractable GD. The proportion of B7-H3⁺ monocytes was higher in the CC genotype of B7H3 rs3816661 C/T than in the other genotypes and was lower in patients with GD and HD than in healthy controls. The concentration of soluble B7-H4 was lower in the TG genotype of B7H4 rs13505T/G than in the TT genotype and was higher in patients with AITD than in healthy controls.

CONCLUSION

B7H3 and B7H4 are associated with AITD susceptibility and prognosis. This article is protected by copyright. All rights reserved.

Search for the Majorana Nature of Neutrinos in the Inverted Mass Ordering Region with KamLAND-Zen

The KamLAND-Zen experiment has provided stringent constraints on the neutrinoless double-beta (0νββ) decay half-life in ^{136}Xe using a xenon-loaded liquid scintillator. We report an improved search using an upgraded detector with almost double the amount of xenon and an ultralow radioactivity container, corresponding to an exposure of 970 kg yr of ^{136}Xe. These new data provide valuable insight into backgrounds, especially from cosmic muon spallation of xenon, and have required the use of novel background rejection techniques. We obtain a lower limit for the 0νββ decay half-life of T_{1/2}^{0ν}>2.3×10^{26}  yr at 90% C.L., corresponding to upper limits on the effective Majorana neutrino mass of 36-156 meV using commonly adopted nuclear matrix element calculations.

Search for Cosmic-Ray Boosted Sub-GeV Dark Matter Using Recoil Protons at Super-Kamiokande

We report a search for cosmic-ray boosted dark matter with protons using the 0.37  megaton×years data collected at Super-Kamiokande experiment during the 1996-2018 period (SKI-IV phase). We searched for an excess of proton recoils above the atmospheric neutrino background from the vicinity of the Galactic Center. No such excess is observed, and limits are calculated for two reference models of dark matter with either a constant interaction cross section or through a scalar mediator. This is the first experimental search for boosted dark matter with hadrons using directional information. The results present the most stringent limits on cosmic-ray boosted dark matter and exclude the dark matter-nucleon elastic scattering cross section between 10^{-33}cm^{2} and 10^{-27}cm^{2} for dark matter mass from 1  MeV/c^{2} to 300  MeV/c^{2}.

Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections

BACKGROUND

Bats harbor various viruses without severe symptoms and act as their natural reservoirs. The tolerance of bats against viral infections is assumed to originate from the uniqueness of their immune system. However, how immune responses vary between primates and bats remains unclear. Here, we characterized differences in the immune responses by peripheral blood mononuclear cells to various pathogenic stimuli between primates (humans, chimpanzees, and macaques) and bats (Egyptian fruit bats) using single-cell RNA sequencing.

RESULTS

We show that the induction patterns of key cytosolic DNA/RNA sensors and antiviral genes differed between primates and bats. A novel subset of monocytes induced by pathogenic stimuli specifically in bats was identified. Furthermore, bats robustly respond to DNA virus infection even though major DNA sensors are dampened in bats.

CONCLUSIONS

Overall, our data suggest that immune responses are substantially different between primates and bats, presumably underlying the difference in viral pathogenicity among the mammalian species tested.

Automation of yeast spot assays using an affordable liquid handling robot

The spot assay of the budding yeast Saccharomyces cerevisiae is an experimental method that is used to evaluate the effect of genotypes, medium conditions, and environmental stresses on cell growth and survival. Automation of the spot assay experiments from preparing a dilution series to spotting to observing spots continuously has been implemented based on large laboratory automation devices and robots, especially for high-throughput functional screening assays. However, there has yet to be an affordable solution for the automated spot assays suited to researchers in average laboratories and with high customizability for end-users. To make reproducible spot assay experiments widely available, we have automated the plate-based yeast spot assay of budding yeast using Opentrons OT-2 (OT-2), an affordable liquid-handling robot, and a flatbed scanner. We prepared a 3D-printed mount for the Petri dish to allow for precise placement of the Petri dish inside the OT-2. To account for the uneven height of the agar plates, which were made by human hands, we devised a method to adjust the z-position of the pipette tips based on the weight of each agar plate. During the incubation of the agar plates, a flatbed scanner was used to automatically take images of the agar plates over time, allowing researchers to quantify and compare the cell density within the spots at optimal time points a posteriori. Furthermore, the accuracy of the newly developed automated spot assay was verified by performing spot assays with human experimenters and the OT-2 and quantifying the yeast-grown area of the spots. This study will contribute to the introduction of automated spot assays and the automated acquisition of growth processes in conventional laboratories that are not adapted for high-throughput laboratory automation.

CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells

MOTIVATION

Cell-cell communications regulate internal cellular states, e.g. gene expression and cell functions, and play pivotal roles in normal development and disease states. Furthermore, single-cell RNA sequencing methods have revealed cell-to-cell expression variability of highly variable genes (HVGs), which is also crucial. Nevertheless, the regulation of cell-to-cell expression variability of HVGs via cell-cell communications is still largely unexplored. The recent advent of spatial transcriptome methods has linked gene expression profiles to the spatial context of single cells, which has provided opportunities to reveal those regulations. The existing computational methods extract genes with expression levels influenced by neighboring cell types. However, limitations remain in the quantitativeness and interpretability: they neither focus on HVGs nor consider the effects of multiple neighboring cell types.

RESULTS

Here, we propose CCPLS (Cell-Cell communications analysis by Partial Least Square regression modeling), which is a statistical framework for identifying cell-cell communications as the effects of multiple neighboring cell types on cell-to-cell expression variability of HVGs, based on the spatial transcriptome data. For each cell type, CCPLS performs PLS regression modeling and reports coefficients as the quantitative index of the cell-cell communications. Evaluation using simulated data showed our method accurately estimated the effects of multiple neighboring cell types on HVGs. Furthermore, applications to the two real datasets demonstrate that CCPLS can extract biologically interpretable insights from the inferred cell-cell communications.

AVAILABILITY AND IMPLEMENTATION

The R package is available at https://github.com/bioinfo-tsukuba/CCPLS. The data are available at https://github.com/bioinfo-tsukuba/CCPLS_paper.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Metabolic regulation in skeletal muscle is essential for blood glucose homeostasis. Obesity causes insulin resistance in skeletal muscle, leading to hyperglycemia and type 2 diabetes. In this study, we performed multiomic analysis of the skeletal muscle of wild-type (WT) and leptin-deficient obese (ob/ob) mice, and constructed regulatory transomic networks for metabolism after oral glucose administration. Our network revealed that metabolic regulation by glucose-responsive metabolites had a major effect on WT mice, especially carbohydrate metabolic pathways. By contrast, in ob/ob mice, much of the metabolic regulation by glucose-responsive metabolites was lost and metabolic regulation by glucose-responsive genes was largely increased, especially in carbohydrate and lipid metabolic pathways. We present some characteristic metabolic regulatory pathways found in central carbon, branched amino acids, and ketone body metabolism. Our transomic analysis will provide insights into how skeletal muscle responds to changes in blood glucose and how it fails to respond in obesity.

Identifying potential regulators of JAGGED1 expression in portal mesenchymal cells

Objective

Portal mesenchymal cells induce the epithelial differentiation of the bile ducts in the developing liver via one of the Delta-Notch signaling components, JAGGED1. Although this differential induction is crucial for normal liver physiology as its genetic disorder (Alagille syndrome) causes jaundice, the molecular mechanism behind JAGGED1 expression remains unknown. Here, we searched for upstream regulatory transcription factors of JAGGED1 using an integrated bioinformatics method.

Results

According to the DoRothEA database, which integrates multiple lines of evidence on the relationship between transcription factors and their downstream target genes, three transcription factors were predicted to be upstream of JAGGED1: SLUG, SOX2, and EGR1. Among these, SLUG and EGR1 were enriched in ACTA2-expressing portal mesenchymal cells in two previously reported human fetal liver single-cell RNA-seq datasets. JAGGED1-expressing portal mesenchymal cells tended to express SLUG rather than EGR1, supporting that SLUG induced JAGGED1 expression. Together with the higher confidentiality of SLUG (DoRothEA level A) over EGR1 (DoRothEA level D), we concluded that SLUG was one of the most important candidate transcription factors upstream of JAGGED1. These results add mechanistic insights into the developmental biology of how portal mesenchymal cells support biliary development in the liver.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-022-06058-4.

scGR-seq: Integrated analysis of glycan and RNA in single cells

Glycans are structurally diverse molecules found on the surface of living cells. The protocol details a system developed for combined analysis of glycan and RNA in single cells (scGR-seq) using human induced pluripotent stem cells (hiPSCs) and hiPSC-derived neural progenitor cells (NPCs). scGR-seq consists of DNA-barcoded lectin-based glycan profiling by sequencing (scGlycan-seq) and single-cell transcriptome profiling (scRNA-seq). scGR-seq will be an essential technique to delineate the cellular heterogeneity of glycans across multicellular systems.

For complete details on the use and execution of this profile, please refer to Minoshima et al. (2021).

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Protocols for combined analysis of glycan and RNA in single cells (scGR-seq)

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scGR-seq is a DNA-barcoded lectin-based glycan profiling

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scGR-seq analysis of hiPSCs and NPCs were shown as an example

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scGR-seq is adaptable for any cells, tissues, and organs across organisms

Optimal Scheduling for Laboratory Automation of Life Science Experiments with Time Constraints

In automated laboratories consisting of multiple different types of instruments, scheduling algorithms are useful for determining the optimal allocations of instruments to minimize the time required to complete experimental procedures. However, previous studies on scheduling algorithms for laboratory automation have not emphasized the time constraints by mutual boundaries (TCMBs) among operations, which is important in procedures involving live cells or unstable biomolecules. Here, we define the "scheduling for laboratory automation in biology" (S-LAB) problem as a scheduling problem for automated laboratories in which operations with TCMBs are performed by multiple different instruments. We formulate an S-LAB problem as a mixed-integer programming (MIP) problem and propose a scheduling method using the branch-and-bound algorithm. Simulations show that our method can find the optimal schedules of S-LAB problems that minimize overall execution time while satisfying the TCMBs. Furthermore, we propose the use of our scheduling method for the simulation-based design of job definitions and laboratory configurations.

Precise Measurement of the D^{0} and D^{+} Lifetimes at Belle II

We report a measurement of the D^{0} and D^{+} lifetimes using D^{0}→K^{-}π^{+} and D^{+}→K^{-}π^{+}π^{+} decays reconstructed in e^{+}e^{-}→cc[over ¯] data recorded by the Belle II experiment at the SuperKEKB asymmetric-energy e^{+}e^{-} collider. The data, collected at center-of-mass energies at or near the ϒ(4S) resonance, correspond to an integrated luminosity of 72  fb^{-1}. The results, τ(D^{0})=410.5±1.1(stat)±0.8(syst)  fs and τ(D^{+})=1030.4±4.7(stat)±3.1(syst)  fs, are the most precise to date and are consistent with previous determinations.

Search for B^{+}→K^{+}νν[over ¯] Decays Using an Inclusive Tagging Method at Belle II

A search for the flavor-changing neutral-current decay B^{+}→K^{+}νν[over ¯] is performed at the Belle II experiment at the SuperKEKB asymmetric energy electron-positron collider. The data sample corresponds to an integrated luminosity of 63  fb^{-1} collected at the ϒ(4S) resonance and a sample of 9  fb^{-1} collected at an energy 60 MeV below the resonance. Because the measurable decay signature involves only a single charged kaon, a novel measurement approach is used that exploits not only the properties of the B^{+}→K^{+}νν[over ¯] decay, but also the inclusive properties of the other B meson in the ϒ(4S)→BB[over ¯] event, to suppress the background from other B meson decays and light-quark pair production. This inclusive tagging approach offers a higher signal efficiency compared to previous searches. No significant signal is observed. An upper limit on the branching fraction of B^{+}→K^{+}νν[over ¯] of 4.1×10^{-5} is set at the 90% confidence level.

Cell-to-cell interaction analysis of prognostic ligand-receptor pairs in human pancreatic ductal adenocarcinoma

Cell-to-cell interactions (CCIs) through ligand-receptor (LR) pairs in the tumor microenvironment underlie the poor prognosis of pancreatic ductal adenocarcinoma (PDAC). However, there is scant knowledge of the association of CCIs with PDAC prognosis, which is critical to the identification of potential therapeutic candidates. Here, we sought to identify the LR pairs associated with PDAC patient prognosis by integrating survival analysis and single-cell CCI prediction. Via survival analysis using gene expression from cancer cohorts, we found 199 prognostic LR pairs. CCI prediction based on single-cell RNA-seq data revealed the enriched LR pairs associated with poor prognosis. Notably, the CCIs involved epithelial tumor cells, cancer-associated fibroblasts, and tumor-associated macrophages through integrin-related and ANXA1–FPR pairs. Finally, we determined that CCIs involving 33 poor-prognostic LR pairs were associated with tumor grade. Although the clinical implication of the set of LR pairs must be determined, our results may provide potential therapeutic targets in PDAC.

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We found 199 prognostic ligand-receptor pairs of pancreatic ductal adenocarcinoma.

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PDAC scRNA-seq data showed cell-cell interactions for the prognostic LR pairs.

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We determined that CCIs involving 33 LR pairs were associated with tumor grade.

Integrated analysis of glycan and RNA in single cells

Single-cell sequencing has emerged as an indispensable technology to dissect cellular heterogeneity but never been applied to the simultaneous analysis of glycan and RNA. Using oligonucleotide-labeled lectins, we first established lectin-based glycan profiling of single cells by sequencing (scGlycan-seq). We then combined the scGlycan-seq with single-cell transcriptome profiling for joint analysis of glycan and RNA in single cells (scGR-seq). Using scGR-seq, we analyzed the two modalities in human induced pluripotent stem cells (hiPSCs) before and after differentiation into neural progenitor cells at the single-cell resolution. The combination of RNA and glycan separated the two cell types clearer than either one of them. Furthermore, integrative analysis of glycan and RNA modalities in single cells found known and unknown lectins that were specific to hiPSCs and coordinated with neural differentiation. Taken together, we demonstrate that scGR-seq can reveal the cellular heterogeneity and biological roles of glycans across multicellular systems.

Antimony from brake dust to the combined sewer collection system via road effluent under rainy conditions

Abrasion of the brake lining of automobiles is one of the main antimony (Sb) sources on the road. Therefore, the road effluent possibly supplies Sb to the combined sewer collection system. However, Sb in road-sewer systems has attracted little concern, although heavy metals such as copper (Cu), zinc (Zn), cadmium (Cd), and lead (Pb) in sewer water have been studied by many previous authors. We investigated the effect of road effluent on Sb in the combined sewer water by collecting road effluent, road dust, and sewer water under rainy and dry weather conditions. Sb in road effluent showed a significantly higher concentration than the other types of samples, and the Sb concentration in sewer during wet weather was significantly higher than that during dry weather. Furthermore, the Sb concentration in sewer water decreased with time during a wash-off event. Clear positive relationships between Sb and Cu and between Sb and Ba in both road effluent and road dust extract indicate the effect of brake abrasion because the brake lining contains Cu, Sb, and Ba in high concentrations. Approximately 42% of Sb load occurred during the wash-off event, while the loads of Cu and Ba were much less. Unlike Cu and Ba, we conclude that Sb in combined sewer water largely depends on road effluent in wet weather due to the wash-off of road dust, which is probably associated with brake lining abrasion.

Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle

Systemic metabolic homeostasis is regulated by inter-organ metabolic cycles involving multiple organs. Obesity impairs inter-organ metabolic cycles, resulting in metabolic diseases. The systemic landscape of dysregulated inter-organ metabolic cycles in obesity has yet to be explored. Here, we measured the transcriptome, proteome, and metabolome in the liver and skeletal muscle and the metabolome in blood of fasted wild-type and leptin-deficient obese (ob/ob) mice, identifying components with differential abundance and differential regulation in ob/ob mice. By constructing and evaluating the trans-omic network controlling the differences in metabolic reactions between fasted wild-type and ob/ob mice, we provided potential mechanisms of the obesity-associated dysfunctions of metabolic cycles between liver and skeletal muscle involving glucose-alanine, glucose-lactate, and ketone bodies. Our study revealed obesity-associated systemic pathological mechanisms of dysfunction of inter-organ metabolic cycles.

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Multi-omic data in liver and skeletal muscle of WT and ob/ob mice were measured

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We developed the trans-omic network of differentially regulated metabolic reactions

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Dysregulation of inter-organ metabolic cycles associated with obesity was revealed

Oncolytic activity of naturally attenuated herpes-simplex virus HF10 against an immunocompetent model of oral carcinoma

Prognosis for advanced oral carcinoma remains poor. Oncolytic virotherapy uses replication-competent viruses to infect and kill only the tumor cells. However, it has been difficult to investigate the oncolytic activity of viruses against oral carcinomas in mouse models. This study established a mouse model of oral cancer and investigated the in vitro and in vivo anti-tumor effects of HF10, a highly attenuated, replication-competent herpes simplex virus (HSV)-1. Mouse tongue cancer was induced by injecting 4-nitroquinoline 1-oxide into the mouse tongue. The murine oral cancer cell line isolated from this tumor, named NMOC1, formed invasive carcinoma within a week when injected into mouse tongue. HF10 successfully infected, replicated, and spread in the cancer cells in vitro. HF10 was able to kill cancer cells isolated from human or mouse tongue tumor. HF10 injection into tongue carcinomas prolonged mouse survival without any side effects or weight loss. Intertumoral injection of GFP-expressing HF10 confirmed that viral spread was confined within the tumors. Immunohistochemical staining showed that HF10 induced infiltration of CD8-positive T cells around HSV-infected cells in the tumor mass, implying increased anti-tumor immunity. We successfully established an oral cancer cell line and showed that HF10 is a promising therapeutic agent for oral cancer.

Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity

Impaired glucose tolerance associated with obesity causes postprandial hyperglycemia and can lead to type 2 diabetes. To study the differences in liver metabolism in healthy and obese states, we constructed and analyzed transomics glucose-responsive metabolic networks with layers for metabolites, expression data for metabolic enzyme genes, transcription factors, and insulin signaling proteins from the livers of healthy and obese mice. We integrated multiomics time course data from wild-type and leptin-deficient obese (ob/ob) mice after orally administered glucose. In wild-type mice, metabolic reactions were rapidly regulated within 10 min of oral glucose administration by glucose-responsive metabolites, which functioned as allosteric regulators and substrates of metabolic enzymes, and by Akt-induced changes in the expression of glucose-responsive genes encoding metabolic enzymes. In ob/ob mice, the majority of rapid regulation by glucose-responsive metabolites was absent. Instead, glucose administration produced slow changes in the expression of carbohydrate, lipid, and amino acid metabolic enzyme-encoding genes to alter metabolic reactions on a time scale of hours. Few regulatory events occurred in both healthy and obese mice. Thus, our transomics network analysis revealed that regulation of glucose-responsive liver metabolism is mediated through different mechanisms in healthy and obese states. Rapid changes in allosteric regulators and substrates and in gene expression dominate the healthy state, whereas slow changes in gene expression dominate the obese state.

Search for Axionlike Particles Produced in e^{+}e^{-} Collisions at Belle II

We present a search for the direct production of a light pseudoscalar a decaying into two photons with the Belle II detector at the SuperKEKB collider. We search for the process e^{+}e^{-}→γa, a→γγ in the mass range 0.2<m_{a}<9.7  GeV/c^{2} using data corresponding to an integrated luminosity of (445±3)  pb^{-1}. Light pseudoscalars interacting predominantly with standard model gauge bosons (so-called axionlike particles or ALPs) are frequently postulated in extensions of the standard model. We find no evidence for ALPs and set 95% confidence level upper limits on the coupling strength g_{aγγ} of ALPs to photons at the level of 10^{-3}  GeV^{-1}. The limits are the most restrictive to date for 0.2<m_{a}<1  GeV/c^{2}.

Stability of RNA sequences derived from the coronavirus genome in human cells

Most viruses inhibit the innate immune system and/or the RNA degradation processes of host cells to construct an advantageous intracellular environment for their survival. Characteristic RNA sequences within RNA virus genomes or RNAs transcribed from DNA virus genomes contribute toward this inhibition. In this study, we developed a method called “Fate-seq” to comprehensively identify the RNA sequences derived from RNA and DNA viruses, contributing RNA stability in the cells. We examined the stabilization activity of 5,924 RNA fragments derived from 26 different viruses (16 RNA viruses and 10 DNA viruses) using next-generation sequencing of these RNAs fused 3′ downstream of GFP reporter RNA. With the Fate-seq approach, we detected multiple virus-derived RNA sequences that stabilized GFP reporter RNA, including sequences derived from severe acute respiratory syndrome-related coronavirus (SARS-CoV). Comparative genomic analysis revealed that these RNA sequences and their predicted secondary structures are highly conserved between SARS-CoV and the novel coronavirus, SARS-CoV-2, which is responsible for the global outbreak of the coronavirus-associated disease that emerged in December 2019 (COVID-19). These sequences have the potential to enhance the stability of viral RNA genomes, thereby augmenting viral replication efficiency and virulence.

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RNA stability is an important regulator for viral life-cycle.

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Fate-seq enables measurement of stabilization activity of RNAs derived from viruses.

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Conserved sequences among coronaviruses including SARS-CoV-2 have stabilizing activity.

DDBJ Data Analysis Challenge: a machine learning competition to predict Arabidopsis chromatin feature annotations from DNA sequences

Recently, the prospect of applying machine learning tools for automating the process of annotation analysis of large-scale sequences from next-generation sequencers has raised the interest of researchers. However, finding research collaborators with knowledge of machine learning techniques is difficult for many experimental life scientists. One solution to this problem is to utilise the power of crowdsourcing. In this report, we describe how we investigated the potential of crowdsourced modelling for a life science task by conducting a machine learning competition, the DNA Data Bank of Japan (DDBJ) Data Analysis Challenge. In the challenge, participants predicted chromatin feature annotations from DNA sequences with competing models. The challenge engaged 38 participants, with a cumulative total of 360 model submissions. The performance of the top model resulted in an area under the curve (AUC) score of 0.95. Over the course of the competition, the overall performance of the submitted models improved by an AUC score of 0.30 from the first submitted model. Furthermore, the 1^st- and 2^nd-ranking models utilised external data such as genomic location and gene annotation information with specific domain knowledge. The effect of incorporating this domain knowledge led to improvements of approximately 5%-9%, as measured by the AUC scores. This report suggests that machine learning competitions will lead to the development of highly accurate machine learning models for use by experimental scientists unfamiliar with the complexities of data science.

Search for an Invisibly Decaying Z^{'} Boson at Belle II in e^{+}e^{-}→μ^{+}μ^{-}(e^{±}μ^{∓}) Plus Missing Energy Final States

Theories beyond the standard model often predict the existence of an additional neutral boson, the Z^{'}. Using data collected by the Belle II experiment during 2018 at the SuperKEKB collider, we perform the first searches for the invisible decay of a Z^{'} in the process e^{+}e^{-}→μ^{+}μ^{-}Z^{'} and of a lepton-flavor-violating Z^{'} in e^{+}e^{-}→e^{±}μ^{∓}Z^{'}. We do not find any excess of events and set 90% credibility level upper limits on the cross sections of these processes. We translate the former, in the framework of an L_{μ}-L_{τ} theory, into upper limits on the Z^{'} coupling constant at the level of 5×10^{-2}-1 for M_{Z^{'}}≤6  GeV/c^{2}.

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets

BACKGROUND

Read coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly "full-length" ones, provide read coverage of many individual cells and have the potential to reveal cellular heterogeneity in RNA transcription and processing. However, visualization tools suited to highlighting cell-to-cell heterogeneity in read coverage are still lacking.

RESULTS

Here, we have developed Millefy, a tool for visualizing read coverage of scRNA-seq data in genomic contexts. Millefy is designed to show read coverage of all individual cells at once in genomic contexts and to highlight cell-to-cell heterogeneity in read coverage. By visualizing read coverage of all cells as a heat map and dynamically reordering cells based on diffusion maps, Millefy facilitates discovery of "local" region-specific, cell-to-cell heterogeneity in read coverage. We applied Millefy to scRNA-seq data sets of mouse embryonic stem cells and triple-negative breast cancers and showed variability of transcribed regions including antisense RNAs, 3 ' UTR lengths, and enhancer RNA transcription.

CONCLUSIONS

Millefy simplifies the examination of cellular heterogeneity in RNA transcription and processing events using scRNA-seq data. Millefy is available as an R package (https://github.com/yuifu/millefy) and as a Docker image for use with Jupyter Notebook (https://hub.docker.com/r/yuifu/datascience-notebook-millefy).

An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data

Single-cell RNA sequencing has enabled researchers to quantify the transcriptomes of individual cells, infer cell types and investigate differential expression among cell types, which will lead to a better understanding of the regulatory mechanisms of cell states. Transcript diversity caused by phenomena such as aberrant splicing events have been revealed, and differential expression of previously unannotated transcripts might be overlooked by annotation-based analyses. Accordingly, we have developed an approach to discover overlooked differentially expressed (DE) gene regions that complements annotation-based methods. Our algorithm decomposes mapped count data matrix for a gene region using non-negative matrix factorization, quantifies the differential expression level based on the decomposed matrix, and compares the differential expression level based on annotation-based approach to discover previously unannotated DE transcripts. We performed single-cell RNA sequencing for human neural stem cells and applied our algorithm to the dataset. We also applied our algorithm to two public single-cell RNA sequencing datasets correspond to mouse ES and primitive endoderm cells, and human preimplantation embryos. As a result, we discovered several intriguing DE transcripts, including a transcript related to the modulation of neural stem/progenitor cell differentiation.

Decrescent intensity training concurrently improves maximal anaerobic power, maximal accumulated oxygen deficit, and maximal oxygen uptake

This study aimed to investigate the effects of a gradually decreasing intensity training from that corresponding to maximal anaerobic power (MAnP) to that of near maximal oxygen uptake ([Formula: see text]) (decrescent intensity training) on MAnP, maximal accumulated oxygen deficit (MAOD), and [Formula: see text] in untrained young men. Seventeen untrained young men were randomly divided into either a training (TR; n = 9) group or a control (CON; n = 8) group. The TR group performed the decrescent intensity training, whereas the CON group did not perform any exercises. The mean training time per session throughout the training period was 275 ± 135 s. There was a Group × Time interaction for both absolute and relative (p < 0.01) values of [Formula: see text], MAOD, and MAnP. The TR group had significantly increased values for all variables after the 8-week training program, and the relative values of all variables were significantly higher in the TR group than in the CON group. Muscle thicknesses in the anterior and posterior aspects of the thigh and maximal isokinetic knee extension and flexion strengths improved only in the TR group (p < 0.05). A single-exercise training with gradually decreasing intensity from that corresponding to the MAnP to that of approximately 100% [Formula: see text] improves MAnP, MAOD, and [Formula: see text] concurrently, despite the short training time per session.

Virulence of Escherichia coli Isolates Obtained from Layer Chickens with Colibacillosis Associated with Pericarditis, Perihepatitis, and Salpingitis in Experimentally Infected Chicks and Embryonated Eggs

To evaluate the virulence of avian pathogenic Escherichia coli (APEC) isolates obtained from colibacillosis cases associated with pericarditis, perihepatitis, and salpingitis, the embryo lethality assay and experimental infection model in chicks were used in this study. According to the established criteria based on mortality in the embryo lethality assay for evaluating the virulence of E. coli isolates, 23 of the 26 APEC isolates associated with pericarditis and perihepatitis and 8 of the 20 isolates associated with salpingitis were found to be virulent. Isolate D137, which had been obtained from a case with pericarditis and perihepatitis and had an embryo mortality of 92%, and isolate D445, which had been obtained from a case with pericarditis and perihepatitis and had an embryo mortality of 17%, were used for the experimental infection. Four of the five 11-day-old chickens inoculated through the air sac with isolate D137 died 1 day postinoculation, and the challenge strain was recovered from the air sac, pericardial sac, or liver; however, colibacillosis lesions were found in only one of the five birds postmortem. All five chicks inoculated with isolate D445 survived for 7 days postinoculation and exhibited airsacculitis or pericarditis lesions at 7 days postinoculation; the challenge strain was not recovered from the lesions postmortem. The results obtained in this study suggest that the different APEC isolates tested cause illness in chickens through distinct pathogenesis.

Association of CD58 Polymorphisms and its Protein Expression with the Development and Prognosis of Autoimmune Thyroid Diseases

The prognosis of autoimmune thyroid diseases (AITDs), including Graves' disease (GD) and Hashimoto's disease (HD), varies among patients. The interaction of CD58 and its ligand (CD2) promotes the differentiation of regulatory T cells and suppresses the immune response. To clarify the association of CD58 expression with the pathogenesis and prognosis of AITDs, we genotyped polymorphisms in the CD58 gene including rs12044852A/C (SNP1), rs2300747A/G (SNP2), rs1335532C/T (SNP3), rs1016140G/T (SNP4), rs1414275C/T (SNP5) and rs11588376C/T (SNP6). The CD58 SNPs were genotyped in 177 GD patients, 193 HD patients and 116 healthy volunteers (control subjects). We used the Polymerase chain reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method for the genotyping of SNP1 and SNPs3-6 and the TaqMan® SNP genotyping assay for the genotyping of SNP2. The frequencies of the AA genotype in SNP1 tend to be high in all patients with AITDs than in control subjects, although it was not significant. The GG genotype of SNP2, the CC genotype of SNP3, the TT genotype of SNP4, the CC genotype of SNP5 and the CC genotype of SNP6 were all significantly more frequent in patients with AITDs than in control subjects. The proportion of CD58⁺ cells in monocytes was significantly lower in healthy individuals with each of these risk genotypes of AITDs and lower in GD and HD patients than that in healthy controls. In conclusion, CD58 SNPs are involved in AITD susceptibility through the reduction in CD58 expression, which probably suppresses regulatory T cells.

Functional D-box sequences reset the circadian clock and drive mRNA rhythms

The circadian clock drives gene expression rhythms, leading to daily changes in physiology and behavior. In mammals, Albumin D-site-Binding Protein (DBP) rhythmically activates transcription of various genes through a DNA cis-element, D-box. The DBP-dependent transactivation is repressed by competitive binding of E4BP4 to the D-box. Despite the elaborate regulation, physiological roles of the D-box in the circadian clockwork are still elusive. Here we identified 1490 genomic regions recognized commonly by DBP and E4BP4 in the mouse liver. We comprehensively defined functional D-box sequences using an improved bioinformatics method, MOCCS2. In RNA-Seq analysis of E4bp4-knockout and wild type liver, we showed the importance of E4BP4-mediated circadian repression in gene expression rhythms. In addition to the circadian control, we found that environmental stimuli caused acute induction of E4BP4 protein, evoking phase-dependent phase shifts of cellular circadian rhythms and resetting the clock. Collectively, D-box-mediated transcriptional regulation plays pivotal roles in input and output in the circadian clock system.

Precision Analysis of the ^{136}Xe Two-Neutrino ββ Spectrum in KamLAND-Zen and Its Impact on the Quenching of Nuclear Matrix Elements

We present a precision analysis of the ^{136}Xe two-neutrino ββ electron spectrum above 0.8 MeV, based on high-statistics data obtained with the KamLAND-Zen experiment. An improved formalism for the two-neutrino ββ rate allows us to measure the ratio of the leading and subleading 2νββ nuclear matrix elements (NMEs), ξ_{31}^{2ν}=-0.26_{-0.25}^{+0.31}. Theoretical predictions from the nuclear shell model and the majority of the quasiparticle random-phase approximation (QRPA) calculations are consistent with the experimental limit. However, part of the ξ_{31}^{2ν} range allowed by the QRPA is excluded by the present measurement at the 90% confidence level. Our analysis reveals that predicted ξ_{31}^{2ν} values are sensitive to the quenching of NMEs and the competing contributions from low- and high-energy states in the intermediate nucleus. Because these aspects are also at play in neutrinoless ββ decay, ξ_{31}^{2ν} provides new insights toward reliable neutrinoless ββ NMEs.

Characteristics of Escherichia coli isolated from broiler chickens with colibacillosis in commercial farms from a common hatchery

To investigate the epidemiologic aspects of colibacillosis in broiler chickens, 83 Escherichia coli isolates obtained from the pericarditis and perihepatitis lesions in broiler chickens from 4 commercial farms, 5 isolates recovered from 5 samples of yolk sac contents that were pooled from 25 emaciated chicks, and 4 fecal isolates obtained from a hatchery that supplied chicks to the 4 commercial farms mentioned above were genetically and bacteriologically characterized. Using pulsed-field gel electrophoresis (PFGE), a total of 92 isolates were classified into 33 pulsotypes. Identical pulsotypes were observed in isolates obtained from hatchery samples and the affected broiler chickens on multiple farms at various sampling times. Seventeen representative isolates with no common origin belonging to 6 pulsotypes and an additional 27 isolates with the other pulsotypes were used for further experiments. Isolates with identical pulsotypes exhibited common traits for virulence-associated genes, lipopolysaccharide core types, and phylogenetic groups. Nine of the isolates were serologically typed as O125 with various types of H antigens and 3 were typed as O25:H4. In the 27 isolates resistant to ceftiofur (CTF), which is a third generation cephalosporin, the blaCTX-M-2, blaCMY-2, blaCTX-M-14, blaCTX-M-65 genes were found in 15, 8, 3, and 1 isolate(s), respectively, and another isolate resistant to CTF had both the blaCTX-M-2 and the blaCMY-2 genes. In the 16 isolates with the blaCTX-M-2 gene, the chromosomal location of the gene was identified in 12 isolates. The plasmid-mediated quinolone resistance genes, oqxAB and aac(6')-Ib-cr, were found in 2 and 3 isolates, respectively. Conjugation experiments revealed that the blaCTX-M-2 (4 isolates), blaCTX-M-14 (3 isolates), blaSHV-12 (1 isolate), and oqxAB (2 isolates) genes were transferred. Our data suggest that E. coli strains with identical pulsotypes had been caused the incidences of colibacillosis and that the antimicrobial resistance genes on conjugative plasmids and those integrated into the chromosome may be spread among avian pathogenic E. coli strains in multiple farms.

Disruption of the pacemaker activity of interstitial cells of Cajal via nitric oxide contributes to postoperative ileus

BACKGROUND

Interstitial cells of Cajal (ICC) serve as intestinal pacemakers. Postoperative ileus (POI) is a gastrointestinal motility disorder that occurs following abdominal surgery, which is caused by inflammation-induced dysfunction of smooth muscles and enteric neurons. However, the participation of ICC in POI is not well understood. In this study, we investigated the functional changes of ICC in a mouse model of POI.

METHODS

Intestinal manipulation (IM) was performed to induce POI. At 24 h or 48 h after IM, the field potential of the intestinal tunica muscularis was investigated. Tissues were also examined by immunohistochemistry and electron microscopic analysis.

KEY RESULTS

Gastrointestinal transit was significantly decreased with intestinal tunica muscularis inflammation at 24 h after IM, which was ameliorated at 48 h after IM. The generation and propagation of pacemaker potentials were disrupted at 24 h after IM and recovered to the control level at 48 h after IM. ICC networks, detected by c-Kit immunoreactivity, were remarkably disrupted at 24 h after IM. Electron microscopic analysis revealed abnormal vacuoles in the ICC cytoplasm. Interestingly, the ICC networks recovered at 48 h after IM. Administration of aminoguanidine, an inducible nitric oxide synthase inhibitor, suppressed the disruption of ICC networks. Ileal smooth muscle tissue cultured in the presence of nitric oxide donor, showed disrupted ICC networks.

CONCLUSIONS AND INFERENCES

The generation and propagation of pacemaker potentials by ICC are disrupted via nitric oxide after IM, and this disruption may contribute to POI. When inflammation is ameliorated, ICC can recover their pacemaker function.

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

Total RNA sequencing has been used to reveal poly(A) and non-poly(A) RNA expression, RNA processing and enhancer activity. To date, no method for full-length total RNA sequencing of single cells has been developed despite the potential of this technology for single-cell biology. Here we describe random displacement amplification sequencing (RamDA-seq), the first full-length total RNA-sequencing method for single cells. Compared with other methods, RamDA-seq shows high sensitivity to non-poly(A) RNA and near-complete full-length transcript coverage. Using RamDA-seq with differentiation time course samples of mouse embryonic stem cells, we reveal hundreds of dynamically regulated non-poly(A) transcripts, including histone transcripts and long noncoding RNA Neat1. Moreover, RamDA-seq profiles recursive splicing in >300-kb introns. RamDA-seq also detects enhancer RNAs and their cell type-specific activity in single cells. Taken together, we demonstrate that RamDA-seq could help investigate the dynamics of gene expression, RNA-processing events and transcriptional regulation in single cells.

A sodium binding system alleviates acute salt stress during seawater acclimation in eels

BACKGROUND

Teleosts transiting from freshwater (FW) to seawater (SW) environments face an immediate osmotic stress from ion influxes and water loss, but some euryhaline species such as eels can maintain a stable plasma osmolality during early SW exposure. The time course changes in the gene expression, protein abundance, and localization of key ion transporters suggested that the reversal of the ion transport systems was gradual, and we investigate how eels utilize a Na-binding strategy to slow down the ion invasion and complement the transporter-mediated osmoregulation.

RESULTS

Using an electron probe micro-analyzer, we localized bound Na in various eel tissues in response to SW transfer, suggesting that the Na-binding molecules were produced to sequester excess ionic Na⁺ to negate its osmotic potential, thus preventing acute cellular dehydration. Mucus cells were acutely activated in digestive tract, gill, and skin after SW transfer, producing Na-binding molecule-containing mucus layers that fence off high osmolality of SW. Using gel filtration HPLC, some molecules at 18 kDa were found to bind Na in the luminal secretion of esophagus and intestine, and higher binding was associated with SW transfer. Transcriptome and protein interaction results indicated that downregulation of Notch and β-catenin pathways, and dynamic changes in TGFβ pathways in intestine were involved during early SW transition, supporting the observed histological changes on epithelial desquamation and increased mucus production.

CONCLUSIONS

The timing for the activation of the Na-binding mechanism to alleviate the adverse osmotic gradient was temporally complementary to the subsequent remodeling of branchial ionocytes and transporting epithelia of the digestive tract. The strategy to manipulate the osmotic potential of Na⁺ by specific binding molecules is similar to the osmotically inactive Na described in human skin and muscle. The Na-binding molecules provide a buffer to tolerate the salinity changes, which is advantageous to the estuary and migrating fishes. Our data pave the way to identify this unknown class of molecules and open a new area of vertebrate osmoregulation research.

Zingiberis Siccatum Rhizoma, the active component of the Kampo formula Daikenchuto, induces anti-inflammatory actions through α7 nicotinic acetylcholine receptor activation

BACKGROUND

We previously reported that Daikenchuto (DKT), a gastrointestinal prokinetic Japanese herbal (Kampo) medicine used for the treatment of postoperative ileus (POI), has characteristic potent anti-inflammatory activity. This effect may be partly mediated by the activation of α7 nicotinic acetylcholine receptor (nAChR). In this study, we identified the specific herbs in DKT that induce anti-inflammatory action.

METHODS

The herbal components of DKT were individually administered orally to each mouse four times before and after intestinal manipulation (IM) was carried out on the distal ileum. The anti-inflammatory activity of each crude drug was subsequently evaluated using immunohistochemical analyses of relevant molecules.

KEY RESULTS

Treatment with Zingiberis Siccatum Rhizoma (ZSR) but not the other components inhibited the infiltration of cluster of differentiation 68 (CD68)-positive macrophages as effectively as DKT treatment. Selective α7nAChR antagonists, such as methyllycaconitine citrate, or transient receptor potential ankyrin 1 (TRPA1) antagonists, such as HC-030031, significantly inhibited the amelioration of macrophage infiltration by ZSR. The inhibition of macrophage infiltration by ZSR was abolished in both α7nAChR and 5-hydroxytryptamine 4 receptor (5-HT₄ R) knockout mice.

CONCLUSIONS & INFERENCES

Daikenchuto-induced anti-inflammatory activity, which was mediated by inhibiting macrophage infiltration in POI, is dependent on the effects of ZSR. Zingiberis Siccatum Rhizoma activates TRPA1 channels possibly in enterochromaffin (EC) cells to release 5-HT, which stimulates 5-HT₄ R in the myenteric plexus neurons to release ACh, which in turn activates α7nAChR on macrophages to inhibit inflammation in POI.

Molecular mechanisms underlying active desalination and low water permeability in the esophagus of eels acclimated to seawater

Marine teleosts can absorb imbibed seawater (SW) to maintain water balance, with esophageal desalination playing an essential role. NaCl absorption from luminal SW was enhanced 10-fold in the esophagus of SW-acclimated eels, and removal of Na⁺ or Cl^- from luminal SW abolished the facilitated absorption, indicating coupled transport. Mucosal/serosal application of various blockers for Na⁺/Cl^- transporters profoundly decreased the absorption. Among the transporter genes expressed in eel esophagus detected by RNA-seq, dimethyl amiloride-sensitive Na⁺/H⁺ exchanger (NHE3) and 4,4'-diisothiocyano-2,2'-disulfonic acid-sensitive Cl^-/[Formula: see text] exchanger (AE) coupled by the scaffolding protein on the apical membrane of epithelial cells, and ouabain-sensitive Na⁺-K⁺-ATPases (NKA1α1c and NKA3α) and diphenylamine-2-carboxylic acid-sensitive Cl^- channel (CLCN2) on the basolateral membrane, may be responsible for enhanced transcellular NaCl transport because of their profound upregulation after SW acclimation. Upregulated carbonic anhydrase 2a (CA2a) supplies H⁺ and [Formula: see text] for activation of the coupled NHE and AE. Apical hydrochlorothiazide-sensitive Na⁺-Cl^- cotransporters and basolateral Na⁺-[Formula: see text] cotransporter (NBCe1) and AE1 are other possible candidates. Concerning the low water permeability that is typically seen in marine teleost esophagus, downregulated aquaporin genes (aqp1a and aqp3) and upregulated claudin gene (cldn15a) are candidates for transcellular/paracellular route. In situ hybridization showed that these upregulated transporters and tight-junction protein genes were expressed in the absorptive columnar epithelial cells of eel esophagus. These results allow us to provide a full picture of the molecular mechanism of active desalination and low water permeability that are characteristic to marine teleost esophagus and gain deeper insights into the role of gastrointestinal tracts in SW acclimation.

Publisher's Note: Search for Majorana Neutrinos Near the Inverted Mass Hierarchy Region with KamLAND-Zen [Phys. Rev. Lett. 117, 082503 (2016)]

This corrects the article DOI: 10.1103/PhysRevLett.117.082503.

Search for Majorana Neutrinos Near the Inverted Mass Hierarchy Region with KamLAND-Zen

We present an improved search for neutrinoless double-beta (0νββ) decay of ^{136}Xe in the KamLAND-Zen experiment. Owing to purification of the xenon-loaded liquid scintillator, we achieved a significant reduction of the ^{110m}Ag contaminant identified in previous searches. Combining the results from the first and second phase, we obtain a lower limit for the 0νββ decay half-life of T_{1/2}^{0ν}>1.07×10^{26}  yr at 90% C.L., an almost sixfold improvement over previous limits. Using commonly adopted nuclear matrix element calculations, the corresponding upper limits on the effective Majorana neutrino mass are in the range 61-165 meV. For the most optimistic nuclear matrix elements, this limit reaches the bottom of the quasidegenerate neutrino mass region.

Epidermal growth factor is a critical regulator of the cytokine IL-33 in intestinal epithelial cells

BACKGROUND AND PURPOSE

IL-33 is a novel cytokine that is believed to be involved in inflammation and carcinogenesis. However, its source, its production and its secretion process remain unclear. Recently, we have reported that IL-33 is up-regulated in dextran sulfate sodium (DSS) colitis in mice.

EXPERIMENTAL APPROACH

Production of IL-33 from intestinal tissue was studied in a murine cancer model induced by azoxymethane (AOM) and DSS in vivo and in cultures of IEC-6 epithelial cells. Cytokine levels were measured by real time PCR, immunohistochemistry and elisa.

KEY RESULTS

Mice with AOM/DSS-induced colitis expressed all the characteristic symptoms of colon cancer pathology. Immunohistochemical analysis demonstrated epithelial cell-derived IL-33 in colon tissues from mice with AOM/DSS colitis. Real time PCR and quantitative PCR analysis revealed that AOM/DSS colitis tissues expressed up-regulated IL-1β, IL-33, TGF-β, and EGF mRNA. Gefitinib, an EGFR inhibitor, inhibited IL-33 mRNA expression in AOM/DSS colitis mice. The pathophysiological role of IL-33 in the rat intestinal epithelial cell line (IEC-6 cells) was then investigated. We found that EGF, but not TGF-β1 or PDGF, greatly enhanced mRNA expression of IL-33 and its receptor ST2. In accordance with the gene expression and immunohistochemical analysis of IL-33 levels, elisa-based analysis of cytoplasmic and nuclear extracts showed increased IL-33 protein levels in IEC-6 cells after treatment with EGF.

CONCLUSIONS AND IMPLICATIONS

Our results suggest that EGF is a key growth factor that increased IL-33 production and ST2 receptor expression during intestinal inflammation and carcinogenesis. The EGF/IL-33/ST2 axis represents a novel therapeutic target in colon cancer.