HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis

Background Integrated analysis that uses multiple sample gene expression data measured under the same stress can detect stress response genes more accurately than analysis of individual sample data. However, the integrated analysis is challenging since experimental conditions (strength of stress and the number of time points) are heterogeneous across multiple samples. Results HTRgene is a computational method to perform the integrated analysis of multiple heterogeneous time-series data measured under the same stress condition. The goal of HTRgene is to identify response order preserving DEGs that are defined as genes not only which are differentially expressed but also whose response order is preserved across multiple samples. The utility of HTRgene was demonstrated using 28 and 24 time-series sample gene expression data measured under cold and heat stress in Arabidopsis. HTRgene analysis successfully reproduced known biological mechanisms of cold and heat stress in Arabidopsis. Also, HTRgene showed higher accuracy in detecting the documented stress response genes than existing tools. Conclusions HTRgene, a method to find the ordering of response time of genes that are commonly observed among multiple time-series samples, successfully integrated multiple heterogeneous time-series gene expression datasets. It can be applied to many research problems related to the integration of time series data analysis.This work, including publication costs, was supported by National Research Foundation of Korea(NRF) funded by the Ministry of Science, ICT (No.NRF-2017M3C4A7065887). This work was also supported by the Collaborative Genome Program for Fostering New Post-Genome Industry of the National Research Foundation (NRF) funded by the Ministry of Science and ICT (MSIT) (No. NRF-2014M3C9A3063541), and a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI15C3224). This work was supported for W.J. by the Agenda program (No.PJ012465032019), Rural Development of dministration of Republic of Korea

StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis

Background Recently, a number of studies have been conducted to investigate how plants respond to stress at the cellular molecular level by measuring gene expression profiles over time. As a result, a set of time-series gene expression data for the stress response are available in databases. With the data, an integrated analysis of multiple stresses is possible, which identifies stress-responsive genes with higher specificity because considering multiple stress can capture the effect of interference between stresses. To analyze such data, a machine learning model needs to be built. Results In this study, we developed StressGenePred, a neural network-based machine learning method, to integrate time-series transcriptome data of multiple stress types. StressGenePred is designed to detect single stress-specific biomarker genes by using a simple feature embedding method, a twin neural network model, and Confident Multiple Choice Learning (CMCL) loss. The twin neural network model consists of a biomarker gene discovery and a stress type prediction model that share the same logical layer to reduce training complexity. The CMCL loss is used to make the twin model select biomarker genes that respond specifically to a single stress. In experiments using Arabidopsis gene expression data for four major environmental stresses, such as heat, cold, salt, and drought, StressGenePred classified the types of stress more accurately than the limma feature embedding method and the support vector machine and random forest classification methods. In addition, StressGenePred discovered known stress-related genes with higher specificity than the Fisher method. Conclusions StressGenePred is a machine learning method for identifying stress-related genes and predicting stress types for an integrated analysis of multiple stress time-series transcriptome data. This method can be used to other phenotype-gene associated studies.This work and publication costs were supported by National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT (No. NRF2017M3C4A7065887), and the Collaborative Genome Program for Fostering New Post-Genome Industry of the National Research Foundation (NRF) funded by the Ministry of Science and ICT (MSIT) (No. NRF-2014M3C9A3063541). This work was supported for W.J. by the Agenda program (No. PJ014307), Rural Development of Administration of Republic of Korea

Changes of fat-mass and obesity-associated protein expression in the hippocampus in animal models of high-fat diet-induced obesity and D-galactose-induced aging

Abstract Fat-mass and obesity-associated protein (Fto) is highly expressed in the brain including, the hippocampus, and its expression is significantly decreased in the brain of Alzheimers disease patients. In the present study, we measured Fto immunoreactivity and protein levels in the hippocampus of obese and aged mice, which were induced by high-fat diet for 12 weeks and D-galactose treatment for 10 weeks, respectively. The obesity and aging phenotypes were assessed by physiological parameters and Morris water maze test, respectively. High fat diet fed mice showed significant increases in body weight and blood glucose levels compared to that in the control or D-galactose-induced aged mice. In addition, treatment with D-galactose significantly decreased the spatial memory. Fto immunoreactivity in the control group was mainly detected in the pyramidal cells of the CA1 and CA3 regions and in the granule cells of the dentate gyrus. In the hippocampus of high-fat diet-fed mice, Fto immunoreactive structures were similarly found in the hippocampus compared to that in the control group, but Fto immunoreactivity in high-fat diet-fed mice was also found in the stratum oriens and radiatum of the CA1 and CA3 regions and the polymorphic layer of the dentate gyrus. In the hippocampus of D-galactose-induced aged mice, fewer Fto immunoreactive structures were detected in the granule cell layer of the dentate gyrus compared to the control group. Fto mRNA and protein levels based on quantitative real-time polymerase chain reaction and western blot assays were slightly increased in the hippocampus of high-fat diet-fed mice compared to that in control mice. In addition, Fto mRNA and protein levels were significantly decreased in the aged hippocampus compared to that in the control group. Fto protein levels are susceptible to the aging process, but not in the hippocampus of high-fat diet-induced obesity. The reduction of Fto in aged mice may be associated with reduced memory impairment in mice

Role of intermediate phase for stable cycling of Na_7V_4(P_2O_7)_4PO_4 in sodium ion battery

Sodium ion batteries offer promising opportunities in emerging utility grid applications because of the low cost of raw materials, yet low energy density and limited cycle life remain critical drawbacks in their electrochemical operations. Herein, we report a vanadium-based ortho-diphosphate, Na_7V_4(P_2O_7)_4PO_4, or VODP, that significantly reduces all these drawbacks. Indeed, VODP exhibits single-valued voltage plateaus at 3.88 V vs. Na/Na+ while retaining substantial capacity (>78%) over 1,000 cycles. Electronic structure calculations reveal that the remarkable single plateau and cycle life originate from an intermediate phase (a very shallow voltage step) that is similar both in the energy level and lattice parameters to those of fully intercalated and deintercalated states. We propose a theoretical scheme in which the reaction barrier that arises from lattice mismatches can be evaluated by using a simple energetic consideration, suggesting that the presence of intermediate phases is beneficial for cell kinetics by buffering the differences in lattice parameters between initial and final phases. We expect these insights into the role of intermediate phases found for VODP hold in general and thus provide a helpful guideline in the further understanding and design of battery materials

Heat shock protein 70 increases cell proliferation, neuroblast differentiation, and the phosphorylation of CREB in the hippocampus

In the present study, we investigated the effects of heat shock protein 70 (HSP70) on novel object recognition, cell proliferation, and neuroblast differentiation in the hippocampus. To facilitate penetration into the blood–brain barrier and neuronal plasma membrane, we created a Tat-HSP70 fusion protein. Eight-week-old mice received intraperitoneal injections of vehicle (10% glycerol), control-HSP70, or Tat-HSP70 protein once a day for 21 days. To elucidate the delivery efficiency of HSP70 into the hippocampus, western blot analysis for polyhistidine was conducted. Polyhistidine protein levels were significantly increased in control-HSP70- and Tat-HSP70-treated groups compared to the control or vehicle-treated group. However, polyhistidine protein levels were significantly higher in the Tat-HSP70-treated group compared to that in the control-HSP70-treated group. In addition, immunohistochemical study for HSP70 showed direct evidences for induction of HSP70 immunoreactivity in the control-HSP70- and Tat-HSP70-treated groups. Administration of Tat-HSP70 increased the novel object recognition memory compared to untreated mice or mice treated with the vehicle. In addition, the administration of Tat-HSP70 significantly increased the populations of proliferating cells and differentiated neuroblasts in the dentate gyrus compared to those in the control or vehicle-treated group based on the Ki67 and doublecortin (DCX) immunostaining. Furthermore, the phosphorylation of cAMP response element-binding protein (pCREB) was significantly enhanced in the dentate gyrus of the Tat-HSP70-treated group compared to that in the control or vehicle-treated group. Western blot study also demonstrated the increases of DCX and pCREB protein levels in the Tat-HSP70-treated group compared to that in the control or vehicle-treated group. In contrast, administration of control-HSP70 moderately increased the novel object recognition memory, cell proliferation, and neuroblast differentiation in the dentate gyrus compared to that in the control or vehicle-treated group. These results suggest that Tat-HSP70 promoted hippocampal functions by increasing the pCREB in the hippocampus.This work was supported by the Promising-Pioneering Researcher Program through Seoul National University (SNU) in 2015 and by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP) (No. NRF-2016R1A2B4009156 and NRF-2018R1A2B6001941). In addition, this study was partially supported by the Research Institute for Veterinary Science of Seoul National University

Neuropathological changes in dorsal root ganglia induced by pyridoxine in dogs

Pyridoxine (PDX; vitamin B6), is an essential vitamin. PDX deficiency induces various symptoms, and when PDX is misused it acts as a neurotoxicant, inducing severe sensory neuropathy. To assess the possibility of creating a reversible sensory neuropathy model using dogs, 150 mg/kg of PDX was injected subcutaneously into dogs for 7 days and body weight measurements, postural reaction assessments, and electrophysiological recordings were obtained. In addition, the morphology of dorsal root ganglia (DRG) and changes in glial fibrillary acidic protein (GFAP) immunoreactive satellite glial cells and ionized calcium-binding adapter molecule 1 (Iba-1) immunoreactive microglia/macrophages were assessed at 1 day, 1 week, and 4 weeks after the last PDX treatment. During the administration period, body weight and proprioceptive losses occurred. One day after the last PDX treatment, electrophysiological recordings showed the absence of the H-reflex in the treated dogs. These phenomena persisted over the four post-treatment weeks, with the exception of body weight which recovered to the pre-treatment level. Staining (CV and HE) results revealed significant losses of large-sized neurons in the DRG at 1 day and 1 week after PDX treatment cessation, but the losses were recovered at 4 weeks post-treatment. The Iba-1 and GFAP immunohistochemistry results showed pronounced increases in reactive microglia/macrophage and satellite glial cell at 1 day and 1 week, respectively, after the last PDX treatment, and thereafter, immunoreactivity decreased with increasing time after PDX treatment. The results suggest that PDX-induced neuropathy is reversible in dogs; thus, dogs can be considered a good experimental model for research on neuropathy.This work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Sci‑ ence, ICT & Future Planning (NRF-2017R1A1A1A05000762). The funding body played no role in the design and interpretation of the experiments. The found‑ ing sponsors had no role in the study design, performance, data collection and analysis, decision to publish, or preparation/writing of the manuscript

Natural Products in the Prevention of Metabolic Diseases: Lessons Learned from the 20th KAST Frontier Scientists Workshop

The incidence of metabolic and chronic diseases including cancer, obesity, inflammation-related diseases sharply increased in the 21st century. Major underlying causes for these diseases are inflammation and oxidative stress. Accordingly, natural products and their bioactive components are obvious therapeutic agents for these diseases, given their antioxidant and anti-inflammatory properties. Research in this area has been significantly expanded to include chemical identification of these compounds using advanced analytical techniques, determining their mechanism of action, food fortification and supplement development, and enhancing their bioavailability and bioactivity using nanotechnology. These timely topics were discussed at the 20th Frontier Scientists Workshop sponsored by the Korean Academy of Science and Technology, held at the University of Hawaii at Manoa on 23 November 2019. Scientists from South Korea and the U.S. shared their recent research under the overarching theme of Bioactive Compounds, Nanoparticles, and Disease Prevention. This review summarizes presentations at the workshop to provide current knowledge of the role of natural products in the prevention and treatment of metabolic diseases

Adult Hippocampal Neurogenesis Can Be Enhanced by Cold Challenge Independently From Beigeing Effects

In this study, we investigated the effects of cold challenge on adult hippocampal neurogenesis (AHN) and hippocampal gene expression and whether these are mediated by beigeing of peripheral fat tissues. Cold challenge (6 ± 2°C) for 1 and 4 weeks was found to induce beigeing effects in inguinal white adipose tissue based on hematoxylin and eosin staining as well as uncoupled protein-1 immunohistochemical staining. In the hippocampus, cold challenge for 1 or 4 weeks increased dentate gyrus neurogenesis and expression of genes related to AHN, including notch signaling, G protein-coupled receptor signaling, and adrenergic beta receptor-1. However, this enhancement of neurogenesis and gene expression by cold challenge was not shown by administration of CL 316,243, which induces peripheral beigeing similar to cold challenge but does not cross the blood–brain barrier. These results suggest that cold challenge promotes AHN and central expression of AHN-related, signaling, and β1-adrenergic receptors genes, and that peripheral beigeing by itself is not sufficient to mediate these effects. Considering the increase in AHN and gene expression changes, cold challenge may offer a novel approach to hippocampal modulation

The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

Abstract Background Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Panax ginseng C.A.Meyer) in Korea have migrated from mid to northern parts of the Korean peninsula to escape from the various higher temperature related stresses. Under the high ambient temperature, vegetative growth was accelerated, which resulted in early flowering. This precocious phase change led to yield loss. Despite of its importance as a traditional medicine, biological mechanisms of ginseng has not been well studied and even the genome sequence of ginseng is yet to be determined due to its complex genome structure. Thus, it is challenging to investigate the molecular biology mechanisms at the transcript level. Results To investigate how ginseng responds to the high ambient temperature environment, we performed high throughput RNA sequencing and implemented a bioinformatics pipeline for the integrated analysis of small-RNA and mRNA-seq data without a reference genome. By performing reverse transcriptase (RT) PCR and sanger sequencing of transcripts that were assembled using our pipeline, we validated that their sequences were expressed in our samples. Furthermore, to investigate the interaction between genes and non-coding small RNAs and their regulation status under the high ambient temperature, we identified potential gene regulatory miRNAs. As a result, 100,672 contigs with significant expression level were identified and 6 known, 214 conserved and 60 potential novel miRNAs were predicted to be expressed under the high ambient temperature. Conclusion Collectively, we have found that development, flowering and temperature responsive genes were induced under high ambient temperature, whereas photosynthesis related genes were repressed. Functional miRNAs were down-regulated under the high ambient temperature. Among them are miR156 and miR396 that target flowering (SPL6/9) and growth regulating genes (GRF) respectively