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  1. Fulltext Cloning and mutagenetic modification of the firefly luciferase gene and its use for bioluminescence microscopy of engrailed expression during Drosophila metamorphosis
    Ogoh K, Akiyoshi R, Suzuki H
    Biochem Biophys Rep, 2020 Sep;23:100771.
    PMID: 32490216 DOI: 10.1016/j.bbrep.2020.100771
    Bioluminescence microscopy is an area attracting considerable interest in the field of cell biology because it offers several advantages over fluorescence microscopy, including no requirement for excitation light and being phototoxicity free. This method requires brighter luciferase for imaging; however, suitable genetic resource material for this purpose is not available at present. To achieve brighter bioluminescence microscopy, we developed a new firefly luciferase. Using the brighter luciferase, a reporter strain of Drosophila Gal4-UAS (Upstream Activating Sequence) system was constructed. This system demonstrated the expression pattern of engrailed, which is a segment polarity gene, during Drosophila metamorphosis by bioluminescence microscopy, and revealed drastic spatiotemporal change in the engrailed expression pattern during head eversion in the early stage of pupation.
  2. Fulltext Neuron-specific splicing
    Hakim NH, Majlis BY, Suzuki H, Tsukahara T
    Biosci Trends, 2017 Mar 22;11(1):16-22.
    PMID: 28049883 DOI: 10.5582/bst.2016.01169
    During pre-mRNA splicing events, introns are removed from the pre-mRNA, and the remaining exons are connected together to form a single continuous molecule. Alternative splicing is a common mechanism for the regulation of gene expression in eukaryotes. More than 90% of human genes are known to undergo alternative splicing. The most common type of alternative splicing is exon skipping, which is also known as cassette exon. Other known alternative splicing events include alternative 5' splice sites, alternative 3' splice sites, intron retention, and mutually exclusive exons. Alternative splicing events are controlled by regulatory proteins responsible for both positive and negative regulation. In this review, we focus on neuronal splicing regulators and discuss several notable regulators in depth. In addition, we have also included an example of splicing regulation mediated by the RBFox protein family. Lastly, as previous studies have shown that a number of splicing factors are associated with neuronal diseases such as Alzheime's disease (AD) and Autism spectrum disorder (ASD), here we consider their importance in neuronal diseases wherein the underlying mechanisms have yet to be elucidated.
  3. Fulltext Peptic ulcer diseases: genetics, mechanism, and therapies
    Chuah SK, Wu DC, Suzuki H, Goh KL, Kao J, Ren JL
    Biomed Res Int, 2014;2014:898349.
    PMID: 25610875 DOI: 10.1155/2014/898349
  4. Infantile neuroaxonal dystrophy in a pair of Malaysian siblings with progressive cerebellar atrophy: Description of an expanded phenotype with novel PLA2G6 variants
    Li L, Fong CY, Tay CG, Tae SK, Suzuki H, Kosaki K, et al.
    J Clin Neurosci, 2020 Jan;71:289-292.
    PMID: 31493991 DOI: 10.1016/j.jocn.2019.08.111
    Infantile neuroaxonal dystrophy 1 (INAD) (OMIM #256600) is a rare infantile onset neurodegenerative disease characterised by neuroregression and hypotonia, evolving into generalized spasticity, blindness and dementia. We report our diagnostic approach of a pair of siblings with psychomotor regression, hypotonia, optic atrophy and auditory neuropathy. The brain magnetic resonance imaging (MRI) showed progressive cerebellar atrophy. Genetic testing of the PLA2G6 confirmed presence of compound heterozygous novel mutations. As the variant c. 196C>T (p.Gln66X) was a truncating variant, it was considered as pathogenic while the variant c. 2249G>A (p. Cys750Tyr) was considered as "likely pathogenic" by bioinformatics analyses. Our patient expands the clinical phenotype of INAD as it described the first South-East Asian patient with INAD-associated auditory neuropathy. Our report highlights the importance of increased awareness of this condition amongst clinicians, the use of deep phenotyping using neuroimaging and the clinical utility of gene sequencing test in the delineation of syndromes associated with infantile neurodegenerative disease.
  5. The expression of sex steroid receptors and sex steroid-synthesizing/metabolizing enzymes in metastasized lymph nodes of prostate cancer
    Nakamura Y, Ise K, McNamara KM, Azmahani A, Sato S, Fujishima F, et al.
    Hum Pathol, 2019 02;84:124-132.
    PMID: 30290162 DOI: 10.1016/j.humpath.2018.09.011
    The expression statuses of sex steroid receptors and sex steroid-synthesizing/metabolizing enzymes have been reported in primary prostate cancer lesions, but that in metastatic lymph nodes has remained unknown. Therefore, in this study, we immunolocalized these proteins in primary tumors and paired metastatic lymph nodes of prostate cancer and correlated the findings with clinicopathological factors of individual patients. The expression statuses of AR and ER β was significantly increased in metastatic lymph nodes compared with primary lesions, whereas that of 17βHSD1, 17βHSD2, 17βHSD5, and STS immunoreactivity was decreased in metastatic lymph nodes. In metastatic lymph nodes, the status of 5α2 was significantly correlated with that of AR. In addition, 17βHSD5-, 5α1-, STS-, and EST-positive cases were significantly associated with Gleason score (GS) status (GS > 8 versus GS < 7) in metastatic lymph nodes. Results of our present study did demonstrate that in situ androgen and estrogen metabolism and action play roles in pathophysiology of prostate cancer in metastatic lymph nodes, but these steroidogenic effects could be different from those in primary lesions.
  6. Fulltext The Impact of COVID-19 on Gastrointestinal Motility Testing in Asia and Europe
    Mori H, Schol J, Geeraerts A, Huang IH, Jandee S, Gonlachanvit S, et al.
    J Clin Med, 2020 Oct 01;9(10).
    PMID: 33019626 DOI: 10.3390/jcm9103189
    BACKGROUND: The new coronavirus disease (COVID-19) has high infection and mortality rates, and has become a pandemic. The infection and mortality rates are lower in Asian countries than in European countries. This study aimed to conduct a survey on the effects of COVID-19 on the capacity to perform gastrointestinal motility tests in Asian countries compared with European countries.

    METHODS: We used the questionnaire previously established by our team for researchers in European countries. The correlation between the decreased rate of gastrointestinal motility and function tests, and the infection/mortality rates of COVID-19 and stringency of a government's interventions in each country was analysed and protective measures were assessed.

    RESULTS: In total, 58 gastroenterologists/motility experts in Asian countries responded to this survey. The infection/mortality rates of COVID-19 and Stringency Index had a significant impact on the testing capacity of oesophageal manometry and catheter-based pH monitoring. In European countries, most facilities used filtering facepiece 2/3 (FFP2/3) masks during oesophageal motility studies. Meanwhile, in Asian countries, most facilities used surgical masks.

    CONCLUSION: The total infection and mortality rates of COVID-19 can affect the rate of gastrointestinal motility testing and the type of protective equipment that must be used.

  7. Fulltext Genetic Diversity and Phylogeography of Thottapalayam thottimvirus (Hantaviridae) in Asian House Shrew (Suncus murinus) in Eurasia
    Kikuchi F, Aoki K, Ohdachi SD, Tsuchiya K, Motokawa M, Jogahara T, et al.
    Front Cell Infect Microbiol, 2020;10:438.
    PMID: 32974220 DOI: 10.3389/fcimb.2020.00438
    Murid and cricetid rodents were previously believed to be the principal reservoir hosts of hantaviruses. Recently, however, multiple newfound hantaviruses have been discovered in shrews, moles, and bats, suggesting a complex evolutionary history. Little is known about the genetic diversity and geographic distribution of the prototype shrew-borne hantavirus, Thottapalayam thottimvirus (TPMV), carried by the Asian house shrew (Suncus murinus), which is widespread in Asia, Africa, and the Middle East. Comparison of TPMV genomic sequences from two Asian house shrews captured in Myanmar and Pakistan with TPMV strains in GenBank revealed that the Myanmar TPMV strain (H2763) was closely related to the prototype TPMV strain (VRC66412) from India. In the L-segment tree, on the other hand, the Pakistan TPMV strain (PK3629) appeared to be the most divergent, followed by TPMV strains from Nepal, then the Indian-Myanmar strains, and finally TPMV strains from China. The Myanmar strain of TPMV showed sequence similarity of 79.3-96.1% at the nucleotide level, but the deduced amino acid sequences showed a high degree of conservation of more than 94% with TPMV strains from Nepal, India, Pakistan, and China. Cophylogenetic analysis of host cytochrome b and TPMV strains suggested that the Pakistan TPMV strain was mismatched. Phylogenetic trees, based on host cytochrome b and cytochrome c oxidase subunit I genes of mitochondrial DNA, and on host recombination activating gene 1 of nuclear DNA, suggested that the Asian house shrew and Asian highland shrew (Suncus montanus) comprised a species complex. Overall, the geographic-specific clustering of TPMV strains in Asian countries suggested local host-specific adaptation. Additional in-depth studies are warranted to ascertain if TPMV originated in Asian house shrews on the Indian subcontinent.
  8. Fulltext Second Asian Consensus on Irritable Bowel Syndrome
    Gwee KA, Gonlachanvit S, Ghoshal UC, Chua ASB, Miwa H, Wu J, et al.
    J Neurogastroenterol Motil, 2019 Jul 01;25(3):343-362.
    PMID: 31327218 DOI: 10.5056/jnm19041
    Background/Aims: There has been major progress in our understanding of the irritable bowel syndrome (IBS), and novel treatment classes have emerged. The Rome IV guidelines were published in 2016 and together with the growing body of Asian data on IBS, we felt it is timely to update the Asian IBS Consensus.

    Methods: Key opinion leaders from Asian countries were organized into 4 teams to review 4 themes: symptoms and epidemiology, pathophysiology, diagnosis and investigations, and lifestyle modifications and treatments. The consensus development process was carried out by using a modified Delphi method.

    Results: Thirty-seven statements were developed. Asian data substantiate the current global viewpoint that IBS is a disorder of gut-brain interaction. Socio-cultural and environmental factors in Asia appear to influence the greater overlap between IBS and upper gastrointestinal symptoms. New classes of treatments comprising low fermentable oligo-, di-, monosacharides, and polyols diet, probiotics, non-absorbable antibiotics, and secretagogues have good evidence base for their efficacy.

    Conclusions: Our consensus is that all patients with functional gastrointestinal disorders should be evaluated comprehensively with a view to holistic management. Physicians should be encouraged to take a positive attitude to the treatment outcomes for IBS patients.

  9. Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association
    Wu J, Danko D, Afshinnekoo E, Bezdan D, Bhattacharyya M, Castro-Nallar E, et al.
    Environ Res, 2022 May 01;207:112183.
    PMID: 34637759 DOI: 10.1016/j.envres.2021.112183
    In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.
  10. Asia-Pacific guidelines for managing functional dyspepsia overlapping with other gastrointestinal symptoms
    Gwee KA, Lee YY, Suzuki H, Ghoshal UC, Holtmann G, Bai T, et al.
    J Gastroenterol Hepatol, 2023 Feb;38(2):197-209.
    PMID: 36321167 DOI: 10.1111/jgh.16046
    Contemporary systems for the diagnosis and management gastrointestinal symptoms not attributable to organic diseases (Functional GI Disorders, FGID, now renamed Disorders of Gut-Brain Interaction, DGBI) seek to categorize patients into narrowly defined symptom-based sub-classes to enable targeted treatment of patient cohorts with similar underlying putative pathophysiology. However, an overlap of symptom categories frequently occurs and has a negative impact on treatment outcomes. There is a lack of guidance on their management. An Asian Pacific Association of Gastroenterology (APAGE) working group was set up to develop clinical practice guidelines for management of patients with functional dyspepsia (FD) who have an overlap with another functional gastrointestinal disorder: FD with gastroesophageal reflux (FD-GERD), epigastric pain syndrome with irritable bowel syndrome (EPS-IBS), postprandial distress syndrome with IBS (PDS-IBS), and FD-Constipation. We identified putative pathophysiology to provide a basis for treatment recommendations. A management algorithm is presented to guide primary and secondary care clinicians.
  11. Fulltext A history of the MetaSUB consortium: Tracking urban microbes around the globe
    Ryon KA, Tierney BT, Frolova A, Kahles A, Desnues C, Ouzounis C, et al.
    iScience, 2022 Nov 18;25(11):104993.
    PMID: 36299999 DOI: 10.1016/j.isci.2022.104993
    The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.
  12. Rising global burden of cancer attributable to high BMI from 2010 to 2019
    Tan DJH, Ng CH, Muthiah M, Yong JN, Chee D, Teng M, et al.
    Metabolism, 2024 Mar;152:155744.
    PMID: 38029839 DOI: 10.1016/j.metabol.2023.155744
    BACKGROUND: High body mass index (BMI) is a major risk factor for cancer development, but its impact on the global burden of cancer remains unclear.

    METHODS: We estimated global and regional temporal trends in the burden of cancer attributable to high BMI, and the contributions of various cancer types using the framework of the Global Burden of Disease Study.

    RESULTS: From 2010 to 2019, there was a 35 % increase in deaths and a 34 % increase in disability-adjusted life-years from cancers attributable to high BMI. The age-standardized death rates for cancer attributable to high BMI increased over the study period (annual percentage change [APC] +0.48 %, 95 % CI 0.22 to 0.74 %). The greatest number of deaths from cancer attributable to high BMI occurred in Europe, but the fastest-growing age-standardized death rates and disability-adjusted life-years occurred in Southeast Asia. Liver cancer was the fastest-growing cause of cancer mortality (APC: 1.37 %, 95 % CI 1.25 to 1.49 %) attributable to high BMI.

    CONCLUSION: The global burden of cancer-related deaths attributable to high BMI has increased substantially from 2010 to 2019. The greatest increase in age-standardized death rates occurred in Southeast Asia, and liver cancer is the fastest-growing cause of cancer mortality attributable to high BMI. Urgent and sustained measures are required at a global and regional level to reverse these trends and slow the growing burden of cancer attributed to high BMI.

  13. Landscape of global urban environmental resistome and its association with local socioeconomic and medical status
    Wu J, Hu Y, Perlin MH, Danko D, Lu J, Oliveira M, et al.
    Sci China Life Sci, 2024 Mar 12.
    PMID: 38489008 DOI: 10.1007/s11427-023-2504-1
    Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters (BGCs) across different countries, and discovered that the urban environment represents a rich source of novel antibiotics. Our study provides a comprehensive overview of the global urban environmental resistome, and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.
  14. Fulltext 2019 Seoul Consensus on Esophageal Achalasia Guidelines
    Jung HK, Hong SJ, Lee OY, Pandolfino J, Park H, Miwa H, et al.
    J Neurogastroenterol Motil, 2020 04 30;26(2):180-203.
    PMID: 32235027 DOI: 10.5056/jnm20014
    Esophageal achalasia is a primary motility disorder characterized by insufficient lower esophageal sphincter relaxation and loss of esophageal peristalsis. Achalasia is a chronic disease that causes progressive irreversible loss of esophageal motor function. The recent development of high-resolution manometry has facilitated the diagnosis of achalasia, and determining the achalasia subtypes based on high-resolution manometry can be important when deciding on treatment methods. Peroral endoscopic myotomy is less invasive than surgery with comparable efficacy. The present guidelines (the "2019 Seoul Consensus on Esophageal Achalasia Guidelines") were developed based on evidence-based medicine; the Asian Neurogastroenterology and Motility Association and Korean Society of Neurogastroenterology and Motility served as the operating and development committees, respectively. The development of the guidelines began in June 2018, and a draft consensus based on the Delphi process was achieved in April 2019. The guidelines consist of 18 recommendations: 2 pertaining to the definition and epidemiology of achalasia, 6 pertaining to diagnoses, and 10 pertaining to treatments. The endoscopic treatment section is based on the latest evidence from meta-analyses. Clinicians (including gastroenterologists, upper gastrointestinal tract surgeons, general physicians, nurses, and other hospital workers) and patients could use these guidelines to make an informed decision on the management of achalasia.
  15. Evidence for the Higgs Boson Decay to a Z Boson and a Photon at the LHC
    Aad G, Abbott B, Abeling K, Abicht NJ, Abidi SH, Aboulhorma A, et al.
    Phys Rev Lett, 2024 Jan 12;132(2):021803.
    PMID: 38277607 DOI: 10.1103/PhysRevLett.132.021803
    The first evidence for the Higgs boson decay to a Z boson and a photon is presented, with a statistical significance of 3.4 standard deviations. The result is derived from a combined analysis of the searches performed by the ATLAS and CMS Collaborations with proton-proton collision datasets collected at the CERN Large Hadron Collider (LHC) from 2015 to 2018. These correspond to integrated luminosities of around 140  fb^{-1} for each experiment, at a center-of-mass energy of 13 TeV. The measured signal yield is 2.2±0.7 times the standard model prediction, and agrees with the theoretical expectation within 1.9 standard deviations.
  16. Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)
    Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.
    Autophagy, 2016;12(1):1-222.
    PMID: 26799652 DOI: 10.1080/15548627.2015.1100356
  17. Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1
    Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, et al.
    Autophagy, 2021 Jan;17(1):1-382.
    PMID: 33634751 DOI: 10.1080/15548627.2020.1797280
    In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
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