Publications by authors named "Yuko Sato"

309 Publications

Environmental Sampling for Avian Influenza Virus Detection in Commercial Layer Facilities.

Avian Dis 2021 09;65(3):391-400

Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011,

The present study was designed to evaluate the utility of environmental samples for convenient but accurate detection of avian influenza virus (AIV) in commercial poultry houses. First, environmental samples from AIV-negative commercial layer facilities were spiked with an H5N2 low pathogenic AIV and were evaluated for their effect on the detection of viral RNA immediately or after incubation at -20 C, 4 C, 22 C, or 37 C for 24, 48, or 72 hr. Second, Swiffer pads, drag swabs, and boot cover swabs were evaluated for their efficiency in collecting feces and water spiked with the H5N2 LPAIV under a condition simulated for a poultry facility floor. Third, environmental samples collected from commercial layer facilities that experienced an H5N2 highly pathogenic AIV outbreak in 2014-15 were evaluated for the effect of sampling locations on AIV detection. The half-life of AIV was comparable across all environmental samples but decreased with increasing temperatures. Additionally, sampling devices did not differ significantly in their ability to collect AIV-spiked environmental samples from a concrete floor for viral RNA detection. Some locations within a poultry house, such as cages, egg belts, house floor, manure belts, and manure pits, were better choices for sampling than other locations (feed trough, ventilation fan, and water trays) to detect AIV RNA after cleaning and disinfection. Samples representing cages, floor, and manure belts yielded significantly more PCR positives than the other environmental samples. In conclusion, environmental samples can be routinely collected from a poultry barn as noninvasive samples for monitoring AIV.
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http://dx.doi.org/10.1637/0005-2086-65.3.391DOI Listing
September 2021

Comparison of Naturally Occurring . Experimental Infection of Septicemia in Laying Hens in Two Different Age Groups.

Avian Dis 2021 06;65(2):310-320

Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University College of Veterinary Medicine, Ames, IA 50011,

In April and November of 2018, multiple commercial laying hen flocks within the same company presented with a sharp increase in mortality and drop in egg production that persisted for several days. These flocks showed striking necropsy lesions consistent with systemic infection and responded to antimicrobial treatment in the feed. (SA) was the most frequently isolated organism from multiple tissues including comb and wattle lesions, lungs, liver, ovary, spleen, and bone marrow. Given such an uncommon presentation of SA, which is known as a secondary opportunistic pathogen, a challenge study was conducted to evaluate its role in these disease outbreaks. In the present study, laying hens of two ages (22 and 96 wk) were inoculated with SA via three routes: oral gavage, subcutaneous (SC) injection, and intravenous (IV) injection. Both young and old hens in the IV group showed a significant increase in body temperature and drop in body weight; however, the clinical signs observed in the naturally occurring outbreaks were not present. SA was reisolated at multiple time points postchallenge from all challenge groups except the negative control group. While the SC group showed localized necrosis at the injection site, microscopic changes were different from changes observed in birds from the natural outbreaks. Despite observed initial differences in route and age, the SA challenge strain was not capable of reproducing the disease on its own. The results of this study indicate that SA may have played a role in the increased mortality, clinical signs, and necropsy lesions reported with the naturally occurring outbreaks. However, SA should still be considered as a secondary opportunistic pathogen. Other factors that could have caused the initial insult are stress, immunosuppression, or other primary infectious agents. The results of this study may aid veterinary diagnosticians, clinicians, and all poultry professionals to include SA in their differentials list as a secondary opportunistic pathogen in similar cases. This is an uncommon presentation and further field observations and clinical studies are needed to better elucidate the pathogenesis of this disease, which will in turn help to prevent future outbreaks.
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http://dx.doi.org/10.1637/0005-2086-65.2.310DOI Listing
June 2021

SARS-CoV-2 is localized in cardiomyocytes: a postmortem biopsy case.

Int J Infect Dis 2021 Aug 9;111:43-46. Epub 2021 Aug 9.

Department of Emergency and Critical Care Medicine, Fukuoka University Hospital, 7-45-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180, Japan. Electronic address:

A 72-year-old patient was admitted to the intensive care unit due to acute respiratory distress syndrome caused by COVID-19. On day 20, the patient experienced shock. The electrocardiogram showed ST segment elevation in leads V3-V6 and severe left ventricular dysfunction with an ejection fraction of 35%-40%. The left ventricle showed basal hypokinesis and apical akinesis, while the creatine kinase level was normal, indicating Takotsubo cardiomyopathy. On day 24, the patient died of multiple organ failure. In post-mortem biopsy, SARS-CoV-2 antigen was detected in cardiomyocytes by immunostaining. Moreover, SARS-CoV-2 RNA was detected in heart tissue. We need to further analyse the direct link between SARS-CoV-2 and cardiomyocytes.
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http://dx.doi.org/10.1016/j.ijid.2021.08.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8351278PMC
August 2021

Multiplexed Imaging of Posttranslational Modifications of Endogenous Proteins in Live Cells.

Methods Mol Biol 2021 ;2350:31-41

Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.

Posttranslational histone modifications are associated with the regulation of genome function. Some modifications are quite stable to maintain epigenome states of chromatin, and others can exhibit dynamic changes in response to internal and external stimuli. To track the local and global changes in histone modifications, multiplexed imaging in living cells is beneficial. Among live cell probes for detecting histone modifications, genetically encoded modification-specific intracellular antibodies, or mintbodies, are convenient and suitable tools for this purpose. We here describe the mintbody-based methods to monitor the changes in histone modification levels induced by histone methyltransferase and deacetylase inhibitors. By measuring the nuclear to cytoplasmic intensity ratios of mintbodies in living cells, changes in histone H4 lysine 20 methylation states and the increase in histone H3 acetylation were detected.
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http://dx.doi.org/10.1007/978-1-0716-1593-5_3DOI Listing
September 2021

Live-Cell Imaging Probes to Track Chromatin Modification Dynamics.

Microscopy (Oxf) 2021 Jul 30. Epub 2021 Jul 30.

Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.

The spatiotemporal organization of chromatin is regulated at different levels in the nucleus. Epigenetic modifications such as DNA methylation and histone modifications are involved in chromatin regulation and play fundamental roles in genome function. While the one-dimensional epigenomic landscape in many cell types has been revealed by chromatin immunoprecipitation and sequencing, the dynamic changes of chromatin modifications and their relevance to chromatin organization and genome function remain elusive. Live-cell probes to visualize chromatin and its modifications have become powerful tools to monitor dynamic chromatin regulation. Bulk chromatin can be visualized both by small fluorescent dyes and fluorescent proteins, and specific endogenous genomic loci have been detected by adapting genome-editing tools. To track chromatin modifications in living cells, various types of probes have been developed. Protein domains that bind to specific modifications weakly, such as chromodomains for histone methylation, can be repeated to create a tighter binding probe that can then be tagged with a fluorescent protein. It has also been demonstrated that antigen-binding fragments and single-chain variable fragments from modification-specific antibodies can serve as binding probes without disturbing cell division, development and, differentiation. These modification-binding modules are used in modification sensors based on fluorescence/Förster resonance energy transfer to measure the intramolecular conformation changes triggered by modifications. Other probes can be created using a bivalent binding system, such as fluorescence complementation, or luciferase chemiluminescence. Live-cell chromatin modification imaging using these probes will address dynamic chromatin regulation and will be useful for assaying and screening effective epigenome drugs in cells and organisms.
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http://dx.doi.org/10.1093/jmicro/dfab030DOI Listing
July 2021

Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians.

Nature 2021 Jul 29. Epub 2021 Jul 29.

Division of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Ibaraki, Japan.

Centenarians have a decreased susceptibility to ageing-associated illnesses, chronic inflammation and infectious diseases. Here we show that centenarians have a distinct gut microbiome that is enriched in microorganisms that are capable of generating unique secondary bile acids, including various isoforms of lithocholic acid (LCA): iso-, 3-oxo-, allo-, 3-oxoallo- and isoallolithocholic acid. Among these bile acids, the biosynthetic pathway for isoalloLCA had not been described previously. By screening 68 bacterial isolates from the faecal microbiota of a centenarian, we identified Odoribacteraceae strains as effective producers of isoalloLCA both in vitro and in vivo. Furthermore, we found that the enzymes 5α-reductase (5AR) and 3β-hydroxysteroid dehydrogenase (3β-HSDH) were responsible for the production of isoalloLCA. IsoalloLCA exerted potent antimicrobial effects against Gram-positive (but not Gram-negative) multidrug-resistant pathogens, including Clostridioides difficile and Enterococcus faecium. These findings suggest that the metabolism of specific bile acids may be involved in reducing the risk of infection with pathobionts, thereby potentially contributing to the maintenance of intestinal homeostasis.
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http://dx.doi.org/10.1038/s41586-021-03832-5DOI Listing
July 2021

Neuroinvasiveness of the MR766 strain of Zika virus in IFNAR-/- mice maps to prM residues conserved amongst African genotype viruses.

PLoS Pathog 2021 Jul 26;17(7):e1009788. Epub 2021 Jul 26.

Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan.

Zika virus (ZIKV) strains are classified into the African and Asian genotypes. The higher virulence of the African MR766 strain, which has been used extensively in ZIKV research, in adult IFNα/β receptor knockout (IFNAR-/-) mice is widely viewed as an artifact associated with mouse adaptation due to at least 146 passages in wild-type suckling mouse brains. To gain insights into the molecular determinants of MR766's virulence, a series of genes from MR766 were swapped with those from the Asian genotype PRVABC59 isolate, which is less virulent in IFNAR-/- mice. MR766 causes 100% lethal infection in IFNAR-/- mice, but when the prM gene of MR766 was replaced with that of PRVABC59, the chimera MR/PR(prM) showed 0% lethal infection. The reduced virulence was associated with reduced neuroinvasiveness, with MR766 brain titers ≈3 logs higher than those of MR/PR(prM) after subcutaneous infection, but was not significantly different in brain titers of MR766 and MR/PR(prM) after intracranial inoculation. MR/PR(prM) also showed reduced transcytosis when compared with MR766 in vitro. The high neuroinvasiveness of MR766 in IFNAR-/- mice could be linked to the 10 amino acids that differ between the prM proteins of MR766 and PRVABC59, with 5 of these changes affecting positive charge and hydrophobicity on the exposed surface of the prM protein. These 10 amino acids are highly conserved amongst African ZIKV isolates, irrespective of suckling mouse passage, arguing that the high virulence of MR766 in adult IFNAR-/- mice is not the result of mouse adaptation.
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http://dx.doi.org/10.1371/journal.ppat.1009788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8341709PMC
July 2021

Endotracheal Tube Obstruction Experienced during an Anterior Cervical Discectomy and Fusion.

Asian J Neurosurg 2021 Apr-Jun;16(2):381-383. Epub 2021 May 28.

Department of Neurosurgery, Aichi Medical University, Nagakute, Japan.

During anterior cervical discectomy and fusion (ACDF), endotracheal tube difficulties are anticipated at the operative level but are unexpected elsewhere in the airway. We report the case of a 66-year-old woman who underwent C4/C5 ACDF to treat adjacent segment disease following a previous anterior cervical fixation surgery. Shortly after her lower jaw was elevated and the fusion cage was inserted, a rise in airway pressure was observed, indicating impaired breathing. Subsequent examination revealed a bent endotracheal tube in the oral cavity as the cause of the respiratory impairment. During anterior cervical surgery, elevating the lower jaw can cause the tongue root to press against the endotracheal tube. Reinforced endotracheal tubes, with a spiral-wound wire in the inner wall, would effectively prevent this issue. In the unlikely event of impaired breathing during such an operation, the oral cavity should be inspected for confirmation of an open airway.
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http://dx.doi.org/10.4103/ajns.AJNS_258_20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8244709PMC
May 2021

Characteristics of Helicase-Primase Inhibitor Amenamevir-Resistant Herpes Simplex Virus.

Antimicrob Agents Chemother 2021 Sep 6;65(10):e0049421. Epub 2021 Jul 6.

Department of Microbiology, Fukushima Medical University School of Medicine, Fukushima, Japan.

The antiherpetic drug amenamevir (AMNV) inhibits the helicase-primase complex of herpes simplex virus 1 (HSV-1), HSV-2, and varicella-zoster virus directly as well as inhibiting the replication of these viruses. Although several mutated HSV viruses resistant to helicase-primase inhibitors have been reported, the mutations contributing to the resistance remain unclear, as recombinant viruses containing a single mutation have not been analyzed. We obtained AMNV-resistant viruses with amino acid substitutions by several passages under AMNV treatment. Twenty HSV-1 and 19 HSV-2 mutants with mutation(s) in UL5 helicase and/or UL52 primase, but not in cofactor UL8, were isolated. The mutations in UL5 were located downstream of motif IV, with UL5 K356N in HSV-1 and K355N in HSV-2, in particular, identified as having the highest frequency, which was 9/20 and 9/19, respectively. We generated recombinant AMNV-resistant HSV-1 with a single amino acid substitution using bacterial artificial chromosome (BAC) mutagenesis. As a result, G352C in UL5 helicase and F360C/V and N902T in UL52 primase were identified as novel mutations. The virus with K356N in UL5 showed 10-fold higher AMNV resistance than did other mutants and showed equivalent viral growth and virulence as the parent HSV-1, although other mutants showed attenuated virulence. All recombinant viruses were susceptible to the other antiherpetic drugs, acyclovir and foscarnet. In conclusion, based on BAC mutagenesis, this study identified, for the first time, mutations in UL5 and UL52 that contributed to AMNV resistance and found that a mutant with the most frequent K356N mutation in HSV-1 maintained viral growth and virulence equivalent to the parent virus.
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http://dx.doi.org/10.1128/AAC.00494-21DOI Listing
September 2021

Propagation of activated B cells by in vitro SFTSV infection of human peripheral blood mononuclear cells.

J Infect Dis 2021 Jul 5. Epub 2021 Jul 5.

Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan.

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging, life-threatening tick-borne viral hemorrhagic fever (VHF) caused by SFTS virus (SFTSV). Transient appearance of plasmablastic lymphocytes in the peripheral blood of SFTS cases has been reported; however, the pathological significance of this transient burst in peripheral blood plasmablastic lymphocytes is unclear. Here, we show that SFTSV infection of human peripheral blood mononuclear cells (PBMCs) in vitro induced propagation of atypical lymphocytes. These atypical lymphocytes were activated B cells, which were induced by secretory factors other than viral particles; these factors were secreted by SFTSV-infected B cells. Activated B cells shared morphological and immunophenotypic characteristics with B cells of plasmablast lineage observed in peripheral blood and autopsy tissues of SFTS cases. This suggests that SFTSV-infected B cells secrete factors that induce B cell differentiation to plasmablasts, which may play an important role in pathogenesis of SFTS through the SFTSV-B cell axis.
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http://dx.doi.org/10.1093/infdis/jiab343DOI Listing
July 2021

A method for gaining a deeper insight into the aroma profile of olive oil.

NPJ Sci Food 2021 Jul 1;5(1):16. Epub 2021 Jul 1.

The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama-shi, Ehime, Japan.

Volatile compounds in food play a crucial role in affecting food quality and consumer preference, but the volatile compounds in olive oil are not fully understood due to the matrix effect of oil. The oiling-out assisted liquid-liquid extraction (OA-LLE), which we previously reported, is an effective method for isolating volatile compounds from edible oils with a strong matrix effect. However, when we apply OA-LLE to extra virgin olive oil (EVOO), the aromatic extracts contain non-volatile compounds such as pigments because of solvent-based extraction. Solvent-assisted flavor evaporation (SAFE) can remove such non-volatiles from extracts, but SAFE is affected by a matrix effect during distillation, resulting in a decrease in performance. By combining the advantages of OA-LLE and SAFE, we propose an effective approach, OA-LLE followed by SAFE (OA-LLE + SAFE), for extracting aroma compounds from EVOO. The "two assists" should help to better understand the native aroma profile of EVOO.
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http://dx.doi.org/10.1038/s41538-021-00098-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8249399PMC
July 2021

Factors related to specialized palliative care use and aggressive care at end of life in Japanese patients with advanced solid cancers: a cohort study.

Support Care Cancer 2021 Jun 25. Epub 2021 Jun 25.

Department of Palliative Medicine, Tohoku University School of Medicine, Sendai, Japan.

Purpose: This study aimed to (1) describe characteristics of aggressive care at the end of life (EOL) and (2) identify factors associated with specialized palliative care use (SPC) and aggressive care at the EOL among Japanese patients with advanced cancer.

Methods: This single-center, follow-up cohort study involved patients with advanced cancer who received chemotherapy at Tohoku University Hospital. Patients were surveyed at enrollment, and we followed clinical events for 5 years from enrollment in the study. We performed multivariate logistic regression analysis to identify independent factors related to SPC use and chemotherapy in the last month before death.

Results: We analyzed a total of 135 patients enrolled between January 2015 and January 2016. No patients were admitted to the intensive care unit, and few received resuscitation or ventilation. We identified no factors significantly associated with SPC use. Meanwhile, younger age (20-59 years, odds ratio [OR] 4.10; 95% confidence interval [CI] 1.30-12.91; p = 0.02) and no receipt of SPC (OR 4.32; 95% CI 1.07-17.37; p = 0.04) were associated with chemotherapy in the last month before death.

Conclusion: Younger age and a lack of SPC were associated with chemotherapy at the EOL in patients with advanced cancer in Japan. These findings suggest that Japanese patients with advanced cancer may benefit from access to SPC.
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http://dx.doi.org/10.1007/s00520-021-06364-wDOI Listing
June 2021

Dynamic Behavior of Inactive X Chromosome Territory During the Cell Cycle as Revealed by H3K27me3-Specific Intracellular Antibody.

Methods Mol Biol 2021 ;2329:237-247

Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.

Posttranslational histone modifications are critical for the regulation of genome function. The levels of histone modifications oscillate during the cell cycle. Most modifications are diluted after DNA replication and then their levels are restored during the rest of the cell cycle with different kinetics depending on the modification. Some modifications, like histone H4 Lys20 monomethylation (H4K20me1), exhibit cell cycle-dependent dynamic changes. To track histone modifications in living cells, we have developed genetically encoded probes termed modification specific intracellular antibodies, or "mintbodies." As mintbodies shuttle between the cytoplasm and nucleus by diffusion, their nuclear concentration depends on the target modification level. By measuring the nuclear to cytoplasmic intensity ratio of H4K20me1-specific mintbody, we have monitored the increase of H4K20me1 in the G2 phase. Here we describe how the mintbody-based methods can be applied to track a specific chromosome, such as the inactive X chromosome (Xi), on which genes are repressed through histone H3 Lys27 trimethylation (H3K27me3). When H3K27me3-specific mintbodies are expressed in cells that harbor Xi, the mintbodies are concentrated on Xi and the dynamic behavior of Xi can be tracked using a confocal microscope. After acquiring 3D time-lapse images, an image analysis allows measuring the volume, shape and H3K27me3 level of Xi during the cell cycle.
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http://dx.doi.org/10.1007/978-1-0716-1538-6_17DOI Listing
August 2021

A Kidney Transplant Patient Who Died of COVID-19-associated Severe Acute Respiratory Distress Syndrome.

Intern Med 2021 Jul 29;60(14):2297-2300. Epub 2021 May 29.

Department of Respiratory Medicine, National Center for Global Health and Medicine, Japan.

We herein report a 67-year-old kidney transplant patient who died of COVID-19. He was treated with hydroxychloroquine and azithromycin and received mechanical ventilation that temporarily improved his respiratory status. Despite our efforts, however, he later developed respiratory failure and died 43 days after the disease onset. The autopsy revealed prominent organization of alveoli and alveolar ducts, with a massive accumulation of macrophages in the lungs. A few severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen-positive cells were detected in the lung, suggesting delayed virus clearance owing to his long-term immunosuppressed state, leading to constant lung damage and ultimately respiratory failure.
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http://dx.doi.org/10.2169/internalmedicine.7089-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8355385PMC
July 2021

Morphological and genetic identification of fungal genus/species in formalin-fixed, paraffin-embedded specimens obtained from patients with histologically proven fungal infection.

Mycoses 2021 Aug 4;64(8):851-859. Epub 2021 Jun 4.

Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.

Background: Although fungi are found relatively easily by microscopic examination of pathological samples, identification of fungal genus and species in pathological samples is not easy because the morphological features of fungi are similar among genera and species.

Objectives: A multiple real-time PCR was developed for identification of fungal genus/species, and morphological characterizations of fungi were analysed in pathological samples.

Patients/methods: Seventy-five formalin-fixed paraffin-embedded (FFPE) samples morphologically proven to contain any fungus were examined. A multiple real-time PCR system was developed to identify 25 fungal genus/species in pathological samples. Morphology of fungus in the specimens was re-reviewed retrospectively based on the results of real-time PCR.

Results: Real-time PCR identified fungal genus/species in 56 of 75 (74.6%) specimens with histologically proven fungal infection. In 53 specimens of filamentous fungi, Aspergillus spp. (22 specimens), Cladosporium (8), Scedosporium apiospermum (4), Malassezia sympodialis (1) and Candida albicans (1) were identified. Pseudohyphae of Candida were confused with filamentous fungus in a case. Morphological observation suggested differences in the presence of septated or non-septated hyphae, the filament size, and the branch angle among genus/species of filamentous fungi; however, genus/species was not able to be determined by their morphological features. In 22 specimens of yeasts, real-time PCR allowed for the identification of Candida albicans (12 specimens), Candida glabrata (2), Cladosporium (2), Scedosporium apiospermum (2), Pichia kudriavzevii (1) and Aspergillus sydowii (1).

Conclusions: These data suggest that it is difficult to identify fungal genus/species by morphological features alone. Real-time PCR is useful to identify fungal genus/species in pathological samples.
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http://dx.doi.org/10.1111/myc.13325DOI Listing
August 2021

Near-Complete Genome Sequence of GI-17 Lineage Infectious Bronchitis Virus, Circulating in Iowa.

Microbiol Resour Announc 2021 May 20;10(20). Epub 2021 May 20.

Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA

Avian infectious bronchitis virus (AvIBV) is the causative agent of a highly contagious respiratory disease in chickens which results in significant economic losses in the poultry industry. Here, we report a near-complete genome sequence of the strain, designated IA1162/2020, identified in tracheal swabs from chickens in Iowa in 2020.
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http://dx.doi.org/10.1128/MRA.01406-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8188336PMC
May 2021

A live imaging system to analyze spatiotemporal dynamics of RNA polymerase II modification in Arabidopsis thaliana.

Commun Biol 2021 05 14;4(1):580. Epub 2021 May 14.

Graduate School of Frontier Sciences, Department of Integrated Biosciences, The University of Tokyo, Kashiwa, Chiba, Japan.

Spatiotemporal changes in general transcription levels play a vital role in the dynamic regulation of various critical activities. Phosphorylation levels at Ser2 in heptad repeats within the C-terminal domain of RNA polymerase II, representing the elongation form, is an indicator of transcription. However, rapid transcriptional changes during tissue development and cellular phenomena are difficult to capture in living organisms. We introduced a genetically encoded system termed modification-specific intracellular antibody (mintbody) into Arabidopsis thaliana. We developed a protein processing- and 2A peptide-mediated two-component system for real-time quantitative measurement of endogenous modification level. This system enables quantitative tracking of the spatiotemporal dynamics of transcription. Using this method, we observed that the transcription level varies among tissues in the root and changes dynamically during the mitotic phase. The approach is effective for achieving live visualization of the transcription level in a single cell and facilitates an improved understanding of spatiotemporal transcription dynamics.
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http://dx.doi.org/10.1038/s42003-021-02106-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8121908PMC
May 2021

The Acute Host-Response of Turkeys Colonized With .

Front Vet Sci 2021 6;8:613203. Epub 2021 Apr 6.

Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Services, U.S. Department of Agriculture, Ames, IA, United States.

Consumption of contaminated poultry products is one of the main sources of human campylobacteriosis, of which subsp. () and are responsible for ~98% of the cases. In turkeys, the ceca are an important anatomical site where asymptomatically colonizes. We previously demonstrated that commercial turkey poults colonized by showed acute changes in cytokine gene expression profiles, and histological intestinal lesions at 2 days post-inoculation (dpi). Cecal tonsils (CT) are an important part of the gastrointestinal-associated lymphoid tissue that surveil material passing in and out of the ceca, and generate immune responses against intestinal pathogens. The CT immune response toward remains unknown. In this study, we generated a kanamycin-resistant construct (CcK) to facilitate its enumeration from cecal contents after experimental challenge. analysis of CcK demonstrated no changes in motility when compared to the parent isolate. Poults were inoculated by oral gavage with CcK (5 × 10 colony forming units) or sterile-media (mock-colonized), and euthanized at 1 and 3 dpi. At both time points, CcK was recovered from cecal contents, but not from the mock-colonized group. As a marker of acute inflammation, serum alpha-1 acid glycoprotein was significantly elevated at 3 dpi in CcK inoculated poults compared to mock-infected samples. Significant histological lesions were detected in cecal and CT tissues of CcK colonized poults at 1 and 3 dpi, respectively. RNAseq analysis identified 250 differentially expressed genes (DEG) in CT from CcK colonized poults at 3 dpi, of which 194 were upregulated and 56 were downregulated. From the DEG, 9 significantly enriched biological pathways were identified, including platelet aggregation, response to oxidative stress and negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway. These data suggest that induced an acute inflammatory response in the intestinal tract of poults, and that platelet aggregation and oxidative stress in the CT may affect the turkey's ability to resist colonization. These findings will help to develop and test mitigation strategies to promote food safety in commercial turkeys.
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http://dx.doi.org/10.3389/fvets.2021.613203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8057350PMC
April 2021

Age and Inoculation Route Differentially Alter Metabolic Potential and Immune Cell Populations in Laying Hens.

Front Vet Sci 2021 26;8:653129. Epub 2021 Mar 26.

Department of Animal Science, Iowa State University, Ames, IA, United States.

In 2018 and 2019, was isolated from multiple post-molt commercial laying hens with unusually high mortality. A challenge study was conducted to elucidate the role of in this disease outbreak and the work herein represents the assessment of immunological responses in laying hens experimentally infected with isolates from these cases. A total of 200 laying hens at 22 or 96 weeks of age (100/ age group) were assigned to 1 of 4 experimental inoculation groups (negative control, oral gavage, subcutaneous injection, or intravenous injection) after a 72 h acclimation period. Blood samples were taken prior to inoculation (baseline), 6 h post-inoculation (pi), 24 hpi, 3 dpi, and 7 dpi. Additional spleen samples to further assess systemic immunity were taken at baseline, 3 and 8 dpi. Metabolic phenotypes of peripheral blood mononuclear cells (PBMC) were isolated and assessed by Seahorse metabolic assay. Immune cell profiles in the spleen and PBMC were assessed by multicolor flow cytometry. At baseline, 96-week-old laying hens had 26.7% fewer PBMC-derived T cells compared to 22-week-old birds. Older hens had 28.9% increased helper T cell (T) populations and 60.5% reduced γδ T cells ( = 0.03 and < 0.0001) which may contribute to variable clinical responses between age groups; however, no age-related differences in metabolic potential were observed. Metabolic outcomes showed that birds remained stressed from transport and re-housing past a 72 h acclimation period and through 24 h- 3 days post-inoculation. Inoculation with generally reduced oxidative and glycolytic potentials compared to the control, with the greatest reductions observed in birds inoculated by intravenous injection ( < 0.05). Overall CD3 T cell populations showed significant reductions in the intravenous group compared to other inoculation routes from 24 hpi to 7 dpi (23.6-39.0%; ≤ 0.0001). These results suggest that age-related baseline differences in T cell populations and changes to T cell subpopulations and other immune cells due to inoculation route may have an additive effect on - induced reductions in metabolic potential; however, further research linking metabolic potential and immune cell profiles is needed.
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http://dx.doi.org/10.3389/fvets.2021.653129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8032939PMC
March 2021

Pitfalls in chest CT findings of COVID-19 patients infected during hospitalisation.

Clin Imaging 2021 Oct 26;78:146-153. Epub 2021 Mar 26.

Department of Radiology, Nerima Hikarigaoka Hospital, Japan Association for Development of Community Medicine, 2-11-1 Hikarigaoka, Nerima-ku, Tokyo 179-0072, Japan.

Objective: This study evaluated the differences in the appearance of COVID-19 pneumonia on chest computed tomography (CT) images of outpatient and cases that developed during hospitalisation.

Method: Chest CT images of 66 patients (median age, 76 years; range, 29-94 years) who underwent the severe acute respiratory syndrome coronavirus-2 reverse-transcription polymerase chain reaction (RT-PCR) test were included in this retrospective study. The chest CT appearance was categorised as "typical," "indeterminate," "atypical," or "negative" in accordance with the recommendations of the Radiological Society of North America for COVID-19 pneumonia and compared among the following four subgroups: PCR-positive outpatient (n = 14); PCR-positive hospitalised (n = 7); PCR-negative outpatient (n = 9); and PCR-negative hospitalised (n = 36).

Findings: The frequency of "typical" findings in the PCR-positive outpatient cases (13/14, 92.9%) was significantly higher than that of those in the PCR-positive hospitalised cases (2/7, 28.6%, P = 0.022). There was no significant difference between the frequency of the "typical" appearance in PCR-positive hospitalised cases and that of those in the PCR-negative hospitalised cases (1/36, 2.8%, P = 0.192).

Conclusions: When COVID-19 patients acquire infections while hospitalised, their chest CT images are less likely to show typical findings than those of outpatient cases. Comprehensive and careful assessments of CT findings and consideration of the possibility of concomitant infections with other pathogens and clinical information, such as underlying diseases, background lung structure, and time course of the infection, are required for the management of such cases.
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http://dx.doi.org/10.1016/j.clinimag.2021.03.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7997701PMC
October 2021

Transcription organizes euchromatin via microphase separation.

Nat Commun 2021 03 1;12(1):1360. Epub 2021 Mar 1.

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

In eukaryotes, DNA is packed inside the cell nucleus in the form of chromatin, which consists of DNA, proteins such as histones, and RNA. Euchromatin, which is permissive for transcription, is spatially organized into transcriptionally inactive domains interspersed with pockets of transcriptional activity. While transcription and RNA have been implicated in euchromatin organization, it remains unclear how their interplay forms and maintains transcription pockets. Here we combine theory and experiment to analyze the dynamics of euchromatin organization as pluripotent zebrafish cells exit mitosis and begin transcription. We show that accumulation of RNA induces formation of transcription pockets which displace transcriptionally inactive chromatin. We propose that the accumulating RNA recruits RNA-binding proteins that together tend to separate from transcriptionally inactive euchromatin. Full phase separation is prevented because RNA remains tethered to transcribed euchromatin through RNA polymerases. Instead, smaller scale microphases emerge that do not grow further and form the typical pattern of euchromatin organization.
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http://dx.doi.org/10.1038/s41467-021-21589-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7921102PMC
March 2021

Accumulation of cellular prion protein within β-amyloid oligomer plaques in aged human brains.

Brain Pathol 2021 Sep 23;31(5):e12941. Epub 2021 Feb 23.

Experimental Dementia Research Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden.

Alzheimer's disease (AD) is the main cause of dementia, and β-amyloid (Aβ) is a central factor in the initiation and progression of the disease. Different forms of Aβ have been identified as monomers, oligomers, and amyloid fibrils. Many proteins have been implicated as putative receptors of respective forms of Aβ. Distinct forms of Aβ oligomers are considered to be neurotoxic species that trigger the pathophysiology of AD. It was reported that cellular prion protein (PrP ) is one of the most selective and high-affinity binding partners of Aβ oligomers. The interaction of Aβ oligomers with PrP is important to synaptic dysfunction and loss. The binding of Aβ oligomers to PrP has mostly been studied with synthetic peptides, cell culture, and murine models of AD by biochemical and biological methods. However, the molecular mechanisms underlying the relationship between Aβ oligomers and PrP remain unclear, especially in the human brain. We immunohistochemically investigated the relationship between Aβ oligomers and PrP in human brain tissue with and without amyloid pathology. We histologically demonstrate that PrP accumulates with aging in human brain tissue even prior to AD mainly within diffuse-type amyloid plaques, which are composed of more soluble Aβ oligomers without stacked β-sheet fibril structures. Our results suggest that PrP accumulating plaques are associated with more soluble Aβ oligomers, and appear even prior to AD. The investigation of PrP accumulating plaques may provide new insights into AD.
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http://dx.doi.org/10.1111/bpa.12941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8412093PMC
September 2021

H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing.

EMBO Rep 2021 03 19;22(3):e51989. Epub 2021 Feb 19.

EMBL Heidelberg, Heidelberg, Germany.

During X chromosome inactivation (XCI), in female placental mammals, gene silencing is initiated by the Xist long non-coding RNA. Xist accumulation at the X leads to enrichment of specific chromatin marks, including PRC2-dependent H3K27me3 and SETD8-dependent H4K20me1. However, the dynamics of this process in relation to Xist RNA accumulation remains unknown as is the involvement of H4K20me1 in initiating gene silencing. To follow XCI dynamics in living cells, we developed a genetically encoded, H3K27me3-specific intracellular antibody or H3K27me3-mintbody. By combining live-cell imaging of H3K27me3, H4K20me1, the X chromosome and Xist RNA, with ChIP-seq analysis we uncover concurrent accumulation of both marks during XCI, albeit with distinct genomic distributions. Furthermore, using a Xist B and C repeat mutant, which still shows gene silencing on the X but not H3K27me3 deposition, we also find a complete lack of H4K20me1 enrichment. This demonstrates that H4K20me1 is dispensable for the initiation of gene silencing, although it may have a role in the chromatin compaction that characterises facultative heterochromatin.
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http://dx.doi.org/10.15252/embr.202051989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7926250PMC
March 2021

Live-cell epigenome manipulation by synthetic histone acetylation catalyst system.

Proc Natl Acad Sci U S A 2021 01;118(4)

Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan;

Chemical modifications of histones, such as lysine acetylation and ubiquitination, play pivotal roles in epigenetic regulation of gene expression. Methods to alter the epigenome thus hold promise as tools for elucidating epigenetic mechanisms and as therapeutics. However, an entirely chemical method to introduce histone modifications in living cells without genetic manipulation is unprecedented. Here, we developed a chemical catalyst, PEG-LANA-DSSMe 11, that binds with nucleosome's acidic patch and promotes regioselective, synthetic histone acetylation at H2BK120 in living cells. The size of polyethylene glycol in the catalyst was a critical determinant for its in-cell metabolic stability, binding affinity to histones, and high activity. The synthetic acetylation promoted by 11 without genetic manipulation competed with and suppressed physiological H2B ubiquitination, a mark regulating chromatin functions, such as transcription and DNA damage response. Thus, the chemical catalyst will be a useful tool to manipulate epigenome for unraveling epigenetic mechanisms in living cells.
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http://dx.doi.org/10.1073/pnas.2019554118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7848698PMC
January 2021

Comparison of naturally-occurring versus experimental infection of Staphylococcus aureus septicemia in Laying Hens in two different age groups.

Avian Dis 2021 Jan 19. Epub 2021 Jan 19.

Iowa State University Assistant Professor Veterinary Preventive Medicine 1809 South River Drive UNITED STATES Ames IA 50011 17065403037.

In April and November of 2018, multiple commercial laying hen flocks within the same company presented with a sharp increase in mortality and drop in egg production that persisted for several days. These flocks showed striking necropsy lesions consistent with systemic infection and responded to antimicrobial treatment in the feed. Staphylococcus aureus (SA) was the most frequently isolated organism from multiple tissues including comb and wattle lesions, lungs, liver, ovary, spleen, and bone marrow. Given such an uncommon presentation of SA, which is known as a secondary opportunistic pathogen, a challenge study was conducted to evaluate its role is these disease outbreaks. In the present study, laying hens of 2 ages (22 and 96 weeks) were inoculated with SA via 3 routes: oral gavage (OG), subcutaneous injection (SC), and intravenous injection (IV). Both young and old hens in the IV group showed a significant increase in body temperature and drop in body weight; however, the clinical signs observed in the naturally-occurring outbreaks were not present. SA was re-isolated at multiple time points post-challenge from all challenge groups except the negative control group. While the SC group showed localized necrosis at the injection site, microscopic changes were different from changes observed in birds from the natural outbreaks. Despite observed initial differences in route and age, the SA challenge strain was not capable of reproducing the disease on its own. The results of this study indicate that SA may have played a role in the increased mortality, clinical signs, and necropsy lesions reported with the naturally-occurring outbreaks. However, SA should still be considered as a secondary opportunistic pathogen. Other factors that could have caused the initial insult are stress, immunosuppression, or other primary infectious agents. The results of this study may aid veterinary diagnosticians, clinicians, and all poultry professionals to include SA in their differentials list as a secondary opportunistic pathogen in similar cases. This is an uncommon presentation and further field observations and clinical studies are needed to better elucidate the pathogenesis of this disease, which will in turn help to prevent future outbreaks.
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http://dx.doi.org/10.1637/aviandiseases-D-20-00118DOI Listing
January 2021

Lung Pathology of Mutually Exclusive Co-infection with SARS-CoV-2 and Streptococcus pneumoniae.

Emerg Infect Dis 2021 03 14;27(3):919-923. Epub 2021 Jan 14.

Postmortem lung pathology of a patient in Japan with severe acute respiratory syndrome coronavirus 2 infection showed diffuse alveolar damage as well as bronchopneumonia caused by Streptococcus pneumoniae infection. The distribution of each pathogen and the accompanying histopathology suggested the infections progressed in a mutually exclusive manner within the lung, resulting in fatal respiratory failure.
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http://dx.doi.org/10.3201/eid2703.204024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7920656PMC
March 2021

Syngamus asphyxiation in a captive ring-necked pheasant.

Vet Parasitol Reg Stud Reports 2020 12 10;22:100493. Epub 2020 Nov 10.

Department of Veterinary Pathology, College of Veterinary Medicine, Iowa State University, USA. Electronic address:

A deceased ring-necked pheasant (Phasianus colchicus) presented for necropsy following a history of chronic wasting. Necropsy revealed nematodes consistent with the genus Syngamus partially obstructing the trachea. Phylogentic analysis failed to reveal conclusive results regarding the species. Syngamus spp. can cause obstruction of the trachea in several different hosts. Additional genetic data from this taxon would aid in the more precise identification of diagnostic specimens.
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http://dx.doi.org/10.1016/j.vprsr.2020.100493DOI Listing
December 2020

Oiling-out effect improves the efficiency of extracting aroma compounds from edible oil.

NPJ Sci Food 2020 Nov 4;4(1):18. Epub 2020 Nov 4.

The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama-shi, Ehime, 790-8566, Japan.

Volatile compounds in foods are a significant factor that affects food intake and preference. However, volatile components in edible oils are poorly understood due to a strong matrix effect. In this study, we developed a method of extracting volatile compounds from extra virgin coconut oil (EVCO) by means of oiling-out assisted liquid-liquid extraction (OA-LLE). Consequently, 44 aroma compounds were isolated and identified from only 5 g of EVCO. Various aroma compounds were detected in addition to δ-lactones. The ratio of the natural abundance of the enantiomers of δ-lactones in EVCO was also revealed. Compared with the conventional methods of solvent assisted flavor evaporation (SAFE) and head-space solid-phase micro extraction (HS-SPME), OA-LLE was able to isolate a wide range and large number of volatile compounds from EVCO without leaving oil residues. Therefore, isolating aroma compounds from edible oil based on the oiling-out effect should provide an innovative extraction method.
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http://dx.doi.org/10.1038/s41538-020-00079-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642429PMC
November 2020

Potency of gastrointestinal colonization and virulence of Candida auris in a murine endogenous candidiasis.

PLoS One 2020 2;15(12):e0243223. Epub 2020 Dec 2.

Department of Chemotherapy and Mycoses, National Institute of Infectious Diseases, Tokyo, Japan.

Background: Candida auris infections have recently emerged worldwide, and this species is highly capable of colonization and is associated with high levels of mortality. However, strain-dependent differences in colonization capabilities and virulence have not yet been reported.

Objectives: In the present study, we aimed to clarify the differences between clinically isolated invasive and non-invasive strains of C. auris.

Methods: We evaluated colonization, dissemination, and survival rates in wild C57BL/6J mice inoculated with invasive or non-invasive strains of C. auris under cortisone acetate immunosuppression, comparing with those of Candida albicans and Candida glabrata infections. We also evaluated the potency of biofilm formation.

Results: Stool fungal burdens were significantly higher in mice inoculated with the invasive strains than in those infected with the non-invasive strain. Along with intestinal colonization, liver and kidney fungal burdens were also significantly higher in mice inoculated with the invasive strains. In addition, histopathological findings revealed greater dissemination and colonization of the invasive strains. Regarding biofilm-forming capability, the invasive strain of C. auris exhibited a significantly higher capacity of producing biofilms. Moreover, inoculation with the invasive strains resulted in significantly greater loss of body weight than that noted following infection with the non-invasive strain.

Conclusions: Invasive strains showed higher colonization capability and rates of dissemination from gastrointestinal tracts under cortisone acetate immunosuppression than non-invasive strains, although the mortality rates caused by C. auris were lower than those caused by C. albicans.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0243223PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710084PMC
January 2021
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