Publications by authors named "Guoyan Zhao"

72 Publications

Ascending dorsal column sensory neurons respond to spinal cord injury and downregulate genes related to lipid metabolism.

Sci Rep 2021 Jan 11;11(1):374. Epub 2021 Jan 11.

Department of Neuroscience, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8108, St. Louis, MO, 63110-1093, USA.

Regeneration failure after spinal cord injury (SCI) results in part from the lack of a pro-regenerative response in injured neurons, but the response to SCI has not been examined specifically in injured sensory neurons. Using RNA sequencing of dorsal root ganglion, we determined that thoracic SCI elicits a transcriptional response distinct from sciatic nerve injury (SNI). Both SNI and SCI induced upregulation of ATF3 and Jun, yet this response failed to promote growth in sensory neurons after SCI. RNA sequencing of purified sensory neurons one and three days after injury revealed that unlike SNI, the SCI response is not sustained. Both SCI and SNI elicited the expression of ATF3 target genes, with very little overlap between conditions. Pathway analysis of differentially expressed ATF3 target genes revealed that fatty acid biosynthesis and terpenoid backbone synthesis were downregulated after SCI but not SNI. Pharmacologic inhibition of fatty acid synthase, the enzyme generating palmitic acid, decreased axon growth and regeneration in vitro. These results support the notion that decreased expression of lipid metabolism-related genes after SCI, including fatty acid synthase, may restrict axon regenerative capacity after SCI.
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http://dx.doi.org/10.1038/s41598-020-79624-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801468PMC
January 2021

Astrocyte deletion of α2-Na/K ATPase triggers episodic motor paralysis in mice via a metabolic pathway.

Nat Commun 2020 12 2;11(1):6164. Epub 2020 Dec 2.

Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.

Familial hemiplegic migraine is an episodic neurological disorder characterized by transient sensory and motor symptoms and signs. Mutations of the ion pump α2-Na/K ATPase cause familial hemiplegic migraine, but the mechanisms by which α2-Na/K ATPase mutations lead to the migraine phenotype remain incompletely understood. Here, we show that mice in which α2-Na/K ATPase is conditionally deleted in astrocytes display episodic paralysis. Functional neuroimaging reveals that conditional α2-Na/K ATPase knockout triggers spontaneous cortical spreading depression events that are associated with EEG low voltage activity events, which correlate with transient motor impairment in these mice. Transcriptomic and metabolomic analyses show that α2-Na/K ATPase loss alters metabolic gene expression with consequent serine and glycine elevation in the brain. A serine- and glycine-free diet rescues the transient motor impairment in conditional α2-Na/K ATPase knockout mice. Together, our findings define a metabolic mechanism regulated by astrocytic α2-Na/K ATPase that triggers episodic motor paralysis in mice.
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http://dx.doi.org/10.1038/s41467-020-19915-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710756PMC
December 2020

Cellular diversity of the regenerating caudal fin.

Sci Adv 2020 Aug 12;6(33):eaba2084. Epub 2020 Aug 12.

Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.

Zebrafish faithfully regenerate their caudal fin after amputation. During this process, both differentiated cells and resident progenitors migrate to the wound site and undergo lineage-restricted, programmed cellular state transitions to populate the new regenerate. Until now, systematic characterizations of cells comprising the new regenerate and molecular definitions of their state transitions have been lacking. We hereby characterize the dynamics of gene regulatory programs during fin regeneration by creating single-cell transcriptome maps of both preinjury and regenerating fin tissues at 1/2/4 days post-amputation. We consistently identified epithelial, mesenchymal, and hematopoietic populations across all stages. We found common and cell type-specific cell cycle programs associated with proliferation. In addition to defining the processes of epithelial replenishment and mesenchymal differentiation, we also identified molecular signatures that could better distinguish epithelial and mesenchymal subpopulations in fish. The insights for natural cell state transitions during regeneration point to new directions for studying this regeneration model.
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http://dx.doi.org/10.1126/sciadv.aba2084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7423392PMC
August 2020

The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain.

Nat Commun 2020 07 9;11(1):3419. Epub 2020 Jul 9.

Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA.

The development and function of the brain require tight control of gene expression. Genome architecture is thought to play a critical regulatory role in gene expression, but the mechanisms governing genome architecture in the brain in vivo remain poorly understood. Here, we report that conditional knockout of the chromatin remodeling enzyme Chd4 in granule neurons of the mouse cerebellum increases accessibility of gene regulatory sites genome-wide in vivo. Conditional knockout of Chd4 promotes recruitment of the architectural protein complex cohesin preferentially to gene enhancers in granule neurons in vivo. Importantly, in vivo profiling of genome architecture reveals that conditional knockout of Chd4 strengthens interactions among developmentally repressed contact domains as well as genomic loops in a manner that tightly correlates with increased accessibility, enhancer activity, and cohesin occupancy at these sites. Collectively, our findings define a role for chromatin remodeling in the control of genome architecture organization in the mammalian brain.
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http://dx.doi.org/10.1038/s41467-020-17065-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7347877PMC
July 2020

Robust principal component analysis for accurate outlier sample detection in RNA-Seq data.

BMC Bioinformatics 2020 Jun 29;21(1):269. Epub 2020 Jun 29.

Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA.

Background: High throughput RNA sequencing is a powerful approach to study gene expression. Due to the complex multiple-steps protocols in data acquisition, extreme deviation of a sample from samples of the same treatment group may occur due to technical variation or true biological differences. The high-dimensionality of the data with few biological replicates make it challenging to accurately detect those samples, and this issue is not well studied in the literature currently. Robust statistics is a family of theories and techniques aim to detect the outliers by first fitting the majority of the data and then flagging data points that deviate from it. Robust statistics have been widely used in multivariate data analysis for outlier detection in chemometrics and engineering. Here we apply robust statistics on RNA-seq data analysis.

Results: We report the use of two robust principal component analysis (rPCA) methods, PcaHubert and PcaGrid, to detect outlier samples in multiple simulated and real biological RNA-seq data sets with positive control outlier samples. PcaGrid achieved 100% sensitivity and 100% specificity in all the tests using positive control outliers with varying degrees of divergence. We applied rPCA methods and classical principal component analysis (cPCA) on an RNA-Seq data set profiling gene expression of the external granule layer in the cerebellum of control and conditional SnoN knockout mice. Both rPCA methods detected the same two outlier samples but cPCA failed to detect any. We performed differentially expressed gene detection before and after outlier removal as well as with and without batch effect modeling. We validated gene expression changes using quantitative reverse transcription PCR and used the result as reference to compare the performance of eight different data analysis strategies. Removing outliers without batch effect modeling performed the best in term of detecting biologically relevant differentially expressed genes.

Conclusions: rPCA implemented in the PcaGrid function is an accurate and objective method to detect outlier samples. It is well suited for high-dimensional data with small sample sizes like RNA-seq data. Outlier removal can significantly improve the performance of differential gene detection and downstream functional analysis.
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http://dx.doi.org/10.1186/s12859-020-03608-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7324992PMC
June 2020

Characterization and bioremediation potential of nickel-resistant endophytic bacteria isolated from the wetland plant Tamarix chinensis.

FEMS Microbiol Lett 2020 06;367(12)

College of Life Science, Shandong Normal University, Jinan 250014, P. R. China.

Wetlands have been proposed as a sink for pollutants such as heavy metals. Wetland plants play a significant role in the phytoremediation of heavy metals. Here, we isolated and characterized three novel nickel (Ni)-resistant endophytic bacteria (NiEB) from the wetland plant Tamarix chinensis. The NiEB were identified as Stenotrophomonas sp. S20, Pseudomonas sp. P21 and Sphingobium sp. S42. All isolates tolerated 50 mg L-1 Ni, with isolates S20 and P21 being more tolerant to Ni at up to 400 mg L-1. Moreover, isolate S42 removed 33.7% of nickel sulfate from the water by forming white precipitates. The three isolates exhibited different plant growth-promoting (PGP) traits related to the production of indole acetic acid (IAA), siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Phytotoxicity studies revealed that the growth of the wetland plants in a high Ni concentration (200 mg L-1) recovered after co-incubation with isolate S42. Overall, this study presents the first report of NiEB isolation from wetland plants and provides novel insights into the diverse functions of endophytic bacteria in a plant host with the potential to improve Ni phytoremediation.
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http://dx.doi.org/10.1093/femsle/fnaa098DOI Listing
June 2020

Ginsenoside Rd Ameliorates High Fat Diet-Induced Obesity by Enhancing Adaptive Thermogenesis in a cAMP-Dependent Manner.

Obesity (Silver Spring) 2020 04 6;28(4):783-792. Epub 2020 Mar 6.

College of Public Health, Jilin Medical University, Jilin, China.

Objective: With the discovery of thermogenic adipocytes in humans, it has been hypothesized that enhancing adaptive thermogenesis may improve obesity. Although many studies have found that ginseng can improve obesity, the beneficial effects of ginsenoside Rd on obesity and its mechanisms have not been studied.

Methods: High-fat diet-induced obese mice were used as the study subjects, with intraperitoneal injection of Rd daily at a dose of 15 mg/kg. Body weight and energy metabolism were observed. The effects of Rd on glucose tolerance, insulin sensitivity, and cold tolerance were tested. The expression of genes associated with thermogenesis was analyzed. Finally, the mechanisms by which Rd regulates adaptive thermogenesis were studied.

Results: Rd ameliorated obesity and insulin resistance. Rd increased cold tolerance through enhancing thermogenic gene expression in brown adipose tissue and increased the browning of white adipose tissue induced by cold stress. Rd increased intracellular cyclic adenosine monophosphate (cAMP) content. Decreasing intracellular cAMP levels by an inhibitor of adenylyl cyclase SQ22536 abolished the promoting effects of Rd on the expression of thermogenic genes.

Conclusions: Rd improves obesity and insulin resistance. The upregulation of thermogenesis by Rd is dependent on the cAMP/protein kinase A signaling pathway.
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http://dx.doi.org/10.1002/oby.22761DOI Listing
April 2020

Bioremediation of malachite green by cyanobacterium Synechococcus elongatus PCC 7942 engineered with a triphenylmethane reductase gene.

Appl Microbiol Biotechnol 2020 Apr 18;104(7):3193-3204. Epub 2020 Feb 18.

College of Life Science, Shandong Normal University, Jinan, 250014, People's Republic of China.

Malachite green is a carcinogenic dye that has been detected in fish tissues and freshwater. Here we evaluated the malachite green decoloring ability of a photoautotrophic cyanobacterium, Synechococcus elongatus PCC 7942 (Synechococcus), that lives in freshwater. Results show that 99.5% of the dye was removed by Synechococcus through bioabsorption and bioaccumulation; however, the dye was not degraded or chemically modified. Next, we established an engineered Synechococcus strain to degrade the dye after uptake. The triphenylmethane reductase gene katmr was heterologously expressed, resulting in high production of a soluble recombinant protein. The engineered strain showed advanced decoloring abilities at a low cell density and in stressful environments. It degraded malachite green into the smaller molecules 4-methylaminobenzoic acid and 4-hydroxyl-aniline. After treatment with the engineered cyanobacterium, the growth of wheat seeds was fully recovered in the presence of malachite green. These results demonstrate the potential application of the engineered Synechococcus as a photosynthetic cell factory for the removal of malachite green from wastewater.
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http://dx.doi.org/10.1007/s00253-020-10438-wDOI Listing
April 2020

MeCP2 Represses Enhancers through Chromosome Topology-Associated DNA Methylation.

Mol Cell 2020 01 26;77(2):279-293.e8. Epub 2019 Nov 26.

Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA. Electronic address:

The genomes of mammalian neurons contain uniquely high levels of non-CG DNA methylation that can be bound by the Rett syndrome protein, MeCP2, to regulate gene expression. How patterns of non-CG methylation are established in neurons and the mechanism by which this methylation works with MeCP2 to control gene expression is unclear. Here, we find that genes repressed by MeCP2 are often located within megabase-scale regions of high non-CG methylation that correspond with topologically associating domains of chromatin folding. MeCP2 represses enhancers found in these domains that are enriched for non-CG and CG methylation, with the strongest repression occurring for enhancers located within MeCP2-repressed genes. These alterations in enhancer activity provide a mechanism for how MeCP2 disruption in disease can lead to widespread changes in gene expression. Hence, we find that DNA topology can shape non-CG DNA methylation across the genome to dictate MeCP2-mediated enhancer regulation in the brain.
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http://dx.doi.org/10.1016/j.molcel.2019.10.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980697PMC
January 2020

Vertical transmission in nematodes of RNA molecules encoding a viral RNA-dependent RNA polymerase.

Proc Natl Acad Sci U S A 2019 12 18;116(49):24738-24747. Epub 2019 Nov 18.

Institute of Biology of the Ecole Normale Supérieure, CNRS, INSERM, Paris Sciences et Lettres Research University, 75005 Paris, France;

Here, we report on the discovery in nematodes of multiple vertically transmitted RNAs coding for putative RNA-dependent RNA polymerases. Their sequences share similarity to distinct RNA viruses, including bunyaviruses, narnaviruses, and sobemoviruses. The sequences are present exclusively as RNA and are not found in DNA form. The RNAs persist in progeny after bleach treatment of adult animals, indicating vertical transmission of the RNAs. We tested one of the infected strains for transmission to an uninfected strain and found that mating of infected animals with uninfected animals resulted in infected progeny. By in situ hybridization, we detected several of these RNAs in the cytoplasm of the male and female germline of the nematode host. The hosts were found defective in degrading exogenous double-stranded RNAs, which may explain retention of viral-like RNAs. Strikingly, one strain, QG551, harbored three distinct virus-like RNA elements. Specific patterns of small RNAs complementary to the different viral-like RNAs were observed, suggesting that the different RNAs are differentially recognized by the RNA interference (RNAi) machinery. While vertical transmission of viruses in the family Narnaviridae, which are known as capsidless viruses, has been described in fungi, these observations provide evidence that multicellular animal cells harbor similar viruses.
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http://dx.doi.org/10.1073/pnas.1903903116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6900638PMC
December 2019

Effects of Atorvastatin on Transient Sodium Currents in Rat Normal, Simulated Ischemia, and Reperfusion Ventricular Myocytes.

Pharmacology 2020 6;105(5-6):320-328. Epub 2019 Nov 6.

Department of Cardiovascular Disease, Tian Jin Medical University General Hospital, Tianjin, China,

Objectives: (1) To detect the whether the effects of simulated ischemia on INa of rat left ventricular myocytes in a time-dependent manner and the effects of atorvastatin on ischemia INa; (2) To investigate the effects of atorvastatin on INa of rat-simulated ischemia/reperfusion (I/R) ventricular cells.

Materials And Methods: Ventricular cells were enzymatically isolated by Langendorff perfusion system. Whole-cell patch clamp was applied to detect INa level. Some elements of extracellular fluid were hanged to simulate the status of normal, I and R condition. Then the effects of atorvastatin on INa were observed.

Results: (1) During simulated reperfusion, INa decreased and atorvastatin further suppressed the reduction degree. (2) At test potential -40 mV, no difference was detected among peak INa amplitude of ischemia for 20 min, reperfusion phase 3/5/7/9 min in continuous ischemia (I) group (p = 0.275). In I/R group, peak INa amplitude continuously decreased at 3 min (p = 0.005) and 9 min (p = 0.041). In atorvastatin intervention + I/R (Statin + I/R) group, peak INa amplitude at reperfusion 3 min decreased compared with ischemia phase (p = 0.000), while no significant difference was detected between 3 and 9 min (p = 0.858). The differences were significant at the same time point between groups. At reperfusion 3/5/7/9 min, peak INa of the I/R group was lower than the ischemia group (all p = 0.000), same as the Statin + I/R group (p = 0.000, p = 0.003, p = 0.006, and p = 0.001). Peak INa of the Statin + I/R group was higher than the I/R group at the same time point (p = 0.011, p = 0.033, p = 0.003, p = 0.003). There was no change in the I group during reperfusion phase (p > 0.05). In I/R group, V1/2 (mV) shifted from -58.87 ± 3.36 to -54.33 ± 2.40, k (mV) shifted from 1.25 ± 0.59 to 1.91 ± 0.84 (p < 0.05). In the Statin + I/R group, V1/2 (mV) increased from -57.80 ± 2.97 to -52.76 ± 3.14 (p < 0.01), no change was observed in k (p > 0.05).

Conclusions: (1) In the status of reperfusion, INa decreased more than that in the status of ischemia. (2) Atorvastatin protected the cells from reduction of INa during long-time simulated (>15 min) I/R. (3) Overall, atorvastatin affected INa of the normal, simulated ischemic/reperfusion cell in rat left ventricle by blocking sodium channel -directly.
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http://dx.doi.org/10.1159/000503793DOI Listing
February 2021

Linguistic neutrosophic power Muirhead mean operators for safety evaluation of mines.

PLoS One 2019 24;14(10):e0224090. Epub 2019 Oct 24.

School of Resources and Safety Engineering, Central South University, Changsha, Hunan, China.

Safety is the fundamental guarantee for the sustainable development of mining enterprises. As the safety evaluation of mines is a complex system engineering project, consistent and inconsistent, even hesitant evaluation information may be contained simultaneously. Linguistic neutrosophic numbers (LNNs), as the extensions of linguistic terms, are effective means to entirely and qualitatively convey such evaluation information with three independent linguistic membership functions. The aim of our work is to investigate several mean operators so that the safety evaluation issues of mines are addressed under linguistic neutrosophic environment. During the safety evaluation process of mines, many influence factors should be considered, and some of them may interact with each other. To this end, the Muirhead mean (MM) operators are adopted as they are powerful tools to deal with such situation. On the other hand, to diminish the impacts of irrational data provided by evaluators, the power average (PA) operators are under consideration. Thus, with the combination of MM and PA, the power MM operators and weighted power MM operators are proposed to aggregate linguistic neutrosophic information. Meanwhile, some key points and special cases are studied. The advantages of these operators are that not only the interrelations among any number of inputs can be reflected, but also the effects of unreasonable information can be reduced. Thereafter, a new linguistic neutrosophic ranking technique based on these operators is developed to evaluate the mine safety. Moreover, in-depth discussions are made to show the robust and flexible abilities of our method. Results manifest that the proposed method is successful in dealing with mine safety evaluation issues within linguistic neutrosophic circumstances.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224090PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6813029PMC
March 2020

Therapeutic efficacy of favipiravir against Bourbon virus in mice.

PLoS Pathog 2019 06 13;15(6):e1007790. Epub 2019 Jun 13.

Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America.

Bourbon virus (BRBV) is an emerging tick-borne RNA virus in the orthomyxoviridae family that was discovered in 2014. Although fatal human cases of BRBV have been described, little is known about its pathogenesis, and no antiviral therapies or vaccines exist. We obtained serum from a fatal case in 2017 and successfully recovered the second human infectious isolate of BRBV. Next-generation sequencing of the St. Louis isolate of BRBV (BRBV-STL) showed >99% nucleotide identity to the original reference isolate. Using BRBV-STL, we developed a small animal model to study BRBV-STL tropism in vivo and evaluated the prophylactic and therapeutic efficacy of the experimental antiviral drug favipiravir against BRBV-induced disease. Infection of Ifnar1-/- mice lacking the type I interferon receptor, but not congenic wild-type animals, resulted in uniformly fatal disease 6 to 10 days after infection. RNA in situ hybridization and viral yield assays demonstrated a broad tropism of BRBV-STL with highest levels detected in liver and spleen. In vitro replication and polymerase activity of BRBV-STL were inhibited by favipiravir. Moreover, administration of favipiravir as a prophylaxis or as post-exposure therapy three days after infection prevented BRBV-STL-induced mortality in immunocompromised Ifnar1-/- mice. These results suggest that favipiravir may be a candidate treatment for humans who become infected with BRBV.
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http://dx.doi.org/10.1371/journal.ppat.1007790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6564012PMC
June 2019

Viral complementation of immunodeficiency confers protection against enteric pathogens via interferon-λ.

Nat Microbiol 2019 07 1;4(7):1120-1128. Epub 2019 Apr 1.

Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA.

Commensal microbes profoundly impact host immunity to enteric viral infections. We have shown that the bacterial microbiota and host antiviral cytokine interferon-λ (IFN-λ) determine the persistence of murine norovirus in the gut. However, the effects of the virome in modulating enteric infections remain unexplored. Here, we report that murine astrovirus can complement primary immunodeficiency to protect against murine norovirus and rotavirus infections. Protection against infection was horizontally transferable between immunocompromised mouse strains by co-housing and fecal transplantation. Furthermore, protection against enteric pathogens corresponded with the presence of a specific strain of murine astrovirus in the gut, and this complementation of immunodeficiency required IFN-λ signalling in gut epithelial cells. Our study demonstrates that elements of the virome can protect against enteric pathogens in an immunodeficient host.
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http://dx.doi.org/10.1038/s41564-019-0416-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588490PMC
July 2019

Biodegradation of malachite green by an endophytic bacterium Klebsiella aerogenes S27 involving a novel oxidoreductase.

Appl Microbiol Biotechnol 2019 Mar 6;103(5):2141-2153. Epub 2019 Jan 6.

College of Life Science, Shandong Normal University, Jinan, 250014, People's Republic of China.

Endophytic microorganisms can metabolize organic contaminants and assist in plant growth, thus facilitating the phytoremediation of polluted environments. An endophytic bacterium capable of decoloring malachite green (MG) was isolated from the leaves of the wetland plant Suaeda salsa and was identified as Klebsiella aerogenes S27. Complete decolorization of MG (100 mg/l) was achieved in 8 h at 30 °C and pH 7.0. Ultraviolet-visible spectroscopy and Fourier-transform infrared spectroscopy analyses indicated the degradation of MG by the isolate. The enzymic assays of the strain showed the triphenylmethane reductase (TMR) activity. A gene encoding putative TMR-like protein (named as KaTMR) was cloned and heterologously expressed in Escherichia coli. KaTMR showed only 42.6-43.3% identities in amino acids compared with well-studied TMRs, and it phylogenetically formed a new branch in the family of TMRs. The degraded metabolites by recombinant KaTMR were detected by liquid chromatography-mass spectrometry, showing differences from the products of reported TMRs. The biotransformation pathway of MG was proposed. Phytotoxicity studies revealed the less-toxic nature of the degraded metabolites compared to the dye. This study presented the first report of an endophyte on the degradation and detoxification of triphenylmethane dye via a novel oxidoreductase, thus facilitating the study of the plant-endophyte symbiosis in the bioremediation processes.
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http://dx.doi.org/10.1007/s00253-018-09583-0DOI Listing
March 2019

Epigenetic regulator UHRF1 inactivates REST and growth suppressor gene expression via DNA methylation to promote axon regeneration.

Proc Natl Acad Sci U S A 2018 12 10;115(52):E12417-E12426. Epub 2018 Dec 10.

Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110;

Injured peripheral sensory neurons switch to a regenerative state after axon injury, which requires transcriptional and epigenetic changes. However, the roles and mechanisms of gene inactivation after injury are poorly understood. Here, we show that DNA methylation, which generally leads to gene silencing, is required for robust axon regeneration after peripheral nerve lesion. Ubiquitin-like containing PHD ring finger 1 (UHRF1), a critical epigenetic regulator involved in DNA methylation, increases upon axon injury and is required for robust axon regeneration. The increased level of UHRF1 results from a decrease in miR-9. The level of another target of miR-9, the transcriptional regulator RE1 silencing transcription factor (REST), transiently increases after injury and is required for axon regeneration. Mechanistically, UHRF1 interacts with DNA methyltransferases (DNMTs) and H3K9me3 at the promoter region to repress the expression of the tumor suppressor gene phosphatase and tensin homolog (PTEN) and REST. Our study reveals an epigenetic mechanism that silences tumor suppressor genes and restricts REST expression in time after injury to promote axon regeneration.
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http://dx.doi.org/10.1073/pnas.1812518115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310844PMC
December 2018

Virome biogeography in the lower gastrointestinal tract of rhesus macaques with chronic diarrhea.

Virology 2019 01 20;527:77-88. Epub 2018 Nov 20.

Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA. Electronic address:

The composition of gastrointestinal tract viromes has been associated with multiple diseases. Our understanding of virus communities in the GI tract is still very limited due to challenges in sampling from different GI sites. Here we defined the GI viromes of 15 rhesus macaques with chronic diarrhea. Luminal content samples from terminal ileum, proximal and distal colon were collected at necropsy while samples from the rectum were collected antemortem using a fecal loop. The composition of and ecological parameters associated with the terminal ileum virome were distinct from the colon and rectum samples; these differences were driven by bacteriophages rather than eukaryotic viruses. The six contigs that were most discriminative of the viromes were distantly related to bacteriophages from three different families. Our analysis provides support for using fecal loop sampling of the rectum as a proxy of the colonic virome in humans.
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http://dx.doi.org/10.1016/j.virol.2018.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333316PMC
January 2019

The Transcriptional Regulator SnoN Promotes the Proliferation of Cerebellar Granule Neuron Precursors in the Postnatal Mouse Brain.

J Neurosci 2019 01 13;39(1):44-62. Epub 2018 Nov 13.

Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri 63110,

Control of neuronal precursor cell proliferation is essential for normal brain development, and deregulation of this fundamental developmental event contributes to brain diseases. Typically, neuronal precursor cell proliferation extends over long periods of time during brain development. However, how neuronal precursor proliferation is regulated in a temporally specific manner remains to be elucidated. Here, we report that conditional KO of the transcriptional regulator SnoN in cerebellar granule neuron precursors robustly inhibits the proliferation of these cells and promotes their cell cycle exit at later stages of cerebellar development in the postnatal male and female mouse brain. In laser capture microdissection followed by RNA-Seq, designed to profile gene expression specifically in the external granule layer of the cerebellum, we find that SnoN promotes the expression of cell proliferation genes and concomitantly represses differentiation genes in granule neuron precursors Remarkably, bioinformatics analyses reveal that SnoN-regulated genes contain binding sites for the transcription factors N-myc and Pax6, which promote the proliferation and differentiation of granule neuron precursors, respectively. Accordingly, we uncover novel physical interactions of SnoN with N-myc and Pax6 in cells. In behavior analyses, conditional KO of SnoN impairs cerebellar-dependent learning in a delayed eye-blink conditioning paradigm, suggesting that SnoN-regulation of granule neuron precursor proliferation bears functional consequences at the organismal level. Our findings define a novel function and mechanism for the major transcriptional regulator SnoN in the control of granule neuron precursor proliferation in the mammalian brain. This study reports the discovery that the transcriptional regulator SnoN plays a crucial role in the proliferation of cerebellar granule neuron precursors in the postnatal mouse brain. Conditional KO of SnoN in granule neuron precursors robustly inhibits the proliferation of these cells and promotes their cycle exit specifically at later stages of cerebellar development, with biological consequences of impaired cerebellar-dependent learning. Genomics and bioinformatics analyses reveal that SnoN promotes the expression of cell proliferation genes and concomitantly represses cell differentiation genes Although SnoN has been implicated in distinct aspects of the development of postmitotic neurons, this study identifies a novel function for SnoN in neuronal precursors in the mammalian brain.
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http://dx.doi.org/10.1523/JNEUROSCI.0688-18.2018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325268PMC
January 2019

Linguistic neutrosophic Hamacher aggregation operators and the application in evaluating land reclamation schemes for mines.

PLoS One 2018 6;13(11):e0206178. Epub 2018 Nov 6.

School of Systems Engineering, National University of Defense Technology, Changsha, China.

Land reclamation has become a significant way for the improvement of ecological environment in mining areas. When selecting the optimal land reclamation scheme, LNNs (linguistic neutrosophic numbers) are suitable to describe the complex fuzzy evaluation information through linguistic truth, indeterminacy and falsity membership degrees. Furthermore, the Hamacher aggregation operators are good tools to handle multi-criteria decision making problems. Accordingly, the aim of this paper is to extend Hamacher aggregation operators with LNNs and then build a decision making framework for evaluating land reclamation schemes in mining areas. First, new operational laws of LNNs based on Hamacher t-norm and t-conorm are defined. Then, several linguistic neutrosophic Hamacher aggregation operators, including the linguistic neutrosophic Hamacher weighted mean aggregation operators and linguistic neutrosophic Hamacher hybrid weighted mean aggregation operators are developed. Meanwhile, their desirable properties are proved. Thereafter, a method for decision making with linguistic neutrosophic information based on these operators is proposed to deal with complex decision problems. At last, the validity of this method is confirmed by an illustrative example of evaluating the land reclamation schemes in mining areas. In addition, the impact of the parameter in extended Hamacher aggregation operators is discussed. The merits of the proposed method are also highlighted by comparing with other decision making methods. The results show that the proposed linguistic neutrosophic Hamacher aggregation operators have great flexibility and advantages, and can provide powerful ways for the evaluation of land reclamation schemes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0206178PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219779PMC
April 2019

Complete Genome Sequence of the Heavy-Metal-Tolerant Endophytic Type Strain of .

Genome Announc 2018 Apr 19;6(16). Epub 2018 Apr 19.

College of Life Science, Shandong Normal University, Jinan, People's Republic of China

The first complete genome sequence of a recently described species was determined for the strain F01 (=CCTCC AB 2015304 =KCTC 42855). The strain was isolated from the leaves of wetland plant Lour and shows a high tolerance to heavy metals, such as manganese, nickel, lead, and copper ions.
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http://dx.doi.org/10.1128/genomeA.00358-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5908926PMC
April 2018

Mining the Virome for Insights into Type 1 Diabetes.

DNA Cell Biol 2018 May 13;37(5):422-425. Epub 2018 Mar 13.

Department of Pathology and Immunology, Washington University School of Medicine , St. Louis, Missouri.

Type 1 diabetes (T1D) is characterized by the autoimmune destruction of insulin-producing pancreatic beta cells. Although environmental factors interplay with genetic susceptibility to promote immune dysregulation and disease, it remains unclear as to which potential environmental factors are causative and not simply correlative. Despite many hints that the microbiome can have a profound effect on T1D, significant changes in bacterial gut flora and diversity appear to emerge only after the detection of early signs of T1D. Surprisingly, we recently found significant differences in the gut virome preceding the initial signs of T1D, raising the tantalizing possibility that the state of the virome may influence or predict whether susceptible individuals progress on the path to disease. The challenge will be to discern whether there is likely a causative relationship between detected virome differences and T1D.
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http://dx.doi.org/10.1089/dna.2018.4185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5944395PMC
May 2018

LysMD3 is a type II membrane protein without an role in the response to a range of pathogens.

J Biol Chem 2018 04 1;293(16):6022-6038. Epub 2018 Mar 1.

From the Departments of Pathology and Immunology and.

Germline-encoded receptors recognizing common pathogen-associated molecular patterns are a central element of the innate immune system and play an important role in shaping the host response to infection. Many of the innate immune molecules central to these signaling pathways are evolutionarily conserved. LysMD3 is a novel molecule containing a putative peptidoglycan-binding domain that has orthologs in humans, mice, zebrafish, flies, and worms. We found that the lysin motif (LysM) of LysMD3 is likely related to a previously described peptidoglycan-binding LysM found in bacteria. Mouse LysMD3 is a type II integral membrane protein that co-localizes with GM130+ structures, consistent with localization to the Golgi apparatus. We describe here two lines of mLysMD3-deficient mice for characterization of mLysMD3 function. We found that mLysMD3-deficient mice were born at Mendelian ratios and had no obvious pathological abnormalities. They also exhibited no obvious immune response deficiencies in a number of models of infection and inflammation. mLysMD3-deficient mice exhibited no signs of intestinal dysbiosis by 16S analysis or alterations in intestinal gene expression by RNA sequencing. We conclude that mLysMD3 contains a LysM with cytoplasmic orientation, but we were unable to define a physiological role for the molecule .
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http://dx.doi.org/10.1074/jbc.RA117.001246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5912457PMC
April 2018

Rapid Cloning of Novel Rhesus Adenoviral Vaccine Vectors.

J Virol 2018 03 26;92(6). Epub 2018 Feb 26.

Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA

Human and chimpanzee adenovirus vectors are being developed to circumvent preexisting antibodies against common adenovirus vectors such as Ad5. However, baseline immunity to these vectors still exists in human populations. Traditional cloning of new adenovirus vaccine vectors is a long and cumbersome process that takes 2 months or more and that requires rare unique restriction enzyme sites. Here we describe a novel, restriction enzyme-independent method for rapid cloning of new adenovirus vaccine vectors that reduces the total cloning procedure to 1 week. We developed 14 novel adenovirus vectors from rhesus monkeys that can be grown to high titers and that are immunogenic in mice. All vectors grouped with the unusual adenovirus species G and show extremely low seroprevalence in humans. Rapid cloning of novel adenovirus vectors is a promising approach for the development of new vector platforms. Rhesus adenovirus vectors may prove useful for clinical development. To overcome baseline immunity to human and chimpanzee adenovirus vectors, we developed 14 novel adenovirus vectors from rhesus monkeys. These vectors are immunogenic in mice and show extremely low seroprevalence in humans. Rhesus adenovirus vectors may prove useful for clinical development.
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http://dx.doi.org/10.1128/JVI.01924-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5827402PMC
March 2018

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.

Proc Natl Acad Sci U S A 2017 07 10;114(30):E6166-E6175. Epub 2017 Jul 10.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;

Viruses have long been considered potential triggers of autoimmune diseases. Here we defined the intestinal virome from birth to the development of autoimmunity in children at risk for type 1 diabetes (T1D). A total of 220 virus-enriched preparations from serially collected fecal samples from 11 children (cases) who developed serum autoantibodies associated with T1D (of whom five developed clinical T1D) were compared with samples from controls. Intestinal viromes of case subjects were less diverse than those of controls. Among eukaryotic viruses, we identified significant enrichment of -related sequences in samples from controls in comparison with cases. Enterovirus, kobuvirus, parechovirus, parvovirus, and rotavirus sequences were frequently detected but were not associated with autoimmunity. For bacteriophages, we found higher Shannon diversity and richness in controls compared with cases and observed that changes in the intestinal virome over time differed between cases and controls. Using Random Forests analysis, we identified disease-associated viral bacteriophage contigs after subtraction of age-associated contigs. These disease-associated contigs were statistically linked to specific components of the bacterial microbiome. Thus, changes in the intestinal virome preceded autoimmunity in this cohort. Specific components of the virome were both directly and inversely associated with the development of human autoimmune disease.
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http://dx.doi.org/10.1073/pnas.1706359114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544325PMC
July 2017

A Murine Herpesvirus Closely Related to Ubiquitous Human Herpesviruses Causes T-Cell Depletion.

J Virol 2017 05 13;91(9). Epub 2017 Apr 13.

Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA

The human roseoloviruses human herpesvirus 6A (HHV-6A), HHV-6B, and HHV-7 comprise the genus of the human subfamily. Infections with these viruses have been implicated in many diseases; however, it has been challenging to establish infections with roseoloviruses as direct drivers of pathology, because they are nearly ubiquitous and display species-specific tropism. Furthermore, controlled study of infection has been hampered by the lack of experimental models, and until now, a mouse roseolovirus has not been identified. Herein we describe a virus that causes severe thymic necrosis in neonatal mice, characterized by a loss of CD4 T cells. These phenotypes resemble those caused by the previously described mouse thymic virus (MTV), a putative herpesvirus that has not been molecularly characterized. By next-generation sequencing of infected tissue homogenates, we assembled a contiguous 174-kb genome sequence containing 128 unique predicted open reading frames (ORFs), many of which were most closely related to herpesvirus genes. Moreover, the structure of the virus genome and phylogenetic analysis of multiple genes strongly suggested that this virus is a betaherpesvirus more closely related to the roseoloviruses, HHV-6A, HHV-6B, and HHV-7, than to another murine betaherpesvirus, mouse cytomegalovirus (MCMV). As such, we have named this virus murine roseolovirus (MRV) because these data strongly suggest that MRV is a mouse homolog of HHV-6A, HHV-6B, and HHV-7. Herein we describe the complete genome sequence of a novel murine herpesvirus. By sequence and phylogenetic analyses, we show that it is a betaherpesvirus most closely related to the roseoloviruses, human herpesviruses 6A, 6B, and 7. These data combined with physiological similarities with human roseoloviruses collectively suggest that this virus is a murine roseolovirus (MRV), the first definitively described rodent roseolovirus, to our knowledge. Many biological and clinical ramifications of roseolovirus infection in humans have been hypothesized, but studies showing definitive causative relationships between infection and disease susceptibility are lacking. Here we show that MRV infects the thymus and causes T-cell depletion, suggesting that other roseoloviruses may have similar properties.
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http://dx.doi.org/10.1128/JVI.02463-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391440PMC
May 2017

Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals.

Virology 2017 04 30;504:36-44. Epub 2017 Jan 30.

Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA. Electronic address:

Next-generation sequencing has expanded our understanding of the viral populations that constitute the mammalian virome. We describe a novel taxon of viruses named Statoviruses, for Stool associated Tombus-like viruses, present in multiple metagenomic datasets. These viruses define a novel clade that is phylogenetically related to the RNA virus families Tombusviridae and Flaviviridae. Five distinct statovirus types were identified in human, macaque, mouse, and cow gastrointestinal tract samples. The prototype genome, statovirus A, was frequently identified in macaque stool samples from multiple geographically distinct cohorts. Another genome, statovirus C1, was discovered in a stool sample from a human child with fever, cough, and rash. Further experimental data will clarify whether these viruses are infectious to mammals or if they originate from another source present in the mammalian gastrointestinal tract.
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http://dx.doi.org/10.1016/j.virol.2017.01.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515247PMC
April 2017

VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.

Virology 2017 03 18;503:21-30. Epub 2017 Jan 18.

Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA. Electronic address:

The advent of Next Generation Sequencing (NGS) has vastly increased our ability to discover novel viruses and to systematically define the spectrum of viruses present in a given specimen. Such studies have led to the discovery of novel viral pathogens as well as broader associations of the virome with diverse diseases including inflammatory bowel disease, severe acute malnutrition and HIV/AIDS. Critical to the success of these efforts are robust bioinformatic pipelines for rapid classification of microbial sequences. Existing computational tools are typically focused on either eukaryotic virus discovery or virome composition analysis but not both. Here we present VirusSeeker, a BLAST-based NGS data analysis pipeline designed for both purposes. VirusSeeker has been successfully applied in several previously published virome studies. Here we demonstrate the functionality of VirusSeeker in both novel virus discovery and virome composition analysis.
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http://dx.doi.org/10.1016/j.virol.2017.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5326578PMC
March 2017

Isolation of a simian immunodeficiency virus from a malbrouck (Chlorocebus cynosuros).

Arch Virol 2017 Feb 1;162(2):543-548. Epub 2016 Nov 1.

Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan.

To investigate the diversity of simian immunodeficiency virus (SIV) among nonhuman primates (NHPs) in Zambia, next-generation sequencing was performed to determine the complete genome sequence of a novel SIV recovered by co-culturing African green monkey (AGM) peripheral blood lymphocytes with human CD4 T-cell lines. We report the first described SIV (SIVagmMAL-ZMB) from a malbrouck (Chlorocebus cynosuros). SIVagmMAL-ZMB was detected by real-time PCR analysis of splenic RNA in 3.2% (3/94) of AGMs and was undetectable in baboons (0/105). SIVagmMAL-ZMB possessed <80% nucleotide sequence identity to known SIV isolates and was located basally to vervet monkey SIV strains in all phylogenies.
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http://dx.doi.org/10.1007/s00705-016-3129-8DOI Listing
February 2017

Predictive analysis of shaft station radon concentrations in underground uranium mine: A case study.

J Environ Radioact 2016 Jul 18;158-159:129-37. Epub 2016 Apr 18.

Beijing Research Institute of Chemical Engineering and Metallurgy, China National Nuclear Corporation, Beijing 101149, China.

This paper presented a method for predicting shaft station radon concentrations in a uranium mine of China through theoretical analysis, mathematical derivation and Monte-Carlo simulation. Based upon the queuing model for tramcars, the average waiting time of tramcars and average number of waiting tramcars were determined, which were further used in developing the predictive model for calculating shaft station radon concentrations. The results exhibit that the extent of variation of shaft station radon concentration in the case study mine is not significantly affected by the queuing process of tramcars, and is always within the allowable limit of 200 Bq m(-3). Thus, the empirical limit of 100,000 T annual ore-hoisting yields has no value in ensuring radiation safety for this mine. Moreover, the developed model has been validated and proved useful in assessing shaft station radon levels for any uranium mine with similar situations.
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http://dx.doi.org/10.1016/j.jenvrad.2016.04.007DOI Listing
July 2016

Hyperexpansion of RNA Bacteriophage Diversity.

PLoS Biol 2016 Mar 24;14(3):e1002409. Epub 2016 Mar 24.

Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America.

Bacteriophage modulation of microbial populations impacts critical processes in ocean, soil, and animal ecosystems. However, the role of bacteriophages with RNA genomes (RNA bacteriophages) in these processes is poorly understood, in part because of the limited number of known RNA bacteriophage species. Here, we identify partial genome sequences of 122 RNA bacteriophage phylotypes that are highly divergent from each other and from previously described RNA bacteriophages. These novel RNA bacteriophage sequences were present in samples collected from a range of ecological niches worldwide, including invertebrates and extreme microbial sediment, demonstrating that they are more widely distributed than previously recognized. Genomic analyses of these novel bacteriophages yielded multiple novel genome organizations. Furthermore, one RNA bacteriophage was detected in the transcriptome of a pure culture of Streptomyces avermitilis, suggesting for the first time that the known tropism of RNA bacteriophages may include gram-positive bacteria. Finally, reverse transcription PCR (RT-PCR)-based screening for two specific RNA bacteriophages in stool samples from a longitudinal cohort of macaques suggested that they are generally acutely present rather than persistent.
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http://dx.doi.org/10.1371/journal.pbio.1002409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807089PMC
March 2016