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  1. Article ; Online: Collagen Remodeling Biomarkers in Lupus Nephritis.

    Caster, Dawn J / Merchant, Michael L

    Kidney360

    2021  Volume 2, Issue 9, Page(s) 1395–1398

    MeSH term(s) Biomarkers ; Collagen ; Humans ; Kidney ; Lupus Nephritis/diagnosis ; Nephritis, Interstitial
    Chemical Substances Biomarkers ; Collagen (9007-34-5)
    Language English
    Publishing date 2021-09-30
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Extramural ; Comment
    ISSN 2641-7650
    ISSN (online) 2641-7650
    DOI 10.34067/KID.0004732021
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Can the Urinary Peptidome Outperform Creatinine and Albumin to Predict Renal Function Decline?

    Merchant, Michael L

    Journal of the American Society of Nephrology : JASN

    2015  Volume 26, Issue 8, Page(s) 1760–1761

    MeSH term(s) Female ; Humans ; Male ; Peptides/urine ; Renal Insufficiency, Chronic/urine
    Chemical Substances Peptides
    Language English
    Publishing date 2015-08
    Publishing country United States
    Document type Comment ; Editorial ; Research Support, N.I.H., Extramural
    ZDB-ID 1085942-1
    ISSN 1533-3450 ; 1046-6673
    ISSN (online) 1533-3450
    ISSN 1046-6673
    DOI 10.1681/ASN.2014121243
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    Zs.A 3344: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  3. Article: Circular RNAs as diagnostic tool for renal transplant patients with acute rejection.

    Moore, Joseph B / Merchant, Michael L / Uchida, Shizuka

    Annals of translational medicine

    2020  Volume 7, Issue Suppl 8, Page(s) S302

    Language English
    Publishing date 2020-01-10
    Publishing country China
    Document type Editorial ; Comment
    ZDB-ID 2893931-1
    ISSN 2305-5847 ; 2305-5839
    ISSN (online) 2305-5847
    ISSN 2305-5839
    DOI 10.21037/atm.2019.11.08
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  4. Article ; Online: Eligibility of emergency department patients for public benefit programs.

    Harrison, Joseph / McDermott, Grace / Dixon, Erica L / Mehta, Michael / Haider, Aliza / Rareshide, Charles / Southwick, Lauren / Agarwal, Anish K / Merchant, Raina M / Kilaru, Austin S

    Academic emergency medicine : official journal of the Society for Academic Emergency Medicine

    2024  

    Language English
    Publishing date 2024-03-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1329813-6
    ISSN 1553-2712 ; 1069-6563
    ISSN (online) 1553-2712
    ISSN 1069-6563
    DOI 10.1111/acem.14870
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    Zs.A 4479: Show issues Location:
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  5. Article ; Online: Chronic Aroclor 1260 exposure alters the mouse liver proteome, selenoproteins, and metals in steatotic liver disease.

    Piell, Kellianne M / Petri, Belinda J / Xu, Jason / Cai, Lu / Rai, Shesh N / Li, Ming / Wilkey, Daniel W / Merchant, Michael L / Cave, Matthew C / Klinge, Carolyn M

    Environmental toxicology and pharmacology

    2024  Volume 107, Page(s) 104430

    Abstract: The prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) continues to increase due in part to the obesity epidemic and to environmental exposures to metabolism disrupting chemicals. A single gavage exposure of male mice to ... ...

    Abstract The prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) continues to increase due in part to the obesity epidemic and to environmental exposures to metabolism disrupting chemicals. A single gavage exposure of male mice to Aroclor 1260 (Ar1260), an environmentally relevant mixture of non-dioxin-like polychlorinated biphenyls (PCBs), resulted in steatohepatitis and altered RNA modifications in selenocysteine tRNA 34 weeks post-exposure. Unbiased approaches identified the liver proteome, selenoproteins, and levels of 25 metals. Ar1260 altered the abundance of 128 proteins. Enrichment analysis of the liver Ar1260 proteome included glutathione metabolism and translation of selenoproteins. Hepatic glutathione peroxidase 4 (GPX4) and Selenoprotein O (SELENOO) were increased and Selenoprotein F (SELENOF), Selenoprotein S (SELENOS), Selenium binding protein 2 (SELENBP2) were decreased with Ar1260 exposure. Increased copper, selenium (Se), and zinc and reduced iron levels were detected. These data demonstrate that Ar1260 exposure alters the (seleno)proteome, Se, and metals in MASLD-associated pathways.
    MeSH term(s) Male ; Mice ; Animals ; Proteome/metabolism ; Glutathione Peroxidase/metabolism ; Selenoproteins/genetics ; Selenoproteins/metabolism ; Liver/metabolism ; Selenium ; Fatty Liver ; Aroclors
    Chemical Substances Proteome ; Glutathione Peroxidase (EC 1.11.1.9) ; aroclor 1260 (11096-82-5) ; Selenoproteins ; Selenium (H6241UJ22B) ; Aroclors
    Language English
    Publishing date 2024-03-27
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1318302-3
    ISSN 1872-7077 ; 1382-6689
    ISSN (online) 1872-7077
    ISSN 1382-6689
    DOI 10.1016/j.etap.2024.104430
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    Zs.A 4490: Show issues Location:
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  6. Article ; Online: Multiomics Analysis of PCB126's Effect on a Mouse Chronic-Binge Alcohol Feeding Model.

    Gripshover, Tyler C / Wahlang, Banrida / Head, Kimberly Z / Luo, Jianzhu / Bolatimi, Oluwanifemi E / Smith, Melissa L / Rouchka, Eric C / Chariker, Julia H / Xu, Jason / Cai, Lu / Cummins, Timothy D / Merchant, Michael L / Zheng, Hao / Kong, Maiying / Cave, Matthew C

    Environmental health perspectives

    2024  Volume 132, Issue 4, Page(s) 47007

    Abstract: Background: Environmental pollutants, including polychlorinated biphenyls (PCBs) have been implicated in the pathogenesis of liver disease. Our group recently demonstrated that PCB126 promoted steatosis, hepatomegaly, and modulated intermediary ... ...

    Abstract Background: Environmental pollutants, including polychlorinated biphenyls (PCBs) have been implicated in the pathogenesis of liver disease. Our group recently demonstrated that PCB126 promoted steatosis, hepatomegaly, and modulated intermediary metabolism in a rodent model of alcohol-associated liver disease (ALD).
    Objective: To better understand how PCB126 promoted ALD in our previous model, the current study adopts multiple omics approaches to elucidate potential mechanistic hypotheses.
    Methods: Briefly, male C57BL/6J mice were exposed to
    Results: Principal component analysis showed that PCB126 uniquely modified the transcriptome in EtOH-fed mice. EtOH feeding alone resulted in
    Discussion: Previous work has demonstrated that PCB126 is a modifying factor in metabolic dysfunction-associated steatotic liver disease (MASLD), and our current work suggests that pollutants also modify ALD. PCB126 may, in part, be contributing to the malnutrition aspect of ALD, where metal deficiency is known to contribute and worsen prognosis. https://doi.org/10.1289/EHP14132.
    MeSH term(s) Male ; Mice ; Animals ; Multiomics ; Mice, Inbred C57BL ; Ethanol/toxicity ; Ethanol/metabolism ; Liver/metabolism ; Polychlorinated Biphenyls/toxicity ; Polychlorinated Biphenyls/metabolism ; Fatty Liver ; Liver Diseases, Alcoholic/etiology ; Liver Diseases, Alcoholic/metabolism ; Liver Diseases, Alcoholic/pathology ; Environmental Pollutants/toxicity ; Environmental Pollutants/metabolism ; Zinc/metabolism ; Tyrosine/metabolism
    Chemical Substances 3,4,5,3',4'-pentachlorobiphenyl (TSH69IA9XF) ; Ethanol (3K9958V90M) ; Polychlorinated Biphenyls (DFC2HB4I0K) ; Environmental Pollutants ; Zinc (J41CSQ7QDS) ; Tyrosine (42HK56048U)
    Language English
    Publishing date 2024-04-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 195189-0
    ISSN 1552-9924 ; 0091-6765 ; 1078-0475
    ISSN (online) 1552-9924
    ISSN 0091-6765 ; 1078-0475
    DOI 10.1289/EHP14132
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    Zs.B 1360: Show issues Location:
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  7. Article ; Online: Macaque monkeys and humans sample temporal regularities in the acoustic environment.

    Criscuolo, Antonio / Schwartze, Michael / Prado, Luis / Ayala, Yaneri / Merchant, Hugo / Kotz, Sonja A

    Progress in neurobiology

    2023  Volume 229, Page(s) 102502

    Abstract: Many animal species show comparable abilities to detect basic rhythms and produce rhythmic behavior. Yet, the capacities to process complex rhythms and synchronize rhythmic behavior appear to be species-specific: vocal learning animals can, but some ... ...

    Abstract Many animal species show comparable abilities to detect basic rhythms and produce rhythmic behavior. Yet, the capacities to process complex rhythms and synchronize rhythmic behavior appear to be species-specific: vocal learning animals can, but some primates might not. This discrepancy is of high interest as there is a putative link between rhythm processing and the development of sophisticated sensorimotor behavior in humans. Do our closest ancestors show comparable endogenous dispositions to sample the acoustic environment in the absence of task instructions and training? We recorded EEG from macaque monkeys and humans while they passively listened to isochronous equitone sequences. Individual- and trial-level analyses showed that macaque monkeys' and humans' delta-band neural oscillations encoded and tracked the timing of auditory events. Further, mu- (8-15 Hz) and beta-band (12-20 Hz) oscillations revealed the superimposition of varied accentuation patterns on a subset of trials. These observations suggest convergence in the encoding and dynamic attending of temporal regularities in the acoustic environment, bridging a gap in the phylogenesis of rhythm cognition.
    MeSH term(s) Animals ; Humans ; Acoustic Stimulation ; Macaca ; Haplorhini ; Auditory Perception ; Acoustics ; Electroencephalography
    Language English
    Publishing date 2023-07-12
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 185535-9
    ISSN 1873-5118 ; 0301-0082
    ISSN (online) 1873-5118
    ISSN 0301-0082
    DOI 10.1016/j.pneurobio.2023.102502
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    Se 205: Show issues Location:
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  8. Article ; Online: Outer Membrane Vesicles Released from Garlic Exosome-like Nanoparticles (GaELNs) Train Gut Bacteria that Reverses Type 2 Diabetes via the Gut-Brain Axis.

    Sundaram, Kumaran / Teng, Yun / Mu, Jingyao / Xu, Qingbo / Xu, Fangyi / Sriwastva, Mukesh K / Zhang, Lifeng / Park, Juw Won / Zhang, Xiang / Yan, Jun / Zhang, Shuang Qin / Merchant, Michael L / Chen, Shao-Yu / McClain, Craig J / Dryden, Gerald W / Zhang, Huang-Ge

    Small (Weinheim an der Bergstrasse, Germany)

    2024  , Page(s) e2308680

    Abstract: Gut microbiota function has numerous effects on humans and the diet humans consume has emerged as a pivotal determinant of gut microbiota function. Here, a new concept that gut microbiota can be trained by diet-derived exosome-like nanoparticles (ELNs) ... ...

    Abstract Gut microbiota function has numerous effects on humans and the diet humans consume has emerged as a pivotal determinant of gut microbiota function. Here, a new concept that gut microbiota can be trained by diet-derived exosome-like nanoparticles (ELNs) to release healthy outer membrane vesicles (OMVs) is introduced. Specifically, OMVs released from garlic ELN (GaELNs) trained human gut Akkermansia muciniphila (A. muciniphila) can reverse high-fat diet-induced type 2 diabetes (T2DM) in mice. Oral administration of OMVs released from GaELNs trained A. muciniphila can traffick to the brain where they are taken up by microglial cells, resulting in inhibition of high-fat diet-induced brain inflammation. GaELNs treatment increases the levels of OMV Amuc-1100, P9, and phosphatidylcholines. Increasing the levels of Amuc-1100 and P9 leads to increasing the GLP-1 plasma level. Increasing the levels of phosphatidylcholines is required for inhibition of cGas and STING-mediated inflammation and GLP-1R crosstalk with the insulin pathway that leads to increasing expression of Insulin Receptor Substrate (IRS1 and IRS2) on OMV targeted cells. These findings reveal a molecular mechanism whereby OMVs from plant nanoparticle-trained gut bacteria regulate genes expressed in the brain, and have implications for the treatment of brain dysfunction caused by a metabolic syndrome.
    Language English
    Publishing date 2024-01-15
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2168935-0
    ISSN 1613-6829 ; 1613-6810
    ISSN (online) 1613-6829
    ISSN 1613-6810
    DOI 10.1002/smll.202308680
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  9. Article ; Online: Zfp281 and Zfp148 control CD4

    Chopp, Laura B / Zhu, Xiaoliang / Gao, Yayi / Nie, Jia / Singh, Jatinder / Kumar, Parimal / Young, Kelly Z / Patel, Shil / Li, Caiyi / Balmaceno-Criss, Mariah / Vacchio, Melanie S / Wang, Michael M / Livak, Ferenc / Merchant, Juanita L / Wang, Lie / Kelly, Michael C / Zhu, Jinfang / Bosselut, Rémy

    Science immunology

    2023  Volume 8, Issue 89, Page(s) eadi9066

    Abstract: ... How ... ...

    Abstract How CD4
    MeSH term(s) Animals ; Mice ; CD4-Positive T-Lymphocytes/metabolism ; Cell Differentiation/genetics ; Cytokines/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances Cytokines ; DNA-Binding Proteins ; Transcription Factors ; Zfp148 protein, mouse ; Zfp281 protein, mouse
    Language English
    Publishing date 2023-11-10
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Intramural
    ISSN 2470-9468
    ISSN (online) 2470-9468
    DOI 10.1126/sciimmunol.adi9066
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  10. Article ; Online: A Comprehensive Survey of Statistical Approaches for Differential Expression Analysis in Single-Cell RNA Sequencing Studies.

    Das, Samarendra / Rai, Anil / Merchant, Michael L / Cave, Matthew C / Rai, Shesh N

    Genes

    2021  Volume 12, Issue 12

    Abstract: Single-cell RNA-sequencing (scRNA-seq) is a recent high-throughput sequencing technique for studying gene expressions at the cell level. Differential Expression (DE) analysis is a major downstream analysis of scRNA-seq data. DE analysis the in presence ... ...

    Abstract Single-cell RNA-sequencing (scRNA-seq) is a recent high-throughput sequencing technique for studying gene expressions at the cell level. Differential Expression (DE) analysis is a major downstream analysis of scRNA-seq data. DE analysis the in presence of noises from different sources remains a key challenge in scRNA-seq. Earlier practices for addressing this involved borrowing methods from bulk RNA-seq, which are based on non-zero differences in average expressions of genes across cell populations. Later, several methods specifically designed for scRNA-seq were developed. To provide guidance on choosing an appropriate tool or developing a new one, it is necessary to comprehensively study the performance of DE analysis methods. Here, we provide a review and classification of different DE approaches adapted from bulk RNA-seq practice as well as those specifically designed for scRNA-seq. We also evaluate the performance of 19 widely used methods in terms of 13 performance metrics on 11 real scRNA-seq datasets. Our findings suggest that some bulk RNA-seq methods are quite competitive with the single-cell methods and their performance depends on the underlying models, DE test statistic(s), and data characteristics. Further, it is difficult to obtain the method which will be best-performing globally through individual performance criterion. However, the multi-criteria and combined-data analysis indicates that DECENT and EBSeq are the best options for DE analysis. The results also reveal the similarities among the tested methods in terms of detecting common DE genes. Our evaluation provides proper guidelines for selecting the proper tool which performs best under particular experimental settings in the context of the scRNA-seq.
    MeSH term(s) Algorithms ; Animals ; Databases, Nucleic Acid ; Gene Expression Profiling/methods ; Humans ; Mice ; RNA-Seq/methods ; Sequence Analysis, RNA/methods ; Sequence Analysis, RNA/statistics & numerical data ; Single-Cell Analysis/methods ; Single-Cell Analysis/statistics & numerical data ; Software/statistics & numerical data
    Language English
    Publishing date 2021-12-02
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12121947
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