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  1. AU=Patterson Andrew D
  2. AU="Kim, Joyce Mary"
  3. AU="Saribay, S Adil"
  4. AU="Couderc, M."
  5. AU="Macerlane de Lira Silva"
  6. AU=Neal Michael S
  7. AU="Nakai, Kozo"
  8. AU="Debatin, Jörg F."
  9. AU="Plant, Laura"
  10. AU="Manuel Tisminetzky"
  11. AU="Monaco, Carlo"
  12. AU="Srivastava, Rupesh"
  13. AU="Nathan, Jaimie D"
  14. AU="Schnegelberger, Regina D"
  15. AU=Doshi Paresh
  16. AU="Cecilia Hognon"
  17. AU="Mason, Jeremy K."
  18. AU=Hasumi Hisashi
  19. AU="Swati Sethi"
  20. AU="Martin G. Myers, Jr."
  21. AU="Marcus-Sekura, Carol"
  22. AU="Petagine, Lucy"
  23. AU="Jessa R. Alexander"
  24. AU=Rauner Martina
  25. AU="Richlen, Mindy L"
  26. AU="Merghani, Nada M"
  27. AU=Splitt M P
  28. AU="Zlatanović, Gordana"

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  1. Artikel: Estimation of spatial demographic maps from polymorphism data using a neural network.

    Smith, Chris C R / Patterson, Gilia / Ralph, Peter L / Kern, Andrew D

    bioRxiv : the preprint server for biology

    2024  

    Abstract: A fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and source sink dynamics of dispersal should shape ... ...

    Abstract A fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and source sink dynamics of dispersal should shape genetic variation over space, however there are few tools currently available that can deal with these ubiquitous complexities. Geographically referenced single nucleotide polymorphism (SNP) data are increasingly accessible, presenting an opportunity to study genetic variation across geographic space in myriad species. We present a new inference method that uses geo-referenced SNPs and a deep neural network to estimate spatially heterogeneous maps of population density and dispersal rate. Our neural network trains on simulated input and output pairings, where the input consists of genotypes and sampling locations generated from a continuous space population genetic simulator, and the output is a map of the true demographic parameters. We benchmark our tool against existing methods and discuss qualitative differences between the different approaches; in particular, our program is unique because it infers the magnitude of both dispersal and density as well as their variation over the landscape, and it does so using SNP data. Similar methods are constrained to estimating relative migration rates, or require identity by descent blocks as input. We applied our tool to empirical data from North American grey wolves, for which it estimated mostly reasonable demographic parameters, but was affected by incomplete spatial sampling. Genetic based methods like ours complement other, direct methods for estimating past and present demography, and we believe will serve as valuable tools for applications in conservation, ecology, and evolutionary biology. An open source software package implementing our method is available from https://github.com/kr-colab/mapNN.
    Sprache Englisch
    Erscheinungsdatum 2024-03-17
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2024.03.15.585300
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  2. Artikel ; Online: Role of bile acids and gut bacteria in healthy ageing of centenarians.

    Rimal, Bipin / Patterson, Andrew D

    Nature

    2021  Band 599, Heft 7885, Seite(n) 380–381

    Mesh-Begriff(e) Aged, 80 and over ; Bacteria/genetics ; Bile Acids and Salts ; Centenarians ; Gastrointestinal Microbiome ; Healthy Aging ; Humans
    Chemische Substanzen Bile Acids and Salts
    Sprache Englisch
    Erscheinungsdatum 2021-10-04
    Erscheinungsland England
    Dokumenttyp News ; Comment
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-021-02196-0
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  3. Artikel ; Online: Comparative urine metabolomics of mice treated with non-toxic and toxic oral doses of (-)-epigallocatechin-3-gallate.

    Hwang, Soomee / Koo, Imhoi / Patterson, Andrew D / Lambert, Joshua D

    Food & function

    2023  Band 14, Heft 20, Seite(n) 9434–9445

    Abstract: The green tea polyphenol, (-)-epigallocatechin-3-gallate (EGCG), has been studied for its potential positive health effects, but human and animal model studies have reported potential toxicity at high oral bolus doses. This study used liquid ... ...

    Abstract The green tea polyphenol, (-)-epigallocatechin-3-gallate (EGCG), has been studied for its potential positive health effects, but human and animal model studies have reported potential toxicity at high oral bolus doses. This study used liquid chromatography-mass spectrometry-based metabolomics to compare the urinary EGCG metabolite profile after administration of a single non-toxic (100 mg kg
    Mesh-Begriff(e) Humans ; Mice ; Male ; Animals ; Glucuronides ; Catechin ; Tea ; Sulfates
    Chemische Substanzen epigallocatechin gallate (BQM438CTEL) ; Glucuronides ; Catechin (8R1V1STN48) ; Tea ; Sulfates
    Sprache Englisch
    Erscheinungsdatum 2023-10-16
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2612033-1
    ISSN 2042-650X ; 2042-6496
    ISSN (online) 2042-650X
    ISSN 2042-6496
    DOI 10.1039/d3fo02710d
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  4. Artikel ; Online: Immune cell-intrinsic Ah receptor facilitates the expression of antimicrobial REG3G in the small intestine.

    Chakraborty, Debopriya / Coslo, Denise M / Murray, Iain A / Vijay, Anitha / Patterson, Andrew D / Perdew, Gary H

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology

    2024  Band 38, Heft 4, Seite(n) e23471

    Abstract: The intestinal epithelial layer is susceptible to damage by chemical, physiological and mechanical stress. While it is essential to maintain the integrity of epithelium, the biochemical pathways that contribute to the barrier function have not been ... ...

    Abstract The intestinal epithelial layer is susceptible to damage by chemical, physiological and mechanical stress. While it is essential to maintain the integrity of epithelium, the biochemical pathways that contribute to the barrier function have not been completely investigated. Here we demonstrate an aryl hydrocarbon receptor (AHR)-dependent mechanism facilitating the production of the antimicrobial peptide AMP regenerating islet-derived protein 3 gamma (REG3G), which is essential for intestinal homeostasis. Genetic ablation of AHR in mice impairs pSTAT3-mediated REG3G expression and increases bacterial numbers of Segmented filamentous bacteria (SFB) and Akkermansia muciniphila in the small intestine. Studies with tissue-specific conditional knockout mice revealed that the presence of AHR in the epithelial cells of the small intestine is not required for the production of REG3G through the phosphorylated STAT3-mediated pathway. However, immune-cell-specific AHR activity is necessary for normal expression of REG3G in all regions of the small intestine. A diet rich in broccoli, capable of inducing AHR activity, increases REG3G production when compared to a semi-purified diet that is devoid of ligands that can potentially activate the AHR, thus highlighting the importance of AHR in antimicrobial function. Overall, these data suggest that homeostatic antimicrobial REG3G production is increased by an AHR pathway intrinsic to the immune cells in the small intestine.
    Mesh-Begriff(e) Animals ; Mice ; Anti-Infective Agents ; Cytoskeleton ; Epithelial Cells ; Intestine, Small ; Mice, Knockout ; Receptors, Aryl Hydrocarbon/genetics
    Chemische Substanzen Anti-Infective Agents ; Receptors, Aryl Hydrocarbon ; Reg3g protein, mouse ; Ahr protein, mouse
    Sprache Englisch
    Erscheinungsdatum 2024-02-14
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 639186-2
    ISSN 1530-6860 ; 0892-6638
    ISSN (online) 1530-6860
    ISSN 0892-6638
    DOI 10.1096/fj.202302319R
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  5. Artikel ; Online: Individualized microbiotas dictate the impact of dietary fiber on colitis sensitivity.

    Bonazzi, Erica / Bretin, Alexis / Vigué, Lucile / Hao, Fuhua / Patterson, Andrew D / Gewirtz, Andrew T / Chassaing, Benoit

    Microbiome

    2024  Band 12, Heft 1, Seite(n) 5

    Abstract: Background: The observation that the intestinal microbiota is  central in the development of IBD suggests that dietary fiber, the microbiota's primary source of nourishment, could play a central role in these diseases. Accordingly, enriching diets with ... ...

    Abstract Background: The observation that the intestinal microbiota is  central in the development of IBD suggests that dietary fiber, the microbiota's primary source of nourishment, could play a central role in these diseases. Accordingly, enriching diets with specific soluble fibers remodels microbiota and modulates colitis sensitivity. In humans, a recent study suggests that the microbiota of select IBD patients might influence the impacts they would experience upon fiber exposure. We sought here to define the extent to which individual microbiotas varied in their responsiveness to purified soluble fiber inulin and psyllium. Moreover, the extent to which such variance might impact proneness to colitis.
    Results: We observed a high level of inter-individual variation in microbiota responsiveness to fiber inulin and psyllium: while microbiotas from select donors exhibited stark fiber-induced modulation in composition, pro-inflammatory potential, and metabolomic profile, others were only minimally impacted. Mice transplanted with fiber-sensitive microbiomes exhibited colitis highly modulated by soluble fiber consumption, while mice receiving fiber-resistant microbiotas displayed colitis severity irrespective of fiber exposure.
    Conclusion: The extent to which select soluble fibers alter proneness to colitis is highly influenced by an individual's microbiota composition and further investigation of individual microbiota responsiveness toward specific dietary fiber could pave the way to personalized fiber-based intervention, both in IBD patients and healthy individuals. Video Abstract.
    Mesh-Begriff(e) Humans ; Mice ; Animals ; Psyllium/adverse effects ; Inulin ; Colitis/chemically induced ; Dietary Fiber ; Gastrointestinal Microbiome ; Inflammatory Bowel Diseases
    Chemische Substanzen Psyllium (8063-16-9) ; Inulin (9005-80-5) ; Dietary Fiber
    Sprache Englisch
    Erscheinungsdatum 2024-01-05
    Erscheinungsland England
    Dokumenttyp Video-Audio Media ; Journal Article
    ZDB-ID 2697425-3
    ISSN 2049-2618 ; 2049-2618
    ISSN (online) 2049-2618
    ISSN 2049-2618
    DOI 10.1186/s40168-023-01724-6
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  6. Artikel ; Online: Individualized microbiotas dictate the impact of dietary fiber on colitis sensitivity

    Erica Bonazzi / Alexis Bretin / Lucile Vigué / Fuhua Hao / Andrew D. Patterson / Andrew T. Gewirtz / Benoit Chassaing

    Microbiome, Vol 12, Iss 1, Pp 1-

    2024  Band 14

    Abstract: Abstract Background The observation that the intestinal microbiota is central in the development of IBD suggests that dietary fiber, the microbiota’s primary source of nourishment, could play a central role in these diseases. Accordingly, enriching diets ...

    Abstract Abstract Background The observation that the intestinal microbiota is central in the development of IBD suggests that dietary fiber, the microbiota’s primary source of nourishment, could play a central role in these diseases. Accordingly, enriching diets with specific soluble fibers remodels microbiota and modulates colitis sensitivity. In humans, a recent study suggests that the microbiota of select IBD patients might influence the impacts they would experience upon fiber exposure. We sought here to define the extent to which individual microbiotas varied in their responsiveness to purified soluble fiber inulin and psyllium. Moreover, the extent to which such variance might impact proneness to colitis. Results We observed a high level of inter-individual variation in microbiota responsiveness to fiber inulin and psyllium: while microbiotas from select donors exhibited stark fiber-induced modulation in composition, pro-inflammatory potential, and metabolomic profile, others were only minimally impacted. Mice transplanted with fiber-sensitive microbiomes exhibited colitis highly modulated by soluble fiber consumption, while mice receiving fiber-resistant microbiotas displayed colitis severity irrespective of fiber exposure. Conclusion The extent to which select soluble fibers alter proneness to colitis is highly influenced by an individual's microbiota composition and further investigation of individual microbiota responsiveness toward specific dietary fiber could pave the way to personalized fiber-based intervention, both in IBD patients and healthy individuals. Video Abstract
    Schlagwörter Microbiota ; Dietary fiber ; Inflammation ; Personalized response ; Microbial ecology ; QR100-130
    Thema/Rubrik (Code) 621
    Sprache Englisch
    Erscheinungsdatum 2024-01-01T00:00:00Z
    Verlag BMC
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research.

    Morgan, Ethan W / Perdew, Gary H / Patterson, Andrew D

    Toxicological sciences : an official journal of the Society of Toxicology

    2022  Band 187, Heft 2, Seite(n) 189–213

    Abstract: Microbial communities on and within the host contact environmental pollutants, toxic compounds, and other xenobiotic compounds. These communities of bacteria, fungi, viruses, and archaea possess diverse metabolic potential to catabolize compounds and ... ...

    Abstract Microbial communities on and within the host contact environmental pollutants, toxic compounds, and other xenobiotic compounds. These communities of bacteria, fungi, viruses, and archaea possess diverse metabolic potential to catabolize compounds and produce new metabolites. Microbes alter chemical disposition thus making the microbiome a natural subject of interest for toxicology. Sequencing and metabolomics technologies permit the study of microbiomes altered by acute or long-term exposure to xenobiotics. These investigations have already contributed to and are helping to re-interpret traditional understandings of toxicology. The purpose of this review is to provide a survey of the current methods used to characterize microbes within the context of toxicology. This will include discussion of commonly used techniques for conducting omic-based experiments, their respective strengths and deficiencies, and how forward-looking techniques may address present shortcomings. Finally, a perspective will be provided regarding common assumptions that currently impede microbiome studies from producing causal explanations of toxicologic mechanisms.
    Mesh-Begriff(e) Bacteria ; Gastrointestinal Microbiome ; Metabolomics/methods ; Microbiota ; Xenobiotics/toxicity
    Chemische Substanzen Xenobiotics
    Sprache Englisch
    Erscheinungsdatum 2022-03-14
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 1420885-4
    ISSN 1096-0929 ; 1096-6080
    ISSN (online) 1096-0929
    ISSN 1096-6080
    DOI 10.1093/toxsci/kfac029
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  8. Artikel ; Online: A Comparison of Patient Characteristics and Outcomes Between Patients Receiving Flexor Digitorum Superficialis Slip Excision or Isolated A1 Pulley Release for Trigger Finger.

    Fisher, Margaret M / Allen, Andrew D / Jeffs, Alexander D / Wellborn, Patricia K / Hu, Di / Patterson, J Megan M / Draeger, Reid W

    The Journal of hand surgery

    2024  

    Abstract: Purpose: Resection of the radial or ulnar slip of the flexor digitorum superficialis (FDS) tendon is a known treatment option for persistent trigger finger. Risk factors for undergoing FDS slip excision are unclear. We hypothesized that patients who ... ...

    Abstract Purpose: Resection of the radial or ulnar slip of the flexor digitorum superficialis (FDS) tendon is a known treatment option for persistent trigger finger. Risk factors for undergoing FDS slip excision are unclear. We hypothesized that patients who underwent A1 pulley release with FDS slip excision secondary to persistent triggering would have a higher comorbidity burden compared to those receiving A1 pulley release alone.
    Methods: We identified all adult patients who underwent A1 pulley release with FDS slip excision because of persistent triggering either intraoperatively or postoperatively from 2018 to 2023. We selected a 3:1 age- and sex-matched control group who underwent isolated A1 pulley release. Charts were retrospectively reviewed for demographics, selected comorbidities, trigger finger history, and postoperative course. We performed multivariable logistic regression to assess the probability of FDS slip excision after adjusting for several variables that were significant in bivariate comparisons.
    Results: We identified 48 patients who underwent A1 pulley release with FDS slip excision and 144 controls. Our multivariable model showed that patients with additional trigger fingers and a preoperative proximal interphalangeal (PIP) joint contracture were significantly more likely to undergo FDS slip excision.
    Conclusions: Patients who underwent A1 pulley release with FDS slip excision were significantly more likely to have multiple trigger fingers or a preoperative PIP joint contracture. Clinicians should counsel patients with these risk factors regarding the potential for FDS slip excision in addition to A1 pulley release to alleviate triggering of the affected digit.
    Type of study/level of evidence: Therapeutic III.
    Sprache Englisch
    Erscheinungsdatum 2024-03-18
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 605716-0
    ISSN 1531-6564 ; 0363-5023
    ISSN (online) 1531-6564
    ISSN 0363-5023
    DOI 10.1016/j.jhsa.2024.02.003
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  9. Artikel: Molecular networking identifies an AHR-modulating benzothiazole from white button mushrooms (

    Chen, Xiaoling / Patterson, Andrew D / Perdew, Gary H / Murray, Iain A / Kellogg, Joshua J

    Journal of functional foods

    2023  Band 106

    Abstract: Diet-derived aryl hydrocarbon receptor (AHR) ligands have potential to maintain gut health. However, among the myriad bioactive compounds from foods, identifying novel functional ligands which would significantly impact gastrointestinal health is a ... ...

    Abstract Diet-derived aryl hydrocarbon receptor (AHR) ligands have potential to maintain gut health. However, among the myriad bioactive compounds from foods, identifying novel functional ligands which would significantly impact gastrointestinal health is a challenge. In this study, a novel AHR modulator is predicted, identified, and characterized in the white button mushroom (
    Sprache Englisch
    Erscheinungsdatum 2023-06-07
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article
    ZDB-ID 2511964-3
    ISSN 1756-4646
    ISSN 1756-4646
    DOI 10.1016/j.jff.2023.105602
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  10. Artikel ; Online: Human Intestinal Microbiome Determines Individualized Inflammatory Response to Dietary Emulsifier Carboxymethylcellulose Consumption.

    Daniel, Noëmie / Wu, Gary D / Walters, William / Compher, Charlene / Ni, Josephine / Delaroque, Clara / Albenberg, Lindsey / Ley, Ruth E / Patterson, Andrew D / Lewis, James D / Gewirtz, Andrew T / Chassaing, Benoit

    Cellular and molecular gastroenterology and hepatology

    2023  Band 17, Heft 2, Seite(n) 315–318

    Mesh-Begriff(e) Humans ; Gastrointestinal Microbiome ; Carboxymethylcellulose Sodium ; Intestines ; Microbiota ; Diet
    Chemische Substanzen Carboxymethylcellulose Sodium (K679OBS311)
    Sprache Englisch
    Erscheinungsdatum 2023-11-04
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2819778-1
    ISSN 2352-345X ; 2352-345X
    ISSN (online) 2352-345X
    ISSN 2352-345X
    DOI 10.1016/j.jcmgh.2023.11.001
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