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  • 1
    Call number: M 97.0368
    In: SEPM short course ; 36, No. 36
    Type of Medium: Monograph available for loan
    Pages: iii, 174 S. + Disk.
    ISBN: 1565760212
    Series Statement: SEPM short course no. 36
    Classification:
    Sedimentology
    Language: English
    Location: Upper compact magazine
    Branch Library: GFZ Library
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  • 2
    Call number: SR 90.0001(1808-L)
    In: U.S. Geological Survey bulletin
    Type of Medium: Series available for loan
    Pages: III, L-19 S.
    Series Statement: U.S. Geological Survey bulletin 1808-L
    Language: English
    Location: Lower compact magazine
    Branch Library: GFZ Library
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  • 3
    Publication Date: 2022-05-25
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Sedimentary Geology 202 (2007): 402-408, doi:10.1016/j.sedgeo.2007.03.020.
    Description: For more than a century, studies of sedimentology and sediment transport have measured bed-sediment grain size by collecting samples and transporting them back to the laboratory for grain-size analysis. This process is slow and expensive. Moreover, most sampling systems are not selective enough to sample only the surficial grains that interact with the flow; samples typically include sediment from at least a few centimeters beneath the bed surface. New hardware and software are available for in situ measurement of grain size. The new technology permits rapid measurement of surficial bed sediment. Here we describe several systems we have deployed by boat, by hand, and by tripod in rivers, oceans, and on beaches.
    Keywords: Underwater microscope ; Bed sediment ; Grain size ; In situ measurement ; Colorado River ; Adriatic Sea
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 4
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 5 (2017): 50, doi:10.1186/s40168-017-0270-x.
    Description: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits. We used shotgun metagenomics together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from fecal samples of a single FMT donor. We then used metagenomic mapping to track the occurrence and distribution patterns of donor MAGs in two FMT recipients. Our analyses revealed that 22% of the 92 highly complete bacterial MAGs that we identified from the donor successfully colonized and remained abundant in two recipients for at least 8 weeks. Most MAGs with a high colonization rate belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales, and colonization success was negatively correlated with the number of genes related to sporulation. Our analysis of 151 publicly available gut metagenomes showed that the donor MAGs that colonized both recipients were prevalent, and the ones that colonized neither were rare across the participants of the Human Microbiome Project. Although our dataset showed a link between taxonomy and the colonization ability of a given MAG, we also identified MAGs that belong to the same taxon with different colonization properties, highlighting the importance of an appropriate level of resolution to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems. The analytical strategy adopted in our study can provide genomic insights into bacterial populations that may be critical to the efficacy of FMT due to their success in gut colonization and metabolic properties, and guide cultivation efforts to investigate mechanistic underpinnings of this procedure beyond associations.
    Description: AME was supported by the Frank R. Lillie Research Innovation Award and startup funds from the University of Chicago. This project was supported by the Mutchnik Family Charitable Fund and the University of Chicago Gastro-Intestinal Research Foundation.
    Keywords: Fecal microbiota transplantation ; Colonization ; Metagenomics ; Metagenome-assembled genomes
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mBio 7 (2016): e01713-16, doi:10.1128/mBio.01713-16.
    Description: A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of Bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified Bacteroides populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of Bacteroides isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of Bacteroides fragilis from the mucosa versus lumen. Each patient harbored Bacteroides spp. that are closely related to commonly occurring clinical isolates, including Bacteroides ovatus, B. thetaiotaomicron, B. vulgatus, and B. fragilis, which contained unique loci in different patients for synthesis of capsular polysaccharides. The presence of unique Bacteroides capsular polysaccharide loci within different hosts and between the lumen and mucosa may represent adaptations to stimulate, suppress, and evade host-specific immune responses at different microsites of the ileal pouch.
    Description: Leona M. and Harry B. Helmsley Charitable Trust; Bay and Paul Foundations; Frank R. Lillie Research Innovation Award; Gastrointestinal Research Foundation of Chicago
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here by permission of American Physiological Society for personal use, not for redistribution. The definitive version was published in American Journal of Physiology-Gastrointestinal and Liver Physiology 310 (2016): G973-G988, doi:10.1152/ajpgi.00017.2016.
    Description: Gut dysbiosis, host genetics, and environmental triggers are implicated as causative factors in inflammatory bowel disease (IBD), yet mechanistic insights are lacking. Longitudinal analysis of ulcerative colitis patients following total colectomy with ileal anal anastomosis (IPAA) where 〉50% develop pouchitis, offers a unique setting to examine cause vs. effect. To recapitulate human IPAA, we employed a mouse model of surgically created blind self-filling (SFL) and self- emptying (SEL) ileal loops using wild-type (WT), IL-10 KO (IL10), and TLR4 KO (T4), and IL10/T4 double KO mice. After 5 weeks, loop histology, host gene/protein expression, and bacterial 16s rRNA profiles were examined. SFL exhibit fecal stasis due to directional motility oriented towards the loop end, whereas SEL remain empty. In wild type mice, SFL, but not SEL, develop pouch-like microbial communities without accompanying active inflammation. However, in genetically susceptible IL-10-/- deficient mice, SFL, but not SEL, exhibit severe inflammation and mucosal transcriptomes resembling human pouchitis. The inflammation associated with IL- 10-/- required TLR4, as animals lacking both pathways displayed little disease. Furthermore, germ-free IL10-/- mice conventionalized with SFL, but not SEL, microbiota populations develop severe colitis. These data support essential roles of stasis-induced, colon-like microbiota, TLR4- mediated colonic metaplasia, and genetic susceptibility in the development of pouchitis and possibly UC. However, these factors by themselves are not sufficient. Similarities between this model and human UC/pouchitis provide opportunities for gaining insights into the mechanistic basis of IBD and for identification of targets for novel preventative and therapeutic interventions.
    Description: NIDDK DK42086 (DDRCC), UH3 DK083993, Leona and Harry Helmsley Trust (SHARE), R37 DK47722, T32 DK07074, F32 DK105728, Gastrointestinal Research Foundation of Chicago, Peter and Carol Goldman Family Research grant.
    Description: 2017-06-01
    Keywords: Pouchitis ; Inflammatory Bowel Disease ; Ulcerative Coltiis ; Dysbiosis
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 7
    Publication Date: 2024-04-03
    Description: Background: Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. Results: Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. Conclusions: These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of “dysbiosis” that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
    Format: application/pdf
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  • 8
    ISSN: 1520-510X
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1520-6041
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1365-3091
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences
    Notes: In settings where the transport of sand is partially or fully supply limited, changes in the upstream supply of sand are coupled to changes in the grain size of sand on the bed. In this manner, the transport of sand under the supply-limited case is ‘grain-size regulated’. Since the closure of Glen Canyon Dam in 1963, the downstream reach of the Colorado River in Marble and Grand Canyons has exhibited evidence of sand-supply limitation. Sand transport in the river is now approximately equally regulated by changes in the discharge of water and changes in the grain sizes of sand on the channel bed and eddy sandbars. Previous work has shown that changes in the grain size of sand on the bed of the channel (driven by changes in the upstream supply of sand owing to both tributary floods and high dam releases) are important in regulating sand transport over timescales of days to months. In this study, suspended-sand data are analysed in conjunction with bed grain-size data to determine whether changes in the grain size of sand on the bed of the channel or changes in the grain size of sand on the surface of eddy sandbars have been more important in regulating sand transport in the post-dam Colorado River over longer, multi-year timescales. The results of this study show that this combined theory- and field-based approach can be used to deduce which environments in a complicated setting are the most important environments for regulating sediment transport. In the case of the regulated Colorado River in Marble and Upper Grand Canyons, suspended-sand transport has been regulated mostly by changes in the surface grain size of eddy sandbars.
    Type of Medium: Electronic Resource
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