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  1. AU="Lipton, Mary S"
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  1. Book: Mass spectrometry of proteins and peptides

    Lipton, Mary S.

    methods and protocols

    (Methods in molecular biology ; 492 ; Springer protocols)

    2009  

    Author's details ed. by Mary S. Lipton
    Series title Methods in molecular biology ; 492
    Springer protocols
    Collection
    Keywords Proteins / analysis ; Mass Spectrometry / methods ; Peptides / analysis ; Proteins/Analysis ; Peptides/Analysis ; Mass spectrometry ; Proteine ; Analysenmesstechnik ; Peptide ; Massenspektrometrie ; Elektrophorese ; Flüssigkeitschromatographie ; Matrix-unterstützte Laser-Desorption
    Subject Eiweiss ; Protein ; Matrix-unterstützte Photodesorption ; MALDI ; Flüssigchromatographie ; Ionographie ; Massenspektrographie ; Massenspektroskopie
    Subject code 572.633
    Language English
    Size XIV, 470 S., [2] Bl. : Ill., graph. Darst., 26cm
    Edition 2. ed.
    Publisher Humana
    Publishing place Totowa, NJ
    Publishing country United States
    Document type Book
    HBZ-ID HT015820167
    ISBN 978-1-934115-48-0 ; 1-934115-48-7 ; 9781597454933 ; 1597454931
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2009 A 1085 order for loan Magazin

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  2. Article ; Online: Bulk and Spatially Resolved Extracellular Metabolome of Free-Living Nitrogen Fixation.

    Smercina, Darian N / Kim, Young-Mo / Lipton, Mary S / Velickovic, Dusan / Hofmockel, Kirsten S

    Applied and environmental microbiology

    2022  Volume 88, Issue 12, Page(s) e0050522

    Abstract: Soil nitrogen (N) transformations constrain terrestrial net primary productivity and are driven by the activity of soil microorganisms. Free-living N fixation (FLNF) is an important soil N transformation and key N input to terrestrial systems, but the ... ...

    Abstract Soil nitrogen (N) transformations constrain terrestrial net primary productivity and are driven by the activity of soil microorganisms. Free-living N fixation (FLNF) is an important soil N transformation and key N input to terrestrial systems, but the forms of N contributed to soil by FLNF are poorly understood. To address this knowledge gap, a focus on microorganisms and microbial scale processes is needed that links N-fixing bacteria and their contributed N sources to FLNF process rates. However, studying the activity of soil microorganisms
    MeSH term(s) Bacteria/metabolism ; Ecosystem ; Metabolome ; Nitrogen/metabolism ; Nitrogen Fixation ; Soil/chemistry ; Soil Microbiology
    Chemical Substances Soil ; Nitrogen (N762921K75)
    Language English
    Publishing date 2022-06-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 223011-2
    ISSN 1098-5336 ; 0099-2240
    ISSN (online) 1098-5336
    ISSN 0099-2240
    DOI 10.1128/aem.00505-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 201: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  3. Article: Real-Time and Rapid Respiratory Response of the Soil Microbiome to Moisture Shifts.

    Smith, Montana L / Weitz, Karl K / Thompson, Allison M / Jansson, Janet K / Hofmockel, Kirsten S / Lipton, Mary S

    Microorganisms

    2023  Volume 11, Issue 11

    Abstract: Microbial response to changing environmental factors influences the fate of soil organic carbon, and drought has been shown to affect microbial metabolism and respiration. We hypothesized that the access of microbes to different carbon pools in response ... ...

    Abstract Microbial response to changing environmental factors influences the fate of soil organic carbon, and drought has been shown to affect microbial metabolism and respiration. We hypothesized that the access of microbes to different carbon pools in response to dry-rewet events occurs sequentially at different rates. We amended desiccated soils with
    Language English
    Publishing date 2023-10-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms11112630
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments.

    Rodríguez-Ramos, Josué / Nicora, Carrie D / Purvine, Samuel O / Borton, Mikayla A / McGivern, Bridget B / Hoyt, David W / Lipton, Mary S / Wrighton, Kelly C

    Microbiology resource announcements

    2024  , Page(s) e0003324

    Abstract: Rivers are critical ecosystems that impact global biogeochemical cycles. Nonetheless, a mechanistic understanding of river microbial metabolisms and their influences on geochemistry is lacking. Here, we announce metaproteomes of river sediments that are ... ...

    Abstract Rivers are critical ecosystems that impact global biogeochemical cycles. Nonetheless, a mechanistic understanding of river microbial metabolisms and their influences on geochemistry is lacking. Here, we announce metaproteomes of river sediments that are paired with metagenomes and metabolites, enabling an understanding of the microbial underpinnings of river respiration.
    Language English
    Publishing date 2024-04-23
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00033-24
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities.

    Berrios, Louis / Bogar, Glade D / Bogar, Laura M / Venturini, Andressa M / Willing, Claire E / Del Rio, Anastacia / Ansell, T Bertie / Zemaitis, Kevin / Velickovic, Marija / Velickovic, Dusan / Pellitier, Peter T / Yeam, Jay / Hutchinson, Chelsea / Bloodsworth, Kent / Lipton, Mary S / Peay, Kabir G

    mSystems

    2024  , Page(s) e0036924

    Abstract: Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF ... ...

    Abstract Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew
    Language English
    Publishing date 2024-05-08
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN (online) 2379-5077
    DOI 10.1128/msystems.00369-24
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Cysteine: an ancestral Cu binding ligand in green algae?

    Strenkert, Daniela / Schmollinger, Stefan / Hu, Yuntao / Hofmann, Christian / Holbrook, Kristen / Liu, Helen W / Purvine, Samuel O / Nicora, Carrie D / Chen, Si / Lipton, Mary S / Northen, Trent R / Clemens, Stephan / Merchant, Sabeeha S

    bioRxiv : the preprint server for biology

    2023  

    Abstract: ... Growth ... ...

    Abstract Growth of
    Language English
    Publishing date 2023-03-15
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.15.532757
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes.

    Kleiner, Manuel / Kouris, Angela / Violette, Marlene / D'Angelo, Grace / Liu, Yihua / Korenek, Abigail / Tolić, Nikola / Sachsenberg, Timo / McCalder, Janine / Lipton, Mary S / Strous, Marc

    Microbiome

    2023  Volume 11, Issue 1, Page(s) 24

    Abstract: Background: Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying ... ...

    Abstract Background: Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput.
    Results: Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50-99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC-MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using
    Conclusions: We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
    MeSH term(s) Humans ; Carbon Isotopes/analysis ; Carbon Isotopes/metabolism ; Chromatography, Liquid ; Tandem Mass Spectrometry/methods ; Microbiota ; DNA Probes
    Chemical Substances Carbon Isotopes ; DNA Probes
    Language English
    Publishing date 2023-02-09
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2697425-3
    ISSN 2049-2618 ; 2049-2618
    ISSN (online) 2049-2618
    ISSN 2049-2618
    DOI 10.1186/s40168-022-01454-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Zn deficiency disrupts Cu and S homeostasis in Chlamydomonas resulting in over accumulation of Cu and Cysteine.

    Strenkert, Daniela / Schmollinger, Stefan / Hu, Yuntao / Hofmann, Christian / Holbrook, Kristen / Liu, Helen W / Purvine, Samuel O / Nicora, Carrie D / Chen, Si / Lipton, Mary S / Northen, Trent R / Clemens, Stephan / Merchant, Sabeeha S

    Metallomics : integrated biometal science

    2023  Volume 15, Issue 7

    Abstract: Growth of Chlamydomonas reinhardtii in zinc (Zn) limited medium leads to disruption of copper (Cu) homeostasis, resulting in up to 40-fold Cu over-accumulation relative to its typical Cu quota. We show that Chlamydomonas controls its Cu quota by ... ...

    Abstract Growth of Chlamydomonas reinhardtii in zinc (Zn) limited medium leads to disruption of copper (Cu) homeostasis, resulting in up to 40-fold Cu over-accumulation relative to its typical Cu quota. We show that Chlamydomonas controls its Cu quota by balancing Cu import and export, which is disrupted in a Zn deficient cell, thus establishing a mechanistic connection between Cu and Zn homeostasis. Transcriptomics, proteomics and elemental profiling revealed that Zn-limited Chlamydomonas cells up-regulate a subset of genes encoding "first responder" proteins involved in sulfur (S) assimilation and consequently accumulate more intracellular S, which is incorporated into L-cysteine, γ-glutamylcysteine, and homocysteine. Most prominently, in the absence of Zn, free L-cysteine is increased ∼80-fold, corresponding to ∼2.8 × 109 molecules/cell. Interestingly, classic S-containing metal binding ligands like glutathione and phytochelatins do not increase. X-ray fluorescence microscopy showed foci of S accumulation in Zn-limited cells that co-localize with Cu, phosphorus and calcium, consistent with Cu-thiol complexes in the acidocalcisome, the site of Cu(I) accumulation. Notably, cells that have been previously starved for Cu do not accumulate S or Cys, causally connecting cysteine synthesis with Cu accumulation. We suggest that cysteine is an in vivo Cu(I) ligand, perhaps ancestral, that buffers cytosolic Cu.
    MeSH term(s) Cysteine/metabolism ; Chlamydomonas/metabolism ; Zinc/metabolism ; Copper/metabolism ; Homeostasis
    Chemical Substances Cysteine (K848JZ4886) ; Zinc (J41CSQ7QDS) ; Copper (789U1901C5)
    Language English
    Publishing date 2023-07-01
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 2474317-3
    ISSN 1756-591X ; 1756-5901
    ISSN (online) 1756-591X
    ISSN 1756-5901
    DOI 10.1093/mtomcs/mfad043
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Hi-C metagenome sequencing reveals soil phage-host interactions.

    Wu, Ruonan / Davison, Michelle R / Nelson, William C / Smith, Montana L / Lipton, Mary S / Jansson, Janet K / McClure, Ryan S / McDermott, Jason E / Hofmockel, Kirsten S

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 7666

    Abstract: Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi-C) to directly capture phage-host relationships. Some hosts have high ... ...

    Abstract Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi-C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lytic infections result in more host death and inversely influence host abundance. This study provides empirical evidence of phage-mediated bacterial population dynamics in soil by directly capturing specific phage-host interactions.
    MeSH term(s) Bacteriophages/genetics ; Metagenome ; Soil ; Bacteria/genetics ; Lysogeny/genetics
    Chemical Substances Soil
    Language English
    Publishing date 2023-11-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-42967-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Daylight-driven carbon exchange through a vertically structured microbial community.

    Moran, James J / Bernstein, Hans C / Mobberley, Jennifer M / Thompson, Allison M / Kim, Young-Mo / Dana, Karl L / Cory, Alexandra B / Courtney, Steph / Renslow, Ryan S / Fredrickson, James K / Kreuzer, Helen W / Lipton, Mary S

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1139213

    Abstract: Interactions between autotrophs and heterotrophs are central to carbon (C) exchange across trophic levels in essentially all ecosystems and metabolite exchange is a frequent mechanism for distributing C within spatially structured ecosystems. Yet, ... ...

    Abstract Interactions between autotrophs and heterotrophs are central to carbon (C) exchange across trophic levels in essentially all ecosystems and metabolite exchange is a frequent mechanism for distributing C within spatially structured ecosystems. Yet, despite the importance of C exchange, the timescales at which fixed C is transferred in microbial communities is poorly understood. We employed a stable isotope tracer combined with spatially resolved isotope analysis to quantify photoautotrophic uptake of bicarbonate and track subsequent exchanges across a vertical depth gradient in a stratified microbial mat over a light-driven diel cycle. We observed that C mobility, both across the vertical strata and between taxa, was highest during periods of active photoautotrophy. Parallel experiments with
    Language English
    Publishing date 2023-05-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1139213
    Database MEDical Literature Analysis and Retrieval System OnLINE

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