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  1. Article: The impacts of a logging road on the soil microbial communities, and carbon and nitrogen components in a Northern Zone Costa Rican forest

    Eaton, William D / McGee, Katie M / Donnelly, Robert / Lemenze, Alex / Larimer, Morgan / Hajibabaei, Mehrdad

    Applied soil ecology. 2021 Aug., v. 164

    2021  

    Abstract: Logging road development is considered as potentially more damaging to a tropical forest than the felling of the actual trees. However, little work has been conducted to determine how logging road development impacts the soil microbial communities and ... ...

    Abstract Logging road development is considered as potentially more damaging to a tropical forest than the felling of the actual trees. However, little work has been conducted to determine how logging road development impacts the soil microbial communities and associated C and N cycle activities in tropical forests. This study was conducted within an upland tropical forest in the Northern Zone of Costa Rica that had a 2-year abandoned logging road system (used for harvesting trees felled during a tornado) to determine how development of logging roads affected soil C and N cycle activities, efficiency of organic C use, and bacterial and fungal community compositions. Soil samples from a set of logging roads, the road edges, and adjacent primary forests were analyzed for C, N metrics, the Microbial Quotients, and DNA-based microbial taxonomic community compositions; which were tested for differences using multivariate statistical analyses. The logging road soils had significantly greater bulk density and clay, and lower levels of sand, TN, NO₃⁻, NO₃⁻/NH₄⁺, TOC, C Biomass, and Microbial Quotients compared to the road edge and forest soils. The composition of the total bacterial genera of the road edge and forest soils were similar to one another and different from that of the logging road soils, and the composition of the total fungal genera was unique within each of the three areas sampled. The relative abundance of DNA sequences of N-cycle bacteria were greater, and lignin degrading bacteria and wood rot/lignin degrading fungi were less in the logging roads compared to the edge and forest soils. These results suggest that the rate of recovery of both the C and N cycle activities and associated microbial groups in the soils from the road edges is occurring more rapidly than in the abandoned logging road soils. Thus, we suggest that a new tropical forest management practice should include the movement of the slash and debris from the road edge regions onto the logging roads after abandonment, as it would enhance the rate of recovery of both the C and N cycle activities in the soils, and perhaps begin to address the concern that logging roads add an additional 10–15 years to tropical forest recovery following deforestation.
    Keywords DNA ; biomass ; bulk density ; carbon ; clay ; decayed wood ; deforestation ; forest management ; fungal communities ; fungi ; highlands ; lignin ; nitrogen ; nitrogen cycle ; sand ; slash ; soil ecology ; tropical forests ; Costa Rica
    Language English
    Dates of publication 2021-08
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1196758-4
    ISSN 0929-1393
    ISSN 0929-1393
    DOI 10.1016/j.apsoil.2021.103937
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: The impact of ovarian stimulation on the human endometrial microenvironment.

    Chemerinski, Anat / Shen, May / Valero-Pacheco, Nuriban / Zhao, Qingshi / Murphy, Trystn / George, Lea / Lemenze, Alex / Sherman, Lauren / Heller, Debra / Chen, Xiaowei / Wu, Tracy / McGovern, Peter G / Morelli, Sara S / Arora, Ripla / Beaulieu, Aimee M / Douglas, Nataki C

    Human reproduction (Oxford, England)

    2024  Volume 39, Issue 5, Page(s) 1023–1041

    Abstract: Study question: How does ovarian stimulation (OS), which is used to mature multiple oocytes for ART procedures, impact the principal cellular compartments and transcriptome of the human endometrium in the periovulatory and mid-secretory phases?: ... ...

    Abstract Study question: How does ovarian stimulation (OS), which is used to mature multiple oocytes for ART procedures, impact the principal cellular compartments and transcriptome of the human endometrium in the periovulatory and mid-secretory phases?
    Summary answer: During the mid-secretory window of implantation, OS alters the abundance of endometrial immune cells, whereas during the periovulatory period, OS substantially changes the endometrial transcriptome and impacts both endometrial glandular and immune cells.
    What is known already: Pregnancies conceived in an OS cycle are at risk of complications reflective of abnormal placentation and placental function. OS can alter endometrial gene expression and immune cell populations. How OS impacts the glandular, stromal, immune, and vascular compartments of the endometrium, in the periovulatory period as compared to the window of implantation, is unknown.
    Study design, size, duration: This prospective cohort study carried out between 2020 and 2022 included 25 subjects undergoing OS and 25 subjects in natural menstrual cycles. Endometrial biopsies were performed in the proliferative, periovulatory, and mid-secretory phases.
    Participants/materials, setting, methods: Blood samples were processed to determine serum estradiol and progesterone levels. Both the endometrial transcriptome and the principal cellular compartments of the endometrium, including glands, stroma, immune, and vasculature, were evaluated by examining endometrial dating, differential gene expression, protein expression, cell populations, and the three-dimensional structure in endometrial tissue. Mann-Whitney U tests, unpaired t-tests or one-way ANOVA and pairwise multiple comparison tests were used to statistically evaluate differences.
    Main results and the role of chance: In the periovulatory period, OS induced high levels of differential gene expression, glandular-stromal dyssynchrony, and an increase in both glandular epithelial volume and the frequency of endometrial monocytes/macrophages. In the window of implantation during the mid-secretory phase, OS induced changes in endometrial immune cells, with a greater frequency of B cells and a lower frequency of CD4 effector T cells.
    Large scale data: The data underlying this article have been uploaded to the Genome Expression Omnibus/National Center for Biotechnology Information with accession number GSE220044.
    Limitations, reasons for caution: A limited number of subjects were included in this study, although the subjects within each group, natural cycle or OS, were homogenous in their clinical characteristics. The number of subjects utilized was sufficient to identify significant differences; however, with a larger number of subjects and additional power, we may detect additional differences. Another limitation of the study is that proliferative phase biopsies were collected in natural cycles, but not in OS cycles. Given that the OS cycle subjects did not have known endometrial factor infertility, and the comparisons involved subjects who had a similar and robust response to stimulation, the findings are generalizable to women with a normal response to OS.
    Wider implications of the findings: OS substantially altered the periovulatory phase endometrium, with fewer transcriptomic and cell type-specific changes in the mid-secretory phase. Our findings show that after OS, the endometrial microenvironment in the window of implantation possesses many more similarities to that of a natural cycle than does the periovulatory endometrium. Further investigation of the immune compartment and the functional significance of this cellular compartment under OS conditions is warranted.
    Study funding/competing interests: Research reported in this publication was supported by the National Institute of Allergy and Infectious Diseases (R01AI148695 to A.M.B. and N.C.D.), Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD109152 to R.A.), and the March of Dimes (5-FY20-209 to R.A.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or March of Dimes. All authors declare no conflict of interest.
    MeSH term(s) Humans ; Female ; Endometrium/metabolism ; Ovulation Induction ; Adult ; Transcriptome ; Cellular Microenvironment ; Prospective Studies ; Estradiol/blood ; Embryo Implantation/physiology ; Progesterone/blood ; Progesterone/metabolism ; Pregnancy ; Menstrual Cycle
    Chemical Substances Estradiol (4TI98Z838E) ; Progesterone (4G7DS2Q64Y)
    Language English
    Publishing date 2024-03-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 632776-x
    ISSN 1460-2350 ; 0268-1161 ; 1477-741X
    ISSN (online) 1460-2350
    ISSN 0268-1161 ; 1477-741X
    DOI 10.1093/humrep/deae048
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Differences in the soil microbial community and carbon‐use efficiency following development of Vochysia guatemalensis tree plantations in unproductive pastures in Costa Rica

    Eaton, William D / Donnelly, Robert / Hajibabaei, Mehrdad / Karas, Olivia / Lemenze, Alex / McGee, Katie M

    Restoration ecology. 2019 Nov., v. 27, no. 6

    2019  

    Abstract: This study shows that Vochysia guatemalensis tree plantations were associated with enhanced soil biotic and abiotic characteristics in previously cleared forests in the northern zone of Costa Rica, suggesting the possible use of this practice as a ... ...

    Abstract This study shows that Vochysia guatemalensis tree plantations were associated with enhanced soil biotic and abiotic characteristics in previously cleared forests in the northern zone of Costa Rica, suggesting the possible use of this practice as a restoration strategy for local land owners. Soil samples from a primary forest, secondary forest, and a 13‐year‐old plantation of V. guatemalensis had greater relative abundances of DNA sequences of microbial genera critical for carbon‐use (C‐use) efficiency (i.e. the saprobe, complex C and wood rot/lignin decomposer fungi, and bacterial lignin and other complex C degraders), and greater levels of total organic carbon, C‐biomass, and microbial quotients as indicators of enhanced C‐use efficiency, than found in soils of adjacent 5‐year‐old V. guatemalensis plantations and abandoned non‐productive pasture/grasslands (GRs). The major research conclusions were that (1) conversion of forested land into abandoned pasture/GRs decreased the C‐use efficiency in the soils and the microbial groups associated with C‐use efficiency; (2) soils in plantations of V. guatemalensis were associated with increased abundances of the DNA of these same microbial groups and enhanced C‐use efficiency; (3) DNA‐based taxonomic analysis of microbes and analysis of the microbial quotient values can be used to monitor soil ecosystems for assessment of the efficacy of restoration activities. Thus, planting V. guatemalensis on damaged lands in the Maquenque National Wildlife Refuge should be encouraged to provide a sustainable forestry crop that can be harvested rotationally, while improving soil ecosystem health and reducing the pressure to harvest other forest sites.
    Keywords conservation areas ; decayed wood ; DNA ; environmental health ; grasslands ; harvesting ; land ownership ; lignin ; nucleotide sequences ; pastures ; plantations ; planting ; saprophytes ; secondary forests ; soil ; soil ecosystems ; soil microorganisms ; soil sampling ; sustainable forestry ; total organic carbon ; Vochysia guatemalensis ; Costa Rica
    Language English
    Dates of publication 2019-11
    Size p. 1263-1273.
    Publishing place Wiley Periodicals, Inc.
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 914746-9
    ISSN 1526-100X ; 1061-2971
    ISSN (online) 1526-100X
    ISSN 1061-2971
    DOI 10.1111/rec.12978
    Database NAL-Catalogue (AGRICOLA)

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  4. Article: Gut Microbial Shifts Indicate Melanoma Presence and Bacterial Interactions in a Murine Model.

    Rossi, Marco / Aspromonte, Salvatore M / Kohlhapp, Frederick J / Newman, Jenna H / Lemenze, Alex / Pepe, Russell J / DeFina, Samuel M / Herzog, Nora L / Donnelly, Robert / Kuzel, Timothy M / Reiser, Jochen / Guevara-Patino, Jose A / Zloza, Andrew

    Diagnostics (Basel, Switzerland)

    2022  Volume 12, Issue 4

    Abstract: Through a multitude of studies, the gut microbiota has been recognized as a significant influencer of both homeostasis and pathophysiology. Certain microbial taxa can even affect treatments such as cancer immunotherapies, including the immune checkpoint ... ...

    Abstract Through a multitude of studies, the gut microbiota has been recognized as a significant influencer of both homeostasis and pathophysiology. Certain microbial taxa can even affect treatments such as cancer immunotherapies, including the immune checkpoint blockade. These taxa can impact such processes both individually as well as collectively through mechanisms from quorum sensing to metabolite production. Due to this overarching presence of the gut microbiota in many physiological processes distal to the GI tract, we hypothesized that mice bearing tumors at extraintestinal sites would display a distinct intestinal microbial signature from non-tumor-bearing mice, and that such a signature would involve taxa that collectively shift with tumor presence. Microbial OTUs were determined from 16S rRNA genes isolated from the fecal samples of C57BL/6 mice challenged with either B16-F10 melanoma cells or PBS control and analyzed using QIIME. Relative proportions of bacteria were determined for each mouse and, using machine-learning approaches, significantly altered taxa and co-occurrence patterns between tumor- and non-tumor-bearing mice were found. Mice with a tumor had elevated proportions of
    Language English
    Publishing date 2022-04-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662336-5
    ISSN 2075-4418
    ISSN 2075-4418
    DOI 10.3390/diagnostics12040958
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Intrabacterial Metabolism Obscures the Successful Prediction of an InhA Inhibitor of

    Wang, Xin / Perryman, Alexander L / Li, Shao-Gang / Paget, Steve D / Stratton, Thomas P / Lemenze, Alex / Olson, Arthur J / Ekins, Sean / Kumar, Pradeep / Freundlich, Joel S

    ACS infectious diseases

    2019  Volume 5, Issue 12, Page(s) 2148–2163

    Abstract: Tuberculosis, caused ... ...

    Abstract Tuberculosis, caused by
    MeSH term(s) Amines/metabolism ; Antitubercular Agents/pharmacology ; Bacterial Proteins/antagonists & inhibitors ; Binding Sites ; High-Throughput Screening Assays ; Ligands ; Molecular Docking Simulation ; Mycobacterium tuberculosis/drug effects ; Mycobacterium tuberculosis/metabolism ; Nitric Oxide/metabolism ; Oxadiazoles/chemistry ; Oxadiazoles/pharmacology ; Oxidoreductases/antagonists & inhibitors ; Protein Conformation
    Chemical Substances Amines ; Antitubercular Agents ; Bacterial Proteins ; Ligands ; Oxadiazoles ; Nitric Oxide (31C4KY9ESH) ; Oxidoreductases (EC 1.-) ; InhA protein, Mycobacterium (EC 1.3.1.9)
    Language English
    Publishing date 2019-11-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2373-8227
    ISSN (online) 2373-8227
    DOI 10.1021/acsinfecdis.9b00295
    Database MEDical Literature Analysis and Retrieval System OnLINE

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