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  1. Article ; Online: Photoacoustic imaging provides an in vivo assessment of the preeclamptic placenta remodeling and function in response to therapy.

    Lawrence, Dylan J / Bayer, Carolyn L

    Placenta

    2022  Volume 126, Page(s) 46–53

    Abstract: Introduction: There is a lack of effective therapeutic interventions for preeclampsia. A central factor in the etiology of the disease is the development of placental hypoxia due to abnormal vascular remodeling. However, methods to assess the impact of ... ...

    Abstract Introduction: There is a lack of effective therapeutic interventions for preeclampsia. A central factor in the etiology of the disease is the development of placental hypoxia due to abnormal vascular remodeling. However, methods to assess the impact of potential therapies on placental growth and remodeling are currently lacking. Here, we develop and validate ultrasound-guided photoacoustic imaging methods to monitor the placental response to therapeutic intervention. Establishing non-invasive tools to image placental function opens up previously unachievable understandings of placental therapeutic response.
    Methods: Studies were performed in the reduced uterine perfusion pressure (RUPP) rat model of preeclampsia. Preclinical research has identified tempol, a superoxide dismutase mimetic, and the phosphodiesterase inhibitor sildenafil as potential therapeutics for preeclampsia, as both improve in vivo maternal outcomes. PA images of the placental environment were acquired in RUPP rats receiving tempol (n = 8) or sildenafil (n = 8) to assess the longitudinal effects of treatment on placental oxygenation and vascular remodeling. Imaging measurements were validated with ex vivo histological analysis.
    Results: Spectral photoacoustic imaging non-invasively measured placental hypoxia and impaired vascular growth two days after the RUPP procedure was implemented. Sildenafil significantly improved (p < 0.05) placental oxygenation and promoted vascular remodeling in RUPP animals, while RUPP animals treated with tempol had a diminished placental therapeutic response.
    Discussion: We demonstrate that photoacoustic imaging provides in vivo measures of placental oxygenation and vascular remodeling, a previously unobtainable assessment of preeclamptic therapeutic response. These imaging tools have tremendous potential to accelerate the search for effective therapies for preeclampsia.
    MeSH term(s) Animals ; Disease Models, Animal ; Female ; Humans ; Hypoxia ; Ischemia ; Photoacoustic Techniques/adverse effects ; Placenta/blood supply ; Pre-Eclampsia/diagnostic imaging ; Pre-Eclampsia/drug therapy ; Pre-Eclampsia/etiology ; Pregnancy ; Rats ; Rats, Sprague-Dawley ; Sildenafil Citrate/pharmacology ; Vascular Remodeling
    Chemical Substances Sildenafil Citrate (BW9B0ZE037)
    Language English
    Publishing date 2022-06-21
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 603951-0
    ISSN 1532-3102 ; 0143-4004
    ISSN (online) 1532-3102
    ISSN 0143-4004
    DOI 10.1016/j.placenta.2022.06.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Extracellular vesicles and their effect on vascular haemodynamics: a systematic review.

    Cheung, Sharon W Y / Chamley, Lawrence W / Barrett, Carolyn J / Lau, Sien Yee S

    Hypertension research : official journal of the Japanese Society of Hypertension

    2024  

    Abstract: Extracellular vesicles (EVs) are released from all cell types studied to date and act as intercellular communicators containing proteins, nucleic acids and lipid cargos. They have been shown to be involved in maintaining homoeostasis as well as playing a ...

    Abstract Extracellular vesicles (EVs) are released from all cell types studied to date and act as intercellular communicators containing proteins, nucleic acids and lipid cargos. They have been shown to be involved in maintaining homoeostasis as well as playing a role in the development of pathology including hypertension and cardiovascular disease. It is estimated that there is 10
    Language English
    Publishing date 2024-04-10
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1175297-x
    ISSN 1348-4214 ; 0916-9636
    ISSN (online) 1348-4214
    ISSN 0916-9636
    DOI 10.1038/s41440-024-01659-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: In vivo noninvasive systemic myography of acute systemic vasoactivity in female pregnant mice.

    Huda, Kristie / Lawrence, Dylan J / Thompson, Weylan / Lindsey, Sarah H / Bayer, Carolyn L

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 6286

    Abstract: Altered vasoactivity is a major characteristic of cardiovascular and oncological diseases, and many therapies are therefore targeted to the vasculature. Therapeutics which are selective for the diseased vasculature are ideal, but whole-body selectivity ... ...

    Abstract Altered vasoactivity is a major characteristic of cardiovascular and oncological diseases, and many therapies are therefore targeted to the vasculature. Therapeutics which are selective for the diseased vasculature are ideal, but whole-body selectivity of a therapeutic is challenging to assess in practice. Vessel myography is used to determine the functional mechanisms and evaluate pharmacological responses of vascularly-targeted therapeutics. However, myography can only be performed on ex vivo sections of individual arteries. We have developed methods for implementation of spherical-view photoacoustic tomography for non-invasive and in vivo myography. Using photoacoustic tomography, we demonstrate the measurement of acute vascular reactivity in the systemic vasculature and the placenta of female pregnant mice in response to two vasodilators. Photoacoustic tomography simultaneously captures the significant acute vasodilation of major arteries and detects selective vasoactivity of the maternal-fetal vasculature. Photoacoustic tomography has the potential to provide invaluable preclinical information on vascular response that cannot be obtained by other established methods.
    MeSH term(s) Pregnancy ; Mice ; Female ; Animals ; Arteries/diagnostic imaging ; Arteries/physiology ; Vasodilator Agents ; Vasodilation/physiology ; Placenta/diagnostic imaging ; Myography/methods
    Chemical Substances Vasodilator Agents
    Language English
    Publishing date 2023-10-09
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-42041-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: In vivo noninvasive systemic myography of acute systemic vasoactivity in female pregnant mice

    Kristie Huda / Dylan J. Lawrence / Weylan Thompson / Sarah H. Lindsey / Carolyn L. Bayer

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 10

    Abstract: Abstract Altered vasoactivity is a major characteristic of cardiovascular and oncological diseases, and many therapies are therefore targeted to the vasculature. Therapeutics which are selective for the diseased vasculature are ideal, but whole-body ... ...

    Abstract Abstract Altered vasoactivity is a major characteristic of cardiovascular and oncological diseases, and many therapies are therefore targeted to the vasculature. Therapeutics which are selective for the diseased vasculature are ideal, but whole-body selectivity of a therapeutic is challenging to assess in practice. Vessel myography is used to determine the functional mechanisms and evaluate pharmacological responses of vascularly-targeted therapeutics. However, myography can only be performed on ex vivo sections of individual arteries. We have developed methods for implementation of spherical-view photoacoustic tomography for non-invasive and in vivo myography. Using photoacoustic tomography, we demonstrate the measurement of acute vascular reactivity in the systemic vasculature and the placenta of female pregnant mice in response to two vasodilators. Photoacoustic tomography simultaneously captures the significant acute vasodilation of major arteries and detects selective vasoactivity of the maternal-fetal vasculature. Photoacoustic tomography has the potential to provide invaluable preclinical information on vascular response that cannot be obtained by other established methods.
    Keywords Science ; Q
    Subject code 610
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Gene function annotations for the maize NAM founder lines.

    Fattel, Leila / Yanarella, Colleen F / Ngara, Blessing / Johnson, Olivia T / Campbell, Darwin A / Wimalanathan, Kokulapalan / Lawrence-Dill, Carolyn J

    BMC research notes

    2024  Volume 17, Issue 1, Page(s) 9

    Abstract: Objectives: We annotated the latest published sequences of the 26 Zea mays Nested Association Mapping (NAM) founder lines using GOMAP, the Gene Ontology Meta Annotator for Plants. The maize NAM panel enables researchers to understand and identify the ... ...

    Abstract Objectives: We annotated the latest published sequences of the 26 Zea mays Nested Association Mapping (NAM) founder lines using GOMAP, the Gene Ontology Meta Annotator for Plants. The maize NAM panel enables researchers to understand and identify the genetic basis of complex traits. Annotations of predicted functions for genes can help researchers investigate gene-phenotype associations, prioritize candidate genes for phenotypes of interest, and formulate testable hypotheses about gene function/phenotype associations. The creation and release of high-confidence, high-coverage gene function annotation sets for the NAM founder lines is critical to accelerate the generation of knowledge in maize genetics research. GOMAP is a high-throughput computational pipeline that annotates gene functions genome-wide in plant genomes using Gene Ontology functional class terms. Here we report and share GOMAP-generated functional annotations for the NAM founder lines.
    Data description: Datasets include the protein sequences used as input, GOMAP-generated annotation files, scripts used to update obsolete terms, and GAF-formatted tab-delimited text files of gene function annotations along with README files that describe formatting, content, and how files relate to each other.
    MeSH term(s) Zea mays/genetics ; Genome, Plant/genetics ; Phenotype
    Language English
    Publishing date 2024-01-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2413336-X
    ISSN 1756-0500 ; 1756-0500
    ISSN (online) 1756-0500
    ISSN 1756-0500
    DOI 10.1186/s13104-023-06668-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Gene function annotations for the maize NAM founder lines

    Leila Fattel / Colleen F. Yanarella / Blessing Ngara / Olivia T. Johnson / Darwin A. Campbell / Kokulapalan Wimalanathan / Carolyn J. Lawrence-Dill

    BMC Research Notes, Vol 17, Iss 1, Pp 1-

    2024  Volume 5

    Abstract: Abstract Objectives We annotated the latest published sequences of the 26 Zea mays Nested Association Mapping (NAM) founder lines using GOMAP, the Gene Ontology Meta Annotator for Plants. The maize NAM panel enables researchers to understand and identify ...

    Abstract Abstract Objectives We annotated the latest published sequences of the 26 Zea mays Nested Association Mapping (NAM) founder lines using GOMAP, the Gene Ontology Meta Annotator for Plants. The maize NAM panel enables researchers to understand and identify the genetic basis of complex traits. Annotations of predicted functions for genes can help researchers investigate gene-phenotype associations, prioritize candidate genes for phenotypes of interest, and formulate testable hypotheses about gene function/phenotype associations. The creation and release of high-confidence, high-coverage gene function annotation sets for the NAM founder lines is critical to accelerate the generation of knowledge in maize genetics research. GOMAP is a high-throughput computational pipeline that annotates gene functions genome-wide in plant genomes using Gene Ontology functional class terms. Here we report and share GOMAP-generated functional annotations for the NAM founder lines. Data description Datasets include the protein sequences used as input, GOMAP-generated annotation files, scripts used to update obsolete terms, and GAF-formatted tab-delimited text files of gene function annotations along with README files that describe formatting, content, and how files relate to each other.
    Keywords Maize ; GOMAP ; Genomics ; NAM ; GO ; Gene function ; Medicine ; R ; Biology (General) ; QH301-705.5 ; Science (General) ; Q1-390
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Gene Ontology Meta Annotator for Plants (GOMAP).

    Wimalanathan, Kokulapalan / Lawrence-Dill, Carolyn J

    Plant methods

    2021  Volume 17, Issue 1, Page(s) 54

    Abstract: Annotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment ... ...

    Abstract Annotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions. The Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation of plants. We containerized GOMAP to increase portability and reproducibility and also optimized its performance for HPC environments. Here we report on the pipeline's availability and performance for annotating large, repetitive plant genomes and describe how GOMAP was used to annotate multiple maize genomes as a test case. Assessment shows that GOMAP expands and improves the number of genes annotated and annotations assigned per gene as well as the quality (based on [Formula: see text]) of GO assignments in maize. GOMAP has been deployed to annotate other species including wheat, rice, barley, cotton, and soy. Instructions and access to the GOMAP Singularity container are freely available online at https://bioinformapping.com/gomap/ . A list of annotated genomes and links to data is maintained at https://dill-picl.org/projects/gomap/ .
    Language English
    Publishing date 2021-05-25
    Publishing country England
    Document type Journal Article
    ISSN 1746-4811
    ISSN 1746-4811
    DOI 10.1186/s13007-021-00754-1
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  8. Article ; Online: Gene Ontology Meta Annotator for Plants (GOMAP)

    Kokulapalan Wimalanathan / Carolyn J. Lawrence-Dill

    Plant Methods, Vol 17, Iss 1, Pp 1-

    2021  Volume 14

    Abstract: Abstract Annotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO ... ...

    Abstract Abstract Annotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions. The Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation of plants. We containerized GOMAP to increase portability and reproducibility and also optimized its performance for HPC environments. Here we report on the pipeline’s availability and performance for annotating large, repetitive plant genomes and describe how GOMAP was used to annotate multiple maize genomes as a test case. Assessment shows that GOMAP expands and improves the number of genes annotated and annotations assigned per gene as well as the quality (based on $$F_{max}$$ F max ) of GO assignments in maize. GOMAP has been deployed to annotate other species including wheat, rice, barley, cotton, and soy. Instructions and access to the GOMAP Singularity container are freely available online at https://bioinformapping.com/gomap/ . A list of annotated genomes and links to data is maintained at https://dill-picl.org/projects/gomap/ .
    Keywords Functional annotation ; Gene ontology ; CAFA ; Plant genomes ; Plant culture ; SB1-1110 ; Biology (General) ; QH301-705.5
    Subject code 580
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Longitudinal characterization of local perfusion of the rat placenta using contrast-enhanced ultrasound imaging.

    Lawrence, Dylan J / Huda, Kristie / Bayer, Carolyn L

    Interface focus

    2019  Volume 9, Issue 5, Page(s) 20190024

    Abstract: The placenta performs many physiological functions critical for development. Insufficient placental perfusion, due to improper vascular remodelling, has been linked to many pregnancy-related diseases. To study ... ...

    Abstract The placenta performs many physiological functions critical for development. Insufficient placental perfusion, due to improper vascular remodelling, has been linked to many pregnancy-related diseases. To study longitudinal
    Language English
    Publishing date 2019-08-16
    Publishing country England
    Document type Journal Article
    ISSN 2042-8898
    ISSN 2042-8898
    DOI 10.1098/rsfs.2019.0024
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Automated Methods Enable Direct Computation on Phenotypic Descriptions for Novel Candidate Gene Prediction.

    Braun, Ian R / Lawrence-Dill, Carolyn J

    Frontiers in plant science

    2020  Volume 10, Page(s) 1629

    Abstract: Natural language descriptions of plant phenotypes are a rich source of information for genetics and genomics research. We computationally translated descriptions of plant phenotypes into structured representations that can be analyzed to identify ... ...

    Abstract Natural language descriptions of plant phenotypes are a rich source of information for genetics and genomics research. We computationally translated descriptions of plant phenotypes into structured representations that can be analyzed to identify biologically meaningful associations. These representations include the entity-quality (EQ) formalism, which uses terms from biological ontologies to represent phenotypes in a standardized, semantically rich format, as well as numerical vector representations generated using natural language processing (NLP) methods (such as the bag-of-words approach and document embedding). We compared resulting phenotype similarity measures to those derived from manually curated data to determine the performance of each method. Computationally derived EQ and vector representations were comparably successful in recapitulating biological truth to representations created through manual EQ statement curation. Moreover, NLP methods for generating vector representations of phenotypes are scalable to large quantities of text because they require no human input. These results indicate that it is now possible to computationally and automatically produce and populate large-scale information resources that enable researchers to query phenotypic descriptions directly.
    Language English
    Publishing date 2020-01-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2019.01629
    Database MEDical Literature Analysis and Retrieval System OnLINE

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