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  1. Article: Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing.

    Marrella, Mackenzie A / Biase, Fernando H

    Journal of animal science and biotechnology

    2023  Volume 14, Issue 1, Page(s) 62

    Abstract: Background: A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait, and expression quantitative trait loci (eQTL) studies provide important information to help close that gap. However, two concerns that ... ...

    Abstract Background: A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait, and expression quantitative trait loci (eQTL) studies provide important information to help close that gap. However, two concerns that arise with eQTL analyses using RNA-sequencing data are normalization of data across samples and the data not following a normal distribution. Multiple pipelines have been suggested to address this. For instance, the most recent analysis of the human and farm Genotype-Tissue Expression (GTEx) project proposes using trimmed means of M-values (TMM) to normalize the data followed by an inverse normal transformation.
    Results: In this study, we reasoned that eQTL analysis could be carried out using the same framework used for differential gene expression (DGE), which uses a negative binomial model, a statistical test feasible for count data. Using the GTEx framework, we identified 35 significant eQTLs (P < 5 × 10
    Conclusions: Our results show that transforming RNA-sequencing data to fit a normal distribution prior to eQTL analysis is not required when the DGE framework is employed. Our proposed approach detected biologically relevant variants that otherwise would not have been identified due to data transformation to fit a normal distribution.
    Language English
    Publishing date 2023-05-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2630162-3
    ISSN 2049-1891 ; 1674-9782
    ISSN (online) 2049-1891
    ISSN 1674-9782
    DOI 10.1186/s40104-023-00861-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A multi-omics analysis identifies molecular features associated with fertility in heifers (Bos taurus).

    Marrella, Mackenzie A / Biase, Fernando H

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 12664

    Abstract: Infertility or subfertility is a critical barrier to sustainable cattle production, including in heifers. The development of heifers that do not produce a calf within an optimum window of time is a critical factor for the profitability and sustainability ...

    Abstract Infertility or subfertility is a critical barrier to sustainable cattle production, including in heifers. The development of heifers that do not produce a calf within an optimum window of time is a critical factor for the profitability and sustainability of the cattle industry. In parallel, heifers are an excellent biomedical model for understanding the underlying etiology of infertility because well-nourished heifers can still be infertile, mostly because of inherent physiological and genetic causes. Using a high-density single nucleotide polymorphism (SNP) chip, we collected genotypic data, which were analyzed using an association analysis in PLINK with Fisher's exact test. We also produced quantitative transcriptome data and proteome data. Transcriptome data were analyzed using the quasi-likelihood test followed by the Wald's test, and the likelihood test and proteome data were analyzed using a generalized mixed model and Student's t-test. We identified two SNPs significantly associated with heifer fertility (rs110918927, chr12: 85648422, P = 6.7 × 10
    MeSH term(s) Cattle ; Female ; Animals ; Multiomics ; Proteome ; Fertility/genetics ; Infertility ; Genotype
    Chemical Substances Proteome
    Language English
    Publishing date 2023-08-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-39858-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Cleavage kinetics is a better indicator of embryonic developmental competency than brilliant cresyl blue staining of oocytes.

    Nix, Jada / Marrella, Mackenzie A / Oliver, Mary Ali / Ealy, Alan D / Biase, Fernando H

    Animal reproduction science

    2022  Volume 248, Page(s) 107174

    Abstract: In vitro production of embryos (IVP) is a valuable technology to produce embryos of high genetic value. Despite advances in IVP, the efficiency of culture systems remains low. One method to increase IVP success is the early selection of oocytes or ... ...

    Abstract In vitro production of embryos (IVP) is a valuable technology to produce embryos of high genetic value. Despite advances in IVP, the efficiency of culture systems remains low. One method to increase IVP success is the early selection of oocytes or embryos that may have greater developmental potential. Here, we investigated two methods of selection, namely BCB staining and cleavage kinetics, both individually and in conjunction, for improved developmental outcomes in vitro. We hypothesized that a synergistic use of both BCB staining and cleavage kinetics would result in identification of embryos of greater developmental potential. The selection of oocytes by BCB staining does select for those oocytes with higher developmental potential, as noted by a greater blastocyst development between BCB positive (32.6%) and BCB negative (22.0%) on day 8 post-fertilization. However, the utilization of BCB staining and cleavage kinetics in tandem resulted in a complete masking of the effect observed when using BCB alone. We obtained the highest proportion of blastocyst development per selection group using cleavage kinetics alone, in which 53.1% of embryos grouped as Fast produced a blastocyst, which was significantly different from the three other groups (Fast+, Slow, not cleaved). We observed, however, that the separation of embryos by cleavage kinetics did not predict their survival to cryopreservation. In conclusion, in standard culture systems, cleavage kinetics is an effective method for the selection of embryos with increased developmental potential to develop blastocysts, however, it may not be effective to select healthy embryos for transfer following cryopreservation.
    Language English
    Publishing date 2022-12-07
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 429674-6
    ISSN 1873-2232 ; 0378-4320
    ISSN (online) 1873-2232
    ISSN 0378-4320
    DOI 10.1016/j.anireprosci.2022.107174
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Tight gene co-expression in BCB positive cattle oocytes and their surrounding cumulus cells.

    Walker, Bailey N / Nix, Jada / Wilson, Chace / Marrella, Mackenzie A / Speckhart, Savannah L / Wooldridge, Lydia / Yen, Con-Ning / Bodmer, Jocelyn S / Kirkpatrick, Laila T / Moorey, Sarah E / Gerrard, David E / Ealy, Alan D / Biase, Fernando H

    Reproductive biology and endocrinology : RB&E

    2022  Volume 20, Issue 1, Page(s) 119

    Abstract: Background: Cytoplasmic and nuclear maturation of oocytes, as well as interaction with the surrounding cumulus cells, are important features relevant to the acquisition of developmental competence.: Methods: Here, we utilized Brilliant cresyl blue ( ... ...

    Abstract Background: Cytoplasmic and nuclear maturation of oocytes, as well as interaction with the surrounding cumulus cells, are important features relevant to the acquisition of developmental competence.
    Methods: Here, we utilized Brilliant cresyl blue (BCB) to distinguish cattle oocytes with low activity of the enzyme Glucose-6-Phosphate Dehydrogenase, and thus separated fully grown (BCB positive) oocytes from those in the growing phase (BCB negative). We then analyzed the developmental potential of these oocytes, mitochondrial DNA (mtDNA) copy number in single oocytes, and investigated the transcriptome of single oocytes and their surrounding cumulus cells of BCB positive versus BCB negative oocytes.
    Results: The BCB positive oocytes were twice as likely to produce a blastocyst in vitro compared to BCB- oocytes (P < 0.01). We determined that BCB negative oocytes have 1.3-fold more mtDNA copies than BCB positive oocytes (P = 0.004). There was no differential transcript abundance of genes expressed in oocytes, however, 172 genes were identified in cumulus cells with differential transcript abundance (FDR < 0.05) based on the BCB staining of their oocyte. Co-expression analysis between oocytes and their surrounding cumulus cells revealed a subset of genes whose co-expression in BCB positive oocytes (n = 75) and their surrounding cumulus cells (n = 108) compose a unique profile of the cumulus-oocyte complex.
    Conclusions: If oocytes transition from BCB negative to BCB positive, there is a greater likelihood of producing a blastocyst, and a reduction of mtDNA copies, but there is no systematic variation of transcript abundance. Cumulus cells present changes in transcript abundance, which reflects in a dynamic co-expression between the oocyte and cumulus cells.
    MeSH term(s) Animals ; Blastocyst ; Cattle ; Cumulus Cells ; Cytoplasm ; DNA, Mitochondrial/genetics ; Female ; Oocytes
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2022-08-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 2119215-7
    ISSN 1477-7827 ; 1477-7827
    ISSN (online) 1477-7827
    ISSN 1477-7827
    DOI 10.1186/s12958-022-00994-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Comparison of reproductive performance of AI- and natural service-sired beef females under commercial management.

    Marrella, Mackenzie A / White, Robin R / Dias, Nicholas W / Timlin, Claire / Pancini, Stefania / Currin, J / Clark, Sherrie / Stewart, Jamie L / Mercadante, Vitor R G / Bradford, Heather L

    Translational animal science

    2021  Volume 5, Issue 3, Page(s) txab114

    Abstract: The objective of this study was to assess differences in reproductive performance of natural service and artificial insemination ( ...

    Abstract The objective of this study was to assess differences in reproductive performance of natural service and artificial insemination (
    Language English
    Publishing date 2021-06-30
    Publishing country England
    Document type Journal Article
    ISSN 2573-2102
    ISSN (online) 2573-2102
    DOI 10.1093/tas/txab114
    Database MEDical Literature Analysis and Retrieval System OnLINE

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