Biology subjects

Goddard, A.

Publications and source records attributed to Goddard, A..

4 recordsLinked to original sources

bioRxiv2022

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

Adventitious rooting is critical to the propagation, breeding, and genetic engineering or editing of trees. The capacity for plants to undergo these processes is highly heritable; however, the basis of its genetic variation is largely uncharacterized. To identify genetic regulators of these processes, we performed a genome-wide association study (GWAS) using 1,148 genotypes of Populus trichocarpa. GWAS are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale; to help overcome this limitation, we developed a computer vision system to measure an array of traits related to adventitious root development in poplar, including temporal measures of lateral and basal root length and area. GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics, and to gain statistical power. These analyses yielded a total of 277 unique associations, suggesting that genes that control rooting include regulators of hormone signaling, cell division and structure, and reactive oxygen species signaling. Genes related to other processes with known roles in root development, and numerous genes with uncharacterized functions and/or cryptic roles, were also identified. These candidates provide targets for functional analysis, including physiological and epistatic analyses, to better characterize the complex polygenic regulation of adventitious rooting.

plant biology↗

bioRxiv2022

GWAS identifies candidate regulators of in planta regeneration in Populus trichocarpa

Plant regeneration is an important dimension of plant propagation, and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. While association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover the genetic basis of trait variation in plants, the power of these methods relies on the accuracy and scale of phenotypic data used. To enable a largescale GWAS of in planta regeneration in model tree Populus, we implemented a workflow involving semantic segmentation to quantify regenerating plant tissues (callus and shoot) over time. We found the resulting statistics are of highly non-normal distributions, which necessitated transformations or permutations to avoid violating assumptions of linear models used in GWAS. While transformations can lead to a loss of statistical power, we demonstrate that this can be mitigated by the application of the Augmented Rank Truncation method, or avoided altogether using the Multi-Threaded Monte Carlo SNP-set (Sequence) Kernel Association Test to compute empirical p-values in GWAS. We report over 200 statistically supported candidate genes, with top candidates including regulators of cell adhesion, stress signaling, and hormone signaling pathways, as well as other diverse functions. We demonstrate that sensitive genetic discovery for complex developmental traits can be enabled by a workflow based on computer vision and adaptation of several statistical approaches necessitated by to the complexity of regeneration trait expression and distribution.

plant biology↗

bioRxiv2021

Kinetics of the inflammatory response during experimental Babesia rossi infection of beagle dogs

Babesia rossi causes severe morbidity and mortality in dogs in sub-Saharan Africa, and the complications associated with this disease are likely caused by an unfocused, excessive inflammatory response. During this experimental B. rossi study we investigated inflammatory marker and cytokine kinetics during infection and after treatment. We aimed to determine whether infectious dose and treatment would influence the progression of the inflammatory response and clinical disease. Five healthy male beagle dogs were infected with B. rossi, three with a high infectious dose (HD group) and two with a low infectious dose (LD group). Clinical examination, complete blood count (CBC) and C-reactive protein (CRP) were determined daily. Cytokines were quantified on stored plasma collected during the study, using a canine specific cytokine magnetic bead panel (Milliplex(C)). The experiment was terminated when predetermined endpoints were reached. Parasitemia occurred on day 1 and 3 in the HD group and LD group respectively. The rate of increase in parasitemia in the HD group was significantly faster than that seen in the LD group. Significant differences were found in heart rate, blood pressure, interferon gamma (INF{gamma}), keratinocyte chemoattractant (KC), INF{gamma}-induced protein 10 (IP10), granulocyte-macrophage colony-stimulating factor (GM-CSF), monocyte chemoattractant protein 1 (MCP1), tumor necrosis factor alpha (TNF), interleukin 2 (IL-2), IL-6, IL-7, IL-8, IL-10 IL-15, IL-18, CRP, neutrophils and monocytes between groups at multiple time points during the course of the infection. Our findings suggest that the initiation of inflammation occurs before the onset of clinical disease in B. rossi infection and infectious dose influences the onset of the inflammatory response. Treatment not only fails to curb the inflammatory response but may enhance it. Finally, we found that there is an imbalance in pro/anti-inflammatory cytokine concentrations during infection which may promote parasite replication.

immunology↗

bioRxiv2020

The ammonia oxidizing bacterium Nitrosomonas eutropha D23 blocks T helper 2 cell polarization via IL-10 mediated interference with dendritic cell activation

ABSTRACTThe prevalence of atopic diseases has been steadily increasing since the mid 20th century, a rise that has been linked to modern hygienic lifestyles that limit exposure to microbes and immune system maturation. Overactive type 2 CD4+ helper T (Th2) cells are known to be closely associated with atopy and represent a key target for treatment. In this study, we report that the ammonia oxidizing bacteria (AOB) Nitrosomonas eutropha D23, an environmental microbe that is not associated with human pathology, effectively suppresses the polarization of Th2 cells and production of Th2-associated cytokines (IL-5, IL-13, & IL-4) by human peripheral blood mononuclear cells (PBMC). We show that AOB inhibit Th2 cell polarization not through Th1-mediated suppression, but rather through an IL-10-mediated mechanism that interferes with the activation of dendritic cells, as evidenced by a reduction in Major Histocompatibility Complex Class II (MHC II) and CD86 expression following AOB treatment. This is the first report of immunomodulatory properties of AOB and supports the development of AOB as a potential therapeutic for atopic diseases.GRAPHICAL ABSTRACTCreated with BioRender.comCompeting Interest StatementThe authors were employed by AOBiome Therapeutics at the time of this study; AOBiome Therapeutics is currently investigating the clinical use of AOB for treatment of atopic dermatitis.View Full Text

immunology↗