Michael A. Grillo
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View article: Training Generalized Segmentation Networks with Real and Synthetic Cryo-ET data
Training Generalized Segmentation Networks with Real and Synthetic Cryo-ET data Open
Deep learning excels at segmenting objects within noisy cryo-electron tomograms, but the approach is typically bottlenecked by access to ground truth training data. To address this issue we have developed CryoTomoSim (CTS), an open-source …
View article: Floral traits underlying mating system differentiation in the wind-pollinated sister species <i>Oryza rufipogon</i> and <i>Oryza nivara</i>
Floral traits underlying mating system differentiation in the wind-pollinated sister species <i>Oryza rufipogon</i> and <i>Oryza nivara</i> Open
The shift from outcrossing to predominantly selfing is one of the most common transitions in plant evolution. This evolutionary shift has received considerable attention from biologists; however, this work has almost exclusively been focus…
View article: Conventional management has a greater negative impact on Phaseolus vulgaris L. rhizobia diversity and abundance than water scarcity
Conventional management has a greater negative impact on Phaseolus vulgaris L. rhizobia diversity and abundance than water scarcity Open
Introduction Drought is one of the biggest problems for crop production and also affects the survival and persistence of soil rhizobia, which limits the establishment of efficient symbiosis and endangers the productivity of legumes, the ma…
View article: Extensive local geographic variation in locoweed toxin produced by a fungal endophyte
Extensive local geographic variation in locoweed toxin produced by a fungal endophyte Open
Legumes are notorious for coevolutionary arms races where chemical defenses are employed to ward off herbivores—particularly insect seed predators. Locoweeds are a group of plants containing the toxic alkaloid swainsonine which can poison …
View article: Farm management has a greater impact on common bean rhizobia diversity and abundance than rainfed treatment
Farm management has a greater impact on common bean rhizobia diversity and abundance than rainfed treatment Open
Drought is one of the biggest problems for crop production and affects the survival and persistence of soil rhizobia. The reduced presence of rhizobia limits the establishment of symbiosis and endangers the productivity of legumes, which i…
View article: Fragment-Based NMR Screening of the BPTF PHD Finger Methyl Lysine Reader Leads to the First Small Molecule Inhibitors
Fragment-Based NMR Screening of the BPTF PHD Finger Methyl Lysine Reader Leads to the First Small Molecule Inhibitors Open
Methyl lysine readers, specifically PHD fingers, are emerging epigenetic targets in human diseases. For example, several PHD finger fusions are implicated in clinical cases of acute myeloid leukemia, highlighting the potential for PHD inhi…
View article: Agrochemical inputs and management have a greater impact on common bean rhizobia diversity than drought
Agrochemical inputs and management have a greater impact on common bean rhizobia diversity than drought Open
Drought is one of the biggest problems for crop production and also affects the survival and persistence of soil rhizobia. The reduced presence of rhizobia limits the establishment of symbiosis and endangers the productivity of legumes, th…
View article: Rapid Synthesis of Cryo-ET Data for Training Deep Learning Models
Rapid Synthesis of Cryo-ET Data for Training Deep Learning Models Open
Deep learning excels at cryo-tomographic image restoration and segmentation tasks but is hindered by a lack of training data. Here we introduce cryo-TomoSim (CTS), a MATLAB-based software package that builds coarse-grained models of macrom…
View article: Deep Learning-Based Segmentation of Cryo-Electron Tomograms
Deep Learning-Based Segmentation of Cryo-Electron Tomograms Open
Cryo-electron tomography (cryo-ET) allows researchers to image cells in their native, hydrated state at the highest resolution currently possible. The technique has several limitations, however, that make analyzing the data it generates ti…
View article: Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes
Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes Open
Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the e…
View article: Discordant population structure among rhizobium divided genomes and their legume hosts
Discordant population structure among rhizobium divided genomes and their legume hosts Open
Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. …
View article: Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis
Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis Open
The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhiz…
View article: Discordant population structure within rhizobium divided genomes and between rhizobia and legume hosts in their native range
Discordant population structure within rhizobium divided genomes and between rhizobia and legume hosts in their native range Open
Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Bacterial symbionts often have genomes comprised of multiple replicons with distinct rates of evolution and horizontal transmissio…
View article: Partners in space: Discordant population structure between legume hosts and rhizobium symbionts in their native range
Partners in space: Discordant population structure between legume hosts and rhizobium symbionts in their native range Open
Coevolution is predicted to depend on how the genetic diversity of interacting species is geographically structured. Plant-microbe symbioses such as the legume-rhizobium mutualism are ecologically and economically important, but distinct l…
View article: Cofilin Regulates Filopodial Structure and Flexibility in Neuronal Growth Cones
Cofilin Regulates Filopodial Structure and Flexibility in Neuronal Growth Cones Open
Cofilin is best known for its ability to sever actin filaments, and facilitate cytoskeletal recycling inside of cells. At higher concentrations, in vitro , cofilin stabilizes a more flexible, hyper-twisted state of actin known as “cofilact…
View article: Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes
Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes Open
A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research a…
View article: Ultrastructural Analysis of Cytoskeletal Networks in Neuronal Growth Cones by Light and Electron Microscopy
Ultrastructural Analysis of Cytoskeletal Networks in Neuronal Growth Cones by Light and Electron Microscopy Open
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View article: Partners in space: Discordant population structure between legume hosts and rhizobium symbionts in their native range
Partners in space: Discordant population structure between legume hosts and rhizobium symbionts in their native range Open
Coevolution is predicted to depend on how the genetic diversity of interacting species is geographically structured. Plant-microbe symbioses such as the legume-rhizobium mutualism are ecologically and economically important, but distinct l…
View article: Neurodegeneration, Neuroprotection and Regeneration in the Zebrafish Retina
Neurodegeneration, Neuroprotection and Regeneration in the Zebrafish Retina Open
Neurodegenerative retinal diseases, such as glaucoma and diabetic retinopathy, involve a gradual loss of neurons in the retina as the disease progresses. Central nervous system neurons are not able to regenerate in mammals, therefore, an o…
View article: Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula
Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula Open
Background Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form …
View article: Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula
Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula Open
Background Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form …
View article: Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula
Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula Open
Background: Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form…
View article: Additional file 10 of Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula
Additional file 10 of Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula Open
Additional file 10: Table S7 Sequencing and Assembly Information for Metagenomic Samples. Count of sequences per sample before and after quality control, as well as count of sequences considered plant sequences and Ensifer sequences for ea…
View article: Additional file 9 of Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula
Additional file 9 of Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula Open
Additional file 9:. Table S6 Primer and MID sequence information for 16S rRNA gene amplicon sequencing, with sample identifications. MIDs and forward primer (515f) were used for secondary PCR reactions.
View article: Additional file 1 of Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula
Additional file 1 of Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula Open
Additional file 1:. Table S1 Full matrix of sequence counts for OTUs (retained) with sample identification. Listed in sample name are soil location (C – Corsica; F – France), genotype (1, 27, 96), replication number (a, b, c, d, e), and pl…
View article: Additional file 7 of Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula
Additional file 7 of Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula Open
Additional file 7: Table S5 Results of BLASTn identification of all demarcated Ensifer MED nodes. Where these MED nodes best matched Ensifer sp. or our OTU1 representative sequence, full blast results are also presented. The four nodes tha…
View article: Additional file 5 of Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula
Additional file 5 of Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula Open
Additional file 5:. Table S3 Core OTUs with taxonomy found within nodule communities across sampling design, an OTU was defined as core if present in >50% nodule samples