Juan I. Bravo
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View article: A multi-omics analysis of human fibroblasts overexpressing an Alu transposon reveals widespread disruptions in aging-associated pathways
A multi-omics analysis of human fibroblasts overexpressing an Alu transposon reveals widespread disruptions in aging-associated pathways Open
During aging and cellular senescence, repetitive elements are frequently transcriptionally derepressed across species and cell types. Among these, the most abundant repeats by copy number in the human genome are Alu retrotransposons. Thoug…
View article: A multi-omics analysis of human fibroblasts overexpressing an <i>Alu</i> transposon reveals widespread disruptions in aging-associated pathways
A multi-omics analysis of human fibroblasts overexpressing an <i>Alu</i> transposon reveals widespread disruptions in aging-associated pathways Open
During aging and cellular senescence, repetitive elements are frequently transcriptionally derepressed across species and cell types. Among these, the most abundant repeats by copy number in the human genome are Alu retrotransposons. Thoug…
View article: Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers
Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers Open
LINE-1 (L1) and Alu are two families of transposable elements (TEs) occupying ~17% and ~11% of the human genome, respectively. Though only a small fraction of L1 copies is able to produce the machinery to mobilize autonomously, Alu and deg…
View article: Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers
Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers Open
LINE-1 (L1) and Alu are two families of transposable elements (TEs) occupying ∼17% and ∼11% of the human genome, respectively. Though only a small fraction of L1 copies is able to produce the machinery to mobilize autonomously, Alu and deg…
View article: An eQTL-based approach reveals candidate regulators of LINE-1 RNA levels in lymphoblastoid cells
An eQTL-based approach reveals candidate regulators of LINE-1 RNA levels in lymphoblastoid cells Open
Long interspersed element 1 (LINE-1; L1) are a family of transposons that occupy ~17% of the human genome. Though a small number of L1 copies remain capable of autonomous transposition, the overwhelming majority of copies are degenerate an…
View article: An eQTL-based Approach Reveals Candidate Regulators of LINE-1 RNA Levels in Lymphoblastoid Cells
An eQTL-based Approach Reveals Candidate Regulators of LINE-1 RNA Levels in Lymphoblastoid Cells Open
Long interspersed element 1 (L1) are a family of autonomous, actively mobile transposons that occupy ∼17% of the human genome. A number of pleiotropic effects induced by L1 (promoting genome instability, inflammation, or cellular senescenc…
View article: Population and comparative genetics of thermotolerance divergence between yeast species
Population and comparative genetics of thermotolerance divergence between yeast species Open
Many familiar traits in the natural world—from lions’ manes to the longevity of bristlecone pine trees—arose in the distant past, and have long since fixed in their respective species. A key challenge in evolutionary genetics is to figure …
View article: Protocol for isolation of adult mouse ear pinnae-derived primary fibroblasts
Protocol for isolation of adult mouse ear pinnae-derived primary fibroblasts Open
Researchers need in vitro models that mirror the biology of organisms. Primary fibroblasts play essential roles in wound healing and are present in many tissues. They are widely used in studies of cell cycle control, reprogramming, and agi…
View article: Purity of Primary Mouse Ear/Pinnae-derived Fibroblasts
Purity of Primary Mouse Ear/Pinnae-derived Fibroblasts Open
Primary fibroblasts were extracted from the ears/pinnae of three young C57BL/6 mice of each sex (male and female) from the NIA. Cells were frozen at the end of passage 3 and then thawed for analysis by flow cytometry. As a control, cells f…
View article: Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation
Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation Open
Our understanding of the molecular regulation of aging and age-related diseases is still in its infancy, requiring in-depth characterization of the molecular landscape shaping these complex phenotypes. Emerging classes of molecules with pr…
View article: Remodeling of the H3 nucleosomal landscape during mouse aging
Remodeling of the H3 nucleosomal landscape during mouse aging Open
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and deregulation of gene expression correlates with aging. A key layer in the study of gene regulation me…
View article: Remodeling of the H3 nucleosomal landscape during mouse aging
Remodeling of the H3 nucleosomal landscape during mouse aging Open
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and deregulation of gene expression correlates with aging. A key layer in the study of gene regulation me…
View article: Bacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in a Rhizosphere Model System
Bacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in a Rhizosphere Model System Open
The microbiomes of plants are critical to host physiology and development. Microbes are attracted to the rhizosphere due to massive secretion of plant photosynthates from roots. Microorganisms that successfully join the rhizosphere communi…
View article: Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior
Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior Open
The manipulation and engineering of microbiomes could lead to improved human health, environmental sustainability, and agricultural productivity. However, microbiomes have proven difficult to alter in predictable ways, and their emergent p…
View article: Multi-level remodeling of transcriptional landscapes in aging and longevity
Multi-level remodeling of transcriptional landscapes in aging and longevity Open
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and gene expression has been observed to be deregulated with aging. In this review, we discuss the curren…
View article: Introducing THOR, a model microbiome for genetic dissection of community behavior
Introducing THOR, a model microbiome for genetic dissection of community behavior Open
The quest to manipulate microbiomes has intensified, but many microbial communities have proven recalcitrant to sustained change. Developing model communities amenable to genetic dissection will underpin successful strategies for shaping m…
View article: Bacterial analogs of plant piperidine alkaloids mediate microbial interactions in a rhizosphere model system
Bacterial analogs of plant piperidine alkaloids mediate microbial interactions in a rhizosphere model system Open
Plants expend significant resources to select and maintain rhizosphere communities that benefit their growth and protect them from pathogens. A better understanding of assembly and function of rhizosphere microbial communities will provide…
View article: Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere
Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere Open
Pseudomonas koreensis CI12 was coisolated with Bacillus cereus from a root of a soybean plant grown in a field in Arlington, WI. Here, we report the draft genome sequence of P. koreensis CI12 obtained by Illumina sequencing.
View article: Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere
Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere Open
Flavobacterium johnsoniae CI04 was coisolated with Bacillus cereus from a root of a field-grown soybean plant in Arlington, WI, and selected as a model for studying commensalism between members of the Cytophaga-Flavobacterium-Bacteroides g…