Peredo Elena L.

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Elena L.

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Now showing 1 - 5 of 5
  • Article
    Extraction of high-quality, high-molecular-weight DNA depends heavily on cell homogenization methods in green microalgae
    (Wiley Open Access, 2020-03-10) Stark, Jordan R. ; Cardon, Zoe G. ; Peredo, Elena L.
    Premise New sequencing technologies have facilitated genomic studies in green microalgae; however, extracting high‐quality DNA is often a bottleneck for long‐read sequencing. Methods and Results Here, we present a low‐cost, highly transferrable method for the extraction of high‐molecular‐weight (HMW), high‐purity DNA from microalgae. We first determined the effect of sample preparation on DNA quality using three homogenization methods: manual grinding using a mini‐pestle, automatic grinding using a vortex adapter, and grinding in liquid nitrogen. We demonstrated the versatility of grinding in liquid nitrogen followed by a modified cetyltrimethylammonium bromide (CTAB) extraction across a suite of aquatic‐ and desert‐evolved algal taxa. Finally, we tested the protocol's robustness by doubling the input material to increase yield, producing per sample up to 20 μg of high‐purity DNA longer than 21.2 kbp. Conclusions All homogenization methods produced DNA within acceptable parameters for purity, but only liquid nitrogen grinding resulted in HMW DNA. The optimization of cell lysis while minimizing DNA shearing is therefore crucial for the isolation of DNA for long‐read genomic sequencing because template DNA length strongly affects read output and length.
  • Article
    Najas flexilis (Hydrocharitaceae) in Alaska : a reassessment
    (New England Botanical Club, 2015-09-23) Les, Donald H. ; Les, Angela M. ; King, Ursula M. ; Peredo, Elena L.
    Fifteen Najas flexilis collections were made in Alaska during the summer of 2012, with 13 of the stations representing either new or formerly undocumented localities for this imperiled Alaskan species. These field collections characterize the Alaskan habitats of N. flexilis as shallow water sites (<1.5 m) with sand-dominated substrates (71% of sites) and have documented an additional 28 species associates (a 300% increase). However, the additional collections have not extended the elevational, latitudinal, or longitudinal extent of N. flexilis from the limits indicated by previous Alaskan collections. Najas flexilis remains rare in Alaska as evidenced by a low specimen recovery rate (10%) from potentially suitable sites, and a total of only 12 geographically distinct localities known across the entire state. The new collections have furnished valuable study material for morphological and genetic analyses, which have confirmed the identity of Alaskan populations as N. flexilis, rather than N. canadensis, a recently identified, cryptic, allotetraploid derivative. A synthesis of information indicates that N. flexilis is indigenous to Alaska, where it originated via past (versus recent) migrations from other North American rather than Old World populations.
  • Article
    Leaf-FISH : microscale imaging of bacterial taxa on phyllosphere
    (Frontiers Media, 2018-01-09) Peredo, Elena L. ; Simmons, Sheri L.
    Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents.
  • Article
    A model suite of green algae within the Scenedesmaceae for investigating contrasting desiccation tolerance and morphology
    (The Company of Biologists, 2018-04-10) Cardon, Zoe G. ; Peredo, Elena L. ; Dohnalkova, Alice C. ; Gershone, Hannah L. ; Bezanilla, Magdalena
    Microscopic green algae inhabiting desert microbiotic crusts are remarkably diverse phylogenetically, and many desert lineages have independently evolved from aquatic ancestors. Here we worked with five desert and aquatic species within the family Scenedesmaceae to examine mechanisms that underlie desiccation tolerance and release of unicellular versus multicellular progeny. Live cell staining and time-lapse confocal imaging coupled with transmission electron microscopy established that the desert and aquatic species all divide by multiple (rather than binary) fission, although progeny were unicellular in three species and multicellular (joined in a sheet-like coenobium) in two. During division, Golgi complexes were localized near nuclei, and all species exhibited dynamic rotation of the daughter cell mass within the mother cell wall at cytokinesis. Differential desiccation tolerance across the five species, assessed from photosynthetic efficiency during desiccation/rehydration cycles, was accompanied by differential accumulation of intracellular reactive oxygen species (ROS) detected using a dye sensitive to intracellular ROS. Further comparative investigation will aim to understand the genetic, ultrastructural and physiological characteristics supporting unicellular versus multicellular coenobial morphology, and the ability of representatives in the Scenedesmaceae to colonize ecologically diverse, even extreme, habitats.
  • Article
    Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae
    (National Academy of Sciences, 2020-07-21) Peredo, Elena L. ; Cardon, Zoe G.
    Among green plants, desiccation tolerance is common in seeds and spores but rare in leaves and other vegetative green tissues. Over the last two decades, genes have been identified whose expression is induced by desiccation in diverse, desiccation-tolerant (DT) taxa, including, e.g., late embryogenesis abundant proteins (LEA) and reactive oxygen species scavengers. This up-regulation is observed in DT resurrection plants, mosses, and green algae most closely related to these Embryophytes. Here we test whether this same suite of protective genes is up-regulated during desiccation in even more distantly related DT green algae, and, importantly, whether that up-regulation is unique to DT algae or also occurs in a desiccation-intolerant relative. We used three closely related aquatic and desert-derived green microalgae in the family Scenedesmaceae and capitalized on extraordinary desiccation tolerance in two of the species, contrasting with desiccation intolerance in the third. We found that during desiccation, all three species increased expression of common protective genes. The feature distinguishing gene expression in DT algae, however, was extensive down-regulation of gene expression associated with diverse metabolic processes during the desiccation time course, suggesting a switch from active growth to energy-saving metabolism. This widespread downshift did not occur in the desiccation-intolerant taxon. These results show that desiccation-induced up-regulation of expression of protective genes may be necessary but is not sufficient to confer desiccation tolerance. The data also suggest that desiccation tolerance may require induced protective mechanisms operating in concert with massive down-regulation of gene expression controlling numerous other aspects of metabolism.