Jessica Audrey Lee

NASA · Ames Research Center

We present CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation), an extension of CFDEM®Coupling to model biological flows, growth, and mass transfer in artificial microgravity devices. For microbes that accompany humans into space, microgravity-induced alterations in the fluid environment are likely to be a major f...

Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well-studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously...

Pink-pigmented facultative methylotrophs have long been studied for their ability to grow on reduced single-carbon (C1) compounds. The C1 groups that support methylotrophic growth may come from a variety of sources. Here, we describe a group of Methylobacterium strains that can engage in methoxydotrophy: they can metabolize the methoxy groups from...

Pink-pigmented facultative methylotrophs have long been studied for their ability to grow on reduced single-carbon (C1) compounds. The C1 groups that support methylotrophic growth may come from a variety of sources. Here, we describe a group of Methylobacterium strains that can engage in methoxydotrophy: they can metabolize the methoxy groups from...

Methylothon is an inquiry-based high school learning module in microbial ecology, molecular biology, and bioinformatics that centers around pink-pigmented plant-associated methylotrophic bacteria. Here we present an overview of the module's learning goals, describe course resources (available for public use on http://methylothon.com), and relate le...

Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such as Methylorubrum extorquens face an acute challenge due to their production of formaldehyde as an obligate central int...

For bacteria to thrive they must be well-adapted to their environmental niche, which may involve specialized metabolism, timely adaptation to shifting environments, and/or the ability to mitigate numerous stressors. These attributes are highly dependent on cellular machinery that can sense both the external and intracellular environment. Methylorub...

The recalcitrance of complex organic polymers such as lignocellulose is one of the major obstacles to sustainable energy production from plant biomass, and the generation of toxic intermediates can negatively impact the efficiency of microbial lignocellulose degradation. Here, we describe the development of a model microbial consortium for studying...

Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such as Methylorubrum extorquens face an acute challenge due to their production of formaldehyde as an obligate central int...

All spacecraft sent to the Moon carry viable microorganisms with them. Historical measurements and recent mathematical models predict that even after the effect of space exposure and, in some cases, high-velocity impact, most deliver a bioburden of thousands to millions of cells each to the Moon. While it is widely assumed that no life can withstan...

While microbiologists often make the simplifying assumption that genotype determines phenotype in a given environment, it is becoming increasingly apparent that phenotypic heterogeneity (in which one genotype generates multiple phenotypes simultaneously even in a uniform environment) is common in many microbial populations. The importance of phenot...

While microbiologists often make the simplifying assumption that genotype determines phenotype in a given environment, it is becoming increasingly apparent that phenotypic heterogeneity (in which one genotype generates multiple phenotypes simultaneously even in a uniform environment) is common in many microbial populations. The importance of phenot...

Denitrification is a dominant nitrogen loss process in the sediments of San Francisco Bay. In this study, we sought to understand the ecology of denitrifying bacteria by using next-generation sequencing (NGS) to survey the diversity of a denitrification functional gene, nirS (encoding cytchrome-cd1 nitrite reductase), along the salinity gradient of...

Rice is an important staple for over half the world's population, and silicon (Si) is a vital nutrient that helps to improve yields through its role in alleviating biotic and abiotic stresses. Despite Si being abundant in crustal materials, it is only slowly released to soil pore-waters through chemical weathering. However, biocycling of Si through...

Charcoal fragments from five historic campsite locations in the Galápagos Islands were identified and radiocarbon dated to investigate postulated early human presence in the archipelago, historic fuel wood collection patterns and the resultant impact on native vegetation. A variety of taxa and fuel types were revealed to be present in the charcoal...

Saprotrophic woodland fungi form self-organised transport networks as they forage for resources across the forest floor. These networks adapt during development by selective reinforcement of major transport routes and recycling of the intervening redundant mycelium to support further extension. The predicted transport performance of the resulting w...

Transport networks are vital components of multi-cellular organisms, distributing nutrients and removing waste products. Animal cardiovascular and respiratory systems, and plant vasculature, are branching trees whose architecture is thought to determine universal scaling laws in these organisms. In contrast, the transport systems of many multi-cell...

Oceanic phages are critical components of the global ecosystem, where they play a role in microbial mortality and evolution. Our understanding of phage diversity is greatly limited by the lack of useful genetic diversity measures. Previous studies, focusing on myophages that infect the marine cyanobacterium Synechococcus, have used the coliphage T4...

On Mar 14, 2011 this sequence version replaced gi:189397306.

On Mar 14, 2011 this sequence version replaced gi:189397276.

Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic machinery during infection. To study the prevalence...

Phylogenetic Analyses Including All psbA Gene Sequences from Cultured Cyanobacteria and Cyanophages Phages are listed by phage name, followed by their original host. Host range information is designated in parentheses. Phages known to infect both Prochlorococcus and Synechococcus hosts are indicated with a “Δ”; phages that infect only Prochlor...

Neighbor-Nets Analysis of 50 psbD Gene Sequences (including All Cyanophage and Marine Cyanobacterial Sequences Available) Taxa color coding and abbreviations are as in Figure S1. Details of the analysis are as in Figure S3. (249 KB PDF)

Consensus Results from Four Tests for Intragenic Recombination within Gene Sequences in Our psbA Dataset The four tests included (1) RDP, (2) GeneConv, (3) MaxChi, and (4) Chimaera (as described in Materials and Methods), and recombination was considered “detected” only when the following criteria were satisfied: (i) similar regions were detecte...

Phylogenetic Analyses Including All psbD Gene Sequences from Cultured Cyanobacteria and Cyanophages Details are as in Figure S1. (59 KB PPT)

Neighbor-Nets Analysis of 80 psbA Gene Sequences (including All Cyanophage and Marine Cyanobacterial Sequences Available) The analysis was conducted under the HKY85 model of substitution using all codon positions. Taxa color coding and abbreviations are as in Figure S1. The box-like appearance in the basal branches of this phylogeny suggests reg...

Consensus Results from Four Tests for Intragenic Recombination within Gene Sequences in Our psbD Dataset Details are as in Table S1. (28 KB XLS)

Likelihood Ratio Tests for Nonstationary Frequencies among Lineages H 0 denotes the null hypothesis of stationary nucleotide frequencies; this was modeled by specifying one set of nucleotide frequencies for all branches of the tree. H 1 denotes the alternative hypothesis of nonstationary nucleotide frequencies; this was modeled by assigning all bra...

PCR Conditions (38 KB DOC)

PCR Primers (39 KB DOC)

Likelihood Ratio Tests for Variable Evolutionary Rates among Branches For both psbA and psbD, individual sequences exhibiting a signature for intragenic recombination ( Tables S1 and S2) were excluded from analysis. Likelihood scores were obtained under a stationary HKY85 model combined with a gamma correction for among-sites rate variation. All...

Likelihood-Based Statistical Comparison of Competing Evolutionary Hypotheses under a Model of Nonstationary Nucleotide Frequencies P KH denotes the p-value for the KH normal test of [ 83]. P SH denotes the p-value for the SH test [ 84]. P RELL denotes the RELL bootstrap proportion [ 83]. Note that although Tree 1 and Tree 2 were not selected i...