Biology subjects

Bird, L. J.

Publications and source records attributed to Bird, L. J..

4 recordsLinked to original sources

bioRxiv2025

Microbial community of a colloidal activated carbon barrier at a perfluoroalkyl substance impacted site and sorption of perfluorooctanesulfonic acid by bacteria

Per- and polyfluorinated alkyl substances (PFAS) including perfluorooctanesulfonic acid (PFOS) are extremely refractory anthropogenic compounds that are widespread in the environment. Their fate and transport are of increasing interest, including the ways that biological activity may affect the efficiency of state-of-the-art mitigation efforts, such as colloidal activated carbon (CAC) injection. The microbial communities of sediments in and around a CAC barrier from 2.7 to 9 m below surface were investigated using 16S ribosomal RNA amplicon sequencing and strains isolated from the samples. The microbial community consisted of taxa commonly associated with the subsurface environment, including a high proportion of Bathyarchaeota in the deeper samples. The presence of PFAS or the CAC barrier used to treat it affected the microbial community. Bacteria in the order Peptococcales had higher relative abundance in the CAC barrier than upstream or downstream of it. The inverse Simpson index decreased with depth, indicating less variety in the microbes that were present, but was higher in the samples downstream of the CAC barrier, which may indicate an impact of the PFAS on the microbial community. The sorption of PFOS was investigated for six newly isolated strains as well as four other strains, and results indicate that sorption of PFOS by different species or genera of bacteria is more variable than previously thought. These results suggest that the microbial community could play a role in the mobility of PFAS within subsurface waters, and emphasizes the need to understand the subsurface microbial community and its interactions with PFAS.

microbiology↗

bioRxiv2023

Bridging Big Data: Procedures for Combining Non-equivalent Cognitive Measures from the ENIGMA Consortium

Investigators in neuroscience have turned to Big Data to address replication and reliability issues by increasing sample sizes, statistical power, and representativeness of data. These efforts unveil new questions about integrating data arising from distinct sources and instruments. We focus on the most frequently assessed cognitive domain - memory testing - and demonstrate a process for reliable data harmonization across three common measures. We aggregated global raw data from 53 studies totaling N = 10,505 individuals. A mega-analysis was conducted using empirical bayes harmonization to remove site effects, followed by linear models adjusting for common covariates. A continuous item response theory (IRT) model estimated each individuals latent verbal learning ability while accounting for item difficulties. Harmonization significantly reduced inter-site variance while preserving covariate effects, and our conversion tool is freely available online. This demonstrates that large-scale data sharing and harmonization initiatives can address reproducibility and integration challenges across the behavioral sciences. TeaserWe present a global effort to devise harmonization procedures necessary to meaningfully leverage big data.

neuroscience↗

bioRxiv2022

A living conductive marine biofilm engineered to sense and respond to small molecules

Engineered electroactive bacteria have potential applications ranging from sensing to biosynthesis. In order to advance the use of engineered electroactive bacteria, it is important to demonstrate functional expression of electron transfer modules in chassis adapted to operationally relevant conditions, such as non-freshwater environments. Here, we use the Shewanella oneidensis electron transfer pathway to induce current production in a marine bacterium, Marinobacter atlanticus, during biofilm growth in artificial seawater. Genetically encoded sensors optimized for use in E. coli were used to control protein expression in planktonic and biofilm attached cells. Significant current production required addition of menaquinone, which M. atlanticus does not produce, for electron transfer from the inner membrane to the expressed electron transfer pathway. Current through the S. oneidensis pathway in M. atlanticus was observed when inducing molecules were present during biofilm formation. Electron transfer was also reversible, indicating electron transfer into M. atlanticus could be controlled. These results show that an operationally relevant marine bacterium can be genetically engineered for environmental sensing and response using an electrical signal.

microbiology↗

bioRxiv2020

A Prokaryotic Membrane Sculpting BAR Domain Protein

Bin/Amphiphysin/RVS (BAR) domain proteins belong to a superfamily of coiled-coil proteins influencing membrane curvature in eukaryotes and are associated with vesicle biogenesis, vesicle-mediated protein trafficking, and intracellular signaling. Here we report the first prokaryotic BAR domain protein, BdpA, from Shewanella oneidensis MR-1, known to produce redox-active membrane vesicles and micrometer-scale outer membrane extensions (OMEs). BdpA is required for uniform size distribution of membrane vesicles and scaffolding OMEs into a consistent diameter and curvature. Cryogenic transmission electron microscopy reveals a strain lacking BdpA produces lobed, disordered OMEs rather than membrane tubes produced by the wild type strain. Overexpression of BdpA promotes OME formation during conditions where they are less common. Heterologous expression results in OME production in Marinobacter atlanticus and Escherichia coli. Based on the ability of BdpA to alter membrane curvature in vivo, we propose that BdpA and its homologs comprise a newly identified class of prokaryotic BAR (P-BAR) domains.

microbiology↗