Biology subjects

Anderson, S. R.

Publications and source records attributed to Anderson, S. R..

12 recordsLinked to original sources

bioRxiv2026

Air-driven aldehyde synthesis in engineered bacteria via gene deletion and aryl-alcohol oxidase profiling

Engineered bacterial routes for oxidation of non-native alcohols face three challenges: Nicotinamide-dependent enzymes are coupled to cellular redox metabolism, nicotinamide-independent aryl-alcohol oxidases (AAOs) usually express poorly in bacteria, and aldehyde products are rapidly modified by host enzymes. Here, we address these limitations by engineering aldehyde-retaining Escherichia coli for discovery and application of soluble bacterial AAOs. Screening 51 candidates revealed a high-expression sequence cluster containing enzymes that are active on diverse aromatic and furan-based alcohols. Pairing the top-performing AAO with designer pathways in aldehyde-retaining cells enabled modular C-N and C-C bond forming cascades starting from supplied alcohols. By making both the oxidase and its product compatible with the host, this work advances air-driven oxidation of diverse alcohols as a programmable entry point to aldehyde-derived chemistry in engineered bacteria.

synthetic biology↗

bioRxiv2026

A genetically encoded reporter reveals interferon responses in multiple cell lineages

Interferons (IFNs) are canonical antiviral cytokines with emerging homeostatic functions across tissues, including in the brain. However, detecting IFN-responsive cells remains challenging, particularly in the immune-restricted brain environment, limiting our understanding of the full breadth of IFN signaling across diverse cell types. Here we developed a novel mouse reporter that detects IFN responses in the brain and peripheral tissues, including in neurons. This tool, IFN-brite, Bright Reporter of Interferon sTimulated gene Expression, has two copies of the fluorophore mGreenLantern downstream of the native Isg15 IFN response gene. We observed IFN responses across multiple cell lineages. Deletion of the Type I interferon receptor Ifnar1 largely abrogated these responses, including to IFN{gamma}, suggesting that Type II signaling can trigger secondary Type I responses. We observed IFN-responsive cells including neurons in a model of ischemic stroke and during experience-dependent neural plasticity. Furthermore, we found that peripheral infection with Sars-CoV2 but not influenza A leads to IFN-responsive neurons in the brain, suggesting differential impacts of these two pathogens in the nervous system. These data define a broadly useful new tool for studying IFN responsive cells and provide evidence that diverse cell types including neurons can respond to IFNs.

immunology↗

bioRxiv2024

A One-Pot Biocatalytic Cascade to Access Diverse L-Phenylalanine Derivatives from Aldehydes or Carboxylic Acids

Non-standard amino acids (nsAAs) that are L-phenylalanine derivatives with aryl ring functionalization have long been harnessed in natural product synthesis, therapeutic peptide synthesis, and diverse applications of genetic code expansion. Yet, to date these chiral molecules have often been the products of poorly enantioselective and environmentally harsh organic synthesis routes. Here, we reveal the broad specificity of multiple natural pyridoxal 5-phosphate (PLP)-dependent enzymes, specifically an L-threonine transaldolase, a phenylserine dehydratase, and an aminotransferase, towards substrates that contain aryl side chains with diverse substitutions. We exploit this tolerance to construct a one-pot biocatalytic cascade that achieves high-yield synthesis of 18 diverse L-phenylalanine derivatives from aldehydes under mild aqueous reaction conditions. We demonstrate addition of a carboxylic acid reductase module to this cascade to enable the biosynthesis of L-phenylalanine derivatives from carboxylic acids that may be less expensive or less reactive than the corresponding aldehydes. Finally, we investigate the scalability of the cascade by developing a lysate-based route for preparative-scale synthesis of 4-formyl-L-phenylalanine, a nsAA with a bio-orthogonal handle that is not readily market-accessible. Overall, this work offers an efficient, versatile, and scalable route with the potential to lower manufacturing cost and democratize synthesis for many valuable nsAAs.

synthetic biology↗

bioRxiv2024

Assessing the effects of warming and carbonate chemistry parameters on marine microbes in the Gulf of Mexico through basin-scale DNA metabarcoding

Ocean acidification and warming threaten marine life, yet the impact of these processes on microbes remains unclear. Here, we performed basin-scale DNA metabarcoding of prokaryotes (16S V4-V5) and protists (18S V9) in the Gulf of Mexico and applied generalized linear models to reveal group-specific environmental correlates of functionally diverse microbes. Models supported prior physiological trends for some groups, like positive temperature effects on SAR11 and SAR86, and a positive effect of pH on Prochlorococcus that implied a negative response to decreasing pH. New insights were revealed for protists, like Syndiniales and Sagenista (e.g., positive pH effects), which offset positive relationships with temperature and reinforced the importance of considering multiple stressors simultaneously. Indicator analysis revealed phytoplankton, like Ostreococcus sp. and Emiliania huxleyi, that were associated with more acidic waters and may reflect candidate indicators of ocean change. Our findings highlight the need for sustained microbial sampling in marine systems, with implications for carbon export, nutrient cycling, and ecosystem health.

microbiology↗

bioRxiv2024

CD11c-expressing microglia are transient, driven by interactions with apoptotic cells

Microglia, the parenchymal macrophage of the central nervous system serve crucial remodeling functions throughout development. Microglia are transcriptionally heterogenous, suggesting that distinct microglial states confer discrete roles. Currently, little is known about how dynamic these states are, the cues that promote them, or how they impact microglial function. In the developing retina, we previously found a significant proportion of microglia express CD11c (Integrin X, complement receptor 4, Itgax) which has also been reported in other developmental and disease contexts. Here, we sought to understand the regulation and function of CD11c+ microglia. We found that CD11c+ microglia track with prominent waves of neuronal apoptosis in postnatal retina. Using genetic fate mapping, we provide evidence that microglia transition out of the CD11c state to return to homeostasis. We show that CD11c+ microglia have elevated lysosomal content and contribute to the clearance of apoptotic neurons, and found that acquisition of CD11c expression is, in part, dependent upon the TAM receptor Axl. Using selective ablation, we found CD11c+ microglia are not uniquely critical for phagocytic clearance of apoptotic cells. Together, our data suggest CD11c+ microglia are a transient state induced by developmental apoptosis rather than a specialized subset mediating phagocytic elimination.

neuroscience↗

bioRxiv2023

Time Tiling of Learned Stimulus-Based Decision Making in Dorsal CA1 in the Hippocampus

Sequential neural dynamics encoded by "time cells" play a crucial role in hippocampal function. However, the role of hippocampal sequential neural dynamics in associative learning is an open question. In this manuscript, we used two-photon Ca2+ imaging of dorsal CA1 pyramidal neurons in head-fixed mice performing a go-no-go associative learning task. We found that pyramidal cells responded differentially to the rewarded or unrewarded stimuli. The stimuli were decoded accurately from the activity of the neuronal ensemble, and accuracy increased substantially as the animal learned to differentiate the stimuli. Decoding the stimulus from individual pyramidal cells that responded differentially revealed that decision-making took place at discrete times after stimulus presentation. Lick prediction decoded from the ensemble activity of cells in dCA1 correlated linearly with lick behavior indicating that sequential activity of pyramidal cells in dCA1 constitutes a temporal memory map used for decision-making in associative learning.

neuroscience↗

bioRxiv2023

Syndiniales parasites drive species networks and are a biomarker for carbon export in the oligotrophic ocean

Microbial associations that result in phytoplankton mortality are important for carbon transport in the ocean. This includes parasitism, which in microbial food webs, is dominated by the marine alveolate group, Syndiniales. Parasites are expected to contribute to carbon recycling via host lysis; however, knowledge on host dynamics and correlation to carbon export remain unclear and limit the inclusion of parasitism in biogeochemical models. We analyzed a 4-year 18S rRNA metabarcoding dataset (2016-2019), performing network analysis for twelve discrete depths (1- 1000 m) to determine Syndiniales-host associations in the seasonally oligotrophic Sargasso Sea. Analogous water column and sediment trap data were included to define environmental drivers of Syndiniales and their correlation with particulate carbon flux (150 m). Syndiniales accounted for 48-74% of network edges, most often associated with Dinophyceae and Arthropoda (mainly copepods) at the surface and Rhizaria (Polycystinea, Acantharea, and RAD-B) in the aphotic zone. Unlike other major groups, Syndiniales were significantly (and negatively) correlated with particulate carbon flux, suggesting parasites may drive flux attenuation through remineralization. Examination of Syndiniales amplicons revealed a range of depth patterns, including specific ecological niches and vertical connection among a subset (19%) of the community, the latter implying sinking of parasites (infected hosts or spores) on particles. Our findings point to the use of Syndiniales as biomarkers of carbon export, highlighting their importance for marine food webs and biogeochemistry. Significance StatementSyndiniales parasites are widespread in the ocean and represent a potentially important, albeit poorly resolved, source of carbon recycling. Here, we assess Syndiniales population dynamics, trophic relationships, and links to carbon export in the Sargasso Sea. Species networks at all depths were driven by Syndiniales, with parasite-host relationships varying with depth based on shifts in host composition. Syndiniales were the only eukaryote group to be significantly (and negatively) correlated with particulate carbon flux, indicating their contribution to flux attenuation via remineralization. Yet, a subset of parasites was vertically connected between photic and aphotic zones, suggesting continued export. Our findings elevate the critical role of Syndiniales in marine microbial systems and reveal their potential use as biomarkers for carbon export.

microbiology↗

bioRxiv2022

Neuronal apoptosis drives remodeling states of microglia and shifts in survival pathway dependence

Microglia serve critical remodeling roles that shape the developing nervous system, responding to the changing neural environment with phagocytosis or soluble factor secretion. Recent single-cell sequencing (scRNAseq) studies have revealed the context-dependent diversity in microglial properties and gene expression, but the cues promoting this diversity are not well defined. Here, we ask how interactions with apoptotic neurons shape microglial state, including lysosomal and lipid metabolism gene expression and independence from Colony-stimulating factor 1 receptor (CSF1R) for survival. Using early postnatal mouse retina, a CNS region undergoing significant developmental remodeling, we performed scRNAseq on microglia from mice that are wild-type, lack neuronal apoptosis (Bax KO), or are treated with CSF1R inhibitor (PLX3397). We find that interactions with apoptotic neurons drives multiple microglial remodeling states, subsets of which are resistant to CSF1R inhibition. We find that TAM receptor Mer and complement receptor 3 are required for clearance of apoptotic neurons, but that Mer does not drive expression of remodeling genes. We show TAM receptor Axl is negligible for phagocytosis or remodeling gene expression but is consequential for microglial survival in the absence of CSF1R signaling. Thus, interactions with apoptotic neurons shift microglia towards distinct remodeling states and through Axl, alters microglial dependence on survival pathway, CSF1R.

neuroscience↗

bioRxiv2021

Tourmaline: a workflow for rapid and reproducible amplicon sequence analysis using QIIME 2 and Snakemake

BackgroundAmplicon sequencing (metabarcoding) is a common method to survey diversity of environmental communities whereby a single genetic locus is amplified and sequenced from the DNA of whole or partial organisms, organismal traces (e.g., skin, mucus, feces), or microbes in an environmental sample. Several software packages exist for analyzing amplicon data, among which QIIME 2 has emerged as a popular option because of its broad functionality, plugin architecture, provenance tracking, and interactive visualizations. However, each new analysis requires the user to keep track of input and output file names, parameters, and commands; this lack of automation and standardization is inefficient and creates barriers to meta-analysis and sharing of results. FindingsWe developed Tourmaline, a Python-based workflow that implements QIIME 2 and is built using the Snakemake workflow management system. Starting from a configuration file that defines parameters and input files--a reference database, a sample metadata file, and a manifest or archive of FASTQ sequences--it uses QIIME 2 to run either the DADA2 or Deblur denoising algorithm, assigns taxonomy to the resulting representative sequences, performs analyses of taxonomic, alpha, and beta diversity, and generates an HTML report summarizing and linking to the output files. Features include support for multiple cores, automatic determination of trimming parameters using quality scores, representative sequence filtering (taxonomy, length, abundance, prevalence, or ID), support for multiple taxonomic classification and sequence alignment methods, outlier detection, and automated initialization of a new analysis using previous settings. The workflow runs natively on Linux and macOS or via a Docker container. We ran Tourmaline on a 16S rRNA amplicon dataset from Lake Erie surface water, showing its utility for parameter optimization and the ability to easily view interactive visualizations through the HTML report, QIIME 2 viewer, and R- and Python-based Jupyter notebooks. ConclusionsAutomated workflows like Tourmaline enable rapid analysis of environmental and biomedical amplicon data, decreasing the time from data generation to actionable results. Tourmaline is available for download at github.com/aomlomics/tourmaline.

bioinformatics↗

bioRxiv2021

Investigating temperature effects on coastal microbial populations and trophic interactions with 16S and 18S rRNA metabarcoding

Temperature is a universal driver of microbial life, with rising sea surface temperatures expected to differentially influence the physiology, biodiversity, and distribution of bacteria and plankton. The impact of ocean warming on microbial interactions remains unclear, despite the importance of these relationships for ecosystem functioning. We employed weekly to monthly 18S and 16S rRNA gene amplicon metabarcoding over a full year (33 d) in a subtropical estuary, investigating microbial population dynamics and network interactions with respect to a temperature gradient (9-31{degrees}C). Certain microbes (e.g., Acidimicrobiia, Nitrososphaeria, and Syndiniales) increased in relative abundance with rising temperatures (Spearman {rho} > 0.69), whereas other groups (e.g., Alpha- and Gammaproteobacteria, Bacillariophyta, and Dinophyceae) slightly decreased, became saturated, or remained stable. With network analysis, we observed an increase in 18S- 18S interactions in warm (23-31{degrees}C) vs. cold (<23{degrees}C) temperatures, largely involving Syndiniales, Bacillariophyta, and Dinophyceae ASVs. Bacteria ASVs were more connected to other microbes (higher degree and centrality) and became more prominent in the cold network, highlighted by well-established cross-domain relationships (e.g., diatom-bacteria) and positive interactions among bacteria (e.g., SAR11 and Rhodobacterales). These efforts highlight the types of interactions that may be more common under changing temperatures, with implications for modeling biogeochemistry and assessing ecosystem health.

ecology↗

bioRxiv2018

Complement C3-targeted gene therapy restricts onset and progression of neurodegeneration in chronic mouse glaucoma

Dysregulation of the complement system is implicated in neurodegeneration, including human and animal glaucoma. Optic nerve and retinal damage in glaucoma is preceded by local complement upregulation and activation, but whether targeting this early innate immune response could have therapeutic benefit remains undefined. Because complement signals through three pathways that intersect at complement C3 activation, here we targeted this step to restore complement balance in the glaucomatous retina, and to determine its contribution to degeneration onset and/or progression. To achieve this, we combined adeno-associated viral retinal gene therapy with the targeted C3 inhibitor CR2-Crry. We show that intravitreal injection of AAV2.CR2-Crry produced sustained Crry overexpression in the retina, and reduced deposition of the activation product complement C3d on retinal ganglion cells and the inner retina of DBA/2J mice. This resulted in neuroprotection of retinal ganglion cell axons and somata despite continued intraocular pressure elevation, suggesting a direct restriction of neurodegeneration onset and progression, and significant delay to terminal disease stages. Our study uncovers a damaging effect of complement C3 or downstream complement activation in glaucoma and establishes AAV2.CR2-Crry as a viable therapeutic strategy to target pathogenic C3-mediated complement activation in the glaucomatous retina.

neuroscience↗

bioRxiv2017

The Prevalence And Benefits Of Admixture During Species Invasions: A Role For Epistasis?

Species introductions often bring together genetically divergent source populations, resulting in genetic admixture. This geographic reshuffling of diversity has the potential to generate favorable new genetic combinations, facilitating the establishment and invasive spread of introduced populations. Observational support for the superior performance of admixed introductions has been mixed, however, and the broad importance of admixture to invasion questioned. Under most underlying mechanisms, admixtures benefits should be expected to increasewith greater divergence among and lower genetic diversity within source populations. We use a literature survey to quantify the prevalence of admixture and evaluate whether it occurrs under circumstances predicted to be mostbeneficial to introduced species. We find that 39% of species are reported to be admixed when introduced. Admixed introductions come from sources with a wide range of genetic variation, but are disproportionately absent where there is high genetic divergence among native populations. We discuss multiple potential explanations for these patterns, but note that negative epistatic interactions should be expected at high divergence amongpopulations (outbreeding depression). As a case study, we experimentally cross source populations differing in divergence in the invasive plant Centaurea solstitialis. We find many positive (heterotic) interactions, but fitness benefits decline and are ultimately negative at high source divergence, with patterns suggestingcyto-nuclear epistasis. We conclude that admixture is common in species introductions and often happens under conditions expected to be beneficial to invaders, but that these conditions may be constrained by predictable negativegenetic interactions, potentially explaining conflicting evidence for admixture's benefits to invasion.

evolutionary biology↗