Biology subjects

Moore, S. D.

Publications and source records attributed to Moore, S. D..

6 recordsLinked to original sources

bioRxiv2026

qPyCR: A qPCR Data Analyzer for Template Quantification and the Detection of Performance Outliers

Motivation: Real-time qPCR data are commonly analyzed to obtain a Cq values, which are used to compare the relative abundance of a targeted template. However, improper background subtraction distorts Cq and changing the assigned threshold can alter experimental conclusions. In addition, a Cq values provide no information on the quality of the qPCR for a given sample. Alternatively, global fitting of qPCR data provides agnostic quantification without the use of Cq or thresholds, and the fitting terms provide a useful metric of reaction performance. Current implementations of global fitting are limited to custom in-house programs. Results: qPyCR is comprehensive analysis tool written in Python that performs background signal subtractions, computes a threshold, and reports Cq values in a traditional manner. The program also performs global fitting and reports template abundances along with reaction quality values. The quality values can be used to assign performance standards, which allow researchers to distinguish aberrant reactions from true changes in template abundance. Availability and Implementation: Code and example data are freely available on GitHub (https://github.com/sdmoore-labs/qPyCR) and on Zenodo (https://doi.org/10.5281/zenodo.21115342).

bioinformatics↗

bioRxiv2026

Acute Increase of Excitatory Activity in Pyramidal Neurons of Rat Motor Cortex under Static Magnetic Field

ObjectivesTranscranial application of a static magnetic field (SMF) was reported to result in subsequent modulation of neural excitability in the human motor cortex, but the acute mechanisms underlying this effect are unknown. We explore the mechanisms of this phenomenon with patch-clamp recording in rat brain slices during SMF exposure. Materials and MethodsPatch-clamp recording from layer II/III pyramidal neurons in motor cortex of acutely prepared brain slices were conducted during exposure to 0.20-0.35 T SMF or sham. ResultsDuring SMF exposure we observed an increase in the frequency of spontaneous excitatory postsynaptic currents (sEPSCs) as well as miniature excitatory post-synaptic currents (mEPSCs) recorded in the presence of TTX to suppress action potentials and thus also network effects. There was a significant acute increase in sEPSC frequency for SMF exposure duration of both 6 min and 10 min, but not for 10 min sham exposure. After SMF exposure, the sEPSC and mEPSC frequency returned to baseline. The frequency of spontaneous inhibitory postsynaptic currents (sIPSCs) was unaffected by SMF. The amplitude of the postsynaptic currents decreased with time for all recordings regardless of the condition, presumably due to the expected gradual deterioration of the patch clamp seal. ConclusionsThe acute effect of SMF exposure on sEPSC and mEPSC frequency, but not amplitude, is consistent with the assumption of a presynaptic or synaptic site mediating the effect. Furthermore, the consistency of the effect between sEPSCs and mEPSCs suggests that the effect is not related to action potential propagation in the presynaptic axon. The effect of SMF on EPSCs and not IPSCs may be related to the larger length of excitatory axons compared to inhibitory axons, or to effects on extracellular ionic gradients within the slice.

bioengineering↗

bioRxiv2022

Reduced ribosome activity influences the non-uniform evolution of 16S rRNA hypervariable regions

16S rRNA gene sequences are commonly analyzed for taxonomic and phylogenetic studies because they contain hypervariable regions that can help distinguish different genera. However, intra-genus distinction is often difficult due to high sequence identities among closely related species. Although common tools for 16S sequence taxonomic classification weight residue variations equally during comparisons, specific residues within hypervariable regions have not drifted evenly through evolution, suggesting that portions of them may be biologically important. We developed an in vivo test system where 16S variants coexisted among natural ribosome populations which allowed their fitness to be evaluated. We found that versions with evolutionarily disparate hypervariable regions were underpopulated in ribosomes and active translation pools, even for a single nucleotide polymorphism (SNP), which indicates functional constraints to the free evolutionary drift of hypervariable regions. Using an in silico method (positional relative entropy), we analyzed over 12,000 16S V3-V4 sequences across Escherichia and Shigella strains and identified species that can be distinguished by position-specific SNPs present in multiple 16S alleles in a genome. When we evaluated these informative SNPs with our in vivo system, we discovered that ribosomes harboring them were compromised, suggesting that their evolution is indeed biologically constrained. Overall, this study demonstrates that SNPs within hypervariable regions are not necessarily inconsequential and that common computational approaches for taxonomic 16S rRNA sequence classification should not assume an even probability of residues at each position. ImportanceHypervariable regions within 16S rRNA genes are commonly analyzed to determine microbial diversity. However, because sequences within a genus are highly similar, strain- or species-specific identification is often uncertain. Because there are no established functions of hypervariable regions, residue variations within them are often evenly weighted when making taxonomic comparisons. This study established that 16S rRNAs with naturally occurring variations in hypervariable regions can affect ribosome quality, indicating that their residues should not be weighted equally during taxonomic sequence classifications.

microbiology↗

bioRxiv2021

Microbial communities in retail draft beers and the biofilms they produce

In the beer brewing industry, microbial spoilage presents a consistent threat that must be monitored and controlled to ensure the palatability of a finished product. Many of the predominant beer spoilage microbes have been identified and characterized, but the mechanisms of contamination and persistence remain an open area of study. Post-production, many beers are distributed as kegs that are attached to draft delivery systems in retail settings where ample opportunities for microbial spoilage are present. As such, restaurants and bars can experience substantial costs and downtime for cleaning when beer draft lines become heavily contaminated. Spoilage monitoring on the retail side of the beer industry is often overlooked, yet this arena may represent one of the largest threats to the profitability of a beer if its flavor profile becomes substantially distorted. In this study, we sampled and cultured microbial communities found in beers dispensed from a retail draft system to identify the contaminating bacteria and yeasts. We also evaluated their capability to establish new biofilms in a controlled setting. Among four tested beer types, we identified over a hundred different contaminant bacteria and nearly twenty wild yeasts. The culturing experiments demonstrated that most of these microbes were viable and capable of joining new biofilm communities. From these data, we provide an important starting point for the efficient monitoring of beer spoilage in draft systems and provide suggestions for cleaning protocol improvements that can benefit the retail community. ImportanceBeer production, packaging, and service are each vulnerable to contamination by microbes that metabolize beer chemicals and impart undesirable flavors, which can result in the disposal of entire batches. Therefore, great effort is taken by brewmasters to reduce and monitor contamination during production and packaging. A commonly overlooked quality control stage of a beer supply chain is at the retail service end, where beer kegs supply draft lines in bars and restaurants under non-sterile conditions. We found that retail draft line contamination is rampant and that routine line cleaning methods are insufficient to efficiently suppress beer spoilage. Thus, many customers unknowingly experience spoiled versions of the beers they consume. This study identified the bacteria and yeast that were resident in draft beer samples and also assessed their abilities to colonize tubing material as members of stable biofilm communities.

microbiology↗

bioRxiv2021

Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about known gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a ten-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills. Significance StatementThe primary scientific literature catalogs the results from publicly funded scientific research about gene function in human-readable format. Information captured from those studies in a widely adopted, machine-readable standard format comes in the form of Gene Ontology annotations about gene functions from all domains of life. Manual annotations based on inferences directly from the scientific literature, including the evidence used to make such inferences, represents the best return on investment by improving data accessibility across the biological sciences. To supplement professional curation, our CACAO project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in contribution of thousands of validated entries to public resources. These annotations are now being used by scientists worldwide.

bioinformatics↗

bioRxiv2020

RNA-Seq data analysis of a rodent model of adolescent binge drinking reveals pathways and candidate genes involved in neuronal remodeling and neuroimmune activation

IntroductionBinge drinking is common among adolescents and young adults and is associated with an increased risk of developing alcohol use disorder (AUD) and long-term cognitive deficits. We analyzed RNA-seq data from male Sprague Dawley rats to identify candidate genes that may play a role in the acute and chronic changes in cognitive function during binge-like adolescent alcohol/EtOH exposure and after a period of abstinence. MethodsAt postnatal day (PND) 30, male rats received chronic intermittent EtOH across 16 days. RNA was extracted from hippocampal tissue and sequenced at two acute timepoints, PND 35 and PND 46, and after 24 days forced abstinence (PND 70). We processed RNA-seq data, compiled gene counts, and performed normalization and differential expression analysis (DESeq2). Gene set enrichment analysis was performed through the R package fgsea. Gene sets of the Molecular Signatures Database (MSigDB) collections were used to identify gene pathways that were dysregulated following EtOH exposure. We also evaluated overlapping gene pathways that were affected across all timepoints. ResultsMultiple gene pathway analyses revealed that EtOH has robust effects on neuroinflammation, cellular remodeling, sleep, and bioenergetics. Changes were heavily dependent on whether gene expression was assessed during acute EtOH exposure or after abstinence. Genes involved in sleep regulation were selectively impacted during the acute timepoints, whereas dysregulation of genes involved in bioenergetics were only impacted after abstinence. The most striking changes occurred in genes that regulate neuroinflammatory processes and cellular remodeling. ConclusionThese data reveal acute and chronic effects of EtOH on multiple gene pathways that persist across analytic approaches and identify genes that have increased sensitivity to EtOH. These findings contribute to our understanding of the temporal effects of adolescent EtOH exposure and how gene pathway dysregulation contributes to the protracted emergence of neuronal remodeling in the hippocampus during a critical period of brain maturation.

bioinformatics↗