Biology subjects

Graham, K. E.

Publications and source records attributed to Graham, K. E..

6 recordsLinked to original sources

bioRxiv2025

Viral adsorption to Moore swabs in passive wastewater sampling

Moore swabs have been used extensively for passive sampling in wastewater surveillance, typically yielding presence/absence information for targets of interest. Quantitative analysis of Moore swab data is only possible if target uptake is well characterized, specifically the relationship between quantity of the target in the liquid sample matrix and the quantity of target sorbing to the Moore swab as a function of time. The mechanism of Moore swab absorption remains unclear and is important to understand toward using them more quantitatively. We conducted viral adsorption and desorption experiments using nonpathogenic SARS-CoV-2 surrogates: {Phi}6, MHV, and BCoV as well as heat-inactivated Zika virus (ZIKV). We fit empirical adsorption data from batch experiments to Langmuir, Freundlich and Redlich-Peterson isotherm models. We observed the adsorption behavior of viral targets onto Moore swabs is best characterized by the Redlich-Peterson isotherm model. Moore swabs retained the highest viral RNA concentrations after exposure durations between 9-12 hours in the presence of target microbes during kinetic viral adsorption experiments. The results inform current and future use of Moore swabs to produce quantitative data during wastewater surveillance, especially in settings where composite sampling remains infeasible. ImportanceThis paper describes the adsorption behavior of viruses and bacteriophages to Moore swabs. Passive sampling via Moore swabs is among the most scalable form of passive wastewater sampling, considered critical to advance wastewater surveillance globally. But key unknowns constrain the utility of Moore swabs and all passive sampling approaches, including the quantitative relationship between targets in wastewater and recovery via Moore swabs. Practical questions such as how long they should be deployed and whether they can be interpreted quantitatively really depend on a characterization of viral target loading behaviors on Moore swab material as a function of time and concentration in the wastewater. Here, we use an approach that is seldom applied to microbial targets to examine adsorption behavior of viruses to Moore swabs, deriving isotherms that describe the relationships between concentration of the viral targets in wastewater and time on attachment to swab material. This is a critical step in advancing the application of Moore swab passive sampling for wastewater surveillance, with potential relevance to other microbial targets of interest.

microbiology↗

bioRxiv2025

Decay and Solid-Liquid Partitioning of Mpox and Vaccinia Viruses in Primary Influent and Settled Solids to Guide Wastewater-Based Epidemiology Practices

Wastewater-based epidemiology (WBE) has proven to be a powerful tool for tracking the spread of viral pathogens, such as SARS-CoV-2, but as WBE has expanded to include new pathogens, such as mpox virus, more data is needed to guide practitioners on how to design WBE campaigns. Here, we investigated the decay rates of heat-inactivated mpox (HI-MPXV) and attenuated vaccinia virus (VV) in primary influent and settled solids collected from a local POTW at 4{degrees}C, 22{degrees}C, or 35{degrees}C using digital PCR. Subsequently, we studied the solid-liquid partitioning of the viruses in primary influent. Over the 30-day study period, we observed no significant difference in log-linear decay rates between viruses (p=0.5258), with significantly higher decay rates in primary influent (0.109-0.144/day) compared to settled solids (0.019-0.040/day) at both 22{degrees}C (p=0.0030) and 35{degrees}C (p=0.0166). Furthermore, as part of the partitioning experiment, we found that HI-MPXV and VV adsorb to the solids fraction of primary influent at higher intensities than previously studied enveloped viruses (KF = 1,000-31,800 mL/g, n = 1.01-1.41). Likewise, it was determined in the partitioning experiment that a concentration of greater than 103 gc/mL in raw influent was needed for the viable quantification of mpox and vaccinia viruses in the clarified liquid fraction of raw primarily influent. Our study provides essential insights into informative sample collection and storage conditions for the analysis of wastewater and for transport modeling studies. Due to the slow decay observed in settled solids at all tested temperatures in the persistence experiment, this matrix may be most suitable for retrospective analyses of community infection of the mpox virus.

microbiology↗

bioRxiv2024

Predictability of next elements in chimpanzee gesture sequences

Recent research has produced evidence for basic combinatorial abilities in the vocal systems of different animal species. Here, we investigate the structure of gesture sequences in Eastern chimpanzees (Pan troglodytes schweinfurthii) to detect whether gestural communication shows non-random combinations and how combinatorial rules influence predictability. Gesture, as compared to vocalization, offers greater flexibility in how signals are combined--for example overlapping in time -- and as the parsing of signals into sequences is dependent on researcher decisions, we employ a multiverse approach, considering four different definitions of what constitutes a sequence based on varying time thresholds. Our results indicate that sequences tend to be short (even with the most liberal time-window) and that transitions between some gesture types occur more frequently than expected by chance, with some transitions showing significant association across all time-windows. These transitions often involve repetition, suggesting persistence as a key aspect of chimpanzee gestural sequences. Information about previous gestures reduced uncertainty in predicting subsequent gestures. The order of gestures within sequences appears to be less critical than their cooccurrence, challenging assumptions based on the linear patterning derived from vocal communication. Our findings highlight the importance of methodological choices in sequence definition and suggest that chimpanzee gestural communication is characterised by a mix of predictability and flexibility, with implications for understanding the evolution of complex communication systems.

animal behavior and cognition↗

bioRxiv2024

Advancing source tracking: systematic review and source-specific genome database curation of fecally shed prokaryotes

Approaches for shotgun metagenomic sequencing are being adapted to many environmental monitoring tasks but remain poorly suited for source attribution within fecal source tracking (FST) studies due to a lack of knowledge regarding the source specificity of fecally shed microbial populations. To address this gap, we performed a systematic literature review and curated a large collection of genomes (n=26,018) representing fecally shed prokaryotic species across broad and narrow source categories commonly implicated in FST studies of recreational waters (i.e., cats, dogs, cows, seagulls, chickens, pigs, birds, ruminants, human feces, and wastewater). These data include genome sequences recovered from metagenomic and isolation-based studies which we examined extensively with comparative genomic approaches to characterize trends across source categories and produce a finalized genome database for each source category which is available online (n=12,730). We find that across these sources, the total number of genomes recovered varies substantially: from none in seagulls to 9,085 in pigs. According to available data, on average 81% of the genomes representing species-level populations occur only within a single source. Using fecal slurries to test the performance of each source database, we report read capture rates that vary with fecal source alpha diversity and database size. Lastly, while extensive work has been performed on the rumen system of cows and other ruminants, we note the scarcity of genomic characterization of prokaryotes in the feces of these animals. We expect this resource to be useful to FST-related objectives, One Health research, and sanitation efforts globally. Table of Contents Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/598882v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@daeadcorg.highwire.dtl.DTLVardef@713d09org.highwire.dtl.DTLVardef@5e538borg.highwire.dtl.DTLVardef@bed833_HPS_FORMAT_FIGEXP M_FIG C_FIG SynopsisWe curate nine prokaryotic genomic databases for fecal source-tracking, summarize their source-specificity, and show their usefulness by bioinformatically testing mock impaired surface water samples.

bioinformatics↗

bioRxiv2023

Many morphs: parsing gesture signals from the noise

Parsing signals from noise is a general problem for signallers and recipients, as well as for researchers studying communicative systems. Substantial research efforts have been invested in comparing how other species encode information and meaning in their signals, and how signalling is structured. However, our ability to do so depends on identifying and discriminating signals that represent meaningful units of analysis. Early approaches to defining signal repertoires applied top- down approaches, classifying cases into predefined signal types. Recently, more labour-intensive methods have taken a bottom-up approach describing the features of each signal in detail and clustering cases into types based on patterns of similarity between them in multi-dimensional feature-space that were previously undetectable. Nevertheless, it remains essential to assess whether the resulting repertoires are composed of relevant units from the perspective of the species using them, and redefining repertoires when additional data makes more detailed analyses feasible. In this paper we provide a framework that takes data from the largest set of wild chimpanzee (Pan troglodytes) gestures currently available, splitting gesture types at a fine scale based on modifying features of gesture expression and then determining whether this splitting process increases the information content of the communication system. Our method allows different features of interest to be incorporated into the splitting process, providing substantial future flexibility across - for example - species, populations, and levels of signal granularity. In doing so we provide a powerful tool allowing researchers interested in gestural communication to establish repertoires of relevant units for subsequent analyses within and between systems of communication.

animal behavior and cognition↗

bioRxiv2023

Tomato brown rugose fruit virus Mo gene is a novel microbial source tracking marker

Microbial source tracking (MST) identifies sources of fecal contamination in the environment using fecal host-associated markers. While there are numerous bacterial MST markers, there are few viral markers. Here we design and test novel viral MST markers based on tomato brown rugose fruit virus (ToBRFV) genomes. We assembled eight nearly complete genomes of ToBRFV from wastewater and stool samples from the San Francisco Bay Area in the United States of America. Next, we developed two novel probe-based RT-PCR assays based on conserved regions of the ToBRFV genome, and tested the markers sensitivities and specificities using human and non-human animal stool as well as wastewater. TheToBRFV markers are sensitive and specific; in human stool and wastewater, they are more prevalent and abundant than a currently used marker, the pepper mild mottle virus (PMMoV) coat protein (CP) gene. We applied the assays to detect fecal contamination in urban stormwater samples and found that the ToBRFV markers matched cross-assembly phage (crAssphage), an established viral MST marker, in prevalence across samples. Taken together, ToBRFV is a promising viral human-associated MST marker. ImportanceHuman exposure to fecal contamination in the environment can cause transmission of infectious diseases. Microbial source tracking (MST) can identify sources of fecal contamination so that contamination can be remediated and human exposures can be reduced. MST requires the use of fecal host-associated MST markers. Here we design and test novel MST markers from genomes of tomato brown rugose fruit virus (ToBRFV). The markers are sensitive and specific to human stool, and highly abundant in human stool and wastewater samples.

microbiology↗