Biology subjects

Pratt, C.

Publications and source records attributed to Pratt, C..

8 recordsLinked to original sources

bioRxiv2025

Positive Reinforcement Training Insight from Working Elephants in India

Working elephants in India are predominantly trained using dominance-based and punitive methods. Research over the past few decades has shown that these methods, when contrasted with positive reinforcement training techniques, can be detrimental to animals mental and physical well being. Positive reinforcement based methods have also been shown to be effective in obtaining the voluntary participation of many species of animals in husbandry and routine medical procedures. Our study aims to characterize the stress responses of a group of captive working elephants longitudinally while desensitizing certain procedures and training assistive behaviours. We documented the duration and frequency of stress signals presented by elephants during regular training sessions over a four month period. We found that as sessions progressed, elephants displayed fewer stress signals - suggesting a decrease in stress with continued exposure to training. Our findings align well with prior research showing similar patterns across multiple non-human species. Further, our findings suggest that voluntary cooperation can be achieved even under challenging circumstances and provide learning opportunities for both elephants and mahouts. Our work outlines a pathway to reshape captive animal welfare measures in India.

animal behavior and cognition↗

bioRxiv2025

Piromyces struthionis, sp. nov., a new anaerobic gut fungus from the feces of ostriches

Anaerobic gut fungi (AGF, Neocallimastigomycota) are a clade of basal, zoospore-producing fungi within the subkingdom Chytridiomyceta and known inhabitants of the alimentary tract of animal hosts. To date, 22 genera and 38 species have been described, most originating from herbivorous mammals. Here, we report on the isolation and characterization of a novel species of Neocallimastigomycota from an avian host. Multiple AGF strains were isolated from ostrich feces obtained from a local farm in Oklahoma (USA). All strains formed small, irregular-shaped white colonies with darker centers, displayed a filamentous rhizoidal structure with monocentric thallus developmental patterns, and produced mostly monoflagellated zoospores. The type strain produced terminal sporangia that were predominantly globose, often exhibiting cup-shaped, and occasionally elongated sporangiophores. Sporangiophores characteristically exhibited constrictions at irregular intervals, giving them a pearls-on-a-chain-like appearance. Phylogenetic analysis using the D1-D2 region of the LSU rRNA gene (D1-D2 LSU), ribosomal internal transcribed spacer-1 (ITS1), and RNA polymerase II large subunit (RPB-II) grouped all isolates as a separate species within the genus Piromyces. Transcriptomic analysis indicated an average amino acid identity (AAI) of 80.34 % ({+/-} 3.27 %) between the type species and members of the genus Piromyces, and 62.93-76.05 % between the type species and all other AGF taxa outside Piromyces. Based on the morphology, phylogenetic analysis, and AAI values, we propose accommodating these strains as a novel species of Piromyces for which the name Piromyces struthionis is proposed. The type strain for this species is Ost1.

microbiology↗

bioRxiv2023

Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution

The anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Here we report on AGF communities in tortoises (family Testudinidae). Culture-independent surveys of tortoise fecal samples identified a unique AGF community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions at 30{degrees}C or 39{degrees}C. Transcriptomics-enabled phylogenomic and molecular dating analysis indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal- Neocallimastigomycota symbiosis from the early Paleogene (67 Mya) to the early Cretaceous (112 Mya). Further, compared to their mammalian counterparts, tortoise-associated isolates exhibited a more limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate active enzyme (CAZyme) families mediating their degradation. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repretoire in tortoise-associated AGF is driven by the paucity of horizontal gene transfer (HGT) in tortoise-associated AGF genomes, compared to the massive HGT occurrence in mammalian AGF taxa. The reduced CAZyome and overall secretory machinery observed is also reflected in an altered cellulosomal production capacity in tortoise-associated AGF. Our findings provide novel insights into the scope of phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes and traits acquisition in Neocallimastigomycota. SignificanceAnaerobic gut fungi (AGF) are encountered in the rumen and hindgut of mammalian herbivores. However, their occurrence outside their canonical mammalian hosts is currently unclear. We report the identification, isolation, and characterization of novel, deep-branching AGF genera from tortoises. Such discovery expands the phylogenetic diversity and host range of the AGF and revises estimates of the phylums evolutionary time to the early Cretaceous (112 Mya). We also demonstrate that tortoise-sourced AGF lack multiple metabolic features compared to their mammalian counterparts, and identify the relative paucity of HGT events in tortoise-associated genera as a major factor underpinning such differences. Our results alter our understanding of the scope of phylogenetic diversity, ecological distribution, and evolutionary history of the AGF.

microbiology↗

bioRxiv2023

Anaerobic gut fungal communities in marsupial hosts

The anaerobic gut fungi (AGF) inhabit the alimentary tracts of herbivores. In contrast to placental mammals, information regarding the identity, diversity, and community structure of AGF in marsupials is extremely sparse. Here, we characterized AGF communities in sixty one fecal samples from ten marsupial species belonging to four families in the order Diprotodontia: Vombatidae (wombats), Phascolarctidae (koalas), Phalangeridae (possums), and Macropodidae (kangaroos, wallabies, and pademelons). Amplicon-based diversity survey using the D2 region in the large ribosomal subunit (D2 LSU) as a phylogenetic marker indicated that marsupial AGF communities were dominated by eight genera commonly encountered in placental herbivores (Neocallimastix, Caecomyces, Cyllamyces, Anaeromyces, Orpinomyces, Piromyces, Pecoramyces, and Khoyollomyces). Community structure analysis revealed a high level of stochasticity, and ordination approaches did not reveal a significant role for animal host, gut type, dietary preferences, or lifestyle in structuring marsupial AGF communities. Marsupial foregut and hindgut communities displayed diversity and community structure patterns comparable to AGF communities typically encountered in placental foregut hosts, while exhibiting a higher level of diversity and a distinct community structure compared to placental hindgut communities. Quantification of AGF load using quantitative PCR indicated a significantly smaller load in marsupial hosts compared to their placental counterparts. Isolation efforts were only successful from a single red kangaroo fecal sample and yielded a Khoyollomyces ramosus isolate closely related to strains previously isolated from placental hosts. Our results suggest that AGF communities in marsupials are in low abundance, and show little signs of selection based on ecological and evolutionary factors. The observed lack of host-fungal coevolutionary signal suggests a potential recent acquisition and/or a transient nature of AGF communities in marsupial herbivores.

microbiology↗

bioRxiv2023

Clade-Specific MPXV PCR Assays

In an evolving infectious disease outbreak, there are two priorities: rapid and accurate detection of the causative agent and characterization of its spread. The polymerase chain reaction (PCR) assay is an effective and portable diagnostic method that can quickly provide information associated with virulence, transmissibility, and pathogenicity. Compared to genomic sequencing, PCR requires less infrastructure, funding, and training. However, the development of sensitive and specific primer sequences is costly, particularly those with subspecies resolution. The recent mpox (monkeypox) virus outbreak underscores the need for the rapid development of clade-specific primers, particularly when there are differences in morbidity and mortality rates. Current mpox assays use primer sequences that also bind to the broader Orthopoxvirus genus, resulting in suspect diagnoses, delays in treatment, and poor allocation of scarce healthcare resources. Additionally, these orthopox-based primer sets cannot distinguish between different mpox clades and cannot illuminate intra-clade evolution over the course of the outbreak. Here, we present the in silico design and in vitro testing of novel clade-specific mpox assays. ImportanceThere is an ongoing global outbreak of Mpox disease, an illness with a characteristic blistering rash progression. The Mpox virus clusters into two clades with differing levels of virulence and mortality rates. Thus, proper sample identification is critical for surveillance and the public health response programs that rely on such data. Accordingly, the US government specifically lists Clade I under the Federal Select Agent Program. Current diagnostics may fail to identify the virus or its clade membership as the genome mutates. In this work, we demonstrate an end-to-end workflow to quickly evaluate existing PCR assays and design new ones for clade-based identification with respect to large sequence databases in service of preventing a catastrophic fog-of-war from forming during an outbreak.

bioinformatics↗

bioRxiv2022

Detection of Dugbe virus from ticks in Ghana

Vector-borne pathogens historically have impacted U.S. warfighters and active-duty personnel stationed both domestically and globally during deployments or forward operations. Tick-borne diseases continue to spread to new geographical regions affecting both animal and human health. In Ghana, there is limited information on the circulating tick-borne pathogens and their risk of infections. This military-to-military vector surveillance study focused on seven sites in Ghana: Navrongo, Airforce Base, 6th Battalion Infantry, Air Borne Force, Army Recruit Training School, 1st Battalion Infantry and 5th Battalion Infantry for detection of tick-borne pathogens. Ticks from these sites were collected by hand-picking with a pair of forceps from domesticated animals including cattle, sheep, goats and dogs. A total of 2,016 ticks were collected from two main ecological zones; the northern Sahel savannah and the coastal savannah. Amblyomma variegatum was the predominant species, accounting for 59.5% of the collected ticks. Next-generation sequencing allowed for Dugbe virus whole genome detection. This study reports the second detection of Dugbe virus in Ghana, which is closely related to Dugbe virus strains from Kenya and Nigeria. This study (sponsored by the Armed Forces Health Surveillance Branch-Global Emerg-ing Infections Surveillance Section) aimed to better inform Force Health Protection (FHP) decisions within the U.S. AFRICOM area of responsibility, the Ghana Armed Forces, and enhance global health security countermeasures. Further surveillance needs to be conducted within the country to determine the distribution of tick-borne pathogens to formulate effective control measures. Author summaryThe prevalence of Dugbe virus in tick species within Ghana was investigated. This study involved seven sampling sites that covered two ecological zones, the northern Sahel savannah and the coastal savannah. About 2,000 ticks were collected from cattle, sheep, goats and dogs and identified using a dissecting microscope. The most predominant tick species was Amblyomma variegatum (59.5%) also known as the tropical bont tick. Using Next-generation sequencing, the full genome of Dugbe virus was for the first time in Ghana identified in A. variegatum. This positive Amblyomma variegatum was collected from the Greater Accra region of Ghana within a military site. The virus was found to be related to Dugbe virus strains from Kenya and Nigeria. Findings from this study show that the trade of livestock across borders facilitates the spread of tick-borne pathogens hence there is a need to enforce measures that prevent the importation of potentially harmful ticks and tick-borne pathogens.

scientific communication and education↗

bioRxiv2021

Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation

Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, non-soil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes, and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of thirteen distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g. FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine-learning approaches based on a set of 634 genes informative of social lifestyle predicted a non-social behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities, but encoded genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 Mya in response to the rise of soil as a distinct habitat on earth. ImportanceThe Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcoat are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota has been encountered in a wide range of non-soil, predominantly anaerobic habitats; and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remains unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes, and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity we confirmed through detailed comparative genomic analysis of thirteen pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate rductio, and dissimilarity sulfate reduction for energy acquisition. Our result highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcoat has occurred in response to soil formation as a distinct habitat on earth.

microbiology↗

bioRxiv2019

CNTNAP2 is targeted to endosomes by the polarity protein Par3

A decade of genetic studies has established Contactin-associated protein-like 2 (CNTNAP2) as a prominent susceptibility gene associated with multiple neurodevelopmental disorders. The development and characterization of Cntnap2 knockout models in multiple species have bolstered this claim by establishing clear connections with certain endophenotypes. Despite these remarkable in vivo findings, CNTNAP2s molecular functions are relatively unexplored, highlighting the need to identify novel protein partners. Here, we characterized an interaction between CNTNAP2 and Partitioning-defective 3 (Par3) - a polarity molecule we isolated in a yeast-two hybrid screen with CNTNAP2s C-terminus. We provide evidence that the two proteins interact via PDZ domain-mediated binding, that CNTNAP2+/Par3+ complexes are largely associated with clathrin-coated endocytic vesicles, and that Par3 causes an enlargement of these structures. Live imaging and fluorescence recovery after photobleaching (FRAP) reveals that Par3 limits the mobility of CNTNAP2 at endosomes, thus stabilizing it at that location. Finally, expression of Par3 but not Par3{Delta}PDZ can cluster endogenous CNTNAP2 in primary neurons. Collectively, we conclude that Par3 regulates CNTNAP2 spatial localization to endocytic compartments.

neuroscience↗