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At least 91 records · Page 5

Whole Genome Sequencing Links Mycobacterium bovis From Cattle, Cheese and Humans in Baja California, Mexico

Mycobacterium bovis causes tuberculosis (TB) in cattle, which in turn can transmit the pathogen to humans. Tuberculosis in dairy cattle is of particular concern where the consumption of raw milk and dairy products is customary. Baja California (BCA), Mexico, presents high prevalence of TB in both cattle and humans, making it important to investigate the molecular epidemiology of the disease in the region. A long-term study was undertaken to fully characterize the diversity of M. bovis genotypes circulating in dairy cattle, cheese and humans in BCA by whole-genome sequencing (WGS). During a 2-year period, 412 granulomatous tissue samples were collected from local abattoirs and 314 cheese samples were purchased from local stores and vendors in BCA and sent to the laboratory for mycobacterial culture, histology, direct PCR and WGS. For tissue samples M. bovis was recovered from 86.8%, direct PCR detected 90% and histology confirmed 85.9% as mycobacteriosis-compatible. For cheese, M. bovis was recovered from 2.5% and direct PCR detected 6% of the samples. There was good agreement between diagnostic tests. Subsequently, a total of 345 whole-genome SNP sequences were obtained. Phylogenetic analysis grouped these isolates into 10 major clades. SNP analysis revealed putative transmission clusters where the pairwise SNP distance between isolates from different dairies was ≤3 SNP. Also, human and/or cheese isolates were within 8.45 (range 0–17) and 5.8 SNP (range 0–15), respectively, from cattle isolates. Finally, a comparison between the genotypes obtained in this study and those reported previously suggests that the genetic diversity of M. bovis in BCA is well-characterized, and can be used to determine if BCA is the likely source of M. bovis in humans and cattle in routine epidemiologic investigations and future studies. In conclusion, WGS provided evidence of ongoing local transmission of M. bovis among the dairies in this high-TB burden region of BCA, as well as show close relationships between isolates recovered from humans, cheese, and cattle. This confirms the need for a coordinated One Health approach in addressing the elimination of TB in animals and humans. Overall, the study contributes to the knowledge of the molecular epidemiology of M. bovis in BCA, providing insight into the pathogen's dynamics in a high prevalence setting.

59 BASIC BIOLOGICAL SCIENCES↗

Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria

Studying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria from the Candidate Phyla Radiation because their minimal metabolic capabilities require associations with microbial hosts.

59 BASIC BIOLOGICAL SCIENCES↗

MicroRNAs as disease progression biomarkers and therapeutic targets in experimental autoimmune encephalomyelitis model of multiple sclerosis

Multiple sclerosis is an autoimmune neurodegenerative disease of the central nervous system characterized by pronounced inflammatory infiltrates entering the brain, spinal cord and optic nerve leading to demyelination. Focal demyelination is associated with relapsing-remitting multiple sclerosis, while progressive forms of the disease show axonal degeneration and neuronal loss. The tests currently used in the clinical diagnosis and management of multiple sclerosis have limitations due to specificity and sensitivity. MicroRNAs (miRNAs) are dysregulated in many diseases and disorders including demyelinating and neuroinflammatory diseases. A review of recent studies with the experimental autoimmune encephalomyelitis animal model (mostly female mice 6–12 weeks of age) has confirmed miRNAs as biomarkers of experimental autoimmune encephalomyelitis disease and importantly at the pre-onset (asymptomatic) stage when assessed in blood plasma and urine exosomes, and spinal cord tissue. The expression of certain miRNAs was also dysregulated at the onset and peak of disease in blood plasma and urine exosomes, brain and spinal cord tissue, and at the post-peak (chronic) stage of experimental autoimmune encephalomyelitis disease in spinal cord tissue. Therapies using miRNA mimics or inhibitors were found to delay the induction and alleviate the severity of experimental autoimmune encephalomyelitis disease. Interestingly, experimental autoimmune encephalomyelitis disease severity was reduced by overexpression of miR-146a, miR-23b, miR-497, miR-26a, and miR-20b, or by suppression of miR-182, miR-181c, miR-223, miR-155, and miR873. Further studies are warranted on determining more fully miRNA profiles in blood plasma and urine exosomes of experimental autoimmune encephalomyelitis animals since they could serve as biomarkers of asymptomatic multiple sclerosis and disease course. Additionally, studies should be performed with male mice of a similar age, and with aged male and female mice.

59 BASIC BIOLOGICAL SCIENCES↗

Allometric-kinetic model predictions of concentration ratios for anthropogenic radionuclides across animal classes and food selection

Protection of the environment from radiation fundamentally relies on dose assessments for non-human biota. These dose assessments use measured or predicted concentrations of radionuclides in soil or water combined with Concentration Ratios (CRs) to estimate tissue concentrations in animals and plants, yet there is a paucity of CR data relative to the vast number of potential taxa and radioactive contaminants in the environment and their taxon-specific ecosystems. Because there are many taxa each having very different behaviors and biology and many possible bioavailable radionuclides, CRs have the potential to vary by orders-of-magnitude, as often seen in published data. Given the diversity of taxa, the International Commission on Radiological Protection (ICRP) has categorized non-human biota into 12 representative organisms (ROs), while the U.S. Department of Energy (DOE) uses the non-taxon specific categories of terrestrial, riparian, and aquatic animals. The question we examine here is: do these categorizations adequately “represent” the broad diversity of animals? To explore this question, here we analyze an Allometric-Kinetic (A-K) model to calculate radionuclide-specific CRs for common animal classes which are then further subcategorized into herbivores, omnivores, carnivores, and invertebrate detritivores. Comparisons in CRs among animal classes exhibited only small differences, but there was order of magnitude differences between herbivores, carnivores, and especially detritivores, for many radionuclides of interest. These findings suggest that the ICRP ROs and the DOE categories are reasonable, but their accuracy could be improved by including sub-categories related to animal dietary ecology. Finally, comparisons of A-K model predicted CR values to published CRs show order-of-magnitude variations, providing justification for additional studies of assimilation across radionuclides and animal classes.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Resource selection functions based on hierarchical generalized additive models provide new insights into individual animal variation and species distributions

Habitat selection studies are designed to generate predictions of species distributions or inference regarding general habitat associations and individual variation in habitat use. Such studies frequently involve either individually indexed locations gathered across limited spatial extents and analyzed using resource selection functions (RSFs) or spatially extensive locational data without individual resolution typically analyzed using species distribution models. Both analytical methodologies have certain desirable features, but analyses that combine individual- and population-level inference with flexible non-linear functions may provide improved predictions while accounting for individual variation. Here, we describe how RSFs can be fit using hierarchical generalized additive models (HGAMs) using widely available software, providing a means to explore individual variation in habitat associations and to generate species distribution maps. We used GPS tracking data from golden eagles Aquila chrysaetos from across eastern North America with four environmental predictors to generate monthly distribution models. We considered three model structures that assumed different amounts of individual variation in the functional relationship between predictors and habitat use and used k-fold cross-validation to compare model performance. Models accounting for individual variability in shape and smoothness of functional responses performed best. Eagles exhibited the least amount of individual variation in response to land cover variables during winter months, with most individuals more closely adhering to the population-level trend. During the summer months, eagles exhibited more substantial individual variation in shape and smoothness of the functional relationships, suggesting some need to account for individual variation in eagle habitat use for both inferential and predictive purposes, during this time of year. Because they allow users to blend flexible functions with random effects structures and are well-supported by a variety of software platforms, we believe that HGAMs provide a useful addition to the suite of analyses used for modeling habitat associations or predicting species distributions.

54 ENVIRONMENTAL SCIENCES↗

Mongooses ( Urva auropunctata ) as reservoir hosts of Leptospira species in the United States Virgin Islands, 2019–2020

During 2019–2020, the Virgin Islands Department of Health investigated potential animal reservoirs of Leptospira spp., the bacteria that cause leptospirosis. In this cross-sectional study, we investigated Leptospira spp. exposure and carriage in the small Indian mongoose (Urva auropunctata, syn: Herpestes auropunctatus), an invasive animal species. This study was conducted across the three main islands of the U.S. Virgin Islands (USVI), which are St. Croix, St. Thomas, and St. John. We used the microscopic agglutination test (MAT), fluorescent antibody test (FAT), real-time polymerase chain reaction (lipl32 rt-PCR), and bacterial culture to evaluate serum and kidney specimens and compared the sensitivity, specificity, positive predictive value, and negative predictive value of these laboratory methods. Mongooses (n = 274) were live-trapped at 31 field sites in ten regions across USVI and humanely euthanized for Leptospira spp. testing. Bacterial isolates were sequenced and evaluated for species and phylogenetic analysis using the ppkgene. Anti-Leptospira spp. antibodies were detected in 34% (87/256) of mongooses. Reactions were observed with the following serogroups: Sejroe, Icterohaemorrhagiae, Pyrogenes, Mini, Cynopteri, Australis, Hebdomadis, Autumnalis, Mankarso, Pomona, and Ballum. Of the kidney specimens examined, 5.8% (16/270) were FAT-positive, 10% (27/274) were culture-positive, and 12.4% (34/274) were positive by rt-PCR. Of the Leptospira spp. isolated from mongooses, 25 were L. borgpetersenii, one was L. interrogans, and one was L. kirschneri. Positive predictive values of FAT and rt-PCR testing for predicting successful isolation of Leptospira by culture were 88% and 65%, respectively. The isolation and identification of Leptospira spp. in mongooses highlights the potential role of mongooses as a wildlife reservoir of leptospirosis; mongooses could be a source of Leptospira spp. infections for other wildlife, domestic animals, and humans.

59 BASIC BIOLOGICAL SCIENCES↗

PS3: The Pheno-Synthesis software suite for integration and analysis of multi-scale, multi-platform phenological data

Phenology is the study of recurring plant and animal life-cycle stages which can be observed across spatial and temporal scales that span orders of magnitude (e.g., organisms to landscapes). The variety of scales at which phenological processes operate is reflected in the range of methods for collecting phenologically relevant data, and the programs focused on these collections. Consideration of the scale at which phenological observations are made, and the platform used for observation, is critical for the interpretation of phenological data and the application of these data to both research questions and land management objectives. However, there is currently little capacity to facilitate access, integration and analysis of cross-scale, multi-platform phenological data. This paper reports on a new suite of software and analysis tools – the “Pheno-Synthesis Software Suite,” or PS3 – to facilitate integration and analysis of phenological and ancillary data, enabling investigation and interpretation of phenological processes at scales ranging from organisms to landscapes and from days to decades. We use PS3 to investigate phenological processes in a semi-aride, mixed shrub-grass ecosystem, and find that the apparent importance of seasonal precipitation to vegetation activity (i.e., “greenness”) is affected by the scale and platform of observation. We end by describing potential applications of PS3 to phenological modeling and forecasting, understanding patterns and drivers of phenological activity in real-world ecosystems, and supporting agricultural and natural resource management and decision-making.

54 ENVIRONMENTAL SCIENCES↗

Mutational signatures in tumours induced by high and low energy radiation in Trp53 deficient mice

Lonising radiation (IR) is a recognised carcinogen responsible for cancer development in patients previously treated using radiotherapy, and in individuals exposed as a result of accidents at nuclear energy plants. However, the mutational signatures induced by distinct types and doses of radiation are unknown. Here, we analyse the genetic architecture of mammary tumours, lymphomas and sarcomas induced by high ( 56 Fe-ions) or low (gamma) energy radiation in mice carrying Trp53 loss of function alleles. In mammary tumours, high-energy radiation is associated with induction of focal structural variants, leading to genomic instability and Met amplification. Gamma-radiation is linked to large-scale structural variants and a point mutation signature associated with oxidative stress. The genomic architecture of carcinomas, sarcomas and lymphomas arising in the same animals are significantly different. Our study illustrates the complex interactions between radiation quality, germline Trp53 deficiency and tissue/cell of origin in shaping the genomic landscape of IR-induced tumours.

Science & Technology - Other Topics↗

Fluorescent and Bioluminescent Reporter Mouse-Adapted Ebola Viruses Maintain Pathogenicity and Can Be Visualized in Vivo

Abstract Ebola virus (EBOV) causes lethal disease in humans but not in mice. Here, we generated recombinant mouse-adapted (MA) EBOVs, including 1 based on the previously reported serially adapted strain (rMA-EBOV), along with single-reporter rMA-EBOVs expressing either fluorescent (ZsGreen1 [ZsG]) or bioluminescent (nano-luciferase [nLuc]) reporters, and dual-reporter rMA-EBOVs expressing both ZsG and nLuc. No detriment to viral growth in vitro was seen with inclusion of MA-associated mutations or reporter proteins. In CD-1 mice, infection with MA-EBOV, rMA-EBOV, and single-reporter rMA-EBOVs conferred 100% lethality; infection with dual-reporter rMA-EBOV resulted in 73% lethality. Bioluminescent signal from rMA-EBOV expressing nLuc was detected in vivo and ex vivo using the IVIS Spectrum CT. Fluorescent signal from rMA-EBOV expressing ZsG was detected in situ using handheld blue-light transillumination and ex vivo through epi-illumination with the IVIS Spectrum CT. These data support the use of reporter MA-EBOV for studies of Ebola virus in animal disease models.

Immunology↗

MiNAA: Microbiome Network Alignment Algorithm

A microbial network is a mathematical representation of a microbial community where nodes represent microbes and edges represent interactions. It is well-recognized that microbes are among the main drivers of biological phenotypes in soil, plants, and animals alike, and thus, their study has vast implications for soil, plant and human health. In particular, recognizing the microbial, environmental, and agricultural factors that drive plant and soil phenotypes is crucial to comprehend processes connected to plant and soil health, to identify global practices of sustainable agriculture, as well as to predict plant and soil responses to environmental perturbations such as climate change. The adaptability of microbes to thrive in every environment poses challenges for scientists who try to understand their communities. Indeed, two microbial communities with the exact same players can interact differently depending on the environmental conditions. It is thus desirable to identify commonalities and differences on two microbial networks, hence the need for computational tools that can match (or align) them.

97 MATHEMATICS AND COMPUTING↗

Design and implementation of a real-time underwater acoustic telemetry system for fish behavior study and environmental sensing

Underwater acoustic telemetry is an important tool for studying the behavior of aquatic animals and assessing the environmental impact of man-made structures such as water power turbines. However, current design of the acoustic telemetry system lacks the ability to transmit collected data continuously in real-time and requires manual retrieval of the recorded measurements, leading to a long delay of data retrieval, high operational cost associated with manpower as well as safety risk for the operators. In addition, there is no efficient way to monitor the status of the acoustic telemetry system, including acoustic transmitters and receivers. For example, if multiple receivers in an array fail, the detection efficiency could be significantly reduced. Herein, we developed a cloud-based, real-time underwater acoustic telemetry system that can be used to estimate behavior or survival of tagged aquatic animals and monitor environmental parameters in near-real-time (< 2 hours). The system incorporates microcontrollers and integrated circuits to create real-time data communication and processing units with a cloud-based service that processes the transmitted data stream to derive behavior and survival information of the tagged animals.

Yang, Yang↗

Hofmeister Effect in RT-QuIC Seeding Activity of Chronic Wasting Disease Prions

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy (TSE) that causes a fatal neurodegenerative disease in cervids. Cases of CWD are rapidly increasing in North America among wild and farmed cervid populations, and potential for zoonotic transmission is not yet determined. Therefore, in order to manage the disease, it is imperative to devise a system that can detect CWD during its early phases to prevent spread to new captive herds through introduction of CWD-affected animals into otherwise CWD-free herds. Real-time quaking–induced conversion (RT-QuIC) assays have been applied to detect the presence of disease-associated prions from various samples in both animals and humans. In this study, we have tested the use of five Hofmeister anions that range from weakly hydrating to strongly hydrating: Na 3 citrate, Na 2 SO 4 , NaCl, NaI, and NaClO 4 in RT-QuIC reactions for CWD seeding activity using different recombinant prion proteins as substrates. This work shows how the ionic environment of the RT-QuIC reaction can enhance or diminish the seeding activity. The use of Na 2 SO 4 or NaI as the sodium salt for RT-QuIC using bank vole recombinant prion substrate for the detection of CWD using brain samples reduces the lag time to detect with reasonable specificity. For detection of the CWD in fecal samples, only NaI showed comparable reduction in lag time relative to NaCl but required reduced temperature to alleviate spontaneous fibril formation in negative control samples. Selection of the proper ion environment and recombinant prion protein substrate will make RT-QuIC a powerful diagnostic tool for early detection of CWD prions, further supporting CWD surveillance in wild and captive cervids.

59 BASIC BIOLOGICAL SCIENCES↗

Comprehensive Genome-Wide Natural Variation and Expression Analysis of Tubby-like Proteins Gene Family in Brachypodium distachyon

The Tubby-like proteins (TLPs) gene family is a group of transcription factors found in both animals and plants. In this study, we identified twelve B. distachyon TLPs, divided into six groups based on conserved domains and evolutionary relationships. We predicted cis-regulatory elements involved in light, hormone, and biotic and abiotic stresses. The expression patterns in response to light and hormones revealed that BdTLP3, 4, 7, and 14 are involved in light responses, and BdTLP1 is involved in ABA responses. Furthermore, BdTLP2, 7, 9, and 13 are expressed throughout vegetative and reproductive stages, whereas BdTLP1, 3, 5, and 14 are expressed at germinating grains and early vegetative development, and BdTLP4, 6, 8, and 10 are expressed at the early reproduction stage. The natural variation in the eleven most diverged B. distachyon lines revealed high conservation levels of BdTLP1-6 to high variation in BdTLP7-14 proteins. Based on diversifying selection, we identified amino acids in BdTLP1, 3, 8, and 13, potentially substantially affecting protein functions. This analysis provided valuable information for further functional studies to understand the regulation, pathways involved, and mechanism of BdTLPs.

Plant Sciences↗

Modulation of Neuroinflammation by Low-Dose Radiation Therapy in an Animal Model of Alzheimer's Disease

Recently, several studies have reported that low-dose radiation therapy (RT) suppresses the release of proinflammatory cytokines in inflammatory-degenerative disorders, including Alzheimer disease (AD). AD is the most common cause of dementia, and neuroinflammation is one of the major contributing factors in AD pathogenesis. Therefore, low-dose RT may be used clinically for treating AD. However, the appropriate doses, effects, and underlying mechanisms of RT in AD have not been determined. In this study, we aimed to determine the appropriate RT dose and schedule for AD treatment and to investigate the therapeutic effects and mechanisms of low-dose RT in AD.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

A three-dimensional model of terrain-induced updrafts for movement ecology studies

Abstract Background Spatially explicit simulation models of animal movements through the atmosphere necessarily require a representation of the spatial and temporal variation of atmospheric conditions. In particular, for movements of soaring birds that rely extensively on vertical updrafts to avoid flapping flight, accurate and reliable estimation of the vertical component of wind is critical. The interaction between wind and complex terrain shapes both the horizontal and vertical wind fields, highlighting the need to model the coupling between local terrain features and atmospheric conditions at scales relevant to animal movement. Methods In this work, we propose a new empirical model for estimating the orographic updraft field. The model is developed using computational fluid dynamics simulations of canonical atmospheric conditions over moderately complex terrain. To isolate buoyancy and thermal effects, and focus on terrain-induced effects, we use only simulations of a neutrally stratified atmosphere to develop the model. The model, which we name Engineering Vertical Velocity Estimator (EVVE), is simple to implement and is a function of the underlying terrain elevation map, the desired height above ground level (AGL), and wind conditions at a reference height (80 m). We validate the model with data from the Alaiz mountain (Spain) field campaign. Results Compared to observations, the proposed improved model estimates the updrafts at 120 m AGL with a mean error of 0.11 m/s ( $$\sigma =0.28$$ σ = 0.28 m/s), compared to 0.85 m/s ( $$\sigma =0.58$$ σ = 0.58 m/s) for its baseline. For typical land-based wind turbine hub heights of 80 m AGL, the proposed model has a mean error of 0.04 m/s ( $$\sigma =0.25$$ σ = 0.25 m/s), compared to baseline 0.54 m/s ( $$\sigma =0.45$$ σ = 0.45 m/s) estimations. We illustrate an application of the model in movement ecology by comparing simulated tracks and presence maps of golden eagles ( Aquila chrysaetos ) moving across two distinct landscapes. The tracks and presence maps are obtained using a simple heuristic-based movement model, with the updraft field given by the proposed model and a wind vector-based estimation approach that is currently in wide use in movement ecology studies of raptors and other soaring birds. Conclusions We highlight that movement model results can be sensitive to the underlying orographic updraft model, especially in studies of fine-scale movements in regions of complex topography. We suggest adopting the proposed model rather than the wind vector estimation method for studies of soaring bird movements.

17 WIND ENERGY↗

Pulsar Movement Animation and its Corresponding Signal Visualization for Timing Source

The global positioning system, widely used for synchronization in energy systems, faces vulnerabilities, while Pulsars—natural cosmic clocks—offer long-term stability as potential backup timing sources. Existing research lacks sufficient exploration of Pulsar signal animation under astrophysical factors, limiting practical applications. This study establishes a mathematical model based on the rotation dynamics of dual-beam Pulsars and implements dynamic signal visualization through MATLAB. The model dynamically illustrates the relative motion between Pulsar beams and observers via timeline calculations, beam intensity modeling, and rotation matrix derivation. A case study on the millisecond Pulsar J1939+2134 reveals that observer angles influence signal peak timing, while beam widths determine signal duration, highlighting the critical role of parameter calibration for timing accuracy. Open-source code and animation results are publicly shared, providing tools for interdisciplinary research. This study validates the feasibility of Pulsar-based timing in energy systems, offering new insights to enhance synchronization robustness.

Wu, Ori [ORNL] (ORCID:0000000326723410)↗

Translocations are induced in hematopoietic stem cells after irradiation of fetal mice

Abstract Although mammalian fetuses have been suggested to be sensitive to radiation, an increased frequency of translocations was not observed in blood lymphocytes from atomic bomb (A-bomb) survivors who were exposed to the bomb in utero and examined as adults. Since experiments using hematopoietic cells of mice and rats confirmed this finding, it was hypothesized that either irradiated fetal hematopoietic stem cells (f-HSCs) cannot generate exchange-type chromosomal aberrations or cells bearing induced aberrations are eliminated before the animals reach adulthood. In the present study, pregnant mice (12.5–15.5 days post coitum [dpc]) were irradiated with 2 Gy of X-rays and long-term HSCs (LT-HSCs) were isolated 24 h later. Multicolor fluorescence in situ hybridization (mFISH) analysis of LT-HSC clones proliferated in vitro showed that nine out of 43 (21%) clones from fetuses and 21 out of 41 (51%) clones from mothers bore translocations. These results indicate that cells with translocations can arise in mouse f-HSCs but exist at a lower frequency than in the mothers 24 h after X-ray exposure. Thus, it seems likely that translocation-bearing f-HSCs are generated but subsequently disappear, so that the frequency of lymphocyte translocations may decrease and reach the control level by the time the animals reach adulthood.

60 APPLIED LIFE SCIENCES↗

Structural and functional analysis of the human cone‐rod homeobox transcription factor

Abstract The cone‐rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone‐rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 25 years since its initial characterization, there are no high‐resolution structures in the published literature for the CRX protein. In this study, we use bioinformatic approaches and small‐angle X‐ray scattering (SAXS) structural analysis to further understand the biochemical complexity of the human CRX homeodomain (CRX‐HD). We find that the CRX‐HD is a compact, globular monomer in solution that can specifically bind functional cis‐regulatory elements encoded upstream of retina‐specific genes. This study presents the first structural analysis of CRX, paving the way for a new approach to studying the biochemistry of this protein and its disease‐causing mutant protein variants.

59 BASIC BIOLOGICAL SCIENCES↗