Scholarly Works, School of Animal Sciences

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Ruminally Protected Isoleucine, Leucine, Methionine, and Threonine Supplementation of Low-Protein Diets Improved the Performance and Nitrogen Efficiency of Dairy Cows
Qin, Xiaoli; Lin, Xueyan; Hanigan, Mark D.; Zhao, Kai; Hu, Zhiyong; Wang, Yun; Hou, Qiuling; Wang, Zhonghua (MDPI, 2025-04-24)
This study evaluated the effects of supplementing rumen-protected methionine, threonine, isoleucine, and leucine to low-protein diets on lactating dairy cow performance. Sixty Holstein cows were assigned to one of four dietary treatments in a 9-week randomized complete block design: positive control (16% crude protein diet; 16% CP), negative control (12% CP), 12% CP plus the four essential amino acids (12% CP + EAA), and 14% CP supplemented with the four EAA (14% CP + EAA). The milk protein yield was significantly decreased in the 12% CP group compared to the 16% CP group but was restored to comparable levels with EAA supplementation of both the 12% and 14% CP diets. Dietary nitrogen intake and urinary nitrogen excretion both increased with higher dietary CP levels. Nitrogen utilization efficiency in milk was significantly improved by EAA supplementation, with the highest efficiency observed in the 12% CP + EAA treatment (39.0% vs. 33.3% in the 16% CP diet). Plasma urea levels increased with elevated dietary CP and EAA supplementation. Moreover, EAA supplementation significantly elevated venous methionine levels and showed a tendency to increase venous leucine levels. Additionally, compared to the negative control, EAA supplementation increased concentrations of glucagon and prolactin (p < 0.05). EAA supplementation of low-protein diets, particularly the 14% CP diet, improved the dietary protein efficiency of lactating cows without a concomitant decrease in milk protein yield.
Monoubiquitination of histone H2B is a crucial regulator of the transcriptome during memory formation
Navabpour, Shaghayegh; Farrell, Kayla; Kincaid, Shannon E.; Omar, Nour; Musaus, Madeline; Lin, Yu; Xie, Hehuang; Jarome, Timothy J. (Cold Spring Harbor Laboratory Press, 2024-03)
Posttranslational modification of histone proteins is critical for memory formation. Recently, we showed that monoubiquitination of histone H2B at lysine 120 (H2Bub) is critical for memory formation in the hippocampus. However, the transcriptome controlled by H2Bub remains unknown. Here, we found that fear conditioning in male rats increased or decreased the expression of 86 genes in the hippocampus but, surprisingly, siRNA-mediated knockdown of the H2Bub ligase, Rnf20, abolished changes in all but one of these genes. These findings suggest that monoubiquitination of histone H2B is a crucial regulator of the transcriptome during memory formation.
Increasing H2B Monoubiquitination Improves the Transcriptome and Memory in the Aged Hippocampus
Kincaid, Shannon; Setenet, Gueladouan; Preveza, Natalie J.; Arndt, Kaiser C.; Gwin, Phillip; Lin, Yu; Xie, Hehuang; Jarome, Timothy J. (Society for Neuroscience, 2025-04)
A decline in cognitive abilities is associated with the aging process, affecting nearly 33% of US adults over the age of 70, and is a risk factor for the development of dementia and Alzheimer's disease. Several studies have reported age-related alterations in the transcriptome in the hippocampus, a major site of memory storage that is among the first regions impacted with age, dementia, and Alzheimer's disease. However, much remains unknown about why these transcriptional changes exist in the aged hippocampus and how this impacts memory late in life. Here, we show that monoubiquitination of histone H2B (H2Bubi), an epigenetic mechanism recently reported to be major regulator of the epigenome and transcriptome during memory formation in the young adult brain, decreases with age in the hippocampus of male rats. In vivo CRISPR-dCas9-mediated upregulation of Rnf20, the only ubiquitin E3 ligase for H2B, in the hippocampus significantly improved memory retention in aged rats. Remarkably, RNA-seq analysis revealed that in addition to the 18 genes typically upregulated in the aged rat hippocampus following contextual fear conditioning, Rnf20 upregulation caused learning-related increases and decreases in 40 and 11 unique genes, respectively, suggesting that these 51 genes may be among those most critical for improving memory in advanced age. Together, these data suggest that H2B monoubiquitination is a significant regulator of age-related dysregulation of the transcriptome and impairments in memory.
Effects of Embryonic Thermal Manipulation on Body Performance and Cecum Microbiome in Broiler Chickens Following a Post-Hatch Lipopolysaccharide Challenge
Hundam, Seif; Al-Zghoul, Mohammad Borhan; Ababneh, Mustafa; Alanagreh, Lo’ai; Dahadha, Rahmeh; Mayyas, Mohammad; Alghizzawi, Daoud; Mustafa, Minas A.; Gerrard, David E.; Dalloul, Rami A. (MDPI, 2025-04-17)
Thermal manipulation (TM) during embryogenesis has emerged as a promising strategy to enhance post-hatch performance and improve resilience to environmental and bacterial stress, which offers a potential alternative to reduce the reliance on antibiotic growth promoters (AGPs) in broiler production. This study investigated TM’s ability to modulate broilers’ cecal microbiota and enhance resilience to lipopolysaccharide (LPS)-induced stress. Eggs in the control group (CON) were incubated at 37.8 °C and 56% relative humidity (RH), while TM eggs were exposed to 39 °C and 65% RH for 18 h daily from embryonic days 10–18. Post-hatch, the LPS subgroups (LPS-CON, LPS-TM) received intraperitoneal LPS injections, and body weight (BW) and temperature (BT) were monitored. Cecal samples were collected for microbiome sequencing. Alpha diversity showed no differences (p > 0.05), but beta diversity revealed differences between groups (PERMANOVA, p < 0.05). Firmicutes and Bacteroidota dominated the microbiota at the phylum level. Oscillospirales were enriched in the TM groups (p < 0.001) and Lactobacillales were increased in the LPS-CON group (p < 0.019). LPS reduced BT in the CON group (p < 0.01), but LPS-TM birds bypassed hypothermia. LPS significantly reduced BW (p < 0.001), while TM had no significant effect. These findings demonstrate TM’s enduring influence on gut microbiota and stress resilience, highlighting its potential to reduce antibiotic reliance and mitigate antimicrobial resistance (AMR) in poultry production.
KHAIT: K-9 Handler Artificial Intelligence Teaming for Collaborative Sensemaking
Wilchek, Matthew; Wang, Linhan; Dickinson, Sally; Feuerbacher, Erica N.; Luther, Kurt; Batarseh, Feras A. (ACM, 2025-03-24)
In urban search and rescue (USAR) operations, communication between handlers and specially trained canines is crucial but often complicated by challenging environments and the specific behaviors canines are trained to exhibit when detecting a person. Since a USAR canine often works out of sight of the handler, the handler lacks awareness of the canine’s location and situation, known as the “sensemaking gap.” In this paper, we propose KHAIT, a novel approach to close the sensemaking gap and enhance USAR effectiveness by integrating object detection-based Artificial Intelligence (AI) and Augmented Reality (AR). Equipped with AI-powered cameras, edge computing, and AR headsets, KHAIT enables precise and rapid object detection from a canine’s perspective, improving survivor localization. We evaluate this approach in a real-world USAR environment, demonstrating an average survival allocation time decrease of 22%, enhancing the speed and accuracy of operations.
Frustration and its impact on search and rescue canines
Dickinson, Sally; Feuerbacher, Erica N. (Frontiers, 2025-03-07)
Despite advances in modern technology, dogs remain the primary detection tool in search and rescue (SAR) missions, locating missing persons across diverse and dynamic environments, including wilderness, avalanche zones, water, and disaster areas. Their exceptional olfactory abilities, combined with their capacity to process complex discrimination tasks and adapt to varied environmental stimuli, make them uniquely suited for this work. However, SAR operations can be both physically and psychologically demanding, requiring sustained focus, endurance, and consistent performance under stressful conditions. Frustration, a form of psychological stress, arises when a dog encounters blocked access to a goal or when an expectation is violated, triggering physiological and behavioral changes that may impact performance. This study investigated the physiological and behavioral responses of SAR dogs to two distinct stress conditions: psychological stress induced by frustration and physiological stress induced by moderate exercise. We measured heart rate variability as an indicator of autonomic nervous system response to stress and analyzed search task performance to assess how frustration and exercise affected the dogs’ latency and accuracy in executing their trained final response to the target odor. Our results revealed significant decreases in heart rate variability following frustration and increased latency in the search task, suggesting that frustration had a more pronounced impact on the dogs’ physiological state and performance compared to exercise. By examining the effects of psychological and physiological stress, this study contributes to a deeper understanding of how different stressors influence SAR dog performance and welfare. These findings provide valuable insights for optimizing training methodologies and operational preparedness, ensuring both the effectiveness and well-being of SAR dogs in the field.
Phytochemical Composition and Effects of Aqueous Extracts from Moringa oleifera Leaves on In Vitro Ruminal Fermentation Parameters
Oliveira, Inessa Steffany Torres de; Fernandes, Tatiane; Santos, Aylpy Renan Dutra; González Aquino, Carolina; Vega Britez, Gustavo Daniel; Vargas Junior, Fernando Miranda de (MDPI, 2025-01-20)
This study evaluated the phytochemical composition of aqueous extracts of Moringa oleifera (MO) obtained by maceration, decoction, and infusion of fresh or dried leaves and their effects on in vitro ruminal fermentation parameters. Phytochemical prospecting analyses were conducted to determine the bioactive compounds in each aqueous extract. Regarding the in vitro ruminal fermentation study, the seven treatments were the following: no addition of extract or control (CON); extract obtained by maceration of fresh leaves (MFL); extract obtained by maceration of dry leaves (MDL); extract obtained by decoction of the fresh leaves (DFL); extract obtained by decoction of dry leaves (DDL); extract obtained by infusion of fresh leaves (IFL) and extract obtained by infusion of dry leaves (IDL). The concentration of all bioactives (saponins, flavonoids, tannins, and alkaloids) quantified was higher when fresh MO leaves were used (p < 0.001). DFL and DDL provided less elimination of azino-bis radicals. On the other hand, MFL resulted in a greater elimination of these radicals. Extracts obtained from fresh leaves resulted in a greater total production of short-chain fatty acids, acetate, and butyrate (p < 0.05). Compared to the control treatment, the inclusion of extracts obtained from fresh leaves provided a higher concentration of propionate (p = 0.049). It is thereby concluded that the use of fresh MO leaves for the production of aqueous extracts is the most recommended, as it results in a higher concentration of bioactive compounds. The use of aqueous extracts of fresh MO leaves increases the total production of fatty acids but does not change their proportion.
Effects of Monensin, Calcareous Algae, and Essential Oils on Performance, Carcass Traits, and Methane Emissions Across Different Breeds of Feedlot-Finished Beef Cattle
Guerreiro, Pedro; Costa, Diogo F. A.; Limede, Arnaldo C.; Congio, Guilhermo F. S.; Meschiatti, Murillo A. P.; Bernardes, Priscila A.; Santos, Flavio A. Portela (MDPI, 2025-01-08)
With the growing use of crossbred cattle in Brazilian feedlots and increasing pressure to reduce antibiotic use as growth promoters, this study examines the impact of three feed additives—monensin (MON), monensin with Lithothamnium calcareum (LCM), and a blend of essential oils (BEO)—on the performance of Nellore (NEL) and crossbred (CROSS) cattle. A total of 90 Nellore and 90 crossbred bulls were assigned to a completely randomized block design with a 2 × 3 factorial design for 112 days, and all received the same diet with varying additives. Their methane (CH₄) emissions were estimated. All data were analyzed using the emmeans package of R software (version 4.4.1). Crossbred cattle outperformed Nellore in average daily gain (ADG), hot carcass weight (HCW), and dry matter intake (DMI), though feed efficiency remained unaffected. Across additives, no significant differences were observed in ADG, HCW, or dressing percentage. However, LCM had a lower DMI than the BEO, while MON showed better feed efficiency than the BEO. A breed-by-additive interaction trend was noted for DMI as a percentage of body weight (DMI%BW), with Nellore bulls on LCM diets showing the lowest DMI%BW. Crossbreeds had greater net energy (NE) requirements for maintenance (NEm) and gain (NEg), and MON-fed animals had greater NEm and NEg than the BEO. Crossbred bulls had greater daily methane (CH₄) emissions than Nellore bulls. Animals on the BEO had greater daily CH₄ emissions and greater g CH₄/kg metabolic BW than LCM bulls. In conclusion, the addition of Lithothamnium calcareum to monensin did not enhance performance compared to monensin alone. Monensin outperformed the BEO in feed efficiency and nutrient utilization.
Predicting Dairy Calf Body Weight from Depth Images Using Deep Learning (YOLOv8) and Threshold Segmentation with Cross-Validation and Longitudinal Analysis
Liao, Mingsi; Morota, Gota; Bi, Ye; Cockrum, Rebecca R. (MDPI, 2025-03-18)
Monitoring calf body weight (BW) before weaning is essential for assessing growth, feed efficiency, health, and weaning readiness. However, labor, time, and facility constraints limit BW collection. Additionally, Holstein calf coat patterns complicate image-based BW estimation, and few studies have explored non-contact measurements taken at early time points for predicting later BW. The objectives of this study were to (1) develop deep learning-based segmentation models for extracting calf body metrics, (2) compare deep learning segmentation with threshold-based methods, and (3) evaluate BW prediction using single-time-point cross-validation with linear regression (LR) and extreme gradient boosting (XGBoost) and multiple-time-point cross-validation with LR, XGBoost, and a linear mixed model (LMM). Depth images from Holstein (n = 63) and Jersey (n = 5) pre-weaning calves were collected, with 20 Holstein calves being weighed manually. Results showed that You Only Look Once version 8 (YOLOv8) deep learning segmentation (intersection over union = 0.98) outperformed threshold-based methods (0.89). In single-time-point cross-validation, XGBoost achieved the best BW prediction (R² = 0.91, mean absolute percentage error (MAPE) = 4.37%), while LMM provided the most accurate longitudinal BW prediction (R² = 0.99, MAPE = 2.39%). These findings highlight the potential of deep learning for automated BW prediction, enhancing farm management.
Are smelly toys more fun? Shelter dogs' preferences for toys, scents, and scented toys
Howard, Skyler; Gunter, Lisa M.; Feuerbacher, Erica N. (Elsevier, 2024-09)
As dogs reside in shelters awaiting adoption, it is critical that they remain behaviorally healthy. A variety of enrichment strategies improve the welfare of shelter dogs, including object (usually in the form of toys) and scent enrichment. However, for these interventions to be enriching, dogs must engage with the items and their welfare be positively affected. Thus, by identifying dogs’ preferences, shelters can improve the function of their enrichment. Using a 15 min free operant preference assessment, an assessment in which the subject is given free access to a variety of items and the duration of their engagement with each item is recorded, we investigated 34 shelter dogs’ preferences for four different toys: a stuffed toy, tennis ball, Nylabone, and flying disc. We also investigated dog’ preferences for four scents: hotdog, peppermint, duck, and an unfamiliar dog. Finally, we applied the dog's preferred scent to their most and least preferred toys to investigate whether adding their preferred scent would increase the amount of time they engaged with those items compared to unscented duplicates. During the toy preference assessment, we observed that dogs, on average, only interacted with toys 3.35 % of the 15 min session. However, we found that dogs engaged over eight times longer with the stuffed toy as compared to all other toys, F (1, 134) = 64.40, p <.001. There was a marginal effect of type during the scent assessment, F (3, 132) = 2.50, p =.062, but post hoc comparisons were not significant. When we applied each dog's preferred scent to their most and least preferred toys, we found statistically significant main effects for preference, F (1, 132) = 54.95, p <.001, and scent, F (1, 132) = 7.16, p =.008, and a significant preference-by-scent interaction, F (1, 132) = 4.66, p =.033. The addition of scent increased engagement with both toys, such that dogs spent 4.2 and 13.7 times more seconds with their most and least preferred toys, respectively. In addition to our results aligning with prior research demonstrating that dogs prefer soft versus hard toys, these findings suggest that combining objects and scents can increase dogs’ engagement with enrichment and may be especially impactful when providing shelter dogs with less preferred objects, such as hard toys.
Functionalized Graphene-Based Biosensors for Early Detection of Subclinical Ketosis in Dairy Cows
Chick, Shannon; Kachouei, Matin Ataei; Knowlton, Katharine; Ali, Md Azahar (American Chemical Society, 2024-08-22)
Precision livestock farming utilizing advanced diagnostic tools, including biosensors, can play a key role in the management of livestock operations to improve the productivity, health, and well-being of animals. Detection of ketosis, a metabolic disease that occurs in early lactation dairy cows due to a negative energy balance, is one potential on-farm use of biosensors. Beta-hydroxybutyrate (βHB) is an excellent biomarker for monitoring ketosis in dairy cows because βHB is one of the main ketones produced during this metabolic state. In this report, we developed a low-cost, Keto-sensor (graphene-based sensor) for the detection of βHB concentrations in less than a minute. On this device, graphene nanosheets were layered onto a screen-printed electrode (SPE), and then, a stabilized enzyme (beta-hydroxybutyrate dehydrogenase, NAD+, and glycerol) was used to functionalize the graphene surface enabled by EDC-NHS conjugation chemistry. The Keto-sensor offers an analytical sensitivity of 10 nm and a limit of detection (LoD) of 0.24 nm within a detection range of 0.01 μm-3.00 mm. Spike testing indicates that the Keto-sensor can detect βHB in serum samples from bovines with subclinical ketosis. The Keto-sensor developed in this study shows promising results for early detection of subclinical ketosis on farms.
Regulation of the expression of αS₁ and αS₂ casein genes in bovine mammary epithelial cells by STAT5A
Wang, A.; Pokhrel, Binod; Perez Hernandez, Gabriela; Jiang, Hongliang (Elsevier, 2024)
Cow milk is rich in protein. Major cow milk proteins include αS₁ casein (CSN1S1), αS₂ casein (CSN1S2), β casein (CSN2), κ casein (CSN3), lactalbumin α (LALBA), and β-LG. These milk proteins are produced through gene expression in the mammary epithelial cells. Little is known about the molecular mechanism that mediates the expression of milk protein genes in cows. In this study, we tested the hypothesis that the expression of milk protein genes in cows is mediated by STAT5A, a transcription factor that is induced to bind and activate the transcription of target genes by extracellular signals such as prolactin. To circumvent the need for prolactin-responsive bovine mammary epithelial cells, we generated a plasmid that expresses a constitutively active bovine STAT5A variant, bSTAT5ACA. Transfection of the bovine mammary epithelial cell line MAC-T cells with the bSTAT5ACA expression plasmid caused a more than 100,000-fold and 600-fold increase in the expression of CSN1S1 and CSN1S2 mRNAs, respectively, compared with transfection of the wild-type bovine STAT5A (bSTAT5A) expression plasmid. Transfection of bSTAT5ACA, however, had no significant effect on the expression of CSN2, CSN3, LALBA, or LGB mRNA in MAC-T cells. Transfection of bSTAT5ACA caused a more than 260-fold and 120-fold increase in the expression of a luciferase reporter gene linked to the bovine CSN1S1 and CSN1S2 promoters in MAC-T cells, respectively, compared with that of bSTAT5A. The bovine CSN1S1 and CSN1S2 promoters each contain a putative STAT5 binding site, and gel-shift and super-shift assays confirmed bSTAT5ACA binding to both sites. These results together suggest that STAT5A plays a major role in regulating the expression of CSN1S1 and CSN1S2 genes in the bovine mammary epithelial cells and that STAT5A regulates the expression of these genes at least in part by binding to the STAT5 binding sites in their promoter regions. These results also suggest that STAT5A does not play a major role in regulating the expression of other major milk protein genes.
Indirectly acquired fear memories have distinct, sex-specific molecular signatures from directly acquired fear memories
Navabpour, Shaghayegh; Patrick, Morgan B.; Omar, Nour A.; Kincaid, Shannon E.; Bae, Yeeun; Abraham, Jennifer; McGrew, Jacobi; Musaus, Madeline; Ray, W. Keith; Helm, Richard F.; Jarome, Timothy J. (PLOS, 2024-12-23)
Post-traumatic stress disorder (PTSD) is a severe anxiety disorder that affects women more than men. About 30% of patients suffering from PTSD develop the disorder by witnessing a traumatic event happen to someone else. However, as the focus has remained on those directly experiencing the traumatic event, whether indirectly acquired fear memories that underlie PTSD have the same molecular signature as those that are directly acquired remains unknown. Here, using a rodent indirect fear learning paradigm where one rat (observer) watches another rat (demonstrator) associate an auditory cue with foot shock, we found that fear can be indirectly acquired by both males and females regardless of the sex or novelty (familiarity) of the demonstrator animal. However, behaviorally, indirectly acquired fear responses resemble those of pseudoconditioning, a behavioral response that is thought to not represent learning. Despite this, using unbiased proteomics, we found that indirectly acquired fear memories have distinct protein degradation profiles in the amygdala and anterior cingulate cortex (ACC) relative to directly acquired fear memories and pseudoconditioning, which further differed significantly by sex. Additionally, Egr2 and c-fos expression in the retrosplenial cortex of observer animals resembled that of demonstrator rats but was significantly different than that of pseudoconditioned rats. Together, these findings reveal that indirectly acquired fear memories have sex-specific molecular signatures that differ from those of directly acquired fear memories or pseudoconditioning. These data have important implications for understanding the neurobiology of indirectly acquired fear memories that may underlie bystander PTSD.
Human Recombinant Interleukin-6 and Leukemia Inhibitory Factor Improve Inner Cell Mass Cell Number but Lack Cryoprotective Activities on In Vitro-Produced Bovine Blastocysts
Oliver, Mary A.; Alward, Kayla J.; Rhoads, Michelle L.; Ealy, Alan D. (MDPI, 2025-02-25)
This work explored whether supplementing recombinant human interleukin-6 (IL6), interleukin-11 (IL11), or leukemia inhibitory factor (LIF) improves IVP bovine embryo development, morphology, and cryosurvivability. Embryos were treated from day 5 to 8 post-fertilization with either the carrier only (control) or 100 ng/mL of IL6, IL11, or LIF. Blastocyst formation and stage were determined on day 7 and 8. A subset of day 8 blastocysts was processed for immunofluorescence to count trophectoderm (TE) and inner cell mass (ICM) cell numbers and another subset was slow frozen and stored in liquid nitrogen until thawing. No differences in the blastocyst rate or blastocyst stage of development were detected. Increases in ICM cell numbers were observed for IL6 and LIF but not the IL11 treatment. None of the cytokine treatments applied before freezing affected post-thaw survival, TE or ICM cell number, or cell death 24 h after thawing. In conclusion, supplementing IL6 and LIF improves ICM cell numbers in non-frozen blastocysts, but there was no evidence that any of these cytokine treatments contain cryoprotective properties in bovine embryos.
Effect of Supplemental Trace Mineral Source on Haircoat and Activity Levels in Senior Dogs
Amundson, Laura A.; Millican, Allison A.; Swensson, Erik; McGilliard, Michael L.; Tomlinson, Dana (MDPI, 2025-02-26)
Trace minerals (TMs) are pivotal for animal wellbeing and appearance. This study evaluated the effects of TM (Zn, Mn, Cu, and Fe) sources on senior dogs’ haircoat and activity. Dogs (mean age 9.16 yr) were fed a control diet (inorganic TM) for 14 d before being assigned to one of three treatments for 3 mo. Treatments included inorganic (Control; n = 10), amino acid-complexed (TMC; n = 17; ZINPRO^® ZnMet + Zinpro^® Availa^® Mins) or lysine and glutamic acid-complexed (TMC-LG; n = 16; Zinpro^® ProPath^®) supplemental TM. Treatments were formulated to provide standard (Control—100 ppm Zn, 5 ppm Mn, 12 ppm Cu, 45 ppm Fe) or product-recommended (TMC and TMC-LG—100 ppm Zn, 25 ppm Mn, 7 ppm Cu, 45 ppm Fe) TM levels (DM basis). Hair length, regrowth, and shedding were measured along with activity. Dogs fed TMC (26.43 mm; 11.64 mm/mo) and TMC-LG (27.87 mm; 12.6 mm/mo) had significantly (p ≤ 0.05) longer hair that grew faster compared to the Control (18.93 mm; 9.14 mm/mo). At 3 mo TMC-LG-fed dogs had 0.38 g less shed hair, and TMC-fed dogs had 0.87 h more active time/d compared to the Control (p ≤ 0.05). Dogs fed TMC and TMC-LG had superior haircoat characteristics and activity compared to the Control.
Open-source carbon dioxide and volatile organic compound sensing and associations with defecation and urination events in horses
Wright, Ryan K.; Ganino, Alyssa; White, Robin R. (2025-03-03)
Management of non-point-source emissions from pastured livestock is complicated by spatial and temporal distribution of emissions and how they interplay with equally complex landscape typological distributions. Wearable sensing of CO2 concentrations near the tailhead may enable real-time, spatially-explicit monitoring of manure emissions, if concentrations correlate with defecation and urination events. The objective of this research was to explore the association between measured CO2 concentrations from wearable sensors placed on the tailhead of horses and the occurrence of defecation and urination events. CO2 sensors consisted of a TTGO-T-Beam microprocessor equipped with GPS and LoRa radio, soldered to a CJMCU-8128 environmental sensing board capable of measuring temperature, pressure, relative humidity, CO2 and total volatile organic compounds (TVOC). Tail wraps were placed on 4 stalled horses for a total of 9 days. Surveillance videos were collected over the same time frame and viewed to determine the time of defecation and urination occurrence. Data were analyzed visually for coherence, and quantitatively using analysis of variance, random forest regression, support vector machines, and extreme gradient boosting. Because defecation and urination events were in much lower quantity than non-events, random oversampling and undersampling were attempted on the classification approaches to improve accuracy and precision of signaling algorithms. Visual inspection revealed that although defecation and urination events corresponded to CO2 peaks, there was considerable noise in CO2 data suggesting that peaks in CO2 also frequently occur in the absence of defecation and urination events. All classification algorithms showed poor accuracies (0.50 to 0.51), which were only marginally improved by over- (< 0.51) and undersampling (< 0.69). This preliminary assessment revealed considerable noise in sensing CO2 emissions in production settings, which may preclude usefulness in manure sensing.
Multi-Input Deep Learning Models for Weight Forecasting of Pigs Using Depth Images
Ranjan, Pranjal; Ha, Dong Sam; Morota, Gota; Shin, Sook (2024-10-01)
Accurate weight forecasting is essential for optimizing swine farming operations and enhancing animal welfare. This paper introduces a novel approach for pig weight forecasting, employing multi-input deep learning models that harness both depth images and statistical descriptors. The study conducts a comprehensive comparison of traditional machine learning (ML) models, deep learning (DL) models, hybrid ML and DL models, and multi-input models integrating both time-series data and image features. A meticulously curated dataset comprising timeseries weight measurements and corresponding depth images of pigs forms the foundation of the study. Image descriptors such as length, width, depth, and volume were extracted from the depth images. The proposed multi-input models, employing architectures based on ResNet, XCeption, LSTM, and GRU layers, are meticulously trained and evaluated using this dataset. The performance evaluation is conducted using mean absolute error (MAE) and mean absolute percentage error (MAPE) metrics. The results underscore the superiority of the multi-input models over traditional ML, DL, and hybrid models. Notably, the best-performing model achieves a test MAE of 1.81 kg and a test MAPE of 5.56%. This exceptional performance highlights the importance of leveraging both time-series data and image features for precise weight forecasting in pigs. These findings can hold significant implications for improving the efficiency and sustainability of swine farming practices, offering a pathway towards improved decision-making and animal management protocols.
The Impact Aerobic and Anaerobic Incubations of Poultry Litter Have on Class 1 Integron Resistome and Microbiome
Maurer, John J.; Hoke, Alexa; Das, Keshav C.; Wu, Jian; Williams, Mark A.; Kinstler, Sydney; Ritz, Casey; Pittman, Gregory P.; Berghaus, Roy; Lee, Margie D. (MDPI, 2025-02-13)
Animal manure is a desirable fertilizer because of its rich nitrogen, but it also contains a large and diverse reservoir of antimicrobial resistance (AMR) genes (ARGs). To reduce this AMR reservoir, five treatments (passive aeration, forced aeration, static or anaerobic incubations, autoclaving) were assessed for their impact on the poultry litter resistome. Bacterial DNA was extracted from the litter and the qPCR-estimated copy number of 16S rrs, class1 integrons (intI1) and associated resistance genes (aadA, sul1). Then, 16S amplicon metagenomic sequencing was used to determine community diversity and composition. Depending on incubation conditions, class 1 integrons and their associated ARGs were reduced by 0.5 to 1.0 Log₁₀/g poultry litter. Only autoclaving reduced integrons and associated AMR genes by three Log₁₀. Changes in AMR abundance reflected fluctuations in litter bacteriome composition at the family, genus, and sequence variant level. There was a negative correlation between class 1 integron and AMR genes, with genera belonging to Actinobacteria, Firmicutes, and Proteobacteria phyla. While these poultry litter treatments failed to reduce AMR abundance, aerobic and anaerobic treatments reduced taxons that contained pathogenic species. The approach to remediating resistance in poultry litter may be more effective if is focused on reducing bacterial pathogens.
Verify the effectiveness of various inclusions of butyrate on male broilers raised on used litter without antibiotics
Fritzlen, Cooper J.; Maurer, John J.; Wong, Eric A.; Persia, Michael E. (Elsevier, 2024-12)
An experiment was conducted to verify the effectiveness of butyrate (BA) in diets of broiler chickens raised without antibiotics and exposed to used litter. Dietary treatments included: negative control (NC), a nonsupplemented diet on fresh shavings; positive control (PC), the same nonsupplemented diet on used litter; 500 BA, similar diet with 500 ppm BA on used litter; 1,000 BA, similar diet with 1,000 ppm BA on used litter; 500/250 BA, similar diet with 500 ppm BA from 0 to 8 d and 250 ppm BA from 8 to 42 d on used litter; 1,000/250 BA, similar diet with 1,000 ppm BA from 0 to 8 d and 250 ppm BA from 8 to 42 d on used litter. From 0 to 8 d, the PC resulted in a 6.8 g decrease in BW gain (BWG) compared to NC, but this response was lost from 0 to 25 d or 0 to 42 d. There were no differences in mortality corrected, FCR (FCRm) between PC and NC. All BA treatments increased BWG in comparison to PC from 0 to 8 d, with no differences from NC. Butyrate improved 0 to 8 d FCRm compared to both PC and NC (P ≤ 0.05), but these responses were lost over time (P > 0.05). Butyrate increased apparent ileal digestibility of energy and DM (P > 0.05). Butyrate had no effect on oocyst shedding compared to PC (P > 0.05). Butyrate was able to ameliorate the negative performance effects with reused litter over the 8-d starter period and was able to increase ileal digestibility of energy and DM.
Effects of dietary enteric-released or pure benzoic acid on Ross 708 male broilers
Fritzlen, Cooper J.; Maurer, John J.; Chen, W.; Tan, Z.; Liu, H.; Peng, X.; Qin, Z.; Peng, Y.; Persia, Michael E. (Elsevier, 2024-12)
An experiment was conducted to evaluate the effects of pure benzoic acid (PBA) or enteric-released benzoic acid (EBA) on performance, intestinal histology, apparent ileal digestibility (AID), cecal coliform and enterococci abundance, and litter moisture of broilers raised on used litter. Day-old male broiler chicks were assigned to control (Con), nontreated diet; positive control (BMD), Con + 50 ppm bacitracin methylene disalicylate; PBA, Con +1,000 ppm of PBA; EBA, Con +330 ppm of EBA. From 0 to 28 and 0 to 42 d, BMD outperformed the Con in either BW gain (BWG) or mortality corrected FCR (FCRm) (P ≤ 0.05). Over 0 to 28 d, EBA and PBA improved BWG and FCRm compared to the Con (P ≤ 0.05). When the entire 0 to 42 d period was considered, EBA improved both BWG and FCRm in comparison to Con (P ≤ 0.05). Supplementation with EBA and PBA resulted in inconsistent responses in duodenum and jejunum morphology; specifically, PBA decreased 28 d duodenal crypt depth and increased villus height to crypt depth ratio, while EBA decreased 28 d jejunum crypt depth (P ≤ 0.05). There were no differences in AID or cecal coliform counts (P > 0.05) due to treatment. However, PBA significantly reduced enterococcus counts at 42 d by 0.48 Log10 CFU/g compared to CON. These results suggest that EBA can increase BWG and decrease FCRm, while PBA performance was similar to CON. Additionally, benzoic acid decreased crypt depth, with the response being tissue-specific depending on the form of benzoic used.

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