Defining optimal dietary starch, oil, and amino acid inclusion levels for broilers experiencing a coccidiosis challenge

Alternative methods to alleviate coccidiosis in broilers are of interest to producers, including dietary strategies to minimize disruptions in growth rate and efficiency when faced with health challenges. Our objective was to determine optimal combinations of dietary starch, amino acids (AA), and oil to benefit productivity of broilers experiencing Eimeria-induced immune activation. Two trials were conducted using 1,536 male Ross 308 broiler chicks in floor pens randomly assigned to 1 of 17 experimental treatments. All birds received common starter (d 0-10) and finisher (d 24-35) diets, and only differed based on their assigned experimental grower diet (d 10-24). Trial 1 experimental grower diets ranged from 2,700 to 3,300 kcal/kg AME. Trial 2 included 10 experimental grower diets following a simplex lattice design consisting of 3 basal lots formulated to have the highest starch (45.4%), oil (10.2%), or AA density (120, 1.33% digestible Lys) and mixed in 4 equally spaced levels for each component (0, 0.33, 0.67, 1). These mixtures enabled varying densities of AA (80-120% of recommendation), starch:oil (4:1-20:1), and AME (2,940-3,450 kcal/kg). Bird and feeder weights were collected on d 0, 10, 24, and 35, and birds were exposed to an Eimeria challenge on d 11 or 12. In trial 2, excreta samples were collected for AME determination and carcasses were processed on d 36. Data were analyzed using ANOVA, t test, or regression. In Trial 1, BW gain and feed conversion were improved (P < 0.05) by increasing dietary AME. In Trial 2, birds receiving diets containing AA at 93 to 107% of recommendations and higher oil exhibited improved (P < 0.05) performance, but increased starch at the expense of oil reduced performance (P < 0.05). Relative breast and fat pad weights were not influenced by diet in Trial 2. We determined that broilers mildly challenged with Eimeria would exhibit highest BW gain when receiving diets containing 35.8% starch, 8.9% oil, and 101.3% of AA recommendations, which can be utilized by producers to maintain productivity under health-challenged conditions.

Ability of three dairy feed evaluation systems to predict postruminal outflows of amino acids in dairy cows: A meta-analysis

Adequate prediction of postruminal outflows of essential AA (EAA) is the starting point of balancing rations for EAA in dairy cows. The objective of this meta-analysis was to compare the performance of 3 dairy feed evaluation systems (National Research Council [NRC], Cornell Net Protein and Carbohydrate System version 6.5.5 [CNCPS], and National Academies of Sciences, Engineering and Medicine [NASEM]) to predict EAA outflows (Trp was not tested). The data set included a total of 354 treatment means from 70 duodenal and 24 omasal studies. To avoid Type I error, mean and linear biases were considered of concern if statistically significant and representing > 5.0% of the observed mean. Analyses were conducted on raw observed values and on observations adjusted for the random effect of study. The analysis on raw data indicates the ability of the feed evaluation system to predict absolute values whereas the analysis on adjusted values indicates its ability to predict responses of EAA outflows to dietary changes. For the prediction of absolute values (based on raw data), NRC underpredicted outflows of all EAA, from 5.3 to 8.6% of the observed mean (%obs.mean) except for Leu, Lys, and Val; NASEM overpredicted Lys (10.8%obs.mean); and CNCPS overpredicted Arg, His, Lys, Met, and Val (5.2 to 26.0%obs.mean). No EAA had a linear bias of concern with NASEM, followed by NRC for His (6.8%obs.mean), and CNCPS for all EAA (5.6 to 12.2%obs.mean) except Leu, Phe, and Thr. On the other hand, for the prediction of responses to dietary changes (based on adjusted data), NRC had 2 EAA presenting a linear bias of concern, followed by NASEM and CNCPS with 4 and 6 EAA, respectively. Predictions of His showed a linear bias of concern (5.3 to 9.6%obs.mean) with the 3 feed evaluation systems. Measured chemistry of crude protein and EAA were reported for 1 or more feed ingredients of the ration in 36% of the studies, and resulted in decreased linear biases in the 3 feed evaluation systems. The difference in mean biases of Met outflows was systematically positive when comparing omasal versus duodenal studies. Predictions of Met outflows with NRC had a higher concordance correlation coefficient in duodenal (used to develop NRC equations) versus omasal studies, whereas the opposite was observed with CNCPS, the latter showing the lowest mean bias for Met in omasal sampling studies. The 30% difference in Met mean biases between sampling sites appeared related to a similar difference found for observed Met versus NAN outflows between duodenal and omasal studies, which is independent of predictions. In conclusion, NRC and NASEM yielded accurate predictions of EAA outflows, with a small superiority of NASEM to predict absolute values, and slight superiority of NRC to predict the responses to dietary changes. In comparison, CNCPS may present mean and linear biases of concern for many EAA. Moreover, it remains to determine which sampling site is more representative of the true supply of EAA to the cows.

Ability of three dairy feed evaluation systems to predict postruminal outflows of nitrogenous compounds in dairy cows: A meta-analysis

Adequate prediction of postruminal outflow of protein fractions is the starting point for the determination of metabolizable protein supply in dairy cows. The objective of this meta-analysis was to compare the performance of 3 dairy feed evaluation systems (National Research Council [NRC], Cornell Net Protein and Carbohydrate System [CNCPS], and National Academies of Sciences, Engineering and Medicine [NASEM]) to predict outflows (g/d) of nonammonia nitrogren (NAN), microbial N (MiN), and nonammonia nonmicrobial N (NANMN). Predictions of rumen degradabilities (% of nutrient) of protein (RDP), NDF, and starch were also evaluated. The data set included 1,294 treatment means from 312 digesta flow studies. The 3 feed evaluation systems were compared using the concordance correlation coefficient (CCC), the ratio of root mean square prediction error (RMSPE) on standard deviation of observed values (RSR), and the slope between observed and predicted values. Mean and linear biases were deemed biologically relevant and are discussed if higher than a threshold of 5% of the mean of observed values. The comparisons were done on observed values adjusted or not for the study effect; the adjustment had a small effect on the mean bias but the linear bias reflected a response to a dietary change rather than absolute predictions. For the absolute predictions of NAN and MiN, CNCPS had the best-fit statistics (8% greater CCC; 6% lower RMSPE) without any bias; NRC and NASEM underpredicted NAN and MiN, and NASEM had an additional linear bias indicating that the underprediction of MiN increased at increased predictions. For NANMN, fit statistics were similar among the 3 feed evaluation systems with no mean bias; however, the linear bias with NRC and CNCPS indicated underprediction at low predictions and overprediction at elevated predictions. On average, the CCC were smaller and RSR ratios were greater for MiN versus NAN indicating increased prediction errors for MiN. For NAN responses to a dietary change, CNCPS also had the best predictions, although the mean bias with NASEM was not biologically relevant and the 3 feed evaluation systems did not present a linear bias. However, CNCPS, but not the 2 other feed evaluation systems, presented a linear bias for MiN, with responses being overpredicted at increased predictions. For NANMN, responses were overpredicted at increased predictions for the 3 feed evaluation systems, but to a lesser extent with NASEM. The site of sampling had an effect on the mean bias of MiN and NANMN in the 3 feed evaluation systems. The mean bias of MiN was higher in omasal than duodenal studies in the 3 feed evaluation systems (from 55 to 61 g/d) and this mean bias was twice as large when 15N labeling was used as a microbial marker compared with purines. Such a difference was not observed for duodenal studies. The reasons underlying these systematic differences are not clear as the type of measurements used in the current meta-analysis does not allow to delineate if one site or one microbial marker is yielding the "true" postruminal N outflows. Rumen degradabilities of protein was underpredicted with CNCPS, and RDP responses to a dietary change was underpredicted by the 3 feed evaluation systems with increased RDP predictions. Rumen degradability of NDF was underpredicted and had poor fit statistics for NASEM compared with CNCPS. Fit statistics were similar between CNCPS and NASEM for rumen degradability of starch, but with an underprediction of the response with NASEM and absolute values being overpredicted with CNCPS. Multivariate regression analyses showed that diet characteristics were correlated with prediction errors of N outflows in each feed evaluation system. Globally, compared with NAN and NANMN, residuals of MiN were correlated with several moderators in the 3 feed evaluation systems reflecting the complexity to measure and model this outflow. In addition, residuals of NANMN were correlated positively with RDP suggesting an overestimation of this parameter. In conclusion, although progress is still to be made to improve equations predicting postruminal N outflows, the current feed evaluation systems provide sufficient precision and accuracy to predict postruminal outflows of N fractions.

Global contributions of milk to nutrient supplies and greenhouse gas emissions

Globally, ruminant production systems used to synthesize meat and milk differ tremendously in terms of their efficiency, productivity, and environmental impacts. Regardless of this variability, milk has been repeatedly identified as an essential source of nutrients for humans. The objective of this work was to characterize global contributions of fluid milk to human food and nutrient supplies, greenhouse gas emissions, and water withdrawal. Data were leveraged from the United Nations Food and Agriculture Organization to estimate global supplies of agricultural products. Trade of agricultural products and waste of those products, along with use of human food for livestock feed were accounted for before estimating human nutrient supplies. The contributions of milk to human-edible nutrient supplies were then enumerated in terms of their proportion of total nutrients supplied by the agricultural system and in terms of the human population's requirement for that nutrient. We identified that fluid milk provides over 10% of consumable supplies of vitamin B₁₂, vitamin A, riboflavin, and calcium available for humans globally. In terms of human nutrient requirements, milk provides sufficient vitamin B₁₂ to meet the needs of over 60% of the global population, riboflavin to satisfy 50% of the population, and calcium and phosphorus for over 35% of the population. Compared with other foods, milk ranked among the highest in terms of nutrient-to-calorie ratio for numerous amino acids, phosphorus, calcium, and riboflavin. Conditional dependencies were identified between greenhouse gas emissions and ruminant milk and meat, but not between water withdrawal and milk production. When evaluating the trade-offs in nutrient use versus nutrient provision for producing milk or producing all ruminant products, the production of ruminants worldwide was associated with both net increases and net decreases of several key nutrients. Continued work focusing on strategies to reduce the environmental impact of milk production will improve the utility of milk for feeding the growing global population.

Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer

Fanconi anaemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink repair resulting in chromosome breakage^1-3. The FA repair pathway protects against endogenous and exogenous carcinogenic aldehydes^4-7. Individuals with FA are hundreds to thousands fold more likely to develop head and neck (HNSCC), oesophageal and anogenital squamous cell carcinomas⁸ (SCCs). Molecular studies of SCCs from individuals with FA (FA SCCs) are limited, and it is unclear how FA SCCs relate to sporadic HNSCCs primarily driven by tobacco and alcohol exposure or infection with human papillomavirus⁹ (HPV). Here, by sequencing genomes and exomes of FA SCCs, we demonstrate that the primary genomic signature of FA repair deficiency is the presence of high numbers of structural variants. Structural variants are enriched for small deletions, unbalanced translocations and fold-back inversions, and are often connected, thereby forming complex rearrangements. They arise in the context of TP53 loss, but not in the context of HPV infection, and lead to somatic copy-number alterations of HNSCC driver genes. We further show that FA pathway deficiency may lead to epithelial-to-mesenchymal transition and enhanced keratinocyte-intrinsic inflammatory signalling, which would contribute to the aggressive nature of FA SCCs. We propose that the genomic instability in sporadic HPV-negative HNSCC may arise as a result of the FA repair pathway being overwhelmed by DNA interstrand crosslink damage caused by alcohol and tobacco-derived aldehydes, making FA SCC a powerful model to study tumorigenesis resulting from DNA-crosslinking damage.

Global human-edible nutrient supplies, their sources, and correlations with agricultural environmental impact

Food production, sustainable development, population growth, and agricultural environmental impacts are linked global problems that require complex solutions. Many efforts evaluating these challenges primarily evaluate dietary strategies designed for health and environmental objectives without considering the subsequent adaptations required by the global food supply. Here we use a complementary approach to summarize trends and variability in the current agricultural system in the context of the growing population and impending environmental challenges. Globally, agricultural systems produce sufficient nutrients to feed 10 billion people with the exception of Ca, DHA + EPA, vitamins B4, D, and E. In a network analysis, greenhouse gas emissions were conditionally dependent on ruminant meat and milk, while water use was conditionally dependent on vegetable and fruit production; however, supplies of most nutrients were also dependent on these same production categories, suggesting trade-offs between nutritional and environmental objectives. Future work should evaluate strategies to address these compromises (i.e., improving water use efficiency and reducing greenhouse gas emissions), to explore to what extent such compromises are biophysically essential or merely a product of the current agricultural system structures. Given the time-sensitive nature of population growth and environmental concerns, strategies to make more effective use of currently produced agricultural products will also be critical complementary strategies to sustainably feed the growing population which can work in concert with other agricultural-, diet- and policy-focused efforts.

Abstract 6196: Fanconi anemia pathway deficiency drives copy number variation in squamous cell carcinoma

Fanconi anemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink (ICL) repair resulting in chromosome breakage. The FA repair pathway comprises at least 22 FANC proteins including BRCA1 and BRCA2 and protects against carcinogenic endogenous and exogenous aldehydes. Individuals with FA are hundreds to thousands-fold more likely to develop head and neck (HNSCC), esophageal and anogenital squamous cell carcinomas (SCCs) with a median onset age of 31 years. The aggressive nature of these tumors and poor patient tolerance of platinum and radiation-based therapy have been associated with short survival in FA. Molecular studies of SCCs from individuals with FA (FA SCCs) have been limited, and it is unclear how they relate to sporadic HNSCCs primarily driven by tobacco and alcohol exposure or human papillomavirus (HPV) infection. Here, by sequencing FA SCCs, we demonstrate that the primary genomic signature of FA-deficiency is the presence of a high number of structural variants (SVs). SVs are enriched for small deletions, unbalanced translocations, and fold-back inversions that arise in the context of TP53 loss. The SV breakpoints preferentially localize to early replicating regions, common fragile sites, tandem repeats, and SINE elements. SVs are often connected forming complex rearrangements. Resultant genomic instability underlies elevated copy number alteration (CNA) rates of key HNSCC-associated genes, including PIK3CA, MYC, CSMD1, PTPRD, YAP1, MXD4, and EGFR. In contrast to sporadic HNSCC, we find no evidence of HPV infection in FA HNSCC, although positive cases were identified in gynecologic tumors. A murine allograft model of FA pathway-deficient SCC was enriched in SVs, exhibited dramatic tumor growth advantage, more rapid epithelial-to-mesenchymal transition, and enhanced autonomous inflammatory signaling when compared to an FA pathway-proficient model. In light of the protective role of the FA pathway against SV formation uncovered here, and recent findings of FA pathway insufficiency in the setting of increased formaldehyde load resulting in hematopoietic stem cell failure and carcinogenesis, we propose that high copy-number instability in sporadic HNSCC may result from functional overload of the FA pathway by endogenous and exogenous DNA crosslinking agents. Our work lays the foundation for improved FA patient treatment and demonstrates that FA SCC is a powerful model to study tumorigenesis resulting from DNA crosslinking damage.

Citation Format: Andrew L. Webster, Mathijs A. Sanders, Krupa Patel, Ralf Dietrich, Raymond J. Noonan, Francis P. Lach, Ryan R. White, Audrey M. Goldfarb, Kevin Hadi, Matthew M. Edwards, Frank X. Donovan, Moonjung Jung, Sunandini Sridhar, Olivier Fedrigo, Huasong Tian, Joel Rosiene, Thomas Heineman, Jennifer Kennedy, Lorenzo Bean, Rasim O. Rosti, Rebecca Tryon, Ashlyn-Maree Gonzalez, Allana Rosenberg, Ji-Dung Luo, Thomas Carrol, Eunike Velleuer, Jeff C. Rastatter, Susanne I. Wells, Jordi Surrallés, Grover Bagby, Margaret L. MacMillan, John E. Wagner, Maria Cancio, Farid Boulad, Theresa Scognamiglio, Roger Vaughan, Amnon Koren, Marcin Imielinski, Settara Chandrasekharappa, Arleen D. Auerbach, Bhuvanesh Singh, David Kutler, Peter J. Campbell, Agata Smogorzewska. Fanconi anemia pathway deficiency drives copy number variation in squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6196.

Inhibition of SUMOylation modulates the immunosuppressive microenvironment of pancreatic cancer

Objective

Pancreatic cancer (PC) is a highly aggressive disease that is poorly responsive to available immunotherapy approaches, such as checkpoint inhibitors. Post-translational protein modification (PTM) by small ubiquitin-like modifier (SUMO) is upregulated in cancer, and high expression of SUMOylation-related factors correlates with poor survival in PC. TAK-981 is a novel inhibitor of SUMOylation that has demonstrated induction of anti-tumor immune responses in preclinical models. Our hypothesis is that TAK-981 will decrease SUMOylated proteins and subsequently modulate the tumor microenvironment to increase anti-tumor immunity.

Methods

In order to recapitulate the microenvironment of human PC, a 3-dimensional organoid cell line derived from a genetically-engineered “KPC” mouse was used. Organoids were injected orthotopically into the head of the pancreas via laparotomy. Once tumors reached 5–7 mm in diameter on ultrasound imaging, mice were randomized to one of two treatment groups: Control/Vehicle versus TAK-981 (15 mg/kg) delivered daily via intraperitoneal injection. Tumors were harvested on day 14 for gene expression analysis by quantitative real time PCR (RT-qPCR).

Results

Tumor growth (Fig. 1) in the TAK-981 15 mg/KG daily group (mean + SD volume = 207 + 109 mm3) was significantly inhibited compared to the vehicle group (595 + 141 mm3, p &lt; 0.01). Immunohistochemical staining for CD 31 (Fig. 2) and Caspase 3 indicated a reduction of angiogenesis and increased apoptosis of tumor cells, consistent with the well-established roles of SUMOylation in angiogenesis and tumorigenesis. Gene expression analysis of tumor lysates showed a 26-fold increase in expression of Interferon beta (p&lt;0.05), and an almost 2-fold increase in expression of genes related to dendritic cell activation, including CD80 (p&lt;0.05) and CD86 (p=0.14) in the TAK-981 group, suggesting a modulation of the immune microenvironment.

Conclusion

Our results suggest that the inhibition of SUMOylation with TAK-981 is associated with improved local tumor control and changes in the immunosuppressive tumor microenvironment. We expect that TAK-981 will improve PC responsiveness to immunotherapy, such as with checkpoint inhibitors.

Practical challenges and potential approaches to predicting low-incidence diseases on farm using individual cow data: A clinical mastitis example

Clinical mastitis (CM) incidence is considerable in terms of cows affected per year, but cases are much less common in terms of detections per cow per milking. From a modeling perspective, where predictions are made every time any cow is milked, low CM incidence per cow day makes training, evaluating, and applying CM prediction models a challenge. The objective of this study was to build models for predicting CM incidence using time-series sensor data and choose models that maximize net return based on a cost matrix. Data collected from 2 university dairy farms, the University of Florida and Virginia Polytechnic Institute and State University, were used to gather representative data, including 110,156 milkings and 333 CM cases. Variables used in the models were milk yield, protein, lactose, fat, electrical conductivity, days in milk, lactation number, and activity as the number of steps, lying time, lying bouts, and lying bout duration. Models that predicted either likelihood of CM caused by gram-negative (GN) or gram-positive (GP) bacteria on each day were derived using extreme gradient boosting with weighting favoring true-positive cases, logistic responses, and log-loss errors. Model accuracies were determined using data randomly held out from the training set on each run. All variables considered were in terms of change (slope) over previous days, including the day CM was visually detected. The GN models had a median sensitivity (Se) of 52.6% and specificity (Sp) of 99.8%, whereas the GP models had a median Se of 37.5% and Sp of 99.9% when tested on the held-out data. In our models optimized to reduce cost from predictions, the Se was much less than Sp, suggesting that CM models might benefit from greater model weighting placed on Sp. Results also highlight the importance of positive predictive value (true positive cases per predicted positive case) along with Sp and Se, as models built on sparse data tend to predict too many false-positive cases. The calculated partial net return of our GN and GP models were -$0.15 and -$0.10 per cow per lactation, respectively, whereas International Organization for Standardization (ISO) standard models with Se of 80% and Sp of 99% would return -$1.32 per cow per lactation. Models chosen that minimized the cost to the farmer differed markedly from models that met ISO guidelines, showing asymmetry in targets between Sp and Se when the disease incidence rate is low. Because of the unique challenges that low-incidence diseases like CM present, we recommend that future CM predictive models consider the economic and practical implications in addition to the traditional model evaluation metrics.

Rumen fermentation and epithelial gene expression responses to diet ingredients designed to differ in ruminally degradable protein and fiber supplies

Although numerous studies exist relating ruminal volatile fatty acid (VFA) concentrations to diet composition and animal performance, minimal information is available describing how VFA dynamics respond to diets within the context of the whole rumen environment. The objective of this study was to characterize how protein and fiber sources affect dry matter intake, rumen pH, fluid dynamics, fermentation parameters, and epithelial gene expression. Four diet treatments (soybean meal or heat-treated soybean meal and beet pulp or timothy hay) were delivered to 10 wethers. The soybean meals served as crude protein (CP) sources while the beet pulp and timothy hay represented neutral detergent fiber (NDF) sources. Feed intake, rumen pH, fluid pool size, and fluid passage rate were unaffected by treatment. Butyrate synthesis and absorption were greater on the beet pulp treatment whereas synthesis and absorption of other VFA remained unchanged. Both CP and NDF treatment effects were associated with numerous VFA interconversions. Expression levels of rumen epithelial genes were not altered by diet treatment. These results indicate that rumen VFA dynamics are altered by changes in dietary sources of nutrients but that intake, rumen environmental parameters, and the rumen epithelium may be less responsive to such changes.

A LoRa sensor network for monitoring pastured livestock location and activity

Precision technologies for confinement animal agricultural systems have increased rapidly over the past decade, though precision technology solutions for pastured livestock remain limited. There are a number of reasons for this limited expansion of technologies for pastured animals, including networking availability and reliability, power requirements, and expense, among others. The objective of this work was to demonstrate a rapidly deployable long-range radio (LoRa) based, low-cost sensor suite that can be used to track location and activity of pastured livestock. The sensor is comprised of an inexpensive Arduino-compatible microprocessor, a generic MPU-9250 motion sensor which contains a 3-axis accelerometer, 3-axis magnetometer, and a 3-axis gyroscope, a generic GPS receiver, and a RFM95W generic LoRa radio. The microprocessor can be programmed flexibly using the open source Arduino IDE software to adjust the frequency of sampling, the data packet to send, and what conditions are needed to operate. The LoRa radio transmits to a Dragino LoRa gateway which can also be flexibly programmed through the Arduino IDE software to send data to local storage or, in cases where a web or cellular connection is available, to cloud storage. The sensor was powered using a USB cord connected to a 3,350 mAh lithium-ion battery pack. The Dragino gateway was programmed to upload data to the ThingSpeak IoT application programming interface for data storage, handling, and visualization. Evaluations showed minimal benefit associated with reducing sampling frequency as a strategy to preserve battery life. Packet loss ranged from 40% to 60%. In a 3 d evaluation on pastured sheep, the sensor suite was able to report GPS locations, inertial sensor readings, and temperature. Preliminary demonstrations of our system are satisfactory to detect animal location based on GPS data in real-time. This system has clear utility as a lower-cost strategy to deploy flexible, useful precision technologies for pasture-based livestock species.

Rumen volatile fatty acid molar proportions, rumen epithelial gene expression, and blood metabolite concentration responses to ruminally degradable starch and fiber supplies

The objective of this work was to characterize rumen volatile fatty acid (VFA) concentrations, rumen epithelial gene expression, and blood metabolite responses to diets with different starch and fiber sources. Six ruminally cannulated yearling Holstein heifers (body weight = 330 ± 11.3 kg) were arranged in a partially replicated Latin square experiment with 4 treatments consisting of different starch [barley (BAR) or corn (CRN)] and fiber [timothy hay (TH) or beet pulp (BP)] sources. Treatments were arranged as a 2 × 2 factorial. Beet pulp and TH were used to create relative changes in apparent ruminal fiber disappearance, whereas CRN and BAR were used to create relative changes in apparent ruminal starch disappearance. Each period consisted of 3 d of diet adaptation and 15 d of dietary treatment. In situ disappearance of fiber and starch were estimated from bags incubated in the rumen from d 10 to 14. From d 15 to 17, rumen fluid was collected every hour from 0500 to 2300 h. Rumen fluid samples were pooled by animal/period and analyzed for pH and VFA concentrations. On d 18, 60 to 80 papillae were biopsied from the epithelium and preserved for gene expression analysis. On d 18, one blood sample per heifer was collected from the coccygeal vessel. In situ ruminal starch disappearance rate (7.30 to 8.72%/h for BAR vs. 7.61 to 10.5%/h for CRN) and the extent of fiber disappearance (22.2 to 33.4% of DM for TH vs. 34.4 to 38.7% of DM for BP) were affected by starch and fiber source, respectively. Analysis of VFA molar proportions showed a shift from propionate to acetate, and valerate to isovalerate on TH diets compared with BP. Corn diets favored propionate over butyrate in comparison to BAR diets. Corn diets also had higher molar proportions of valerate. Expression of 1 gene (SLC9A3) were increased in BP diets and 2 genes (BDH1 and SLC16A4) tended to be increased in TH diets. Plasma acetate demonstrated a tendency for a starch by fiber interaction with BAR-BP diets having the highest plasma acetate, but other metabolites measured were not significant. These results suggest that TH has the greatest effect on shifts in VFA molar proportions and epithelial transporters, but does not demonstrate shifts in blood metabolite concentrations.

CENP-A chromatin prevents replication stress at centromeres to avoid structural aneuploidy

Chromosome segregation relies on centromeres, yet their repetitive DNA is often prone to aberrant rearrangements under pathological conditions. Factors that maintain centromere integrity to prevent centromere-associated chromosome translocations are unknown. Here, we demonstrate the importance of the centromere-specific histone H3 variant CENP-A in safeguarding DNA replication of alpha-satellite repeats to prevent structural aneuploidy. Rapid removal of CENP-A in S phase, but not other cell-cycle stages, caused accumulation of R loops with increased centromeric transcripts, and interfered with replication fork progression. Replication without CENP-A causes recombination at alpha-satellites in an R loop-dependent manner, unfinished replication, and anaphase bridges. In turn, chromosome breakage and translocations arise specifically at centromeric regions. Our findings provide insights into how specialized centromeric chromatin maintains the integrity of transcribed noncoding repetitive DNA during S phase.

Contributions of dairy products to environmental impacts and nutritional supplies from United States agriculture

Questions regarding the balance between the contribution to human nutrition and the environmental impact of livestock food products rarely evaluate specific species or how to accomplish the recommended depopulation. The objective of this study was to assess current contributions of the US dairy industry to the supply of nutrients and environmental impact, characterize potential impacts of alternative land use for land previously used for crops for dairy cattle, and evaluate the impacts of these approaches on US dairy herd depopulation. We modeled 3 scenarios to reflect different sets of assumptions for how and why to remove dairy cattle from the US food production system coupled with 4 land-use strategies for the potential newly available land previously cropped for dairy feed. Scenarios also differed in assumptions of how to repurpose land previously used to grow grain for dairy cows. The current system provides sufficient fluid milk to meet the annual energy, protein, and calcium requirements of 71.2, 169, and 254 million people, respectively. Vitamins supplied by dairy products also make up a high proportion of total domestic supplies from foods, with dairy providing 39% of the vitamin A, 54% of the vitamin D, 47% of the riboflavin, 57% of the vitamin B₁₂, and 29% of the choline available for human consumption in the United States. Retiring (maintaining animals without milk harvesting) dairy cattle under their current management resulted in no change in absolute greenhouse gas emissions (GHGE) relative to the current production system. Both depopulation and retirement to pasture resulted in modest reductions (6.8-12.0%) in GHGE relative to the current agricultural system. Most dairy cow removal scenarios reduced availability of essential micronutrients such as α-linolenic acid, Ca, and vitamins A, D, B₁₂, and choline. Those removal scenarios that did not reduce micronutrient availability also did not improve GHGE relative to the current production system. These results suggest that removal of dairy cattle to reduce GHGE without reducing the supply of the most limiting nutrients to the population would be difficult.

Factors that affect heat production in lactating Jersey cows

Heat production (HP) represents a major energy cost in lactating dairy cows. Better understanding of factors that affect HP will improve our understanding of energy metabolism. Our objective was to derive models to explain variation in HP of lactating Jersey cows. Individual animal-period data from 9 studies (n = 293) were used. The data set included cows with a wide range (min to max) in days in milk (44-410) and milk yield (7.8-43.0 kg/d). Diets included corn silage as the predominate forage source, but diets varied (min to max on DM basis) in crude protein (CP; 15.2-19.5%), neutral detergent fiber (NDF; 35.5-43.0%), starch (16.2-31.1%), and crude fat (2.2 to 6.4%) contents. Average HP was (mean ± standard deviation) 22.1 ± 2.86 Mcal/d, or 28.1 ± 3.70% of gross energy intake. Eight models were fit to explain variation in HP: (1) dry matter intake (DMI; INT); (2) milk fat, protein, and lactose yield (MILKCOMP); (3) INT and milk yield (INT+MY); (4) INT and MILKCOMP/DMI (INT+MILKCOMP); (5) mass of digested NDF, CP, and starch (DIG); (6) INT and digested energy (INT+DE); (7) INT and NDF, CP, and starch digestibility (INT+DIG); or (8) INT+MILKCOMP model plus urinary N excretion (INT+MILKCOMP+UN). For all HP models, metabolic body weight was included. All models were derived via a backward elimination approach and included the random effects of study, cow, and period within block within study. The INT models adequately explained variation in HP with a nonrandom effect-adjusted concordance correlation coefficient of 0.84. Similar adjusted concordance correlation coefficients (0.79-0.85) were observed for other HP models. The HP associated with milk protein yield and supply of digestible protein was greater than other milk production and nutrient digestibility variables. The HP associated with urinary N excretion was 5.32. Overall, HP can be adequately predicted from metabolic body weight and DMI. Milk component yield, nutrient digestibility, or urinary N excretion explained similar variation as DMI. Coefficients for milk protein and protein digestion suggest that digestion and metabolism of protein and synthesis of milk protein contribute substantially to HP of a dairy cow.

FOXO3a acts to suppress DNA double-strand break-induced mutations

Genomic instability is one of the hallmarks of aging, and both DNA damage and mutations have been found to accumulate with age in different species. Certain gene families, such as sirtuins and the FoxO family of transcription factors, have been shown to play a role in lifespan extension. However, the mechanism(s) underlying the increased longevity associated with these genes remains largely unknown and may involve the regulation of responses to cellular stressors, such as DNA damage. Here, we report that FOXO3a reduces genomic instability in cultured mouse embryonic fibroblasts (MEFs) treated with agents that induce DNA double‐strand breaks (DSBs), that is, clastogens. We show that DSB treatment of both primary human and mouse fibroblasts upregulates FOXO3a expression. FOXO3a ablation in MEFs harboring the mutational reporter gene lacZ resulted in an increase in genome rearrangements after bleomycin treatment; conversely, overexpression of human FOXO3a was found to suppress mutation accumulation in response to bleomycin. We also show that overexpression of FOXO3a in human primary fibroblasts decreases DSB‐induced γH2AX foci. Knocking out FOXO3a in mES cells increased the frequency of homologous recombination and non‐homologous end‐joining events. These results provide the first direct evidence that FOXO3a plays a role in suppressing genome instability, possibly by suppressing genome rearrangements.

Inducible aging in Hydra oligactis implicates sexual reproduction, loss of stem cells, and genome maintenance as major pathways

Freshwater polyps of the genus Hydra do not age. However, temperature stress induces aging and a shift from reproduction by asexual budding to sexual gamete production in a cold-sensitive (CS) strain of H. oligactis. We sequenced the transcriptome of a male CS strain before and after this life history shift and compared changes in gene expression relative to those seen in a cold-resistant (CR) strain that does not undergo a life history shift in response to altered temperature. We found that the switch from non-aging asexual reproduction to aging and sexual reproduction involves upregulation of genes not only involved in gametogenesis but also genes involved in cellular senescence, apoptosis, and DNA repair accompanied by a downregulation of genes involved in stem cell maintenance. These results suggest that aging is a byproduct of sexual reproduction-associated cellular reprogramming and underscore the power of these H. oligactis strains to identify intrinsic mechanisms of aging.

Breeding animals to feed people: The many roles of animal reproduction in ensuring global food security

As the population grows and shifts demographically, the resulting increase in demand for beef and milk necessitates improvements in the sustainability of ruminant livestock production systems. Ruminant livestock contribute to ensuring global food security because they have the ability to up-cycle non-human-edible products into meat and milk products with notable nutritional value. However, ruminant livestock also pose a challenge to global food sustainability because they are resource-intensive to produce and contribute substantially to agricultural greenhouse gas emissions. As such, improving environmental impacts of ruminant livestock production globally is an essential goal. There are a number of strategies that can be employed to enhance sustainability of ruminant production systems; however, improving reproductive efficiency is among the more efficient, because an increase in reproductive success will reduce the number of cows needed to produce a target quantity of beef. This reduction in the cow herd size helps limit the number of unproductive animals retained in the herd, thereby reducing the environmental maintenance cost of livestock production. Additionally, proper application of reproductive technologies enables faster and more targeted advances in genetic gains, which can be leveraged to produce phenotypes that are resource-use-efficient and well-adapted to their production environment. Optimizing reproductive efficiency can be accomplished through improved genetic selection for fertility and fecundity; applying more effective use of assisted reproductive technologies; and coupling reproductive and nutritional management to optimize likelihood of reproductive success. Collectively, applying these approaches will be essential when working to ensure ruminant livestock's contribution to global food security.

Identifying gram-negative and gram-positive clinical mastitis using daily milk component and behavioral sensor data

Opportunities exist for automated animal health monitoring and early detection of diseases such as mastitis with greater on-farm adoption of precision technologies. Our objective was to evaluate time series changes in individual milk component or behavioral variables for all clinical mastitis (CM) cases (ACM), for CM caused by gram-negative (GN) or gram-positive (GP) pathogens, or CM cases in which no pathogen was isolated (NPI). We developed algorithms using a combination of milk and activity parameters for predicting each of these infection types. Milk and activity data were collated for the 14 d preceding a CM event (n = 170) and for controls (n = 166) matched for breed, parity, and days in milk. Explanatory variables in the univariate and multiple regression models were the slope change in milk (milk yield, conductivity, somatic cell count, lactose percentage, protein percentage, and fat percentage) and activity parameters (steps, lying time, lying bout duration, and number of lying bouts) over 7 d. Slopes were estimated using linear regression between d -7 and -5, d -7 and -4, d -7 and -3, d -7 and -2, and d -7 and -1 relative to CM detection for all parameters. Univariate analyses determined significant slope ranges for explanatory variables against the 4 responses: ACM, GN, GP, and NPI. Next, all slope ranges were offered into the multivariate models for the same 4 responses using 3 baselines: d -10, -7, and -3 relative to CM detection. In the univariate analysis, no explanatory variables were significant indicators of ACM, whereas at least 1 parameter was significant for each of GN, GP, and NPI models. Superior sensitivity (Se) and specificity (Sp) estimates were observed for the best GP (Se = 82%, Sp = 87%) and NPI (Se = 80%, Sp = 94%) multiple regression models compared with the best ACM (Se = 73%, Sp = 75%) and GN (Se = 71%, Sp = 74%) models. Sensitivity for the GN model was greater at the baseline closest to the day of CM detection (d -3), whereas the opposite was observed for the GP and NPI model as Se was maximized at the d -10 baseline. Based on this screening of relationships, milk and activity sensor data could be used in CM detection systems.

Predictions of ruminal outflow of essential amino acids in dairy cattle

The objective of this work was to update and evaluate predictions of essential AA (EAA) outflows from the rumen. The model was constructed based on previously derived equations for rumen-undegradable (RUP), microbial (MiCP), and endogenous (EndCP) protein outflows from the rumen, and revised estimates of ingredient composition and EAA composition of the protein fractions. Corrections were adopted to account for incomplete recovery of EAA during 24-h acid hydrolysis. The predicted ruminal protein and EAA outflows were evaluated against a data set of observed values from the literature. Initial evaluations indicated a minor mean bias for non-ammonia, non-microbial nitrogen flow ([RUP + EndCP]/6.25) of 16 g of N per day. Root mean squared errors (RMSE) of EAA predictions ranged from 26.8 to 40.6% of observed mean values. Concordance correlation coefficients (CCC) of EAA predictions ranged from 0.34 to 0.55. Except for Leu, all ruminal EAA outflows were overpredicted by 3.0 to 32 g/d. In addition, small but significant slope biases were present for Arg [2.2% mean squared error (MSE)] and Lys (3.2% MSE). The overpredictions may suggest that the mean recovery of AA from acid hydrolysis across laboratories was less than estimates encompassed in the recovery factors. To test this hypothesis, several regression approaches were undertaken to identify potential causes of the bias. These included regressions of (1) residual errors for predicted EAA flows on each of the 3 protein-driven EA flows, (2) observed EAA flows on each protein-driven EAA flow, including an intercept, (3) observed EAA flows on the protein-driven EAA flows, excluding an intercept term, and (4) observed EAA flows on RUP and MiCP. However, these equations were deemed unsatisfactory for bias adjustment, as they generated biologically unfeasible predictions for some entities. Future work should focus on identifying the cause of the observed prediction bias.

The effect of J5 bacterins on clinical, behavioral, and antibody response following an Escherichia coli intramammary challenge in dairy cows at peak lactation

Vaccination against coliform mastitis has become part of mastitis control programs in the past 3 decades, as a means of reducing the severity of clinical mastitis. Our study objective was to evaluate the effect of 2 commercially available vaccines on clinical, behavioral, and antibody response following Escherichia coli intramammary challenge in cows near peak lactation. Cows (n = 12 per group) were vaccinated with vaccine 1 (V1) or vaccine 2 (V2) at dry-off, 21 d pre-calving, and 14 d post-calving. Twelve cows served as unvaccinated controls (CTL). Cows were challenged with E. coli in a rear quarter at approximately 100 d in milk. Milk samples were collected pre- and post-challenge to enumerate E. coli and determine somatic cell count. Serum was collected before each vaccination and at d 0, 1, 2, 3, 6, 30, and 60 relative to challenge, to study antibody response. Milk IgA and tumor necrosis factor-α concentrations were determined in whey. Vaginal temperature, cow activity, and milk yield and components were monitored post-challenge. Bacterial count, somatic cell score, milk yield and component decline, vaginal temperature, activity measures, and antibody and cytokine response were analyzed for treatment differences. The effects of parity, breed, and a repeated measure of time were also tested. Seven cows had to be removed from the study post-challenge for antibiotic treatment (CTL and V1, n = 3 each; V2, n = 1), 2 of which were euthanized (both CTL). Vaccinated cows exhibited fever (vaginal temperature ≥39.4°C) 3 h earlier than CTL cows, but we found no differences between treatments for bacterial count, somatic cell score, or milk yield reduction. Vaccinated cows spent more time lying per rest bout 2 d post-challenge, but total daily lying time was not different from CTL cows during the 7 d post-challenge. The vaccines differed in antibody response: V1 cows had greater serum IgG₁ and IgG₂ post-challenge. A parity effect was also evident: primiparous cows had lower bacterial counts, somatic cell score and a smaller milk yield decline than multiparous cows, but also had lower antibody production. Immunization with either J5 bacterin did not reduce clinical signs of mastitis in cows challenged at 100 d in milk, demonstrating that the effects of J5 vaccination had diminished at peak lactation.

Form of calf diet and the rumen. II: Impact on volatile fatty acid absorption

Diet is known to affect rumen growth and development. Calves fed an all-liquid diet have smaller and less developed rumens and a decreased ability to absorb volatile fatty acids (VFA) compared to calves fed both liquid and dry feed. However, it is unknown how rumens respond when challenged with a defined concentration of VFA. The objective of this study was to assess the effects of 2 different feeding programs on VFA absorption in preweaned calves. Neonatal Holstein bull calves were individually housed and randomly assigned to 1 of 2 diets. The diets were milk replacer only (MRO; n = 5) or milk replacer with starter (MRS; n = 6). Diets were isoenergetic (3.87 ± 0.06 Mcal of metabolizable energy per day) and isonitrogenous (0.17 ± 0.003 kg/d of apparent digestible protein). Milk replacer was 22% crude protein, 21.5% fat (dry matter basis). The textured calf starter was 21.5% crude protein (dry matter basis). Feed and ad libitum water intakes were recorded daily. Calves were exposed to a defined concentration of VFA buffer (acetate 143 mM, propionate 100 mM, butyrate 40.5 mM) 6 h before euthanasia on d 43 ± 1. Rumen fluid samples were obtained every 15 to 30 min for 6 h to measure the rate of VFA absorption. Rumen tissues were obtained from the ventral sac region and processed for morphological and immunohistochemical analyses of the VFA transporters monocarboxylate transporter 1 (MCT1) and 4 (MCT4). Body growth did not differ between diets, but empty reticulorumens were heavier in MRS than MRO calves (0.67 vs. 0.39 ± 0.04 kg) and MRS calves had larger papillae areas (0.76 vs. 15 ± 0.08 mm²). We observed no differences between diets in terms of the abundance of MCT1 and MCT4 per unit area. These results indicate that the extrapolated increase in total abundance of MCT1 or MCT4 in MRS calves was not due to increased transporter density per unit area. Modeled VFA absorption metrics (flux, mmol/h, or 6 h absorbed VFA in mmol) were not different across diets. These results demonstrate that the form of calfhood diet, whether solely MR or MR and starter, does not alter VFA absorption capacity when the rumen is exposed to a defined concentration of VFA at 6 wk of age.

Short-term lactation and mammary metabolism responses in lactating goats to graded removal of methionine from an intravenously infused complete amino acid mixture

To investigate the possible pathways of Met deficiency to depress milk protein synthesis, 4 lactating goats fitted with jugular vein, mammary vein, and carotid artery catheters and transonic blood flow detectors on the external pudic artery were used in a 4 × 4 Latin square experiment. Goats were fasted for 24 h followed by a 9-h intravenous infusion of an AA mixture plus glucose. Milk yield was recorded and samples were taken in h 2 to 8 of the infusion period, and mammary biopsy was performed in the last hour. Treatments were graded removal of Met from the infused AA mixture to achieve Met content in the infusate of 100 (complete), 60, 30, or 0% of that in casein. Graded Met removal decreased yield of milk, milk protein, and lactose linearly and tended to decrease yield of milk fat linearly. Milk protein yield decreased to 82, 78, and 69% that of complete mixture infusion, respectively, when the 60, 30, and 0% Met infusate was infused. Circulating Met decreased linearly with graded Met removal. Arterial and venous Met decreased to 36 and 23% that of complete mixture infusion, respectively, when all Met was removed out of the mixture. Concomitant with the decreased circulating concentration was a similar increase in mammary Met affinity as reflected by the linearly increased mammary Met clearance rate. The increased affinity plus the linearly increased mammary blood flow totally offset the negative effect of decreased circulating Met concentration on mammary Met uptake. The overall result was similar mammary Met uptakes across treatments ranging from 285.9 to 339.5 μmol/h. Mammary uptakes of the other AA measured were generally not affected by treatments except for a linearly decreased Thr uptake and a trend of linearly increased Glu uptake. Consistent with the behavior of an AA mainly catabolized in the liver and mainly used for protein synthesis in peripheral tissues, mammary uptake to milk output ratios of Met measured in the present study ranged from 1.25 to 1.49 and was not affected by treatments. For the other AA measured, the ratio of Thr was linearly decreased and that of Glu was linearly increased by graded Met removal. Graded Met removal linearly elevated circulating urea N and glucose concentrations, indicating enhanced whole-body catabolism of AA and hepatic gluconeogenesis. Treatments had no significant effects on circulating insulin, growth hormone, and the other hormones and metabolites measured. Phosphorylation status of eIF4E binding protein 1 tended to decrease linearly and that of p70S6k was linearly decreased by graded Met removal, indicating depressed signal in the intracellular mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway. In conclusion, results of the present study indicated that the mTORC1 pathway and whole-body AA catabolism rather than mammary uptake appeared the drivers for changes in milk protein synthesis in response to varying Met supply.

Technical note: A muscle biopsy technique for stratifying cattle by skeletal muscle metabolic activity

Tissue biopsy metabolic activity, assessed using the oxidation-reduction indicator resazurin, may serve as a proxy to assess energy expenditure associated with maintenance in nongrowing animals or growth rate in growing animals. Herein, we evaluate the repeatability, practicality, and sensitivity of a resazurin-based assay for ranking bovine skeletal muscle biopsies based on metabolic activity. Six yearling Holstein heifers (body weight = 330 ± 11.3 kg) were fed 4 dietary treatments consisting of high or low rumen-degradable starch and fiber arranged factorially in a partially replicated Latin square design. Periods were 18 d, consisting of 3 d for diet transition, 14 d for diet adaptation, and 1 d for sample collection. Semitendinosus biopsies were collected into ice-cold Dulbecco's modified Eagle medium (Fisher Scientific, Hampton, NH) from each heifer during each period. Analysis was initiated within an hour of sample collection. To assess tissue metabolic rate, biopsies were transferred to Dulbecco's modified Eagle medium with resazurin and incubated at 37°C. Fluorescence of each sample was read at time 0 and at 15-min intervals for 2 h. Change in fluorescence was representative of skeletal muscle reducing equivalent production. Fluorescent signal strength increased with time and relative rank of treatments did not change with time; accordingly, future studies may compare fluorescence at a single time point. Change in fluorescence at 120 min was used for analysis of the fixed effects of fiber, starch, and animal when accounting for a random effect of period. Samples collected when animals were on a high-ruminally degradable starch diet were more metabolically active than samples collected from animals on low-starch diets. Significant differences in metabolic activity among individual animals were also identified. Average relative fluorescence was correlated with dry matter intake, average daily gain, and feed-to-gain ratio. The relative fluorescence tended to correlate with average daily gain (r = 0.749) and feed-to-gain ratio (r = -0.783); change in fluorescence did not correlate with dry matter intake. Although evaluated on a small sample size, this technique shows promise as a potential means of ranking animals by growth or feed efficiency. Further work on a larger experimental population is needed to confirm the usefulness of this assay as a consistent and reliable predictor of these important phenotypic parameters.

Association between prophylactic low-molecular-weight heparin use in pregnancy and macrosomia: analysis of the Ottawa and Kingston birth cohort

Essentials Low-molecular-weight heparin (LMWH) is used to prevent venous thromboembolism (VTE) in pregnancy. We evaluated the association between LMWH and large for gestational age (LGA) infants. We found no significant associations between LMWH use and LGA. LMWH does not appear to increase the risk for the delivery of an LGA infant. SUMMARY: Background Low-molecular-weight heparin (LMWH), an anticoagulant, is the recommended drug for thromboprophylaxis and treatment of venous thromboembolism (VTE) in pregnancy. During pregnancy, LMWH is routinely prescribed to mothers with an increased risk of VTE or with a history of thrombosis. Although clinical reports of larger offspring born to women administered LMWH have been noted, no studies to date have evaluated or associated the use of LMWH and large for gestational age (LGA) infants. Objectives To determine whether there is an association between LMWH usage in mothers and the prevalence of LGA. Patients/Methods We performed an analysis of the Ottawa and Kingston (OaK) Birth Cohort and report characteristics of LMWH and association LGA (> 10%ile). We used coarsened exact matching (CEM) methods to account for bias and confounding. Results A total of 7519 women from the OaK Birth Cohort were included; 59 were administered LMWH during pregnancy (0.78%). Mothers prescribed LMWH had significantly greater BMI (P = 0.0001), age (P = 0.0001) and parity (P = 0.02). Gestational length was shorter among women administered LMWH compared to those without treatment (37.7 ± 2.0 vs. 39.2 ± 2.0, P < 0.0001), an iatrogenic finding. The odds ratio of an LGA delivery among women administered LMWH was 1.02 (95% confidence interval [CI], 0.48-2.16; P = 0.96) in unadjusted analyses and was 1.15 (95% CI, 0.49-2.71) in the matched sample adjusted for maternal age, BMI and gestational age. Conclusions These results, although exploratory, provide indirect evidence of no increased risk of LGA infants among women prescribed LMWH.

Propionate Affects Insulin Signaling and Progesterone Profiles in Dairy Heifers

Emerging data highlighting gut microbiome influences on health support evaluation of how microbial fermentation end-products influence postabsorptive systems. This study aimed to investigate the effect of increased propionate status on progesterone profiles and insulin sensitivity in dairy heifers. Eleven Holstein heifers, synchronized in estrus, were assigned to one of two continuous, 5-day IV treatments: sodium propionate (PRO; n = 5) or saline (CON; n = 6). These infusions culminated in a hyperglycemic clamp with daily blood samples for an additional 7 days. Plasma propionate concentrations increased over the first 9 h in PRO heifers, then decreased until day 3 when they matched CON heifers. Maximum plasma progesterone concentrations tended to be greater in PRO heifers than CON heifers (4.19 vs 3.73 ng/mL; P = 0.087). Plateau insulin concentrations in CON animals were significantly greater than those in PRO animals (249.4 ± 25.1 vs 123.9 ± 35.8; P = 0.008) with a trend for an increased insulin sensitivity index in PRO heifers compared to CON heifers (P = 0.06). These changes in plasma propionate clearance leading to increased progesterone response and changes in insulin sensitivity suggest a role for SCFA metabolism in reproductive hormone regulation.

Effects of dirty housing and a Typhimurium DT104 challenge on pig growth performance, diet utilization efficiency, and gas emissions from stored manure

The objectives of this study were to elucidate the effects of a dirty environment and a challenge plus associated environmental contamination on pig growth performance, diet utilization efficiency, and gas emissions (CO, NH, CH, NO, and HS) from stored manure. Twenty-four weaned barrows, aged 31 d at initiation of the trial, were randomly allotted to 3 different treatments in a completely randomized design. Treatments were: pigs housed in cages with manure removed and cages washed daily (Clean); pigs housed in cages sprayed daily with manure slurry mixtures (Dirty); or pigs challenged with Typhimurium DT104 and housed in cages that were not washed, but manure was removed daily ( challenge). Rectal temperature, body weight, daily feed intake, manure output, manure composition, and gas emissions from stored manure were measured throughout the 24-d animal phase. The Dirty and challenge treatments were statistically compared to the Clean treatment to evaluate individual effects. Dirty housing tended to decrease ADG from d 1 to 24 ( = 0.06) but there were no other effects on pig performance compared with the Clean treatment. In contrast, a challenge was associated with a marked reduction in each of the measured indicators of pig performance. challenge increased the carbon to nitrogen ratio, ether extract, and lignin concentrations in excreted manure ( = 0.02, 0.01, 0.003, respectively), and increased manure and head space temperatures in manure tanks ( < 0.0001). Gas emissions from stored manure of pigs on the Dirty or treatments were increased for each of the measured gases as compared to the Clean treatment ( < 0.01) when expressed per unit of BW gain. When gas emissions from manure of pigs housed in the Dirty treatment were expressed per unit of manure volatile solids (VS), they were increased for NH, CH, and HS ( < 0.02). challenge was associated with increased emissions of CO, and NO and decreased emissions of HS per kilogram manure VS compared to the Clean treatment ( = 0.06, 0.03, 0.04, respectively). Collectively, these results indicated that a challenge and associated housing contamination caused depressed growth rate and increased manure gas emissions, while exposure to a Dirty environment slightly reduced growth performance and clearly increased manure gas emissions per unit of BW gain as compared to Clean control.

Do DNA Double-Strand Breaks Drive Aging?

DNA double-strand breaks (DSBs) are rare, but highly toxic, lesions requiring orchestrated and conserved machinery to prevent adverse consequences, such as cell death and cancer-causing genome structural mutations. DSBs trigger the DNA damage response (DDR) that directs a cell to repair the break, undergo apoptosis, or become senescent. There is increasing evidence that the various endpoints of DSB processing by different cells and tissues are part of the aging phenotype, with each stage of the DDR associated with specific aging pathologies. In this Perspective, we discuss the possibility that DSBs are major drivers of intrinsic aging, highlighting the dynamics of spontaneous DSBs in relation to aging, the distinct age-related pathologies induced by DSBs, and the segmental progeroid phenotypes in humans and mice with genetic defects in DSB repair. A model is presented as to how DSBs could drive some of the basic mechanisms underlying age-related functional decline and death.

Cow-calf reproductive, genetic, and nutritional management to improve the sustainability of whole beef production systems

Optimizing efficiency in the cow-calf sector is an important step toward improving beef sustainability. The objective of the study was to use a model to identify the relative roles of reproductive, genetic, and nutritional management in minimizing beef production systems' environmental impact in an economically viable, socially acceptable manner. An economic and environmental diet optimizer was used to identify ideal nutritional management of beef production systems varying in genetic and reproductive technology use. Eight management scenarios were compared to a least cost baseline: average U.S. production practices (CON), CON with variable nutritional management (NUT), twinning cattle (TWN), early weaning (EW), sire selection by EPD using either on-farm bulls (EPD-B) or AI (EPD-AI), decreasing the calving window (CW), or selecting bulls by EPD and reducing the calving window (EPD-CW). Diets to minimize land use, water use, and/or greenhouse gas (GHG) emissions were optimized under each scenario. Increases in diet cost attributable to reducing environmental impact were constrained to less than stakeholder willingness to pay for improved efficiency and reduced environmental impact. Baseline land use, water use, and GHG emissions were 188 m, 712 L, and 21.9 kg/kg HCW beef. The NUT scenario, which assessed opportunities to improve sustainability by altering nutritional management alone, resulted in a simultaneous 1.5% reduction in land use, water use, and GHG emissions. The CW scenario improved calf uniformity and simultaneously decreased land use, water use, and GHG emissions by 3.2%. Twinning resulted in a 9.2% reduction in the 3 environmental impact metrics. The EW scenario allowed for an 8.5% reduction in the 3 metrics. The EPD-AI scenario resulted in an 11.1% reduction, which was comparable to the 11.3% reduction achieved by EPD-B in the 3 metrics. Improving genetic selection by using AI or by purchasing on-farm bulls based on their superior EPD demonstrated clear opportunity to improve sustainability. When genetic and reproductive technologies were adopted, up to a 12.4% reduction in environmental impact was achievable. Given the modeling assumptions used in this study, optimizing nutritional management while concurrently improving genetic and reproductive efficiency may be promising avenues to improve productivity and sustainability of U.S. beef systems.

Comprehensive transcriptional landscape of aging mouse liver

BACKGROUND

Mammalian aging is a highly complex process, a full mechanistic understanding of which is still lacking. One way to help understand the molecular changes underlying aging is through a comprehensive analysis of the transcriptome, the primary determinant of age-related phenotypic diversity. Previous studies have relied on microarray analysis to examine gene expression profiles in different tissues of aging organisms. However, studies have shown microarray-based transcriptional profiling is less accurate and not fully capable of capturing certain intricacies of the global transcriptome.

METHODS

Here, using directional whole transcriptome RNA-sequencing of aged mouse liver we have identified a comprehensive high-resolution profile of differentially expressed liver transcripts comprised of canonical protein-coding transcripts, transcript isoforms, and non-coding RNA transcripts, including pseudogenes, long non-coding RNAs and small RNA species.

RESULTS

Results show extensive age-related changes in every component of the mouse liver transcriptome and a pronounced increase in inter-individual variation. Functional annotation of the protein-coding mRNAs and isoforms indicated broad alterations in immune response, cell activation, metabolic processes, and RNA modification. Interestingly, multiple lncRNAs (Meg3, Rian, Mirg) from the Dlk-Dio3 microRNA locus were found up-regulated in aging liver, classifying this locus as a putative regulatory hotspot locus in aging liver. Moreover, integration of the altered non-coding RNAs and protein-coding transcripts into interaction networks of age-related change revealed inflammation, cellular proliferation, and metabolism as the dominant aging phenotypes in mouse liver.

CONCLUSIONS

Our analyses provide the first comprehensive dissection of the transcriptional landscape in aging mouse liver.

High-throughput sequencing in mutation detection: A new generation of genotoxicity tests?

The advent of next generation sequencing (NGS) technology has provided the means to directly analyze the genetic material in primary cells or tissues of any species in a high throughput manner for mutagenic effects of potential genotoxic agents. In principle, direct, genome-wide sequencing of human primary cells and/or tissue biopsies would open up opportunities to identify individuals possibly exposed to mutagenic agents, thereby replacing current risk assessment procedures based on surrogate markers and extrapolations from animal studies. NGS-based tests can also precisely characterize the mutation spectra induced by genotoxic agents, improving our knowledge of their mechanism of action. Thus far, NGS has not been widely employed in genetic toxicology due to the difficulties in measuring low-abundant somatic mutations. Here, we review different strategies to employ NGS for the detection of somatic mutations in a cost-effective manner and discuss the potential applicability of these methods in testing the mutagenicity of genotoxic agents.

Rapid mitochondrial DNA isolation method for direct sequencing

Standard methods for mitochondrial DNA (mtDNA) extraction do not provide the level of enrichment for mtDNA sufficient for direct sequencing and must be followed by long-range-PCR amplification, which can bias the sequence results. Here, we describe a reliable method for the preparation of mtDNA-enriched samples from eukaryotic cells ready for direct sequencing. This protocol utilizes a conventional miniprep kit, in conjunction with a paramagnetic bead-based purification step.

Double-strand break repair by interchromosomal recombination: an in vivo repair mechanism utilized by multiple somatic tissues in mammals

Homologous recombination (HR) is essential for accurate genome duplication and maintenance of genome stability. In eukaryotes, chromosomal double strand breaks (DSBs) are central to HR during specialized developmental programs of meiosis and antigen receptor gene rearrangements, and form at unusual DNA structures and stalled replication forks. DSBs also result from exposure to ionizing radiation, reactive oxygen species, some anti-cancer agents, or inhibitors of topoisomerase II. Literature predicts that repair of such breaks normally will occur by non-homologous end-joining (in G1), intrachromosomal HR (all phases), or sister chromatid HR (in S/G²). However, no in vivo model is in place to directly determine the potential for DSB repair in somatic cells of mammals to occur by HR between repeated sequences on heterologs (i.e., interchromosomal HR). To test this, we developed a mouse model with three transgenes—two nonfunctional green fluorescent protein (GFP) transgenes each containing a recognition site for the I-SceI endonuclease, and a tetracycline-inducible I-SceI endonuclease transgene. If interchromosomal HR can be utilized for DSB repair in somatic cells, then I-SceI expression and induction of DSBs within the GFP reporters may result in a functional GFP+ gene. Strikingly, GFP+ recombinant cells were observed in multiple organs with highest numbers in thymus, kidney, and lung. Additionally, bone marrow cultures demonstrated interchromosomal HR within multiple hematopoietic subpopulations including multi-lineage colony forming unit–granulocyte-erythrocyte-monocyte-megakaryocte (CFU-GEMM) colonies. This is a direct demonstration that somatic cells in vivo search genome-wide for homologous sequences suitable for DSB repair, and this type of repair can occur within early developmental populations capable of multi-lineage differentiation.

DNA damage in normally and prematurely aged mice

Steady-state levels of spontaneous DNA damage, the by-product of normal metabolism and environmental exposure, are controlled by DNA repair pathways. Incomplete repair or an age-related increase in damage production and/or decline in repair could lead to an accumulation of DNA damage, increasing mutation rate, affecting transcription, and/or activating programmed cell death or senescence. These consequences of DNA damage metabolism are highly conserved, and the accumulation of lesions in the DNA of the genome could therefore provide a universal cause of aging. An important corollary of this hypothesis is that defects in DNA repair cause both premature aging and accelerated DNA damage accumulation. While the former has been well-documented, the reliable quantification of the various lesions thought to accumulate in DNA during aging has been a challenge. Here, we quantified inhibition of long-distance PCR as a measure of DNA damage in liver and brain of both normal and prematurely aging, DNA repair defective mice. The results indicate a marginal, but statistically significant, increase in spontaneous DNA damage with age in normal mouse liver but not in brain. Increased levels of DNA damage were not observed in the DNA repair defective mice. We also show that oxidative lesions do not increase with age. These results indicate that neither normal nor premature aging is accompanied by a dramatic increase in DNA damage. This suggests that factors other than DNA damage per se, for example, cellular responses to DNA damage, are responsible for the aging phenotype in mice.

Isolation and Characterization of a Protective Antigen-Containing Particle from Culture Supernatant Fluids of Erysipelothrix rhusiopathiae

The mouse-protective activity of Erysipelothrix rhusiopathiae culture supernatant fluids exists in a polydisperse form, ranging in density from aggregates which sediment at 10,000 x g for 3 hr to soluble units which will not sediment at 198,000 x g for 12 hr. A partially purified protective antigen has been isolated from the aggregates sedimented from a concentrate of the culture supernatant fluid at 20,000 x g for 3 hr. These aggregates contained the major protective antigen or antigens of E. rhusiopathiae, since, in addition to inducing active immunity, they adsorbed essentially all of the passively protecting antibody from rabbit antiserum produced by immunization with whole culture. The protective activity in these aggregates was destroyed by trypsin and greatly diminished by muramidase and heating at 64 C, but was not affected by lipase or ribonuclease.

Solubilization and Characterization of a Protective Antigen of Erysipelothrix rhusiopathiae

A particulate fraction of Erysipelothrix rhusiopathiae cultures has been subjected to butanol extraction and treatment with surface-active agents in an attempt to solubilize a protective antigen. The particulate fraction was partitioned into the butanol layer but was not solubilized. Only sodium dodecyl sulfate solubilized the particles. The soluble protective activity was not sedimented by centrifugation at 198,000 x g for 12 hr but was excluded by Sephadex G-200. Immunodiffusion studies of the soluble fraction demonstrated eight antigens, five of horse serum origin and three of E. rhusiopathiae origin. Ultracentrifugation indicated that spontaneous reaggregation occurred after removal of the sodium dodecyl sulfate. Analytical ultracentrifugation showed that 90% of the sodium dodecyl sulfatetreated material migrated as a single homogeneous 3.5S component. The physical and biological characteristics of the protective activity suggest that the protective antigen is a glyco-lipoprotein.

Rates and patterns of recurrence for percutaneous radiofrequency ablation and open wedge resection for solitary colorectal liver metastasis

INTRODUCTION

The purpose of this study was to compare rates and patterns of disease progression following percutaneous, image-guided radiofrequency ablation (RFA) and nonanatomic wedge resection for solitary colorectal liver metastases.

METHODS

We identified 30 patients who underwent nonanatomic wedge resection for solitary liver metastases and 22 patients who underwent percutaneous RFA because of prior major hepatectomy (50%), major medical comorbidities (41%), or relative unresectability (9%). Serial imaging studies were retrospectively reviewed for evidence of local tumor progression.

RESULTS

Patients in the RFA group were more likely to have undergone prior liver resection, to have a disease-free interval greater than 1 year, and to have had an abnormal carcinoembryonic antigen (CEA) level before treatment. Two-year local tumor progression-free survival (PFS) was 88% in the Wedge group and 41% in the RFA group. Two patients in the RFA group underwent re-ablation, and two patients underwent resection to improve the 2-year local tumor disease-free survival to 55%. Approximately 30% of patients in each group presented with distant metastasis as a component of their first recurrence. Median overall survival from the time of resection was 80 months in the Wedge group vs 31 months in the RFA group. However, overall survival from the time of treatment of the colorectal primary was not significantly different between the two groups.

CONCLUSIONS

Local tumor progression is common after percutaneous RFA. Surgical resection remains the gold standard treatment for patients who are candidates for resection. For patients who are poor candidates for resection, RFA may help to manage local disease, but close follow-up and retreatment are necessary to achieve optimal results.

Fixation of Vancouver B1 peri-prosthetic fractures by broad metal plates without the application of strut allografts

The use of allograft struts and cerclage wire, possibly augmented by plate fixation, for the treatment of Vancouver type-B1 peri-prosthetic fractures around a total hip replacement has been strongly advocated. We examined our results using plate fixation without allograft struts and compared them with the results of the use of struts alone or when combined with plate fixation. Of 20 consecutive patients with type-B1 fractures treated by open reduction and plate fixation, 19 were available for follow-up. The fractures healed in 18 patients with a mean time to weight-bearing of ten weeks (4 to 19). There were no cases of infection or malunion. Nonunion occurred in one patient and required a second plate fixation to achieve union.

Safe, cost-effective treatment of Vancouver type-B1 fractures can be performed by plate fixation without the addition of cortical struts. This procedure may allow earlier weight-bearing than allograft strut fixation alone.

Energy input and response from prompt and early optical afterglow emission in γ-ray bursts

The taxonomy of optical emission detected during the critical first few minutes after the onset of a gamma-ray burst (GRB) defines two broad classes: prompt optical emission correlated with prompt gamma-ray emission, and early optical afterglow emission uncorrelated with the gamma-ray emission. The standard theoretical interpretation attributes prompt emission to internal shocks in the ultra-relativistic outflow generated by the internal engine; early afterglow emission is attributed to shocks generated by interaction with the surrounding medium. Here we report on observations of a bright GRB that, for the first time, clearly show the temporal relationship and relative strength of the two optical components. The observations indicate that early afterglow emission can be understood as reverberation of the energy input measured by prompt emission. Measurements of the early afterglow reverberations therefore probe the structure of the environment around the burst, whereas the subsequent response to late-time impulsive energy releases reveals how earlier flaring episodes have altered the jet and environment parameters. Many GRBs are generated by the death of massive stars that were born and died before the Universe was ten per cent of its current age, so GRB afterglow reverberations provide clues about the environments around some of the first stars.

A link between prompt optical and prompt γ-ray emission in γ-ray bursts

The prompt optical emission that arrives with the gamma-rays from a cosmic gamma-ray burst (GRB) is a signature of the engine powering the burst, the properties of the ultra-relativistic ejecta of the explosion, and the ejecta's interactions with the surroundings. Until now, only GRB 990123 had been detected at optical wavelengths during the burst phase. Its prompt optical emission was variable and uncorrelated with the prompt gamma-ray emission, suggesting that the optical emission was generated by a reverse shock arising from the ejecta's collision with surrounding material. Here we report prompt optical emission from GRB 041219a. It is variable and correlated with the prompt gamma-rays, indicating a common origin for the optical light and the gamma-rays. Within the context of the standard fireball model of GRBs, we attribute this new optical component to internal shocks driven into the burst ejecta by variations of the inner engine. The correlated optical emission is a direct probe of the jet isolated from the medium. The timing of the uncorrelated optical emission is strongly dependent on the nature of the medium.

Modeling the environmental fate of manganese from methylcyclopentadienyl manganese tricarbonyl in urban landscapes

The environmental impacts of gasoline additives such as lead (Pb) and Methyl Tertiary Butyl Ether (MTBE) are well documented, leading to the phasing out of these additives. In contrast, little is known about the health and environmental impacts of potential replacement chemicals such as Methylcyclopentadienyl Manganese Tricarbonyl (MMT). The combustion of MMT in gasoline leads to the formation of MnPO4 and MnSO4 and MMT is considered a recent source of inorganic Mn in urban landscapes particularly in high traffic areas. The main objective of this study is to estimate the automotive deposition of Mn from MMT relative to the traffic volume at sites near a major highway in the Greater Toronto Area of Canada, where MMT is currently being used. Manganese emission levels were estimated for two sites that varied according to Annual Average Daily Traffic (AADT) density, fuel consumption, distance traveled by automobiles, and Mn concentration (mg l(-1)) in gasoline. Multiple regression analysis was used to predict the AADT volume from year 2002-2010. Comparison of the mass balance between the ANOVA means of 15% Mn emitted from the automobile tailpipes at 10, and 18 mg of Mn l(-1) in gasoline was conducted for both study sites. The percentage difference between the Mn input at the selected concentrations of Mn in gasoline and output into surface soil were found to be 99% significant for both sites. Thus the predicted 15% tailpipe emission levels for 10 mg of Mn l(-1) of gasoline used in automobiles, which represented 1290.03 g/year for site 1 and 555.94 g/year for site 2, will add 5.73 and 2.47 mg/kg of Mn annually, respectively. These input levels are considered negligible when compared to the natural abundance of Mn in soil. Based on these data, it could take more than 95-256 years of continuous MMT usage in the region to double the content of Mn in surface soils at the respective sites.

The effect of reverberation on the damping of bubbles

The measurement of an acoustic emission, or scatter, from a bubble is not difficult. However, an accurate interpretation of that signal in terms of the bubble dynamics may require careful consideration. The study presented here is at first sight relatively simple: comparison of the predicted and measured quality factors of injected bubbles. While the measurement is normally done by monitoring the decay of passive emissions from a bubble, this technique becomes difficult with smaller bubbles. Therefore an active technique is introduced, which removes all the frequency-dependent effects on the measurement (such as transducer response) bar one. That, critically, is the effect of the change in the bubble resonance (frequency and damping) which results from the loading on the bubble due to the reverberant field. The vast majority of theoretical treatments of bubble acoustics assume free field conditions, yet the environmental conditions rarely if ever match these. Therefore measurements of bubble damping are compared both with the established free field theory, and with a new theory relevant to the prevailing reverberant conditions (whether caused by tank surfaces, monochromatic neighboring bubbles, or both).

Neoadjuvant chemoradiation for localized adenocarcinoma of the pancreas

BACKGROUND

The use of neoadjuvant (preoperative) chemoradiotherapy (CRT) for pancreatic cancer has been advocated for its potential ability to optimize patient selection for surgical resection and to downstage locally advanced tumors. This article reports our experience with neoadjuvant CRT for localized pancreatic cancer.

METHODS

Since 1995, 111 patients with radiographically localized, pathologically confirmed pancreatic adenocarcinoma have received neoadjuvant external beam radiation therapy (EBRT; median, 4500 cGy) with 5-flourouracil-based chemotherapy. Tumors were defined as potentially resectable (PR, n = 53) in the absence of arterial involvement and venous occlusion and locally advanced (LA, n = 58) with arterial involvement or venous occlusion by CT.

RESULTS

Five patients (4.5%) were not restaged due to death (n = 3) or intolerance of therapy (n = 2). Twenty-one patients (19%) manifested distant metastatic disease on restaging CT. Twenty-eight patients with initially PR tumors (53%) and 11 patients with initially LA tumors (19%) were resected after CRT. Histologic examination revealed significant fibrosis in all resected specimens and two complete responses. Surgical margins were negative in 72%, and lymph nodes were negative in 70% of resected patients. Median survival in resected patients has not been reached at a median follow-up of 16 months.

CONCLUSIONS

Neoadjuvant CRT provided an opportunity for patients with occult metastatic disease to avoid the morbidity of resection and resulted in tumor downstaging in a minority of patients with LA tumors. Survival after neoadjuvant CRT and resection appears to be at least comparable to survival after resection and adjuvant (postoperative) CRT.

Staging of pancreatic cancer before and after neoadjuvant chemoradiation

Neoadjuvant chemoradiation therapy is used at many institutions for treatment of localized adenocarcinoma of the pancreas. Accurate staging before neoadjuvant therapy identifies patients with distant metastatic disease, and restaging after neoadjuvant therapy selects patients for laparotomy and attempted resection. The aims of this study were to (1) determine the utility of staging laparoscopy in candidates for neoadjuvant therapy and (2) evaluate the accuracy of restaging CT following chemoradiation. Staging laparoscopy was performed in 98 patients with radiographically potentially resectable (no evidence of arterial abutment or venous occlusion) or locally advanced (arterial abutment or venous occlusion) adenocarcinoma of the pancreas. Unsuspected distant metastasis was identified in 8 (18%) of 45 patients with potentially resectable tumors and 13 (24%) of 55 patients with locally advanced tumors by CT. Neoadjuvant chemoradiation therapy and restaging CT were completed in a total of 103 patients. Thirty-three patients with potentially resectable tumors by restaging CT underwent surgical exploration and resections were performed in 27 (82%). Eleven (22%) of 49 patients with locally advanced tumors by restaging CT were resected, with negative margins in 55%; the tumors in these 11 patients had been considered locally advanced because of arterial involvement on restaging CT. Staging laparoscopy is useful for the exclusion of patients with unsuspected metastatic disease from aggressive neoadjuvant chemoradiation protocols. Following neoadjuvant chemoradiation, restaging CT guides the selection of patients for laparotomy but may overestimate unresectability to a greater extent than does prechemoradiation CT.