Flexible feeding: Dairy cow personality affects changes in feeding behavior and milk production under feed competition conditions.

The objective of this study was to determine the effect of individual cow personality traits on feeding behavior and production under low levels of feeding competition, and to determine whether personality traits influence how feeding behavior changes in response to greater feeding competition. Forty-two Holstein cows were assigned to 1 automated feed bin per cow (low competition condition) from 15 to 28 d in milk (DIM; period 1, P1), and 2 feed bins per 3 cows (higher competition condition) from 63 to 76 DIM (period 2, P2). A total mixed ration (TMR) was fed into the automated feed bins which recorded each feed bin visit time, duration, and intake. Cow personality traits were assessed at 21 DIM during P1 and at 70 DIM during P2 using a combined arena test, measuring behavioral responses to a novel environment, novel object, and novel human. Principal components analysis of behaviors observed during the P1 combined arena test revealed 1 factor (interpreted as active-explorative) from the novel environment test explaining 51% of the variance, and 3 factors (interpreted as fearfulness, active-explorative, and sociability toward conspecifics) from each of the novel object (76% cumulative variance) and human (75% cumulative variance) tests. The principal components analysis of behaviors observed during the P2 combined arena test revealed 2 factors jointly from the environment, object, and human tests (interpreted as fearfulness and active-explorative) that together explained 68% of the variance. Fearfulness and active-explorative trait scores were correlated across P1 and P2, indicating stability of personality over a challenging period and advancing DIM. In P2 when competition for feed was increased at greater stage of lactation, the more active-explorative cows appeared to make few alterations to their feeding behavior, yet still maintained their milk yield, compared with lower competition in P1. In contrast, cows who were more fearful increased their feed bin visits from P1 to P2, and less fearful cows increased their eating rate, without increased milk production, despite advanced lactation. Overall, the results indicate that cows of different personalities adopt different feeding strategies in response to a change in their environment, and may benefit from tailored management during challenging periods.

Effects of concentrate allowance and individual dairy cow personality traits on behavior and production of dairy cows milked in a free-traffic automated milking system.

The primary objective of this study was to determine whether the level of concentrate allowance in an automated milking system (AMS) affects the feed intake, eating behavior, milking activity, and performance of lactating dairy cows. The secondary objective of this study was to describe how the response to concentrate allocation, specifically in feeding and milking behavior, varies with cow personality traits. Fifteen Holstein cows were used in a crossover design with two 28-d periods, each including 14 d of adaptation and 14 d of data collection. The cows were housed in a freestall pen with free-traffic access to the AMS. Treatments consisted of a basal partial mixed ration (PMR) common to both treatment groups, with a concentrate allowance (on dry matter basis) of (1) 3.0 kg/d in the AMS (L-AMS) or (2) 6.0 kg/d in the AMS (H-AMS). Between the 2 treatment periods, each cow was assessed for personality traits using a combined arena test consisting of exposure to a novel environment, novel object, and novel human. Principal component analysis of behaviors observed during the novel environment and object tests revealed 3 factors (interpreted as active, social, and alert-curious) that together explained 76% of the variance, whereas principal component analysis of the novel human test revealed 2 factors (interpreted as active-vocal and fearful of novel humans) that together explained 77% of the variance. When on the H-AMS treatment, PMR dry matter intake (DMI) was less (24.5 vs. 26.0 kg/d) and AMS concentrate delivery was greater (5.9 vs. 3.1 kg/d), as per design. Consequently, total DMI was greater on the H-AMS treatment (30.4 vs. 29.1 kg/d). When on the H-AMS treatment, cows who were more alert-curious consumed more PMR, whereas cows who were more fearful of the novel human were less likely to receive the maximum amount of AMS concentrate available, limiting their total DMI and increasing the day-to-day variability of that intake. Although this was a preliminary study, these data suggest an association between dairy cow personality traits and how cows respond to increased AMS concentrate allowance.

Feed restriction and type of forage influence performance and behaviour of outdoor gestating sows.

Forages can contribute to the nutrient supply for sows but the extent to which they can replace concentrate feeding is not well known. The objective of this study was to assess the effect of level of feed restriction and type of forage on the performance and activity of gestating sows under outdoor conditions. A total of 45 sows were distributed among three treatments, with five replicates of three sows/treatment, from week 5 of gestation until farrowing. Treatments differed in the daily level of concentrate feed provided and the type of forage offered during gestation: 90% of metabolisable energy (ME) requirements provided by concentrates and free access to a pasture (P90); 40% of ME requirements provided by concentrates and free access to a pasture (P40); and 40% of ME requirements provided by concentrates and free access to a bare paddock with hay ad libitum (H40). From farrowing to weaning (5 weeks), concentrate feed was offered to all sows ad libitum. Body weight and backfat thickness (BF) were measured seven times during gestation and lactation. Postures of sows and time spent in the pasture were assessed at the beginning, middle and end of gestation. Forage intake was estimated with a method based on sow performance using the InraPorc® model. At farrowing, P90 sows were heavier and had greater BF than P40 and H40 sows. At weaning, P90 sows maintained a higher BW and tended to have greater BF than H40 sows, but no longer differed from P40 sows. Treatments did not influence litter size, but piglets from P40 sows were lighter at birth than those from P90 sows (1.44 vs. 1.69 kg, P = 0.004). In late gestation, P90 sows spent less time standing over 24 h and less time in the pasture during daytime than P40 sows, suggesting less foraging behaviour. Sows fed concentrates to meet 40% of ME requirements during gestation did not consume enough forage to maintain the same body condition as sows fed at 90% of ME requirements. Despite their inability to fully compensate for concentrate restriction during gestation by consuming more forage, P40 sows reached a similar body condition to P90 sows at weaning. In conclusion, forage intake for outdoor gestating sows can compensate a concentrate feed reduction of 10% and possibly more, but not as much as 60%.

Endotoxin-induced cytokine, chemokine and white blood cell profiles of variable stress-responding sheep.

Individual variation of the hypothalamic-pituitary-adrenal (HPA) axis response to stress could contribute to variable stress resiliency of livestock. During stress events, the innate immune system can also become activated and work in concert with the neuroendocrine system to restore homeostasis, while minimizing tissue damage. The purpose of this study was to assess immune function in variable stress-responding sheep in response to bacterial lipopolysaccharide (LPS) endotoxin immune-challenge. High (HSR, n = 12), middle (MSR, n = 12), and low-stress responders (LSR, n = 12) were selected from a population of 112 female lambs and classified based on serum cortisol concentration after receiving an intravenous bolus of LPS (400 ng/kg). Blood was collected from the jugular vein at 0 and 4 hrs post-LPS challenge to monitor changes in serum pro- and anti-inflammatory cytokines and chemokines, and white blood cell populations. Rectal temperature was recorded hourly to monitor fever. HSR had the greatest increase in rectal temperature and strongest pro-inflammatory IL-6 and IFN-γ cytokine responses compared to MSR and LSR. HSR and MSR had stronger anti-inflammatory IL-10 cytokine and CCL2 chemokine responses than LSR. White blood cell counts changed between 0 and 4 h; however, no differences were detected among the variable stress response groups. The distinct inflammatory response in variable stress responding sheep could contribute to individual differences in stress resiliency and this warrants investigation in the context of other types of stress.

LAY SUMMARYAcute inflammation was studied in sheep stress-phenotyped using bacterial lipopolysaccharide. Sheep selected based on stress responsiveness (i.e. serum cortisol concentration) have different immune responses to bacterial stress. Specifically, high-stress responders have a more pronounced inflammatory response than low-stress responders.

Sows' preferences for different forage mixtures offered as fresh or dry forage in relation to botanical and chemical composition.

Providing forage to feed-restricted pregnant sows may improve their welfare by reducing their high feeding motivation. The aim of this study was to determine sows' preferences for four forage mixtures cultivated in Canada. Forage mixtures were compared when offered either fresh or dry. The four forage mixtures were composed of different proportions and species of legumes (alfalfa (Alf) or red clover (Clo)) and grasses (tall fescue (F) and/or timothy (T)): (1) Alf-F, (2) Alf-F-T, (3) Clo-T and (4) Clo-F-T. Voluntary intake was measured, and preference tests were carried out for two experiments: one in spring for fresh forages ( n = 8) and the other in autumn for hays ( n = 8) with different sows housed in individual pens and fed a concentrated diet meeting their nutritional requirements for maintenance and foetal growth. Voluntary intake was measured by offering each forage mixture separately (one forage mixture/day) during 90 min according to a 4 × 4 Latin square design replicated four times. During preference tests, all six combinations of two forage mixtures were offered once (one combination/day) for 45 min to each sow. Individual forage intake was measured, and feeding behaviour was observed. Forages were analysed for botanical and chemical composition. Difference in voluntary intake among the four forage mixtures was determined using a variance analysis followed by Tukey tests for post hoc comparisons. In preference tests, differences between the two forage mixtures offered were determined using a paired Student's t test, and the most ingested forage mixture was considered the preferred one. Results from both experiments revealed clear preferences for some forage mixtures when offered either fresh or dry. Forage mixtures with a greater proportion of legumes (AlfT and CloT) were preferred over forage mixtures with a higher proportion of grasses (AlfFT and CloFT). The AlfFT and CloFT forage mixtures contained at least 30% of fescue; therefore, the greater preference for the AlfT and CloT forage mixtures could also be due to the absence of fescue. Sows preferred forages with low DM and NDF concentrations and high CP and non-structural carbohydrates concentrations. Based on results from previous studies, the preferences seen in the present study are most likely due to the greater proportion of legumes, although an effect of tall fescue in preference cannot be excluded. Therefore, offering forages with a high proportion of legumes would be a good strategy to maximise both fresh and dry forage intake in pregnant sows.

Marker genes as predictors of shared genomic function.

BACKGROUND: Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacity. Recently, scientists have shown a general desire to predict functional profiles of microbial communities based on phylogenetic identification inferred from marker genes, and recent tools have been developed to link the two. However, to date, no large-scale examination has quantified the correlation between the marker gene based taxonomic identity and protein coding gene conservation. Here we utilize 4872 representative prokaryotic genomes from NCBI to investigate the relationship between marker gene identity and shared protein coding gene content. RESULTS: Even at 99-100% marker gene identity, genomes share on average less than 75% of their protein coding gene content. This occurs regardless of the marker gene(s) used: V4 region of the 16S rRNA, complete 16S rRNA, or single copy orthologs through a multi-locus sequence analysis. An important aspect related to this observation is the intra-organism variation of 16S copies from a single genome. Although the majority of 16S copies were found to have high sequence similarity (> 99%), several genomes contained copies that were highly diverged (< 97% identity). CONCLUSIONS: This is the largest comparison between marker gene similarity and shared protein coding gene content to date. The study highlights the limitations of inferring a microbial community's functions based on marker gene phylogeny. The data presented expands upon the results of previous studies that examined one or few bacterial species and supports the hypothesis that 16S rRNA and other marker genes cannot be directly used to fully predict the functional potential of a bacterial community.

Effects of alternative deep bedding options on dairy cow preference, lying behavior, cleanliness, and teat end contamination.

Cows spend more time lying down when stalls are soft and dry, and bedding plays a key role in the comfort of the lying surface. The first objective of this study (experiment 1) was to compare cow preference for 2 types of alternative deep-bedding materials, switchgrass and switchgrass-lime, using wheat straw on a rubber mat as a control. Nine Holstein lactating cows were submitted in trios to a 3-choice preference test over 14 d (2 d of adaptation, 3 d of restriction to each stall, and 3 d of free access to all 3 stalls). Cows were housed individually in pens containing 3 stalls with different lying surfaces: (1) rubber mat with chopped wheat straw (WS); (2) deep-bedded switchgrass (SG); and (3) deep-bedded switchgrass, water, and lime mixture (SGL). The second objective (experiment 2) was to test, in freestall housing, the effects of these 3 types of bedding on lying behavior, cow cleanliness, and teat end bacterial contamination. Bedding treatments were compared in a 3 × 3 Latin square design using 24 cows split into groups of 8, with bedding materials being switched every 4 wk. Lying behavior was measured with data loggers in both studies. During experiment 1, cows chose to spend more time lying and had more frequent lying bouts on SG (9.4 h/d; 8.2 bouts/d) than on SGL (1.0 h/d; 0.9 bouts/d). They also spent more time standing and stood more frequently in stalls with SG (2.0 h/d; 10.1 bouts/d) than in those with SGL (0.6 h/d; 2.6 bouts/d), and stood longer in stalls with SG than with WS (0.6 h/d). In experiment 2, the total lying time, frequency of lying bouts, and mean lying bout duration were, on average, 9.7 ± 1.03 h/d, 8.2 ± 0.93 bouts/d, and 1.2 ± 0.06 h/bout, respectively, and did not differ between treatments. No treatment effects were found for cow cleanliness scores. Bedding dry matter was highest for SG (74.1%), lowest for SGL (63.5%), and intermediate for WS (68.6%) [standard error of the mean (SEM) = 1.57%]. This may explain the higher teat end count of coliforms for cows on SGL (0.92 log10 cfu/g) compared with WS (0.13 log10 cfu/g) (SEM = 0.144 log10 cfu/g). In conclusion, cows preferred the deep-bedded switchgrass surface over the other 2 surfaces, and deep-bedded switchgrass appears to be a suitable bedding alternative for dairy cows.

A method of outdoor housing dairy calves in pairs using individual calf hutches.

Interest in housing dairy calves in groups is currently growing. Group housing using individual calf hutches, a resource already available in most dairy farms in North America, could provide a novel housing method that can be a simple way to implement group housing on farm. The main objective of this study was to determine whether pair housing dairy calves in hutches outdoors would result in similar weight gain and milk intake compared with individual housing in hutches. The study was designed to avoid competition for resources (including milk and solid feed, teat, bucket, outdoor space, and hutch) to test a setup that has the potential to maximize performance and calf growth. Secondary objectives were to document how calves in both treatments use their environment in terms of time spent and behaviors performed in each area, how paired calves interact, and the time they spend together. Single calves (n = 6/season) were housed in 1 hutch with an attached outdoor environment; paired calves (n = 6 pairs/season) were given twice the resources. Calves were fed up to 16 L/d of milk replacer. Daily milk intake and weekly weight gains were recorded. Behavioral observations were recorded live once per week for 5 (summer) or 4 (winter) nonconsecutive periods. Paired and single calves had similar weight gain (averaging from 1.1 to 1.3 kg/d across trials) and milk intake (averaging from 11.1 to 13.7 kg/d across trials), showing no difference in performance between treatments. Low occurrences of cross sucking (averaging from 0.1 to 0.4 bouts/h of observation per pen across trials) and displacements at the teat (0.8 to 1.4 bouts/h of observation per pen across trials) were found. All calves altered their behavior in some way to accommodate companions; paired calves were seen interacting and spending time together (i.e., lying in the same hutch), and in the summer trial single calves spent less time lying inside the hutch than paired calves, presumably to have visual access to other calves. The solution of mixed indoor and outdoor housing environments tested as part of this study showed that calves make use of all spaces provided to them in winter and in summer conditions while maintaining good performance. Housing calves in pairs using individual hutches can be a suitable alternative to housing calves individually in hutches outdoors.

Technical note: Assessing lameness in tie-stalls using live stall lameness scoring.

Video stall lameness scoring (SLS) has been shown to be comparable to video locomotion scoring for evaluating lameness in dairy cows housed in tie-stalls and may be a more practical and easier method to measure lameness in a herd. We compared live SLS to video SLS and to live locomotion scoring. A total of 685 lactating cows subsampled from 27 commercial dairy herds were examined for lameness through live and video SLS. Cows scored with the live or video SLS system were scored for 4 behavioral indicators while still in their stall: weight shifting (shift), standing on the edge of the stall (edge), uneven weight bearing while standing (rest), and uneven weight bearing while moving from side to side (uneven). Two observers live scored and video scored for SLS. Lameness prevalence from video SLS and live SLS were similar (31 vs. 30%, respectively). Prevalence of the behavioral indicators varied from 0.59 to 58.2%. Sensitivity and specificity of live SLS was calculated using video SLS as the gold standard for lameness detection in tie-stalls. Sensitivity of live SLS was 0.83 and specificity was 0.94. False positives and false negatives for lameness were 14.4 and 16.8%, respectively. When comparing the prevalence of lameness measured through video or live SLS at the herd level, live SLS for lameness was correlated to video SLS (r = 0.91) with a Cohen's kappa coefficient of 0.79 (95% confidence limit = 0.73-0.84). Average exact agreement in the behavior indicators observed ranged from 80 to 100%. A subsample of 250 cows from 5 herds were scored for live SLS and live locomotion by a third observer. Intra- and interobserver reliability for live SLS and live locomotion scoring were found to have a kappa coefficient of 0.53 (95% confidence limit = 0.43-0.64) when determining a cow as lame through SLS or locomotion scoring. Live SLS was correlated with live locomotion scoring (r = 0.92). However, lameness prevalence was lower when using live SLS (28.4%) compared with locomotion scoring (38%). In summary, live SLS may be an acceptable method to replace video SLS to identify lame cows and rank tie-stall herds in terms of lameness prevalence without having to remove the cows from their stalls or view videos to score; however, it may underestimate lameness prevalence compared with locomotion scoring methods.

PALADIN: protein alignment for functional profiling whole metagenome shotgun data.

MOTIVATION: Whole metagenome shotgun sequencing is a powerful approach for assaying the functional potential of microbial communities. We currently lack tools that efficiently and accurately align DNA reads against protein references, the technique necessary for constructing a functional profile. Here, we present PALADIN-a novel modification of the Burrows-Wheeler Aligner that provides accurate alignment, robust reporting capabilities and orders-of-magnitude improved efficiency by directly mapping in protein space. RESULTS: We compared the accuracy and efficiency of PALADIN against existing tools that employ nucleotide or protein alignment algorithms. Using simulated reads, PALADIN consistently outperformed the popular DNA read mappers BWA and NovoAlign in detected proteins, percentage of reads mapped and ontological similarity. We also compared PALADIN against four existing protein alignment tools: BLASTX, RAPSearch2, DIAMOND and Lambda, using empirically obtained reads. PALADIN yielded results seven times faster than the best performing alternative, DIAMOND and nearly 8000 times faster than BLASTX. PALADIN's accuracy was comparable to all tested solutions. AVAILABILITY AND IMPLEMENTATION: PALADIN was implemented in C, and its source code and documentation are available at https://github.com/twestbrookunh/paladin. CONTACT: anthonyw@wildcats.unh.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Investigation of dairy cattle ease of movement on new methyl methacrylate resin aggregate floorings.

Freestall dairy farms commonly present issues with cattle slips and falls caused by smooth flooring and manure slurry. This study examined the effect of 4 new methyl methacrylate (MMA) resin aggregate flooring types (1-4) compared with rubber (positive) and concrete (negative control) on dairy cow (n=18) ease of movement when walking on straight and right-angled corridors. Our hypothesis was that cow ease of movement when walking on the MMA surfaces would be better than when walking on traction milled concrete, and at least as good as when walking on rubber. Cattle ease of movement was measured using kinematics, accelerometers, and visual observation of gait and associated behaviors. Stride length, swing time, stance time, and hoof height were obtained from kinematic evaluation. Acceleration and asymmetry of variance were measured with accelerometers. Locomotion score and behaviors associated with lameness, such as arch back, head bob, tracking up, step asymmetry, and reluctance to bear weight were visually observed. Stride length, swing time, stance time, and the number of steps taken were the only variables affected by flooring type. Differences between flooring types for these variables were tested using a generalized linear mixed model with cow as a random effect, week as a random block factor, and flooring type as a fixed effect. Multiple comparisons with a Scheffé adjustment were done to analyze differences among flooring types. Stride length was 0.14 m longer (better) on rubber when compared with concrete, and 0.11 and 0.17 m shorter on MMA 1 and 2 compared with rubber. On MMA 3 and 4, stride length did not differ from either rubber or concrete. Swing time was 0.04 s shorter (worse) on MMA 1 than on rubber, but did not differ from any other flooring. Stance time was 0.18 s longer (worse) on MMA 2 when compared with rubber, but it did not differ from any other treatment. The number of steps was higher on MMA 4 compared with rubber (4.57 vs. 3.95 steps), but did not differ from any other treatment. Of all the MMA floors tested, MMA 3 was the only one that was consistently as good as rubber (positive control). All 4 MMA floors never differed from concrete (negative control) in any of the ease of movement variables measured. These results suggest that MMA 3 may improve cow ease of movement, compared with the other MMA floors, but more research is required to confirm these findings.

The Good and Bad Sides of NAAG.

Why has such a small peptide been the source of controversy in neuroscience over the last 5 decades? Is N-acetyl-aspartyl-glutamate (NAAG) a neurotransmitter? Is NAAG located in neuronal tissue or in astrocytes? Is NAAG involved in neuropsychiatric and neurodegenerative disorders? Is NAAG therapeutically beneficial in the treatment of stroke or in initiating cascades of events leading to psychosis? After many years of intense research there is no clear consensus within the scientific community on how NAAG behaves in the brain. One of the major controversies about NAAG is its physiological action at N-methyl-d-aspartate (NMDA) receptors. While some researchers strongly argue that NAAG acts as a weak agonist at NMDA receptors, others have suggested that NAAG could behave as a potent antagonist. Published data from our laboratory demonstrate that the effect of NAAG on NMDA receptors could be influenced by a number of factors including the subcellular localization and subunit composition of NMDA receptors, as well as protons. In this chapter, we will summarize the knowledge of the literature on NAAG, however, we will place emphasis on our recently published data. More specifically, we have reported interesting findings on the effects of NAAG on NMDA receptors at synaptic and extrasynaptic sites using a pharmacological paradigm to distinguish the two populations of NMDA receptors. Additionally, we have evaluated the role of NAAG on GluN2A- and GluN2B-containing NMDA receptors using a HEK293 cell recombinant system. Finally, we have studied the effects of NAAG on GluN2A- and GluN2B-containing NMDA receptors in different extracellular pH conditions. We believe that our findings could potentially resolve some aspects of the debate regarding the role of NAAG at NMDA receptors.

Effect of feed type and method of presentation on feeding behavior, intake, and growth of dairy calves fed a high level of milk.

The objective of this study was to assess the effect of different feed types and method of feed presentation in the first 12 wk of life on the feeding behavior, intake, and growth of calves fed a high milk level. Forty-eight neonatal Holstein calves were individually housed and randomly assigned to 1 of 4 treatments and fed solid feed ad libitum: silage-based total mixed ration (TMR), concentrate (CON), and chopped hay and concentrate presented in 2 manners: mixed (MIX) or separate (SEP). All calves were offered 12 L/d of acidified milk replacer (1.8 kg of dry matter) until d 38 at which time step-down weaning by 1 L/d began. At d 50 calves no longer received milk, and all calves on SEP and CON treatments were offered the MIX diet until the end of the trial, whereas TMR and MIX calves did not change feeds. Feed intakes were recorded daily, and calves were weighed twice per week. Rumination time was observed on the last 3 d of alternate weeks (wk 3, 5, 7, 9, and 11) for 1h beginning at 1500 h. Time spent feeding was determined for the last 2 d of alternate weeks. In the preweaning stage (d 1-37) average daily gain was similar for all calves (1.1 kg/d). The TMR calves had lower average daily gain than calves on the other 3 treatments during both the weaning (d 38-49; 0.2 vs. 0.7 kg/d) and postweaning (d 50-84; 0.5 vs. 1.2 kg/d) stages. This result is related to the lower dry matter intake of calves fed TMR in comparison with MIX, SEP, and CON calves in the weaning (0.2 vs. 0.5 kg/d) and postweaning (1.8 vs. 2.8 kg/d) stages. Given dry matter content of the feeds (TMR=52%, other diets=89%), the as-fed intake of the calves was similar across treatments in all 3 stages. Calves offered hay in addition to concentrate showed no difference in concentrate intake in the first 7 wk of life. Interestingly, TMR calves spent more time feeding during the postweaning stage than MIX, SEP, and CON calves (308 vs. 194 min/d) and exhibited a slower feeding rate postweaning (5.9 vs. 14.4 g of dry matter per minute). It appears that during weaning, and postweaning, calves fed TMR were attempting to maximize their nutrient intake but were unable to match that of calves in other treatments because of the high moisture content of their feed, and thus were unable to achieve similar average daily gain. Additionally, growth and total intake throughout the preweaning and weaning stages were similar for calves fed chopped hay along with concentrate and those not offered hay, suggesting no detrimental effect of feeding forage.

Incidence rate of pathogen-specific clinical mastitis on conventional and organic Canadian dairy farms.

Mastitis is a common and costly production disease on dairy farms. In Canada, the incidence rate of clinical mastitis (IRCM) has been determined for conventionally managed dairy farms; however, no studies to date have assessed rates in organically managed systems. The objectives of this observational study were (1) to determine the producer-reported IRCM and predominant pathogen types on conventional and organic dairy farms in Southern Ontario, Canada, and (2) to evaluate the association of both mean overall IRCM and pathogen-specific IRCM with management system, housing type, and pasture access. Data from 59 dairy farms in Southern Ontario, Canada, distributed across conventional (n=41) and organic management (n=18) systems, were collected from April 2011 to May 2012. In addition to management system, farms were categorized by housing method (loose or tie-stall) and pasture access for lactating cows. Participating producers identified and collected samples from 936 cases of clinical mastitis. The most frequently isolated mastitis pathogens were coagulase-negative staphylococci, Bacillus spp., Streptococcus spp., Staphylococcus aureus, and Escherichia coli. The IRCM was higher on conventional farms than organic (23.7 vs. 13.2 cases per 100 cow-years) and was not associated with housing type (loose or tie-stall), pasture access, or herd-average milk yield. Bulk tank somatic cell count tended to be lower on conventional farms than organic (222,000 vs. 272,000 cells/mL). Pathogen-specific IRCM attributed to Staph. aureus, Bacillus spp., and E. coli was greater on conventional than organic farms, but was not associated with housing or any other factors. In conclusion, organic management was associated with reduced overall and pathogen-specific IRCM.

Effects of season, truck type, and location within truck on gastrointestinal tract temperature of market-weight pigs during transport.

Two experiments were done to assess the effects of season, truck type, and location in the truck on the gastrointestinal tract temperature (GTT) of market-weight pigs during transport. In Exp. 1, a total of 504 sentinel pigs were selected from a total load of 3,756 pigs over 12 wk in summer or winter and transported in either a double-decked (DD) hydraulic truck or a pot-belly (PB) trailer for 2 h. In Exp. 2, a total of 330 sentinel pigs were selected from a total load of 2,145 pigs over 11 wk in summer or winter and transported in a PB trailer for 8 h. In both experiments, sentinel pigs were equipped with a temperature data logger for the real-time GTT recording from the farm to slaughter. Transport was divided into 8 periods in Exp. 1 (rest, pretravel, initial travel, prearrival 1, prearrival 2, unloading, lairage 1, and lairage 2) and in Exp. 2 (rest, pretravel 1, pretravel 2, travel, prearrival 1, prearrival 2, lairage 1, and lairage 2). A delta GTT (ΔGTT) was calculated as the difference between the measured GTT at any determined event and the GTT measured at rest. In Exp. 1, the ΔGTT of pigs was greater ( < 0.001) in summer than in winter and only during the pretravel and initial travel periods. No difference was observed in the ΔGTT between the 2 truck types ( > 0.10). In summer, pigs located in the front top and rear top compartments of the PB trailer presented greater ( < 0.05) ΔGTT values than those transported in the middle top and front belly compartments during initial travel. In summer, during prearrival 1 and 2, a greater ( < 0.05) loss of GTT was found in pigs located in the rear top compartment of the DD truck compared with the rear lower compartment and in the front middle compartment compared with the rear middle compartment of the PB trailer. In Exp. 2, the ΔGTT of pigs was greater ( = 0.03) in summer than in winter during pretravel 2. Pigs in the front top compartment had a greater ( < 0.05) ΔGTT compared with pigs in the middle top, lower deck, and front belly compartments during the pretravel periods. Based on the results of the 2 experiments, modifications of the PB trailer model are recommended to limit body temperature increase due to physical stress at loading and unloading, and during transport due to inconsistent ventilation rate across vehicle locations.

Feeding preferences and voluntary feed intake of dairy cows: Effect of conservation and harvest time of birdsfoot trefoil and chicory.

Bioactive forages contain compounds, such as tannins, that are active against pathogens. They have been successfully used in ruminants to control parasite infections. Because cattle may find bioactive forages unpalatable, it is of interest to know if an afternoon harvest time, which has been shown to increase the percentage of nonstructural carbohydrates (NSC), hence palatability, may mitigate this. The objectives of this study were to quantify voluntary intake and preference of dairy cows for 2 bioactive forages, harvested in the morning and evening, in addition to determining their time spent grazing on each forage species. The forage species evaluated were fresh chicory harvested at 0700 h (FCAM) and 1800 h (FCPM), fresh birdsfoot trefoil harvested at 0700 h (FBAM) and 1800 h (FBPM), birdsfoot trefoil baleage harvested the previous summer at 0700 h (BBAM) and at 1800 h (BBPM), and third-cut alfalfa baleage harvested the previous summer and used as control (CON). Single forages were offered ad libitum in 30-min tests to 14 dairy cows to determine intake in a 7 × 7 Latin square (experiment 1). Every possible pair of forages (21 pairs) was then presented for a 30-min test to 8 different dairy cows, and feed intake was measured (experiment 2). Finally, time spent grazing on chicory and birdsfoot trefoil was measured on 12 dairy cows (experiment 3). The tests consisted of 2 d of restriction on 1 of the 2 fields for 1h, and 2 d of free-choice sessions (1h) between the 2 fields adjacent to each other. Grazing time and location of the animals on the field was assessed through 2-min scan sampling. In experiment 1, the highest voluntary intakes were for CON, BBPM, and BBAM. In experiment 2, BBPM was preferentially consumed over all other forages followed by CON and BBAM. Multidimensional scaling showed that preference for BBPM, CON, and BBAM in dimension 1 was positively associated with dry matter and nitrogen content, and negatively associated with hemicellulose and soluble N/total N. No relationships between dimension coordinates and any of the measured chemical composition variables could be found for the other 2 dimensions. In experiment 3, cows spent 71% of their time grazing in the birdsfoot trefoil field and 23% in the chicory field during the free-choice sessions. In conclusion, cows in the present experiments showed an overall preference toward baled forages compared with fresh forages, most notably toward birdsfoot trefoil baleage. Cow preference did not appear to be linked to harvest time (a.m. vs. p.m.).

The effects of providing portable shade at pasture on dairy cow behavior and physiology.

Access to pasture has advantages for cows such as reduced lameness and improved udder health, but also may expose cows to stressors such as extreme heat. The objective of this study was to understand how portable shade affected physiological and behavioral responses of pastured dairy cows in a Canadian summer. Over 8wk, a total of 24 lactating Holstein cows were separated into 2 treatments, one with access to shade and a control without access to shade. The cows were pastured in groups of 4, with 3 field sections per treatment. Instantaneous scan sampling of behaviors (drinking, lying, grazing, other) performed in the shade or not were recorded every 5min for 3h/d during the hottest part of the day (peak hours: 1130-1530h) 3d/wk. Ambient temperature, humidity, and vaginal temperature were recorded at 10-min intervals. Daily milk production was also recorded. Differences between treatments by week were analyzed using the generalized linear mixed model with group as random effect and treatment as fixed effect. Cows with shade access were observed at the water trough up to 6.42 times less and lying down up to 1.75 times more. Cows with shade access grazed up to 1.5 times more but only when the temperature-humidity index was above their comfort threshold (≥72) during the hottest part of the day (wk 2). Cows sought shade when it was made available, but spent less than half of their time observed (%) in the shade (40.8±4.67) with the exception of wk 2 when most of the time was spent under the shade (74.3±4.77). Daily lying time was highest during peak hours for cows with shade access. However, no overall difference in total lying time between the 2 treatments was observed. No differences were found in vaginal temperature or milk production between treatments with the exception of wk 1 for daily milk production, which was higher for cows in the control treatment. In conclusion, cows sought shade when it was provided at pasture, whereas cows without access to shade seemed to alter their behavior to cope with heat stress, as seen from the lack of physiological differences between treatments. The results indicate that providing cows with access to pasture under a temperate climate does not seem to have any detrimental physiological or production effects and providing them with shade can potentially decrease production costs and help with water conservation strategies as fewer cows were observed at the water when shade was provided.

Measure and characterization of lameness in gestating sows using force plate, kinematic, and accelerometer methods.

The objective was to assess sows' lameness by measuring weight distribution on limbs using a force plate made up of 4 individual platforms each resting on 4 single-ended beam load cells. The weight was recorded at an average rate of 14 readings per s over a 15 min period. Ten sows (5 lame sows and 5 sound sows) were weighed twice on 2 different days to assess the repeatability of the measure. Sixty-one sows were then selected in 2 different sites and visually scored for lameness, using a 3-point scoring system (0=normal gait; 1=abnormal gait, and/or stiffness; and 2=shortened stride, and/or the sow puts less weight or avoids putting weight on 1 leg). Various measures were recorded from each sow using the force plate (percentage of weight, the ratio between the weights applied by contralateral legs, weight shifting, and amplitude of weight bearing and weight removing), kinematics (speed, stride length, swing time, stance time, foot height, and carpal and tarsal joints angle average and amplitude), and accelerometers (time spent standing during 24 h, frequency of stepping behavior during feeding, and latency to lie down after feed delivery). The within-sow CV for each measure taken from the force plate were lower than 15%, which reflects a good repeatability. Among force plate measures, only the weight shifting frequency and the ratio between the weights applied by contralateral legs differed between lameness scores. Sows that scored 2 had a higher frequency of weight shifting for fore legs (P=0.0003) and hind legs (P=0.0007) than sows scored 0 and 1. The ratio between the weights applied by contralateral legs decreased with the increase of lameness score for the hind limbs (P=0.014). However, these measures also differed between sites (P<0.01). These differences may be due to various reasons, including but not limited to genetics and housing systems. Nevertheless, the results suggest that force plate measures such as the asymmetry in the weight applied between a pair of legs and weight shifting are good indicators of lameness. Multivariate analysis on fore and hind legs showed independency between variables related to animals in movement (measures from kinematics) and variables related to static animals (measures from the force plate and accelerometers). Therefore, both static and dynamic methods need to be used to detect various lame sows.

An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits.

BACKGROUND: Although Daphnia is increasingly recognized as a model for ecological genomics and biomedical research, there is, as of yet, no high-resolution genetic map for the genus. Such a map would provide an important tool for mapping phenotypes and assembling the genome. Here we estimate the genome size of Daphnia magna and describe the construction of an SNP array based linkage map. We then test the suitability of the map for life history and behavioural trait mapping. The two parent genotypes used to produce the map derived from D. magna populations with and without fish predation, respectively and are therefore expected to show divergent behaviour and life-histories. RESULTS: Using flow cytometry we estimated the genome size of D. magna to be about 238 mb. We developed an SNP array tailored to type SNPs in a D. magna F2 panel and used it to construct a D. magna linkage map, which included 1,324 informative markers. The map produced ten linkage groups ranging from 108.9 to 203.6 cM, with an average distance between markers of 1.13 cM and a total map length of 1,483.6 cM (Kosambi corrected). The physical length per cM is estimated to be 160 kb. Mapping infertility genes, life history traits and behavioural traits on this map revealed several significant QTL peaks and showed a complex pattern of underlying genetics, with different traits showing strongly different genetic architectures. CONCLUSIONS: The new linkage map of D. magna constructed here allowed us to characterize genetic differences among parent genotypes from populations with ecological differences. The QTL effect plots are partially consistent with our expectation of local adaptation under contrasting predation regimes. Furthermore, the new genetic map will be an important tool for the Daphnia research community and will contribute to the physical map of the D. magna genome project and the further mapping of phenotypic traits. The clones used to produce the linkage map are maintained in a stock collection and can be used for mapping QTLs of traits that show variance among the F2 clones.

Competition during the milk-feeding stage influences the development of feeding behavior of pair-housed dairy calves.

This study investigated how the feeding behavior of pair-housed calves develops in response to reduced teat and feed place availability. Twenty Holstein bull calves were pair housed and provided with milk replacer (MR) and grain concentrate ad libitum via either (1) 1 teat and feed bucket/pen, such that calves could not feed simultaneously [competitive feeding (CF)] or (2) 2 teats and feed buckets/pen [noncompetitive feeding (NCF)]. The calves were weaned during wk 7 of life by incrementally diluting the MR. Postweaning, all pens were managed identically and offered a complete pelleted diet ad libitum via 2 feed buckets/pen (NCF) in period 1 (wk 8 and 9) and period 3 (wk 12 and 13) and exposed to a competitive challenge with CF in period 2 (wk 10 and 11). Feeding times and competitive interactions were recorded from video for 3 d/wk in wk 2, 4, and 6 and 2 d/wk in wk 8 to 13. Meal criteria were used to calculate daily meal frequency, meal time, and synchronized meal time (the percentage of meal time when calves within the pen were engaged in simultaneous meals). Milk replacer intake was subject to a treatment × week interaction, with calves in CF pens having lower MR intake (wk 2: 8.3 vs. 10.0 L/calf per day for CF vs. NCF), but compensating by increasing intake to a greater extent over time (wk 4-5: 13.3 vs. 11.7 L/d for CF vs. NCF). Corresponding to MR intake, meal frequencies and feeding times evolved differently over this period, increasing in CF pens and decreasing in NCF pens (wk 2: 5.8 vs. 11.1 and wk 4-6: 6.2 vs. 5.1 meals/d for CF vs. NCF). Calves in CF pens also spent less time engaged in synchronized meals (28 vs. 51% of meal time; standard error=7.1) and displaced each other 5 times more frequently during synchronized eating. Postweaning, calves in previously CF pens maintained 5 times greater displacement frequencies and had fewer overlapping meals than calves in previously NCF pens (34.5 vs. 40.7% of meals, respectively). Postweaning, when calves were all fed noncompetitively (2 buckets/pen in periods 1 and 3), calves previously fed CF had greater intakes in period 3 (4.87 vs. 4.44 kg/d) and a tendency for greater intake in period 1 (2.80 vs. 2.63 kg/d), greater rates of intake in period 3 (87.8 vs. 72.0 g/min) and a tendency for greater rates of intake in period 1 (44.3 vs. 38.9 g/min), and greater meal frequencies in both periods (11.1 vs. 9.9 meals/d). In the competitive challenge period (1 bucket/pen in period 2), intake, rates of intake, and meal frequencies were subject to treatment × week interactions: calves in NCF pens had lower intake and meal frequencies, but increased meal frequency, intake, and rate of intake over time to a greater extent than calves previously in CF pens. These results indicate that calves are able to adapt to moderate competition by increasing meal frequency and that behavioral responses to competition persist postweaning.