Calving body condition score affects indicators of health in grazing dairy cows.

The objectives of this study were to determine the effect of calving body condition score (BCS) on cow health during the transition period in a pasture-based dairying system. Feed inputs were managed during the second half of the previous lactation so that BCS differed at drying off (BCS 5.0, 4.0, and 3.0 for high, medium, and low treatments, respectively: a 10-point scale); feed allowance was managed after cows were dried off, such that the BCS differences established during lactation remained at the subsequent calving (BCS 5.5, 4.5, and 3.5; n=20, 18, and 19, for high, medium, and low treatments, respectively). After calving, cows were allocated pasture and pasture silage to ensure grazing residuals >1,600 kg of DM/ha. Milk production was measured weekly; blood was sampled regularly pre- and postpartum to measure indicators of health, and udder and uterine health were evaluated during the 6 wk after calving. Milk weight, fat, protein, and lactose yields, and fat content increased with calving BCS during the first 6 wk of lactation. The effect of calving BCS on the metabolic profile was nonlinear. Before calving, cows in the low group had lower mean plasma ß-hydroxybutyrate and serum Mg concentrations and greater mean serum urea than cows in the medium and high BCS groups, which did not differ from each other. During the 6 wk after calving, cows in the low group had lower serum albumin and fructosamine concentrations than cows in the other 2 treatment groups, whereas cows in the low- and medium-BCS groups had proportionately more polymorphonucleated cells in their uterine secretions at 3 and 5 wk postpartum than high-BCS cows. In comparison, plasma ß-hydroxybutyrate and nonesterified fatty acid concentrations increased linearly in early lactation with calving BCS, consistent with a greater negative energy balance in these cows. Many of the parameters measured did not vary with BCS. The results highlight that calving BCS and, therefore, BCS through early lactation are not effective indicators of functional welfare, with the analyses presented indicating that both low and high BCS at calving will increase the risk of disease: cows in the low group were more prone to reproductive compromise and fatter cows had an increased risk of metabolic diseases. These results are important in defining the welfare consequences of cow BCS.

Behavioral and physiological effects of a short-term feed restriction in lactating dairy cattle with different body condition scores at calving.

Body condition score (BCS) around calving, and the typical BCS loss for up to 100 d after parturition, is associated with both production and reproductive performance of dairy cattle. In addition, there is public concern that thin cows may have impaired welfare, particularly in early lactation where feed demand exceeds pasture growth, and a lag exists between peak milk energy requirements and intake. The aim of this experiment was to determine how BCS at calving influences behavioral and physiological responses to a short-term feed restriction at 47 DIM. Body condition score (on a 10-point scale) at calving was manipulated by modifying the diets in the previous lactation of healthy dairy cattle to generate 3 treatment groups: low BCS (3.4; n=17), medium BCS (4.6; n=18), or high BCS (5.4; n=20). Cows were tested in 4 groups for 8 consecutive days; testing consisted of different levels of feed allocation (d 1 and 2: 100%; d 3 and 4: 75%; d 5: 50%; d 6 to 8: 125%), where 100% was 15kg of DM/cow per day. All BCS groups had similar and marked behavioral and physiological responses to feed restriction. For example, they increased vocalization, time spent eating silage and grazing, aggressive behavior, and fat metabolism (as measured by concentrations of ß-hydroxybutyrate and nonesterified fatty acids), and reduced milk production. Body condition affected some of these responses. Fewer cows with low BCS engaged in aggressive interactions in a feed competition test (trough filled with silage that could be consumed in 15 min) on the first day of feed restriction (low: 32%; medium: 74%; high: 64%; standard error of difference=15.4%). High BCS cows had greater concentrations of ß-hydroxybutyrate and nonesterified fatty acids throughout the experimental period, which suggests more fat mobilization; however, plasma leptin and fecal glucocorticosteroid metabolite concentrations were unaffected by BCS. Whereas cows demonstrated marked responses to feed restriction, the results suggest that a BCS of 3.4, 4.6, or 5.4 in healthy cows at calving does not overwhelmingly influence this response at 47 DIM.

Dairy cattle prefer shade over sprinklers: effects on behavior and physiology.

Cattle will readily use shade in warm weather, but less is known about voluntary use of sprinklers. We examined preferences of 96 Holstein-Friesian dairy cows (milk yield: 12.7±3.48 kg per day; mean±SD) for sprinklers, shade, or ambient conditions after walking 2.0 km or 0.3 km before afternoon milking (n=48 cows/distance). Each cow was individually tested on 3 consecutive days with a different paired choice each day: 1) shade or sprinklers, 2) shade or ambient conditions, 3) sprinklers or ambient conditions. Average air temperature during testing was 22.3°C. Cows preferred shade over sprinklers (62 vs. 38% ± 5.0%; mean ± SE) and shade over ambient conditions (65 vs. 35% ± 5.1%; mean±SE). Cows showed no preference between sprinklers and ambient conditions (44% of the cows chose sprinklers, SE=5.3%). The preference for shade over sprinklers and ambient conditions increased with air temperature, solar radiation, and wind speed. Walking distance did not influence the preference for any treatment. Respiration rate was decreased most by sprinklers (38% decrease) but also decreased in shade and ambient conditions (17 and 13% decrease, respectively; standard error of the difference=4.7%). Similarly, surface temperature was decreased most by sprinklers (11.4% decrease), compared with that by shade (1.0% decrease), or that by ambient conditions (1.4% increase; standard error of the difference=1.82%). Furthermore, sprinklers reduced insect avoidance behaviors, including number of tail flicks and hoof stamps. In conclusion, dairy cattle preferred to use shade in summer despite sprinklers being more efficient in decreasing heat load and insect avoidance behavior.

The amount of shade influences the behavior and physiology of dairy cattle.

The objective was to understand how the amount of shade (shade cloth blocking 99% of solar radiation) influenced the behavior and physiology of Holstein-Friesian dairy cattle managed on pasture. We compared behavior, body temperature, and respiration rate of cattle provided with 1 of 3 treatments for 5 d: access to 2.4m(2) or 9.6m(2) shade/cow, or no shade (n=4 groups/treatment, 10 animals/group). Behavioral observations were carried out between 1000 and 1550h. Cows spent more than twice as much time in the larger shade (24 vs. 50% of observations for 2.4m(2) and 9.6m(2) shade/cow, respectively, SED: 1.7%) and engaged in fewer aggressive interactions when more shade was provided (10.7 vs. 3.2 aggressive interactions/m(2) during 5.8h of observation for 2.4m(2) and 9.6m(2) shade/cow, respectively, SED: 3.16 interactions/m(2)). Time around the water trough increased when little or no shade was provided (11, 5, and 2% of observations within 4.5m of water trough for no shade, 2.4m(2), and 9.6m(2) shade/cow, SED: 2.4%). Respiration rate was higher when cows had less shade available (62, 57, and 51 breaths/min for no shade, 2.4m(2), and 9.6m(2) shade/cow, respectively, SED: 2.1 breaths/min). All cows used the shade more when 9.6m(2) shade/cow was provided; simultaneous use was observed in 15 versus 0% of observations in the 9.6m(2) and 2.4m(2) treatments on the warmest day, respectively. Weather conditions influenced both the behavioral and physiological responses, and these changes were more pronounced when less or no shade was available. Cows spent more time in shade and less time lying with increasing heat load. In addition, aggressive interactions in the shade, time around the water trough, mean body temperature, and respiration rate increased with environmental heat load. Our findings highlight the importance of determining and providing an effective amount of shade to cattle.

Chronic hepatitis, hepatic dysplasia, fibrosis, and biliary hyperplasia in hamsters naturally infected with a novel Helicobacter classified in the H. bilis cluster.

We recently described helicobacter-associated progressive, proliferative, and dysplastic typhlocolitis in aging (18- to 24-month-old) Syrian hamsters. Other pathogens associated with typhlocolitis in hamsters, Clostridium difficile, Lawsonia intracellularis, and Giardia spp., were not indentified. The presence of Helicobacter genus-specific DNA was noted by PCR in cecal and paraffin-embedded liver samples from aged hamsters by the use of Helicobacter-specific PCR primers. By 16S rRNA analysis, the Helicobacter sp. isolated from the liver tissue was identical to the cecal isolates from hamsters. The six hamster 16S rRNA sequences form a genotypic cluster most closely related to Helicobacter sp. Flexispira taxon 8, part of the Helicobacter bilis/H. cinaedi group. Livers from aged helicobacter-infected hamsters showed various stages of predominantly portocentric and, to a lesser extent, perivenular fibrosis. Within nodules, there was cellular atypia consistent with nodular dysplasia. The livers also exhibited a range of chronic active portal/interface and lobular inflammation, with significant portal hepatitis being present. The inflammation was composed of a mixture of lymphocytes, neutrophils, and macrophages, indicative of its chronic-active nature in these aged hamsters infected with Helicobacter spp. The isolation of novel Helicobacter spp., their identification by PCR from the diseased livers of aged hamsters, and their taxonomic classification as belonging to the Helicobacter bilis cluster strengthen the argument that H. bilis and closely related Helicobacter spp. play an etiological role in hepatobiliary disease in both animals and humans.

Effects of local anesthetic and a nonsteroidal antiinflammatory drug on pain responses of dairy calves to hot-iron dehorning.

This study examined the effects of a nonsteroidal antiinflammatory agent (NSAID) on physiological responses of calves immediately after hot-iron dehorning (DH) and during the time that local anesthetic (LA) wears off (2 to 3 h) after this procedure. Forty-six calves (33 +/- 0.3 d of age) were randomly assigned to 6 treatments: hot-iron DH versus sham DH with either no pain mitigation, LA alone, or LA with NSAID (i.v. Meloxicam). Eye temperature (measured using infrared thermography) was recorded every 5 min for 3 h after treatments. Heart rate (HR) and heart rate variability (HRV) were recorded continuously; for analysis of HRV, short segments of 512 interbeat intervals were examined. After DH without LA or NSAID, HR increased by 35 +/- 3.0 beats/min in the first 5 min and remained elevated above baseline for 3 h. The HRV around the time of DH did not differ between treatments; however, the root mean square of successive differences decreased from 68 to 41 +/- 12.6 ms immediately following DH without pain relief, suggesting a decrease in vagal tone at this time. Between 2 and 3 h following DH with LA, there was a decrease in eye temperature (-0.6 +/- 0.1 degrees C), an increase in HR (8 +/- 3.0 beats per min) and changes in HRV. Changes in HRV at this time included a decreased high-frequency power and an increase in the low-frequency power and low-frequency/high-frequency ratio, indicating a change in sympatho-vagal balance. The changes in eye temperature, HR, and HRV between 2 and 3 h following DH with LA indicated the onset of pain coinciding with the time that the LA effects wear off. In addition, this study demonstrated that the combination of LA and NSAID mitigated the onset of pain responses when the LA wanes.

Brief communication: the Thule migration: rejecting population histories using computer simulation.

Locked within our genetic code are the histories of our genes and the genes of our ancestors. Deciphering a population's history from genetic data often involves lengthy investigations of many loci for many individuals. We test hypothetical population histories of the Thule expansion using a new coalescent simulation method that uses little more than mitochondrial haplogroup data. This new methodology rejects a severe bottleneck at expansion and reveals the range of probable population histories on which to focus future research.

Genetic similarities within and between human populations.

The proportion of human genetic variation due to differences between populations is modest, and individuals from different populations can be genetically more similar than individuals from the same population. Yet sufficient genetic data can permit accurate classification of individuals into populations. Both findings can be obtained from the same data set, using the same number of polymorphic loci. This article explains why. Our analysis focuses on the frequency, omega, with which a pair of random individuals from two different populations is genetically more similar than a pair of individuals randomly selected from any single population. We compare omega to the error rates of several classification methods, using data sets that vary in number of loci, average allele frequency, populations sampled, and polymorphism ascertainment strategy. We demonstrate that classification methods achieve higher discriminatory power than omega because of their use of aggregate properties of populations. The number of loci analyzed is the most critical variable: with 100 polymorphisms, accurate classification is possible, but omega remains sizable, even when using populations as distinct as sub-Saharan Africans and Europeans. Phenotypes controlled by a dozen or fewer loci can therefore be expected to show substantial overlap between human populations. This provides empirical justification for caution when using population labels in biomedical settings, with broad implications for personalized medicine, pharmacogenetics, and the meaning of race.

Human population genetic structure and diversity inferred from polymorphic L1(LINE-1) and Alu insertions.

BACKGROUND/AIMS: The L1 retrotransposable element family is the most successful self-replicating genomic parasite of the human genome. L1 elements drive replication of Alu elements, and both have had far-reaching impacts on the human genome. We use L1 and Alu insertion polymorphisms to analyze human population structure. METHODS: We genotyped 75 recent, polymorphic L1 insertions in 317 individuals from 21 populations in sub-Saharan Africa, East Asia, Europe and the Indian subcontinent. This is the first sample of L1 loci large enough to support detailed population genetic inference. We analyzed these data in parallel with a set of 100 polymorphic Alu insertion loci previously genotyped in the same individuals. RESULTS AND CONCLUSION: The data sets yield congruent results that support the recent African origin model of human ancestry. A genetic clustering algorithm detects clusters of individuals corresponding to continental regions. The number of loci sampled is critical: with fewer than 50 typical loci, structure cannot be reliably discerned in these populations. The inclusion of geographically intermediate populations (from India) reduces the distinctness of clustering. Our results indicate that human genetic variation is neither perfectly correlated with geographic distance (purely clinal) nor independent of distance (purely clustered), but a combination of both: stepped clinal.

Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms.

We have analyzed 35 widely distributed, polymorphic Alu loci in 715 individuals from 31 world populations. The average frequency of Alu insertions (the derived state) is lowest in Africa (.42) but is higher and similar in India (.55), Europe (.56), and Asia (.57). A comparison with 30 restriction-site polymorphisms (RSPs) for which the ancestral state has been determined shows that the frequency of derived RSP alleles is also lower in Africa (.35) than it is in Asia (.45) and in Europe (.46). Neighbor-joining networks based on Alu insertions or RSPs are rooted in Africa and show African populations as separate from other populations, with high statistical support. Correlations between genetic distances based on Alu and nuclear RSPs, short tandem-repeat polymorphisms, and mtDNA, in the same individuals, are high and significant. For the 35 loci, Alu gene diversity and the diversity attributable to population subdivision is highest in Africa but is lower and similar in Europe and Asia. The distribution of ancestral alleles is consistent with an origin of early modern human populations in sub-Saharan Africa, the isolation and preservation of ancestral alleles within Africa, and an expansion out of Africa into Eurasia. This expansion is characterized by increasing frequencies of Alu inserts and by derived RSP alleles with reduced genetic diversity in non-African populations.

Using mitochondrial and nuclear DNA markers to reconstruct human evolution.

Molecular genetic-data have greatly improved our ability to test hypotheses about human evolution. During the past decade, a large amount of nuclear and mitochondrial data have been collected from diverse human populations. Taken together, these data indicate that modern humans are a relatively young species. African populations show the largest amount of genetic diversity, and they are the most genetically divergent population. Modern human populations expanded in size first on the African continent. These findings support a recent African origin of modern humans, but this conclusion should be tempered by the possible effects of factors such as gene flow, population size differences, and natural selection.

Genetic traces of ancient demography.

Patterns of gene differences among humans contain information about the demographic history of our species. Haploid loci like mitochondrial DNA and the nonrecombining part of the Y chromosome show a pattern indicating expansion from a population of only several thousand during the late middle or early upper Pleistocene. Nuclear short tandem repeat loci also show evidence of this expansion. Both mitochondrial DNA and the Y chromosome coalesce within the last several hundred thousand years, and they cannot provide information about the population before their coalescence. Several nuclear loci are informative about our ancestral population size during nearly the whole Pleistocene. They indicate a small effective size, on the order of 10,000 breeding individuals, throughout this time period. This genetic evidence denies any version of the multiregional model of modern human origins. It implies instead that our ancestors were effectively a separate species for most of the Pleistocene.

Microsatellite diversity and the demographic history of modern humans.

We have examined differences in diversity at 60 microsatellite loci among human population samples from three major continental groups to evaluate the hypothesis of greater African diversity in this rapidly evolving class of loci. Application of a statistical test that assumes equal mutation rates at all loci fails to demonstrate differences in microsatellite diversity, while a randomization test that does not make this assumption finds that Africans have significantly greater microsatellite diversity (P < 10(-8)) than do Asians and Europeans. Greater African diversity is most apparent at loci with smaller overall variance in allele size, suggesting that the record of population history has been erased at repeat loci with higher mutation rates. A power analysis shows that only 35-40 microsatellites are needed to establish this difference statistically, demonstrating the considerable evolutionary information contained in these systems. On average, African populations have approximately 20% greater microsatellite diversity than do Asian and European populations. A comparison of continental diversity differences in microsatellites and mtDNA sequences suggests earlier demographic expansion of the ancestors of Africans.

Evolution and human choice over time.

This chapter reviews previous work on an evolutionary model describing the effect of time delays on human preferences. The model explains why the long-term real interest rate is usually near 3% and why rates of crime and driving accidents are highest among young adults. It does not succeed in explaining the phenomenon of preference reversal. The chapter reports new results on uncertainty and on a more comprehensive model allowing consumption to have simultaneous effects on mortality and fertility.

Mitochondrial mismatch analysis is insensitive to the mutational process.

Mismatch distributions are histograms showing the pattern of nucleotide (or restriction) site differences between pairs of individuals in a sample. They can be used to test hypotheses about the history of population size and subdivision (if selective neutrality is assumed) or about selection (if a constant population size is assumed). Previous work has assumed that mutations never strike the same site twice, an assumption that is called the model of infinite sites. Fortunately, the results are surprisingly robust even when this assumption is violated. We show here that (1) confidence regions inferred using the infinite-sites model differ little from those inferred using a model of finite sites with uniform site-specific mutation rates, and (2) even when site-specific mutation rates follow a gamma distribution, confidence regions are little changed until the gamma shape parameter falls well below its plausible range, to roughly 0.01. In addition, we evaluate and reject the proposition that mismatch waves are produced by pooling data from several subdivisions of a structured population.

Listeriolysin O production and pathogenicity of non-growing Listeria monocytogenes stored at refrigeration temperature.

Three haemolytic, pathogenic strains of Listeria monocytogenes (a reference strain NCTC 7973, a food-derived strain L70 and a human strain L94) and a control strain of Listeria innocua L27 were held in phosphate-buffered saline (PBS) of pH 7.0 or 5.5 at 4 degrees C for 4 weeks. The number of viable cells did not change significantly during this storage (the cells were non-growing). Titers of Listeria listeriolysin O (LLO) activity against washed human erythrocytes and the pathogenicity of non-growing bacterial cells for 14-day-old chick embryos were determined before storage and after 1, 2, 3 and 4 weeks of storage. Prolonged storage at 4 degrees C affected both LLO production and pathogenicity of the non-growing cells, but effects were strain- and pH-dependent. At pH 7.0, all three L. monocytogenes strains had lost LLO activity after 2 weeks of storage. At pH 5.5, the reference and the food strains lost LLO activity 1 week later than when stored at neutral pH, and the human strain maintained LLO activity throughout the 4-week period. Pathogenicity of the reference strain stored at pH 7.0 and 5.5 and that of the food strain stored at pH 7.0 decreased during storage at 4 degrees C. However, the human strain stored at pH 7.0 and 5.5, and the food strain stored at pH 5.5, maintained their pathogenicity throughout the 4-week period. In all cases, non-growing L. monocytogenes cells that had ceased LLO production and/or had a reduced pathogenicity, recovered these characteristics after growth in media at 37 degrees C. This study indicates that prolonged storage of chilled-foods in which L. monocytogenes is present, but not growing may have the desirable result that the L. monocytogenes has a reduced ability to cause illness in humans. As well, pathogenicity testing involving growth of L. monocytogenes in laboratory media may not reflect the actual pathogenicity of the organism in the food as eaten.

Estimating sexual dimorphism by method-of-moments.

Estimating the degree of sexual dimorphism is difficult in fossil species because most specimens lack indicators of sex. We present a procedure that estimates sexual dimorphism in samples of unknown sex using method-of-moments. We assume that the distribution of a metric trait is composed of two underlying normal distributions, one for males and one for females. We use three moments around the mean of the combined-sex distribution to estimate the means and the common standard deviation of the two underlying distributions. This procedure has advantages over previous methods: it is relatively simple to use, specimens need not be assigned to sex a priori, no reference to living species analogs is required, and the method provides conservative estimates of dimorphism under a variety of conditions. The method performs best when the male and female distributions overlap minimally but also works well when overlap is substantial. Simulations indicate that this relatively simple method is more accurate and reliable than previous methods for estimating dimorphism.

Genetic admixture in the late pleistocene.

The replacement hypothesis of modern human origins holds that the original population of modern humans expanded throughout the world, replacing existing archaic populations as it went. If this expanding population interbred with the peoples it replaced, then some archaic mitochondria might have been introduced into the early modern gene pool. Such mitochondria would be recognizable today because they should differ from other modern mitochondria at several times the number of sites that we are used to seeing in pairwise comparisons. In this paper we ask what can be inferred from the absence of these "divergent" mitochondria from modern samples. We show that if the effective number of females in our species has been large for the past 40,000 years, then the level of admixture must have been low. For example, if this effective number exceeded 1.6 million, then we can reject the hypothesis that more more than 2/1,000 of the mitochondria in the early modern population derived from admixture with archaic peoples. We argue elsewhere that regional continuity would be detectable in the fossil record only if the rate of admixture exceeded 76%. Here, we show that this level of admixture would require the effective female size of the human population to have been less than 1,777 for the past 40,000 years.

Ascertainment bias in estimates of average heterozygosity.

Population geneticists work with a nonrandom sample of the human genome. Conventional practice ensures that unusually variable loci are most likely to be discovered and thus included in the sample of loci. Consequently, estimates of average heterozygosity are biased upward. In what follows we describe a model of this bias. When the mutation rate varies among loci, bias is increased. This effect is only moderate, however, so that a model of invariant mutation rates provides a reasonable approximation. Bias is pronounced when estimated heterozygosity is < approximately 35% Consequently, it probably affects estimates from classical polymorphisms as well as from restriction-site polymorphisms. Estimates from short-tandem-repeat polymorphisms have negligible bias, because of their high heterozygosity. Bias should vary not only among categories of polymorphism but also among populations. It should be largest in European populations, since these are the populations in which most polymorphisms were discovered. As this argument predicts, European estimates exceed those of Africa and Asia at systems with large bias. The magnitude of this European excess is consistent with the version of our model in which mutation rates vary across loci.