Real-time multiplexed PCR using surface enhanced Raman spectroscopy in a thermoplastic chip.

Surface enhanced Raman spectroscopy (SERS) has the potential to enable point-of-care sensing across the spectrum of chemical and biological analytes. In diagnostic assays, SERS has been demonstrated to increase the multiplexing density while reducing the burden of fluorescence hardware. One particular application of interest is the use of SERS to provide a multiplexed optical read-out following polymerase chain reaction (PCR). To date, however, the reported PCR-SERS assays require endpoint mixing with a plasmonic nanoparticle solution for detection, thus adding manual steps and preventing real-time, quantitative PCR. In this work, we detail a real-time PCR-SERS thermoplastic microsystem that allows simultaneous nucleic acid amplification and product separation into a SERS-active silver colloid for real-time detection. Specifically, a laser cut thermoplastic fluidic chip has been devised to utilize a dialysis membrane capable of isolating a PCR reaction from the silver colloid. As the reaction progresses, a Raman-reporter-labeled DNA probe is degraded, liberating the reporter from probe DNA, allowing passage across the size-restricting dialysis membrane into the SERS-active colloid, where the accumulating reporter can be measured in real time. Here, we demonstrate that this system is capable of real-time and single-well multiplexed readout of a PCR reaction to simultaneously detect two biomarker genes for methicillin-resistant S. aureus (MRSA).

Estimating variance components and predicting breeding values for eventing disciplines and grades in sport horses.

Eventing competitions in Great Britain (GB) comprise three disciplines, each split into four grades, yielding 12 discipline-grade traits. As there is a demand for tools to estimate (co)variance matrices with a large number of traits, the aim of this work was to investigate different methods to produce large (co)variance matrices using GB eventing data. Data from 1999 to 2008 were used and penalty points were converted to normal scores. A sire model was utilised to estimate fixed effects of gender, age and class, and random effects of sire, horse and rider. Three methods were used to estimate (co)variance matrices. Method 1 used a method based on Gibbs sampling and data augmentation and imputation. Methods 2a and 2b combined sub-matrices from bivariate analyses; one took samples from a multivariate Normal distribution defined by the covariance matrix from each bivariate analysis, then analysed these data in a 12-trait multivariate analysis; the other replaced negative eigenvalues in the matrix with positive values to obtain a positive definite (co)variance matrix. A formal comparison of models could not be conducted; however, estimates from all methods, particularly Methods 2a/2b, were in reasonable agreement. The computational requirements of Method 1 were much less compared with Methods 2a or 2b. Method 2a heritability estimates were as follows: for dressage 7.2% to 9.0%, for show jumping 8.9% to 16.2% and for cross-country 1.3% to 1.4%. Method 1 heritability estimates were higher for the advanced grades, particularly for dressage (17.1%) and show jumping (22.6%). Irrespective of the model, genetic correlations between grades, for dressage and show jumping, were positive, high and significant, ranging from 0.59 to 0.99 for Method 2a and 0.78 to 0.95 for Method 1. For cross-country, using Method 2a, genetic correlations were only significant between novice and pre-novice (0.75); however, using Method 1 estimates were all significant and low to moderate (0.36 to 0.70). Between-discipline correlations were all low and of mixed sign. All methods produced positive definite 12 × 12 (co)variance matrices, suitable for the prediction of breeding values. Method 1 benefits from much reduced computational requirements, and by performing a true multivariate analysis.

Genetic parameters of egg defects and egg quality in layer chickens.

Genetic parameters were estimated for egg defects, egg production, and egg quality traits. Eggs from 11,738 purebred brown-egg laying hens were classified as salable or as having one of the following defects: bloody, broken, calcium deposit, dirty, double yolk, misshapen, pee-wee, shell-less, and soft shelled. Egg quality included albumen height, egg weight, yolk weight, and puncture score. Body weight, age at sexual maturity, and egg production were also recorded. Heritability estimates of liability to defects using a threshold animal model were less than 0.1 for bloody and dirty; between 0.1 and 0.2 for pee-wee, broken, misshapen, soft shelled, and shell-less; and above 0.2 for calcium deposit and double yolk. Quality and production traits were more heritable, with estimates ranging from 0.29 (puncture score) to 0.74 (egg weight). High-producing hens had a lower frequency of egg defects. High egg weight and BW were associated with an increased frequency of double yolks, and to a lesser extent, with more shell quality defects. Estimates of genetic correlations among defect traits that were related to shell quality were positive and moderate to strong (0.24-0.73), suggesting that these could be grouped into one category or selection could be based on the trait with the highest heritability or that is easiest to measure. Selection against defective eggs would be more efficient by including egg defect traits in the selection criterion, along with egg production rate of salable eggs and egg quality traits.

Genetic heterogeneity of variance in production traits of laying hens.

Genetic parameters for mean and for environmental variation in egg weight, body weight, age at first egg, and egg production were estimated in eight layer lines. The data were recorded from years 1999-2007, with on average of 6500 birds per line. An iterative mean-variance REML method was applied with a sire-plus-dam model for mean, a sire model for variance, and a fixed effect of hatch within generation for both mean and variance. The estimated heritability of environmental variation averaged about 5% for body weight, 3% for egg weight, and 11% for age at first egg, but was inconsistent among the lines for egg production (0-15%). Correlations between means and variances were slightly positive for body weight, egg weight, and age at first egg; and strongly negative for egg production. Age at first egg had the highest heritability of environmental variation; and favourable correlations with egg production and with variation in other production traits indicate that reducing variation in this trait may have potential benefits for the breeding industry.

Inheritance of hatchability in broiler chickens and its relationship to egg quality traits.

The first objective of this study on broiler breeders was to investigate the genetic basis of variability in hatchability over age using a longitudinal model. Weekly percentage hatch of fertile and hatch of set eggs were available for 23,250 dams mated to 3,106 sires of the same age between the 28th and 54th week of life. Hatch of set was very highly correlated with fertility and showed a similar pattern through lay. There was a genetic contribution of the dam but not the sire to hatch of fertile; its heritability was about 6% from peak lay onward but lower earlier. The second objective was to investigate the relationship between hatchability and internal and external egg quality traits measured at 48 wk of age. These traits, specific gravity, weight loss, egg weight, and Haugh units, had moderate to high heritabilities, 0.53, 0.38, 0.65, and 0.38, respectively. Parameters of the genetic trend in weekly hatchability (mean and persistency) were significantly correlated with these egg quality traits, suggesting that in a bulk mating situation in which individual recording of hatchability is not possible, these quality traits could provide some indication on the trend in flock hatchability.

Contributions of genetic and environmental components to changes in phenotypic variation between generations.

We evaluate the extent to which changes in phenotypic variation among generations of populations kept in the same environment are due to changes in genetic (V(A)) or in environmental (V(E)) variance. Data were available on body weight of adult poultry on a total of 89186 birds (mainly females) from six generations of each of seven lines of layers. There was substantial heterogeneity of variation between generations, shown to be in both V(A) and V(E) components. Based on the Akaike information criterion (AIC), the best fit was with both components changing, and a better fit was obtained if V(A)/V(E) (i.e. heritability) or V(E), rather than V(A), was assumed constant. In analyses of quantitative genetic data spanning environmental groups, attention should be paid to whether and how the variance components change among groups before undertaking detailed variance partition that may be sensitive to such changes.

Evidence of genetic resistance of cattle to infection with Mycobacterium bovis.

Anecdotal evidence points to genetic variation in resistance of cattle to infection with Mycobacterium bovis, the causative agent of bovine tuberculosis (BTB), and published experimental evidence in deer and cattle suggests significant genetic variation in resistance and reactivity to diagnostic tests. However, such genetic variation has not been properly quantified in the United Kingdom dairy cattle population; it is possible that it exists and may be a factor influencing the occurrence of BTB. Using models based on the outcome of the process of diagnosis (ultimate fate models) and on the outcome of a single stage of diagnosis (continuation ratio models, herd test-date models), this study shows that there is heritable variation in individual cow susceptibility to BTB, and that selection for milk yield is unlikely to have contributed to the current epidemic. Results demonstrate that genetics could play an important role in controlling BTB by reducing both the incidence and the severity of herd breakdowns.

African Dacus (Diptera: Tephritidae: molecular data and host plant associations do not corroborate morphology based classifications.

The genus Dacus Fabricius includes economically important pest fruit flies distributed in the Afrotropical and Indo-Australian regions. Two recent revisions based on morphological characters proposed new and partially discordant classifications synonymizing/revalidating several subgeneric names and forming species groups. Regardless these efforts, the phylogenetic relationships among Dacus species remained largely unresolved mainly because of the difficulties in assigning homologous character states. Therefore we investigated the phylogeny of African Dacus by sequencing 71 representatives of 32 species at two mitochondrial (COI, 16S) and one nuclear (period) gene fragments. Phylogenetic relationships were inferred through Bayesian and Maximum Parsimony methods and hypotheses about the monophyly of Dacus subgenera were tested by Shimodaira-Hasegawa tests. The congruence tests and the analyses of the single gene fragments revealed that the nuclear gene supports similar conclusions as the two mitochondrial genes. Levels of intra- and inter-specific differentiation of Dacus species were highly variable and, in some cases, largely overlapping. The analyses of the concatenated dataset resolved two major bootstrap-supported groups as well as a number of well-supported clades and subclades that often comprised representatives of different subgenera. Additionally, specimens of Dacus humeralis from Eastern and Western African localities formed separate clades, suggesting cryptic differentiation within this taxon. The comparisons between the molecular phylogeny and the morphological classification revealed a number of discrepancies and, in the vast majority of cases, the molecular data were not compatible with the monophyly of the currently recognised subgenera. Conversely, the molecular data showed that Apocynaceae feeders are a monophyletic sister group of species feeding on both Cucurbitaceae and Passifloraceae (these latter being also monophyletic). These results show a clear association between the molecular phylogeny of African Dacus and the evolution of host plant choice and provide a basis towards a more congruent taxonomy of this genus.

Genetic variability in residual variation of body weight and conformation scores in broiler chickens.

The aim of the study was to estimate genetic variance in residual variation of BW and body conformation scores of 34-d-old male and female broiler chickens. The data set included performance records of 52,349 female and 49,001 male birds. Two models were used: an iterative mean-variance restricted maximum likelihood sire plus dam model and a Bayesian sire plus dam model, in each case with heterogeneity in residual variances across sire families. They gave similar results. Estimates of heritability for BW in females and males were, respectively, 0.25 and 0.21, and for conformation score were 0.24 and 0.15, and genetic correlations for the same trait between sexes were high. Estimates of genetic correlations between means and variances were positive for both sexes and both traits. Estimates of the heritability of residual variation were low, between 0.023 and 0.038 for both traits, but genetic CV were substantial (between 0.25 and 0.40), indicating the possibility of improving uniformity of BW and conformation by means of selection.

Characterization of the dairy farm environment in Great Britain and the effect of the farm environment on cow life span.

Dairy farms vary a great deal in the feeding and management systems that are used. These differences affect the performance of the cows, and some genotypes may be affected more than others. If effects of such genotype-by-environment interactions (GxE) are large, then farmers must be made aware of them to make informed breeding decisions. To investigate GxE, a classification system for farm environments was developed based on national- and fine-level data from dairy herds across the United Kingdom. The national data included herd and yield characteristics and local weather information. The fine-level data included information on feeding and management systems on farms, and was obtained from survey results from 778 farms. A principal components analysis of the surveys identified 2 major dimensions characterizing the data. The first dimension explained 14.6% of the variation and was related to the level of production intensity. The second dimension explained 11.5% of the variation and was related to climate. Information on milk yield, herd characteristics, and climate was then extracted from national databases for the survey farms. A canonical correlation analysis was used to relate the survey data to the variables extracted from the national data set to determine the most relevant variables. The canonical correlation between the chosen sets of national data and survey variables was 0.62. This environmental classification was then used to determine how the farm environment affects the life span of dairy cows. The life span of the daughters of 1,000 sires was related to the type of farm environment. The daughters of a majority of sires showed a "plastic" response, with increased life span in less intensive farms. The daughters of a smaller number of sires showed a more generalized response, with life span being less affected by the environment. This GxE suggested that sires vary in the sensitivity of their daughters to different farm environments. This variation in response could allow breeding companies and farmers to match sires to particular farm environments.

The relationship between fertility, rump angle, and selected type information in Holstein-Friesian cows.

Some dairy cattle breeders believe that dairy cows with high pin bones will have poorer fertility. The aim of this study was to examine this claim by investigating the relationships, both genetic and phenotypic, between fertility, rump angle, and other selected type traits in first-lactation Holstein-Friesians. Results showed an unfavorable genetic correlation (-0.16) between calving interval and rump angle, suggesting that animals with high pin bones would have a longer calving interval. However, no significant genetic or phenotypic correlation between days to first service and nonreturn rate and rump angle was observed. No evidence of a relationship, linear or quadratic, between any fertility trait and rump angle was found. Udder support and mammary system were unfavorably correlated to calving interval (0.25 and 0.14, respectively), suggesting that cows with more functional udders would have a longer calving interval. Legs and feet score was favorably correlated to nonreturn rate, suggesting that animals with good legs and feet would be less likely to return to service.

Contrasting models for lactation curve analysis.

Several statistical models have been proposed for the genetic evaluation of production traits in dairy cattle based on test-day records. Three main approaches have been put forward in the literature: random regression, orthogonal polynomials, and, more recently, character process models. The aim of this paper is to show how these different approaches are related, to compare their performance for the genetic analysis of lactation curves, and to assess equivalence between sire and animal models for repeated measures analyses. It was found that, with an animal model, a character process model with 11 parameters performed better, regarding the likelihood criterion, than a quartic random regression model (with 31 parameters). However, although the likelihood was higher, the genetic variance was very different with the character process model from the unstructured model, which raises important issues concerning model selection criteria. There are advantages in combining methodologies. A quadratic random regression model for the environmental part, combined with a character process model for the residual, performed better than the quartic random regression model and had fewer parameters. A character process structure allowing for a correlation pattern modeled the residual better than a simple quadratic variance, and had only one extra parameter.

Neuronal activity in dorsomedial frontal cortex and prefrontal cortex reflecting irrelevant stimulus dimensions.

Previous studies of the dorsomedial frontal cortex (DMF) and the prefrontal cortex (PF) have shown that, when monkeys respond to nonspatial features of a discriminative stimulus (e.g., color) and the stimulus appears at a place unrelated to the movement target, neurons nevertheless encode stimulus location. This observation could support the idea that these neurons always encode stimulus location, regardless of its relevance to an instrumentally conditioned behavior. Past studies, however, leave open the possibility that activity observed during one operant task might reflect the contingencies of a different task, performed at different times. To test these alternatives, we examined the activity of DMF and PF neurons in two rhesus monkeys conditioned to perform an operant eye-movement task in which only the color and shape of visual stimuli served as salient discriminative features. Each of eight stimuli was associated with a response to a different eye-movement target. The location of these stimuli varied from trial to trial but was of no behavioral relevance, and the monkeys did not perform any operant task in which stimulus location controlled behavior. A substantial minority of neurons in both DMF and PF nevertheless encoded stimulus location, which indicates that this property does not depend on its relevance in an instrumentally conditioned behavior.

Effects of administering cocaine at the same versus varying times of day on circadian activity patterns and sensitization in rats.

The effects of different schedules of cocaine administration on circadian activity patterns and locomotor sensitization were studied. Rats received intraperitoneal injections of either saline or 20 mg/kg cocaine at either 24- or 33-hr intervals for 8 cycles (development). After a 2-day withdrawal, they were given a cocaine challenge in a novel environment. Rats given cocaine at 24-hr intervals were hypoactive 4 to 9 hr postinjection during development and, during cocaine challenge, showed sensitization of locomotor activity. Rats given cocaine at 33-hr intervals did not show these effects. On the 33-hr-period schedule, activity was enhanced beginning 24 hr after drug receipt. Different intermittent schedules of cocaine receipt may alter the vulnerability to cocaine, and altered vulnerability may be more likely when a subsequent cocaine injection interacts with a distal state of sensitivity produced by a prior injection.

A link function approach to model heterogeneity of residual variances over time in lactation curve analyses.

Several studies with test-day models for the lactation curve show heterogeneity of residual variance over time. The most common approach is to divide the lactation length into subclasses, assuming homogeneity within these classes and heterogeneity between them. The main drawbacks of this approach are that it can lead to many parameters being estimated and that classes have to be arbitrarily defined, whereas the residual variance changes continuously over time. A methodology that overcomes these drawbacks is proposed here. A structural model on the residual variance is assumed in which the covariates are parametric functions of time. In this model, only a few parameters need to be estimated, and the residual variance is then a continuous function of time. The analysis of a sample data set illustrates this methodology.

Effects of MK801 and neuroleptics on prepulse inhibition: re-examination in two strains of rats.

Disruption of prepulse inhibition (PPI) induced by NMDA receptor antagonists, such as MK801, has been used as an animal model of positive and negative symptoms of schizophrenia. Previous studies suggested that atypical, but not typical, neuroleptics can selectively restore MK801-induced PPI disruption and that such selectivity may depend on strain differences. The present study re-examined PPI disruption by systemic MK801 in Wistar (WS) and Sprague-Dawley (SD) strains, and addressed the issue whether clozapine (atypical), compared to haloperidol (typical), effectively antagonizes MK801-induced PPI disruption. In addition, we tested the effects of bilateral microinfusion of MK801 into the ventral hippocampus in WS. Systemic MK801 disrupted PPI in both strains. Neither clozapine nor haloperidol antagonized MK801-induced PPI in either strain. Our clozapine data do not agree with previous reports of clozapine's ability to antagonize MK801-induced PPI disruption. Similar to previous results with SD, MK801 infusion into the ventral hippocampus failed to affect PPI in WS. In our view, the selective ability of atypical neuroleptics to restore PPI disruption by NMDA antagonists, and to serve as a tool for identifying possible atypical neuroleptics, requires further examination. PPI disruption with systemic MK801 may be due to the blockade of NMDA receptors in multiple brain sites.

Rule-dependent neuronal activity in the prefrontal cortex.

We studied single-neuron activity in the prefrontal cortex (PF) while a monkey performed a task according to two different rules, termed conditional and spatial. The monkey viewed a video screen, and its task required a hand movement in response to the dimming of a light spot. There were four light spots on the screen: right, left, up, and down from the center. Only one of the four spots dimmed, and the degree of dimming was slight. Accordingly, the monkey needed to foveate the "correct" light spot to detect the dimming. A visual cue indicated which of the four light spots would be deemed correct and, thus, would dim on each trial. The sequence of events was as follows: a fixation spot appeared at the center of the screen; then, a cue appeared twice at one of the four potential target locations; then, the four target spots appeared; and, finally, one of them dimmed. Except for the color of an initial fixation point, the cues, their locations, and other events were identical for the conditional and spatial rules. The rules differed in one essential way. For the conditional rule, nonspatial attributes of the visual cue indicated which of the four light spots would dim, and the cue's location was irrelevant. For the spatial rule, the cue's location determined the correct target on that trial. The light spot at the location of the cue always dimmed, regardless of which cue appeared there. Our sample included 221 PF neurons showing significant task-related activity modulation, distributed among dorsal, dorsolateral, and ventral PF regions. Between one-third and one-half of the sample in each of those regions showed statistically significant activity differences that could be attributed to the rule. Selectivity for cues and/or their locations was common. However, there was no significant regional segregation of such selectivity. These data support the hypothesis that PF plays a role in the guidance of behavior according to previously learned rules.

Genetic and environmental smoothing of lactation curves with cubic splines.

Most approaches to modeling lactation curves involve parametric curves with fixed or random coefficients. In either case, the resulting models require the specification on an underlying parametric curve. The fitting of splines represents a semiparametric approach to the problem. In the context of animal breeding, cubic smoothing splines are particularly convenient because they can be incorporated into a suitably constructed mixed model. The potential for the use of splines in modeling lactation curves is explored with a simple example, and the results are compared with those using a random regression model. The spline model provides greater flexibility at the cost of additional computation. Splines are shown to be capable of picking up features of the lactation curve that are missed by the random regression model.

Cocaine-induced activation of striatal neurons during focused stereotypy in rats.

As psychomotor stimulants, both amphetamine and cocaine elicit episodes of repetitive motor activation (focused stereotypy) known to involve the mesostriatal dopamine system. During amphetamine-induced focused stereotypy, motor-related neurons in the striatum respond with either an excitation or inhibition, depending on dose and behavioral pattern, whereas nonmotor-related units are inhibited. To assess striatal activity during the focused stereotypy induced by cocaine, both types of striatal units were recorded in ambulant rats. Either 20 or 40 mg/kg cocaine caused highly focused sniffing and head bobbing, which occurred in conjunction with activation of both motor- and nonmotor-related neurons. The activation of motor-related units was evident even when firing rate was compared during periods of matched pre- and post-drug behavior, arguing against movement as the sole basis for the drug-induced neuronal excitation. Subsequent administration of haloperidol (1.0 mg/kg) reversed but did not completely block the neuronal activation, while the behavioral response shifted away from focused stereotypy toward an increase in ambulation. Thus, the level of activation of both motor- and nonmotor-related striatal neurons may play a critical role in the behavioral response pattern induced by cocaine.

Responses of neurons in dorsal striatum during amphetamine-induced focused stereotypy.

The phase of highly focused, repetitive behavior (stereotypy) induced by amphetamine in rats emerges after an initial period of locomotor activation. To assess the neuronal correlates of this behavioral transition, single-unit activity was recorded from the dorsal striatum of awake, unrestrained rats. Units were first characterized in terms of their responsiveness to spontaneous movement. Various types of motor-related neurons were identified. Some increased activity above resting baseline during specific movements such as forward locomotion or turning of the head, while others were excited during periods of general behavioral activation. Neurons that showed no consistent change in firing rate during overt movement were classified separately. Administration of 5.0 mg/kg d-amphetamine caused a steady increase in the overall neuronal response through both the locomotor and stereotypy phases. An analysis of specific neuronal types, however, revealed distinct, phase-related shifts in firing rate. Locomotor-related neurons discharged rapidly during the early phase of the amphetamine response and then declined toward baseline as focused stereotypy emerged. Cells found to be excited primarily during head movements showed relatively small changes shortly after drug administration but increased markedly in conjunction with intense head-movement activity associated with focused stereotypy. Other neurons, which increased activity nonselectively to a wide range of movements, showed progressive increases in firing rate during both behavioral phases elicited by the drug. Subsequent administration of 1.0 mg/kg haloperidol typically reversed the neuronal changes and blocked amphetamine-induced focused stereotypy. Nonmotor-related cells responded inconsistently to amphetamine, showing an inhibition, excitation, or no change in rate. Previous assessments of neuron-behavior relationships have shown that changes in motor-related neuronal activity are not secondary to amphetamine-induced behavioral changes, though this finding may not apply in all cases. At doses capable of eliciting focused stereotypy, therefore, amphetamine appears to trigger a complex pattern of striatal activity that governs the behavioral response. This conclusion supports steadily increasing evidence that the role of striatal neurons in amphetamine-induced focused stereotypy is shaped by multiple synaptic mechanisms.