Impact of volume and expression time in an AAV-delivered channelrhodopsin

Optogenetics has revolutionised neuroscience research, but at the same time has brought a plethora of new variables to consider when designing an experiment with AAV-based targeted gene delivery. Some concerns have been raised regarding the impact of AAV injection volume and expression time in relation to longitudinal experimental designs. In this study, we investigated the efficiency of optically evoked post-synaptic responses in connection to two variables: the volume of the injected virus and the expression time of the virus. For this purpose, we expressed the blue-shifted ChR2, oChIEF, employing a widely used AAV vector delivery strategy. We found that the volume of the injected virus has a minimal impact on the efficiency of optically-evoked postsynaptic population responses. The expression time, on the other hand, has a pronounced effect, with a gradual reduction in the population responses beyond 4 weeks of expression. We strongly advise to monitor time-dependent expression profiles when planning or conducting long-term experiments that depend on successful and stable channelrhodopsin expression.

Analysis of the effect of air temperature on ammonia emission from band application of slurry

Field application of liquid animal manure (slurry) is a significant source of ammonia (NH₃) emission to the atmosphere. It is well supported by theory and previous studies that air temperature effects NH₃ flux from field applied slurry. The objectives of this study was to statistically model the response of temperature at the time of application on cumulative NH₃ emission. Data from 19 experiments measured with the same system of dynamic chambers and online measurements were included. A generalized additive model allowing to represent non-linear functional dependences of the emission on the temperature revealed that a positive response of the cumulative NH₃ emission on the temperature at the time of application up to a temperature of approximately 14 °C. Above that, the temperature effect is insignificant. Average temperature over the measuring period was not found to carry any additional information on the cumulative NH₃ emission. The lack of emission response on temperature above a certain point is assumed to be caused by drying out of the slurry and possible crust formation. This effect is hypothesized to create a physical barrier that reduce diffusion of NH₃ to the soil surface, thereby lowering the emission rate. Furthermore, the effect of the interaction between soil type and application technique and the effect of dry matter content of the slurry was derived from the model, and found to be significant on cumulative NH₃ emission predictions.

Total Phosphorus Determination in Soils Using Laser-Induced Breakdown Spectroscopy: Evaluating Different Sources of Matrix Effects

Laser-induced breakdown spectroscopy (LIBS) is a potential alternative to wet chemical methods for total soil phosphorus determination, but matrix effects related to physical and chemical sample properties need to be further understood. The aim of this study was to explore matrix effects linked to particle size distribution and chemical form of phosphorus on LIBS response and the ability of LIBS to predict total phosphorus in a range of different soil types. Univariate calibration curves were developed by spiking the soils with increasing doses of phosphorus, and limits of detection for LIBS determined phosphorous (P) (LIBS-P) were calculated. Different particle size distributions in otherwise identical soils were obtained by four milling treatments and effects of chemical form of phosphorus were examined by spiking soils with identical amounts of phosphorus in different chemical compounds. The LIBS-P response showed a high correlation (R² > 0.99) with total phosphorus for all soils. Yet, the sensitivity of LIBS differed significantly among soils, as the slope of the calibration curves increased with increasing sand content, resulting in estimated limits of detection of 10 mg kg^-1 for the sandiest and 122 mg · kg^-1 for the most clayey soils. These limits indicate that quantitative evaluation of total phosphorus in sandy and loamy sandy soils by LIBS is feasible, since they are lower than typical total phosphorus concentrations in soil. A given milling treatment created different particle size distributions depending on soil type, and consequently different LIBS-P results. Thus, procedures that specify the required degree of homogenization of soil samples prior to analysis are needed. Sieving after milling could be an option, but that should be tested. The soils spiked with Fe(III) phosphate, potassium phosphate and phytic acid had similar LIBS-P, except for soils with hydroxyapatite, which resulted in markedly lower response. These results suggested that matrix effects related to the chemical nature of phosphorus would be minor for non-calcareous soils in humid regions, where apatites comprise only a small fraction of total phosphorus. Strategies to overcome matrix effects related to particle size and content of apatite-phosphorus by combining multivariate models and soil type groupings should be further investigated.

Methane fluxes from a rewetted agricultural fen during two initial years of paludiculture

Rewetting agricultural peatland abates carbon dioxide (CO₂) emission, but the resulting waterlogged anaerobic soil condition may create hotspots of methane (CH₄) emissions. In this study, we measured CH₄ emissions from side-by-side replicated plots in an agricultural fen cultivated with reed canary grass under a control and two experimental rewetting (i.e., paludiculture) conditions as either continuously flooded to soil surface or semi-flooded where water from the flooded plots intruded from sub-surface. Fluxes were measured for two successive years at 1-2 week intervals (total 59 measurement dates) using static chambers. Annual emissions were estimated by trapezoidal linear interpolation of the measured fluxes between the measurement dates. Two-year time-weighted average ground water tables (GWT) in the flooded, semi-flooded and control plots were 1, 3 and 9 cm below soil surface, respectively. The annual average emissions from flooded plots were 82 and 116 g CH₄ m^-2 yr^-1 in Year 1 and 2, respectively, which were significantly higher than the emissions from semi-flooded plots (35 and 69 g CH₄ m^-2 yr^-1 in Year 1 and 2, respectively) and from control plots (3 and 9 g CH₄ m^-2 yr^-1 in Year 1 and 2, respectively). Overall, the results showed that the GWT in paludiculture should be maintained few cm below soil surface during high temperature periods to prevent risks of high CH₄ emissions.

Nitrate leaching from suction cup data: Influence of method of drainage calculation and concentration interpolation

The use of suctions cups is a common practice for estimating nitrate (NO₃ -N) leaching under agricultural systems despite the various uncertainties associated with the approach. One major uncertainty is water flux, which is required for calculating NO₃ -N leaching loads from measured concentrations. Another problem is the interpolation of NO₃ -N concentrations between measurement days. We investigated how differences in water flux, obtained from two different models (EVACROP and APSIM), affect NO₃ -N leaching loads. The effect of interpolation of NO₃ -N concentrations based on days or drainage was also addressed. The models were set up according to a 2-yr field experiment with spring barley (Hordeum vulgare L. Quinch) with different levels of N fertilization rates on a loamy soil at Flakkebjerg, Denmark. Due to small differences in measured NO₃ -N concentrations between sequential samplings, the method of interpolation did not significantly affect NO₃ -N leaching in the two periods investigated. Although there is no standard against which leaching losses from different approaches can be tested, results highlight that the modeling of water uptake as affected by N supply influences the amount of drainage and thus calculated NO₃ -N leaching. Therefore, for experiments with varying N fertilization levels, the APSIM model, which accounts for N nutrition on crop water use, is likely more accurate. For common fertilization rates, the simpler EVACROP seems appropriate. Thus, when using suction cup data for testing models or for evaluating mitigation options for nitrate leaching, the use of an appropriate model for estimating water fluxes is important.

Seed size and burial depth influence Zostera marina L. (eelgrass) seed survival, seedling emergence and initial seedling biomass development

Seed burial in the sediment is critical for successful seedling establishment in seagrasses because it protects from predation and dispersal into unsuitable sites, and it may enhance germination by exposing the seeds to suitable germination stimuli. However, relatively little is known about the fate of buried seeds and their ability to emerge from greater depths. The goal of this study was to determine seed survival in the sediment, seedling emergence success and initial seedling biomass of Zostera marina in relation to burial depth and to evaluate if large seeds, having larger energy reserves, are more tolerant to burial than small seeds. Seeds from a perennial Z. marina population were buried at 7 different sediment depths (0.1–8 cm), and seeds sorted by size (large and small) were buried at depths of 2, 4 and 6 cm in outdoor mesocosms. Total seedling emergence after 2 months was significantly affected by seed burial depth, with maximum values in the top 2 cm of the sediment (48.1–56.7% of planted seeds), and a marked decline below 4 cm depth to only 5% seedling emergence at the deepest burial depth of 8 cm. Moreover, seeds had shorter time to emergence from shallow compared to deep burial depths. At all burial depths, a small fraction of seeds (<10%) died after germination but before emerging, and 15–30% remained viable after 6 months. Seed mortality was the major limitation to seedling recruitment from the deeper burial depths. The effect of seed size on seedling emergence success and time was not clear, but heavier seeds displayed greater longevity and gave rise to seedlings of significantly higher biomass, indicating that the mobilization of metabolic reserves may be important during initial seedling development.

Vitellogenin expression in the oilseed rape pest Meligethes aeneus

When investigating insecticide resistance of pest insects, for example, the pollen beetle Meligethes aeneus, it is relevant to differentiate toxicological and molecular genetic data between male and female specimens. A molecular sex determination method would allow resistance testing to be run without prior sorting of the samples. A one-step quantitative RT-PCR method for quantification of the yolk protein vitellogenin expression in the pollen beetle was established. The expression level of vitellogenin relative to tubulin was determined. Pollen beetles were tested at different time points during their development to determine if vitellogenin is a reliable molecular marker for detection of sexually mature females. The differentiation between females and males by relative expression of vitellogenin to tubulin is conditional regarding the life cycle. Sexually mature females and males could easily be distinguished, whereas immature specimens could not be seperated. Vitellogenin expression is a successful marker for identification of sexually mature pollen beetles. Females from the spring populations showed vitellogenin expression when the temperature was above 10.2°C. Further, detailed observations of vitellogenin throughout the spring indicated a strong relationship between daily temperatures and vitellogenin expression, which is an indicator of oviposition ability.

A new DNA sensor system for specific and quantitative detection of mycobacteria

In the current study, we describe a novel DNA sensor system for specific and quantitative detection of mycobacteria, which is the causative agent of tuberculosis. Detection is achieved by using the enzymatic activity of the mycobacterial encoded enzyme topoisomerase IA (TOP1A) as a biomarker. The presented work is the first to describe how the catalytic activities of a member of the type IA family of topoisomerases can be exploited for specific detection of bacteria. The principle for detection relies on a solid support anchored DNA substrate with dual functions namely: (1) the ability to isolate mycobacterial TOP1A from crude samples and (2) the ability to be converted into a closed DNA circle upon reaction with the isolated enzyme. The DNA circle can act as a template for rolling circle amplification generating a tandem repeat product that can be visualized at the single molecule level by fluorescent labelling. This reaction scheme ensures specific, sensitive, and quantitative detection of the mycobacteria TOP1A biomarker as demonstrated by the use of purified mycobacterial TOP1A and extracts from an array of non-mycobacteria and mycobacteria species. When combined with mycobacteriophage induced lysis as a novel way of effective yet gentle extraction of the cellular content from the model Mycobacterium smegmatis, the DNA sensor system allowed detection of mycobacteria in small volumes of cell suspensions. Moreover, it was possible to detect M. smegmatis added to human saliva. Depending on the composition of the sample, we were able to detect 0.6 or 0.9 million colony forming units (CFU) per mL of mycobacteria, which is within the range of clinically relevant infection numbers. We, therefore, believe that the presented assay, which relies on techniques that can be adapted to limited resource settings, may be the first step towards the development of a new point-of-care diagnostic test for tuberculosis.

Effect of poplar trees on nitrogen and water balance in outdoor pig production - A case study in Denmark

Nitrate leaching from outdoor pig production is a long-standing environmental problem for surface and groundwater pollution. In this study, the effects of inclusion of poplar trees in paddocks for lactating sows on nitrogen (N) balances were studied for an organic pig farm in Denmark. Vegetation conditions, soil water and nitrate dynamics were measured in poplar and grass zones of paddocks belonging to main treatments: access to trees (AT), no access to trees (NAT) and a control without trees (NT), during the hydrological year April 2015 to April 2016. Soil water drainage for each zone, simulated by two simulation models (CoupModel and Daisy), was used to estimate nitrate leaching from the zones in each paddock. N balances (input minus output) for the treatments were computed and compared. The results showed that, in terms of annual water balance and regardless of treatment, simulated evapotranspiration of poplar was 560-569 and 489-498 mm for CoupModel and Daisy, respectively, and corresponding evapotranspiration of grass-clover was 250 and 400 mm, against precipitation of 1076 mm. Simulated drainage below the root zone varied as 620-723 mm for Daisy and 568-958 mm for CoupModel, the higher end of the latter being probably overestimated. Annual nitrate leaching ranged from 32 kg N ha^-1 in the poplar zone of NAT up to 289 kg N ha^-1 in the control grass zone of NT. The poplar zone showed significantly lower nitrate leaching, by 75-80%, compared to the grass zone. For the control NT treatment, nitrate leaching was approximately 50% higher in the grass zone closest to the hut compared to the grass zone further away. NT treatment also had the largest surface N balance of 468 kg N ha^-1 compared to 436 and 397 kg N ha^-1 for AT and NAT, respectively. When N losses by leaching and volatilisation were included, soil N balances were 118, 157 and 113 kg N ha^-1 for AT, NAT and NT, respectively. Overall, the two simulation models were found useful tools for analyses of water balance for complex agroforestry systems. The findings collectively suggest that it is possible to decrease nitrate leaching from outdoor pig production on sandy soils by inclusion of poplar trees. Additional measures are nevertheless needed to reduce N losses on a mean area basis in paddocks with 20% tree cover.

Catch Crop Residues Stimulate N2O Emissions During Spring, Without Affecting the Genetic Potential for Nitrite and N2O Reduction

Agricultural soils are a significant source of anthropogenic nitrous oxide (N₂O) emissions, because of fertilizer application and decomposition of crop residues. We studied interactions between nitrogen (N) amendments and soil conditions in a 2-year field experiment with or without catch crop incorporation before seeding of spring barley, and with or without application of N in the form of digested liquid manure or mineral N fertilizer. Weather conditions, soil inorganic N dynamics, and N₂O emissions were monitored during spring, and soil samples were analyzed for abundances of nitrite reduction (nirK and nirS) and N₂O reduction genes (nosZ clade I and II), and structure of nitrite- and N₂O-reducing communities. Fertilization significantly enhanced soil mineral N accumulation compared to treatments with catch crop residues as the only N source. Nitrous oxide emissions, in contrast, were stimulated in rotations with catch crop residue incorporation, probably as a result of concurrent net N mineralization, and O₂ depletion associated with residue degradation in organic hotspots. Emissions of N₂O from digested manure were low in both years, while emissions from mineral N fertilizer were nearly absent in the first year, but comparable to emissions from catch crop residues in the second year with higher precipitation and delayed plant N uptake. Higher gene abundances, as well as shifts in community structure, were also observed in the second year, which were significantly correlated to NO3- availability. Both the size and structure of the nitrite- and N₂O-reducing communities correlated to the difference in N₂O emissions between years, while there were no consistent effects of management as represented by catch crops or fertilization. It is concluded that N₂O emissions were constrained by environmental, rather than the genetic potential for nitrite and N₂O reduction.

Detection of the Malaria causing Plasmodium Parasite in Saliva from Infected Patients using Topoisomerase I Activity as a Biomarker

Malaria is among the major threats to global health with the main burden of disease being in rural areas of developing countries where accurate diagnosis based on non-invasive samples is in high demand. We here present a novel molecular assay for detection of malaria parasites based on technology that may be adapted for low-resource settings. Moreover, we demonstrate the exploitation of this assay for detection of malaria in saliva. The setup relies on pump-free microfluidics enabled extraction combined with a DNA sensor substrate that is converted to a single-stranded DNA circle specifically by topoisomerase I expressed by the malaria causing Plasmodium parasite. Subsequent rolling circle amplification of the generated DNA circle in the presence of biotin conjugated deoxynucleotides resulted in long tandem repeat products that was visualized colorimetrically upon binding of horse radish peroxidase (HRP) and addition of 3,3′,5,5′-Tetramethylbenzidine that was converted to a blue colored product by HRP. The assay was directly quantitative, specific for Plasmodium parasites, and allowed detection of Plasmodium infection in a single drop of saliva from 35 out of 35 infected individuals tested. The results could be determined directly by the naked eye and documented by quantifying the color intensity using a standard paper scanner.

Temporal and Spatial Variability of Fungal Structures and Host Responses in an Incompatible Rust-Wheat Interaction

Information about temporal and spatial variability of fungal structures and host responses is scarce in comparison to the vast amount of genetic, biochemical, and physiological studies of host-pathogen interactions. In this study, we used avirulent wild type and virulent mutant isolates of Puccinia striiformis to characterize the interactions in wheat carrying yellow rust Yr2 resistance. Both conventional and advanced microscopic techniques were used for a detailed study of morphology and growth of fungal colonies and associated host cell responses. The growth of the wild type isolates was highly restricted due to hypersensitive response (HR, plant cell death) indicated by autofluorescence and change in the shape of the affected plant cells. The host response appeared post-haustorial, but large variation in the time and stage of arrest was observed for individual fungal colonies, probably due to a delay between detection and response. Some colonies were stopped right after the formation of the primary infection hyphae whereas others formed highly branched mycelia. HR was first observed in host cells in direct contact with fungal structures, after which the defense responses spread to adjacent host cells, and eventually led to encasement of the fungal colony. Several cells with HR contained haustoria, which were small and underdeveloped, but some cells contained normal sized haustoria without signs of hypersensitivity. The growth of the virulent mutants in the resistant plants was similar to the growth in plants without Yr2 resistance, which is a strong indication that the incompatible phenotype was associated with Yr2. The interaction between P. striiformis and wheat with Yr2 resistance was highly variable in time and space, which demonstrate that histological studies are important for a deeper understanding of host-pathogen interactions and plant defense mechanisms in general.

Genetic diversity within and among aecia of the wheat rust fungus Puccinia striiformis on the alternate host Berberis vulgaris

An isolate of the fungus Puccinia striiformis, causing yellow (stripe) rust on cereals and grasses, was selfed on the alternate (sexual) host, Berberis vulgaris. This enabled us to investigate genetic variability of progeny isolates within and among aecia. Nine aecial clusters each consisting of an aecium (single aecial cup) and nine clusters containing multiple aecial cups were selected from 18 B. vulgaris leaves. Aeciospores from each cluster were inoculated on susceptible wheat seedlings and 64 progeny isolates were recovered. Molecular genotyping using 37 simple sequence repeat markers confirmed the parental origin of all progeny isolates. Thirteen molecular markers, which were heterozygous in the parental isolate, were used to analyse genetic diversity within and among aecial cups. The 64 progeny isolates resulted in 22 unique recombinant multilocus genotypes and none of them were resampled in different aecial clusters. Isolates derived from a single cup were always of the same genotype whereas isolates originating from clusters containing up to nine aecial cups revealed one to three genotypes per cluster. These results implied that each aecium was the result of a successful fertilization in a corresponding pycnium and that an aecium consisted of genetically identical aeciospores probably multiplied via repetitive mitotic divisions. Furthermore, the results suggested that aecia within a cluster were the result of independent fertilization events often involving genetically different pycniospores. The application of molecular markers represented a major advance in comparison to previous studies depending on phenotypic responses on host plants. The study allowed significant conclusions about fundamental aspects of the biology and genetics of an important cereal rust fungus.

The parental origin correlates with the karyotype of human embryos developing from tripronuclear zygotes

Objective

It has previously been suggested that embryos developing from intracytoplasmic sperm-injected (ICSI) zygotes with three pronuclei (3PN) are endowed with a mechanism for self-correction of triploidy to diploidy. 3PN are also observed in zygotes after conventional in vitro fertilization (IVF). The parental origin, however, differs between the two fertilization methods. Whereas the vast majority of 3PN IVF zygotes are of dispermic origin and thus more likely to have two centrioles, the 3PN ICSI zygotes are digynic in origin and therefore, more likely to have one centriole. In the present study, we examine whether the parental origin of 3PN embryos correlates with the karyotype.

Methods

The karyotype of each nucleus was estimated using four sequential fluorescence in situ hybridizations-each with two probes-resulting in quantitative information of 8 different chromosomes. The karyotypes were then compared and correlated to the parental origin.

Results

3PN ICSI embryos displayed a significantly larger and more coordinated reduction from the assumed initial 3 sets of chromosomes than 3PN IVF embryos.

Conclusion

The differences in the parental origin-and hence the number of centrioles-between the 3PN IVF and the 3PN ICSI zygotes are likely to be the cause of the differences in karyotypes.

The proto-oncogene TWIST1 is regulated by microRNAs

Upregulation of the proto-oncogene Twist1 is highly correlated with acquired drug resistance and poor prognosis in human cancers. Altered expression of this multifunctional transcription factor is also associated with inherited skeletal malformations. The mammalian Twist1 3′UTRs are highly conserved and contain a number of potential regulatory elements including miRNA target sites. We analyzed the translational regulation of TWIST1 using luciferase reporter assays in a variety of cell lines. Among several miRNAs tested, miR-145a-5p, miR-151-5p and a combination of miR-145a-5p + miR-151-5p and miR-151-5p + miR-337-3p were able to significantly repress Twist1 translation. This phenomena was confirmed with both exogenous and endogenous miRNAs and was dependent on the presence of the predicted target sites in the 3′UTR. Furthermore, the repression was sensitive to LNA-modified miRNA antagonists and resulted in decreased migratory potential of murine embryonic fibroblast cells. Understanding the in vivo mechanisms of this oncogene's regulation might open up a possibility for therapeutic interference by gene specific cancer therapies.

Droplet microfluidics platform for highly sensitive and quantitative detection of malaria-causing Plasmodium parasites based on enzyme activity measurement

We present an attractive new system for the specific and sensitive detection of the malaria-causing Plasmodium parasites. The system relies on isothermal conversion of single DNA cleavage-ligation events catalyzed specifically by the Plasmodium enzyme topoisomerase I to micrometer-sized products detectable at the single-molecule level. Combined with a droplet microfluidics lab-on-a-chip platform, this design allowed for sensitive, specific, and quantitative detection of all human-malaria-causing Plasmodium species in single drops of unprocessed blood with a detection limit of less than one parasite/μL. Moreover, the setup allowed for detection of Plasmodium parasites in noninvasive saliva samples from infected patients. During recent years malaria transmission has declined worldwide, and with this the number of patients with low-parasite density has increased. Consequently, the need for accurate detection of even a few parasites is becoming increasingly important for the continued combat against the disease. We believe that the presented droplet microfluidics platform, which has a high potential for adaptation to point-of-care setups suitable for low-resource settings, may contribute significantly to meet this demand. Moreover, potential future adaptation of the presented setup for the detection of other microorganisms may form the basis for the development of a more generic platform for diagnosis, fresh water or food quality control, or other purposes within applied or basic science.

Short communication: Large-scale study on effects of metritis on reproduction in Danish Holstein cows

A total of 398,237 lactations of Danish Holstein dairy cows were studied with the main objective to investigate the effects of metritis on 2 fertility variables: interval from calving to first insemination (CFI) and nonreturn rate at 56 d after first insemination (NR56), adjusting for milk production and body condition score as confounders. Metritis was defined as a score of at least 5 (indicating purulent vaginal discharge with abnormal smell) on the Danish uterine score scale (from 0 to 9, used to evaluate vaginal discharge in the first 19 d postpartum on all fresh cows in herds participating in a national herd health program). Cows with metritis in early lactation presented a significant delay in first insemination (hazard ratio of 0.80) and a significantly reduced probability of success at first insemination. The effect of metritis was also present after adjusting for possible effects of body condition score, milk production in the first month of lactation, parity, herd, and year-season. Only a small part of the observed effect of metritis could be explained by variation in body condition score at calving and milk production in the first month after calving. The results from this large-scale study underscore the deleterious effects of metritis on the fertility variables CFI and NR56.

Variation of polyphenols and betaines in aerial parts of young, field-grown Amaranthus genotypes

Amaranthus hybridus and Amaranthus mantegazzianus are commonly cultivated and the entire young fresh plants consumed as vegetables in regions of Africa and Asia. A. hybridus and A. mantegazzianus were cultivated at four sites in three climate regions of the world: Santa Rosa, Argentina; Lleida, Spain; and Prague and Olomouc, both in the Czech Republic. The contents of flavonoids (isoquercitrin, rutin, nicotiflorin), hydroxybenzoic acids (protocatechuic acid, 4-hydroxybenzoic acid, vanillic acid), hydroxycinnamic acids (caffeic acid, p-coumaric acid, ferulic acid), hydroxycinnamyl amides (N-trans-feruloyltyramine, N-trans-feruloyl-4-O-methyldopamine), and betaines (glycinebetaine, trigonelline) were determined. The variation in phytochemical content due to species and cultivation site was analyzed utilizing the multivariate statistical methods of principal component analysis (PCA) and graphical model (GM). The Argentinean samples differed from the three other locations due to higher contents of most compounds. The samples from Spain and the Czech Republic differed from each other in the content of the negatively correlated metabolites trigonelline and the flavonoids. The two amaranth species were separated primarily by a higher content of trigonelline and the two hydroxycinnamyl amides in A. mantegazzianus. The GM showed that the quantities of the different analytes within each compound group were intercorrelated except in the case of the betaines. The betaines carried no information on each other that was not given through correlations with other compounds. The hydroxycinnamic acids were a key group of compounds in this analysis as they separated the other groups from each other (i.e., carried information on all of the other groups). This study showed the contents of polyphenols and betaines in the aerial parts of vegetable amaranth to be very dependent on growth conditions, but also revealed that some of the compounds (trigonelline and the two hydroxycinnamyl amides) may be useful as features of a taxonomic classification.

Relationship among seminal quality measures and field fertility of young dairy bulls using low-dose inseminations

Optimal use of genetically superior bulls through artificial insemination (AI) is highly dependent on precise assessment of seminal quality which allows for reasonable estimations of field fertility with normal or low-dose inseminations. In the present study, seminal measures such as sperm motility and morphology, sperm viability, sperm DNA fragmentation, and the ability of the sperm to display an acrosome reaction were tested. The relationships between field fertility and the seminal measures were investigated using 3 ejaculates from each of 195 bulls (156 Holstein and 39 Jersey) participating in a progeny test program. A range of AI doses, varying from 2×10(6) to 15×10(6) sperm/straw, was obtained by a controlled dilution process applied to each ejaculate. The different AI doses were distributed at random among 75,610 experimental first inseminations in 4,721 herds and 208 AI technicians. Most of the seminal measures appeared to contain a predictive value for the nonreturn to estrus at 56 d post-AI (NRR56) regardless of the number of sperm per AI dose and can be regarded as noncompensable sperm traits. But, due to correlations between the individual measures, the best model for describing (and predicting) NRR56 was based on sperm concentration and viability in the neat (raw) semen, and post-thaw sperm viability. The statistical models for describing NRR56 included the following explanatory variables: strength of the estrus, number of sperm per AI dose, breed, parity, and random components representing herds and AI technicians. The present results show that the most precise estimation of a bull's NRR56 can be achieved through flow cytometric detection of sperm concentration and viability in neat semen as well as flow cytometric detection of post-thaw sperm viability.

Body metal concentrations and glycogen reserves in earthworms (Dendrobaena octaedra) from contaminated and uncontaminated forest soil

Stress originating from toxicants such as heavy metals can induce compensatory changes in the energy metabolism of organisms due to increased energy expenses associated with detoxification and excretion processes. These energy expenses may be reflected in the available energy reserves such as glycogen. In a field study the earthworm, Dendrobaena octaedra, was collected from polluted areas, and from unpolluted reference areas. If present in the environment, cadmium, lead and copper accumulated to high concentrations in D. octaedra. In contrast, other toxic metals such as aluminium, nickel and zinc appeared to be regulated and kept at low internal concentrations compared to soil concentrations. Lead, cadmium and copper accumulation did not correlate with glycogen reserves of individual worms. In contrast, aluminium, nickel and zinc were negatively correlated with glycogen reserves. These results suggest that coping with different metals in earthworms is associated with differential energy demands depending on the associated detoxification strategy.

A sequential threshold cure model for genetic analysis of time-to-event data

In analysis of time-to-event data, classical survival models ignore the presence of potential nonsusceptible (cured) individuals, which, if present, will invalidate the inference procedures. Existence of nonsusceptible individuals is particularly relevant under challenge testing with specific pathogens, which is a common procedure in aquaculture breeding schemes. A cure model is a survival model accounting for a fraction of nonsusceptible individuals in the population. This study proposes a mixed cure model for time-to-event data, measured as sequential binary records. In a simulation study survival data were generated through 2 underlying traits: susceptibility and endurance (risk of dying per time-unit), associated with 2 sets of underlying liabilities. Despite considerable phenotypic confounding, the proposed model was largely able to distinguish the 2 traits. Furthermore, if selection is for improved susceptibility rather than endurance, the error of applying a classical survival model was nonnegligible. The difference was most pronounced for scenarios with substantial underlying genetic variation in endurance and when the 2 underlying traits were lowly genetically correlated. In the presence of nonsusceptible individuals, the method provides a novel and more accurate tool for utilization of time-to-event data, and has also been proven successful when applied to zero-inflated longitudinal binary data.

Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests

Background

Chow and Liu showed that the maximum likelihood tree for multivariate discrete distributions may be found using a maximum weight spanning tree algorithm, for example Kruskal's algorithm. The efficiency of the algorithm makes it tractable for high-dimensional problems.

Results

We extend Chow and Liu's approach in two ways: first, to find the forest optimizing a penalized likelihood criterion, for example AIC or BIC, and second, to handle data with both discrete and Gaussian variables. We apply the approach to three datasets: two from gene expression studies and the third from a genetics of gene expression study. The minimal BIC forest supplements a conventional analysis of differential expression by providing a tentative network for the differentially expressed genes. In the genetics of gene expression context the method identifies a network approximating the joint distribution of the DNA markers and the gene expression levels.

Conclusions

The approach is generally useful as a preliminary step towards understanding the overall dependence structure of high-dimensional discrete and/or continuous data. Trees and forests are unrealistically simple models for biological systems, but can provide useful insights. Uses include the following: identification of distinct connected components, which can be analysed separately (dimension reduction); identification of neighbourhoods for more detailed analyses; as initial models for search algorithms with a larger search space, for example decomposable models or Bayesian networks; and identification of interesting features, such as hub nodes.

MHC haplotype and susceptibility to experimental infections (Salmonella Enteritidis, Pasteurella multocida or Ascaridia galli) in a commercial and an indigenous chicken breed

In three independent experimental infection studies, the susceptibility and course of infection of three pathogens considered of importance in most poultry production systems, Ascaridia galli, Salmonella Enteritidis and Pasteurella multocida were compared in two chicken breeds, the indigenous Vietnamese Ri and the commercial Luong Phuong. Furthermore, the association of the Major Histocompatibility Complex (MHC) with disease-related parameters was evaluated, using alleles of the LEI0258 microsatellite as markers for MHC haplotypes. The Ri chickens were found to be more resistant to A. galli and S. Enteritidis than commercial Luong Phuong chickens. In contrast, the Ri chickens were more susceptible to P. multocida, although production parameters were more affected in the Luong Phuong chickens. Furthermore, it was shown that the individual variations observed in response to the infections were influenced by the MHC. Using marker alleles of the microsatellite LEI0258, which is located within the MHC region, several MHC haplotypes were identified as being associated with infection intensity of A. galli. An association of the MHC with the specific antibody response to S. Enteritidis was also found where four MHC haplotypes were shown to be associated with high specific antibody response. Finally, one MHC haplotype was identified as being associated with pathological lesions and mortality in the P. multocida experiment. Although not statistically significant, our analysis suggested that this haplotype might be associated with resistance. These results demonstrate the presence of local genetic resources in Vietnamese chickens, which could be utilized in breeding programmes aiming at improving disease resistance.

Probability of pregnancy as affected by oestrus number and days to first oestrus in dairy cows of three breeds and parities

An improved understanding of the animal factors that affect measures such as conception rate would contribute to solving the problem of impaired reproductive performance in modern dairy cows. A question of particular interest relates to the observed improvement in conception rates from first to second and third oestrus cycle: is the increase in conception rate related to cycle number per se or to increasing days from calving? A 5-year study using three breeds (Holstein, Jersey and Danish Red) allowed this issue to be examined. In 560 lactations, from calving until confirmed pregnancy or until 290 days after calving all cows were observed daily for signs of oestrus. Inseminations were carried out to all clear cases of oestrus after 35 days from calving until the cow was judged to be pregnant or until 290 days post-calving. Days from calving to the first oestrus was modeled using a frailty model. Danish Red cows had a significantly greater rate of occurrence of first oestrus over time. Generalized linear mixed models defined using a binomial distribution and logit link function were used to estimate probability of pregnancy as affected by: breed, parity, oestrus number and days from calving to first oestrus. In order to account for the paradox that the incidence of cows with inherently low fertility increases with oestrus number, different random components for cow were included. There was a significant increase in probability of pregnancy from first to second oestrus but no significant change in probability of pregnancy thereafter. There was a significant increase in probability of pregnancy with increasing days to first oestrus. This indicates that both oestrus number and days from calving play a role in determining the fertility of dairy cows. Correcting for inherent differences in fertility was shown to be important.

Crowding as a risk factor of meningococcal disease in Danish preschool children: A nationwide population-based case-control study

Meningococcal disease (MD) remains an important health problem. Crowding has been suggested to be a risk factor for MD in children, but the evidence is relatively sparse. We performed a nationwide nested case-control study comprising 1222 children with MD and 24,549 population controls. We identified MD cases younger than 6 y in the Danish National Hospital Discharge Registry from 1980 to 1999, and obtained information on household density as a measure of crowding, per capita income and other potential confounders through The Danish Civil Registration System and social registries. The risk of MD associated with household density was estimated by conditional logistic regression for children less than 1 y of age (infants) and children aged 1 to 5 y, respectively. The risk of MD increased with increasing household density. In both age groups, the crude OR was 1.8 (95% confidence interval [CI]: 1.4-2.3) at a density of less than 20 m2 per person compared with the reference of more than 50 m2 per person. The adjusted OR for MD was 1.5 (95% CI: 1.1-1.9) for infants, and 1.5 (95% CI: 1.1-2.0) for children older than 1 y. Household density appears to be a risk factor of MD in preschool children.

Cyclooxygenase-2, multidrug resistance 1, and breast cancer resistance protein gene polymorphisms and inflammatory bowel disease in the Danish population

OBJECTIVE

Crohn's disease (CD) and ulcerative colitis (UC) are characterized by an impaired mucosal defence to normal constituents of the intestinal flora and a dysregulated inflammatory response. The purpose of the study was to investigate whether single nucleotide polymorphisms (SNPs) in genes involved in these processes were associated with CD and UC.

MATERIAL AND METHODS

Allele frequencies of the cyclooxygenase 2 (COX-2/PTGS2/PGHS2) G-765C and breast cancer resistance protein (BCRP/ABCG2) C421A as well as allele and haplotype frequencies of multidrug resistance 1 (MDR1, ABCB1) SNPs G2677T/A, C3435T and G-rs3789243-A (intron 3) were assessed in a Danish case-control study comprising 373 CD and 541 UC patients and 796 healthy controls.

RESULTS

Carriers of the homozygous COX-2 and MDR1 intron 3 variant had a relatively high risk of CD, odds ratio (95% CI) (OR (95% CI))=2.86 ((1.34-5.88) p=0.006) and 1.39 ((0.99-1.92) p=0.054), respectively, and for UC of 2.63 ((1.33-5.26) p=0.005) and 1.28 ((0.96-1.51) p=0.093), respectively, assuming complete dominance. No association was found for BCRP or other MDR1 SNPs, or for selected MDR1 haplotypes. No effect-modification of smoking habit at the time of diagnosis was found.

CONCLUSIONS

An effect of the COX-2 polymorphism on both CD and UC was shown which is compatible with the presence of a recessive allele in linkage equilibrium with the SNP marker in the COX-2 gene. The polymorphism located in intron 3 of the MDR1 gene showed a weak association with CD, and a marginally suggestive association with UC.

Genetic analysis of days from calving to first insemination and days open in Danish Holsteins using different models and censoring scenarios

The objectives of this study were to estimate genetic parameters and evaluate models for genetic evaluation of days from calving to first insemination (ICF) and days open (DO). Data including 509,512 first-parity records of Danish Holstein cows were analyzed using 5 alternative sire models that dealt with censored records in different ways: 1) a conventional linear model (LM) in which a penalty of 21 d was added to censored records; 2) a bivariate threshold-linear model (TLM), which included a threshold model for censoring status (0, 1) of the observations, and a linear model for ICF or DO without any penalty on censored records; 3) a right-censored linear model (CLM); 4) a Weibull proportional hazard model (SMW); and 5) a Cox proportional hazard model (SMC) constructed with piecewise constant baseline hazard function. The variance components for ICF and DO estimated from LM and TLM were similar, whereas CLM gave higher estimates of both additive genetic and residual components. Estimates of heritability from models LM, TLM, and CLM were very similar (0.102 to 0.108 for ICF, and 0.066 to 0.069 for DO). Heritabilities estimated using model SMW were 0.213 for ICF and 0.121 for DO in logarithmic scale. Using SMC, the estimates of heritability, defined as the log-hazard proportional factor for ICF and DO, were 0.013 and 0.009, respectively. Correlations between predicted transmitting ability from different models for sires with records from at least 20 daughters were far from unity, indicating that different models could lead to different rankings. The largest reranking was found between SMW and SMC, whereas negligible reranking was found among LM, TLM, and CLM. The 5 models were evaluated by comparing correlations between predicted transmitting ability from different data sets (the whole data set and 2 subsets, each containing half of the whole data set), for sires with records from at least 20 daughters, and chi(2) statistics based on predicted and observed daughter frequencies using a cross validation. The model comparisons showed that SMC had the best performance in predicting breeding values of the 2 traits. No significant difference was found among models LM, TLM, and CLM. The SMW model had a relatively poor performance, probably because the data are far from a Weibull distribution. The results from the present study suggest that SMC could be a good alternative for predicting breeding values of ICF and DO in the Danish Holstein population.

A major QTL and an SSR marker associated with glycoalkaloid content in potato tubers from Solanum tuberosum x S. sparsipilum located on chromosome I

New potato (Solanum tuberosum) varieties are required to contain low levels of the toxic glycoalkaloids and a potential approach to obtain this is through marker-assisted selection (MAS). Before applying MAS it is necessary to map quantitative trait loci (QTLs) for glycoalkaloid content in potato tubers and identify markers that link tightly to this trait. In this study, tubers of a dihaploid BC(1) population, originating from a cross between 90-HAF-01 (S. tuberosum(1)) and 90-HAG-15 (S. tuberosum(2) x S. sparsipilum), were evaluated for content of alpha-solanine and alpha-chaconine (total glycoalkaloid, TGA) after field trials. In addition, tubers were assayed for TGA content after exposure to light. A detailed analysis of segregation patterns indicated that a major QTL is responsible for the TGA content in tubers of this potato population. One highly significant QTL was mapped to chromosome I of the HAG and the HAF parent. Quantitative trait loci for glycoalkaloid production in foliage of different Solanum species have previously been mapped to this chromosome. In the present research, QTLs for alpha-solanine and alpha-chaconine content were mapped to the same location as for TGA content. Similar results were observed for tubers exposed to light. The simple sequence repeat marker STM5136 was closely linked to the identified QTL.

Gastrointestinal helminths in indigenous and exotic chickens in Vietnam: association of the intensity of infection with the Major Histocompatibility Complex

This study compared the prevalence and intensity of infections of helminths in 2 chicken breeds in Vietnam, the indigenous Ri and the exotic Luong Phuong. Also, possible correlations with the Major Histocompatibility Complex (MHC) were tested. The most prevalent helminths were Ascaridia galli, Heterakis beramporia, Tetrameres mothedai, Capillaria obsignata, Raillietina echinobothrida and Raillietina tetragona. Differences in prevalence and intensity of infection were found between the 2 breeds. Comparing the 2 groups of adult birds, Ri chickens were observed to have higher prevalence and infection intensities of several species of helminths, as well as a higher mean number of helminth species. In contrast, A. galli and C. obsignata were shown to be more prevalent in Luong Phuong chickens. Furthermore, an age-dependent difference was indicated in the group of Ri chickens in which the prevalence and the intensity of infection was higher for the adult than the young chickens for most helminths. The most notable exception was the significantly lower prevalence and intensities of A. galli in the group of adult chickens. In contrast, the prevalence and intensity were very similar in both age groups of Luong Phuong chickens. Using a genetic marker located in the MHC, a statistically significant correlation between several MHC haplotypes and the infection intensity of different helminth species was inferred. This is the first report of an association of MHC haplotype with the intensity of parasite infections in chickens.

Role of suckling in regulating cell turnover and onset and maintenance of lactation in individual mammary glands of sows

This study addressed the mechanisms by which suckling regulates cell turnover and onset and maintenance of lactation of individual mammary glands of sows. The effects of no, transient (through 12 to 14 h postpartum), or regular suckling of individual glands during d 0 to 6 of lactation were studied in 5 sows. Nonsuckling was obtained by taping the glands to prevent access to the nipples. Visual scores confirmed that regularly suckled glands maintained lactation, whereas transiently suckled and nonsuckled glands regressed during lactation. Mammary gland biopsies were collected on d -5, 1, 2, 4, and 6 relative to farrowing in order to evaluate the cell turnover and to quantify the transcription of genes potentially involved in mammary cell turnover and function. The proportion of proliferating cells was greatest prepartum (13.1%). After farrowing, the proportion of proliferating cells declined in all glands, then remained low (5.6%) in nonsuckled glands and increased (P < 0.01) from an average of 7.5% on d 1 to 9.9% on d 6 in regularly suckled and transiently suckled glands. Transcriptional data were analyzed using a gamma-distributed, generalized linear mixed model. Abundance of alpha-lactalbumin mRNA (P < 0.01) increased in regularly suckled glands within the first day of lactation and remained elevated, whereas the expression in taped glands remained at the prepartum level. Prolactin receptor mRNA abundance decreased (P < 0.001), and IGFBP-5 mRNA abundance increased (P < 0.01) in nonsuckled and transiently suckled glands after parturition compared with regularly suckled glands. Mammary mRNA abundances of IGF-I, IGF-II, type I IGF receptor, and caspase 3 were minimally or inconclusively affected by the suckling regimens. In conclusion, suckling during the first 12 to 14 h postpartum is insufficient to initiate and maintain lactation until 24 to 36 h postpartum but sufficient to induce mammary cell proliferation for at least 6 d postpartum. Furthermore, a high prolactin receptor transcription and a low IGFBP-5 transcription seem important for maintaining a functional mammary gland during lactation.

Altered Circulating Levels of Serotonin and Immunological Changes in Laying Hens Divergently Selected for Feather Pecking Behavior

The aim of this study was to investigate the changes in immunological parameters as well as changes with respect to plasma levels of serotonin and tryptophan in lines selected for and against feather pecking (FP) behavior [high FP (HP) line and low FP (LP) line] for 5 generations. The hens from the HP line had a higher plasma serotonin level than those from the LP line (0.059 vs. 0.037 micromol/L, F(2,27) = 0.031, P < 0.05). The plasma level of tryptophan was, on average, 67.30 micromol/L and did not differ between the lines (68.3 vs. 66.3 micromol/L, F(2,28) = 0.36, P < 0.05). The HP line had a higher response to infectious bursal disease virus vaccination after 1 wk post-vaccination compared with the control and LP lines. The number of white blood cells (P < 0.0001) and the expression of MHC class I molecules on CD4 (P < 0.02), CD8beta (P < 0.006) and on B cells (P < 0.03) were highest in the LP line compared with the control and HP lines. Selection for or against FP, therefore, changes the number of white blood cells and the expression of MHC class I molecules on T and B cells, which may influence the health status of the birds.

Expression of genes involved in regulation of cell turnover during milk stasis and lactation rescue in sow mammary glands1

We studied the transcription of selected genes involved in the regulation of cell turnover during milk stasis and lactation rescue in individual mammary glands of sows and evaluated the timeframe for lactation rescue and the subsequent productivity of rescued glands. Suckling was prevented in two glands from each of five sows by taping them the day after farrowing for 1 or 3 d (Closed 24 h and Closed 72 h glands, respectively). After removing the tape, Closed 24 h glands were suckled until weaning. Closed 72 h glands were refused by the piglets and therefore remained unsuckled. Mammary gland biopsies were collected to quantify the transcription of genes involved in cell turnover and the percentage of proliferating and apoptotic cells. Transcriptional data were analyzed with a gamma-distributed generalized linear mixed model. Mammary transcription of alpha-lactalbumin was high in suckled glands the day after farrowing, indicating onset of lactation, but was downregulated after 1 d of milk stasis. The prolactin receptor mRNA was downregulated and IGFBP-5 mRNA was upregulated within 1 d of milk stasis. The downregulation of alpha-lactalbumin and prolactin receptor and upregulation of IGFBP-5 mRNA noted after 1 d of milk stasis was maintained in Closed 72 h glands (those glands regressed) but reversed on d 4 and 6 of lactation in Closed 24 h glands. Mammary IGF-I mRNA was not regulated in response to milk stasis or lactation rescue. The percentage of proliferating cells in mammary glands was high prepartum (13.1%) and intermediate (7.8%) the day after farrowing. By d 6 of lactation, the percentage of proliferating cells was increased to 10.1% (P < 0.01) in glands suckled regularly but decreased to 5.9% (P < 0.05) in regressing glands (Closed 72 h glands). Glands rescued after 1 d of milk stasis had lower productivity throughout lactation than glands suckled regularly, as indicated by the BW of piglets suckling these glands (242 vs. 315 g/d, respectively; P < 0.05). In conclusion, regularly suckled glands had a greater cell proliferation, greater transcriptions of alpha-lactalbumin and prolactin receptor genes, and less IGFBP-5 transcription compared with rescued (Closed 24 h) and regressing (Closed 72 h) glands. Glands that were not suckled for 1 d could be rescued, although their subsequent productivity was lower, whereas glands not suckled for 3 d could not be rescued.

Molecular Characterization of Major Histocompatibility Complex Class I (B-F) mRNA Variants from Chickens Differing in Resistance to Marek's Disease

In this study, the relative distributions of two alternatively polyadenylated chicken major histocompatibility complex (MHC) mRNA isoforms of approximately 1.5 and 1.9 kb were analysed in spleen cells from chickens homozygous for the MHC haplotypes B21 and B19v1 as well as in heterozygous B19v1/B21 birds. Both isoforms are likely to encode classical MHC class I (B-F) alpha chains. The B19v1 and B21 MHC haplotypes confer different levels of protection against Marek's disease (MD), which is caused by infection with MD virus (MDV). In spleen cells, MD-resistant B21 birds were shown to have the highest percentage of the 1.5 kb variant relative to the total MHC class I expression, MD-susceptible B19v1 birds the lowest and B19v1/B21 birds an intermediate percentage. Infection of 4-week-old chickens with the GA strain of MDV was shown to cause a significant increase in the relative amount of 1.5 kb transcripts in B21 birds 32 days postinfection (dpi). Alternatively polyadenylated mRNA isoforms may encode identical proteins, but differences in the 3' untranslated region (UTR) can influence polyadenylation, mRNA stability, intracellular localization and translation efficiency. It was shown that the increased 1.5 kb percentage in B21 birds 32 days postinfection may be a result of a change in the choice of poly(A) site rather than a locus-specific upregulated transcription of the BF1 gene that preferentially expresses the 1.5 kb variant. Furthermore, the 3' end of the 1.5 kb mRNA variants deriving from B19v1 and B21 chickens was characterized by Rapid Amplification of cDNA Ends (RACE) and sequencing. No potentially functional elements were identified in the 3' UTR of the RACE products corresponding to this short isoform. However, variation in polyadenylation site was observed between the BF1 and BF2 mRNA transcripts and alternative splicing-out of the sequence (exon 7) encoding the second segment of the cytoplasmic part of the mature BF2*19 molecules. This alternative exon 7 splice variant was also detected in other MD-susceptible haplotypes, but not in the MD-resistant B21 and B21-like haplotypes, suggesting a potential role of exon 7 in MHC-related MD resistance.