Handling missingness when modeling the force of infection from clustered seroprevalence data

Modeling infectious diseases data is a relatively young research area in which clustering and stratification are key features. It is not unlikely for these data to have missing values. If values are missing completely at random, the analysis on the complete cases is valid. However, in practice this assumption is usually not fulfilled. This article shows the effect of ignoring missing data in modeling the force of infection of the bovine herpesvirus-1 in Belgian cattle and proposes the use of weighted generalized estimating equations with constrained fractional polynomials as a flexible modeling tool.     

Effects of Different Soil Treatments on the Development of <Emphasis Type="Italic">Spongospora subterranea</Emphasis> f. sp. <Emphasis Type="Italic">subterranea</Emphasis> in Potato Roots and Tubers in the Greenhouse

Powdery scab caused by Spongospora subterranea f. sp. subterranea (Sss) causes extensive losses in potato production systems globally. Two pot experiments were established in the greenhouse in summer 2013 and winter 2014 to evaluate the effectiveness of different soil chemicals, fumigant, amendments and biological control agents (BCAs) against Sss in the rhizospheric soil, potato roots and tubers. The study used visual assessment methods to assess the effect of treatments on root galling and zoosporangia production, and qPCR to measure Sss concentration in the soil and in the potato roots and tubers. All six soil treatments, namely metam sodium, fluazinam, ZincMax, calcium cyanamide, Biocult and a combination of Bacillus subtilis and Trichoderma asperellum recorded significantly (P < 0.05) lower numbers of zoosporangia in the roots compared to the untreated control. The same effect was observed on the concentration of Sss DNA in the roots at tuber initiation. A more diverse picture was obtained when root gall scores at tuber initiation and Sss DNA in the rhizospheric soil at tuber initiation and harvesting were compared. Significant differences (P < 0.05) were also noted in disease severity, disease incidence, and tuber yield between metam sodium, fluazinam, ZincMax, calcium cyanamide and the untreated control. Calcium cyanamide gave the highest tuber yield. The study demonstrated the potential of soil treatments such as metam sodium, fluazinam, ZincMax and calcium cyanamide in managing Sss in potatoes by reducing the pathogen both in the rhizospheric soil and the roots of the potato plant.     

Determinants of the biodiversity patterns of ammonia-oxidizing archaea community in two contrasting forest stands

Purpose

The variation in soil microbial community patterns is primarily influenced by ecological processes associated with spatial distance and environmental heterogeneities. However, the relative importance of these processes in determining the patterns of soil microbial biodiversity in different successional forests remains unclear.

Materials and methods

Based on the species data from denaturing gradient gel electrophoresis (DGGE) analysis, we described the composition and beta diversity of ammonia-oxidizing archaea (AOA) community, an important functional microbial group in regulating nitrogen cycle, in a middle-succeed stand (60 years of secondary succession) and an undisturbed native stand in a subtropical forest in southern China. The composition pattern was examined using a multi-response permutation procedure (MRPP), and the beta diversity was described using the Sørensen index. The relative influence of edaphic, vegetational, spatial, and topographical factors on AOA composition and beta diversity was assessed by variation partitioning and multiple regression on distance matrices (MRM), respectively.

Results and discussion

We did not find any stand-specific patterns in AOA community composition in the two stands; however, the influential variables were different between the two stands; 7.3 and 4.5 % of the total variation in AOA community composition could be explained by edaphic (i.e., available potassium and total phosphorus) and spatial variables, respectively, in the middle-succeed stand, while 3.7 and 2.8 % of the variation were explained by spatial variable and available phosphorus, respectively, in the native stand. Soil total phosphorus influenced the beta diversity of AOA community most in the middle-succeed stand, while genetic distance of tree species was found to be the most important factor in driving the beta diversity pattern in the native stand.

Conclusions

Soil nutrients influenced the beta diversity of AOA community in the middle-succeed stand more than that in the native stand, while vegetation is more important in the native stand. The substantial unexplained variations were possibly due to the effects of other unmeasured variables. Nevertheless, dispersal process is more important in controlling AOA community composition in the native stand, while processes associated with environmental heterogeneities are more important in the middle-succeed stand in this subtropical forest.

     

Evaluation of genetic and non-genetic factors on foot and mouth disease (FMD) virus vaccine-elicited immune response in Hardhenu (<Emphasis Type="Italic">Bos taurus</Emphasis> x <Emphasis Type="Italic">Bos indicus</Emphasis>) cattle

Foot and mouth disease (FMD) is the most contagious disease of mammals and a major threat to animal husbandry sector. In India, vaccination with the inactivated trivalent (O, A and Asia1) vaccine is one proven way for protecting the livestock from FMD. However, many outbreaks have been reported in different parts of the country. Therefore, present study was aimed at elucidating the effects of genetic and non-genetic factors on FMD viral vaccine-elicited immune response in Hardhenu cattle. The effect of season of vaccination was not consistent. The effect of status of animal was significant for all the pre and post AB titres except for pre AB titre of serotype O and post AB titre of Asia1.The estimates of heritability for response to vaccination were low to high ranging from 0.11 to 0.45. The highest heritability estimate was obtained for serotype O and the lowest for Asia1. The heritability estimates for pre and post AB titres ranged from 0.15 to 0.33. All the pre and post AB titres and responses to vaccination had genetic correlations ranged from high negative to high positive among them. Results of this study highlight the variation in vaccine response which needs to be further exploited on large-scale animal data for better immunization and protection against highly contagious viral vesicular disease of cloven-hoofed animals.     

Avian predation on wild and cultured sea urchin <Emphasis Type="Italic">Strongylocentrotus intermedius</Emphasis> in a rocky shore habitat

ABSTRACT:   The present study reports the annual variation in consumption of the sea urchin Strongylocentrotus intermedius by avian predators on a rocky shore where the culture of sea urchins has been conducted. Carrion crow and a few gull species were the most abundant avian predators and consumed a large number of sea urchins. Crows consumed mostly natural sea urchins, approximately 36 kg ww/ha per year on the intertidal rocky bench, but the gull species consumed mostly cultured sea urchins, approximately 100 kg ww/ha per year in the culture area. The seasonal variation in the amount of sea urchins consumed by crows was higher than that by the gull species, presumably because of the difference in foraging behavior in association with the seasonal tidal cycle. The natural sea urchins consumed are an allochthonous input from the subtidal to the intertidal habitat, and thus, crow predation may not affect the natural and the cultured populations of the sea urchin. The gull species consumed much of the cultured sea urchin, and thus, may be regarded as an effective predator causing damage to sea urchin culture. The results suggest that further studies are needed to determine why the gull species selectively feed on cultured sea urchins.     

A 192bp allele at the <Emphasis Type="Italic">Xgwm261</Emphasis> locus is not always associated with the <Emphasis Type="Italic">Rht8</Emphasis> dwarfing gene in wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

The height-reducing gene Rht8 was introduced into Italian wheats by breeder Nazareno Strampelli from the Japanese landrace Akakomugi, and has been widely used in wheats adapted to southern and eastern European conditions. Following identification of a close linkage to Rht8, microsatellite marker Gwm261 has been used extensively to screen large numbers of diverse international germplasm. A 192bp allele at this locus has been taken as “diagnostic” for Rht8 and used to infer the international distribution of Rht8. In this paper, we report several instances of cultivars and mapping populations that vary for the presence of the 192bp allele at the Xgwm261 locus (Xgwm261 ₁₉₂ ), but with no associated reduction in height, suggesting a lack of association with Rht8. For instance, in the population derived from a cross between Sunco (Rht-B1b, Xgwm261 ₁₆₅ ) and Tasman (Rht-D1b, Xgwm261 ₁₉₂ ), there were significant height differences associated with the segregation of Rht-B1b and Rht-D1b, but no height differences between Xgwm261 genotypes. Similar results were obtained in a population derived from the cross between Molineux (Rht-B1b, Xgwm261 ₁₉₂ ) and Trident (Rht-D1b Xgwm261 ₂₀₈ ). In contrast, the cross between Trident and Chuanmai 18 (Xgwm261 ₁₉₂ ) gave significant height effects at both the Rht-D1 and Xgwm261 loci, with no epistatic interaction between loci. Chuanmai 18 is closely related to the Strampelli wheat Mara (ancestrally derived from Akakomugi) and is therefore likely to carry Rht8. The old Japanese cultivar Norin 10, used by Norman Borlaug to introduce Rht-B1b and Rht-D1b into Mexican wheats, also has a 192bp allele at the Xgwm261 locus, and the sequence of the amplified product is identical to that of Akakomugi. We suggest that the widespread use of Norin 10-derived germplasm during and after the Green Revolution introduced a second haplotype into international germplasm, in which Xgwm261 ₁₉₂ has no association with Rht8. Therefore, the presence of Xgwm261 ₁₉₂ is only indicative of Rht8 in wheat cultivars that have inherited this allele from Akakomugi or a Strampelli wheat ancestor.     

A review on breeding and genetic strategies in Iranian buffaloes (<Emphasis Type="Italic">Bubalus bubalis</Emphasis>)

The aim of current study was to review breeding progress and update information on genetic strategies in Iranian buffaloes. Iranian buffalo is one of the vital domestic animals throughout north, north-west, south and south-west of Iran with measurable characteristics both in milk and meat production. The species plays an important role in rural economy of the country due to its unique characteristics such as resistance to diseases and parasites, having long productive lifespan and showing higher capability of consuming low-quality forage. In Iran, total production of milk and meat devoted to buffaloes are 293,000 and 24,700 tons, respectively. Selection activities and milk yield recording are carrying out by the central government through the Animal Breeding Centre of Iran. The main breeding activities of Iranian buffaloes included the estimation of genetic parameters and genetic trends for performance traits using different models and methods, estimation of economic values and selection criteria and analysis of population structure. Incorporating different aspects of dairy buffalo management together with improved housing, nutrition, breeding and milking, is known to produce significant improvements in buffalo production. Therefore, identifying genetic potential of Iranian buffaloes, selection of superior breeds, improving nutritional management and reproduction and developing the education and increasing the skills of practical breeders can be useful in order to enhance the performance and profitability of Iranian buffaloes.     

Contrasting phenology and female cone characteristics of the two Macaronesian island endemic cedars (<Emphasis Type="Italic">Juniperus cedrus</Emphasis> and <Emphasis Type="Italic">J. brevifolia</Emphasis>)

Phenology and female cone characteristics of the two endemic cedars (Juniperus cedrus and J. brevifolia) from the Macaronesian islands were studied. Despite their closely taxonomic affinity and their evolution under insular conditions, different trends were recorded. Mature J. cedrus female cones were present throughout the year, while those from J. brevifolia were only present in summer and autumn. J. cedrus female cone size was significantly larger than that of J. brevifolia, a trend consistent with the presence of larger vertebrates (lizards and birds) in the Canary Islands. However, water content was four times higher in J. brevifolia female cones, which can be related with the higher rainfall existing in the Azores. J. cedrus has two or three seeds per cone, whereas J. brevifolia frequently had three. Seeds from J. cedrus were clearly larger and heavier, coinciding with the female cone size trend. However, tetrazolium tests revealed higher viability values in J. brevifolia. The relatively low percentage of filled seeds in J. cedrus could be a consequence of the climatic stress and limits to pollination due to fragmented populations as described for other Juniperus species. In summary, our results reveal that some environmental factors such as the harsh conditions, high population fragmentation and the dependence on large dispersers have compromised the fitness of J. cedrus in the Canary Islands.