Segmentation of 3D images of plant tissues at multiple scales using the level set method

Background

Developmental biology has made great strides in recent years towards the quantification of cellular properties during development. This requires tissues to be imaged and segmented to generate computerised versions that can be easily analysed. In this context, one of the principal technical challenges remains the faithful detection of cellular contours, principally due to variations in image intensity throughout the tissue. Watershed segmentation methods are especially vulnerable to these variations, generating multiple errors due notably to the incorrect detection of the outer surface of the tissue.

Results

We use the level set method (LSM) to improve the accuracy of the watershed segmentation in different ways. First, we detect the outer surface of the tissue, reducing the impact of low and variable contrast at the surface during imaging. Second, we demonstrate a new edge function for a level set, based on second order derivatives of the image, to segment individual cells. Finally, we also show that the LSM can be used to segment nuclei within the tissue.

Conclusion

The watershed segmentation of the outer cell layer is demonstrably improved when coupled with the LSM-based surface detection step. The tool can also be used to improve watershed segmentation at cell-scale, as well as to segment nuclei within a tissue. The improved segmentation increases the quality of analysis, and the surface detected by our algorithm may be used to calculate local curvature or adapted for other uses, such as mathematical simulations.

     

Outbreaks of proliferative haemorrhagic enteropathy on two pig farms

SUMMARY Clinical signs of proliferative haemorrhagic enteropathy (PHE) including anaemia, dysentery and sudden death were observed in finisher pigs and young breeding stock on 2 farms. On farm A, PHE occurred 12 months after repopulation of the farm. Other outbreaks of PHE occurred after the withdrawal of therapeutic concentrations of in-feed antibacterial agents (farm A), or after monensin sodium (100 g/t) replaced olaquindox (100 g/t) in feed (farm B). The outbreaks, the possible sources of contamination and the role of antibacterial feed additives in the treatment and control of PHE are described.     

New pig disease in Hungary: postweaning multisystemic wasting syndrome caused by circovirus (short communication)

Postweaning multisystemic wasting syndrome (PMWS), a new disease in Hungary, was recognized in a swine herd located in Southeast Hungary, during the early winter of 1999. The first clinical signs of paleness, anaemia, and leanness appeared immediately after weaning, at the age of 40-50 days. Pustules were frequently observed on the skin of the trunk, and signs of necrotic dermatitis were also visible. A syndrome of poor growth and wasting was characteristic of the affected pigs. A porcine circovirus (PCV), the suspected causative agent, was detected by polymerase chain reaction (PCR). Sequencing data and restriction endonuclease (RE) analysis of the PCR products suggested that the virus belonged to the PCV-II group where all the causative agents of PMWS are also grouped.     

Sustainable management of the western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), in infested areas: experiences in Italy, Hungary and the USA

The western corn rootworm, Diabrotica virgifera virgifera LeConte, is the most important pest of maize in the Midwestern USA, and since its detection in 1992 in Europe, also in several countries of Central and Eastern Europe. Methods for managing this pest vary from region to region, depending upon: the different cultural practices in maize production, climatic conditions, soil types, pest behaviour, infestation level and socio-economic conditions. Factors including date of planting, amount of rotated or continuous maize, irrigation, date of rootworm hatching and differences in behaviour of the pest, necessitate developing different management strategies in different areas of the infested countries. Pest monitoring, damage evaluation, threshold development, use of insecticides, risk estimation and crop rotation are some of the starting points in the development of management strategies. Approaches and experiences in D. v. virgifera control and management in Italy, Hungary and the USA, based on the understanding of local agro-ecosystems and socio-economic conditions, are reported.     

Cytotoxic pentacyclic triterpenes from Combretum nigricans

A new pentacyclic triterpene, 11alpha-acetoxy-20,24-epoxy-25-hydroxy-dammar-3-one (1), has been isolated from the African tree Combretum nigricans, together with the known corresponding diol, 20,24-epoxy-11alpha, 25-dihydroxy-dammar-3-one (2). They are responsible, at least in part, for the cytotoxic activity of the methanolic extract of the plant.     

First results on synchrony between seasonal pattern of pheromone trap captures of cotton bollworm, <Emphasis Type="Italic">Helicoverpa armigera</Emphasis> and appearance of freshly emerged larvae on developing cobs of corn hybrids

Synchrony between development of five corn hybrid varieties of various seasonal growing rates (FAO numbers), seasonal flight pattern of male cotton bollworm, Helicoverpa armigera Hb. (Lepidoptera: Noctuidae), as monitored by pheromone traps, and the subsequent appearance of newly hatched larvae on developing cobs were studied at Mezőhegyes, South-Hungary, in 2003 and 2004. The phenological stages of corn hybrids were evaluated using the Iowa State University Scale (R₁–R₅), the flight of male moths was monitored by large capacity, funnel type of pheromone traps and the appearance of freshly hatched larvae on developing cobs were counted by visual inspection. The synchrony between the flight peak of male moths and the peak apperance of L₁ larvae on cobs was investigated by cross-correlation. In 2003 (average daily temperatures 20.7°C, average daily relative humidity 59.9% for the period of 4–18 July) “DK 391”, “DK 443” and “Maraton” hybrid varieties already reached silking stage (R₁) by the time when pheromone traps indicated a peak, at 7 July (peak capture at 3-day intervals 755.5 males/traps). The number of L₁ larvae peaked on developing cobs of these varieties also at 7 July (7.0, 4.0 and 3.8 larvae/50 cobs, respectively). The synchrony between the flight peak of male moths and the peak appearance of L₁ larvae on cobs was proven (LAG = 0). A rather similar trend was observed in “Vilma” hybrid variety: it reached R₁ stage at 7 July, and L₁ larvae appeared only a few days later (11 July, 3.8 larvae/50 cobs) (LAG = −1). However, “Maxima” hybrid variety reached R₁ stage 1 week later (14 July) than the time of peak captures. Here L₁ larvae peaked as late as at 18 July (0.8 larvae/50 cobs), i.e., only after the cob had reached R₁ stage (LAG = −3). A reverse order of dates of R₁ stage and peak capture was observed in “Maxima” in 2004 (average daily temperatures; 22.5°C, average daily relative humidities 72.6% for the period of 15 July–6 August): it reached R₁ stage at 19 July, while peak trap captures were recorded at 6 August (peak capture at 3-day intervals 20.5 males/traps). L₁ larvae were found in the highest numbers on 2 August (1.5 larvae/50 cobs), practically in synchrony with peak caputres (LAG = 0). “Káma” reached R₁ stage in 16 July, and L₁ larvae peaked at 2 August (1.3 larvae/50 cobs) (LAG = 0). On the rest of the corn varieties larvae were found only in too numbers for performing statistical analysis. We conclude that in order to predict the appearance of L₁ larvae, the phenological stage of the corn variety and the seasonal flight pattern of moths, as measured by large capacity pheromone traps, should be considered in combination. If the corn variety already reached R₁ stage, L₁ larvae appear on cobs as early as the time of peak flight of moths. However, no young larvae appear on cobs despite of high trap captures, until the corn reaches the R₁ stage. These findings are discussed in the view of specifying optimal timing of a pesticide application.     

Comparative Expression Analysis of Gametogenesis‐Associated Genes in Foetal and Adult Bubaline (Bubalus bubalis) Ovaries and Testes

This study was conducted to identify and analyse the expression of gametogenesis‐associated genes and proteins in foetal and adult buffalo gonads of both the sexes. Relative quantification of the genes was determined by qPCR and Western blotting. Immunohistochemistry was also performed for various gametogenesis‐associated proteins in foetal and adult gonads of both the sexes. We observed significantly (p < 0.05) increased expression of primordial germ cell‐specific, meiotic as well as genes associated with oocyte maturation and development in foetal ovaries as compared to the adult ones. However, significantly (p < 0.05) increased expression of proteins associated with oocyte maturation like GDF9 and ZP4 was found in adult ovaries, indicating temporal regulation of mRNA translation during oogenesis. Meiotic genes showed significantly (p < 0.05) increased expression in adult testes as compared to foetal testes and ovaries, indicating onset of meiosis at a later stage in spermatogenesis. In general, the expression of primordial germ cell‐associated as well as meiotic genes was higher in adult testes, indicating the increased biological activity in the organ. Immunohistochemistry revealed localized expression of gametogenesis‐associated proteins in ovarian follicles and seminiferous tubules of testes, while the surrounding somatic tissues were devoid of these proteins. The study gives an understanding of the sequential and temporal events of gene expression as well as mRNA translation during male and female gametogenesis. It could also be concluded that follicles and seminiferous tubules are the functional units of the female and male gonads, respectively, and their function could be enhanced by appropriate chemical and genetic intervention of the somatic tissue immediately surrounding them. This assumes importance in the context that buffalo attains sexual maturity at an older age of 2–3 years and have smaller ovaries with lesser number of primordial follicles in comparison with cattle, which is suggested to be the main reason of their poor breeding performance.