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.

     

Nursery rearing of kalbasu, Labeo calbasu (Hamilton), at different stocking densities in outdoor concrete tanks

The growth and survival of kalbasu, Labeo calbasu, was evaluated at stocking densities of 5, 10 and 15 million spawn ha⁻¹ in nursery rearing in concrete tanks of 50 m², each for a period of 25 days. Survival of fry was density dependent and significantly higher (54.5%) at 5 million ha⁻¹ than those at 10 million ha⁻¹ (50.1%) and 15 million ha⁻¹ (46.9%). Similarly, growth and specific growth rate were inversely related to the stocking density and varied significantly among the three densities.     

Rice-wheat productivity and nutrient status in a lantana- (Lantana spp.) amended soil

Imbalanced and inadequate use of chemical fertilizers is responsible for low rice- (Oryza sativa L.) wheat (Triticum aestivum L.) productivity in many resource-poor farmers' fields. Wheat yields in post-rice soils are also constrained due to soil conditions created by puddling in rice, especially in fine to medium textured soils. Organic amendments are known to improve soil productivity under rice-wheat cropping by way of improving physical conditions and nutrient status of the soil, but their availability is restricted. There is a need to identify locally available and cost-effective organic materials, which have minimal alternate uses as fodder and fuel. We evaluated lantana (Lantana spp. L.) residues, a fast-growing weed in nearby wastelands, as a potential soil organic amendment. Yield trends, and soil and crop nutrient status in a 12-year rice-wheat experiment at Palampur, India, involving four levels (0, 10, 20, and 30 Mg ha^-1 year^-1 fresh mass) of lantana addition were investigated. Chopped lantana was incorporated into soil 10–15 days before puddling. Lantana additions at 10, 20 and 30 Mg ha^-1 increased rice yields on average by 18%, 23% and 30%, wheat yields by 11%, 14% and 20%, and total system productivity (rice + wheat) by 15%, 20% and 26% over controls, respectively, and at the same time saved NPK fertilizer. Linear regression analyses over 12 years did not show any change in yield trends of rice and wheat at P =0.05. Continuous cultivation of rice-wheat significantly increased total C, labile C, and other C indices of soils. Total N, Olsen's P, and NH₄OAc-extractable K in the lantana-amended plots were higher than in the controls. Nutrient concentrations in crop biomass, however, remained generally unaffected by lantana treatments. Results suggest that lantana residues, which improved the nutrient status of soil and system yield, have the potential for resource conservation and sustaining rice-wheat productivity.     

Effect of long-term manuring and fertilizers on carbon pools,soil structure,and sustainability under different cropping systems in wet-temperate zone of northwest Himalayas

We investigated C management index (CMI; an indicator of sustainability of a management system and is based on total and labile C) and soil aggregation in medium-textured soils (silt loam and silty clay loam) under different cropping systems as follows: maize-wheat (M-W), rice-wheat (R-W), soybean-wheat (S-W), Guinea grass, and Setaria grass. Field experiments were 6–32 years long and were located in the wet-temperate zone of northwest Himalayas. The plant nutrients were applied through chemical fertilizers (urea, superphosphate, and muriate of potash) with or without organic materials (FYM, wheat straw, and Lantana spp.). The content of total C (C_T), labile C (C_L), CMI, mean weight diameter (MWD), and aggregate porosity varied significantly under different cropping systems. The range was 1.59 (R-W)–4.29% (Setaria) for C_T, 1.23 (R-W)–3.89 mg/kg (Guinea grass) for C_L, 52.09 (R-W)–129.77 (Guinea grass) for CMI, 0.90 (R-W)–5.09 (Guinea grass) for MWD, and 41.5 (R-W)–56.8% (S-W) for aggregate porosity. Aggregate porosity was highest (56.8%) under S-W, followed by grasses (50.1–51.2%), and M/R-W (41.5–50.0%). As per these data, (a) continuous use of N alone as urea lowered soil sustainability over control (no fertilizers); (b) use of NPK at recommended rates improved soil productivity over control; (c) the NPK + organic amendments further improved soil sustainability; and (d) the sustainability under different cropping systems followed the order: perennial grasses > soybean-wheat > maize-wheat > rice-wheat.     

Uptake and bioconcentration of dieldrin,dimethoate, and permethrin by Tetrahymena pyriformis

A ciliate protozoan, Tetrahymenapyriformis was exposed to three insecticides, dieldrin, dimethoate, and permethrin for 12 hr to study the uptake and bioconcentration potential. Ciliates concentrated 922, 3547, and 1056 gg g^?1 dry wt. over an initial concentration of 1 gg mL^?1 of dieldrin, dimethoate, and permethrin, respectively. The highest bioconcentration factor for three insecticides was 2095, 3547, and 1110, respectively. It is suggested that if levels in the environment reach 1 gg mL^?1 the chief effects would be reduction of cell population, and accumulation of the toxicants by ciliates. Accumulation of insecticides by ciliates would permit the toxicants to enter aquatic food chains. Thus the compounds could exert toxic effects at higher trophic levels.     

GBP5 promotes NLRP3 inflammasome assembly and immunity in mammals

Inflammasomes are sensory complexes that alert the immune system to the presence of infection or tissue damage. These complexes assemble NLR (nucleotide binding and oligomerization, leucine-rich repeat) or ALR (absent in melanoma 2-like receptor) proteins to activate caspase-1 cleavage and interleukin (IL)-1β/IL-18 secretion. Here, we identified a non-NLR/ALR human protein that stimulates inflammasome assembly: guanylate binding protein 5 (GBP5). GBP5 promoted selective NLRP3 inflammasome responses to pathogenic bacteria and soluble but not crystalline inflammasome priming agents. Generation of Gbp5(-/-) mice revealed pronounced caspase-1 and IL-1β/IL-18 cleavage defects in vitro and impaired host defense and Nlrp3-dependent inflammatory responses in vivo. Thus, GBP5 serves as a unique rheostat for NLRP3 inflammasome activation and extends our understanding of the inflammasome complex beyond its core machinery.     

Landscaping and performance of some aesthetic plant species in hot, arid conditions of India

Establishment of ornamental and aesthetic plants in hot, arid conditions of India is difficult due to the prevailing climatic, edaphic and biotic factors. Effect of turfgrass on the growth of ornamental plants in hot arid conditions has not been studied so far anywhere in the world. A study was conducted on the campus of Arid Forest Research Institute, Jodhpur, India to assess the performance of a few ornamental plant species in combination with turfgrass and without turfgrass with respect to different soil tilling intervals. Growth of plants was better with turfgrass than without turfgrass. We suggest adopting a soil tilling interval of 30 days to achieve optimum growth of ornamental plant species in terms of height and crown diameter. Our results can help reduce labor costs and achieving better landscapes in fewer days in hot urban conditions of Indian sub continent.     

Contingency nature of Helicobacter bizzozeronii oxygen-insensitive NAD(P)H-nitroreductase (HBZC1_00960) and its role in metronidazole resistance

Genomic analysis of a metronidazole resistant H. bizzozeronii strain revealed a frame length extension of the oxygen-insensitive NAD(P)H-nitroreductase HBZC1_00960 (RdxA), associated with the disruption of the C-terminal cysteine-containing conserved region (IACLXALGK). This was the result of the extension (from C₈ to C₉) of a simple sequence cytosine repeat (SSCR) located in the 3’ of the gene. A 3'' SSCR is also present in the rdxA homolog of H. heilmannii sensu stricto, but not in H. pylori. We showed that in the majority of in vitro spontaneous H. bizzozeronii metronidazole resistant mutants, the extension of the 3′ SSCR of rdxA was the only mutation observed. In addition, we observed that H. bizzozeronii ΔrdxA mutant strain showed the same MIC value of metronidazole observed in the spontaneous mutants. These data indicate that loss of function mutations in rdxA and in particular the disruption of the conserved region IACLXALGK is associated with reduced susceptibility to metronidazole in H. bizzozeronii. Slipped-strand mispairing of the SSCR located in the 3′ of the H. bizzozeronii rdxA appears to be the main mechanism. We also observed that H. bizzozeronii acquires resistance to metronidazole at high mutation rate, and that serial passages in vitro without selection induced an increased level of susceptibility. In conclusion, contrary to what was previously described in H. pylori, the H. bizzozeronii rdxA appears to be a contingency gene which undergoes phase variation. The contingency nature of rdxA should be carefully considered when metronidazole is used in the treatment of H. heilmannii-associated gastritis.