Fine Mapping of qroot-yield-1.06, a QTL for Root, Plant Vigor and Yield in Maize

Root-yield-1.06 is a major QTL affecting root system architecture (RSA) and other agronomic traits in maize. The effect of this QTL has been evaluated with the development of near isogenic lines (NILs) differing at the QTL position. The objective of this study was to fine map qroot-yield-1.06 by marker-assisted searching for chromosome recombinants in the QTL interval and concurrent root phenotyping in both controlled and field conditions, through successive generations. Complementary approaches such as QTL meta-analysis and RNA-seq were deployed in order to help prioritizing candidate genes within the QTL target region. Using a selected group of genotypes, field based root analysis by ‘shovelomics’ enabled to accurately collect RSA information of adult maize plants. Shovelomics combined with software-assisted root imaging analysis proved to be an informative and relatively highly automated phenotyping protocol. A QTL interval mapping was conducted using a segregating population at the seedling stage grown in controlled environment. Results enabled to narrow down the QTL interval and to identify new polymorphic markers for MAS in field experiments. A collection of homozygous recombinant NILs was developed by screening segregating populations with markers flanking qroot-yield-1.06. A first set of lines from this collection was phenotyped based on the adapted shovelomics protocol. QTL analysis based on these data highlighted an interval of 1.3 Mb as completely linked with the target QTL but, a larger safer interval of 4.1 Mb was selected for further investigations. QTL meta-analysis allows to synthetize information on root QTLs and two mQTLs were identified in the qroot-yield-1.06 interval. Trascriptomics analysis based on RNA-seq data of the two contrasting QTL-NILs, confirmed alternative haplotypes at chromosome bin 1.06. qroot-yield-1.06 has now been delimited to a 4.1-Mb interval, and thanks to the availability of additional untested homozygous recombinant NILs, the potentially achievable mapping resolution at qroot-yield-1.06 is c. 50 kb.

Development and validation of a liquid chromatography-tandem mass spectrometry method for the quantitation of synthetic cannabinoids of the aminoalkylindole type and methanandamide in serum and its application to forensic samples

After the discovery of synthetic cannabimimetic substances in 'Spice'-like herbal mixtures marketed as 'incense' or 'plant fertilizer' the active compounds have been declared as controlled substances in several European countries. As expected, a monitoring of new herbal mixtures which continue to appear on the market revealed that shortly after control measures have been taken by legal authorities, other compounds were added to existing mixtures and to new products. Several compounds of the aminoalkylindole type have been detected so far in herbal mixtures but still their consumption cannot be detected by commonly used drug-screening procedures, encouraging drug users to substitute cannabis with those products. There is a increasing demand on the part of police authorities, hospitals and psychiatrists for detection and quantification of synthetic cannabinoids in biological samples originating from psychiatric inpatients, emergency units or assessment of fitness to drive. Therefore, a liquid chromatography-tandem mass spectrometry method after liquid-liquid extraction for the quantitation of JWH-015, JWH-018, JWH-073, JWH-081, JWH 200, JWH-250, WIN 55,212-2 and methanandamide and the detection of JWH-019 and JWH-020 in human serum has been developed and fully validated according to guidelines for forensic toxicological analyses. The method was successfully applied to 101 serum samples from 80 subjects provided by hospitals, detoxification and therapy centers, forensic psychiatric centers and police authorities. Fifty-seven samples or 56.4% were found positive for at least one aminoalkylindole. JWH-019, JWH-020, JWH-200, WIN 55,212-2 and methanandamide were not detected in any of the analyzed samples.

Development of a biocrystallisation assay for examining effects of homeopathic preparations ursing cress seedlings

A major challenge in basic research into homeopathic potentisation is to develop bioassays that yield consistent results. We evaluated the potential of a seedling-biocrystallisation method. Cress seeds (Lepidium sativum L.) germinated and grew for 4 days in vitro in Stannum metallicum 30x or water 30x in blinded and randomized assignment. 15 experiments were performed at two laboratories. CuCl2-biocrystallisation of seedlings extracted in the homeopathic preparations was performed on circular glass plates. Resulting biocrystallograms were analysed by computerized textural image analysis. All texture analysis variables analysed yielded significant results for the homeopathic treatment; thus the texture of the biocrystallograms of homeopathically treated cress exhibited specific characteristics. Two texture analysis variables yielded differences between the internal replicates, most probably due to a processing order effect. There were only minor differences between the results of the two laboratories. The biocrystallisation method seems to be a promising complementary outcome measure for plant bioassays investigating effects of homeopathic preparations.

Systemic analysis of microarray data sets towards identifying genes regulating root development

Nitrogen and water are essential for plant growth and development. In this study, we designed experiments to produce gene expression data of poplar roots under nitrogen starvation and water deprivation conditions. We found low concentration of nitrogen led first to increased root elongation followed by lateral root proliferation and eventually increased root biomass. To identify genes regulating root growth and development under nitrogen starvation and water deprivation, we designed a series of data analysis procedures, through which, we have successfully identified biologically important genes. Differentially Expressed Genes (DEGs) analysis identified the genes that are differentially expressed under nitrogen starvation or drought. Protein domain enrichment analysis identified enriched themes (in same domains) that are highly interactive during the treatment. Gene Ontology (GO) enrichment analysis allowed us to identify biological process changed during nitrogen starvation. Based on the above analyses, we examined the local Gene Regulatory Network (GRN) and identified a number of transcription factors. After testing, one of them is a high hierarchically ranked transcription factor that affects root growth under nitrogen starvation. It is very tedious and time-consuming to analyze gene expression data. To avoid doing analysis manually, we attempt to automate a computational pipeline that now can be used for identification of DEGs and protein domain analysis in a single run. It is implemented in scripts of Perl and R.

Evaluation of sugar maple dieback in the Upper Great Lakes region and development of a forest health youth education program

Acer saccharum Marsh., is one of the most valuable trees in the northern hardwood forests. Severe dieback was recently reported by area foresters in the western Upper Great Lakes Region. Sugar Maple has had a history of dieback over the last 100 years throughout its range and different variables have been identified as being the predisposing and inciting factors in different regions at different times. Some of the most common factors attributed to previous maple dieback episodes were insect defoliation outbreaks, inadequate precipitation, poor soils, atmospheric deposition, fungal pathogens, poor management, or a combination of these. The current sugar maple dieback was evaluated to determine the etiology, severity, and change in dieback on both industry and public lands. A network of 120 sugar maple health evaluation plots was established in the Upper Peninsula, Michigan, northern Wisconsin, and eastern Minnesota and evaluated annually from 2009-2012. Mean sugar maple crown dieback between 2009-2012 was 12.4% (ranging from 0.8-75.5%) across the region. Overall, during the sampling period, mean dieback decreased by 5% but individual plots and trees continued to decline. Relationships were examined between sugar maple dieback and growth, habitat conditions, ownership, climate, soil, foliage nutrients, and the maple pathogen sapstreak. The only statistically significant factor was found to be a high level of forest floor impacts due to exotic earthworm activity. Sugar maple on soils with lower pH had less earthworm impacts, less dieback, and higher growth rates than those on soils more favorable to earthworms. Nutritional status of foliage and soil was correlated with dieback and growth suggesting perturbation of nutrient cycling may be predisposing or contributing to dieback. The previous winter's snowfall totals, length of stay on the ground, and number of days with freezing temperatures had a significant positive relationship to sugar maple growth rates. Sapstreak disease, Ceratocystis virescens, may be contributing to dieback in some stands but was not related to the amount of dieback in the region. The ultimate goal of this research is to help forest managers in the Great Lakes Region prevent, anticipate, reduce, and/or salvage stands with dieback and loss in the future. An improved understanding of the complex etiology associated with sugar maple dieback in the Upper Great Lakes Region is necessary to make appropriate silvicultural decisions. Forest Health education helps increase awareness and proactive forest management in the face of changing forest ecosystems. Lessons are included to assist educators in incorporating forest health into standard biological disciplines at the secondary school curricula.

Experimental plant communities develop phylogenetically overdispersed abundance distributions during assembly

The importance of competition between similar species in driving community assembly is much debated. Recently, phylogenetic patterns in species composition have been investigated to help resolve this question: phylogenetic clustering is taken to imply environmental filtering, and phylogenetic overdispersion to indicate limiting similarity between species. We used experimental plant communities with random species compositions and initially even abundance distributions to examine the development of phylogenetic pattern in species abundance distributions. Where composition was held constant by weeding, abundance distributions became overdispersed through time, but only in communities that contained distantly related clades, some with several species (i.e., a mix of closely and distantly related species). Phylogenetic pattern in composition therefore constrained the development of overdispersed abundance distributions, and this might indicate limiting similarity between close relatives and facilitation/complementarity between distant relatives. Comparing the phylogenetic patterns in these communities with those expected from the monoculture abundances of the constituent species revealed that interspecific competition caused the phylogenetic patterns. Opening experimental communities to colonization by all species in the species pool led to convergence in phylogenetic diversity. At convergence, communities were composed of several distantly related but species-rich clades and had overdispersed abundance distributions. This suggests that limiting similarity processes determine which species dominate a community but not which species occur in a community. Crucially, as our study was carried out in experimental communities, we could rule out local evolutionary or dispersal explanations for the patterns and identify ecological processes as the driving force, underlining the advantages of studying these processes in experimental communities. Our results show that phylogenetic relations between species provide a good guide to understanding community structure and add a new perspective to the evidence that niche complementarity is critical in driving community assembly.

Holocene climatic change and the development of the lake-effect snowbelt in Michigan, USA

Lake-effect snow is an important constraint on ecological and socio-economic systems near the North American Great Lakes. Little is known about the Holocene history of lake-effect snowbelts, and it is difficult to decipher how lake-effect snowfall abundance affected ecosystem development. We conducted oxygen-isotope analysis of calcite in lake-sediment cores from northern Lower Michigan to infer Holocene climatic variation and assess snowbelt development. The two lakes experience the same synoptic-scale climatic systems, but only one of them (Huffman Lake) receives a significant amount of lake-effect snow. A 177-cm difference in annual snowfall causes groundwater inflow at Huffman Lake to be 18O-depleted by 2.3‰ relative to O'Brien Lake. To assess when the lake-effect snowbelt became established, we compared calcite-δ18O profiles of the last 11,500 years from these two sites. The chronologies are based on accelerator-mass-spectrometry 14C ages of 11 and 17 terrestrial-plant samples from Huffman and O'Brien lakes, respectively. The values of δ18O are low at both sites from 11,500 to 9500 cal yr BP when the Laurentide Ice Sheet (LIS) exerted a dominant control over the regional climate and provided periodic pulses of meltwater to the Great Lakes basin. Carbonate δ18O increases by 2.6‰ at O'Brien Lake and by 1.4‰ at Huffman Lake between 9500 and 7000 cal yr BP, suggesting a regional decline in the proportion of runoff derived from winter precipitation. The Great Lakes snowbelt probably developed between 9500 and 5500 cal yr BP as inferred from the progressive 18O-depletion at Huffman Lake relative to O'Brien Lake, with the largest increase of lake-effect snow around 7000 cal yr BP. Lake-effect snow became possible at this time because of increasing contact between the Great Lakes and frigid arctic air. These changes resulted from enhanced westerly flow over the Great Lakes as the LIS collapsed, and from rapidly rising Great Lakes levels during the Nipissing Transgression. The δ18O difference between Huffman and O'Brien lakes declines after 5500 cal yr BP, probably because of a northward shift of the polar vortex that brought increasing winter precipitation to the entire region. However, δ18O remains depleted at Huffman Lake relative to O'Brien Lake because of the continued production of lake-effect snow.

Investigation of potential causes for the development of porcine ear necrosis: different study designs--comparable results?

During the last years two studies for the investigation of the etiology of porcine ear necrosis were carried out at the Clinic for Swine of the University of Veterinary Medicine Vienna. In study 1, parameters, which are discussed in this context, were collected by veterinary practitioners by completing specially designed questionnaires in farms with symptoms of the porcine ear necrosis syndrome. In study 2, samples of piglets and feed were collected for laboratory analysis of the most important infectious agents as well as mycotoxins. In the present manuscript, the results of both projects were compared. Even if the selection criteria of both studies differed, the affected age class was comparable (5.5 to ten weeks of life in study 1 and six to ten weeks of life in study 2). The herd-specific prevalence of the porcine ear necrosis syndrome varied considerably with percentages between 2 and 10, respectively, to 100%. The evaluation of questionnaires in study 1 showed that 51% of the farms had problems with cannibalism. Particles of plant material, which were frequently seen on the histologic slides of study 2, could have got into the tissue by chewing the ears of the pen mates or cannibalism. Whereas in study 1 the negative effect of parameters as high pig density, suboptimal climate, missing enrichment material and bad quality of feed and water were considered, in study 2 all these factors were checked at sample collection and ruled out as precursor for cannibalism. In both studies bacterial agents proved to be a crucial co-factor for the expansion of the necroses to deeper tissue layers, whereas viral pathogens were classified less important. In both projects it was not possible to estimate the direct impact of infectious agents and mycotoxins as direct trigger of the necroses as well as their participation as co-factors or precursor in the sense of an immunosuppression or previous damage of blood vessels or tissue.

Peptide and amino acid transporters are differentially regulated during seed development and germination in faba bean

Two peptide transporter (PTR) homologs have been isolated from developing seeds of faba bear, (Vicia faba). VfPTR1 was shown to be a functional peptide transporter through complementation of a yeast mutant. Expression patterns of VfPTR1 and VfPTR2 as well as of the amino acid permease VfAAP1 (Miranda et al., 2001) were compared throughout seed development and germination. In developing seeds, the highest levels of VfPTR1 transcripts were reached during midcotyledon development, whereas VfAAP1 transcripts were most abundant during early cotyledon development, before the appearance of storage protein gene transcripts, and were detectable until late cotyledon development. During early germination, VfPTR1 mRNA appeared first in cotyledons and later, during seedling growth, also in axes and roots. Expression of VfPTR2 and VfAAP1 was delayed compared with VfPTR1, and was restricted to the nascent organs of the seedlings. Localization of VfPTR1 transcripts showed that this FTR is temporally and spatially regulated during cotyledon development. In germinating seeds, VfPTR1 mRNA was localized in root hairs and root epidermal cells, suggesting a role in nutrient uptake from the soil. In seedling roots, VfPTR1 was repressed by a dipeptide and by an amino acid, whereas nitrate was without influence.

Sequence of arrival determines plant-mediated interactions between herbivores

Induced changes in plant quality can mediate indirect interactions between herbivores. Although the sequence of attack by different herbivores has been shown to influence plant responses, little is known about how this affects the herbivores themselves. We therefore investigated how induction by the leaf herbivore Spodoptera frugiperda influences resistance of teosinte (Zea mays mexicana) and cultivated maize (Zea mays mays) against root-feeding larvae of Diabrotica virgifera virgifera. The importance of the sequence of arrival was tested in the field and laboratory. Spodoptera frugiperda infestation had a significant negative effect on colonization by D. virgifera larvae in the field and weight gain in the laboratory, but only when S. frugiperda arrived on the plant before the root herbivore. When S. frugiperda arrived after the root herbivore had established, no negative effects on larval performance were detected. Yet, adult emergence of D. virgifera was reduced even when the root feeder had established first, indicating that the negative effects were not entirely absent in this treatment. The defoliation of the plants was not a decisive factor for the negative effects on root herbivore development, as both minor and major leaf damage resulted in an increase in root resistance and the extent of biomass removal was not correlated with root-herbivore growth. We propose that leaf-herbivore-induced increases in feeding-deterrent and/or toxic secondary metabolites may account for the sequence-specific reduction in root-herbivore performance. Synthesis. Our results demonstrate that the sequence of arrival can be an important determinant of plant-mediated interactions between insect herbivores in both wild and cultivated plants. Arriving early on a plant may be an important strategy of insects to avoid competition with other herbivores. To fully understand plant-mediated interactions between insect herbivores, the sequence of arrival should be taken into account. © 2011 The Authors. Journal of Ecology © 2011 British Ecological Society.

Plant architecture

Plant architecture is species specific, indicating that it is under strict genetic control. Although it is also influenced by environmental conditions such as light, temperature, humidity and nutrient status, here we wish to focus only on the endogenous regulatory principles that control plant architecture. We summarise recent progress in the understanding of the basic patterning mechanisms involved in the regulation of leaf arrangement, the genetic regulation of meristem determinacy, i.e. the decision to stop or continue growth, and the control of branching during vegetative and generative development. Finally, we discuss the basis of leaf architecture and the role of cell division and cell growth in morphogenesis.

Measuring the mechanical properties of plant cells by combining micro-indentation with osmotic treatments

Growth in plants results from the interaction between genetic and signalling networks and the mechanical properties of cells and tissues. There has been a recent resurgence in research directed at understanding the mechanical aspects of growth, and their feedback on genetic regulation. This has been driven in part by the development of new micro-indentation techniques to measure the mechanical properties of plant cells in vivo. However, the interpretation of indentation experiments remains a challenge, since the force measures results from a combination of turgor pressure, cell wall stiffness, and cell and indenter geometry. In order to interpret the measurements, an accurate mechanical model of the experiment is required. Here, we used a plant cell system with a simple geometry, Nicotiana tabacum Bright Yellow-2 (BY-2) cells, to examine the sensitivity of micro-indentation to a variety of mechanical and experimental parameters. Using a finite-element mechanical model, we found that, for indentations of a few microns on turgid cells, the measurements were mostly sensitive to turgor pressure and the radius of the cell, and not to the exact indenter shape or elastic properties of the cell wall. By complementing indentation experiments with osmotic experiments to measure the elastic strain in turgid cells, we could fit the model to both turgor pressure and cell wall elasticity. This allowed us to interpret apparent stiffness values in terms of meaningful physical parameters that are relevant for morphogenesis.