Stem anatomy and adventitious root formation in cuttings of Angophora, Corymbia and Eucalyptus

Many plantation eucalypts are difficult to propagate from cuttings, and their rooted cuttings often possess very few adventitious roots. We microscopically examined the stem anatomy of cuttings from 12 species of eucalypts and we determined whether adventitious root formation in auxin-treated cuttings of four species was limited to particular positions around the vascular tissue. Most species contained a central pith that was arranged in a four-pointed stellate pattern. The surrounding vascular tissue was also arranged in a stellate pattern near the shoot apex but it developed a more rectangular shape at the outer phloem as the stems enlarged radially. Adventitious roots formed at, or slightly peripheral to, the vascular cambium, and they formed at both the corners and the sides of the rectangular-shaped vascular tissue. The study highlighted that auxin-treated eucalypt cuttings can produce roots at multiple positions around the vascular tissue and so propagation methods can aim to produce more than four adventitious roots per rooted cutting. Higher numbers of adventitious roots could improve the root system symmetry, stability, survival and growth rate of clonal eucalypt trees. © 2015 by the authors; licensee MDPI, Basel, Switzerland.

Genomic regions influencing seminal root traits in barley

Water availability is a major limiting factor for crop production, making drought adaptation and its many component traits a desirable attribute of plant cultivars. Previous studies in cereal crops indicate that root traits expressed at early plant developmental stages, such as seminal root angle and root number, are associated with water extraction at different depths. Here, we conducted the first study to map seminal root traits in barley (Hordeum vulgare L.). Using a recently developed high-throughput phenotyping method, a panel of 30 barley genotypes and a doubled-haploid (DH) population (ND24260 × 'Flagship') comprising 330 lines genotyped with diversity array technology (DArT) markers were evaluated for seminal root angle (deviation from vertical) and root number under controlled environmental conditions. A high degree of phenotypic variation was observed in the panel of 30 genotypes: 13.5 to 82.2 and 3.6 to 6.9° for root angle and root number, respectively. A similar range was observed in the DH population: 16.4 to 70.5 and 3.6 to 6.5° for root angle and number, respectively. Seven quantitative trait loci (QTL) for seminal root traits (root angle, two QTL; root number, five QTL) were detected in the DH population. A major QTL influencing both root angle and root number (RAQ2/RNQ4) was positioned on chromosome 5HL. Across-species analysis identified 10 common genes underlying root trait QTL in barley, wheat (Triticum aestivum L.), and sorghum [Sorghum bicolor (L.) Moench]. Here, we provide insight into seminal root phenotypes and provide a first look at the genetics controlling these traits in barley.

On-farm Campylobacter and Escherichia coli in commercial broiler chickens: Re-used bedding does not influence Campylobacter emergence and levels across sequential farming cycles

Limitations in quality bedding material have resulted in the growing need to re-use litter during broiler farming in some countries, which can be of concern from a food-safety perspective. The aim of this study was to compare the Campylobacter levels in ceca and litter across three litter treatments under commercial farming conditions. The litter treatments were (a) the use of new litter after each farming cycle; (b) an Australian partial litter re-use practice; and (c) a full litter re-use practice. The study was carried out on two farms over two years (Farm 1, from 2009–2010 and Farm 2, from 2010–2011), across three sheds (35,000 to 40,000 chickens/shed) on each farm, adopting three different litter treatments across six commercial cycles. A random sampling design was adopted to test litter and ceca for Campylobacter and Escherichia coli, prior to commercial first thin-out and final pick-up. Campylobacter levels varied little across litter practices and farming cycles on each farm and were in the range of log 8.0–9.0 CFU/g in ceca and log 4.0–6.0 MPN/g for litter. Similarly the E. coli in ceca were ∼log 7.0 CFU/g. At first thin-out and final pick-up, the statistical analysis for both litter and ceca showed that the three-way interaction (treatments by farms by times) was highly significant (P < 0.01), indicating that the patterns of Campylobacter emergence/presence across time vary between the farms, cycles and pickups. The emergence and levels of both organisms were not influenced by litter treatments across the six farming cycles on both farms. Either C. jejuni or C. coli could be the dominant species across litter and ceca, and this phenomenon could not be attributed to specific litter treatments. Irrespective of the litter treatments in place, cycle 2 on Farm 2 remained campylobacter-free. These outcomes suggest that litter treatments did not directly influence the time of emergence and levels of Campylobacter and E. coli during commercial farming.

Minimization of Incompletely Specified Sequential Machines

A simple yet efficient method for the minimization of incompletely specified sequential machines (ISSMs) is proposed. Precise theorems are developed, as a consequence of which several compatibles can be deleted from consideration at the very first stage in the search for a minimal closed cover. Thus, the computational work is significantly reduced. Initial cardinality of the minimal closed cover is further reduced by a consideration of the maximal compatibles (MC's) only; as a result the method converges to the solution faster than the existing procedures. "Rank" of a compatible is defined. It is shown that ordering the compatibles, in accordance with their rank, reduces the number of comparisons to be made in the search for exclusion of compatibles. The new method is simple, systematic, and programmable. It does not involve any heuristics or intuitive procedures. For small- and medium-sized machines, it canle used for hand computation as well. For one of the illustrative examples used in this paper, 30 out of 40 compatibles can be ignored in accordance with the proposed rules and the remaining 10 compatibles only need be considered for obtaining a minimal solution.

Fine root dry matter relative to mango (Mangifera indica) tree scion size grafted on size-controlling rootstocks, is negatively related to scion growth rate

Knowledge of root dry matter (DM) allocation, in relation to differing vigour conferred by rootstock cultivars, is required to understand the structural relationships between rootstock and scion. We investigated the mass of roots (four size classes up to 23 mm diameter) by coring proximal to five polyembryonic mango rootstock cultivars known to differ in their effects on the vigour and productivity of scion cultivar ‘Kensington Pride’, in a field trial of 13-year-old trees. Significant differences in fine (<0.64 and 0.64–1.88 mm diameter) and small (1.88–7.50 mm) root DM contents were observed between rootstock cultivars. There was a complex relationship between the amount of feeder (fine and small size classes) roots and scion size (trunk cross sectional area, TCSA), with intermediate size trees on rootstock MYP having the most feeder roots, while the smallest trees, on the rootstock Vellaikulamban had the least of these roots. Across rootstock cultivars, tree vigour (TCSA growth rate) was negatively and significantly related to the ratio of fine root DM/scion TCSA, suggesting this may be a useful indicator of the vigour that different rootstocks confer on the scion. In contrast non-ratio root DM and scion TCSA results had no significant relationships. The significant rootstock effects on orchard root growth and tree size could not be predicted from earlier differences in nursery seedling vigour, nor did seedling vigour predict root DM allocation.

Highly heritable resistance to root-lesion nematode (Pratylenchus thornei) in Australian chickpea germplasm observed using an optimised glasshouse method and multi-environment trial analysis

Pratylenchus thornei is a root-lesion nematode (RLN) of economic significance in the grain growing regions of Australia. Chickpea (Cicer arietinum) is a significant legume crop grown throughout these regions, but previous testing found most cultivars were susceptible to P. thornei. Therefore, improved resistance to P. thornei is an important objective of the Australian chickpea breeding program. A glasshouse method was developed to assess resistance of chickpea lines to P. thornei, which requires relatively low labour and resource input, and hence is suited to routine adoption within a breeding program. Using this method, good differentiation of chickpea cultivars for P. thornei resistance was measured after 12 weeks. Nematode multiplication was higher for all genotypes than the unplanted control, but of the 47 cultivars and breeding lines tested, 17 exhibited partial resistance, allowing less than two fold multiplication. The relative differences in resistance identified using this method were highly heritable (0.69) and were validated against P. thornei data from seven field trials using a multi-environment trial analysis. Genetic correlations for cultivar resistance between the glasshouse and six of the field trials were high (>0.73). These results demonstrate that resistance to P. thornei in chickpea is highly heritable and can be effectively selected in a limited set of environments. The improved resistance found in a number of the newer chickpea cultivars tested shows that some advances have been made in the P. thornei resistance of Australian chickpea cultivars, and that further targeted breeding and selection should provide incremental improvements.

Optimal adaptive sequential spatial sampling of soil using pair-copulas

A spatial sampling design that uses pair-copulas is presented that aims to reduce prediction uncertainty by selecting additional sampling locations based on both the spatial configuration of existing locations and the values of the observations at those locations. The novelty of the approach arises in the use of pair-copulas to estimate uncertainty at unsampled locations. Spatial pair-copulas are able to more accurately capture spatial dependence compared to other types of spatial copula models. Additionally, unlike traditional kriging variance, uncertainty estimates from the pair-copula account for influence from measurement values and not just the configuration of observations. This feature is beneficial, for example, for more accurate identification of soil contamination zones where high contamination measurements are located near measurements of varying contamination. The proposed design methodology is applied to a soil contamination example from the Swiss Jura region. A partial redesign of the original sampling configuration demonstrates the potential of the proposed methodology.

The nonplanar peptide unit III. Quantum chemical calculations for related compounds and experimental X-ray diffraction data

The possible nonplanar distortions of the amide group in formamide, acetamide, N-methylacetamide, and N-ethylacetamide have been examined using CNDO/2 and INDO methods. The predictions from these methods are compared with the results obtained from X-ray and neutron diffraction studies on crystals of small open peptides, cyclic peptides, and amides. It is shown that the INDO results are in good agreement with observations, and that the dihedral angles N and defining the nonplanarity of the amide unit are correlated approximately by the relation N = -2, while C is small and uncorrelated with . The present study indicates that the nonplanar distortions at the nitrogen atom of the peptide unit may have to be taken into consideration, in addition to the variation in the dihedral angles (,), in working out polypeptide and protein structures.

Ecological impacts of Phlebiopsis gigantea biocontrol treatment against Heterobasidion spp. as revealed by fungal community profiling and population analyses

Wood decay fungi belonging to the species complex Heterobasidion annosum sensu lato are among the most common and economically important species causing root rot and stem decay in conifers of the northern temperate regions. New infections by these pathogens can be suppressed by tree stump treatments using chemical or biological control agents. In Finland, the corticiaceous fungus Phlebiopsis gigantea has been formulated into a commercial biocontrol agent called Rotstop (Verdera Ltd.). This thesis addresses the ecological impacts of Rotstop biocontrol treatment on the mycoflora of conifer stumps. Locally, fungal communities within Rotstop-treated and untreated stumps were analyzed using a novel method based on DGGE profiling of small subunit ribosomal DNA fragments amplified directly from wood samples. Population analyses for P. gigantea and H. annosum s.l. were conducted to evaluate possible risks associated with local and/or global distribution of the Rotstop strain. Based on molecular community profiling by DGGE, we detected a few individual wood-inhabiting fungal species (OTUs) that seemed to have suffered or benefited from the Rotstop biocontrol treatment. The DGGE analyses also revealed fungal diversity not retrieved by cultivation and some fungal sequence types untypical for decomposing conifer wood. However, statistical analysis of DGGE community profiles obtained from Rotstop-treated and untreated conifer stumps revealed that the Rotstop treatment had not caused a statistically significant reduction in the species diversity of wood-inhabiting fungi within our experimental forest plots. Locally, ISSR genotyping of cultured P. gigantea strains showed that the Rotstop biocontrol strain was capable of surviving up to six years within treated Norway spruce stumps, while in Scots pine stumps it was sooner replaced by successor fungal species. In addition, the spread of resident P. gigantea strains into Rotstop-treated forest stands seemed effective in preventing the formation of genetically monomorphic populations in the short run. On a global scale, we detected a considerable level of genetic differentiation between the interfertile European and North American populations of P. gigantea. These results strongly suggest that local biocontrol strains should be used in order to prevent global spread of P. gigantea and hybrid formation between geographically isolated populations. The population analysis for H. annosum s.l. revealed a collection of Chinese fungal strains that showed a high degree of laboratory fertility with three different allopatric H. annosum s.l. taxa. However, based on the molecular markers, the Chinese strains could be clearly affiliated with the H. parviporum taxonomical cluster, which thus appears to have a continuous distribution range from Europe through southern Siberia to northern China. Keywords: Rotstop, wood decay, DGGE, ISSR fingerprinting, ribosomal DNA

State Minimization of Incompletely Specified Sequential Machines

A simple procedure for the state minimization of an incompletely specified sequential machine whose number of internal states is not very large is presented. It introduces the concept of a compatibility graph from which the set of maximal compatibles of the machine can be very conveniently derived. Primary and secondary implication trees associated with each maximal compatible are then constructed. The minimal state machine covering the incompletely specified machine is then obtained from these implication trees.

Inflammation-driven bone formation in a mouse model of ankylosing spondylitis: Sequential not parallel processes

Background Ankylosing spondylitis (AS) is an immune-mediated arthritis particularly targeting the spine and pelvis and is characterised by inflammation, osteoproliferation and frequently ankylosis. Current treatments that predominately target inflammatory pathways have disappointing efficacy in slowing disease progression. Thus, a better understanding of the causal association and pathological progression from inflammation to bone formation, particularly whether inflammation directly initiates osteoproliferation, is required. Methods The proteoglycan-induced spondylitis (PGISp) mouse model of AS was used to histopathologically map the progressive axial disease events, assess molecular changes during disease progression and define disease progression using unbiased clustering of semi-quantitative histology. PGISp mice were followed over a 24-week time course. Spinal disease was assessed using a novel semi-quantitative histological scoring system that independently evaluated the breadth of pathological features associated with PGISp axial disease, including inflammation, joint destruction and excessive tissue formation (osteoproliferation). Matrix components were identified using immunohistochemistry. Results Disease initiated with inflammation at the periphery of the intervertebral disc (IVD) adjacent to the longitudinal ligament, reminiscent of enthesitis, and was associated with upregulated tumor necrosis factor and metalloproteinases. After a lag phase, established inflammation was temporospatially associated with destruction of IVDs, cartilage and bone. At later time points, advanced disease was characterised by substantially reduced inflammation, excessive tissue formation and ectopic chondrocyte expansion. These distinct features differentiated affected mice into early, intermediate and advanced disease stages. Excessive tissue formation was observed in vertebral joints only if the IVD was destroyed as a consequence of the early inflammation. Ectopic excessive tissue was predominantly chondroidal with chondrocyte-like cells embedded within collagen type II- and X-rich matrix. This corresponded with upregulation of mRNA for cartilage markers Col2a1, sox9 and Comp. Osteophytes, though infrequent, were more prevalent in later disease. Conclusions The inflammation-driven IVD destruction was shown to be a prerequisite for axial disease progression to osteoproliferation in the PGISp mouse. Osteoproliferation led to vertebral body deformity and fusion but was never seen concurrent with persistent inflammation, suggesting a sequential process. The findings support that early intervention with anti-inflammatory therapies will be needed to limit destructive processes and consequently prevent progression of AS.

Analysis of the amino acid sequences of plant Bowman-Birk inhibitors

Plant seeds contain a large number of protease inhibitors of animal, fungal, and bacterial origin. One of the well-studied families of these inhibitors is the Bowman-Birk family(BBI). The BBIs from dicotyledonous seeds are 8K, double-headed proteins. In contrast, the 8K inhibitors from monocotyledonous seeds are single headed. Monocots also have a 16K, double-headed inhibitor. We have determined the primary structure of a Bowman-Birk inhibitor from a dicot, horsegram, by sequential edman analysis of the intact protein and peptides derived from enzymatic and chemical cleavage. The 76-residue-long inhibitor is very similar to that ofMacrotyloma axillare. An analysis of this inhibitor along with 26 other Bowman-Birk inhibitor domains (MW 8K) available in the SWISSPROT databank revealed that the proteins from monocots and dicots belong to related but distinct families. Inhibitors from monocots show larger variation in sequence. Sequence comparison shows that a crucial disulphide which connects the amino and carboxy termini of the active site loop is lost in monocots. The loss of a reactive site in monocots seems to be correlated to this. However, it appears that this disulphide is not absolutely essential for retention of inhibitory function. Our analysis suggests that gene duplication leading to a 16K inhibitor in monocots has occurred, probably after the divergence of monocots and dicots, and also after the loss of second reactive site in monocots.