The apical control of lateral bud development in excised shoot tips of Cuscuta reflexa cultured in vitro

Excised shoot tips of Cuscuta reflexa Roxb. (dodder), a rootless and leafless angiospermic plant parasite, were cultured in vitro for the study of the control of lateral bud development by the apex. In a chemically defined medium lacking hormones, the basal bud alone developed into a shoot. The addition of coconut milk to the growth medium induced the activation of multiple lateral buds, but only a single bud developed further into a shoot. The decapitation of this shoot induced the development of another shoot and the process could be repeated. This showed the controlling effect of the apex in correlative control of bud development. Application of indole-3-acetic acid to the shoot tip explant delayed the development of the lateral bud. Gibberellic acid A3 induced a marked elongation growth of the explant and reinforced apical dominance. The direct application of cytokinin to an inhibited bud relieved it from apical dominance. A basipetally decreasing concentration gradient of auxin may prevail at the nodes. Bud outgrowth is probably stimulated by cytokinin produced locally in the bud.

Wild dogma: An examination of recent "evidence" for dingo regulation of invasive mesopredator release in Australia

There is growing interest in the role that apex predators play in shaping terrestrial ecosystems and maintaining trophic cascades. In line with the mesopredator release hypothesis, Australian dingoes (Canis lupus dingo and hybrids) are assumed by many to regulate the abundance of invasive mesopredators, such as red foxes Vulpes vulpes and feral cats Felis catus, thereby providing indirect benefits to various threatened vertebrates. Several recent papers have claimed to provide evidence for the biodiversity benefits of dingoes in this way. Nevertheless, in this paper we highlight several critical weaknesses in the methodological approaches used in many of these reports, including lack of consideration for seasonal and habitat differences in activity, the complication of simple track-based indices by incorporating difficult-to-meet assumptions, and a reduction in sensitivity for assessing populations by using binary measures rather than potentially continuous measures. Of the 20 studies reviewed, 15 of them (75%) contained serious methodological flaws, which may partly explain the inconclusive nature of the literature nvestigating interactions between invasive Australian predators. We therefore assert that most of the “growing body of evidence” for mesopredator release is merely an inconclusive growing body of literature only. We encourage those interested in studying the ecological roles of dingoes relative to invasive mesopredators and native prey species to account for the factors we identify, and caution the value of studies that have not done so.

Molecular basis of colorectal cancer predisposition

Colorectal cancer (CRC) is one of the most frequent malignancies in Western countries. Inherited factors have been suggested to be involved in 35% of CRCs. The hereditary CRC syndromes explain only ~6% of all CRCs, indicating that a large proportion of the inherited susceptibility is still unexplained. Much of the remaining genetic predisposition for CRC is probably due to undiscovered low-penetrance variations. This study was conducted to identify germline and somatic changes that contribute to CRC predisposition and tumorigenesis. MLH1 and MSH2, that underlie Hereditary non-polyposis colorectal cancer (HNPCC) are considered to be tumor suppressor genes; the first hit is inherited in the germline and somatic inactivation of the wild type allele is required for tumor initiation. In a recent study, frequent loss of the mutant allele in HNPCC tumors was detected and a new model, arguing against the two-hit hypothesis, was proposed for somatic HNPCC tumorigenesis. We tested this hypothesis by conducting LOH analysis on 25 colorectal HNPCC tumors with a known germline mutation in the MLH1 or MSH2 genes. LOH was detected in 56% of the tumors. All the losses targeted the wild type allele supporting the classical two-hit model for HNPCC tumorigenesis. The variants 3020insC, R702W and G908R in NOD2 predispose to Crohn s disease. Contribution of NOD2 to CRC predisposition has been examined in several case-control series, with conflicting results. We have previously shown that 3020insC does not predispose to CRC in Finnish CRC patients. To expand our previous study the variants R702W and G908R were genotyped in a population-based series of 1042 Finnish CRC patients and 508 healthy controls. Association analyses did not show significant evidence for association of the variants with CRC. Single nucleotide polymorphism (SNP) rs6983267 at chromosome 8q24 was the first CRC susceptibility variant identified through genome-wide association studies. To characterize the role of rs6983267 in CRC predisposition in the Finnish population, we genotyped the SNP in the case-control material of 1042 cases and 1012 controls and showed that G allele of rs6983267 is associated with the increased risk of CRC (OR 1.22; P=0.0018). Examination of allelic imbalance in the tumors heterozygous for rs6983267 revealed that copy number increase affected 22% of the tumors and interestingly, it favored the G allele. By utilizing a computer algorithm, Enhancer Element Locator (EEL), an evolutionary conserved regulatory motif containing rs6983267 was identified. The SNP affected the binding site of TCF4, a transcription factor that mediates Wnt signaling in cells, and has proven to be crucial in colorectal neoplasia. The preferential binding of TCF4 to the risk allele G was showed in vitro and in vivo. The element drove lacZ marker gene expression in mouse embryos in a pattern that is consistent with genes regulated by the Wnt signaling pathway. These results suggest that rs6983267 at 8q24 exerts its effect in CRC predisposition by regulating gene expression. The most obvious target gene for the enhancer element is MYC, residing ~335 kb downstream, however further studies are required to establish the transcriptional target(s) of the predicted enhancer element.

A Story of Organized Crime: Constructing Criminality and Building Institutions

This is a narrative about the way in which a category of crime-to-be-combated is constructed through the discipline of criminology and the agents of discipline in criminal justice. The aim was to examine organized crime through the eyes of those whose job it is to fight it (and define it), and in doing so investigate the ways social problems surface as sites for state intervention. A genealogy of organized crime within criminological thought was completed, demonstrating that there are a range of different ways organized crime has been constructed within the social scientific discipline, and each of these were influenced by the social context, political winds and intellectual climate of the time. Following this first finding, in-depth qualitative interviews were conducted with individuals who had worked at the apex of the policing of organized crime in Australia, in order to trace their understandings of organized crime across recent history. It was found that organized crime can be understood as an object of the discourse of the politics of law and order, the discourse of international securitization, new public management in policing business, and involves the forging of outlaw identities. Therefore, there are multiple meanings of organized crime that have arisen from an interconnected set of social, political, moral and bureaucratic discourses. The institutional response to organized crime, including law and policing, was subsequently examined. An extensive legislative framework has been enacted at multiple jurisdictional levels, and the problem of organized crime was found to be deserving of unique institutional powers and configurations to deal with it. The social problem of organized crime, as constituted by the discourses mapped out in this research, has led to a new generation of increasingly preemptive and punitive laws, and the creation of new state agencies with amplified powers. That is, the response to organized crime, with a focus on criminalization and enforcement, has been driven and shaped by the four discourses and the way in which the phenomenon is constructed within them. An appreciation of the nexus between the emergence of the social problem, and the formation of institutions in response to it, is important in developing a more complete understanding of the various dimensions of organized crime.

Wild dogma II: the role and implications of wild dogma for wild dog management in Australia

The studies of Allen (2011) and Allen et al. (2011) recently examined the methodology underpinning claims that dingoes provide net benefits to biodiversity by suppressing foxes and cats. They found most studies to have design flaws and/or observational methods that preclude valid interpretations from the data, describing most of the current literature as ‘wild dogma’. In this short supplement, we briefly highlight the roles and implications of wild dogma for wild dog management in Australia. We discuss nomenclature, and the influence that unreliable science can have on policy and practice changes related to apex predator management.

The structure of Norway spruce (Picea abies [L.] Karst.) stems in relation to wood properties of sawn timber

An important challenge in forest industry is to get the appropriate raw material out from the forests to the wood processing industry. Growth and stem reconstruction simulators are therefore increasingly integrated in industrial conversion simulators, for linking the properties of wooden products to the three-dimensional structure of stems and their growing conditions. Static simulators predict the wood properties from stem dimensions at the end of a growth simulation period, whereas in dynamic approaches, the structural components, e.g. branches, are incremented along with the growth processes. The dynamic approach can be applied to stem reconstruction by predicting the three-dimensional stem structure from external tree variables (i.e. age, height) as a result of growth to the current state. In this study, a dynamic growth simulator, PipeQual, and a stem reconstruction simulator, RetroSTEM, are adapted to Norway spruce (Picea abies [L.] Karst.) to predict the three-dimensional structure of stems (tapers, branchiness, wood basic density) over time such that both simulators can be integrated in a sawing simulator. The parameterisation of the PipeQual and RetroSTEM simulators for Norway spruce relied on the theoretically based description of tree structure developing in the growth process and following certain conservative structural regularities while allowing for plasticity in the crown development. The crown expressed both regularity and plasticity in its development, as the vertical foliage density peaked regularly at about 5 m from the stem apex, varying below that with tree age and dominance position (Study I). Conservative stem structure was characterized in terms of (1) the pipe ratios between foliage mass and branch and stem cross-sectional areas at crown base, (2) the allometric relationship between foliage mass and crown length, (3) mean branch length relative to crown length and (4) form coefficients in branches and stem (Study II). The pipe ratio between branch and stem cross-sectional area at crown base, and mean branch length relative to the crown length may differ in trees before and after canopy closure, but the variation should be further analysed in stands of different ages and densities with varying site fertilities and climates. The predictions of the PipeQual and RetroSTEM simulators were evaluated by comparing the simulated values to measured ones (Study III, IV). Both simulators predicted stem taper and branch diameter at the individual tree level with a small bias. RetroSTEM predictions of wood density were accurate. For focusing on even more accurate predictions of stem diameters and branchiness along the stem, both simulators should be further improved by revising the following aspects in the simulators: the relationship between foliage and stem sapwood area in the upper stem, the error source in branch sizes, the crown base development and the height growth models in RetroSTEM. In Study V, the RetroSTEM simulator was integrated in the InnoSIM sawing simulator, and according to the pilot simulations, this turned out to be an efficient tool for readily producing stand scale information about stem sizes and structure when approximating the available assortments of wood products.

The effects of thinning and fertilisation on wood and tracheid properties of Norway spruce (Picea abies) the results of long-term experiments

The aim of this thesis was to study the basic relationships between thinning and fertilisation, tree growth rate and wood properties of Norway spruce (Picea abies (L.) Karst.) throughout a stand rotation. The material consisted of a total of 109 trees from both long-term thinning (Heinola, 61°10'N, 26°01'E; Punkaharju, 61°49'N, 29°19'E) and fertilisation-thinning experiments (Parikkala, 61°36'N, 29°22'E; Suonenjoki, 62°45'N, 27°00'E) in Finland. Wood properties, i.e., radial increment, wood density, latewood proportion, tracheid length, cell wall thickness and lumen diameter, as well as relative lignin content, were measured in detail from the pith to the bark, as well as from the stem base towards the stem apex. Intensive thinning and fertilisation treatments of Norway spruce stands increased (8% 64%) the radial increment of studied trees at breast height (1.3 m). At the same time, a faster growth rate slightly decreased average wood density (2% 7%), tracheid length (0% 9%) and cell wall thickness (1% 17%). The faster growth resulted in only small changes (0% 9%) in lumen diameter and relative lignin content (1% 2%; lignin content was 25.4% 26%). However, the random variation in wood properties was large both between and within trees and annual rings. The results of this thesis indicate that the prevailing thinning and fertilisation treatments of Norway spruce stands in Fennoscandia may significantly enhance the radial increment of individual trees, and cause only small or no detrimental changes in wood and tracheid properties.

Regulation of strawberry growth and development

Strawberries (Fragaria sp.) are adapted to diverse environmental conditions from the tropics to about 70ºN, so different responses to environmental conditions can be found. Most genotypes of garden strawberry (F. x ananassa Duch.) and woodland strawberry (F. vesca L.) are short-day (SD) plants that are induced to flowering by photoperiods under a critical limit, but also various photoperiod x temperature interactions can be found. In addition, continuously flowering everbearing (EB) genotypes are found. In addition to flowering, axillary bud differentiation in strawberry is regulated by photoperiod. In SD conditions, axillary buds differentiate to rosette-like structures called "branch crowns", whereas in long-day conditions (LD) they form runners, branches with 2 long internodes followed by a daughter plant (leaf rosette). The number of crown branches determines the yield of the plant, since inflorescences are formed from the apical meristems of the crown. Although axillary bud differentiation is an important developmental process in strawberries, its environmental and hormonal regulation has not been characterized in detail. Moreover, the genetic mechanisms underlying axillary bud differentiation and regulation of flowering time in these species are almost completely unresolved. These topics have been studied in this thesis in order to enhance strawberry research, cultivation and breeding. The results showed that 8-12 SD cycles suppressed runner initiation from the axillary buds of the garden strawberry cv. Korona with the concomitant induction of crown branching, and 3 weeks of SD was sufficient for the induction of flowering in the main crown. Furthermore, a second SD treatment given a few weeks after the first SD period can be used to induce flowering in the primary branch crowns and to induce the formation of secondary branches. Thus, artificial SD treatments effectively stimulate crown branching, providing one means for the increase of cropping (yield) potential in strawberry. It was also shown by growth regulation applications, quantitave hormone analysis and gene expression analysis that gibberellin (GA) is one of the key signals involved in the photoperiod control of shoot differentiation. The results indicate that photoperiod controls GA activity specifically in axillary buds, thereby determining bud fate. It was further shown that chemical control of GA biosynthesis by prohexadione-calcium can be utilized to prevent excessive runner formation and induce crown branching in strawberry fields. Moreover, ProCa increased berry yield up to 50%, showing that it is an easier and more applicable alternative to artificial SD treatments for controlling strawberry crown development and yield. Finally, flowering gene pathways in Fragaria were explored by searching for homologs of 118 Arabidopsis thaliana flowering-time genes. In total, 66 gene homologs were identified, and they distributed to all known flowering pathways, suggesting the presence of these pathways also in strawberry. Expression analysis of selected genes revealed that the mRNA of putative floral identity gene APETALA1 accumulated in the shoot apex of the EB genotype after the induction of flowering, whereas it was absent in vegetative SD genotype, indicating the usefulness of this gene product as the marker of floral initiation. The present data enables the further exploration of strawberry flowering pathways with genetic transformation, gene mapping and transcriptomics methods.

An overview on the role of Hexanchiformes in marine ecosystems: biology, ecology and conservation status of a primitive order of modern sharks

The large size, high trophic level and wide distribution of Hexanchiformes (cow and frilled sharks) should position this order as important apex predators in coastal and deep-water ecosystems. This review synthesizes available information on Hexanchiformes, including information not yet published, with the purpose of evaluating their conservation status and assessing their ecological roles in the dynamics of marine ecosystems. Comprising six species, this group has a wide global distribution, with members occurring from shallow coastal areas to depths of c. 2500 m. The limited information available on their reproductive biology suggests that they could be vulnerable to overexploitation (e.g. small litter sizes for most species and suspected long gestation periods). Most of the fishing pressure exerted on Hexanchiformes is in the form of commercial by-catch or recreational fishing. Comprehensive stock and impact assessments are unavailable for most species in most regions due to limited information on life history and catch and abundance time series. When hexanchiform species have been commercially harvested, however, they have been unable to sustain targeted fisheries for long periods. The potentially high vulnerability to intense fishing pressure warrants a conservative exploitation of this order until thorough quantitative assessments are conducted. At least some species have been shown to be significant apex predators in the systems they inhabit. Should Hexanchiformes be removed from coastal and deep-water systems, the lack of sympatric shark species that share the same resources suggests no other species would be capable of fulfilling their apex predator role in the short term. This has potential ecosystem consequences such as meso-predator release or trophic cascades. This review proposes some hypotheses on the ecology of Hexanchiformes and their role in ecosystem dynamics, highlighting the areas where critical information is required to stimulate research directions.

Interaction of Gibberellic Acid and Indole-3-acetic Acid in the Growth of Excised Cuscuta Shoot Tips in Vitro1

Gibberellic acid (GA3) induced a marked elongation of 2.5-centimeter shoot tips of Cuscuta chinensis Lamk. cultured in vitro. In terms of the absolute amount of elongation, this growth may be the largest reported for an isolated plant system. The response to hormone was dependent on an exogenous carbohydrate supply. The hormone-stimulated growth was due to both cell division and cell elongation. The growth response progressively decreased if GA3 was given at increasingly later times after culturing, but the decreased growth response could be restored by the application of indole-3-acetic acid (IAA) to the apex. Explants deprived of GA3 gradually lost their ability to transport IAA basipetally, but this ability was also restored by auxin application. The observations are explained on the basis that: (a) the growth of Cuscuta shoot tip in vitro requires, at least, both an auxin and a gibberellin; and (b) in the absence of gibberellin the cultured shoot tip explants lose the ability to produce and/or transport auxin.

Regulating supply chains to protect road transport workers: An early assessment of the road safety remuneration tribunal

The Road Safety Remuneration Act 2012 (Cth) (the Act) explicitly enables the Road Safety Remuneration Tribunal to make orders that can impose binding requirements on all the participants in the road transport supply chain, including consignors and consignees at the apex the chain, for the pay and safety of both employee and independent contractor drivers. The tribunal is also specifically empowered to make enforceable orders to reduce or remove remuneration related incentives and pressures that contribute to unsafe work practices in the road transport industry. Recently the tribunal handed down its first order. The article considers whether, and the degree to which, the tribunal has been willing to exercise its explicit power to impose enforceable obligations on consignors and consignees — such as large supermarket chains — at the apex of road transport supply chains. It examines the substance and extent of the obligations imposed by the tribunal, including whether the tribunal has exercised the full range of powers vested in it by the Act. We contend that the tribunal’s first order primarily imposes obligations on direct work providers and drivers without making large, powerful consignors and consignees substantively responsible for driver pay and safety. We argue that the tribunal’s first order could have more comprehensively fulfilled the objectives of the Act by more directly addressing the root causes of low pay and poor safety in the road transport industry.

Drag reduction by a forward facing aerospike for a large angle blunt cone in high enthalpy flows

Drag reduction studies are conducted using a flat disc tipped aerospike for a 120-degree apex angle blunt cone model in high enthalpy flows. Accelerometer based force balance is used for the drag force measurement in the newly established free piston driven shock tunnel, HST3. Drag reduction upto about 58 percent has been achieved for Mach 8 flow of 5 MJ/kg specific enthalpy at zero degree angle of attack.

Drag reduction by counterflow supersonic jet for a blunt cone in high enthalpy flows

Counterflow supersonic jet is used as a drag reduction device during the experiments in free piston driven shock tunnel, HST3. Accelerometer based force balance is employed to measure the drag force experienced by the 60-degree apex angle blunt cone model without and with the supersonic jet opposing the hypersonic flow. It is observed that the drag force decreases with increase in injection pressure ratio until the critical injection pressure is reached. Maximum reduction in drag force of 44 percent is recorded at the critical injection pressure ratio 22.36. Further increase in injection pressure ratio has reduced the percentage drag reduction. Change in nature of the flowfield around the model has also been observed across the critical injection pressure ratio.

Computational Methods for Locating and Analyzing Conserved Gene Regulatory DNA Elements

This thesis presents methods for locating and analyzing cis-regulatory DNA elements involved with the regulation of gene expression in multicellular organisms. The regulation of gene expression is carried out by the combined effort of several transcription factor proteins collectively binding the DNA on the cis-regulatory elements. Only sparse knowledge of the 'genetic code' of these elements exists today. An automatic tool for discovery of putative cis-regulatory elements could help their experimental analysis, which would result in a more detailed view of the cis-regulatory element structure and function. We have developed a computational model for the evolutionary conservation of cis-regulatory elements. The elements are modeled as evolutionarily conserved clusters of sequence-specific transcription factor binding sites. We give an efficient dynamic programming algorithm that locates the putative cis-regulatory elements and scores them according to the conservation model. A notable proportion of the high-scoring DNA sequences show transcriptional enhancer activity in transgenic mouse embryos. The conservation model includes four parameters whose optimal values are estimated with simulated annealing. With good parameter values the model discriminates well between the DNA sequences with evolutionarily conserved cis-regulatory elements and the DNA sequences that have evolved neutrally. In further inquiry, the set of highest scoring putative cis-regulatory elements were found to be sensitive to small variations in the parameter values. The statistical significance of the putative cis-regulatory elements is estimated with the Two Component Extreme Value Distribution. The p-values grade the conservation of the cis-regulatory elements above the neutral expectation. The parameter values for the distribution are estimated by simulating the neutral DNA evolution. The conservation of the transcription factor binding sites can be used in the upstream analysis of regulatory interactions. This approach may provide mechanistic insight to the transcription level data from, e.g., microarray experiments. Here we give a method to predict shared transcriptional regulators for a set of co-expressed genes. The EEL (Enhancer Element Locator) software implements the method for locating putative cis-regulatory elements. The software facilitates both interactive use and distributed batch processing. We have used it to analyze the non-coding regions around all human genes with respect to the orthologous regions in various other species including mouse. The data from these genome-wide analyzes is stored in a relational database which is used in the publicly available web services for upstream analysis and visualization of the putative cis-regulatory elements in the human genome.

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.