Generalised Sandpile Dynamics on Artificial and Real-World Directed Networks

The main finding of this paper is a novel avalanche-size exponent τ ≈ 1.87 when the generalised sandpile dynamics evolves on the real-world Japanese inter-firm network. The topology of this network is non-layered and directed, displaying the typical bow tie structure found in real-world directed networks, with cycles and triangles. We show that one can move from a strictly layered regular lattice to a more fluid structure of the inter-firm network in a few simple steps. Relaxing the regular lattice structure by introducing an interlayer distribution for the interactions, forces the scaling exponent of the avalanche-size probability density function τ out of the two-dimensional directed sandpile universality class τ = 4/3, into the mean field universality class τ = 3/2. Numerical investigation shows that these two classes are the only that exist on the directed sandpile, regardless of the underlying topology, as long as it is strictly layered. Randomly adding a small proportion of links connecting non adjacent layers in an otherwise layered network takes the system out of the mean field regime to produce non-trivial avalanche-size probability density function. Although these do not display proper scaling, they closely reproduce the behaviour observed on the Japanese inter-firm network.     

Cell division versus cell elongation: the control of radicle elongation during thermoinhibition of Tagetes minuta achenes

Endogenous embryo factors, which act mainly in the radicle, prevent germination in Tagetes minuta at high temperatures. These factors act to prevent cell elongation, which is critical for radicle protrusion under optimal conditions. Once the radicle has emerged both cell elongation and cell division are required for post-germination growth. Germination can be induced at high temperatures by fusicoccin, which rapidly stimulates cell elongation. In addition, priming seeds at 25 °C on polyethylene glycol (PEG) 6000 and mannitol could also induce germination on water at 36 °C, indicating that priming prevents radicle protrusion at a point subsequent to the point of control in thermoinhibited achenes. Flow cytometry studies revealed that DNA synthesis occurs during thermoinhibition and the inhibition of DNA synthesis during this process inhibits subsequent germination on water under optimal conditions, suggesting a protective role for DNA synthesis in thermoinhibited achenes of T. minuta.     

Gender and ecological restoration: time to connect the dots

Although the human dimension of ecological restoration has increasingly been recognized in recent years, the gender dimension thereof remains largely unexplored. This article aims to fill this gap in the literature by providing an overview of the current knowledge on gender and ecological restoration. Our analysis of selected academic literature on ecological restoration revealed that scholars have only marginally addressed gender issues in their publications. However, in restoration practice, various initiatives that highlight the importance of including a women's rights and gender perspective can be found. These initiatives seem to indicate that applying a gender approach to restoration practice creates a double benefit. First, integrating gender considerations into restoration efforts is desirable from a human rights and gender equality perspective. Second, different case studies suggest that integrating gender considerations can promote the efficiency and effectiveness of restoration work. Integrating a social and gender dimension into restoration policy and practice should therefore be recommended. This integration process can learn from a wide range of literature on gender and the environment, and from existing practices of gender mainstreaming in this field. Furthermore, international law provides useful policy intentions on gender and restoration that could be used as entry points. To conclude, this article summarizes the main challenges for “connecting the dots” between gender and ecological restoration and formulates some recommendations for the Society for Ecological Restoration.     

Hormone homeostasis and induction of the small-fruit phenotype in ‘Hass’ avocado

Plant hormones play an important regulatory role in growth and development of fleshy fruits and often these are synthesized in a sequence that is tissue- and/or fruit-specific. Previous studies using Hass avocado and its small-fruit phenotype as a model demonstrated a relationship between the cytokinin/abscisic acid ration and final fruit size. More detailed studies revealed that differential activity of molybdenum-cofactor-containing enzymes was in part responsible for the observed increase in abscisic acid in small Hass fruit and that the same suite of enzymes likely impacted levels of indole-3-acetic acid. The present study confirms that the inability of the seed to produce/accumulate indole-3-acetic acid is a major contributing factor and characteristic of fruit that display a small-fruit phenotype, that reduced indole-3-acetic acid levels occur concomitant with increased abscisic acid, and that cytokinin metabolism appears unchanged irrespective of fruit size. Results are discussed in relation to the role of molybdenum-cofactor-requiring enzymes in indole-3-acetic acid and abscisic acid metabolism.     

Saccharomyces cerevisiae-based molecular tool kit for manipulation of genes from gram-negative bacteria

A tool kit of vectors was designed to manipulate and express genes from a wide range of gram-negative species by using in vivo recombination. Saccharomyces cerevisiae can use its native recombination proteins to combine several amplicons in a single transformation step with high efficiency. We show that this technology is particularly useful for vector design. Shuttle, suicide, and expression vectors useful in a diverse group of bacteria are described and utilized. This report describes the use of these vectors to mutate clpX and clpP of the opportunistic pathogen Pseudomonas aeruginosa and to explore their roles in biofilm formation and surface motility. Complementation of the rhamnolipid biosynthetic gene rhlB is also described. Expression vectors are used for controlled expression of genes in two pseudomonad species. To demonstrate the facility of building complicated constructs with this technique, the recombination of four PCR-generated amplicons in a single step at >80% efficiency into one of these vectors is shown. These tools can be used for genetic studies of pseudomonads and many other gram-negative bacteria.     

BaySTDetect: detecting unusual temporal patterns in small area data via Bayesian model choice

Space-time modeling of small area data is often used in epidemiology for mapping chronic disease rates and by government statistical agencies for producing local estimates of, for example, unemployment or crime rates. Although there is typically a general temporal trend, which affects all areas similarly, abrupt changes may occur in a particular area, e.g. due to emergence of localized predictors/risk factor(s) or impact of a new policy. Detection of areas with "unusual" temporal patterns is therefore important as a screening tool for further investigations. In this paper, we propose BaySTDetect, a novel detection method for short-time series of small area data using Bayesian model choice between two competing space-time models. The first model is a multiplicative decomposition of the area effect and the temporal effect, assuming one common temporal pattern across the whole study region. The second model estimates the time trends independently for each area. For each area, the posterior probability of belonging to the common trend model is calculated, which is then used to classify the local time trend as unusual or not. Crucial to any detection method, we provide a Bayesian estimate of the false discovery rate (FDR). A comprehensive simulation study has demonstrated the consistent good performance of BaySTDetect in detecting various realistic departure patterns in addition to estimating well the FDR. The proposed method is applied retrospectively to mortality data on chronic obstructive pulmonary disease (COPD) in England and Wales between 1990 and 1997 (a) to test a hypothesis that a government policy increased the diagnosis of COPD and (b) to perform surveillance. While results showed no evidence supporting the hypothesis regarding the policy, an identified unusual district (Tower Hamlets in inner London) was later recognized to have higher than national rates of hospital readmission and mortality due to COPD by the National Health Service, which initiated various local enhanced services to tackle the problem. Our method would have led to an early detection of this local health issue.     

Fruit size: Towards an understanding of the metabolic control of fruit growth using avocado as a model system

Final fruit size is the consequence of complex metabolic events that occur between fruit set and maturation. Disruption of these biochemical and molecular processes at any stage during fruit growth will impact on final fruit size. Because fruit size is a function of cell number rather than cell size, factors affecting cell division cycle activity assume importance. In this paper, we focus attention on the metabolic control of fruit growth using avocado as a model system. Three areas of current interest are highlighted, viz. the contribution by isoprenoid metabolism in the control of cell proliferation, the role played by carbohydrate content and composition in signalling changes in metabolite status and gene expression and maintenance of plant hormone homeostasis. Central to the process of fruit growth and control of final fruit size by cell division is 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) and activity of the sucrose non-fermenting 1-related protein kinase (SnRK1) complex. It is argued that sugar content and composition of sink cells impact on SnRK1 (and hexokinase) to modulate expression of sugar-metabolizing enzymes, HMGR and molybdenum cofactor (MoCo)-containing enzymes. These changes, in turn, impact on hormone metabolism by affecting allocation of the purine-derived MoCo to aldehyde oxidase and thus the endogenous concentration of indole-3-acetic acid, abscisic acid and cytokinin (CK) to alter plant hormone homeostasis. These aspects are integrated into a model to explain the metabolic control of avocado fruit growth and final fruit size.     

Tracking elusive cargo: Illuminating spatio‐temporal Type 3 effector protein dynamics using reporters

Type 3 secretion systems form an integral part of the arsenal of many pathogenic bacteria. These injection machines, together with their cargo of subversive effector proteins, are capable of manipulating the cellular environment of the host in order to ensure persistence of the pathogen. In order to fully appreciate the functions of Type 3 effectors, it is necessary to gain spatio‐temporal knowledge of each effector during the process of infection. A number of genetic modifications have been exploited in order to reveal effector protein secretion, translocation and subsequent activity, and localisation within host cells. In this review, we will discuss the many available approaches for tracking effector protein dynamics and discuss the challenges faced to improve the current technologies and gain a clearer picture of effector protein function.