Influence of convex and concave curvatures in a coastal dike line on wave run-up

Due to climatic change and the increased usage of coastal areas, there is an increasing risk of dike failures along the coasts worldwide. Wave run-up plays a key role in the planning and design of a coastal structure. Coastal engineers use empirical equations for the determination of wave run-up. These formulae generally include the influence of various hydraulic, geometrical and structural parameters, but neglect the effect of the curvature of coastal dikes on wave run-up and overtopping. The scope of this research is to find the effects of the dike curvature on wave run-up for regular wave attack by employing numerical model studies for various dike-opening angles and comparing it with physical model test results. A numerical simulation is carried out using DualSPHysics, a mesh-less model and OpenFOAM, a mesh-based model. A new influence factor is introduced to determine the influence of curvature along a dike line. For convexly curved dikes (ad = 210° to 270°) under perpendicular wave attack, a higher wave run-up was observed for larger opening angles at the center of curvature whereas for concavely curved dikes (ad = 90° to 150°) under perpendicular wave attack, wave run-up increases at the center of curvature as the opening angle decreases. This research aims to contribute a more precise analysis and understanding the influence of the curvature in a dike line and thus ensuring a higher level of protection in the future development of coastal structures.Peer ReviewedPostprint (published version

Early nodulins in root nodule development

The symbiotic interaction between bacteria of the genus Rhizobium and leguminous plants leads to the formation of root nodules, which are specific nitrogen-fixing organs on the roots of plants. Bacteria enter the root by infection threads, and concomitantly cell divisons are induced in the root cortex, which lead to the formation of a meristern. From this meristern the different tissues of the root nodule originate. In the nodule bacteria are released in plant cells and then differentiate into the endosymbiotic bacteroids. These bacteroids are capable of nitrogen fixation.The formation of root nodules involves expression of both bacterial and plant genes. Rhizobium genes involved in nodule formation are the nodulation ( nod ) genes. Nodulespecific plant genes are termed nodulin genes. According to their timing of expression they can be divided into early and late nodulin genes. Early nodulin genes are expressed well before the onset of nitrogen fixation, at the time that the nodule tissue is formed and the roots become infected by bacteria, while expression of late nodulin genes starts shortly before the onset of nitrogen fixation, when the nodule structure has been formed. Therefore only early nodulins can be involved in the infection process and in nodule development. Early nodulin genes expressed during the pea ( Pisum sativum L.) - Rhizobium leguminosarum bv. viciae interaction are the subject of this thesis. Several cDNA clones representing pea early nodulin genes have been isolated and they have been used to study root nodule development and the communication between bacteria and host plant.In chapter 2 we review general aspects of plant development. Recent progresses in understanding the molecular mechanisms underlying animal development are listed, and the possible significance of such mechanisms for plant development is discussed. The features of the root nodule formation system that make it suitable to study particular questions on the molecular basis of plant development are put forward.In chapter 3 the pea early nodulin cDNA clone pPsENOD2 is characterized. The nature of the encoded polypeptide is compared with that of the soybean early nodulin described before. ENOD2 transcripts are localized both in pea and soybean root nodules throughout successive stages of development by in situ hybridization. Data on the primary structure of the ENOD2 protein and localization data are then combined to hypothesise that the function of this early nodulin is to create an oxygen barrier in the root nodule.In chapter 4 the early nodulin ENOD12 is described. The spatial distribution of the corresponding transcript throughout root nodule development is depicted to demonstrate the involvement of ENOD12 in the infection process. We describe the primary structure of the ENOD12 protein and we examine whether ENOD12 gene expression is related to a defense respons. Using a sensitive detection method based on the polymerase chain reaction (PCR) we demonstrate that ENOD12 gene expression is induced by excreted Rhizobium factors and that bacterial nod genes are involved. ENOD12 transcripts found in flower and stem tissue are compared to the ENOD12 mRNAs in nodules using, among other techniques, a novel adaptation of RNase mapping to determine whether the same genes are expressed in these different tissues or not.In chapter 5 it is demonstrated that the accumulation pattern of the transcripts corresponding to the pPsENOD5, pPsENOD3 and pPsENOD14 cDNA clones differs from that of ENOD2 and ENOD12 mRNA. The distribution of the former three transcripts is compared with the distribution of ENOD12 mRNA and the late nodulin leghemoglobin transcript. It is shown that the different transcripts are present at successive stages of development of the infected cell type. The primary structure of the ENOD5, ENOD3 and ENOD14 early nodulins is determined and these data are combined with the localization data of the transcripts to speculate on functions of these proteins, The involvement of different factors to induce expression of different early and late nodulin genes is discussed.In chapter 6 the results described in the previous three chapters are summarized and some additional data on early nodulins are presented. The significance of the availability of early nodulin gene probes to elucidate the mechanisms of communication between rhizobia and legumes, which underly the process of root nodule formation, is discussed. Finally, in chapter 7, the value of the obtained information on early nodulins for studying both specific and general aspects of root nodule development is discussed

Which executive functioning deficits are associated with AD/HD, ODD/CD and comorbid AD/HD+ODD/CD?

Item does not contain fulltextThis study investigated (1) whether attention deficit/hyperactivity disorder (AD/HD) is associated with executive functioning (EF) deficits while controlling for oppositional defiant disorder/conduct disorder (ODD/CD), (2) whether ODD/CD is associated with EF deficits while controlling for AD/HD, and (3)~whether a combination of AD/HD and ODD/CD is associated with EF deficits (and the possibility that there is no association between EF deficits and AD/HD or ODD/CD in isolation). Subjects were 99~children ages 6–12 years. Three putative domains of EF were investigated using well-validated tests: verbal fluency, working memory, and planning. Independent of ODD/CD, AD/HD was associated with deficits in planning and working memory, but not in verbal fluency. Only teacher rated AD/HD, but not parent rated AD/HD, significantly contributed to the prediction of EF task performance. No EF deficits were associated with ODD/CD. The presence of comorbid AD/HD accounts for the EF deficits in children with comorbid AD/HD+ODD/CD. These results suggest that EF deficits are unique to AD/HD and support the model proposed by R. A. Barkley (1997).17 p

Structural insights into RNA processing by the human RISC-loading complex.

Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC). In humans, Argonaute2 (AGO2) assembles with the guide RNA-generating enzyme Dicer and the RNA-binding protein TRBP to form a RISC-loading complex (RLC), which is necessary for efficient transfer of nascent siRNAs and miRNAs from Dicer to AGO2. Here, using single-particle EM analysis, we show that human Dicer has an L-shaped structure. The RLC Dicer's N-terminal DExH/D domain, located in a short 'base branch', interacts with TRBP, whereas its C-terminal catalytic domains in the main body are proximal to AGO2. A model generated by docking the available atomic structures of Dicer and Argonaute homologs into the RLC reconstruction suggests a mechanism for siRNA transfer from Dicer to AGO2

Quaternary structure of the specific p53-DNA complex reveals the mechanism of p53 mutant dominance

The p53 tumour suppressor is a transcriptional activator that controls cell fate in response to various stresses. p53 can initiate cell cycle arrest, senescence and/or apoptosis via transactivation of p53 target genes, thus preventing cancer onset. Mutations that impair p53 usually occur in the core domain and negate the p53 sequence-specific DNA binding. Moreover, these mutations exhibit a dominant negative effect on the remaining wild-type p53. Here, we report the cryo electron microscopy structure of the full-length p53 tetramer bound to a DNA-encoding transcription factor response element (RE) at a resolution of 21 Å. While two core domains from both dimers of the p53 tetramer interact with DNA within the complex, the other two core domains remain available for binding another DNA site. This finding helps to explain the dominant negative effect of p53 mutants based on the fact that p53 dimers are formed co-translationally before the whole tetramer assembles; therefore, a single mutant dimer would prevent the p53 tetramer from binding DNA. The structure indicates that the Achilles’ heel of p53 is in its dimer-of-dimers organization, thus the tetramer activity can be negated by mutation in only one allele followed by tumourigenesis

Mechanism of eIF6 release from the nascent 60S ribosomal subunit.

SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eIF6 from nascent 60S ribosomal subunits. However, the mechanism is completely unknown. Here, we present cryo-EM structures of human SBDS and SBDS-EFL1 bound to Dictyostelium discoideum 60S ribosomal subunits with and without endogenous eIF6. SBDS assesses the integrity of the peptidyl (P) site, bridging uL16 (mutated in T-cell acute lymphoblastic leukemia) with uL11 at the P-stalk base and the sarcin-ricin loop. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit. Our data reveal the conserved mechanism of eIF6 release, which is corrupted in both inherited and sporadic leukemias.Supported by a Federation of European Biochemical Societies Long term Fellowship (to FW), Specialist Programme from Bloodwise [12048] (AJW), the Medical Research Council [MC_U105161083] (AJW) and [U105115237] (RRK), Wellcome Trust strategic award to the Cambridge Institute for Medal Research [100140], Tesni Parry Trust (AJW), Ted’s Gang (AJW) and the Cambridge NIHR Biomedical Research Centre.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nsmb.311

Molecular basis of caspase-1 polymerization and its inhibition by a new capping mechanism

Inflammasomes are cytosolic caspase-1-activation complexes that sense intrinsic and extrinsic danger signals, and trigger inflammatory responses and pyroptotic cell death. Homotypic interactions among Pyrin domains and caspase recruitment domains (CARDs) in inflammasome-complex components mediate oligomerization into filamentous assemblies. Several cytosolic proteins consisting of only interaction domains exert inhibitory effects on inflammasome assembly. In this study, we determined the structure of the human caspase-1 CARD domain (caspase-1[superscript CARD]) filament by cryo-electron microscopy and investigated the biophysical properties of two caspase-1-like CARD-only proteins: human inhibitor of CARD (INCA or CARD17) and ICEBERG (CARD18). Our results reveal that INCA caps caspase-1 filaments, thereby exerting potent inhibition with low-nanomolar K[subscript i] on caspase-1[superscript CARD] polymerization in vitro and inflammasome activation in cells. Whereas caspase-1[superscript CARD] uses six complementary surfaces of three types for filament assembly, INCA is defective in two of the six interfaces and thus terminates the caspase-1 filament

Structural basis of signal sequence surveillance and selection by the SRP–FtsY complex

Signal-recognition particle (SRP)-dependent targeting of translating ribosomes to membranes is a multistep quality-control process. Ribosomes that are translating weakly hydrophobic signal sequences can be rejected from the targeting reaction even after they are bound to the SRP. Here we show that the early complex, formed by Escherichia coli SRP and its receptor FtsY with ribosomes translating the incorrect cargo EspP, is unstable and rearranges inefficiently into subsequent conformational states, such that FtsY dissociation is favored over successful targeting. The N-terminal extension of EspP is responsible for these defects in the early targeting complex. The cryo-electron microscopy structure of this 'false' early complex with EspP revealed an ordered M domain of SRP protein Ffh making two ribosomal contacts, and the NG domains of Ffh and FtsY forming a distorted, flexible heterodimer. Our results provide a structural basis for SRP-mediated signal-sequence selection during recruitment of the SRP receptor

Interference control in children with attention deficit/hyperactivity disorder

The view that Attention Deficit/Hyperactivity Disorder (ADHD) is associated with a diminished ability to control interfference is controversial and based exclusively on results of (verbal)-visual interference tasks, primarily the Stroop Color Word task. The present study compares medication-naïve children with ADHD (n∈=∈35 and n∈=∈51 in Experiments 1 and 2, respectively) with normal controls (n∈=∈26 and n∈=∈32, respectively) on two interference tasks to assess interference control in both the auditory and the visual modality: an Auditory Stroop task and a Simon task. Both groups showed reliable but equal degrees of interference on both tasks, suggesting that children with ADHD do not differ from normal controls in their ability to control interference in either modality. © 2008 The Author(s)

Risk-taking, delay discounting, and time perspective in adolescent gamblers: an experimental study

Previous research has demonstrated that adult pathological gamblers (compared to controls) show risk-proneness, foreshortened time horizon, and preference for immediate rewards. No study has ever examined the interplay of these factors in adolescent gambling. A total of 104 adolescents took part in the research. Two equal-number groups of adolescent non-problem and problem gamblers, defined using the South Oaks Gambling Screen-Revised for Adolescents (SOGS-RA), were administered the Balloon Analogue Risk Task (BART), the Consideration of Future Consequences (CFC-14) Scale, and the Monetary Choice Questionnaire (MCQ). Adolescent problem gamblers were found to be more risk-prone, more oriented to the present, and to discount delay rewards more steeply than adolescent non-problem gamblers. Results of logistic regression analysis revealed that BART, MCQ, and CFC scores predicted gambling severity. These novel finding provides the first evidence of an association among problematic gambling, high risk-taking proneness, steep delay discounting, and foreshortened time horizon among adolescents. It may be that excessive gambling induces shortsighted behaviors that, in turn, facilitate gambling involvement