Comparative analysis of somitogenesis related genes of the hairy/Enhancer of split class in Fugu and zebrafish

BACKGROUND: Members of a class of bHLH transcription factors, namely the hairy (h), Enhancer of split (E(spl)) and hairy-related with YRPW motif (hey) (h/E(spl)/hey) genes are involved in vertebrate somitogenesis and some of them show cycling expression. By sequence comparison, identified orthologues of cycling somitogenesis genes from higher vertebrates do not show an appropriate expression pattern in zebrafish. The zebrafish genomic sequence is not available yet but the genome of Fugu rubripes was recently published. To allow comparative analysis, the currently known Her proteins from zebrafish were used to screen the genomic sequence database of Fugu rubripes. RESULTS: 20 h/E(spl)/hey-related genes were identified in Fugu, which is twice the number of corresponding zebrafish genes known so far. A novel class of c-Hairy proteins was identified in the genomes of Fugu and Tetraodon. A screen of the human genome database with the Fugu proteins yielded 10 h/E(spl)/hey-related genes. By analysing the upstream sequences of the c-hairy class genes in zebrafish, Fugu and Tetraodon highly similar sequence stretches were identified that harbour Suppressor of hairless paired binding sites (SPS). This motif was also discovered in the upstream sequences of the her1 gene in the examined fish species. Here, the Su(h) sites are separated by longer intervening sequences. CONCLUSIONS: Our study indicates that not all her homologues in zebrafish have been isolated. Comparison to the human genome suggests a selective duplication of h/E(spl) genes in pufferfish or loss of members of these genes during evolution to the human lineage

Mechanism of polarization of Listeria monocytogenes surface protein ActA

The polar distribution of the ActA protein on the surface of the Gram-positive intracellular bacterial pathogen, Listeria monocytogenes, is required for bacterial actin-based motility and successful infection. ActA spans both the bacterial membrane and the peptidoglycan cell wall. We have directly examined the de novo ActA polarization process in vitro by using an ActA–RFP (red fluorescent protein) fusion. After induction of expression, ActA initially appeared at distinct sites along the sides of bacteria and was then redistributed over the entire cylindrical cell body through helical cell wall growth. The accumulation of ActA at the bacterial poles displayed slower kinetics, occurring over several bacterial generations. ActA accumulated more efficiently at younger, less inert poles, and proper polarization required an optimal balance between protein secretion and bacterial growth rates. Within infected host cells, younger generations of L. monocytogenes initiated motility more quickly than older ones, consistent with our in vitro observations of de novo ActA polarization. We propose a model in which the polarization of ActA, and possibly other Gram-positive cell wall-associated proteins, may be a direct consequence of the differential cell wall growth rates along the bacterium and dependent on the relative rates of protein secretion, protein degradation and bacterial growth

Keep them alive! Design and Evaluation of the “Community Fostering Reference Model”

Firms host online communities for commercial purposes, for example in order to integrate customers into ideation for new product development. The success of these firm-hosted online communities depends entirely on the cooperation of a high number of customers that constantly produce valuable knowledge for firms. However, in practice, the majority of successfully implemented communities suffers from stagnation and even a decrease of member activities over time. Literature provides numerous guidelines on how to build and launch these online communities. While these models describe the initial steps of acquiring and activating a community base from scratch very well and explicitly, they neglect continuous member activation and acquistion after a successful launch. Against this background, the authors propose the Community Fostering Reference Model (CoFoRM), which represents a set of general procedures and instruments to continuously foster member activity. In this paper, the authors present the theory-driven design as well as the evaluation of the CoFoRM in a practical use setting. The evaluation results reveal that the CoFoRM represents a valuable instrument in the daily working routine of community managers, since it efficiently helps activating community members especially in the late phases of a community’s LifeCycle

Longest Common Prefixes with kk-Errors and Applications

Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we study the problem of computing the longest prefix of each suffix of a given string of length $n$ over a constant-sized alphabet that occurs elsewhere in the string with $k$-errors. This problem has already been studied under the Hamming distance model. Our first result is an improvement upon the state-of-the-art average-case time complexity for non-constant $k$ and using only linear space under the Hamming distance model. Notably, we show that our technique can be extended to the edit distance model with the same time and space complexities. Specifically, our algorithms run in $\mathcal{O}(n \log^k n \log \log n)$ time on average using $\mathcal{O}(n)$ space. We show that our technique is applicable to several algorithmic problems in computational biology and elsewhere

An exploration of the determinants for decision to migrate existing resources to cloud computing using an integrated TOE-DOI model

Migrating existing resources to cloud computing is a strategic organisational decision that can be difficult. It requires the consideration and evaluation of a wide range of technical and organisational aspects. Although a significant amount of attention has been paid by many industrialists and academics to aid migration decisions, the procedure remains difficult. This is mainly due to underestimation of the range of factors and characteristics affecting the decision for cloud migration. Further research is needed to investigate the level of effect these factors have on migration decisions and the overall complexity. This paper aims to explore the level of complexity of the decision to migrate the cloud. A research model based on the diffusion of innovation (DOI) theory and the technology-organization-environment (TOE) framework was developed. The model was tested using exploratory and confirmatory factor analysis. The quantitative analysis shows the level of impact of the identified variables on the decision to migrate. Seven determinants that contribute to the complexity of the decisions are identified. They need to be taken into account to ensure successful migration. This result has expanded the collective knowledge about the complexity of the issues that have to be considered when making decisions to migrate to the cloud. It contributes to the literature that addresses the complex and multidimensional nature of migrating to the cloud

OC6 Phase I: Investigating the underprediction of low-frequency hydrodynamic loads and responses of a floating wind turbine

Phase I of the OC6 project is focused on examining why offshore wind design tools underpredict the response (loads/motion) of the OC5-DeepCwind semisubmersible at its surge and pitch natural frequencies. Previous investigations showed that the underprediction was primarily related to nonlinear hydrodynamic loading, so two new validation campaigns were performed to separately examine the different hydrodynamic load components. In this paper, we validate a variety of tools against this new test data, focusing on the ability to accurately model the low-frequency loads on a semisubmersible floater when held fixed under wave excitation and when forced to oscillate in the surge direction. However, it is observed that models providing better load predictions in these two scenarios do not necessarily produce a more accurate motion response in a moored configuration.The authors would like to acknowledge the support of the MARINET2 project (European Union’s Horizon 2020 grant agreement 731084), which supplied the tank test time and travel support to accomplish the testing campaign. The support of MARIN in the preparation, execution of the modeltests, and the evaluation of the uncertainties was essential for this study. MARIN’s contribution was partly funded by the Dutch Ministry of Economic Affairs through TKI-ARD funding programs. This work was authored in part by the National Renewable Energy Laboratory, operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36- 08GO28308. Funding provided by the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Wind Energy Technologies Office. The views expressed in the article do not necessarily represent the views of the DOE or the U.S. Government. The U.S. Government retains and the publisher, by accepting the article for publication, acknowledges that the U.S. Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this work, or allow others to do so, for U.S. Government purposes

Conditional Ablation of Ezh2 in Murine Hearts Reveals Its Essential Roles in Endocardial Cushion Formation, Cardiomyocyte Proliferation and Survival

Ezh2 is a histone trimethyltransferase that silences genes mainly via catalyzing trimethylation of histone 3 lysine 27 (H3K27Me3). The role of Ezh2 as a regulator of gene silencing and cell proliferation in cancer development has been extensively investigated; however, its function in heart development during embryonic cardiogenesis has not been well studied. In the present study, we used a genetically modified mouse system in which Ezh2 was specifically ablated in the mouse heart. We identified a wide spectrum of cardiovascular malformations in the Ezh2 mutant mice, which collectively led to perinatal death. In the Ezh2 mutant heart, the endocardial cushions (ECs) were hypoplastic and the endothelial-to-mesenchymal transition (EMT) process was impaired. The hearts of Ezh2 mutant mice also exhibited decreased cardiomyocyte proliferation and increased apoptosis. We further identified that the Hey2 gene, which is important for cardiomyocyte proliferation and cardiac morphogenesis, is a downstream target of Ezh2. The regulation of Hey2 expression by Ezh2 may be independent of Notch signaling activity. Our work defines an indispensible role of the chromatin remodeling factor Ezh2 in normal cardiovascular development

Somitogenesis Clock-Wave Initiation Requires Differential Decay and Multiple Binding Sites for Clock Protein

Somitogenesis is a process common to all vertebrate embryos in which repeated blocks of cells arise from the presomitic mesoderm (PSM) to lay a foundational pattern for trunk and tail development. Somites form in the wake of passing waves of periodic gene expression that originate in the tailbud and sweep posteriorly across the PSM. Previous work has suggested that the waves result from a spatiotemporally graded control protein that affects the oscillation rate of clock-gene expression. With a minimally constructed mathematical model, we study the contribution of two control mechanisms to the initial formation of this gene-expression wave. We test four biologically motivated model scenarios with either one or two clock protein transcription binding sites, and with or without differential decay rates for clock protein monomers and dimers. We examine the sensitivity of wave formation with respect to multiple model parameters and robustness to heterogeneity in cell population. We find that only a model with both multiple binding sites and differential decay rates is able to reproduce experimentally observed waveforms. Our results show that the experimentally observed characteristics of somitogenesis wave initiation constrain the underlying genetic control mechanisms