Sphingosine Phosphate Lyase Expression Is Essential for Normal Development in Caenorhabditis elegans

Sphingolipids are ubiquitous membrane constituents whose metabolites function as signaling molecules in eukaryotic cells. Sphingosine 1-phosphate, a key sphingolipid second messenger, regulates proliferation, motility, invasiveness, and programmed cell death. These effects of sphingosine 1-phosphate and similar phosphorylated sphingoid bases have been observed in organisms as diverse as yeast and humans. Intracellular levels of sphingosine 1-phosphate are tightly regulated by the actions of sphingosine kinase, which is responsible for its synthesis and sphingosine-1-phosphate phosphatase and sphingosine phosphate lyase, the two enzymes responsible for its catabolism. In this study, we describe the cloning of the Caenorhabditis elegans sphingosine phosphate lyase gene along with its functional expression in Saccharomyces cerevisiae. Promoter analysis indicates tissue-specific and developmental regulation of sphingosine phosphate lyase gene expression. Inhibition of C. elegans sphingosine phosphate lyase expression by RNA interference causes accumulation of phosphorylated and unphosphorylated long-chain bases and leads to poor feeding, delayed growth, reproductive abnormalities, and intestinal damage similar to the effects seen with exposure to Bacillus thuringiensis toxin. Our results show that sphingosine phosphate lyase is an essential gene in C. elegans and suggest that the sphingolipid degradative pathway plays a conserved role in regulating animal development

Parallel Metric Tree Embedding based on an Algebraic View on Moore-Bellman-Ford

A \emph{metric tree embedding} of expected \emph{stretch~$\alpha \geq 1$} maps a weighted $n$-node graph $G = (V, E, \omega)$ to a weighted tree $T = (V_T, E_T, \omega_T)$ with $V \subseteq V_T$ such that, for all $v,w \in V$, $\operatorname{dist}(v, w, G) \leq \operatorname{dist}(v, w, T)$ and $operatorname{E}[\operatorname{dist}(v, w, T)] \leq \alpha \operatorname{dist}(v, w, G)$. Such embeddings are highly useful for designing fast approximation algorithms, as many hard problems are easy to solve on tree instances. However, to date the best parallel $(\operatorname{polylog} n)$-depth algorithm that achieves an asymptotically optimal expected stretch of $\alpha \in \operatorname{O}(\log n)$ requires $\operatorname{\Omega}(n^2)$ work and a metric as input. In this paper, we show how to achieve the same guarantees using $\operatorname{polylog} n$ depth and $\operatorname{\tilde{O}}(m^{1+\epsilon})$ work, where $m = |E|$ and $\epsilon > 0$ is an arbitrarily small constant. Moreover, one may further reduce the work to $\operatorname{\tilde{O}}(m + n^{1+\epsilon})$ at the expense of increasing the expected stretch to $\operatorname{O}(\epsilon^{-1} \log n)$. Our main tool in deriving these parallel algorithms is an algebraic characterization of a generalization of the classic Moore-Bellman-Ford algorithm. We consider this framework, which subsumes a variety of previous "Moore-Bellman-Ford-like" algorithms, to be of independent interest and discuss it in depth. In our tree embedding algorithm, we leverage it for providing efficient query access to an approximate metric that allows sampling the tree using $\operatorname{polylog} n$ depth and $\operatorname{\tilde{O}}(m)$ work. We illustrate the generality and versatility of our techniques by various examples and a number of additional results

Regulation of Sphingosine-1-phosphate Lyase Gene Expression by Members of the GATA Family of Transcription Factors

Sphingosine-1-phosphate is a bioactive sphingolipid that regulates proliferation, differentiation, migration, and apoptosis. Sphingosine-1-phosphate is irreversibly degraded by the highly conserved enzyme sphingosine-1-phosphate lyase. Recent studies have suggested that sphingosine-1-phosphate lyase expression affects animal development and cell fate decisions. Despite its crucial role, mechanisms affecting expression of sphingosine-1-phosphate lyase remain poorly understood. In this study, regulation of sphingosine-1-phosphate lyase gene expression was investigated in Caenorhabditis elegans, where lyase expression is spatially restricted to cells of the developing and adult gut and is essential for normal development. Deletion analysis and generation of transgenic worms combined with fluorescence microscopy identified a 350-nucleotide sequence upstream of the ATG start site necessary for maximal lyase expression in adult worms. Site-specific mutagenesis of a GATA transcription factor-binding motif in the promoter led to loss of reporter expression. Knockdown of the gut-specific GATA transcription factor ELT-2 by RNA interference similarly led to loss of reporter expression. ELT-2 interacted with the GATA factor-binding motif in vitro and was also capable of driving expression of a Caenorhabditis elegans lyase promoter-{beta}-galactosidase reporter in a heterologous yeast system. These studies demonstrate that ELT-2 regulates sphingosine-1-phosphate lyase expression in vivo. Additionally, we demonstrate that the human sphingosine-1-phosphate lyase gene is regulated by a GATA transcription factor. Overexpression of GATA-4 led to both an increase in activity of a reporter gene as well as an increase in endogenous sphingosine-1-phosphate lyase protein

Protein engineering of Pseudomonas fluorescens peroxidase Dyp1B for oxidation of phenolic and polymeric lignin substrates

Directed evolution was applied to dye-decolourizing peroxidase Dyp1B from Pseudomonas fluorescens Pf-5, in order to enhance the activity for oxidation of phenolic and lignin substrates. Saturation mutagenesis was used to generate focused libraries at 7 active site residues in the vicinity of the heme cofactor, and the libraries were screened for activity towards 2,6-dichlorophenol. Mutants N193 L and H169 L were found to show 7–8 fold enhanced kcat/KM towards DCP, and replacements at Val205 and Ala209 also showed enhanced activity towards alkali Kraft lignin. Residues near the predicted Mn(II) binding site were also investigated by site-directed mutagenesis, and mutants S223 N and H127R showed 4-7-fold increased kcat/KM for Mn(II) oxidation. Mutant F128R also showed enhanced thermostability, compared to wild-type Dyp1B. Testing of mutants for low molecular weight product release from Protobind alkali lignin revealed that mutant H169 L showed enhanced product release, compared with WT enzyme, and the formation of three low molecular weight metabolites by this mutant was detected by reverse phase HPLC analysis

Interval type-2 intuitionistic fuzzy logic systems - a comparative evaluation

Several fuzzy modeling techniques have been employed for handling uncertainties in data. This study presents a comparative evaluation of a new class of interval type-2 fuzzy logic system (IT2FLS) namely: interval type-2 intuitionistic fuzzy logic system (IT2IFLS) of Takagi Sugeno-Kang (TSK)-type with classical IT2FLS and its type-1 variant (IFLS). Simulations are conducted using a real-world gas compression system (GCS) dataset. Study shows that the performance of the proposed framework with membership functions (MFs) and non-membership functions (NMFs) that are each intervals is superior to classical IT2FLS with only MFs (upper and lower) and IFLS with MFs and NMFs that are not intervals in this problem domain