Along-the-channel modeling and analysis of PEFCs at low stoichiometry: Development of a 1+2D model

Water management remains a key challenge in polymer-electrolyte fuel cells. In this work, a pseudo 3-D (1+2D) model is developed to account better for changes of water management along the channel, as well as verify the possibilities of using differential cells for data capture and translation to integral cell performance. An accurate 2-D membrane-electrode-assembly model is developed for differential cell modeling, which is combined with an along-the-channel stepping algorithm to account for down the channel changes in pressure, temperature, reactant concentration, and relative humidity. Variations in cell performance along the channel due to changes in operating conditions are characterized quantitatively and optimized, where drier feed conditions demonstratively require such an approach. Overall, the study identifies gaps between differential and integral cells including those related to flow velocity and highlights the need for better models to understand and link integral cell performance and water management

Self-assembly mechanism in colloids: perspectives from Statistical Physics

Motivated by recent experimental findings in chemical synthesis of colloidal particles, we draw an analogy between self-assembly processes occurring in biological systems (e.g. protein folding) and a new exciting possibility in the field of material science. We consider a self-assembly process whose elementary building blocks are decorated patchy colloids of various types, that spontaneously drive the system toward a unique and predetermined targeted macroscopic structure. To this aim, we discuss a simple theoretical model -- the Kern-Frenkel model -- describing a fluid of colloidal spherical particles with a pre-defined number and distribution of solvophobic and solvophilic regions on their surface. The solvophobic and solvophilic regions are described via a short-range square-well and a hard-sphere potentials, respectively. Integral equation and perturbation theories are presented to discuss structural and thermodynamical properties, with particular emphasis on the computation of the fluid-fluid (or gas-liquid) transition in the temperature-density plane. The model allows the description of both one and two attractive caps, as a function of the fraction of covered attractive surface, thus interpolating between a square-well and a hard-sphere fluid, upon changing the coverage. By comparison with Monte Carlo simulations, we assess the pros and the cons of both integral equation and perturbation theories in the present context of patchy colloids, where the computational effort for numerical simulations is rather demanding.Comment: 14 pages, 7 figures, Special issue for the SigmaPhi2011 conferenc

Assembly, trafficking and function of gamma-secretase

gamma-Secretase catalyzes the final cleavage of the beta-amyloid precursor protein to generate amyloid-beta peptide, the principal component of amyloid plaques in the brains of patients suffering from Alzheimer's disease. Here, we review the identification of gamma-secretase as a protease complex and its assembly and trafficking to its site(s) of cellular function. In reconstitution experiments, gamma-secretase was found to be composed of four integral membrane proteins, presenilin (PS), nicastrin (NCT), PEN-2 and APH-1 that are essential and sufficient for gamma-secretase activity. PS, which serves as a catalytic subunit of gamma-secretase, was identified as a prototypic member of novel aspartyl proteases of the GxGD type. In human cells, gamma-secretase could be further defined as a heterogeneous activity consisting of distinct complexes that are composed of PS1 or PS2 and APH-1a or APH-1b homologues together with NCT and PEN-2. Using green fluorescent protein as a reporter we localized PS and gamma-secretase activity at the plasma membrane and endosomes. Investigation of gamma-secretase complex assembly in knockdown and knockout cells of the individual subunits allowed us to develop a model of complex assembly in which NCT and APH-1 first stabilize PS before PEN-2 assembles as the last component. Furthermore, we could map domains in PS and PEN-2 that govern assembly and trafficking of the complex. Finally, Rer1 was identified as a PEN-2-binding protein that serves a role as an auxiliary factor for gamma-secretase complex assembly. Copyright (c) 2006 S. Karger AG, Basel

Biochemical analysis of TssK, a core component of the bacterial Type VI secretion system, reveals distinct oligomeric states of TssK and identifies a TssK–TssFG subcomplex

Gram-negative bacteria use the Type VI secretion system (T6SS) to inject toxic proteins into rival bacteria or eukaryotic cells. However, the mechanism of the T6SS is incompletely understood. In the present study, we investigated a conserved component of the T6SS, TssK, using the antibacterial T6SS of Serratia marcescens as a model system. TssK was confirmed to be essential for effector secretion by the T6SS. The native protein, although not an integral membrane protein, appeared to localize to the inner membrane, consistent with its presence within a membrane-anchored assembly. Recombinant TssK purified from S. marcescens was found to exist in several stable oligomeric forms, namely trimer, hexamer and higher-order species. Native-level purification of TssK identified TssF and TssG as interacting proteins. TssF and TssG, conserved T6SS components of unknown function, were required for T6SS activity, but not for correct localization of TssK. A complex containing TssK, TssF and TssG was subsequently purified in vitro, confirming that these three proteins form a new subcomplex within the T6SS. Our findings provide new insight into the T6SS assembly, allowing us to propose a model whereby TssK recruits TssFG into the membrane-associated T6SS complex and different oligomeric states of TssK may contribute to the dynamic mechanism of the system

Functional modelling in evolvable assembly systems

The design and reconfiguration of adaptive production systems is a key driver in modern advanced manufacturing. We summarise the use of an ap-proach from the field of functional modelling to capture the function, behaviour, and structure of a system. This model is an integral part of the Evolvable Assembly Systems architecture, allowing the system to adapt its behaviour in response to changing product requirements. The integrated approach is illustrated with an example taken from a real EAS instantiation

Genomic organization, expression analysis, and chromosomal localization of the mouse PEX3 gene encoding a peroxisomal assembly protein

The peroxin Pex3p has been identified as an integral peroxisomal membrane protein in yeast where pex3 mutants lack peroxisomal remnant structures. Although not proven in higher organisms, a role of this gene in the early peroxisome biogenesis is suggested, We report here the cDNA cloning and the genomic structure of the mouse PEX3 gene. The 2 kb cDNA encodes a polypeptide of 372 amino acids (42 kDa). The gene spans a region of 30 kb, contains 12 exons and 11 introns and is located on band A of chromosome 10, The putative promoter region exhibits characteristic housekeeping features. PEX3 expression was identified in all tissues analyzed, with the strongest signals in liver and in testis, and could not be induced by fenofibrate. The data presented may be useful for the generation of a mouse model defective in PEX3 in order to clarify the yet unknown functional impact of disturbances in early peroxisomal membrane assembly

k mer

Motivation: De novo transcriptome assembly is an integral part for many RNA-seq workflows. Common applications include sequencing of non-model organisms, cancer or meta transcriptomes. Most de novo transcriptome assemblers use the de Bruijn graph (DBG) as the underlying data structure. The quality of the assemblies produced by such assemblers is highly influenced by the exact word length k. As such no single kmer value leads to optimal results. Instead, DBGs over different kmer values are built and the assemblies are merged to improve sensitivity. However, no studies have investigated thoroughly the problem of automatically learning at which kmer value to stop the assembly. Instead a suboptimal selection of kmer values is often used in practice. Results: Here we investigate the contribution of a single kmer value in a multi-kmer based assembly approach. We find that a comparative clustering of related assemblies can be used to estimate the importance of an additional kmer assembly. Using a model fit based algorithm we predict the kmer value at which no further assemblies are necessary. Our approach is tested with different de novo assemblers for datasets with different coverage values and read lengths. Further, we suggest a simple post processing step that significantly improves the quality of multi-kmer assemblies. Conclusion: We provide an automatic method for limiting the number of kmer values without a significant loss in assembly quality but with savings in assembly time. This is a step forward to making multi-kmer methods more reliable and easier to use. Availability and Implementation:A general implementation of our approach can be found under: https://github.com/SchulzLab/KREATION. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: [email protected]

Analysis of the effect of genetic heterogeneity on de novo genome assembly using Xylocopa virginica as a model.

Next generation sequencing (NGS) technology has revolutionized genomic and genetic research, and as a result, de novo genome sequencing and assembly for non-model organisms has now become a common task in genome research. However, the integral properties of a genome such as ploidy, mutations, and repeat content impose issues for current genome assemblers. In this work, we used Xylocopa virginica (Eastern carpenter bees) as a unique model organism for examining on the effect of sequence heterozygosity on quality of de novo genome assembly. Using two de Bruijn graph genome assemblers, we assembled four bee genomes representing different sex and age (unworn male, worn male, unworn female, worn female) using standard Illumina sequencing and one genome using 10X linked-reads library for an unworn female. We discovered that there is a noticeable difference in a variety of genome assembly quality metrics, with the haploid unworn male genome having the highest quality and the worn diploid female genome having the lowest quality. In fact, the N50 value of the unworn male genome was >100 times higher than that of the worn female genome. The genome quality pattern supports the hypothesis that sequence heterozygosity resulting both from ploidy and somatic variants can affect the result of an assembly with former shown to be a much bigger player than the latter. Furthermore, we observed that the density of variants was moderately correlated to the density of breakpoints in the genome assemblies. Overall, our results indicate that increased ploidy and accumulation of somatic variants both negatively affect the quality of the resulting assembly with the former being much more significant than the latter. When considering a de novo assembly project for a non-model organism, whenever possible, haploid samples at the youngest possible age are to be recommended. Furthermore, use of a long-read platform can lead to better genome quality. However, at least for the 10x linked reads, having too much sequencing data does not necessarily lead to a better genome assembly