Prototypes for automating product system model assembly

The International Journal of Life Cycle Assessment - The flexibility of life cycle inventory (LCI) background data selection is increasing with the increasing availability of data, but this comes...     

A global assembly line for cyanobactins

More than 100 cyclic peptides harboring heterocyclized residues are known from marine ascidians, sponges and different genera of cyanobacteria. Here, we report an assembly line responsible for the biosynthesis of these diverse peptides, now called cyanobactins, both in symbiotic and free-living cyanobacteria. By comparing five new cyanobactin biosynthetic clusters, we produced the prenylated antitumor preclinical candidate trunkamide in Escherichia coli culture using genetic engineering.     

Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem

With the consensus human genome sequenced and many other sequencing projects at varying stages of completion, greater attention is being paid to the genetic differences among individuals and the abilities of those differences to predict phenotypes. A significant obstacle to such work is the difficulty and expense of determining haplotypes--sets of variants genetically linked because of their proximity on the genome--for large numbers of individuals for use in association studies. This paper presents some algorithmic considerations in a new approach for haplotype determination: inferring haplotypes from localised polymorphism data gathered from short genome 'fragments.' Formalised models of the biological system under consideration are examined, given a variety of assumptions about the goal of the problem and the character of optimal solutions. Some theoretical results and algorithms for handling haplotype assembly given the different models are then sketched. The primary conclusion is that some important simplified variants of the problem yield tractable problems while more general variants tend to be intractable in the worst case.     

Quality control in the secretory assembly line

As a rule, only proteins that have reached a native, folded and assembled structure are transported to their target organelles and compartments within the cell. In the secretory pathway of eukaryotic cells, this type of sorting is particularly important. A variety of molecular mechanisms are involved that distinguish between folded and unfolded proteins, modulate their intracellular transport, and induce degradation if they fail to fold. This phenomenon, called quality control, occurs at several levels and involves different types of folding sensors. The quality control system provides a stringent and versatile molecular sorting system that guaranties fidelity of protein expression in the secretory pathway.     

Alterations in differentiation and pyrimidine pathway enzymes in 5-azacytidine resistant variants of a myoblast line.

5-azacytidine at concentrations higher than 5 muM inhibited the differentiation of a rat myoblast line in vitro. It was also somewhat cytotoxic at this level. Variants resistant to the cytotoxic effect of 5-azacytidine were obtained which were simultaneously unable to differentiate into myotubes and exhibited altered morphology. These characteristics were retained by the variants when subcultured in the absence of the drug for over 700 generations. Several of the azacytidine resistant cells were more susceptible than the parental line to the lethal action of 5-bromodeoxyuridine and adenosine, but not that of cytosine arabinoside, ouabain or 8-azaguanine. The variants were capable of transporting uridine, thymidine and 5-azacytidine. The uridine kinase activity was one-half to one-third of than in the parental cells but it was not missing completely in any of the variants. Two independently isolated variants selected for detailed study showed a 2- to 3-fold increase in the activity of orotidylic acid decarboxylase. This enzyme in the variants in contrast to that of the parental cells was completely insensitive to the inhibitory effect of a nucleotide generated from ATP and 5-azacytidine in cell extracts (probably 5-azacytidine monophosphate). These observations point to the possibility the 5-azacytidine resistance arises in myoblasts due to an alteration of the components of two target pathways of this drug, viz., the de novo pyrimidine pathway and an undefined sequence leading to the synthesis of membrane components.     

Chemical variation from the neoantimycin depsipeptide assembly line

Here we report the biosynthetic pathway for the neoantimycin and present three novel neoantimycin analogues, neoantimycin D (1), E (2) and F (3), from this assembly system from Streptoverticillium orinoci. Identification of these novel neoantimycin variants was achieved by selective MS/MS interrogation of natural product extracts using diagnostic fragments of the known neoantimycins. Their structures, including the absolute configurations, were elucidated using a combination of NMR experiments, detailed MS/MS experiments and the advanced Marfey’s method. The biosynthetic pathway of neoantimycin was dissected by genome sequencing data analysis for the first time, which includes a hybrid nonribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) assembly lines.     

Glycosaminoglycan variants in the C2 muscle cell line

Using a replica technique, we have isolated and characterized five genetic variants of the C2 mouse muscle cell line that are defective in incorporation of radiolabeled sulfate into glycosaminoglycans (GAGs). The variants incorporate free sulfate into GAGs at 5-20% of wild-type levels. None of the variants is defective in sulfate transport across the cell membrane, and in no case could the deficit in incorporation of sulfate be reversed by addition of an artificial initiator of GAG biosynthesis, p-nitrophenyl beta-D-xyloside. Analysis of the incorporation of [3H]glucosamine into GAGs by the variants revealed three different patterns: one variant incorporated [3H]glucosamine at the wild-type level; one, S27, at a severely reduced level; and three at intermediate levels. Four of the five variants showed marked deficits in their ability to differentiate and fuse. The remaining variant, S27, formed multinucleated myotubes and expressed acetylcholine receptor with a normal time course. Differentiation of the first four variants could not be restored by addition of exogenous GAGs or extracellular matrix. Because of the important roles that GAGs and proteoglycans are thought to play in the differentiation of muscle, these genetic variants should serve as useful tools in functional analyses of these molecules.     

Evaluation of computational techniques for predicting non-synonymous single nucleotide variants pathogenicity

The human genetic diseases associated with many factors, one of these factors is the non-synonymous Single Nucleotide Variants (nsSNVs) cause single amino acid change with another resulting in protein function change leading to disease. Many computational techniques have been released to expect the impacts of amino acid alteration on protein function and classify mutations as pathogenic or neutral. Here in this article, we assessed the performance of eight techniques; FATHMM, SIFT, Provean, iFish, Mutation Assessor, PANTHER, SNAP2, and PON- P2 using a VaribenchSelectedPure dataset of 2144 pathogenic variants and 3777 neutral variants extracted from the free standard database “Varibench.” The first five techniques achieve (45.60–83.75) % specificity, (52.64–94.13) % sensitivity, (51.00–88.90) % AUC, and (49.76–88.24) % ACC on whole dataset, while all eight techniques achieve (36.54–77.88) % specificity, (50.00–75.00) % sensitivity, (51.00–76.40) % AUC, and (25.00–77.78) % ACC on random sample dataset. We also created a Meta classifier (CSTJ48) that combines FATHMM, iFish, and Mutation Assessor. It registers 96.33% specificity, 86.07% sensitivity, 91.20% AUC, and 91.89 ACC. By comparing the results, it's clear that FATHMM gives the highest performance over the seven individual techniques, where it achieves 83.75% and 77.88% specificity, 94.13%, and 75.00% sensitivity, 88.90% and 76.40% AUC, and 88.24% and 77.78% ACC on whole and random sample dataset, respectively. Also, the launched Meta classifier (CSTJ48) is outperforming over all the eight individual tools that compared here.     

Biochemical characterization of actin assembly mechanisms with ALS-associated profilin variants

Eight separate mutations in the actin-binding protein profilin-1 have been identified as a rare cause of amyotrophic lateral sclerosis (ALS). Profilin is essential for many neuronal cell processes through its regulation of lipids, nuclear signals, and cytoskeletal dynamics, including actin filament assembly. Direct interactions between profilin and actin monomers inhibit actin filament polymerization. In contrast, profilin can also stimulate polymerization by simultaneously binding actin monomers and proline-rich tracts found in other proteins. Whether the ALS-associated mutations in profilin compromise these actin assembly functions is unclear. We performed a quantitative biochemical comparison of the direct and formin mediated impact for the eight ALS-associated profilin variants on actin assembly using classic protein-binding and single-filament microscopy assays. We determined that the binding constant of each profilin for actin monomers generally correlates with the actin nucleation strength associated with each ALS-related profilin. In the presence of formin, the A20T, R136W, Q139L, and C71G variants failed to activate the elongation phase of actin assembly. This diverse range of formin-activities is not fully explained through profilin-poly-L-proline (PLP) interactions, as all ALS-associated variants bind a formin-derived PLP peptide with similar affinities. However, chemical denaturation experiments suggest that the folding stability of these profilins impact some of these effects on actin assembly. Thus, changes in profilin protein stability and alterations in actin filament polymerization may both contribute to the profilin-mediated actin disruptions in ALS.     

Solid-phase cloning for high-throughput assembly of single and multiple DNA parts

We describe solid-phase cloning (SPC) for high-throughput assembly of expression plasmids. Our method allows PCR products to be put directly into a liquid handler for capture and purification using paramagnetic streptavidin beads and conversion into constructs by subsequent cloning reactions. We present a robust automated protocol for restriction enzyme based SPC and its performance for the cloning of >60 000 unique human gene fragments into expression vectors. In addition, we report on SPC-based single-strand assembly for applications where exact control of the sequence between fragments is needed or where multiple inserts are to be assembled. In this approach, the solid support allows for head-to-tail assembly of DNA fragments based on hybridization and polymerase fill-in. The usefulness of head-to-tail SPC was demonstrated by assembly of >150 constructs with up to four DNA parts at an average success rate above 80%. We report on several applications for SPC and we suggest it to be particularly suitable for high-throughput efforts using laboratory workstations.     

Use of factor-H sera for the differentiation of the flagellar antigens of Escherichia coli serological variants

The use of factor sera permitting the differentiation of the variants, described in earlier. works, among the flagellar antigens of E. coli, formally denoted as H2, H4, H7, H10 and H34 in accordance with their official nomenclature, has made it possible to reveal that each of these variants is widely spread among E. coli and occurs in bacteria of different O-groups. Besides, this study has shown the possibility of subdividing a number of formal H: O types into 2 or more serovars on the basis of differences in the factor composition of their antigens. The results obtained in this study suggest that in the process of the evolution of E. coli H-antigen variants differing in their factor composition have been formed as independent varieties; therefore, these variants do not reflect the features characteristic of individual strains, but constitute one of the diagnostic signs of serological classification, i. e. the differentiation of the species into various serovars.     

Stimulation of lipid-linked oligosaccharide assembly during oviduct differentiation

Regulation of dolichyl phosphate-linked oligosaccharide assembly has been studied during the course of diethylstilbestrol-induced chick oviduct differentiation. Oviduct membranes from treated chicks form 4.6 times as much GlcNAc-P-P-Dol and GlcNAc2-P-P-Dol upon incubation with UDP-[14C]GlcNAc and MgCl2 than do membranes from untreated chicks. Assembly of oligosaccharide-lipid was studied by incubation of membranes with purified exogenous [14C]GlcNAc2-P-P-Dol and GDP-Man. Man transfer required a divalent cation (10 mM Mg2+) and detergent (0.5% Nonidet P-40 is optimal) and occurs in the presence of amphomycin (500 micrograms/ml). The apparent Km for GDP-Man is 1 microM and for [14C]GlcNAc2-P-P-Dol is 0.45 microM. The products are a series of sequentially formed dolichyl pyrophosphate-linked saccharides up to Man5GlcNAc2, the first of which is Man beta 1,4GlcNAc2. The same products are formed either in the presence or absence of amphomycin. Conversion of GlcNAc2-P-P-Dol to higher oligosaccharides is stimulated 3-fold by estrogen treatment of chicks. Similarly, the conversion of partially purified exogenously added Man beta-[14C]GlcNAc2-P-P-Dol is 4.6-fold higher after diethylstilbestrol treatment.     

Structure and mechanism of assembly line polyketide synthases

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