Synergy between cationic lipid and co-lipid determines the macroscopic structure and transfection activity of lipoplexes

The large number of cytofectin and co-lipid combinations currently used for lipoplex-mediated gene delivery reflects the fact that the optimal cytofectin/co-lipid combination varies with the application. The effects of structural changes in both cytofectin and co-lipid were systematically examined to identify structure–activity relationships. Specifically, alkyl chain length, degree of unsaturation and the head group to which the alkyl side chain was attached were examined to determine their effect on lipoplex structure and biological activity. The macroscopic lipoplex structure was assessed using a dye-binding assay and the biological activity was examined using in vitro transfection in three diverse cell lines. Lipoplexes were formulated in three different vehicles currently in use for in vivo delivery of naked plasmid DNA (pDNA) and lipoplex formulations. The changes in dye accessibility were consistent with structural changes in the lipoplex, which correlated with alterations in the formulation. In contrast, transfection activity of different lipoplexes was cell type and vehicle dependent and did not correlate with dye accessibility. Overall, the results show a correlation between transfection and enhanced membrane fluidity in both the lipoplex and cellular membranes.     

Integration of DNA ligation and rolling circle amplification for the homogeneous,end-point detection of single nucleotide polymorphisms

Association studies using common sequence variants or single nucleotide polymorphisms (SNPs) may provide a powerful approach to dissect the genetic inheritance of common complex traits. Such studies necessitate the development of cost-effective, high throughput technologies for scoring SNPs. The method described in this paper for the co-detection of both alleles of a SNP in a single homogeneous reaction combines the specificity of a high fidelity DNA ligation step with the power of rolling circle amplification. The incorporation of Amplifluor™ energy transfer primers enables signal detection in a homogeneous format, making this approach highly amenable to automation. The adaptation of the genotyping method for high throughput screening using conventional liquid handling systems is described.     

Synaptosome-associated protein of 25 kilodaltons modulates Kv2.1 voltage-dependent K(+) channels in neuroendocrine islet beta-cells through an interaction with the channel N terminus

Insulin secretion is initiated by ionic events involving membrane depolarization and Ca(2+) entry, whereas exocytic SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins mediate exocytosis itself. In the present study, we characterize the interaction of the SNARE protein SNAP-25 (synaptosome-associated protein of 25 kDa) with the beta-cell voltage-dependent K(+) channel Kv2.1. Expression of Kv2.1, SNAP-25, and syntaxin 1A was detected in human islet lysates by Western blot, and coimmunoprecipitation studies showed that heterologously expressed SNAP-25 and syntaxin 1A associate with Kv2.1. SNAP-25 reduced currents from recombinant Kv2.1 channels by approximately 70% without affecting channel localization. This inhibitory effect could be partially alleviated by codialysis of a Kv2.1N-terminal peptide that can bind in vitro SNAP-25, but not the Kv2.1C-terminal peptide. Similarly, SNAP-25 blocked voltage-dependent outward K(+) currents from rat beta-cells by approximately 40%, an effect that was completely reversed by codialysis of the Kv2.1N fragment. Finally, SNAP-25 had no effect on outward K(+) currents in beta-cells where Kv2.1 channels had been functionally knocked out using a dominant-negative approach, indicating that the interaction is specific to Kv2.1 channels as compared with other beta-cell Kv channels. This study demonstrates that SNAP-25 can regulate Kv2.1 through an interaction at the channel N terminus and supports the hypothesis that SNARE proteins modulate secretion through their involvement in regulation of membrane ion channels in addition to exocytic membrane fusion.     

Cellular localization of tissue inhibitors of metalloproteinases in the rat ovary throughout pseudopregnancy

The present study determined the ovarian cellular localization of the mRNA for the tissue inhibitors of metalloproteinases (TIMPs) during pseudopregnancy in the rat. Pseudopregnancy was induced by eCG/hCG stimulation. At Day 1 of pseudopregnancy, intense reaction product for TIMP-1 mRNA was observed surrounding the developing corpus luteum (CL), with less intense expression present in granulosa-lutein cells. With continued luteal development, the TIMP-1 mRNA encircling the CL was lost, although low levels of expression were found within the CL. For TIMP-2 mRNA, intense reaction product was observed surrounding the developing CL but, unlike TIMP-1, was present in granulosa-lutein cells, with high levels near the center of the CL. The localization pattern of TIMP-2 mRNA was unchanged through the latter stages of pseudopregnancy. TIMP-3 mRNA expression was strikingly different from the other TIMPs. At Day 1 of pseudopregnancy, intense reaction product for TIMP-3 mRNA was observed in granulosa-lutein cells of certain developing CL, whereas adjacent follicles did not express TIMP-3 mRNA. With continued luteal development, there was a homogenous, intense localization of TIMP-3 mRNA throughout the CL, which was unchanged during pseudopregnancy. To understand the induction of TIMP-3 mRNA in the developing CL, a series of experiments was performed to compare markers of follicular maturity with the presence of TIMP-3 mRNA. TIMP-3 mRNA appears to be switched on in granulosa cells of follicles destined to ovulate. The distinct pattern of expression of the three TIMPs suggests that each inhibitor may regulate either the site and extent of proteolytic action or specific matrix metalloproteinases at different periods of the luteal life span.     

How plants see themselves--self-incompatibility in flowering plants

Plants have been propagating themselves by cloning for millennia. It is, however, widely recognised that mixing genes with other individuals of the same species makes better evolutionary sense, as it provides the variation that is the raw material for natural selection. How, then, do some plants prevent self-fertilisation?     

Iterative pass optimization of sequence data

The problem of determining the minimum-cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete. This "tree alignment" problem has motivated the considerable effort placed in multiple sequence alignment procedures. Wheeler in 1996 proposed a heuristic method, direct optimization, to calculate cladogram costs without the intervention of multiple sequence alignment. This method, though more efficient in time and more effective in cladogram length than many alignment-based procedures, greedily optimizes nodes based on descendent information only. In their proposal of an exact multiple alignment solution, Sankoff et al. in 1976 described a heuristic procedure--the iterative improvement method--to create alignments at internal nodes by solving a series of median problems. The combination of a three-sequence direct optimization with iterative improvement and a branch-length-based cladogram cost procedure, provides an algorithm that frequently results in superior (i.e., lower) cladogram costs. This iterative pass optimization is both computation and memory intensive, but economies can be made to reduce this burden. An example in arthropod systematics is discussed.     

Search-based optimization

The problem of determining the minimum cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete (Wang and Jiang, 1994). Traditionally, point estimations of hypothetical ancestral sequences have been used to gain heuristic, upper bounds on cladogram cost. These include procedures with such diverse approaches as non-additive optimization of multiple sequence alignment, direct optimization (Wheeler, 1996), and fixed-state character optimization (Wheeler, 1999). A method is proposed here which, by extending fixed-state character optimization, replaces the estimation process with a search. This form of optimization examines a diversity of potential state solutions for cost-efficient hypothetical ancestral sequences and can result in greatly more parsimonious cladograms. Additionally, such an approach can be applied to other NP-complete phylogenetic optimization problems such as genomic break-point analysis.     

Leprosy – clues about the biochemistry of Mycobacterium leprae and its host-dependency from the genome

Deletions and the appearance of pseudogenes in pathways of carbon source utilisation and energy metabolism best explain the host-dependency and failure to culture Mycobacterium leprae axenically. From the genome sequence it is possible to predict that acetate and galactose cannot be used as carbon sources, while pyruvate can only be catabolised. Glycerol, glucose, and fatty acids could be used for glycolysis, the pentose cycle and -oxidation which are complete. Retrospective functional genomics – interpreting work before the completion of the genome project – supports the failure of M. leprae to use acetate as well as another prediction that metabolic flux from pyruvate to acetyl-CoA would be very low. However, the loss of a second icd gene (compared with M. tuberculosis), predicted to encode isocitrate dehydrogenase, did not diminish the specific activity of the enzyme. The genes for respiratory pathways are extremely limited, being present for oxidative phosphorylation as a result of electron transport only using FADH as an electron donor. In contrast, all the major biosynthetic pathways are complete except that M. leprae is a natural methionine auxotroph: this is predicted not to be attenuating, or explain host-dependency since methionine would be present in rich culture media.     

Identification of alanine dehydrogenase and its role in mixed secretion of ammonium and alanine by pea bacteroids

N2-fixation by Rhizobium-legume symbionts is of major ecological and agricultural importance, responsible for producing a substantial fraction of the biosphere's nitrogen. On the basis of 15N-labelling studies, it had been generally accepted that ammonium is the sole secretion product of N2-fixation by the bacteroid and that the plant is responsible for assimilating it into amino acids. However, this paradigm has been challenged in a recent 15N-labelling study showing that soybean bacteroids only secrete alanine. Hitherto, nitrogen secretion has only been assessed from in vitro 15N-labelling studies of isolated bacteroids. We show that both ammonium and alanine are secreted by pea bacteroids. The in vitro partitioning between them will depend on whether the system is open or closed, as well as the ammonium concentration and bacteroid density. To overcome these limitations we identified and mutated the gene for alanine dehydrogenase (aldA) and demonstrate that AldA is the primary route for alanine synthesis in isolated bacteroids. Bacteroids of the aldA mutant fix nitrogen but only secrete ammonium at a significant rate, resulting in lower total nitrogen secretion. Peas inoculated with the aldA mutant are green and healthy, demonstrating that ammonium secretion by bacteroids can provide sufficient nitrogen for plant growth. However, plants inoculated with the mutant are reduced in biomass compared with those inoculated with the wild type. The labelling and plant growth studies suggest that alanine synthesis and secretion contributes to the efficiency of N2-fixation and therefore biomass accumulation.