Recombineering BAC transgenes for protein tagging

Protein tagging offers many advantages for proteomic and regulomic research, particularly due to the use of generic and highly sensitive methods that can be applied with reasonable throughput. Ideally, protein tagging is equivalent to having a high affinity antibody for every chosen protein. However, these advantages are compromised if the tagged protein is overexpressed, which is usually the case from cDNA expression vectors. BAC (bacterial artificial chromosome) transgenes present a way to express a chosen protein at physiological levels with all regulatory elements in their native configurations, including cell cycle, alternative splicing and microRNA regulation. Recombineering has become the method of choice for modifying large constructs like BACs. Here, we present a method for protein tagging by recombineering BACs, transfecting cells and evaluating tagged protein expression.     

Synthesis of phytochelatins in vetiver grass upon lead exposure in the presence of phosphorus

In a hydroponic setting, we investigated the possible role of phytochelatins (metal-binding peptides) in the lead (Pb) tolerance of vetiver grass (Vetiveria zizanioides L.). Pb was added to the nutrient medium at concentrations ranging from 0 to 1,200 mg L^?1. Furthermore, we simulated the effect of soil phosphorus (P) on potentially plant available Pb by culturing vetiver grass in P-rich nutrient media. After 7 days of exposure to Pb, we evaluated the Pb uptake by vetiver grass. Results indicate that vetiver can accumulate Pb up to 3,000 mg kg^?1 dry weight in roots with no toxicity. Formation of lead phosphate inhibited Pb uptake by vetiver, suggesting the need for an environmentally safe chelating agent in conjunction with phytoremediation to clean up soils contaminated with lead-based paint. Unambiguous characterization of phytochelatins (PC_n) was possible using high pressure liquid chromatography coupled with electrospray ionization mass spectrometry (LC-ESMS). Vetiver shows qualitative and quantitative differences in PC_n synthesis between root and shoot. In root tissue from vetiver exposed to 1,200 mg Pb L^-1, phytochelatins ranged from PC₁ to PC₃. Collision-induced dissociation of the parent ion allowed confirmation of each PC_n based on the amino acid sequence. Possible Pb-PC₁ and Pb₂-PC₁ complexes were reported in vetiver root at the highest Pb concentration. The data from these experiments show that the most probable mechanism for Pb detoxification in vetiver is by synthesizing PC_n and forming Pb–PC_n complexes.     

Complete genome sequence of Arcanobacterium haemolyticum type strain (11018)

Arcanobacterium haemolyticum (ex MacLean et al. 1946) Collins et al. 1983 is the type species of the genus Arcanobacterium, which belongs to the family Actinomycetaceae. The strain is of interest because it is an obligate parasite of the pharynx of humans and farm animal; occasionally, it causes pharyngeal or skin lesions. It is a Gram-positive, nonmotile and non-sporulating bacterium. The strain described in this study was isolated from infections amongst American soldiers of certain islands of the North and West Pacific. This is the first completed sequence of a member of the genus Arcanobacterium and the ninth type strain genome from the family Actinomycetaceae. The 1,986,154 bp long genome with its 1,821 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Evaluation of Plasma Trace Elements in Different Stages of Nonalcoholic Fatty Liver Disease

Biological Trace Element Research - Nonalcoholic fatty liver disease (NAFLD) is considered as the hepatic manifestation of metabolic syndrome. Its global prevalence is estimated between 25 and 45%,...     

Preparation and Characterization of Lyophilized Liposomes with Incorporated Quercetin

Liposomes composed of egg-phosphatidylcholine (EPC) incorporating quercetin (QR) were prepared by the thin-film hydration method (TFHM) and the monophase solution method (MSM). A rapid and slow freeze-drying process was applied for both laboratory and industrial scales. The purpose of this study was to compare the two methods of liposome preparation, and further determine whether the lyophilization process affects the liposome physicochemical characteristics (size, polydispersity index, and ζ-potential) and incorporation of quercetin.     

Structural, photolysis and biological studies of the bis(μ2-chloro)-tris(triphenylphosphine)-di-copper(I) and chloro-tris(triphenylphosphine)-copper(I) complexes. Study of copper(I)-copper(I) interactions

Direct reaction of copper(I) chloride with triphenylphosphine (tpp) in molar ratio 2:3 and 1:3, results in the formation of the [(tpp)Cu(μ₂-Cl)₂Cu(tpp)₂] (1) and {[CuCl(tpp)₃]·(CH₃CN)} (2) complexes. The complexes have been characterized by melting point, FT-IR, UV-Vis spectroscopic data and X-ray crystallography. Complex 1 is di-nuclear. Two μ₂-Cl atoms bridge two copper(I) ions with tetrahedral and trigonal geometry respectively. The short copper-copper bond distance of 2.9039(6) ? in case of 1 indicates d¹⁰-d¹⁰ interaction between metal centers. Thus, our studies were extended here in the determination of the quasi-aromaticity, which results in strong Cu-Cu interactions, using the computational method of nucleus-independent chemical shifts (NICS). The NICS calculated at the inner region of the Cu₂Cl₂P₃ core in complex 1 is shielded up to −6.05 ppm. Complex 2 is mono-nuclear where three phosphorus and one chloride atoms form a tetrahedron around the copper(I) ion. Photolysis of both complexes 1 and 2, results in the formation of triphenylphosphine oxide.The complexes 1 and 2, were tested for their in vitro cytotoxic activity against leiomyosarcoma cells (LMS) and human breast adenocarcinoma cells (MCF-7). The type of LMS cell death caused by the complexes was also evaluated by use of a flow cytometry assay. The results show that at concentration of 5 μΜ of complexes 1 and 2, 34.1% (1) and 19.6 (2)% of LMS cells undergo programmed cell death (apoptosis), while at 10 μΜ, 80.4% (1) and 65.2% (2) of LMS cells undergo apoptosis. The light sensitivity of the complex is discussed in relation with the biological activity.     

Next-Generation Sequencing of a 40 Mb Linkage Interval Reveals TSPAN12 Mutations in Patients with Familial Exudative Vitreoretinopathy

Familial exudative vitreoretinopathy (FEVR) is a genetically heterogeneous retinal disorder characterized by abnormal vascularisation of the peripheral retina, often accompanied by retinal detachment. To date, mutations in three genes (FZD4, LRP5, and NDP) have been shown to be causative for FEVR. In two large Dutch pedigrees segregating autosomal-dominant FEVR, genome-wide SNP analysis identified an FEVR locus of ∼40 Mb on chromosome 7. Microsatellite marker analysis suggested similar at risk haplotypes in patients of both families. To identify the causative gene, we applied next-generation sequencing in the proband of one of the families, by analyzing all exons and intron-exon boundaries of 338 genes, in addition to microRNAs, noncoding RNAs, and other highly conserved genomic regions in the 40 Mb linkage interval. After detailed bioinformatic analysis of the sequence data, prioritization of all detected sequence variants led to three candidates to be considered as the causative genetic defect in this family. One of these variants was an alanine-to-proline substitution in the transmembrane 4 superfamily member 12 protein, encoded by TSPAN12. This protein has very recently been implicated in regulating the development of retinal vasculature, together with the proteins encoded by FZD4, LRP5, and NDP. Sequence analysis of TSPAN12 revealed two mutations segregating in five of 11 FEVR families, indicating that mutations in TSPAN12 are a relatively frequent cause of FEVR. Furthermore, we demonstrate the power of targeted next-generation sequencing technology to identify disease genes in linkage intervals.     

The genetic basis of triple A (Allgrove) syndrome in a Greek family

Triple A (or Allgrove) syndrome is an autosomal recessive genetic disorder. Patients typically suffer from chronic adrenal insufficiency due to resistance to ACTH (Addison's disease), achalasia of the cardia, and defective tear formation (alacrima). The syndrome is caused by mutations in the AAAS gene which encodes the protein ALADIN, a constituent of eukaryotic nuclear pore complexes. The multi-systemic nature and variable manifestations of the triple A syndrome often confound its diagnosis and limit our understanding of its exact pathogenesis. We performed mutational screening of the AAAS gene in a Greek family of four individuals, including an affected propositus with typical symptoms of late-onset triple A syndrome. Our results are consistent with an autosomal recessive pattern of inheritance within the family, caused by a functional c.43C > A mutation in exon 1 of the AAAS gene. All members of the family were also homozygous for a silent c.855C > T nucleotide change within exon 9 of the AAAS gene, representing a common single nucleotide polymorphism. The compromising c.43C > A mutation is predicted to cause a p.Gln15Lys amino acid substitution in the ALADIN protein. However, it has been suggested that the functional impact of this mutation may be more severe, causing a shift in the reading frame of AAAS gene via formation of an aberrant premature donor splice site within exon 1. We propose that mutational analysis of the AAAS gene should be considered in adult patients with one or more clinical signs of the disease, as diagnosis of late-onset cases can be ambiguous.     

Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1)

Ilyobacter polytropus Stieb and Schink 1984 is the type species of the genus Ilyobacter, which belongs to the fusobacterial family Fusobacteriaceae. The species is of interest because its members are able to ferment quite a number of sugars and organic acids. I. polytropus has a broad versatility in using various fermentation pathways. Also, its members do not degrade poly-β-hydroxybutyrate but only the monomeric 3-hydroxybutyrate. This is the first completed genome sequence of a member of the genus Ilyobacter and the second sequence from the family Fusobacteriaceae. The 3,132,314 bp long genome with its 2,934 protein-coding and 108 RNA genes consists of two chromosomes (2 and 1 Mbp long) and one plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.