Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses.

Formation of complex inorganic structures is widespread in nature. Diatoms create intricately patterned cell walls of inorganic silicon that are a biomimetic model for design and generation of three-dimensional silica nanostructures. To date, only relatively simple silica structures can be generated in vitro through manipulation of known diatom phosphoproteins (silaffins) and long-chain polyamines. Here, we report the use of genome-wide transcriptome analyses of the marine diatom Thalassiosira pseudonana to identify additional candidate gene products involved in the biological manipulation of silicon. Whole-genome oligonucleotide tiling arrays and tandem mass spectrometry identified transcripts for >8,000 genes, approximately 3,000 of which were not previously described and included noncoding and antisense RNAs. Gene-specific expression profiles detected a set of 75 genes induced only under low concentrations of silicon but not under low concentrations of nitrogen or iron, alkaline pH, or low temperatures. Most of these induced gene products were predicted to contain secretory signals and/or transmembrane domains but displayed no homology to known proteins. Over half of these genes were newly discovered, identified only through the use of tiling arrays. Unexpectedly, a common set of 84 genes were induced by both silicon and iron limitations, suggesting that biological manipulation of silicon may share pathways in common with iron or, alternatively, that iron may serve as a required cofactor for silicon processes. These results provide insights into the transcriptional and translational basis for the biological generation of elaborate silicon nanostructures by these ecologically important microbes.

A scalable method for multiplex LED-controlled synthesis of DNA in capillaries.

As research in synthetic biology and genomic sciences becomes more widespread, the need for diverse oligonucleotide populations has increased. To limit reagent cost, it would be advantageous to obtain high quality populations in minute amounts. Towards that end, synthesis of DNA strands in capillaries utilizing photolabile 3-nitrophenylpropyloxycarbonyl (NPPOC) chemistry and ultraviolet-light emitting diodes (UV-LEDs) was examined. Multiple oligonucleotides were made in single capillaries and were characterized by hybridization, sequencing and gene synthesis. DNA synthesized in capillaries was capable of being hybridized and signal intensities correlated with microarray data. Sequencing demonstrated that the oligonucleotides were of high quality (up to 44% perfect sequences). Oligonucleotides were combined and used successfully for gene synthesis. This system offers a novel, scalable method to synthesize high quality oligonucleotides for biological applications.

Effect of exclusive enteral nutritional treatment on plasma antioxidant concentrations in childhood Crohn's disease.

BACKGROUND & AIMS: Oxidative stress and depletion of antioxidants may play a role in the pathogenesis of Crohn's disease (CD). The aim of this study was to determine the effect of exclusive enteral nutrition, which is increasingly being used as primary therapy for CD, on plasma antioxidant concentrations in children with active CD. METHODS: In a double-blind randomised controlled trial, 15 children with active CD (mean age, 11.3 years, range 6.8-15.7) attending a paediatric gastroenterology referral centre, were assigned to receive either a standard polymeric diet (Group S, n=8) or a glutamine-enriched polymeric diet (Group G, n=7) as primary therapy for active CD. Plasma concentrations of selenium, urates, vitamin A, vitamin E, vitamin C, glutathione, and also malondialdehyde (MDA) were measured at baseline and after 4 weeks of exclusive enteral nutritional treatment. RESULTS: Mean (95% CI) selenium concentration of the cohort increased significantly from 0.82 micromol/l (0.72, 0.91) to 1.14 micromol/l (0.98, 1.3), P<0.001. There were, however, significant reductions in mean concentrations of vitamin C {11.8 mg/l (7.7, 15.8) to 6.5 mg/l (4.5, 8.7), P=0.01} and vitamin E {11.3 mg/l (10.3, 12.4) to 9.4 mg/l (8.7, 10.1), P=0.03}. The concentrations of vitamin A, urates, glutathione and MDA did not change significantly over the study period. Glutamine supplementation did not have any significant effect on plasma antioxidant concentrations. CONCLUSIONS: Significant changes in circulating antioxidant concentrations occurred in children with active CD receiving exclusive enteral nutritional treatment. Glutamine supplementation was not beneficial in improving plasma antioxidant status.

Correcting errors in synthetic DNA through consensus shuffling.

Although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1-3 random errors/kb of DNA. Here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic DNA. In this method, errors are revealed as mismatches by re-hybridization of the population. The DNA is fragmented, and mismatched fragments are removed upon binding to an immobilized mismatch binding protein (MutS). PCR assembly of the remaining fragments yields a new population of full-length sequences enriched for the consensus sequence of the input population. We show that two iterations of consensus shuffling improved a population of synthetic green fluorescent protein (GFPuv) clones from approximately 60 to >90% fluorescent, and decreased errors 3.5- to 4.3-fold to final values of approximately 1 error per 3500 bp. In addition, two iterations of consensus shuffling corrected a population of GFPuv clones where all members were non-functional, to a population where 82% of clones were fluorescent. Consensus shuffling should facilitate the rapid and accurate synthesis of long DNA sequences.

Got silicon? The non-essential beneficial plant nutrient.

Research on a possible nutritional role for the element silicon has been hampered by the diverse beneficial effects that it has on monocots and dicots, and the subsequent difficulties in focusing studies on a single genetic model system. Although deemed a non-essential nutrient for the majority of plants, the benefits of silicon include increasing pest and pathogen resistance, drought and heavy metal tolerance, and the quality and yield of agricultural crops. Although the pathways and molecular mechanisms by which silicon is absorbed and deposited in plants are still unclear, recent progress has been achieved through the use of rice mutants that are deficient in silicon uptake. Additionally, the application of electron-energy-loss spectroscopy (EELS) allows one to determine the composition of silica deposits conclusively. Thereby shedding light upon the role of silicon in heavy metal tolerance. With the complete sequence of the genomes for a dicot (Arabidopsis) and a monocot (rice) available for large-scale genetic analysis, the future bodes well for a more complete understanding of the biological role of silicon and its mode of transport into and through plants.

Amplification and assembly of chip-eluted DNA (AACED): a method for high-throughput gene synthesis.

A basic problem in gene synthesis is the acquisition of many short oligonucleotide sequences needed for the assembly of genes. Photolithographic methods for the massively parallel synthesis of high-density oligonucleotide arrays provides a potential source, once appropriate methods have been devised for their elution in forms suitable for enzyme-catalyzed assembly. Here, we describe a method based on the photolithographic synthesis of long (>60mers) single-stranded oligonucleotides, using a modified maskless array synthesizer. Once the covalent bond between the DNA and the glass surface is cleaved, the full-length oligonucleotides are selected and amplified using PCR. After cleavage of flanking primer sites, a population of unique, internal 40mer dsDNA sequences are released and are ready for use in biological applications. Subsequent gene assembly experiments using this DNA pool were performed and were successful in creating longer DNA fragments. This is the first report demonstrating the use of eluted chip oligonucleotides in biological applications such as PCR and assembly PCR.

Similar structural basis for membrane localization and protein priming by an RNA-dependent RNA polymerase.

Protein primers are used to initiate genomic synthesis of several RNA and DNA viruses, although the structural details of the primer-polymerase interactions are not yet known. Poliovirus polymerase binds with high affinity to the membrane-bound viral protein 3AB but uridylylates only the smaller peptide 3B in vitro. Mutational analysis of the polymerase identified four surface residues on the three-dimensional structure of poliovirus polymerase whose wild-type identity is required for 3AB binding. These mutants also decreased 3B uridylylation, arguing that the binding sites for the membrane tether and the protein primer overlap. Mutation of flanking residues between the 3AB binding site and the polymerase active site specifically decreased 3B uridylylation, likely affecting steps subsequent to binding. The physical overlap of sites for protein priming and membrane association should facilitate replication initiation in the membrane-associated complex.