Kathryn E. Richmond

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.

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, ≈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.

Infection ofArabidopsis thaliana ecotype columbia by tomato spotted wilt virus

Mechanical inoculation ofArabidopsis thaliana ecotype Columbia with tomato spotted wilt virus led to viral replication and spread as determined by dot blot and ELISA analysis. Severe symptoms were observed three to four weeks post-inoculation. Early symptoms were manifested as chlorotic spots on uninoculated leaves. Later in the infection process, some plants showed complete chlorosis and wilting prior to bolting. Bolts that were developed by infected plants were chlorotic and deformed. These preliminary results suggest thatA. thaliana could become a model system for the genetic analysis of host factors required for the replication of viruses in the family Bunyaviridae, which includes viruses that cause important diseases of both plants and animals.

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.