5′-Coterminal Subgenomic RNAs in Citrus Tristeza Virus-Infected Cells

AbstractThree unusual 5′ coterminal positive-stranded subgenomic (sg) RNAs, two of about 0.8 kb and one of 10 kb (designated LMT1, LMT2, and LaMT, respectively), from Citrus spp. plants and Nicotiana benthamiana protoplasts infected with Citrus tristeza virus (CTV) were characterized. The 5′ termini of the LMT RNAs were mapped by runoff reverse transcription and found to correspond with the 5′ terminus of the genomic RNA. The LMT 5′-coterminal sgRNAs consisted of two modal lengths of 744–746 and 842–854 nts. The 3′ of the LaMT RNAs terminated near the junction of ORF 1b and ORF 2 (p33). None of the 5′ sgRNAs had detectable amounts of corresponding negative-sense RNAs, as occurs with the genomic and 3′ coterminal subgenomic RNAs of CTV. The abundance of the short and long 5′ sgRNAs differed considerably in infected cells. The LMT RNAs were considerably more abundant than the genomic RNAs, while the larger LaMT RNA accumulated to much lower levels. The kinetics of accumulation of LMT1 and LMT2 in synchronously infected protoplasts differed. The larger RNA, LMT1, accumulated earlier with a strong hybridization signal at 2 days postinfection, a time when only traces of genomic and 3′ sgRNAs were detected. The lack of corresponding RNAs, that could be 3′ cleavage products corresponding to the 5′ coterminal sgRNAs and the lack of complementary negative strands, suggest that these sgRNAs were produced by termination during the synthesis of the genomic positive strands

Nanog transforms NIH3T3 cells and targets cell-type restricted genes

The transcription factor Nanog is uniquely expressed in embryonic stem (ES) cells and in germ cell tumors and is important for selfrenewal. To understand the relation between this and cell transformation, we expressed Nanog in NIH3T3 cells, and these cells showed an increased growth rate and a transformed phenotype as demonstrated by foci formation and colony growth in soft agar. This suggests that Nanog possesses an oncogenic potential that may be related to the role it plays in germ cell tumors and to its function in self renewal of ES cells. We studied the transcription targets of Nanog using microarrays to identify Nanog regulated genes. The list of genes regulated by Nanog was unique for each cell type and more than 10 % of the Nanog regulated genes, including transcription factors, are primary Nanog targets since their promoters bind Nanog in ES cells. Some of these target genes can explain the transformation o

Rose Scent: Genomics Approach to Discovering Novel Floral Fragrance–Related Genes

For centuries, rose has been the most important crop in the floriculture industry; its economic importance also lies in the use of its petals as a source of natural fragrances. Here, we used genomics approaches to identify novel scent-related genes, using rose flowers from tetraploid scented and nonscented cultivars. An annotated petal EST database of ∼2100 unique genes from both cultivars was created, and DNA chips were prepared and used for expression analyses of selected clones. Detailed chemical analysis of volatile composition in the two cultivars, together with the identification of secondary metabolism–related genes whose expression coincides with scent production, led to the discovery of several novel flower scent–related candidate genes. The function of some of these genes, including a germacrene D synthase, was biochemically determined using an Escherichia coli expression system. This work demonstrates the advantages of using the high-throughput approaches of genomics to detail traits of interest expressed in a cultivar-specific manner in nonmodel plants

Diffraction-free pulsed optical beams via space-time correlations

Diffraction places a fundamental limitation on the distance an optical beam propagates before its size increases and spatial details blur. We show here that imposing a judicious correlation between spatial and spectral degrees of freedom of a pulsed beam can render its transverse spatial profile independent of location along the propagation axis, thereby arresting the spread of the time-averaged beam. Such correlation introduced into a beam with arbitrary spatial profile enables spatio-temporal dispersion to compensate for purely spatial dispersion that underlies diffraction. As a result, the spatio-temporal profile in the local time-frame of the pulsed beam remains invariant at all positions along the propagation axis. One-dimensional diffraction-free space-time beams are described - including non-accelerating Airy beams, despite the well-known fact that cosine waves and accelerating Airy beams are the only one-dimensional diffraction-free solutions to the monochromatic Helmholtz equation