Plants respond to day/night cycling in a number of physiological ways. At the mRNA level, the expression of some genes changes during the 24-hr period. To identify novel genes regulated in this way, we used microarrays containing 11,521 Arabidopsis expressed sequence tags, representing an estimated 7800 unique genes, to determine gene expression levels at 6-hr intervals throughout the day. Eleven percent of the genes, encompassing genes expressed at both high and low levels, showed a diurnal expression pattern. Approximately 2% cycled with a circadian rhythm. By clustering microarray data from 47 additional nonrelated experiments, we identified groups of genes regulated only by the circadian clock. These groups contained the already characterized clock-associated genes LHY , CCA1 , and GI , suggesting that other key circadian clock genes might be found within these clusters. INTRODUCTIONPlants have adapted their growth and development to use the diurnal cycling of light and dark. This is manifested at both the physiological level, with leaf movement, growth, and stomatal opening, and the molecular level, with expression of some genes occurring only at certain times of the day. The day/night cycling of gene expression is called a diurnal rhythm and is achieved primarily by two mechanisms: first, by light, and second, by a free-running internal circadian clock. Circadian clocks have been well characterized in animals, fungi, and bacteria, and in all cases they have a central oscillator that measures time with a molecular feedback loop that cycles over a 24-hr period (Dunlap, 1999). Although a growing number of genes either regulated by the clock or affecting clock function have been identified in plants, a full picture has yet to emerge.The ability of plants to respond to light is achieved through photoreceptors. In Arabidopsis, two classes of photoreceptors are known: the red/far-red receptors, phytochrome A to E (Sharrock and Quail, 1989;Clack et al., 1994), and the blue light receptors, CRY1 (Ahmad and Cashmore, 1993), CRY2 (Guo et al., 1998), and NPH1 (Liscum and Briggs, 1995). Using these photoreceptors, a plant can detect a range of light intensities and wavelengths, with which it senses not only whether light is present but also from which direction the light is coming and whether there is competing vegetation (reviewed in Ballare, 1999). The best characterized of the photoreceptors are the phytochromes, for which the events that convert the light signal into transcriptional regulation have been described. Phytochrome is transported into the nucleus in a light-dependent manner (Sakamoto and Nagatani, 1996;Kircher et al., 1999). In the nucleus, it interacts with a basic helix-loop-helix transcription factor, PIF3 (Ni et al., 1998(Ni et al., , 1999, which has been shown to bind to the G box element found in the promoters of many light-activated genes (Giuliano et al., 1988;Martinez-Garcia et al., 2000). This chain of events allows the plants to respond to light after germination, by stopping hypocotyl elongat...

Two Brassicaceae species, Physaria fendleri and Camelina sativa, are genetically very closely related to each other and to Arabidopsis thaliana. Physaria fendleri seeds contain over 50% hydroxy fatty acids (HFAs), while Camelina sativa and Arabidopsis do not accumulate HFAs. To better understand how plants evolved new biochemical pathways with the capacity to accumulate high levels of unusual fatty acids, transcript expression and protein sequences of developing seeds of Physaria fendleri, wild-type Camelina sativa, and Camelina sativa expressing a castor bean (Ricinus communis) hydroxylase were analyzed. A number of potential evolutionary adaptations within lipid metabolism that probably enhance HFA production and accumulation in Physaria fendleri, and, in their absence, limit accumulation in transgenic tissues were revealed. These adaptations occurred in at least 20 genes within several lipid pathways from the onset of fatty acid synthesis and its regulation to the assembly of triacylglycerols. Lipid genes of Physaria fendleri appear to have co-evolved through modulation of transcriptional abundances and alterations within protein sequences. Only a handful of genes showed evidence for sequence adaptation through gene duplication. Collectively, these evolutionary changes probably occurred to minimize deleterious effects of high HFA amounts and/or to enhance accumulation for physiological advantage. These results shed light on the evolution of pathways for novel fatty acid production in seeds, help explain some of the current limitations to accumulation of HFAs in transgenic plants, and may provide improved strategies for future engineering of their production.

Relating single-nucleotide polymorphisms (SNP) to cows with acceptable productivity could benefit cattle breeders in areas where tall fescue is the predominant forage. This study aimed to (i) identify SNPs in bovine cytochrome P450 3A28 (CYP3A28) and (ii) determine the associations between SNP genotype, forage and cow body condition (BC). Genotype (CC, CG or GG) and forage [Kentucky-31 wild-type endophyte-infected tall fescue (KY+) vs. bermudagrass] effects on milk volume and quality were determined in Herd 1 cows (123 cows); in Herd 2 (99 cows), genotype and BC (low vs. moderate) effects on ovarian follicle size, calving date and calving per cent were determined; and in Herd 3 (114 cows), effects of genotype and fescue cultivar [KY+ vs. non-toxic endophyte-infected tall fescue (HiMag4)] were related to calving per cent, calving date and weaning weights of both cow and her calf. A cytosine (C) to guanine (G) transversion at base 994 (C994G) in CYP3A28 was identified. There was a genotype × forage type interaction (p < 0.05) on milk protein in Herd 1 cows; CC cows grazing bermudagrass had greater milk protein percentage in relation to other cows in the herd. In Herd 2, BC and genotype × BC tended (p < 0.10) to influence follicle size and Julian calving date respectively. Diameter of the largest follicle tended to be larger in moderate BC than in low-BC cows; whereas, CC and CG cows in moderate BC and homozygous (CC and GG) cows in low BC tended to calve 14 days earlier in relation to CG cows in low BC. In Herd 3, there was a genotype × forage type interaction (p < 0.05) on calving per cent, Julian calving date and calf weaning weight. In this study, genetic alterations (G allele at C994G) coupled with nutritional factors (low BC and toxic tall fescue) resulted in overall lower productivity in cows.

Myotonic dystrophy (DM) is an autosomal dominant neuromuscular disease with highly variable multisystemic manifestations. The mutation underlying DM is an unstable (CTG)n expansion in the 3´ UTR of the myotonic dystrophy protein kinase gene (DMPK). The pathophysiological mechanism(s) of the expanded (CTG)n repeat remains unclear. Various effects have been proposed, most recently a gain of function for mutant DMPK transcripts that results in a generalized RNA metabolism defect, mediated through one or several trans-acting proteins involved in RNA processing. This would in turn lead to the loss of function of multiple genes by qualitatively or quantitatively affecting post-transcriptional RNA processing, splicing or nuclear export of their transcripts. To test these hypotheses, we examined global mRNA expression changes between DM patients and normal controls by comprehensively and simultaneously profiling more than 6,800 human genes with oligo-based Genechip microarrays (Affymetrix). Total, nuclear and cytoplasmic RNA fractions of DM patient lymphoblastoid cell lines (four adult-onset, one congenital) as well as primary undifferentiated myoblasts and differentiated myotubes (one adult-onset, one congenital) were profiled. DM myoblasts in culture showed a reduced differentiation rate to myotubes and a tendency to dedifferentiate, suggesting a general block in or reprogramming of differentiation. Expression profiles of DM cell lines differed considerably from controls. Between the different DM cell lines profiled, many of the more than 6,800 genes assayed showed dysregulation. Moreover, comparison of nuclear and cytoplasmic fractions suggested a defect in the nuclear export of some processed transcripts. The number of genes dysregulated and the degree of dysregulation correlated with expansion size. Functions of the dysregulated genes were highly varied. In conclusion, DNA microarray expression profiling identified several novel DM phenotype effector candidate genes that may explain the complex pathogenesis of DM.Incyte has developed a new gene expression microarray (GEM) for analysis of the plant functional genomic system Arabidopsis thaliana. This GEM features over 7,000 array elements from a non-redundant cDNA collection; nearly 30% of the estimated 25,000 genes in this organism. Over 2,000 of these clones represent genes that have functional annotation in public databases. We are offering hybridization and analysis services for the Arabidopsis GEM via Incyte and Genome Systems. Arabidopsis is the primary model system for the study of dicot plant genomics. Academic and commercial groups are using the combination of genomic and genetic tools available for Arabidopsis to study complex problems in plant biology. We have performed a few biological studies using the Arabidopsis GEM to validate the platform and provide examples of possible applications. We will present sample data on these studies.The microarray facility at MSU is part of the Arabidopsis Functional Genomics Consortium (AFGC), a collaboration recently f...