Strike while the ionome is hot: making the most of plant genomic advances

Research into plant nutrition focuses on how plants maintain elemental differences from the surrounding environment. Classic genetic analysis has been hindered because it is not possible to accurately screen for perturbations in this disequilibrium. Recent work by Lahner and colleagues has enabled efficient screening and identification of plants that have altered elemental profiles.     

Phylogenetic utility of the nuclear gene arginine decarboxylase: an example from Brassicaceae

Arginine decarboxylase (ADC) is an important enzyme in the production of putrescine and polyamines in plants. It is encoded by a single or low-copy nuclear gene that lacks introns in sequences studied to date. The rate of Adc amino acid sequence evolution is similar to that of ndhF for the angiosperm family studied. Highly conserved regions provide several target sites for PCR priming and sequencing and aid in nucleotide and amino acid sequence alignment across a range of taxonomic levels, while a variable region provides an increased number of potentially informative characters relative to ndhF for the taxa surveyed. The utility of the Adc gene in plant molecular systematic studies is demonstrated by analysis of its partial nucleotide sequences obtained from 13 representatives of Brassicaceae and 3 outgroup taxa, 2 from the mustard oil clade (order Capparales) and 1 from the related order Malvales. Two copies of the Adc gene, Adc1 and Adc2, are found in all members of the Brassicaceae studied to data except the basal genus Aethionema. The resulting Adc gene tree provides robust phylogenetic data regarding relationships within the complex mustard family, as well as independent support for proposed tribal realignments based on other molecular data sets such as those from chloroplast DNA.      

The number distribution for involved lymph nodes in cancer

The number of involved lymph nodes exhibits considerable heterogeneity within populations. Here, the implications of population heterogeneity are explored with respect to the kinematics of nodal metastases. Data from the National Cancer Institute's Surveillance, Epidemiology, and End Results program for 224656 breast, 12404 gastric, 18015 rectal, 4117 cervical and 2443 laryngeal cancers as well as 9118 melanomas were used to construct frequency distributions for the number of involved nodes which were then fitted to the negative binomial distribution. The negative binomial distribution described the heterogeneity in nodal involvement well. The patterns of nodal involvement can be explained by either of two models: one where involved nodes could seed further nodal metastases, the other where the number of nodal metastases in any individual was randomly distributed, with the deviations between patients accounted for by population heterogeneity. Since the number of sampled nodes similarly approximated a negative binomial distribution, random involvement with superimposed population heterogeneity would more credibly explain both sets of observations.     

In planta regulation of the Arabidopsis Ca(2+)/H(+) antiporter CAX1

Vacuolar localized Ca(2+)/H(+) exchangers such as Arabidopsis thaliana cation exchanger 1 (CAX1) play important roles in Ca(2+) homeostasis. When expressed in yeast, CAX1 is regulated via an N-terminal autoinhibitory domain. In yeast expression assays, a 36 amino acid N-terminal truncation of CAX1, termed sCAX1, and variants with specific mutations in this N-terminus, show CAX1-mediated Ca(2+)/H(+) antiport activity. Furthermore, transgenic plants expressing sCAX1 display increased Ca(2+) accumulation and heightened activity of vacuolar Ca(2+)/H(+) antiport. Here the properties of N-terminal CAX1 variants in plants and yeast expression systems are compared and contrasted to determine if autoinhibition of CAX1 is occurring in planta. Initially, using ionome analysis, it has been demonstrated that only yeast cells expressing activated CAX1 transporters have altered total calcium content and fluctuations in zinc and nickel. Tobacco plants expressing activated CAX1 variants displayed hypersensitivity to ion imbalances, increased calcium accumulation, heightened concentrations of other mineral nutrients such as potassium, magnesium and manganese, and increased activity of tonoplast-enriched Ca(2+)/H(+) transport. Despite high in planta gene expression, CAX1 and N-terminal variants of CAX1 which were not active in yeast, displayed none of the aforementioned phenotypes. Although several plant transporters appear to contain N-terminal autoinhibitory domains, this work is the first to document clearly N-terminal-dependent regulation of a Ca(2+) transporter in transgenic plants. Engineering the autoinhibitory domain thus provides a strategy to enhance transport function to affect agronomic traits.     

Drosophila modeling of heritable neurodevelopmental disorders

Heritable neurodevelopmental disorders are multifaceted disease conditions encompassing a wide range of symptoms including intellectual disability, cognitive dysfunction, autism and myriad other behavioral impairments. In cases where single, causative genetic defects have been identified, such as Angelman syndrome, Rett syndrome, Neurofibromatosis Type 1 and Fragile X syndrome, the classical Drosophila genetic system has provided fruitful disease models. Recent Drosophila studies have advanced our understanding of UBE3A, MECP2, NF1 and FMR1 function, respectively, in genetic, biochemical, anatomical, physiological and behavioral contexts. Investigations in Drosophila continue to provide the essential mechanistic understanding required to facilitate the conception of rational therapeutic treatments.     

Fathoming fragile X in fruit flies

Fragile X syndrome (FraX) is the most common inherited mental retardation disease. It is caused by mutation of the fragile X mental retardation 1 (fmr1) gene. The FMR1 protein (FMRP) is a widely expressed RNA-binding translational regulator with reportedly hundreds of potential targets. Recent work has focused on putative roles of FMRP in regulating the development and plasticity of neuronal synaptic connections. The newest animal model of FraX, the fruit fly Drosophila, has revealed several novel mechanistic insights into the disease. This review focuses on Drosophila FMRP as (i) a negative regulator of translation via noncoding RNA, including microRNA and adaptor BC1 RNA-mediated silencing mechanisms; (ii) a negative regulator of microtubule cytoskeleton stability; and (iii) a negative regulator of neuronal architectural complexity.     

Protein expression profiling of the drosophila fragile X mutant brain reveals up-regulation of monoamine synthesis

Fragile X syndrome is the most common form of inherited mental retardation, associated with both cognitive and behavioral anomalies. The disease is caused by silencing of the fragile X mental retardation 1 (fmr1) gene, which encodes the mRNA-binding, translational regulator FMRP. Previously we established a disease model through mutation of Drosophila fmr1 (dfmr1) and showed that loss of dFMRP causes defects in neuronal structure, function, and behavioral output similar to the human disease state. To uncover molecular targets of dFMRP in the brain, we use here a proteomic approach involving two-dimensional difference gel electrophoresis analyses followed by mass spectrometry identification of proteins with significantly altered expression in dfmr1 null mutants. We then focus on two misregulated enzymes, phenylalanine hydroxylase (Henna) and GTP cyclohydrolase (Punch), both of which mediate in concert the synthetic pathways of two key monoamine neuromodulators, dopamine and serotonin. Brain enzymatic assays show a nearly 2-fold elevation of Punch activity in dfmr1 null mutants. Consistently brain neurochemical assays show that both dopamine and serotonin are significantly increased in dfmr1 null mutants. At a cellular level, dfmr1 null mutant neurons display a highly significant elevation of the dense core vesicles that package these monoamine neuromodulators for secretion. Taken together, these data indicate that dFMRP normally down-regulates the monoamine pathway, which is consequently up-regulated in the mutant condition. Elevated brain levels of dopamine and serotonin provide a plausible mechanistic explanation for aspects of cognitive and behavioral deficits in human patients.     

Ligand concentration is a driver of divergent signaling and pleiotropic cellular responses to FGF

Fibroblast growth factors (FGFs) are soluble ligands important for embryonic patterning, limb and brain development, and stem cell proliferation. They activate specific receptors (FGFR) to elicit changes in gene expression and cellular responses such as proliferation, differentiation, and survival, but the extent to which these pleiotropic responses are driven by FGF concentration gradients has not been systematically addressed. Here, we show that a single cell type exhibits divergent, even opposing, responses to a single FGF dependent on the exposure concentration, and that this is controlled by differential signaling with specific negative feedback inhibition. Low concentrations of FGF2 stimulate survival and differentiation but actively inhibit proliferation while intermediate concentrations stimulate proliferation in the presence of serum but apoptosis in its absence. Intriguingly, high concentrations reverse the proliferation and apoptosis effects, and mirror the low concentration effects: inhibition of proliferation and stimulation of survival and differentiation. By screening for activation of sampled signaling intermediates across the FGF2 concentration range in fibroblasts, we show that the peak in proliferation and apoptosis correlates with abrupt activation of FRS-2 and Erk that is specifically down-regulated by high concentrations of FGF2, a pattern that contrasts with an incremental increase in activation of p38 MAP kinase and the FGFR itself, across the FGF2 concentration range. Whilst proliferation stimulated by FGF2 was dependent on p38 MAP kinase, apoptosis stimulated by proliferative concentrations of FGF2 under serum-free conditions was, in contrast, dependent on Erk MAP kinase. These findings indicate that FGF exposure concentration precisely controls intracellular signaling and cellular responses to the growth factor, and have important implications for understanding how FGF gradients influence cell proliferation, survival, and differentiation during processes such as limb development.