Inference of S-system models of genetic networks using Product Unit Neural Networks

In this study, we proposed the method of inference of genetic networks which expresses the regulation of genes. The proposed method does not solve the differential equations, learns the genetic networks using Product-Unit-Neural- Network (PUNN) and infer the S-system model of genetic networks which describes a set of differential equations. The experimental results show the proposal method is 160 times faster than the previous method which estimated S-system model of genetic networks while maintaining equivalent performance to the previous method. © 2008 IEEE

Initial Evaluation of AF78: a Rationally Designed Fluorine-18-Labelled PET Radiotracer Targeting Norepinephrine Transporter

Purpose Taking full advantage of positron emission tomography (PET) technology, fluorine-18-labelled radiotracers targeting norepinephrine transporter (NET) have potential applications in the diagnosis and assessment of cardiac sympathetic nerve conditions as well as the delineation of neuroendocrine tumours. However, to date, none have been used clinically. Drawbacks of currently reported radiotracers include suboptimal kinetics and challenging radiolabelling procedures. Procedures We developed a novel fluorine-18-labelled radiotracer targeting NET, AF78, with efficient one-step radiolabelling based on the phenethylguanidine structure. Radiosynthesis of AF78 was undertaken, followed by validation in cell uptake studies, autoradiography, and in vivo imaging in rats. Results [18F]AF78 was successfully synthesized with 27.9 ± 3.1 % radiochemical yield, > 97 % radiochemical purity and > 53.8 GBq/mmol molar activity. Cell uptake studies demonstrated essentially identical affinity for NET as norepinephrine and meta-iodobenzylgaunidine. Both ex vivo autoradiography and in vivo imaging in rats showed homogeneous and specific cardiac uptake. Conclusions The new PET radiotracer [18F]AF78 demonstrated high affinity for NET and favourable biodistribution in rats. A structure-activity relationship between radiotracer structures and affinity for NET was revealed, which may serve as the basis for the further design of NET targeting radiotracers with favourable features

Expression Analysis of an R3-Type MYB Transcription Factor CPC-LIKE MYB4 (TRICHOMELESS2) and CPL4-Related Transcripts in Arabidopsis

The CAPRICE (CPC)-like MYB gene family encodes R3-type MYB transcription factors in Arabidopsis. There are six additional CPC-like MYB sequences in the Arabidopsis genome, including TRYPTICHON (TRY), ENHANCER OF TRY AND CPC1 and 2 (ETC1 and ETC2), ENHANCER OF TRY AND CPC3/CPC-LIKE MYB3 (ETC3/CPL3), and TRICHOMELESS1 and 2 (TCL1 and TCL2). We independently identified CPC-LIKE MYB4 (CPL4), which was found to be identical to TCL2. RT-PCR analysis showed that CPL4 is strongly expressed in shoots, including true leaves, but not in roots. Promoter-GUS analyses indicated that CPL4 is specifically expressed in leaf blades. Although CPC expression was repressed in 35S::ETC1, 35S::ETC2 and 35S::CPL3 backgrounds, CPL4 expression was not affected by ETC1, ETC2 or CPL3 over-expression. Notably, several chimeric transcripts may result from inter-genic alternative splicing of CPL4 and ETC2, two tandemly repeated genes on chromosome II. At least two chimeric transcripts named CPL4-α and CPL4-β are expected to encode complete CPC-like MYB proteins

Distinct relationships between GLABRA2 and single-repeat R3 MYB transcription factors in the regulation of trichome and root hair patterning in Arabidopsis

• The patterning of epidermal cell types in Arabidopsis is an excellent model for studying the molecular basis of cell specification. Trichome and root hair formation is controlled by a transcriptional activator complex that induces the homeobox gene GLABRA2 (GL2) and some single-repeat R3 MYB genes (single MYB ). However, it remains unclear how the actions of GL2 and single MYBs are coordinated to regulate epidermal patterning. • GL2 is thought to act downstream of single MYBs to regulate trichome and root hair development. In order to test this hypothesis genetically, double and higher order mutants between gl2 and single myb were generated. • In these mutants, the glabrous phenotypes observed in the gl2 single mutants were partially recovered, suggesting that single MYBs may not act solely through GL2 to regulate trichome development. On the other hand, double and higher order mutants between gl2 and single myb phenocopied the root hair phenotype of gl2 single mutants, suggesting that GL2 and single MYBs act in a common pathway to regulate root hair patterning. • These findings reveal distinct relationships between GL2 and single MYBs in the regulation of trichome vs root hair development, and provide new insights into the molecular mechanism of epidermal patterning.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78641/1/j.1469-8137.2009.03067.x.pd

Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research

Prior to the availability of the genome sequence, the root of Arabidopsis had attracted a small but ardent group of researchers drawn to its accessibility and developmental simplicity. Roots are easily observed when grown on the surface of nutrient agar media, facilitating analysis of responses to stimuli such as gravity and touch. Developmental biologists were attracted to the simple radial organization of primary root tissues, which form a series of concentric cylinders around the central vascular tissue. Equally attractive was the mode of propagation, with stem cells at the tip giving rise to progeny that were confined to cell files. These properties of root development reduced the normal four-dimensional problem of development (three spatial dimensions and time) to a two-dimensional problem, with cell type on the radial axis and developmental time along the longitudinal axis. The availability of the complete Arabidopsis genome sequence has dramatically accelerated traditional genetic research on root biology, and has also enabled entirely new experimental strategies to be applied. Here we review examples of the ways in which availability of the Arabidopsis genome sequence has enhanced progress in understanding root biology.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79263/1/j.1365-313X.2010.04129.x.pd

Manganese deficiency alters the patterning and development of root hairs in Arabidopsis

Manganese (Mn) is the second most prevalent transition metal in the Earth's crust but its availability is often limited due to rapid oxidation and low mobility of the oxidized forms. Acclimation to low Mn availability was studied in Arabidopsis seedlings subjected to Mn deficiency. As reported here, Mn deficiency caused a thorough change in the arrangement and characteristics of the root epidermal cells. A proportion of the extra hairs formed upon Mn deficiency were located in atrichoblast positions, indicative of a post-embryonic reprogramming of the cell fate acquired during embryogenesis. When plants were grown under a light intensity of >50 μmol m−2 s−1 in the presence of manganese root hair elongation was substantially inhibited, whereas Mn-deficient seedlings displayed stimulated root hair development. GeneChip analysis revealed several candidate genes with potential roles in the reprogramming of rhizodermal cells. None of the genes that function in epidermal cell fate specification were affected by Mn deficiency, indicating that the patterning mechanism which controls the differentiation of rhizodermal cells during embryogenesis have been bypassed under Mn-deficient conditions. This assumption is supported by the partial rescue of the hairless cpc mutant by Mn deficiency. Inductively coupled plasma-optical emission spectroscopy (ICP-OES) analysis revealed that, besides the anticipated reduction in Mn concentration, Mn deficiency caused an increase in iron concentration. This increase was associated with a decreased transcript level of the iron transporter IRT1, indicative of a more efficient transport of iron in the absence of Mn

Positional Signaling and Expression of ENHANCER OF TRY AND CPC1 Are Tuned to Increase Root Hair Density in Response Phosphate Deficiency in Arabidopsis thaliana

Phosphate (Pi) deficiency induces a multitude of responses aimed at improving the acquisition of Pi, including an increased density of root hairs. To understand the mechanisms involved in Pi deficiency-induced alterations of the root hair phenotype in Arabidopsis (Arabidopsis thaliana), we analyzed the patterning and length of root epidermal cells under control and Pi-deficient conditions in wild-type plants and in four mutants defective in the expression of master regulators of cell fate, CAPRICE (CPC), ENHANCER OF TRY AND CPC 1 (ETC1), WEREWOLF (WER) and SCRAMBLED (SCM). From this analysis we deduced that the longitudinal cell length of root epidermal cells is dependent on the correct perception of a positional signal (‘cortical bias’) in both control and Pi-deficient plants; mutants defective in the receptor of the signal, SCM, produced short cells characteristic of root hair-forming cells (trichoblasts). Simulating the effect of cortical bias on the time-evolving probability of cell fate supports a scenario in which a compromised positional signal delays the time point at which non-hair cells opt out the default trichoblast pathway, resulting in short, trichoblast-like non-hair cells. Collectively, our data show that Pi-deficient plants increase root hair density by the formation of shorter cells, resulting in a higher frequency of hairs per unit root length, and additional trichoblast cell fate assignment via increased expression of ETC1

A frontal attention mechanism in the visual mismatch negativity

Automatic detection of environmental change is a core component of attention. The mismatch negativity (MMN), an electrophysiological marker of this mechanism, has been studied prominently in the auditory domain, with cortical generators identified in temporal and frontal regions. Here, we combined electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) to assess whether the underlying frontal regions associated with auditory change detection also play a role in visual change detection. Twenty healthy young adults completed a visual MMN task in separate EEG and fMRI sessions. Region of interest analyses were conducted on left and right middle frontal (MFG) and inferior frontal (IFG) gyri, i.e., the frontal areas identified as potential auditory MMN generators. A significant increase in activation was observed in the left IFG and MFG in response to blocks containing deviant stimuli. These findings suggest that a frontal mechanism is involved in the detection of change in the visual MMN. Our results support the notion that frontal mechanisms underlie attention switching, as measured via MMN, across multiple modalities

Genome-Wide Identification of R2R3-MYB Genes and Expression Analyses During Abiotic Stress in

The R2R3-MYB is one of the largest families of transcription factors, which have been implicated in multiple biological processes. There is great diversity in the number of R2R3-MYB genes in different plants. However, there is no report on genome-wide characterization of this gene family in cotton. In the present study, a total of 205 putative R2R3-MYB genes were identified in cotton D genome (Gossypium raimondii), that are much larger than that found in other cash crops with fully sequenced genomes. These GrMYBs were classified into 13 groups with the R2R3-MYB genes from Arabidopsis and rice. The amino acid motifs and phylogenetic tree were predicted and analyzed. The sequences of GrMYBs were distributed across 13 chromosomes at various densities. The results showed that the expansion of the G. Raimondii R2R3-MYB family was mainly attributable to whole genome duplication and segmental duplication. Moreover, the expression pattern of 52 selected GrMYBs and 46 GaMYBs were tested in roots and leaves under different abiotic stress conditions. The results revealed that the MYB genes in cotton were differentially expressed under salt and drought stress treatment. Our results will be useful for determining the precise role of the MYB genes during stress responses with crop improvement