The specification of SBML Level 1 is freely available from http://www.sbml.org/

Vesicular transport to and from the lysosome and late endosome is defective in patients with Chediak-Higashi syndrome (CHS) and in mutant beige (bg) mice. CHS and bg cells have giant, perinuclear vesicles with characteristics of late endosomes and lysosomes that arise from dysregulated homotypic fusion. CHS and bg lysosomes also exhibit compartmental missorting of proteins, such as elastase, glucuronidase and cathepsin G. Lyst, a candidate gene for bg, was identified by direct complementary DNA selection from a yeast artificial chromosome (YAC) clone containing a 650-kilobase segment of the bg-critical region on mouse chromosome 13. Lyst is disrupted by a 5-kilobase deletion in bg mice, and Lyst messenger RNA is markedly reduced in bg homozygotes. The homologous human gene, LYST, is highly conserved with mouse Lyst, and contains a frame-shift mutation at nucleotides 117-118 of the coding domain in a CHS patient. Thus bg mice and human CHS patients have homologous disorders associated with Lyst mutations. Lyst encodes a protein with a carboxy-terminal prenylation motif and multiple potential phosphorylation sites. Lyst protein is predicted to form extended helical domains, and has a region of sequence similar to stathmin, a coiled-coil phosphoprotein thought to act as a relay integrating cellular signal response coupling.

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In plants, genomic DNA methylation which contributes to development and stress responses can be actively removed by DEMETER-like DNA demethylases (DMLs). Indeed, in Arabidopsis DMLs are important for maternal imprinting and endosperm demethylation, but only a few studies demonstrate the developmental roles of active DNA demethylation conclusively in this plant. Here, we show a direct cause and effect relationship between active DNA demethylation mainly mediated by the tomato DML, SlDML2, and fruit ripeningan important developmental process unique to plants. RNAi SlDML2 knockdown results in ripening inhibition via hypermethylation and repression of the expression of genes encoding ripening transcription factors and rate-limiting enzymes of key biochemical processes such as carotenoid synthesis. Our data demonstrate that active DNA demethylation is central to the control of ripening in tomato.active DNA demethylation | DNA glycosylase lyase | epigenetic | tomato | fruit ripening G enomic DNA methylation is a major epigenetic mark that is instrumental to many aspects of chromatin function, including gene expression, transposon silencing, or DNA recombination (1-4). In plants, DNA methylation can occur at cytosine both in symmetrical (CG or CHG) and nonsymmetrical (CHH) contexts and is controlled by three classes of DNA methyltransferases, namely, the DNA Methyltransferase 1, Chromomethylases, and the Domain Rearranged Methyltransferases (5-7). Indeed, in all organisms, cytosine methylation can be passively lost after DNA replication in the absence of methyltransferase activity (1). However, plants can also actively demethylate DNA via the action of DNA GlycosylaseLyases, the so-called DEMETER-Like DNA demethylases (DMLs), that remove methylated cytosine, which is then replaced by a nonmethylated cytosine (8

Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAAbased reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 908 gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 408 to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.environmental sensing | systems biology R oot gravitropism has fascinated researchers since Knight (1) and Darwin (2). More recently, reorientation of Arabidopsis seedlings has been shown to trigger the asymmetric release of the growth regulator auxin from gravity-sensing columella cells at the root apex (Fig. 1A) (3-5). The resulting lateral auxin gradient is hypothesized to drive a differential growth response, where cell expansion on the lower side of the elongation zone is reduced relative to the upper side, causing the root to bend downward (6-8). Despite representing one of the oldest hypotheses in plant biology, key questions about auxin-regulated root gravitropism remain to be experimentally determined. How rapidly does the lateral auxin gradient form? Is this timescale consistent with the theory that auxin redistribution drives root bending? How long does the lateral auxin gradient persist? What triggers auxin redistribution to return to equal levels?Our understanding of gravity-induced auxin redistribution has been limited by the tools available to monitor auxin concentrations at high spatiotemporal resolution. Currently, the most widely used tools to follow auxin distribution in tissues are auxin-inducible reporters such as DR5::GFP (3, 4). However, as an output of the auxin response pathway (Fig. 1B), the activity of the DR5 reporter does not directly relate to endogenous auxin abundance, but also depends on additional parameters including local auxin signaling capacities and rates of transcription and translation (Fig. 1B). In practice, these intermediate processes confer a time delay of ∼1.5-2 h between changes in auxin abundance and DR5 reporter activity (9, 4), making it difficult to quantify the speed and magnitude of fold changes in auxin distribution during a root gravitropic response.Auxi...