Fruit indehiscence caused by enhanced expression of NO TRANSMITTING TRACT in Arabidopsis thaliana

In flowering plants, fruit dehiscence enables seed dispersal. Here we report that ntt-3D, an activation tagged allele of NO TRANSMITTING TRACT (NTT), caused a failure of fruit dehiscence in Arabidopsis. We identified ntt-3D, in which the 35S enhancer was inserted adjacent to AT3G-57670, from our activation tagged mutant library. ntt-3D mutants showed serrated leaves, short siliques, and indehiscence phenotypes. NTT-overexpressing plants largely phenocopied the ntt-3D plants. As the proximate cause of the indehiscence, ntt-3D plants exhibited a near absence of valve margin and lignified endocarp b layer in the carpel. In addition, the replum was enlarged in ntt-3D mutants. NTT expression reached a peak in flowers at stage 11 and gradually decreased thereafter and pNTT::GUS expression was mainly observed in the replum, indicating a potential role in fruit patterning. NTT:GFP localized in the nucleus and cytoplasm. FRUITFULL (FUL) expression was downregulated in ntt-3D mutants and ntt-3D suppressed upregulation of FUL in replumless mutants. These results indicate that NTT suppresses FUL, indicating a potential role in patterning of the silique. In seed crops, a reduction in pod dehiscence can increase yield by decreasing seed dispersal; therefore, our results may prove useful as a basis to improve crop yield.     

Sample size calculation for studies comparing binary outcomes using historical controls

In historical control trials (HCTs), the experimental therapy is compared with a control therapy that has been evaluated in a previously conducted trial. Makuch and Simon developed a sample size formula where the observations from the HC group were considered not subject to sampling variability. Many researchers have pointed out that the Makuch–Simon sample size formula does not preserve the nominal power and type I error. We develop a sample size calculation approach that properly accounts for the uncertainty in the true response rate of the HC group. We demonstrate that the empirical power and type I error, obtained over the simulated HC data, have extremely skewed distributions. We then derive a closed‐form sample size formula that enables researchers to control percentiles, instead of means, of the power and type I error accounting for the skewness of the distributions. A simulation study demonstrates that this approach preserves the operational characteristics in a more realistic scenario where the true response rate of the HC group is unknown. We also show that the controlling percentiles can be used to describe the joint behavior of the power and type I error. It provides a new perspective on the assessment of HCTs.     

Soluble oligomers of the intramembrane serine protease YqgP are catalytically active in the absence of detergents

Rhomboid, a polytopic membrane serine protease, represents a unique class of proteases that cleave substrates within the transmembrane domain. Elucidating the mechanism of this extraordinary catalysis comes with inherent challenges related to membrane-associated peptide hydrolysis. Here we established a system that allows expression and isolation of YqgP, a rhomboid homologue from Bacillus subtilis, as a soluble protein. Intriguingly, soluble YqgP is able to specifically cleave a peptide substrate that contains the transmembrane domain of Spitz. Mutation of the catalytic dyad abolished protease activity, and substitution of another highly conserved residue, Asn241, with Ala or Asp significantly reduced the catalytic efficiency of YqgP. We have identified the cleavage site that resides in the middle of the transmembrane domain of Spitz. Replacement of two residues that contribute to the scissile bond by Ala did not eliminate cleavage, but rather led to additional or alternative cleavages. Moreover, we have demonstrated that soluble YqgP exists as oligomers that are required for catalytic activity. These results suggest that soluble oligomers of maltose binding protein-YqgP complexes form micellelike structures that are able to retain the active conformation of the protease for catalysis. Therefore, this work not only provides a unique system for elucidating the reaction mechanism of rhomboid but also will facilitate the characterization of other intramembrane proteases as well as non-protease membrane proteins.     

Zinc metal solubilization by Gluconacetobacter diazotrophicus and induction of pleomorphic cells

Gluconacetobacter diazotrophicus strain PAl5 exhibited a minimum inhibitory concentration value of 11 mM in an LGI medium amended with ZnCl2. When an LGI medium was amended with Zn metal, solubilization halos were observed in a plate assay, and further solubilization was confirmed in a broth assay. The maximum solubilization was recorded after 120 h with a 0.1% Zn metal amendment. During solubilization, the culture growth and pH of the broth were indirectly correlated. Using a Fourier Transform Infrared Spectroscopy analysis, one of the agents solubilizing the Zn metal was identified as gluconic acid. When the Zn-amended broth was observed under a bright field microscope, long involution cells were observed, and further analysis with Atomic Force Microscopy revealed highly deformed, pleomorphic, aggregate-like cells.     

A systemic administration of NMDA induces immediate early gene pip92 in the hippocampus

Abstract : In the mammalian CNS, aspartate and glutamate are major excitatory amino acids, and their receptors are believed to mediate a wide range of physiological and pathological processes, including neurotransmission, plasticity, excitotoxicity, and various forms of neurodegeneration. The immediate early gene pip92 has been identified in serum-stimulated BALB/c 3T3 fibroblasts, activated T lymphocytes treated with cycloheximide, and fibroblast growth factor-stimulated hippocampal cells during neuronal differentiation. In this study we have demonstrated that pip92 is expressed in the mouse brain after a single intraperitoneal injection of NMDA. The distribution of pip92 mRNA levels in the NMDA-treated mouse brain was investigated using in situ RT-PCR. The region-specific activation of pip92 in the CNS was observed 3 h after NMDA injection, and high levels of pip92 mRNA were detected in the hippocampal dentate gyrus and piriform cortex regions. In addition, the activation of pip92 by NMDA was mediated by activation of mitogen-activated protein kinases (MAPKs), such as c-Jun N-terminal kinase (JNK) and p38 kinase, but not extracellular signal-regulated kinase (ERK) in the mouse hippocampus and immortalized rat hippocampal progenitor cells. This study suggests that pip92 is likely to play an important role in neuronal cell death induced by excitotoxic NMDA injury in the CNS.     

Evidence for linkage and association with reading disability on 6p21.3-22

Reading disability (RD), or dyslexia, is a common heterogeneous syndrome with a large genetic component. Several studies have consistently found evidence for a quantitative-trait locus (QTL) within the 17 Mb (14.9 cM) that span D6S109 and D6S291 on chromosome 6p21.3-22. To characterize further linkage to the QTL, to define more accurately the location and the effect size, and to identify a peak of association, we performed Haseman-Elston and DeFries-Fulker linkage analyses, as well as transmission/disequilibrium, total-association, and variance-components analyses, on 11 quantitative reading and language phenotypes. One hundred four families with RD were genotyped with a new panel of 29 markers that spans 9 Mb of this region. Linkage results varied widely in degree of statistical significance for the different linkage tests, but multipoint analysis suggested a peak near D6S461. The average 6p QTL heritability for the 11 reading and language phenotypes was 0.27, with a maximum of 0.66 for orthographic choice. Consistent with the region of linkage described by these studies and others, there was a peak of transmission disequilibrium with a QTL centered at JA04 (chi2=9.48; empirical P=.0033; orthographic choice), and there was strong evidence for total association at this same marker (chi2=11.49; P=.0007; orthographic choice). Although the boundaries of the peak could not be precisely defined, the most likely location of the QTL is within a 4-Mb region surrounding JA04.