Intracellular localization of histone deacetylase HDA6 in plants

Journal of Plant Research - Histone modification is an important epigenetic mechanism in eukaryotes. Histone acetyltransferase and deacetylase regulate histone acetylation levels antagonistically,...     

An Early Arising Role of the MicroRNA156/529-SPL Module in Reproductive Development Revealed by the Liverwort Marchantia polymorpha

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An Arabidopsis example of association mapping in structured samples

A potentially serious disadvantage of association mapping is the fact that marker-trait associations may arise from confounding population structure as well as from linkage to causative polymorphisms. Using genome-wide marker data, we have previously demonstrated that the problem can be severe in a global sample of 95 Arabidopsis thaliana accessions, and that established methods for controlling for population structure are generally insufficient. Here, we use the same sample together with a number of flowering-related phenotypes and data-perturbation simulations to evaluate a wider range of methods for controlling for population structure. We find that, in terms of reducing the false-positive rate while maintaining statistical power, a recently introduced mixed-model approach that takes genome-wide differences in relatedness into account via estimated pairwise kinship coefficients generally performs best. By combining the association results with results from linkage mapping in F2 crosses, we identify one previously known true positive and several promising new associations, but also demonstrate the existence of both false positives and false negatives. Our results illustrate the potential of genome-wide association scans as a tool for dissecting the genetics of natural variation, while at the same time highlighting the pitfalls. The importance of study design is clear; our study is severely under-powered both in terms of sample size and marker density. Our results also provide a striking demonstration of confounding by population structure. While statistical methods can be used to ameliorate this problem, they cannot always be effective and are certainly not a substitute for independent evidence, such as that obtained via crosses or transgenic experiments. Ultimately, association mapping is a powerful tool for identifying a list of candidates that is short enough to permit further genetic study.     

Signal-transducing adaptor protein-2 modulates Fas-mediated T cell apoptosis by interacting with caspase-8

We found that an adaptor protein, signal-transducing adaptor protein (STAP)-2, is a new member of the Fas-death-inducing signaling complex and participates in activation-induced cell death in T cells. STAP-2 enhanced Fas-mediated apoptosis and caspase-8 aggregation and activation in Jurkat T cells. Importantly, STAP-2 directly interacted with caspase-8 and Fas, resulting in enhanced interactions between caspase-8 and FADD in the Fas-death-inducing signaling complex. Moreover, STAP-2 protein has a consensus caspase-8 cleavage sequence, VEAD, in its C-terminal domain, and processing of STAP-2 by caspase-8 was crucial for Fas-induced apoptosis. Physiologic roles of STAP-2 were confirmed by observations that STAP-2-deficient mice displayed impaired activation-induced cell death and superantigen-induced T cell depletion. Therefore, STAP-2 is a novel participant in the regulation of T cell apoptosis after stimulation.     

Functional interaction between plastidial starch phosphorylase and starch branching enzymes from rice during the synthesis of branched maltodextrins

The present study established the way in which plastidial α-glucan phosphorylase (Pho1) synthesizes maltodextrin (MD) which can be the primer for starch biosynthesis in rice endosperm. The synthesis of MD by Pho1 was markedly accelerated by branching enzyme (BE) isozymes, although the greatest effect was exhibited by the presence of branching isozyme I (BEI) rather than by isozyme IIa (BEIIa) or isozyme IIb (BEIIb). The enhancement of the activity of Pho1 by BE was not merely due to the supply of a non-reducing ends. At the same time, Pho1 greatly enhanced the BE activity, possibly by generating a branched carbohydrate substrate which is used by BE with a higher affinity. The addition of isoamylase to the reaction mixture did not prevent the concerted action of Pho1 and BEI. Furthermore, in the product, the branched structure was, at least to some extent, maintained. Based on these results we propose that the interaction between Pho1 and BE is not merely due to chain-elongating and chain-branching reactions, but occurs in a physically and catalytically synergistic manner by each activating the mutual capacity of the other, presumably forming a physical association of Pho1, BEI and branched MDs. This close interaction might play a crucial role in the synthesis of branched MDs and the branched MDs can act as a primer for the biosynthesis of amylopectin molecules.     

Presence of supercooling-facilitating (anti-ice nucleation) hydrolyzable tannins in deep supercooling xylem parenchyma cells in <Emphasis Type="Italic">Cercidiphyllum japonicum</Emphasis>

Xylem parenchyma cells (XPCs) in trees adapt to subzero temperatures by deep supercooling. Our previous study indicated the possibility of the presence of diverse kinds of supercooling-facilitating (SCF; anti-ice nucleation) substances in XPCs of katsura tree (Cercidiphyllum japonicum), all of which might have an important role in deep supercooling of XPCs. In the previous study, a few kinds of SCF flavonol glycosides were identified. Thus, in the present study, we tried to identify other kinds of SCF substances in XPCs of katsura tree. SCF substances were purified from xylem extracts by silica gel column chromatography and Sephadex LH-20 column chromatography. Then, four SCF substances isolated were identified by UV, mass and nuclear magnetic resonance analyses. The results showed that the four kinds of hydrolyzable gallotannins, 2,2′,5-tri-O-galloyl-α,β-d-hamamelose (trigalloyl Ham or kurigalin), 1,2,6-tri-O-galloyl-β-d-glucopyranoside (trigalloyl Glc), 1,2,3,6-tetra-O-galloyl-β-d-glucopyranoside (tetragalloyl Glc) and 1,2,3,4,6-penta-O-galloyl-β-d-glucopyranoside (pentagalloyl Glc), in XPCs exhibited supercooling capabilities in the range of 1.5–4.5°C, at a concentration of 1 mg mL⁻¹. These SCF substances, including flavonol glycosides and hydrolyzable gallotannins, may contribute to the supercooling in XPCs of katsura tree.     

Augmentation of innate immunity by low-dose irradiation

The effect of low-dose irradiation on the immune system was investigated in mice. When a 0.2 Gy dose of X-ray irradiation was administered every other day for a total of four times, the number of lymphocytes yielded by the liver, spleen and thymus decreased at the initial stage (around day 10). At this stage, NK cells, extrathymic T cells and NKT cells were found to be radioresistant. In other words, conventional lymphocytes were radiosensitive, even in the case of low-dose irradiation. However, the number of lymphocytes in all tested immune organs increased beyond the control level at the recovery stage (around day 28). Enumeration of the absolute number of lymphocyte subsets showed that the most prominently expanding populations were NK cells, extrathymic T cells and NKT cells, especially in the liver where primordial lymphocytes are primarily present. Functional and phenotypic activation of these populations also occurred at the recovery stage. It raised a possibility that an initial activation of macrophages by low-dose irradiation then mediated the present phenomenon. These results suggest that low-dose irradiation eventually has the potential to induce a hormesis effect on the immune system.     

NOVEL PROTEINS COMPRISING THE STRAMENOPILE TRIPARTITE MASTIGONEME IN OCHROMONAS DANICA (CHRYSOPHYCEAE)1

Two‐dimensional (2‐D) protein analysis of the mastigoneme fraction of the chromophyte alga Ochromonas danica E. G. Pringsh. showed the presence of several component proteins of the tubular mastigoneme. Adding to the reported gene Ocm1, three new genes (Ocm2, Ocm3, and Ocm4) belonging to the Ocm gene family were isolated using degenerate primers designed from predicted Ocm1 amino acid sequences. The predicted polypeptides encoded by Ocm2, Ocm3, and Ocm4 were smaller in size than Ocm1. However, they shared four highly conserved, cysteine‐rich, epithelial growth factor (EGF)‐like motifs, potentially involved in protein–protein interaction. In addition, Ocm2, Ocm3, and Ocm4 showed homology to the SIG protein family in the centric diatom Thalassiosira weissflogii (Grunow) Fryxell et Hasle, which is up‐regulated during early stages of sexual reproduction. Immunofluorescence analysis with a polyclonal antibody against the partial amino acid sequences of Ocm2, Ocm3, and Ocm4 showed that Ocm2 and Ocm3 were located in the basal segment region of mastigonemes attached on the surface of the anterior flagellum, and that Ocm4 was located within the tubular shaft portion similar to Ocm1.     

EFFECT OF LATRUNCULIN B AND BREFELDIN A ON CYTOKINESIS IN THE BROWN ALGA SCYTOSIPHON LOMENTARIA (SCYTOSIPHONALES,PHAEOPHYCEAE)1

In zygotes of the brown alga Scytosiphon lomentaria (Lyngb.) Link, cytokinesis proceeds by growth of membranous sacs, which are formed by fusion of Golgi vesicles and flat cisternae accumulated at the future cytokinetic plane. It has been reported that depolymerization of actin filaments by latrunculin B does not inhibit mitosis. However, this molecule prevents the formation of the actin plate, which appears at the region of intermingled microtubules from each centrosome just before and during cytokinesis. In this study, zygotes treated with latrunculin B were observed using EM. Remarkably, this reagent inhibited the formation of flat cisternae. Golgi vesicles gathered around the midzone between the two daughter nuclei and fused with the plasma membrane there. As a result, the plasma membrane invaginated, in a complicated manner, into the cytoplasm. However, these invaginations of the plasma membrane never produced a continuous partition membrane. The ultrastructure of zygotes treated with brefeldin A, which prevents Golgi‐mediated secretion, was also examined. Flat cisternae appeared at the future cytokinetic plane, and a new cell partition membrane was formed. However, the partition membrane became thick, because it was filled with amorphous material rather than the normal rigid fibrous material. These results suggested that actin is involved in the formation of flat cisternae, where it is necessary for completion of the new cell partition membrane, and that Golgi vesicles may play an important role in the deposition of cell wall material.