A novel promoter from soybean that is active in a complex developmental pattern with and without its proximal 650 base pairs

We report the isolation of a novel soybean gene, Msg, which is highly expressed in developing soybean pods. The gene shows significant homology to a family of fruit- and flower-specific genes, designated the major latex protein (MLP) homologues, so far reported in only a few species and whose functions are unknown. The MLPs are more distantly related to a group of pathogenesis-related proteins (IPR or PR-10) whose functions are likewise unknown. This is the first report of a MLP homologue in a plant for which there is already an IPR-protein reported. We performed an analysis of the Msg promoter with 14 different promoter fragments ranging from 0.65 kb to 2.26 kb, fused to the uidA (GUS) gene. High transient expression was obtained with all the constructs upon particle bombardment in soybean and green bean pods. Stable Arabidopsis transformants were obtained with the Agrobacterium vacuum infiltration method. The promoter is fully active in Arabidopsis only in plants transformed with the 2.26 kb fragment promoter, expressing GUS in nectaries, nodes, short style and in guard cells of the silique, pedicel and stem but not in mature leaves. Surprisingly, the proximal 650 bp TATA-containing region cannot function on its own in Arabidopsis and can be deleted without a change in expression pattern in both Arabidopsis and soybean. Thus, tissue-specific regions of the complex Msg promoter reside in the distal 5 regions upstream of a dispensable TATA box in contrast to many examples of tissue-specific elements that reside much closer to the TATA box.     

Oxalate-induced and cell-cycle-dependent expression of nuclear pore complex oxalate binding protein gp210

The effect of oxalate, a constituent of renal stone, on the expression of nuclear pore complex oxalate binding protein (gp210) in Vero monkey kidney cells was examined. The expression of this protein was found to increase more in mitotic phase than in S phase, suggesting cell cycle dependency. Exposure of cells to oxalate-containing growth medium resulted in a relative increase in nuclear pore complex oxalate binding protein in each stage of cell cycle. The concentration of this protein was found to increase six times in the telophase stage of the cells exposed to high concentrations of oxalate in the growth medium, though slight reduction in cell density was observed. Structural analogues of oxalate did not show any stimulatory effect on expression of this oxalate binding protein. Hence, the expression of the nuclear pore complex oxalate binding protein gp210 was specific to oxalate and is cell cycle dependent.     

Clarification of yeast by colloidal gas aphrons

Summary Colloidal gas aphrons or CGAs were employed in a flotation column for the recovery of yeast from aqueous solutions. The CGAs sparging rate was a critical factor that governed the efficiency of the process. The separation efficiency was less than 30% at a sparging rate of 1.3 ml sec^–1 and increased exponentially up to 90% as the sparging rate was increased to 2.4 ml sec^–1. Whereas there was no appreciable change in the separation efficiency with CGAs sparging rates for high initial feed concentrations, the maximum achievable efficiency decreased with an increase in the initial feed concentration. In general, a decrease in pH will improve the separation efficiency.     

Structure and functions of γ-dodecalactone isolated from Antrodia camphorata for NK cell activation

The preserved fungal species Antrodia camphorata has diverse health-promoting effects and has been popularly used in East Asia as a traditional herb. We isolated a volatile compound from the culture medium of A. camphorata and identified it as γ-dodecalactone (γ-DDL). Cytomic screening for immune-modulating activity revealed that γ-DDL can activate human NK cells to express the early activation marker CD69. Further experiments showed that γ-DDL not only can induce NK cells to express CD69 but also stimulate NK cells to secrete cytotoxic molecules (FasL and granzyme B) and Th1 cytokines (TNF-α and INF-γ).Measuring the distribution of γ-DDL in the subcellular compartments of NK cells revealed that γ-DDL has been converted to 4-hydroxydodecanoic acid (an acyclic isomer of γ-DDL) in a time-dependent manner in the cytoplasm.Synthetic (R,S)-4-hydroxydodecanoic acid activated NK cells to express CD69 mRNA within 10 min, in contrast to γ-DDL, which activated NK cells to express CD69 within 50 min. This faster activation suggests that γ-DDL has converted to 4-hydroxydodecanoic acid and to stimulate the NK cells to express CD69.Optically pure (R)-(+)-4-hydroxydodecanoic acid and (S)-(?)-4-hydroxydodecanoic acid were obtained via: (1) synthesis of its diastereomeric esters of (R,S)-4-hydroxydodecanoic (R)-(?)-2-phenylpropionate; (2) separation of diastereomers via preparative HPLC, and (3) subsequent hydrolysis of the obtained optical pure ester of (R)-(+)-4-hydroxydodecanoic acid (R)-(?)-2-phenylpropionate and (R)-(?)-4-hydroxydodecanoic acid (R)-(?)-2-phenylpropionate, respectively. Further assays of NK cells activation using each enantiomer showed that only the (R)-(+)-4-hydroxydodecanoic acid can activate NK cells.     

PCA and Clustering Reveal Alternate mtDNA Phylogeny of N and M Clades

Phylogenetic trees based on mtDNA polymorphisms are often used to infer the history of recent human migrations. However, there is no consensus on which method to use. Most methods make strong assumptions which may bias the choice of polymorphisms and result in computational complexity which limits the analysis to a few samples/polymorphisms. For example, parsimony minimizes the number of mutations, which biases the results to minimizing homoplasy events. Such biases may miss the global structure of the polymorphisms altogether, with the risk of identifying a "common" polymorphism as ancient without an internal check on whether it either is homoplasic or is identified as ancient because of sampling bias (from oversampling the population with the polymorphism). A signature of this problem is that different methods applied to the same data or the same method applied to different datasets results in different tree topologies. When the results of such analyses are combined, the consensus trees have a low internal branch consensus. We determine human mtDNA phylogeny from 1737 complete sequences using a new, direct method based on principal component analysis (PCA) and unsupervised consensus ensemble clustering. PCA identifies polymorphisms representing robust variations in the data and consensus ensemble clustering creates stable haplogroup clusters. The tree is obtained from the bifurcating network obtained when the data are split into k = 2,3,4,...,kmax clusters, with equal sampling from each haplogroup. Our method assumes only that the data can be clustered into groups based on mutations, is fast, is stable to sample perturbation, uses all significant polymorphisms in the data, works for arbitrary sample sizes, and avoids sample choice and haplogroup size bias. The internal branches of our tree have a 90% consensus accuracy. In conclusion, our tree recreates the standard phylogeny of the N, M, L0/L1, L2, and L3 clades, confirming the African origin of modern humans and showing that the M and N clades arose in almost coincident migrations. However, the N clade haplogroups split along an East-West geographic divide, with a "European R clade" containing the haplogroups H, V, H/V, J, T, and U and a "Eurasian N subclade" including haplogroups B, R5, F, A, N9, I, W, and X. The haplogroup pairs (N9a, N9b) and (M7a, M7b) within N and M are placed in nonnearest locations in agreement with their expected large TMRCA from studies of their migrations into Japan. For comparison, we also construct consensus maximum likelihood, parsimony, neighbor joining, and UPGMA-based trees using the same polymorphisms and show that these methods give consistent results only for the clade tree. For recent branches, the consensus accuracy for these methods is in the range of 1-20%. From a comparison of our haplogroups to two chimp and one bonobo sequences, and assuming a chimp-human coalescent time of 5 million years before present, we find a human mtDNA TMRCA of 206,000 +/- 14,000 years before present.     

Cyclic somatic embryogenesis and efficient plant regeneration from callus of safflower

Efficient plant regeneration through somatic embryogenesis was established for safflower (Carthamus tinctorius L.) cv. NARI-6. Embryogenic calli were induced from 10 to 17-d-old cotyledon and leaf explants from in vitro seedlings. High frequency (94.3 %) embryogenic callus was obtained from cotyledon explants cultured on Murashige and Skoog’s germination (MSG) basal medium supplemented with thidiazuron, 2-isopentenyladenine and indole-3-butyric acid. Primary, secondary and cyclic somatic embryos were formed from embryogenic calli in a different media free of plant growth regulators, however, 100 % cyclic somatic embryogenesis was obtained from cotyledon derived embryogenic calli cultured on MSG. Somatic embryos matured and germinated in quarter-strength MSG medium supplemented with gibberellic acid. Cotyledons with root poles or non root poles were converted to normal plantlets and produced adventitious roots in rooting medium. Rooted plants were acclimatized and successfully transferred to the field.     

The arginine-rich motif of Bamboo mosaic virus satellite RNA-encoded P20 mediates self-interaction, intracellular targeting, and cell-to-cell movement

Satellite RNA of Bamboo mosaic virus (satBaMV) has a single open reading frame for a nonstructural, RNA-binding protein, P20, which facilitates the long-distance movement of satBaMV in Nicotiana benthamiana. Here, we elucidate various biological properties of P20 and the involvement of a single domain in its activities. P20 displayed a strong self-interaction in vitro and in vivo, and cross-linking assays demonstrated its oligomerization. Domain mapping, using the bacterial two-hybrid system, indicated that the self-interacting domain overlaps the RNA-binding domain in the N-terminal arginine-rich motif (ARM) of P20. The deletion of the ARM abolished the self-interaction of P20 in vitro and in vivo and impaired its intracellular targeting and efficient cell-to-cell movement in N. benthamiana leaves. Moreover, RNA and protein accumulation of the ARM deletion mutant of satBaMV was significantly reduced in leaves systemically coinfected with Bamboo mosaic potexvirus and satBaMV. This is the first report of the involvement of ARM in various biological activities of a satellite RNA-encoded protein during infection of its host.     

Zinc Modulates the Interaction of Protein C and Activated Protein C with Endothelial Cell Protein C Receptor

Zinc is an essential trace element for human nutrition and is critical to the structure, stability, and function of many proteins. Zinc ions were shown to enhance activation of the intrinsic pathway of coagulation but down-regulate the extrinsic pathway of coagulation. The protein C pathway plays a key role in blood coagulation and inflammation. At present there is no information on whether zinc modulates the protein C pathway. In the present study we found that Zn²⁺ enhanced the binding of protein C/activated protein C (APC) to endothelial cell protein C receptor (EPCR) on endothelial cells. Binding kinetics revealed that Zn²⁺ increased the binding affinities of protein C/APC to EPCR. Equilibrium dialysis with ⁶⁵Zn²⁺ revealed that Zn²⁺ bound to the Gla domain as well as sites outside of the Gla domain of protein C/APC. Intrinsic fluorescence measurements suggested that Zn²⁺ binding induces conformational changes in protein C/APC. Zn²⁺ binding to APC inhibited the amidolytic activity of APC, but the inhibition was reversed by Ca²⁺. Zn²⁺ increased the rate of APC generation on endothelial cells in the presence of physiological concentrations of Ca²⁺ but did not further enhance increased APC generation obtained in the presence of physiological concentrations of Mg²⁺ with Ca²⁺. Zn²⁺ had no effect on the anticoagulant activity of APC. Zn²⁺ enhanced APC-mediated activation of protease activated receptor 1 and p44/42 MAPK. Overall, our data show that Zn²⁺ binds to protein C/APC, which results in conformational changes in protein C/APC that favor their binding to EPCR.     

Functional Comparison of Human Adenomatous Polyposis Coli (APC) and APC-Like in Targeting Beta-Catenin for Degradation

Truncating mutations affect the adenomatous polyposis coli (APC) gene in most cases of colon cancer, resulting in the stabilization of β-catenin and uncontrolled cell proliferation. We show here that colon cancer cell lines express also the paralog APC-like (APCL or APC2). RNA interference revealed that it controls the level and/or the activity of β-catenin, but it is less efficient and binds less well to β-catenin than APC, thereby providing one explanation as to why the gene is not mutated in colon cancer. A further comparison indicates that APCL down-regulates the β-catenin level despite the lack of the 15R region known to be important in APC. To understand this discrepancy, we performed immunoprecipitation experiments that revealed that phosphorylated β-catenin displays a preference for binding to the 15 amino acid repeats (15R) rather than the first 20 amino acid repeat of APC. This suggests that the 15R region constitutes a gate connecting the steps of β-catenin phosphorylation and subsequent ubiquitination/degradation. Using RNA interference and domain swapping experiments, we show that APCL benefits from the 15R of truncated APC to target β-catenin for degradation, in a process likely involving heterodimerization of the two partners. Our data suggest that the functional complementation of APCL by APC constitutes a substantial facet of tumour development, because the truncating mutations of APC in colorectal tumours from familial adenomatous polyposis (FAP) patients are almost always selected for the retention of at least one 15R.