BioBrick-based 'Quick Gene Assembly' in vitro.

Because of the technological limitations of de novo DNA synthesis in (i) making constructs containing tandemly repeated DNA sequence units, (ii) making an unbiased DNA library containing DNA fragments with sequence multiplicity in a specific region of target genes, and (iii) replacing DNA fragments, development of efficient and reliable biochemical gene assembly methods is still anticipated. We succeeded in developing a biological standardized genetic parts that are flanked between a common upstream and downstream nucleotide sequences in an appropriate plasmid DNA vector (BioBrick)-based novel assembly method that can be used to assemble genes composed of 25 tandemly repeated BioBricks in the correct format in vitro. We named our new DNA part assembly system: 'Quick Gene Assembly (QGA)'. The time required for finishing a sequential fusion of five BioBricks is less than 24 h. We believe that the QGA method could be one of the best methods for 'gene construction based on engineering principles' at the present time, and is also a method suitable for automation in the near future.

Fiber knob domain lacking the shaft sequence but fused to a coiled coil is a candidate subunit vaccine against egg-drop syndrome.

Egg-drop syndrome (EDS) virus is an avian adenovirus that causes a sudden drop in egg production and in the quality of the eggs when it infects chickens, leading to substantial economic losses in the poultry industry. Inactivated EDS vaccines produced in embryonated duck eggs or cell culture systems are available for the prophylaxis of EDS. However, recombinant subunit vaccines that are efficacious and inexpensive are a desirable alternative. In this study, we engineered chimeric fusion proteins in which the trimeric fiber knob domain lacking the triple ß-spiral motif in the fiber shaft region was genetically fused to trimeric coiled coils, such as those of the engineered form of the GCN4 leucine zipper peptide or chicken cartilage matrix protein (CMP). The fusion proteins were expressed predominantly as soluble trimeric proteins in Escherichia coli at levels of 15-80mg/L of bacterial culture. The single immunization of chickens with the purified fusion proteins, at a dose equivalent to 10µg of the knob moiety, elicited serum antibodies with high hemagglutination inhibition (HI) activities, similar to those induced by an inactivated EDS vaccine. A dose-response analysis indicated that a single immunization with as little as 1µg of the knob moiety of the CMP-knob fusion protein was as effective as the inactivated vaccine in inducing antibodies with HI activity. The immunization of laying hens had no apparent adverse effects on egg production and effectively prevented clinical symptoms of EDS when the chickens were challenged with pathogenic EDS virus. This study demonstrates that the knob domain lacking the shaft sequence but fused to a trimeric coiled coil is a promising candidate subunit vaccine for the prophylaxis of EDS in chickens.

The Arabidopsis transcriptional repressor ERF9 participates in resistance against necrotrophic fungi.

Complex plant defenses that include the hypersensitive response (HR) are mediated by plant hormones, such as salicylic acid (SA), jasmonic acid (JA) and ethylene. We previously isolated the Arabidopsis DEAR1 (DREB AND EAR MOTIF PROTEIN 1) regulator and showed that its overexpression DEAR1 (DEAR1ox) resulted in a dwarf phenotype and lesion-like cell death, accompanied by elevated expression of PR (PATHOGENESIS-RELATED) genes. Here, we show that transgenic Arabidopsis overexpressing DEAR1 (DEAR1ox) has enhanced resistance to the necrotrophic fungus Botrytis cinerea (B. cinerea). This result indicates that DEAR1 represses negative regulators of plant defense responses, including transcriptional repressors belonging to the ERF (ETHYLEN RESPONSE FACTOR) family. Knockout mutants of ERF9 (erf9), which were down-regulated in DEAR1ox plants, showed transcriptional promotion of PDF1.2 (PATHOGEN-INDUCIBLE PLANT DEFENSIN) genes, which serve as positive markers for the ethylene/jasmonic acid (JA) signaling pathway and provide enhanced resistance to B. cinerea. Biochemical assays demonstrated that the ERF9 in capable of binding to the GCC box, a cis-element contained in the promoters of the PDF1.2 gene that possesses trans-repression activity. Moreover, infection with B. cinerea resulted in the promotion of the PDF1.2 expression, coinciding with suppression of the ERF9 gene under the control of the DEAR1 gene. These results indicate that the transcriptional repressor ERF9 participates in plant defense mechanisms against necrotic fungi mediated by the DEAR1-dependent ethylene/JA signaling pathway.

MBF1s regulate ABA-dependent germination of Arabidopsis seeds.

Transcriptional co-activators of the multiprotein bridging factor 1 (MBF1) controls gene expression by connecting transcription factors and the basal transcription machinery. In Arabidopsis thaliana functions of MBF1 genes have been related to stress tolerance and developmental alterations. Endogenous ABA plays a major role in the regulation of Arabidopsis seed dormancy and germination. Seed dormancy and ABA sensitivity are enhanced in ethylene insensitive mutants suggesting that ethylene signal transduction pathway is necessary to fully develop ABA-dependent germination. In this report we showed that a triple knock-down mutant for Arabidopsis MBF1 genes (abc-) has enhanced seed dormancy and displays hypersensitivity to exogenous ABA. In addition, higher ABA contents were detected in abc- seeds after imbibition. These evidences suggest a negative role of MBF1s genes in ABA-dependent inhibition of germination. The participation of MBF1s in ethylene signal transduction pathway is also discussed.

Biodegradation of melamine and its hydroxy derivatives by a bacterial consortium containing a novel Nocardioides species.

Melamine has recently been recognized as a food contaminant with adverse human health effects. Melamine contamination in some crops arises from soil and water pollution from various causes. To remove melamine from the polluted environment, a novel bacterium, Nocardioides sp. strain ATD6, capable of degrading melamine was enriched and isolated from a paddy soil sample. The enrichment culture was performed by the soil-charcoal perfusion method in the presence of triazine-degrading bacteria previously obtained. Strain ATD6 degraded melamine and accumulated cyanuric acid and ammonium, via the intermediates ammeline and ammelide. No gene known to encode for triazine-degrading enzymes was detected in strain ATD6. A mixed culture of strain ATD6 and a simazine-degrading Methyloversatilis sp. strain CDB21 completely degraded melamine, but the degradation rate of cyanuric acid was slow. The degradation of melamine and its catabolites by the mixed culture was greatly enhanced by including Bradyrhizobium japonicum strain CSB1 in the inoculum and adding ethanol to the culture medium. The melamine-degrading consortium consisting of strains ATD6, CDB21, and CSB1 appears to be potentially safer than other known melamine-degrading bacteria for the bioremediation of farmland and other contaminated sites, as no known pathogens were included in the consortium.

The analysis of an Arabidopsis triple knock-down mutant reveals functions for MBF1 genes under oxidative stress conditions.

Transcriptional co-activators of the multiprotein bridging factor 1 (MBF1) type belong to a small multigenic family that controls gene expression by connecting transcription factors and the basal transcription machinery. In this report, a triple knock-down mutant (abc-) for the Arabidopsis thaliana MBF1 genes AtMBF1a, AtMBF1b and AtMBF1c was generated. The phenotypic characterization using oxidative agents such as hydrogen peroxide and methyl viologen revealed that the abc- mutant was more sensitive to oxidative stress. The triple knock-down mutant, abc- was also sensitive to osmotic stress mediated by high concentrations of sorbitol. Furthermore, the abc- phenotype was partially or completely rescued by AtMBF1c cDNA over-expression (abc- +c) depending on physiological and developmental conditions. AtMBF1s regulate the expression of ABR1, which is a member of the ethylene-response factor family and acts as ABA repressor. Thus, we conclude that AtMBF1 gene family may function as a regulatory component of the cross-talk node between ethylene, ABA and stress signal pathways. Furthermore, higher levels of a HSP70 mRNA and an immunoreactive HSP70 protein were detected in the abc- mutant. The participation of MBF1c as a possible negative regulator of HSP genes was discussed.

Immune deviation and alleviation of allergic reactions in mice subjected to dietary restriction.

We examined cytokine production and allergic reactions in mice fed ad libitum (AL) and subjected to dietary restriction (DR). DR retarded the increase in body weight, and peripheral blood T cells in the DR mice produced less IFN-gamma and more IL-4 in response to immobilized anti-CD3 mAb. Systemic immunization and intranasal challenge with ovalbumin (OVA) induced accumulation of leukocytes into the lung, increase in IL-4 level in bronchoalveolar lavage fluid (BALF), and rise in serum IgE in the AL mice. In contrast, these allergic symptoms were alleviated in the DR mice. Furthermore, the relative proportion of IL-4-producing T cells responsive to OVA was less in the DR mice than the AL mice. DR tended to decrease the proportion and cytolytic activity of NK cells in the spleen, especially in younger mice. These results indicate that DR can prevent the expansion of allergen-specific IL-4-producing T cells followed by suppression of the allergic reaction, but might dampen NK cell activity.

Arabidopsis MBF1s control leaf cell cycle and its expansion.

Multiprotein bridging factor 1 (MBF1) is known as a transcriptional co-activator that enhances transcription of its target genes by bridging between transcription factors and TATA-box-binding protein in eukaryotes. Arabidopsis thaliana has three MBF1 genes: AtMBF1a-AtMBF1c. However, details of the functions of AtMBF1 remain unclear. For this study, transgenic Arabidopsis overexpressing AtMBF1 fused to an active transcriptional repression domain (SRDX) was constructed. The chimeric protein putatively functions as a transcriptional co-repressor and as a suppressor of functions of endogenous AtMBF1 in transgenic plants. Transgenic Arabidopsis overexpressing AtMBF1-SRDX (AtMBF1-SRDX(OE)) showed an extremely small leaf phenotype under a continuous white light condition. Its leaf cells-especially those around vascular tissues, where strong expression of endogenous AtMBF1s is observed-were much smaller than those from the wild type (WT). In addition, a lower cell number was observed in leaves from AtMBF1-SRDX(OE) plants. Time course analysis of cell size revealed that cell expansion of leaves of AtMBF1-SRDX(OE) plants was dramatically suppressed during the late leaf developmental stage (cell expansion stage), when endogenous AtMBF1b is strongly expressed in the WT. The results show that ploidy levels of leaves from AtMBF1-SRDX(OE) plants were dramatically lower than those from the WT; moreover, expression levels of several negative regulators of endoreduplication were more elevated in AtMBF1s-SRDX(OE) plants than those in the WT. These observations suggest that AtMBF1-SRDX interacts with regulators of endoreduplication. Therefore, AtMBF1s are considered to affect not only leaf cell expansion but also regulation of the ploidy level in leaf cells during the leaf expansion stage.

Direct determination of estrogenic and antiestrogenic activities using an enhanced plant two-hybrid system.

This paper reports a simple, low-cost, and extremely sensitive reporter-gene assay system for comprehensive analysis of estrogenic activity using transgenic Arabidopsis thaliana: the EPTH system. It had the capability to detect 17beta-estradiol at a concentration of 10 pM. The system was rendered 5 times more sensitive than a previous system [Tojo, T.; Tsuda, K.; Wada, T.; Yamazaki, K. Ecotoxicol. Environ. Saf. 2006, 64, 106-114) (1)] by increasing the copy number of the transactivation domain fused to a nuclear receptor co-activator. The system can efficiently detect other estrogenic and antiestrogenic substances. Estrogenic activities were determined in treated sewage samples from four distinct sewage farms using the system. Results showed that the system can detect estrogenic activity directly and more efficiently than a yeast two-hybrid system without any manipulation for extraction and condensation of hydrophobic compounds and aseptic treatment. Furthermore, the system also is useful as a powerful tool for discovery of a new category of natural estrogenic substances that are undetectable by previous plant and yeast systems.

Pathogenicity of fowl adenovirus isolated from gizzard erosions to immuno-suppressed chickens.

Pathogenicity of a fowl adenovirus (FAV), JM1/1 strain of serotype 1 derived from gizzard erosions of a broiler chicken, was examined to specific pathogen-free (SPF) chickens pre-treated with infectious bursal disease viruses (IBDVs) or cyclophosphamide (CY). Virulent IBDVs, classical type, were inoculated orally at 3 days of age of SPF chickens. CY was treated subcutaneously for 3 days after hatch. FAV was given orally at 30 days of age. At 40 days of age, all chickens were bled and autopsied for serology and gross observation. Gizzard lesions were ranked by the scores depending on their severities. IBDV- or CY-treated chickens showed significantly higher gizzard lesion scores than non treated birds. There were no gross lesions in any other organs except for bursal atrophy. Serologically, antibody production against FAV was highly suppressed by IBDV infection or CY treatment.

A simple and extremely sensitive system for detecting estrogenic activity using transgenic Arabidopsis thaliana.

Numerous physiological processes are regulated by endocrine systems in animals. Endocrine-disrupting chemicals (EDCs) can affect physiological processes of organisms by binding to hormone receptors. Therefore, it is necessary to develop methods for detecting EDCs and removing them from the environment. We have developed a simple and low-cost reporter gene assay system for the comprehensive analysis of estrogenic activity using transgenic Arabidopsis thaliana. This transgenic plant constantly expresses two effector proteins: a chimeric estrogen receptor and a chimeric nuclear receptor coactivator. Estrogen-dependent interaction between the two effector proteins triggers transcriptional activation of reporter gene, beta-glucuronidase. We have demonstrated this transgenic plant's capability of detecting the existence of 17beta-estradiol at a concentration of 50 pM (13 pg/ml) in agar medium. This plant can also detect other estrogenic substances, such as diethylstilbestrol, p-n-nonylphenol, bisphenol A, and Genistein.

Transcriptional coactivator MBF1s from Arabidopsis predominantly localize in nucleolus.

Multiprotein bridging factor 1 (MBF1) is a transcriptional coactivator. It has been reported that MBF1 changed its subcellular localization from cytoplasm into nuclei with a transcriptional activator for activation of a target gene expression in animals. We found that Arabidopsis MBF1s (AtMBF1s) predominantly localize in nucleolus. We previously reported that plant MBF1s were rapidly induced by several stresses, whereas animal MBF1s were not induced. Therefore, we suggest that MBF1-function in plants is controlled on the level of transcriptional induction but not by nuclear translocation, dissimilar from the case of MBF1s from animals.

Accumulation of intestinal intraepithelial lymphocytes in association with lack of polymeric immunoglobulin receptor.

Immunoglobulin A (IgA) is transported by the polymeric immunoglobulin receptor (pIgR) through epithelial cells of the gut, the airways, the tear and salivary glands, and the lactating mammary gland, and IgA accumulates in serum and the intestinal lamina propria of pIgR-deficient (pIgR(-/-)) mice. Intraepithelial lymphocytes (IEL) increased in number and Thy-1(+)CD8alphabeta(+)TCRalphabeta(+) IEL preferentially expanded in the small intestine (SI) of pIgR(-/-) mice. Cytotoxic activity of SI-IEL was comparable in pIgR(+/+) and pIgR(-/-) mice. Accumulation and cytotoxic activity of SI-IEL was attenuated in germ-free pIgR(-/-) mice. Furthermore, Thy-1(+)CD8alphabeta(+) IEL did not expand in pIgR(-/-)TCRbetadelta(-/-) mice compared with TCRbetadelta(-/-) mice, and SI-IEL from pIgR(-/-)TCRbetadelta(-/-) mice as well as TCRbetadelta(-/-) mice expressed perforin and granzyme B mRNA and serine esterase. The proliferative status of SI-IEL from pIgR(+/+) and pIgR(-/-) mice was similar, but adoptive transfer experiment showed that SI-IEL from pIgR(-/-) mice might have a stronger tendency to migrate into the intestinal epithelia than those from pIgR(+/+) mice. These results demonstrate that the accumulation of Thy-1(+)CD8alphabeta(+)TCRalphabeta(+) IEL in pIgR(-/-) mice triggered by intestinal microorganisms needed the expression of functional TCR and might be caused by lymphocyte migration into the intestinal epithelia.

Structure and expression analysis of three subtypes of Arabidopsis MBF1 genes.

Multiprotein bridging factor 1 (MBF1) is a transcriptional co-activator that mediates transcriptional activation by bridging between an activator and a TATA-box binding protein (TBP). Recently, we have reported that three Arabidopsis MBF1s play roles as transcriptional co-activators. This study shows that AtMBF1c is totally different from the other two in its structure and expression pattern, and that MBF1c genes also occur in other plant species, including monocots. We performed histochemical analysis of these genes using beta-glucuronidase (GUS) assays to characterize the expression profile of each AtMBF1 gene extensively. In pAtMBF1a Colon, two colons GUS transformants, GUS staining was observed only in anthers and seeds, whereas strong GUS activity in pAtMBF1b Colon, two colons GUS transformants was detected in leaf veins, stems, anthers, and seeds. In mature pAtMBF1c Colon, two colons GUS transformants, GUS staining was observed in almost all tissues. It is noteworthy that intense GUS staining was observed in anthers of all transformants. We also found that AtMBF1c expression was up-regulated upon diverse stress treatments including exposure to heat, hydrogen peroxide, dehydration, and high concentrations of salt. These findings suggest that AtMBF1c may be involved in stress response pathway.

Three Arabidopsis MBF1 homologs with distinct expression profiles play roles as transcriptional co-activators.

Multiprotein bridging factor 1 (MBF1) is known to be a transcriptional co-activator that mediates transcriptional activation by bridging between an activator and a TATA-box binding protein (TBP). We demonstrated that expression of every three MBF1 from Arabidopsis partially rescues the yeast mbf1 mutant phenotype, indicating that all of them function as co-activators for GCN4-dependent transcriptional activation. We also report that each of their subtypes shows distinct tissue-specific expression patterns and responses to phytohormones. These observations suggest that even though they share a similar biochemical function, each MBF1 has distinct roles in various tissues and conditions.

Differentially expressed genes associated with CIS-diamminedichloroplatinum (II) resistance in head and neck cancer using differential display and CDNA microarray.

BACKGROUND: The mechanism by which cancer cells become resistant to cis-Diamminedichloroplatinum (II) (cDDP) is not completely understood. To investigate the molecular markers involved in the cDDP resistance, we compared the gene expression profiles between a head and neck squamous cell carcinoma (HNSCC) line sensitive to cDDP and its cDDP-resistant variant. METHODS: Both a fluorescent differential display and a cDNA microarray analysis were applied to distinguish the gene profiles between KB, a human HNSCC line, and its cDDP-resistant variant (KB/cDDP). These results were confirmed by Northern blot analysis. RESULTS: One up-regulated gene, glycoprotein hormone alpha-subunit, and two down-regulated genes coding membrane proteins, human folate receptor and tumor-associated antigen L6, were identified in KB/cDDP cells. CONCLUSIONS: Our findings suggest that development of the cDDP-resistant phenotype is accompanied by alternations of gene expression including a glycoprotein hormone and membrane proteins. These gene products could be new molecular markers for resistance to cDDP.