Cloning of the RNase H genes from a metagenomic DNA library: identification of a new type 1 RNase H without a typical active-site motif

AIMS

The study aimed to combine a metagenomics approach with complementary genetics to identify novel bacterial genes with orthologous functions, with the identification of novel RNase H genes as a test case.

METHODS AND RESULTS

A metagenomic DNA library was prepared from leaf-and-branch compost and used to screen for the RNase H genes by their abilities to complement the temperature-sensitive growth phenotype of the rnhA mutant Escherichia coli strain MIC3001. Determination of the nucleotide sequences of the cloned DNA fragments allowed us to identify 12 different genes encoding type 1 RNases H. Eleven of them encode novel RNases H, which show 40-72% amino acid sequence identities to those available from database. One of them lacks a typical DEDD/E active-site motif, which is almost fully conserved in various RNases H.

CONCLUSIONS

Functional screening of environmental DNA without cultivation of microbes is a useful procedure to isolate novel RNase H genes.

SIGNIFICANCE AND IMPACT OF THE STUDY

One of the identified RNase H genes had no sequence similarity to a previously assumed conserved motif, suggesting multiple catalytic mechanisms exist. This test case illustrates that metagenomics combined with complementary genetics can identify novel genes that are orthologous without sequence similarity to those from cultivated bacteria.

Subtilisin-like serine protease from hyperthermophilic archaeon Thermococcus kodakaraensis with N- and C-terminal propeptides

The genome of the hyperthermophilic archaeon Thermococcus kodakaraensis contains three genes encoding subtilisin-like serine proteases, Tk-1689, Tk-0076 and Tk-subtilisin. Of them, the structure and function of Tk-subtilisin have been extensively studied. To examine whether Tk-1689 is matured to an active form and functions as a hyperthermostable protease as is Tk-subtilisin, the gene encoding the Tk-1689 derivative without a putative N-terminal signal sequence, termed Pro-Tk-SP, was overexpressed in Escherichia coli. Pro-Tk-SP is composed of 640 amino acid residues and its molecular mass is 68.6 kDa. The recombinant protein was purified, however, as an active 44 kDa protease, termed Tk-SP, which lacks the N-terminal 113 and C-terminal 101 amino acid residues. This result suggests that Pro-Tk-SP consists of an N-terminal propeptide (Ala1-Ala113), a mature domain (Tk-SP, Val114-Val539) and a C-terminal propeptide (Asp540-Gly640). Like Tk-subtilisin, Tk-SP showed a broad substrate specificity and was highly thermostable. Its optimum temperature for activity was approximately 100 degrees C and its half-life at 100 degrees C was 100 min. It was fully resistant to treatment with 5% SDS, 8 M urea or 10% Triton X-100. However, unlike Tk-subtilisin and bacterial subtilisins, Tk-SP requires neither Ca2+ nor propeptide for folding. As a result, Tk-SP was fully active even in the presence of 10 mM EDTA. Thus, Tk-SP has a great advantage over other proteases in high resistance to heat, denaturants, detergents and chelating agents and therefore has great potential for application in biotechnology fields.

Antitumor activity of NK012 combined with cisplatin against small-cell lung cancer and intestinal mucosal changes in tumor-bearing mouse after treatment

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Background: The novel SN-38-incorporating polymeric micelles NK012 has been shown to have significant antitumor activity against several cancer mouse models compared with CPT-11. The phase I study demonstrated that patients treated with NK012 did not develop grade 3/4 diarrhea, one of the major adverse effects of CPT-11. The aim of this study is to investigate the advantages of NK012 combined with cisplatin (cis-dichlorodiammineplatinum (II): CDDP) over CPT-11/CDDP, one of the most active regimens against small-cell and non-small-cell lung cancers in the clinic, in mice bearing a small-cell lung cancer (SCLC) xenograft in terms of antitumor activity and toxicity, particularly intestinal toxicity. Methods: Cytotoxic effects were evaluated in human SCLC cell lines (H69, H82, vascular endothelial growth factor [VEGF]-secreting cells, SBC-3/VEGF and its mock transfectant SBC-3/Neo). In vivo antitumor effects were evaluated in SBC-3/Neo-and SBC-3/VEGF-bearing mice after NK012/CDDP or CPT-11/CDDP administration on days 0, 7, and 14. Drug distribution was analyzed by high-performance liquid chromatography or fluorescence microscopy, and the small intestine was pathologically examined. Results: The in vitro growth inhibitory effects of NK012 were 198- to 532-fold more potent than those of CPT-11. A significant difference in the relative tumor volume on day 30 was found between NK012/CDDP and CPT- 11/CDDP treatments (P=0.0058). Inflammatory changes in the small intestinal mucosa were rare in all NK012-treated mice, but were commonly observed in CPT-11-treated mice. Moreover, a large amount of CPT-11 was excreted into the feces and high CPT-11 concentration was detected in the small intestinal epithelium. On the other hand, a small amount of NK012 was found in the feces and NK012 was weakly and uniformly distributed in the mucosal interstitium. Conclusions: NK012/CDDP combination may be a promising candidate regimen against lung cancer without severe diarrhea toxicity, and therefore warrants further clinical evaluation.

No significant financial relationships to disclose.

[Pulmonary atresia with intact ventricular septum showing Fontan-like circulation after biventricular repair]

A 6-year-old girl was referred to our institute for cardiac evaluation. She had been diagnosed as pulmonary atresia with intact ventricular septum (PAIVS) at 16 days after birth and she had underwent balloon atrial septostomy and bilateral Blalock-Taussig shunts. A cardiac catheterization at 5 months showed that her right ventricular end diastolic volume was 58% of normal, the Z value (standard deviation units) of the diameter of the tricuspid valve was -3.3, and a biventricular repair was performed. After the operation, she suffered from severe congestive heart failure for 10 months. A cardiac catheterization at the age of 6 years demonstrated that the pulmonary blood flow was generated during the diastolic phase like Fontan circulation. Although biventricular repair had been performed at 5 months, the circulation may be less advantageous for long term survival than if the patient had undergone the staged Fontan procedure. Careful and continuous hemodynamic assessment is essential for surgical therapy of PAIVS.

Effect of intestinal microbiota on the induction of regulatory CD25+ CD4+ T cells

When oral tolerance was induced in either specific pathogen-free (SPF) or germ-free (GF) mice, ovalbumin (OVA) feeding before immunization induced oral tolerance successfully in SPF mice. On the other hand, OVA-specific immunoglobulin G1 (IgG1) and IgE titres in OVA-fed GF mice were comparable to those in phosphate-buffered saline-fed GF mice, thus demonstrating that oral tolerance could not be induced in GF mice. The frequencies of CD25(+) CD4(+)/CD4(+) cells in the mesenteric lymph node (MLN) and the absolute number of CD25(+) CD4(+) cells in the Peyer's patches and MLN of naive GF mice were significantly lower than those in naive SPF mice. In an in vitro assay, the CD25(+) CD4(+) cells from the naive SPF mice suppressed more effectively the proliferation of responder cells in a dose-dependent manner than those from the GF mice. In addition, the CD25(+) CD4(+) regulatory T (T(reg)) cells from the naive SPF mice produced higher amounts of interleukin (IL)-10 and transforming growth factor (TGF)-beta than those from the GF mice. When anti-TGF-beta neutralizing antibody, but not anti-IL-10 neutralizing antibody, was added to the in vitro proliferation assay, the suppressive effect of the CD25(+) CD4(+) T(reg) cells from the SPF mice was attenuated to the same level as that of the CD25(+) CD4(+) cells from the GF mice. In conclusion, the TGF-beta-producing CD25(+) CD4(+) T(reg) cells from the MLN of SPF mice played a major role in oral tolerance induction. In addition, as the regulatory function of the CD25(+) CD4(+) cells from the naive GF mice was much lower than that of the CD25(+) CD4(+) T(reg) cells from the SPF mice, indigenous microbiota are thus considered to contribute to the induction and maintenance of CD25(+) CD4(+) T(reg) cells.

Flat adenoma-carcinoma sequence with high-malignancy potential as demonstrated by CD10 and beta-catenin expression: a different pathway from the polypoid adenoma-carcinoma sequence

AIMS

CD10+ colorectal carcinomas have a high risk of giving rise to liver metastasis. The aim was to examine phenotypic expression in colorectal neoplasia and to elucidate changes in such expression through the adenoma-carcinoma sequence.

METHODS AND RESULTS

We examined the expression of various proteins immunohistochemically in 111 flat [non-polypoid growth (NPG)] colorectal neoplasms, categorized into 28 low-grade (NPG-LGN), 44 high-grades (NPG-HGN) and 39 cases of invasive neoplasia (NPG-IN), as well as in 96 polypoid [polypoid growth (PG)] neoplasms, categorized into 26 PG-LGN, 39 PG-HGN and 31 PG-IN according to the Vienna classification. CD10 was more frequently expressed in NPG than in PG neoplasia. MUC2 and MUC5AC were more frequently expressed in PG than in NPG neoplasias. Nuclear beta-catenin was more frequently expressed in NPG-LGN than in PG-LGN. No difference in p53 expression was found between NPG and PG neoplasia.

CONCLUSIONS

From the viewpoint of the expression of CD10 and beta-catenin, it would appear that NPG-LGN differs significantly from PG-LGN, thereby indicating that NPG-LGN is a precursor of CD10+ carcinoma. It is important to ensure that NPG neoplasia is not overlooked if cases of CD10+ carcinoma are to be detected at an early stage.

Kirkwood-Buff integrals of aqueous alcohol binary mixtures

The Kirkwood-Buff integrals of some binary aqueous alcohol mixtures are computed from the available vapor pressure measurements and compared with previous results as well as small angle neutron scattering experiments. The emphasis of the present report is on accuracy of the results that can be achieved by these two different types of measurements. This seems to be needed, mainly in view of the discrepancies between the various published results, as shown herein. It is argued that agreement in peak positions is more important than that in magnitude. In general, very good agreement is obtained by both methods, and sources of disagreements are discussed. The issue of the computer simulations of aqueous systems and the problematics related to correlations, microheterogeneity, and consequently the Kirkwood-Buff integrals are equally discussed herein.

Multiple self-healing squamous epithelioma in different ethnic groups: more than a founder mutation disorder?

Multiple self-healing squamous epithelioma (MSSE), also known as Ferguson-Smith Disease, is a rare cancer-associated genodermatosis with an autosomal dominant inheritance. Affected patients suffer from recurrent skin lesions, which clinically and histologically resemble keratoacanthomas or well-differentiated squamous cell carcinomas, but which, if left, undergo spontaneous regression, leaving pronounced scarring. The majority of MSSE cases previously described were of Scottish ancestry and all shared the same at-risk haplotype, suggesting that this disorder was caused by a founder mutation. The candidate locus for MSSE lies in a region of <4 cM in chromosome 9q22, between the markers D9S197 and D9S1809. We recently investigated MSSE families of non-Scottish origin. For every patient of these families, we obtained a detailed clinical history, with particular attention to the age of onset, distribution, and clinical course of their skin lesions. Once confirmed that they were really affected by MSSE, we performed haplotype analysis on them and their families. The haplotypes for polymorphic markers segregating with MSSE in non-Scottish and Scottish families differ, suggesting that MSSE is not caused by a founder mutation and might be more common than originally thought.

Directed evolution of Tk-subtilisin from a hyperthermophilic archaeon: identification of a single amino acid substitution responsible for low-temperature adaptation

Tk-subtilisin from the hyperthermophilic archaeon Thermococcus kodakaraensis is synthesized in a prepro-form (prepro-Tk-subtilisin), secreted in a pro-form (pro-Tk-subtilisin), and matured to an active form (mat-Tk-subtilisin*; a Ca(2+)-bound active form of matured domain of Tk-subtilisin) upon autoprocessing and degradation of the propeptide [Tk-propeptide; propeptide of Tk-subtilisin (Gly1-Leu69)]. Pro-Tk-subtilisin exhibited halo-forming activity only at 80 degrees C, but not at 70 and 60 degrees C, because Tk-propeptide is not effectively degraded by mat-Tk-subtilisin* and forms an inactive complex with mat-Tk-subtilisin* at <80 degrees C. Random mutagenesis in the entire prepro-Tk-subtilisin gene, followed by screening for mutant proteins with halo-forming activity at 70 and 60 degrees C, allowed us to identify single Gly56 --> Ser mutation in the propeptide region responsible for low-temperature adaptation of pro-Tk-subtilisin. SDS-PAGE analyses and mat-Tk-subtilisin* activity assay of pro-G56S-subtilisin indicated more rapid maturation than pro-Tk-subtilisin. The resultant active form was indistinguishable from mat-Tk-subtilisin* in activity and stability, indicating that Gly56 --> Ser mutation does not seriously affect the folding of the mature domain. However, this mutation greatly destabilized the propeptide, making it unstructured in an isolated form. As a result, Tk-propeptide with Gly56 --> Ser mutation (G56S-propeptide) was more susceptible to proteolytic degradation and less effectively inhibited mat-Tk-subtilisin* activity than Tk-propeptide. These results suggest that pro-G56S-subtilisin is more effectively matured than pro-Tk-subtilisin at lower temperatures, because autoprocessed G56S-propeptide is unstructured upon dissociation from mat-Tk-subtilisin* and is therefore effectively degraded by mat-Tk-subtilisin*.

Determination of formoterol in rat plasma by liquid chromatography-electrospray ionisation mass spectrometry

A sensitive method for the determination of formoterol in rat plasma is described, using high performance liquid chromatographic separation with tandem mass spectrometry. Samples were purified using liquid-liquid extraction and separated on CAPCELL PAK C18 UG120 (2.0 x 150 mm) with a mobile phase consisting of a mixture of methanol- 50 mM ammonium hydrogen carbonate (1:1 v/v). Detection was performed with a TSQ 7000 mass spectrometer using positive ion electrospray ionisation, monitoring the shift from precursor ions for formoterol at m/z 344.9 to product ions of m/z 121.0. The limit of quantitation of the method was found to be 0.1 ng/ml, when using 0.1 ml plasma. Plasma concentrations of formoterol could be quantified from 0.15 to 7.01 ng/ml, allowing the analysis of samples up to 32 h after a single oral dose of formoterol fumarate (0.25 mg) to rats.

Hemi-orbicularis oculi switch flap for upper eyelid defects

BACKGROUND

The technique chosen to reconstruct anterior lamellar defects of the upper eyelid requires careful consideration. We modified pre-existing techniques used to reconstruct anterior lamellar defects after tumour resection and have called this procedure a hemi-orbicularis oculi switch flap.

METHODS

This musculocutaneous flap is elevated with underlying orbicularis and its base abuts the anterior lamellar defect. The flap, which is half the height of the defect, is elevated and inset to cover the defect. Then, taking into consideration the extensibility of upper eyelid skin, the remainder of the defect and the donor site are closed directly.

RESULTS

Five patients with basal cell carcinoma, haemangioma, and xanthoma of the upper eyelid were treated by this method. All flaps survived and complications were minimal. Aesthetically and functionally good results were obtained by this method.

CONCLUSIONS

We have developed a surgical method for the reconstruction of anterior lamellar defects of the upper eyelid. The proposed method is technically simple and safe and provides consistent results for a potentially wide variety of upper eyelid tumours.