Search

A novel catechin, pilosanol N (1), was isolated from Agrimonia pilosa Ledeb and its structure was determined by (1)H, (13)C NMR and HRESI-MS analyses. Compound 1 inhibited nitric oxide (NO) production in LPS/IFN-γ -induced RAW264.7 macrophages, and then the iNOS gene expression and its protein production with LPS/IFN-γ treatment cells were also suppressed in the presence of 1. In addition, compound 1 scavenged NO or nitrogen radicals generated from NOR3 (4-ethyl-2-hydroxyamino-5-nitro-3-hexenamide) as an NO donor. These results indicated that pilosanol N can decrease the level of NO through a mechanism that involved both a decrease in the NO production and NO scavenging., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

A homozygous mutational change in the Ataxia-Telangiectasia and RAD3 related (ATR) gene was previously reported in two related families displaying Seckel Syndrome (SS). Here, we provide the first identification of a Seckel Syndrome patient with mutations in ATRIP, the gene encoding ATR-Interacting Protein (ATRIP), the partner protein of ATR required for ATR stability and recruitment to the site of DNA damage. The patient has compound heterozygous mutations in ATRIP resulting in reduced ATRIP and ATR expression. A nonsense mutational change in one ATRIP allele results in a C-terminal truncated protein, which impairs ATR-ATRIP interaction; the other allele is abnormally spliced. We additionally describe two further unrelated patients native to the UK with the same novel, heterozygous mutations in ATR, which cause dramatically reduced ATR expression. All patient-derived cells showed defective DNA damage responses that can be attributed to impaired ATR-ATRIP function. Seckel Syndrome is characterised by microcephaly and growth delay, features also displayed by several related disorders including Majewski (microcephalic) osteodysplastic primordial dwarfism (MOPD) type II and Meier-Gorlin Syndrome (MGS). The identification of an ATRIP-deficient patient provides a novel genetic defect for Seckel Syndrome. Coupled with the identification of further ATR-deficient patients, our findings allow a spectrum of clinical features that can be ascribed to the ATR-ATRIP deficient sub-class of Seckel Syndrome. ATR-ATRIP patients are characterised by extremely severe microcephaly and growth delay, microtia (small ears), micrognathia (small and receding chin), and dental crowding. While aberrant bone development was mild in the original ATR-SS patient, some of the patients described here display skeletal abnormalities including, in one patient, small patellae, a feature characteristically observed in Meier-Gorlin Syndrome. Collectively, our analysis exposes an overlapping clinical manifestation between the disorders but allows an expanded spectrum of clinical features for ATR-ATRIP Seckel Syndrome to be defined., Competing Interests: The authors have declared that no competing interests exist.

Pentylphenols 1 and 2, cyclopropane fatty acid 3, and cyclopentenones 4 and 5, were isolated from an ascidian, Diplosoma sp. The structures of 1-5 were determined by spectroscopic analysis and/or synthesis. Compound 1 inhibited the division of fertilized sea urchin eggs and compound 4 showed mild cytotoxity against HCT116 cells (human colorectal cancer cell).

MRE11 and NBS1 function together as components of a MRE11/RAD50/NBS1 protein complex, however deficiency of either protein does not result in the same clinical features. Mutations in the NBN gene underlie Nijmegen breakage syndrome (NBS), a chromosomal instability syndrome characterized by microcephaly, bird-like faces, growth and mental retardation, and cellular radiosensitivity. Additionally, mutations in the MRE11A gene are known to lead to an ataxia-telangiectasia-like disorder (ATLD), a late-onset, slowly progressive variant of ataxia-telangiectasia without microcephaly. Here we describe two unrelated patients with NBS-like severe microcephaly (head circumference -10.2 SD and -12.8 SD) and mutations in the MRE11A gene. Both patients were compound heterozygotes for a truncating or missense mutation and carried a translationally silent mutation. The truncating and missense mutations were assumed to be functionally debilitating. The translationally silent mutation common to both patients had an effect on splicing efficiency resulting in reduced but normal MRE11 protein. Their levels of radiation-induced activation of ATM were higher than those in ATLD cells., (Copyright © 2010 Elsevier B.V. All rights reserved.)

Tyrosinase, trypsin, and tryptase are known to play important roles in melanin production of human skin. This paper describes the study of the inhibitory effect of Balanophora fungosa on melanin. The 50% EtOH extract obtained from B. fungosa indicated an inhibitory effect on mushroom tyrosinase activity with an IC(50) value of 15 μg/mL. Bioassay-guided fractionation of the active extract resulted in the isolation of four known compounds. Their structures were identified as 1-O-(E)-caffeoyl-3-O-galloyl-4,6-(S)-HHDP-β-d-glucopyranose (1), 1-O-(E)-caffeoyl-3,4,6-tri-O-galloyl-β-d-glucopyranose (2), caffeoyl-β-d-glucopyranose (3), and abietin (4) on the basis of spectroscopic analyses and comparison of their spectral data with those in the literature. Compounds 1 and 2 prevented pigmentation of melanin in a three-dimensional cultured human skin model. Furthermore, compounds 1 and 2 indicated inhibitory activities against trypsin and tryptase.

A rare case of severe intestinal bleeding caused by sinistral portal hypertension after pylorus-preserving pancreatoduodenectomy is reported. Examinations revealed that the developed collateral vessels adjacent to the pancreas and elevated jejunum in the right upper abdomen were the source of the intestinal bleeding, and typical gastric varices were not identified. The present case showed atypical development of collateral vessels due to the postoperative state, which made diagnosis difficult.

An experimental system for the study of ion-induced nucleation in a SO(2)/H(2)O/N(2) gas mixture was developed, employing a soft x-ray at different pressure and temperature levels. The difficulties associated with these experiments included the changes in physical properties of the gas mixture when temperature and pressure were varied. Changes in the relative humidity (RH) as a function of pressure and temperature also had a significant effect on the different behaviors of the mobility distributions of particles. In order to accomplish reliable measurement and minimize uncertainties, an integrated on-line control system was utilized. As the pressure decreased in a range of 500-980 hPa, the peak concentration of both ions and nanometer-sized particles decreased, which suggests that higher pressure tended to enhance the growth of particles nucleated by ion-induced nucleation. Moreover, the modal diameters of the measured particle size distributions showed a systematic shift to larger sizes with increasing pressure. However, in the temperature range of 5-20 °C, temperature increases had no significant effects on the mobility distribution of particles. The effects of residence time, RH (7%-70%), and SO(2) concentration (0.08-6.7 ppm) on ion-induced nucleation were also systematically investigated. The results show that the nucleation and growth were significantly dependent on the residence time, RH, and SO(2) concentration, which is in agreement with both a previous model and previous observations. This research will be inevitable for a better understanding of the role of ions in an atmospheric nucleation mechanism.

Magnesium fluoride particles with controllable size (from several nanometers to submicrometers) and morphology (spherical and cubic forms) were successfully prepared via liquid-phase synthesis. The particles were synthesized from the reaction of MgCl(2) and NH(4)F in an aqueous solution at 75 degrees C for 1 h under a nitrogen atmosphere. Control of particle size was accomplished mainly by changing the concentration of the reactants, which could be qualitatively explained by conventional nucleation theory. Flexibility of the process in controlling particle morphology, from a spherical to a cubical form, was predominantly achieved by varying the concentration of MgCl(2). Since the same XRD pattern was detected in particles with varying morphologies, the shape transformation was due to changes in particle growth. With the ability to control particle size and morphology, the creation of other inorganic particles is possible and has potential for many field applications.

Nucleotide excision repair (NER) removes the major UV-photolesions from cellular DNA. In humans, compromised NER activity is the cause of several photosensitive diseases, one of which is the skin-cancer predisposition disorder, xeroderma pigmentosum (XP). Two assays commonly used in measurement of NER activity are 'unscheduled DNA synthesis (UDS)', and 'recovery of RNA synthesis (RRS)', the latter being a specific measure of the transcription-coupled repair sub-pathway of NER. Both assays are key techniques for research in NER as well as in diagnoses of NER-related disorders. Until very recently, reliable methods for these assays involved measurements of incorporation of radio-labeled nucleosides. We have established non-radioactive procedures for determining UDS and RRS levels by incorporation of recently developed alkyne-conjugated nucleoside analogues, 5-ethynyl-2'-deoxyuridine (EdU) and 5-ethynyuridine (EU). EdU and EU are respectively used as alternatives for (3)H-thymidine in UDS and for (3)H-uridine in RRS. Based on these alkyne-nucleosides and an integrated image analyser, we have developed a semi-automated assay system for NER-activity. We demonstrate the utility of this system for NER-activity assessments of lymphoblastoid samples as well as primary fibroblasts. Potential use of the system for large-scale siRNA-screening for novel NER defects as well as for routine XP diagnosis are also considered., ((c) 2010 Elsevier B.V. All rights reserved.)

Nucleotide excision repair (NER) is the most versatile DNA repair system that deals with the major UV photoproducts in DNA, as well as many other DNA adducts. The early steps of NER are well understood, whereas the later steps of repair synthesis and ligation are not. In particular, which polymerases are definitely involved in repair synthesis and how they are recruited to the damaged sites has not yet been established. We report that, in human fibroblasts, approximately half of the repair synthesis requires both pol kappa and pol delta, and both polymerases can be recovered in the same repair complexes. Pol kappa is recruited to repair sites by ubiquitinated PCNA and XRCC1 and pol delta by the classical replication factor complex RFC1-RFC, together with a polymerase accessory factor, p66, and unmodified PCNA. The remaining repair synthesis is dependent on pol epsilon, recruitment of which is dependent on the alternative clamp loader CTF18-RFC., ((c) 2010 Elsevier Inc. All rights reserved.)

Topoisomerase inhibitors such as camptothecin and etoposide are used as anti-cancer drugs and induce double-strand breaks (DSBs) in genomic DNA in cycling cells. These DSBs are often covalently bound with polypeptides at the 3' and 5' ends. Such modifications must be eliminated before DSB repair can take place, but it remains elusive which nucleases are involved in this process. Previous studies show that CtIP plays a critical role in the generation of 3' single-strand overhang at "clean" DSBs, thus initiating homologous recombination (HR)-dependent DSB repair. To analyze the function of CtIP in detail, we conditionally disrupted the CtIP gene in the chicken DT40 cell line. We found that CtIP is essential for cellular proliferation as well as for the formation of 3' single-strand overhang, similar to what is observed in DT40 cells deficient in the Mre11/Rad50/Nbs1 complex. We also generated DT40 cell line harboring CtIP with an alanine substitution at residue Ser332, which is required for interaction with BRCA1. Although the resulting CtIP(S332A/-/-) cells exhibited accumulation of RPA and Rad51 upon DNA damage, and were proficient in HR, they showed a marked hypersensitivity to camptothecin and etoposide in comparison with CtIP(+/-/-) cells. Finally, CtIP(S332A/-/-)BRCA1(-/-) and CtIP(+/-/-)BRCA1(-/-) showed similar sensitivities to these reagents. Taken together, our data indicate that, in addition to its function in HR, CtIP plays a role in cellular tolerance to topoisomerase inhibitors. We propose that the BRCA1-CtIP complex plays a role in the nuclease-mediated elimination of oligonucleotides covalently bound to polypeptides from DSBs, thereby facilitating subsequent DSB repair., Competing Interests: The authors have declared that no competing interests exist.

A series of new C(11) cyclopentenones 1-7 was isolated, together with four known metabolites 9/10, 12 and 13, from the extract of the didemnid ascidian Lissoclinum sp. The other didemnid ascidian Diplosoma sp. contained didemnenones 1, 2 and 5, and five known metabolites 8-12. The structures of 1-7 were elucidated by spectroscopic analyses. Cytotoxicity of the isolated compounds was evaluated against three human cancer cell lines (HCT116, A431 and A549).

Objective: Stent grafts are increasingly recognized as useful devices for endovascular repair of aortic aneurysms and other vascular diseases. Stent graft-mediated gene delivery into the vascular wall is expected to improve their therapeutic effects. This study evaluated the efficacy of genetically engineered cationized gelatin (CG) hydrogel-coated partially-covered polyester stent grafts that facilitate delivery of an expression plasmid DNA in rabbit aortic wall., Methods: Partially covered polyester stent grafts coated with CG hydrogel impregnated with 10.0 mg/mL of beta-galactosidase (LacZ)-expression plasmid vector (pCAGGS-LacZ) or empty vector (pCAGGS) solutions were implanted via the femoral artery in rabbit balloon-injured aortas. The aortic segments were removed at 1, 3, or 7 days (4 rabbits/each group) after implantation and evaluated for the transgene (LacZ) delivery and expression by real-time reverse transcriptase polymerase chain reaction (RT-PCR) and X-gal (5-bromo-4-chloro-3-indolyl-beta-D-galactoside) staining. Partially-covered polyester stent grafts coated with CG hydrogel impregnated with various amounts (0.1 mg/mL, 1.0 mg/mL, and 10.0 mg/mL) of pCAGGS-LacZ or pCAGGS were also implanted in rabbits' balloon-injured aortas (4 rabbits/each group) to evaluate transgene delivery and expression in the aortic wall 3 days after implantation. The difference of transgene efficiency among each group was compared using one-way analysis of variance (ANOVA) and Newman-Keuls' test according to the result of quantitative RT-PCR., Results: In all animals, LacZ gene transduction into the aortic wall was detected at the implantation site of pCAGGS-LacZ-loaded, but not pCAGGS-loaded, stent grafts. LacZ expression was not detected in aortic segments immediately proximal or distal to the implanted pCAGGS-LacZ-loaded stent graft or remote organs including the brain, heart, liver, and kidney by either RT-PCR or X-gal staining. The X-gal staining-positive cells were observed at or near the luminal surface in the aortic segments only in contact with the stent graft and the ingrowth tissues within stent grafts. Immunohistochemical studies suggested that the LacZ-positive cells were mainly the neointimal alpha-smooth-muscle actin-positive cells and macrophages. The extent of the transgene expression was dependent on the quantity of the plasmid DNA loaded onto the stent graft (10.0 mg/mL plasmid vs 1.0 mg/mL plasmid, P < .01 and 10.0 mg/mL plasmid vs 0.1 mg/mL plasmid, P < .05). LacZ mRNA expression was maximal at day 1 and declined at day 7 (P < .05) but was still detectable., Conclusion: Plasmid-loaded CG hydrogel-coated stent graft is a promising vehicle for local transgene delivery to the aortic wall and offers the possibility of transduction of therapeutic genes into the vascular wall.

Purpose: To present a new endovascular technique for placing handmade partially covered stent-grafts in rabbit aortas that is promising for experimental study of direct gene delivery to the aortic wall., Methods: A 7-mm-diameter Z-stent made from the inner core of a guidewire was covered with a 7-mm-diameter, 10-mm-long polyester fabric tube (2268 mL porosity). To decrease stent profile and make delivery possible through a 6-F introducer, one third of the fabric was cut away to form a partially covered polyester stent-graft. Two stent-grafts were delivered sequentially into the descending thoracic aorta of 12 male Japanese White rabbits; a third device was positioned in each aorta so that the orifices of the celiac trunk and superior mesenteric artery were not occluded., Results: The implantation was successful in 10 animals. One rabbit died during the procedure due to sheath laceration of the infrarenal abdominal aorta. Another animal died within 2 days after the procedure owing to occlusion of the celiac trunk by graft fabric. At 2 weeks, the stent-grafts in the 10 surviving rabbits remained patent, and there was no migration. Gross examination of the lumens showed that both the metal stent and the polyester graft material were completely covered with thin transparent tissue, without massive thrombosis. Histological staining revealed incomplete neointima formation between the stent-graft and the aorta. Incomplete linear endothelial cells on the luminal side of the tissue ingrowth into the stent-graft were also observed. Foreign body giant cells and macrophages represented inflammatory reactions related to the graft material., Conclusion: Partially covered stent-grafts can be safely placed in relatively small animals and potentially used in research.

Xeroderma pigmentosum (XP) is an autosomal recessive genetic disorder. Afflicted patients show extreme sun-sensitivity and skin cancer predisposition. XP is in most cases associated with deficient nucleotide excision repair (NER), which is the process responsible for removing photolesions from DNA. Measuring NER activity by nucleotide incorporation into repair patches, termed 'unscheduled DNA synthesis (UDS)', is one of the most commonly used assays for XP-diagnosis and NER research. We have established a rapid and accurate procedure for measuring UDS by replacement of thymidine with 5-ethynyl-2'-deoxyuridine (EdU). EdU incorporated into repair patches can be directly conjugated to fluorescent azide derivatives, thereby obviating the need for either radiolabeled thymidine or denaturation and antibody detection of incorporated bromodeoxyuridine (BrdU). We demonstrate that the EdU incorporation assay is compatible with conventional techniques such as immunofluorescent staining and labeling of cells with micro-latex beads. Importantly, we can complete the entire UDS assay within half a day from preparation of the assay coverslips; this technique may prove useful as a method for XP diagnosis.

The unstable isomeric compounds 5-hydroxy-7-prop-2-en-(E)-ylidene-7,7adihydro-2H-cyclopenta[b]pyran-6-one (1) and 5-hydroxy-7-prop-2-en-(Z)-ylidene-7,7adihydro-2H-cyclopenta[b]pyran-6-one (2), previously described as antimicrobial metabolites from the sponge Ulosa sp., were isolated and identified as major components of the ascidian Diplosoma virens. In this paper, full spectral data for 2 and complete 13CNMR data for 1, based on 2D NMR measurements, are provided for the first time. Compounds 1 and 2 showed cytotoxity against HCT116 cells (human colorectal cancer cells) by triggering apoptotic cell death.

Purpose: To evaluate the local reaction of the aortic wall induced by basic fibroblast growth factor (bFGF) released from a gelatin hydrogel coated on the outer surface of a stent-graft for the purpose of biological fixation., Methods: A total of 18 nitinol-based, polyester-covered stent-grafts were implanted in 6 porcine aortas for 1 month. The implanted stent-grafts were divided into 3 groups: the control group (uncoated), the hydrogel group (coated with hydrogel containing water), and the bFGF group (coated with hydrogel containing bFGF). After stent-graft implantation, the results of intravascular ultrasound (IVUS) and qualitative and quantitative microscopic examinations were compared among the groups., Results: In the bFGF group, a thin white lamellar tissue was observed on IVUS images. Significantly more new intimal tissue formation was observed in all the bFGF group animals than in the other 2 groups, and alpha smooth muscle (SM) actin-positive cells (alphaSMCs) were detected in this new tissue. The alphaSMCs within the fabric of tightly woven grafts were significantly more abundant in the bFGF group than in the other groups., Conclusion: The local controlled release of bFGF from the stent-graft significantly accelerated the proliferation of new intimal tissue between the aorta and the stent-graft and within the graft materials. These findings suggest that a graft can be fixed biologically to the aortic wall, which may contribute to the shrinkage of aneurysms following stent-grafting.

Replicative DNA polymerases are blocked at DNA lesions. Synthesis past DNA damage requires the replacement of the replicative polymerase by one of a group of specialised translesion synthesis (TLS) polymerases, most of which belong to the Y-family. Each of these has different substrate specificities for different types of damage. In eukaryotes mono-ubiquitination of PCNA plays a crucial role in the switch from replicative to TLS polymerases at stalled forks. All the Y-family polymerases have ubiquitin binding sites that increase their binding affinity for ubiquitinated PCNA at the sites of stalled forks.

To successfully colonize their mammalian hosts, many bacteria produce multiple virulence factors that play essential roles in disease processes and pathogenesis. Some of these molecules are adhesins that allow efficient attachment to host cells, a prerequisite for successful host colonization. Bordetella spp. express a number of proteins which either play a direct role in attachment to the respiratory epithelia or exhibit similarity to known bacterial adhesins. One such recently identified protein is BipA. Despite the similarity of BipA to intimins and invasins, deletion of this protein from B. bronchiseptica did not result in any significant defect in respiratory tract colonization. In this study, we identified an open reading frame in B. bronchiseptica, designated bcfA (encoding BcfA [bordetella colonization factor A]), that is similar to bipA. In contrast to the maximal expression of bipA in the Bvg intermediate (Bvg(i)) phase, bcfA is expressed at high levels in both the Bvg(+) and Bvg(i) phases. We show here that BvgA and phosphorylated BvgA bind differentially to the bcfA promoter region. Utilizing immunoblot assays, we found that BcfA is localized to the outer membrane and that it is expressed during animal infection. While deletion of either bipA or bcfA did not significantly affect respiratory tract colonization, concomitant deletion of both genes resulted in a defect in colonization of the rat trachea. Our results indicate that the two paralogous proteins have a combinatorial role in mediating efficient respiratory tract colonization.

DNA polymerase kappa (pol kappa) is a member of the Y-family of DNA polymerases that are thought to function in translesion synthesis (TLS) past different types of DNA damage. Here, we show that pol kappa-deficient mouse cells have substantially reduced (but not absent) levels of nucleotide excision repair (NER) of UV damage, as measured by several methods. Our results provide evidence for an unexpected role for pol kappa in mammalian NER.

DNA lesions that escape excision repair pathways can cause arrested DNA replication. This replication block can be processed by translesion DNA synthesis (TLS), which is carried out by a number of specialized DNA polymerases. A sequential lesion bypass model has been proposed; one of the lesion-specific polymerases inserts nucleotide(s) opposite the damaged template, followed by extension from the inserted nucleotide by the same or another polymerase. Polzeta and Polkappa have been proposed as candidates for executing the extension step in eukaryotic cells. We previously disrupted separately Rev3, the catalytic subunit of Polzeta, and Polkappa in chicken B lymphocyte DT40 cells. We found that each cell line showed significant UV sensitivity, implying that both contribute to UV radiation damage repair. In the present studies we generated REV3(-/-)POLK(/-) double knock-out cells to determine whether they participate in the same or different pathways. The double mutant was viable and proliferated with the same kinetics as parental REV3(-/-) cells. The cells showed the same sensitivity as REV3(-/-) cells to UV, ionizing radiation, and chemical cross-linking agents. In contrast, they were more sensitive than REV3(-/-) cells to monofunctional alkylating agents, even though POLK(/-) cells barely exhibited increased sensitivity to those. Moreover Polk-deficient mouse embryonic stem and fibroblast cells, both of which have previously been shown to be sensitive to UV radiation, also showed moderate sensitivity to methyl methanesulfonate, a monofunctional alkylating agent. These data imply that Polkappa has a function in TLS past alkylated base adducts as well as UV radiation DNA damage in vertebrates.

The gene hierarchy directing biogenesis of peritrichous flagella on the surface of Escherichia coli and other enterobacteria is controlled by the heterotetrameric master transcriptional regulator FlhD(2)C(2). To assess the extent to which FlhD(2)C(2) directly activates promoters of a wider regulon, a computational screen of the E. coli genome was used to search for gene-proximal DNA sequences similar to the 42-44 bp inverted repeat FlhD(2)C(2) binding consensus. This identified the binding sequences upstream of all eight flagella class II operons, and also putative novel FlhD(2)C(2) binding sites in the promoter regions of 39 non-flagellar genes. Nine representative non-flagellar promoter regions were all bound in vitro by active reconstituted FlhD(2)C(2) over the K(D) range 38-356 nM, and of the nine corresponding chromosomal promoter-lacZ fusions, those of the four genes b1904, b2446, wzz(fepE) and gltI showed up to 50-fold dependence on FlhD(2)C(2) in vivo. In comparison, four representative flagella class II promoters bound FlhD(2)C(2) in the K(D) range 12-43 nM and were upregulated in vivo 30- to 990-fold. The FlhD(2)C(2)-binding sites of the four regulated non-flagellar genes overlap by 1 or 2 bp the predicted -35 motif of the FlhD(2)C(2)-activated sigma(70) promoters, as is the case with FlhD(2)C(2)-dependent class II flagellar promoters. The data indicate a wider FlhD(2)C(2) regulon, in which non-flagellar genes are bound and activated directly, albeit less strongly, by the same mechanism as that regulating the flagella gene hierarchy.

Polyamic acid (PAA) containing free-base porphyrin and zinc(II) porphyrin chromophores was synthesized by copolymerization of diphenylether-type tetracarboxylic dianhydride and diamines. The monolayer of the alkylamine salts of PAA (PAASs) at the air/water interface was deposited on solid substrates by the Langmuir-Blodgett (LB) technique. The PAAS LB films thus obtained were converted to polyimide (PI) LB films by chemical treatment. The fluorescence of porphyrin moieties in the PI LB film was observed, because of the weak electron-accepting properties of the diphenylether unit. Therefore, the photophysically important processes, such as photoinduced electron transfer, excitation energy transfer, and excitation energy migration could be investigated in relation to the layered nanostructures of the ultrathin PI films. The fluorescence spectrum suggested that the aggregation of porphyrin moieties in the PI LB films was effectively prevented by the use of polymeric films. The surface plasmon (SP) measurement showed that the thickness of the monolayers was 0.9-1.0 nm for PAAS films and 0.32-0.40 nm on average for PI LB films. The absorption dichroism of the Soret band of porphyrin indicated that porphyrin moieties in the PAAS and PI LB films are oriented in parallel with the substrate. These results showed that the orientation and the spatial distribution of porphyrin units can be efficiently regulated in the PI LB films in a nanometer dimension.

DNA polymerases of the Y-family are involved in translesion DNA synthesis past different types of DNA damage. Previous work has shown that DNA polymerases eta and iota are localised in replication factories during S phase, where they colocalise one-to-one with PCNA. Cells with factories containing these polymerases accumulate after treatment with DNA damaging agents because replication forks are stalled at sites of damage. We now show that DNA polymerase kappa (pol(kappa)) has a different localisation pattern. Although, like the other Y-family polymerases, it is exclusively localised in the nucleus, pol(kappa) is found in replication foci in only a small proportion of S-phase cells. It does not colocalise in those foci with proliferating cell nuclear antigen (PCNA) in the majority of cells. This reduced number of cells with pol(kappa) foci, when compared with those containing pol(eta) foci, is observed both in untreated cells and in cells treated with hydroxyurea, UV irradiation or benzo[a]pyrene. The C-terminal 97 amino acids of pol(kappa)are sufficient for this limited localisation into nuclear foci, and include a C2HC zinc finger, bipartite nuclear localisation signal and putative PCNA binding site.

It is currently widely accepted that genetic instability is key to cancer development. Many types of cancers arise as a consequence of a gradual accumulation of nucleotide aberrations, each mutation conferring growth and/or survival advantage. Genetic instability could also proceed in sudden bursts leading to a more drastic upheaval of structure and organization of the genome. Genetic instability, as an operative force, will produce genetic variants and the greater the instability, the larger the number of variants. We report here that the overexpression of human DNA polymerase kappa, an error-prone enzyme that is up-regulated in lung cancers, induces DNA breaks and stimulates DNA exchanges as well as aneuploidy. Probably as the result of so many perturbations, excess polymerase kappa favors the proliferation of competent tumor cells as observed in immunodeficient mice. These data suggest that altered regulation of DNA metabolism might be related to cancer-associated genetic changes and phenotype.

Cyclins, cyclin-dependent kinases (Cdks), and Cdk inhibitors (CdkIs) are frequently altered in human cancer. p18INK4C, a member of the INK4 family of CdkIs, is a potential tumor-suppressor gene product. However, the expression of p18INK4C in hepatocellular carcinoma (HCC) remains unknown. The aim of this study was to examine the expression of p18INK4C in various liver diseases including HCC and to assess its clinical significance in HCC. To that end, we examined the expression of p18INK4C by immunohistochemistry in various liver diseases, including 51 HCCs, and also studied the relationship between p18INK4C expression, the phosphorylation of retinoblastoma protein (pRb), and the activity level of Cdk4 and Cdk6. Immunohistochemical analysis revealed the frequent loss of p18INK4C expression in HCC, especially in poorly differentiated HCC. The loss of p18INK4C expression was shown to be associated with a poor prognosis compared with that associated with p18INK4C- positivity. Further, the kinase activity of Cdk4 was found to be higher in p18INK4C-negative HCCs than in p18INK4C- positive HCCs. However, the level of Cdk6 activity was similar in the 2 groups of HCCs. In p18INK4C- positive HCCs, p18INK4C dominantly interacted with Cdk4 rather than with Cdk6. pRb phosphorylated at serine(Ser) 780 was detected more frequently in p18INK4C - negative than in p18INK4C - positive HCCs. In conclusion, the loss of p18INK4C expression may play a role in the differentiation and development of HCC through the up-regulation of Cdk4 activity., (Copyright 2004 American Association for the Study of Liver Diseases)

DNA polymerase kappa (POLkappa) is a low fidelity translesional DNA polymerase implicated in spontaneous and DNA damage-induced mutagenesis. We have previously shown that POLkappa was frequently overexpressed in human lung cancer tissues as compared with their matched non-tumorous tissue counterpart. In the present study, we found a close correlation between elevated POLkappa expression and p53 inactivation in lung cancer tissues. To investigate whether POLK expression might be regulated by p53, we have determined the transcriptional initiation site of POLK gene and examined its promoter activity in A549, H358-129, and PC-3 human lung cancer cell lines. Wild-type p53, but not a mutant p53 (R273H) devoid of the DNA-binding activity, strongly inhibited POLK promoter activity in these cells. In addition, POLK promoter exhibited a significantly higher activity in p53-/- murine embryo fibroblasts (MEF) than in p53+/- and p53+/+ MEF. These results link p53 status with POLkappa expression and suggest that loss of p53 function may in part contribute to the observed POLkappa upregulation in human lung cancers.

During the immune response to T cell-dependent antigen, somatic hypermutation (SHM) is introduced into immunoglobulin (Ig) genes. The variable region is the target for SHM and it is here that DNA lesions are introduced and mutations are generated. It has been suggested that error-prone DNA polymerase(s) may play an important role in this mutagenesis phase. Recently, DNA polymerase kappa (Polkappa), which belongs to the Y-family of DNA polymerases, was identified. Since a hot spot of SHMs (RGYW motif) is also a hot spot of mutations by human Polkappa, this enzyme was suggested to be an SHM instigator. In order to address the question whether Polkappa is involved in SHM, we immunized Polkappa-deficient mice and analyzed the SHM of the Ig heavy chain gene. We found that the SHM frequency and spectrum were indistinguishable between the Polkappa knockout mice and control mice. These results suggested that Polkappa is not essential for this process.

There are two interrelated acyl-homoserine lactone quorum-sensing-signaling systems in Pseudomonas aeruginosa. These systems, the LasR-LasI system and the RhlR-RhlI system, are global regulators of gene expression. We performed a transcriptome analysis to identify quorum-sensing-controlled genes and to better understand quorum-sensing control of P. aeruginosa gene expression. We compared gene expression in a LasI-RhlI signal mutant grown with added signals to gene expression without added signals, and we compared a LasR-RhlR signal receptor mutant to its parent. In all, we identified 315 quorum-induced and 38 quorum-repressed genes, representing about 6% of the P. aeruginosa genome. The quorum-repressed genes were activated in the stationary phase in quorum-sensing mutants but were not activated in the parent strain. The analysis of quorum-induced genes suggests that the signal specificities are on a continuum and that the timing of gene expression is on a continuum (some genes are induced early in growth, most genes are induced at the transition from the logarithmic phase to the stationary phase, and some genes are induced during the stationary phase). In general, timing was not related to signal concentration. We suggest that the level of the signal receptor, LasR, is a critical trigger for quorum-activated gene expression. Acyl-homoserine lactone quorum sensing appears to be a system that allows ordered expression of hundreds of genes during P. aeruginosa growth in culture.

Several low-fidelity DNA polymerases have recently been discovered that are able to bypass DNA lesions during DNA synthesis in vitro. The efficiency and accuracy of lesion bypass is, however, both polymerase and lesion specific. For example, in vitro studies revealed that human DNA polymerase kappa (Polkappa) is unable to insert a base opposite a cis-syn thymine-thymine dimer or cisplatin adduct, yet can bypass some DNA lesions such as abasic site and acetylaminofluorene-adducted guanine in an error-prone manner. More importantly, Polkappa is able to bypass benzo[a]pyrene (B[a]P)-adducted guanine accurately and efficiently. To investigate the biological function of Polkappa, we have generated mouse embryonic stem (ES) cells deficient in the Polk gene encoding the enzyme. Polk-deficient ES cells grow normally and their sensitivities to UV and x-ray radiation are only slightly affected. In contrast, the mutant cells are highly sensitive to both killing and mutagenesis induced by B[a]P. Furthermore, the spectrum of mutations recovered in the Polk-deficient cells is different from that in the wild-type cells. Thus, our results indicate that Polkappa plays an important role in suppressing mutations at DNA lesions generated by B[a]P.

Background: Human polkappa is a newly identified low-fidelity DNA polymerase. While the enzyme bypasses an abasic site and acetylaminofluorene-adduct in an error-prone manner, it bypasses benzo[a]pyrene-N2-dG lesions in a mostly error-free manner by incorporating predominantly dC opposite the bulky lesions. Benzo[a]pyrene (B[a]P) is activated through intracellular process mediated by the arylhydrocarbon receptor (AhR, also called the dioxin receptor), which is a ligand-activated transcription factor with high affinities for aromatic compounds such as B[a]P and dioxin., Results: We examined promoter structures of the human POLK and mouse Polk genes to study how their expressions are regulated. The mouse Polk gene is developmentally regulated in testis and utilizes two transcription start sites during spermatogenesis, while it utilizes only one site in tissues other than testis. Both of the mouse Polk and the human POLK genes have two AhR-binding sites in the promoter regions and the expression of the mouse Polk gene is indeed enhanced upon AhR-activation., Conclusions: The AhR activation increases expression of the mouse Polk gene and probably the human POLK gene, the product of which bypasses benzo[a]pyrene-N2-dG lesions in a mostly accurate manner. Thus, polkappa seems to function to reduce mutagenesis at benzo[a]pyrene-adducts, although it may also have a role related to spermatogenesis.

Microalgal cultivation in a solution recovered from the low-temperature catalytic gasification of the microalga itself was studied. The growth of Chlorella vulgaris in 75-300-fold diluted recovered solution containing phosphate, magnesium ions and micro-elements was comparable to that in the standard culture medium. It was suggested that C. vulgaris could use ammonium in the recovered solution as its nitrogen source and at the same time could provide a source of biomass which was recycled via gasification.

The Escherichia coli protein DinB is a newly identified error-prone DNA polymerase. Recently, a human homolog of DinB was identified and named DINB1. We report that the DINB1 gene encodes a DNA polymerase (designated polkappa), which incorporates mismatched bases on a nondamaged template with a high frequency. Moreover, polkappa bypasses an abasic site and N-2-acetylaminofluorene (AAF)-adduct in an error-prone manner but does not bypass a cis-syn or (6-4) thymine-thymine dimer or a cisplatin-adduct. Therefore, our results implicate an important role for polkappa in the mutagenic bypass of certain types of DNA lesions.

Exposure of Escherichia coli to a variety of DNA-damaging agents results in the induction of the global 'SOS response'. Expression of many of the genes in the SOS regulon are controlled by the LexA protein. LexA acts as a transcriptional repressor of these unlinked genes by binding to specific sequences (LexA boxes) located within the promoter region of each LexA-regulated gene. Alignment of 20 LexA binding sites found in the E. coli chromosome reveals a consensus of 5'-TACTG(TA)5CAGTA-3'. DNA sequences that exhibit a close match to the consensus are said to have a low heterology index and bind LexA tightly, whereas those that are more diverged have a high heterology index and are not expected to bind LexA. By using this heterology index, together with other search criteria, such as the location of the putative LexA box relative to a gene or to promoter elements, we have performed computational searches of the entire E. coli genome to identify novel LexA-regulated genes. These searches identified a total of 69 potential LexA-regulated genes/operons with a heterology index of <15 and included all previously characterized LexA-regulated genes. Probes were made to the remaining genes, and these were screened by Northern analysis for damage-inducible gene expression in a wild-type lexA+ cell, constitutive expression in a lexA(Def) cell and basal expression in a non-inducible lexA(Ind-) cell. These experiments have allowed us to identify seven new LexA-regulated genes, thus bringing the present number of genes in the E. coli LexA regulon to 31. The potential function of each newly identified LexA-regulated gene is discussed.

Background: The Escherichia coli dinB gene is an SOS gene known to be required for lambda phage untargeted mutagenesis. When over-expressed, it exhibits a potent mutagenic activity without any exogenous treatment to damage DNA. Frameshift mutations at a run of identical bases are most enhanced. The product DinB is structurally related to the E. coli UmuC protein and the Saccharomyces cerevisiae Rev1 and Rad30 proteins, all of which are shown to be involved in bypass synthesis at a DNA lesion., Results: We have cloned and sequenced human and mouse cDNAs encoding a DinB homologue. Their products are highly similar to DinB and less similar to UmuC, Rev1 or Rad30, and hence the genes were named DINB1 for human and Dinb1 for mouse. Both genes were expressed most abundantly in testis. Transient expression of the mouse cDNA in cultured mouse cells resulted in a nearly 10-fold increase in the incidence of point mutations, among which about 30% were frameshift mutations., Conclusions: The above results suggest that a mutagenic mechanism, a so-called untargeted type, also operates in mammalian cells. Taken together with recent findings that human cells have multiple DNA polymerases for translesion synthesis which are homologous to the S. cerevisiae Rev3 and Rad30 proteins, our results imply that multiple mutagenic pathways are conserved from bacteria to higher eukaryotes.

The effects of glucose addition and light on the current outputs in electrochemical cells using a cyanobacterium Synechocystis sp. PCC6714 were investigated under photo- and chemoheterotrophical conditions. The addition of glucose to the anode solutions of the electrochemical cells resulted in a rapid increase in the current outputs under both light and dark conditions. Although the coulombic outputs were almost the same between under light and dark conditions, the rate of glucose consumption was faster under illumination than in the dark. The total sugar content in the cells of strain PCC6714 increased with the addition of glucose and the total sugar accumulated remained intact during the discharge under illumination, while it decreased gradually in the dark. When the light was switched off after the addition of glucose, the current output markedly increased. The coulombic outputs obtained after darkening were 10 to 80 times larger than that obtained by the addition of glucose under the continuous light or dark conditions. Synechocystis sp. completely incorporated 0.14 mM and 0.42 mM glucose for 1 h and 3 h, respectively, under illumination. There was no difference in the coulombic outputs between 1 h and 12 h illumination times in the electrochemical cells with 0.14 mM glucose. When the light was switched off after 1 h illumination in the electrochemical cells with 0.42 mM glucose, the coulombic output obtained from the electrochemical cell was lower than that in the electrochemical cell with 12 h illumination. This indicates that the current output was produced with higher efficiency with glucose incorporated under illumination than that in the case of glucose incorporated after darkening. The highest coulombic yield of 54% in this experiment was obtained by darkening in the electrochemical cell with 0.14 mM glucose.

Thermochemical liquidization as a pretreatment for anaerobic digestion of food waste was studied using a laboratory-scale upflow anaerobic sludge blanket (UASB) reactor for a period of 82 d. Model food waste (approximately 90 wt% moisture content) was thermochemically liquidized at 175 degrees C for 1 h. The liquidized food waste was separated into a solid phase (6-10 wt%) and a liquid phase (85-89 wt%). The diluted liquid phase was continuously treated by anaerobic digestion using a UASB reactor at 35 degrees C. The volumetric loading rate was increased stepwise to 6.4-7.2 g total organic carbon (TOC)/l-reactor/d. Methane production was found to be approximately 0.35-0.61 l/g-TOC removed. The range of TOC removal efficiencies was 67-69% at an influent TOC concentration of 10.1-11.1 g/l and a volumetric loading rate of 4.8-5.3 g-TOC/l-reactor/d. This treatment process using an UASB reactor could be suitable for resource recovery from food waste.