Archaeal integrases and mechanisms of gene capture

Archaeal integrases facilitate the formation of two distinctive types of integrated element within archaeal chromosomes: the SSV type and pNOB8 type. The former carries a smaller N-terminal and a larger C-terminal integrase gene fragment, and the latter an intact integrase gene. All integrated elements overlap tRNA genes that were target sites for integration. It has been demonstrated that SSV (Sulfolobus spindle virus) viruses, carrying an SSV-type integrase gene, and conjugative plasmids, carrying a pNOB8-type integrase, are integrative elements. Two mechanisms have been proposed for stably maintaining an integrated element within archaeal chromosomes. There is also evidence for changes having occurred in the captured integrated elements present in archaeal genomes. Thus we infer that site-specific integration constitutes an important mechanism for horizontal gene transfer and genome evolution.

Retroviral delivery of GAD-IgG fusion construct induces tolerance and modulates diabetes: a role for CD4+ regulatory T cells and TGF-beta?

Previous studies have demonstrated that antigen-specific tolerance could be induced by lipopolysaccharide (LPS)-stimulated B cells retrovirally transduced with an immunoglobulin-antigen (or epitope-containing peptide) fusion construct. To investigate the mechanism of this gene therapy system, we now adapted this approach to immunotherapy of spontaneous diabetes in nonobese diabetic (NOD) mice, a T-cell-mediated autoimmune disease triggered, in part, by a pathogenic response to glutamate decarboxylase (GAD) 65. We demonstrate that LPS-stimulated splenocytes, retrovirally transfected with GAD-IgG fusion construct, induce a significant antigen-specific hyporesponsiveness at both cellular and humoral levels and reduce the incidence of diabetes in female NOD mice. Parallel with disease protection, we observed a prolonged increase of the numbers of CD4+CD25+ T cells in the periphery of GAD-IgG-treated mice, compared to those treated with a control IgG vector, both in the prediabetic period and persisting even 8 months after gene therapy. This increase appeared to be induced by the repeated stimulation of the antigen in the periphery instead of a result of differentiation of T-cell precursor in the thymus. Moreover, CD4+CD25+ T cells induced by GAD-IgG fusion construct were capable of suppressing the proliferative response of CD4+CD25- T cells in vitro; and ablation of the activity of CD4+CD25+ T cells by blocking antibody against CD25 could reverse GAD-specific T-cell hyporesponsiveness. These results suggested that CD4+CD25+ T-cell subset induced in GAD-IgG-treated NOD mice represented the regulatory or suppressive CD4+CD25+ T cells (Treg) and might play an important role in the induction and maintenance of tolerance in NOD mice. Furthermore, the numbers of splenic CD4+CD62L+ regulatory T cells in GAD-IgG-treated mice during the prediabetic period and serum TGF-beta levels in 34-38-week-old GAD-IgG-protected mice were also increased, compared to control IgG-treated ones. Therefore, we propose that the induction of tolerance and the prevention of diabetes incidence in NOD female mice induced by the GAD-IgG fusion construct may require CD4+ regulatory T cells, and the possible mediation of TGF-beta.

[Cloning and identification of deltamethrin-resistance or susceptibility associated genes of Culex pipiens pallens]

OBJECTIVE

To obtain deltamethrin-resistance or susceptibility associated genes of Culex pipiens pallens.

METHODS

The differentially expressed genes were obtained by suppression subtractive hybridization (SSH), and identified by cDNA microarray and reverse Northern blotting.

RESULTS

523 and 286 clones were selected respectively in the two directional SSH. 155 and 42 genes were respectively expressed 2-3 and > 3 times higher in the insecticide-resistant strain than in the susceptible strain; 15 and 9 genes were respectively expressed 2-3 and > 3 times higher in the susceptible strain than in the resistant strain. There were 2 genes only expressed in the insecticide-resistant strain. 51 three times differentially expressed clones and 2 specially expressed clones were sequenced. 44 sequences were obtained which belong to 13 new genes. There were 8 over-expressed genes in resistant strain, 7 of which were similar respectively to mitochondrion rRNA gene, 60S ribosomal protein gene, 40S ribosomal protein S4 gene, trypsin gene, chymotrypsin A gene, ospin gene, and 16S ribosomal RNA gene. There were 5 over-expressed genes in susceptible strain, 2 of them being similar with 40S ribosomal protein S29 gene and myosin regulatory light chain 2 gene. In addition, 2 genes specially expressed in resistant strain were similar respectively to glycogen branching enzyme gene and ribosomal protein 46 gene.

CONCLUSION

The differentially expressed genes may be associated with deltamethrin-resistance or susceptibility of Culex pipiens pallens.

Induction of matrix metalloproteinase-2 and -3 activity in ovine nucleus pulposus cells grown in three-dimensional agarose gel culture by interleukin-1beta: a potential pathway of disc degeneration

Degeneration of the intervertebral disc is an important clinical problem, which often contributes to low back pain. Since approximately 80-90% of the general population will be subject to back pain at some stage during their lifetime, this has major socioeconomic consequences. Matrix metalloproteinases (MMPs) have been implicated in the excessive breakdown of extracellular matrix components during disc degeneration. The aim of the present study was to evaluate the regulation of MMP-2 (gelatinase-A) and MMP-3 (stromelysin) produced by cultured ovine nucleus pulposus (NP) cells stimulated with interleukin-1beta (IL-1beta). NP cells were established in three-dimensional agarose culture and stimulated with IL-1beta under serum-free conditions. Conditioned media samples were evaluated by gelatin and casein zymography and by fluorimetry using an MMP-specific substrate. Time-course and dose dependencies were established for MMP-2, -3 production by the NP cells in response to the IL-1beta. Gelatin and casein zymography indicated that elevated levels of proMMP-2 and proMMP-3 were present in media samples in response to the IL-1beta treatment. After 24-96 h culture, levels of the active 43 and 45 kDa active MMP-3 were significantly elevated, whereas MMP-2 was present mainly as its 72 kDa pro-form. Additional 36, 28 and 21 kDa MMP species were also present after prolonged incubation with IL-1beta, probably representing MMP breakdown species. IL-1beta was a potent catabolic mediator for the NP cells, resulting in the production of elevated levels of MMP-2 and -3 in culture. However, approximately 70% of the MMP-2 was present as the 72 kDa pro-form, which suggests that some additional steps are involved in its activation in vivo.

[Abuse of "pheticol" and its interference to the analysis of methamphetamine]

The study was to eliminate interference from ephedrine in the analysis of methamphetamine. The extraction procedure for methamphetamine was modified to include an oxidation step (2 ml urine specimen was treated with 0.5 ml of 1 mol/L phosphate buffer (pH 6.8) and 0.5 ml 0.3 mol/L sodium periodate). Results showed that ephedrine could be oxidized in the presence of periodate ions into smaller fragments while leaving methamphetamine intact. It is recommended that specimens be treated with sodium periodate prior to extraction in order to eliminate any interference caused by ephedrine.

Independent dose calculations for the corvus MLC IMRT

Two independent dose calculation methods have been explored to validate MLC-based IMRT plans from the NOMOS CORVUS system. After the plan is generated on the CORVUS planning system, the beam parameters are imported into an independent workstation. The beam parameters consist of intensity maps at each gantry angle. In addition, CT scans of the patient are imported into the independent workstation to obtain the external contour of the patient. The coordinate system is defined relative to the alignment point chosen in the CORVUS plan. The 2 independent calculation methods are based on a pencil beam kernel convolution and a Clarkson-type differential scatter summation, respectively. The pencil beam data for a 1 x 1-cm beam, as formed by the multileaf collimator, were measured for the 6-MV photon beam from a Siemens PRIMUS linear accelerator using film dosimetry. In the pencil beam method, the dose at a point is calculated using the depth and off-axis distance from a given pencil beam, corrected for beam intensity. The scatter summation method used the conversion of measured depth dose data into scatter maximum ratios. In this method, the differential scatter from each pencil beam is corrected for the beam intensity. Isodose distributions were generated using the independent dose calculations and compared to the CORVUS plans. Although isodose distributions from both methods show good agreement with the CORVUS plan, our implementation of the differential scatter summation approach seems more favorable. The 2 independent dose calculation algorithms are described in this paper.

[Distribution of F13A01, FESFPS and vWA loci in ten minority populations in Yunnan of China]

The short tandem repeats (STR) is a kind of DNA sequence formed repeatedly and connectively subjected to a core unit of several base pairs. The non-interfered multi-PCR was applied with 3 loci in the same reaction system. By using the technique of denaturing polyacrylamide gel electrophoresis and silver stain, the allele frequencies distributions of 3 loci: F13A01, FESFPS and vWA in 10 minority populations only resided in Yunnan Province: Bai, Dai, Achang, Jingpo, Deang, Lahu, Bulang, Hani, Pumi and Jino. A satisfactory result was obtained and some significant genetic differences were noticed in different populations.

[A novel erythroid differentiation related gene EDRF1 upreguated globin gene expression in HEL cells]

OBJECTIVE

To observe the differentiation-inducing properties of the novel erythroid differentiation related gene EDRF1, and demonstrate its functioning pathway involved in regulation of alpha- and gamma-globin gene expression.

METHODS

EDRF1 sense and antisense constructs were transfected into HEL cells, then the expression of globin and erythropoietin receptor gene was identified by Northern blot analysis. RT-PCR and electrophoresis mobility shift assay (EMSA) were carried out to monitor the expression and DNA-binding activity of erythroid specific transcription factor GATA-1 and NF-E2.

RESULTS

In HEL cells with transfection of sense expression carrier, the experssion of EDRF1 mRNA was upregulated. In HEL cells with transfection of antisense expression carrier, the experession of EDRF1 mRNA was downregulated. In HEL cells with overexpression of EDRF1, production of alpha-globin was increased. In antisense EDRF1 overexpressed HEL cells, significant loss of alpha- and gamma-globin mRNA synthesis was observed. The expression of erythropoietin receptor was unchanged in HEL cells transfected with EDRF1 sense and antisense expression carriers. No significant change was found in expression of transcription factors GATA-1 and NF-E2 in HEL cells transfected with empty carrier, sense expression carrier, and antisense expression carrier. However, the transcription activity of GATA-1 was severely impaired. Expression of erythropoietin receptor gene was not influenced by EDRF1 gene overexpression.

CONCLUSION

EDRF1 regulates alpha- and gamma-globin gene synthesis by modulating DNA-binding activity of GATA-1 transcription factor. Overexpression and underexpression of EDRF1 do not significantly regulate the expression of GATA-1 and NF-E2 mRNA. Monitoring the EPOR signal pathway is not the mechanism by which EDRF1 influences the differentiation of erythrocyte.

Medical management of postoperative complications of inflammatory bowel disease: pouchitis and Crohn's disease recurrence

Surgical intervention is often required for patients with inflammatory bowel disease. Total proctocolectomy with ileal pouch-anal anastomosis is the surgical treatment of choice for patients with ulcerative colitis. The main long-term complication of this surgery is pouchitis, with 10-year cumulative incidence rates between 24% and 46%. For patients with Crohn's disease, postoperative recurrence is a significant problem, with clinical recurrence rates as high as 55% at 5 years and 76% at 15 years. Increasing evidence suggests that postoperative medical therapy has the potential to decrease the risk of postoperative Crohn's disease recurrence.

Affinity and Western blotting reveal homologies between ovine intervertebral disc serine proteinase inhibitory proteins and bovine pancreatic trypsin inhibitor

The objective of this study was to assess any similarities between ovine intervertebral disc (IVD) serine proteinase inhibitory proteins (SPIs) and known mammalian IVD SPIs. Ovine IVDs were dissected into the annulus fibrosus and nucleus pulposus and the tissue finely diced then extracted with 4 M guanidine hydrochloride. The tissue extracts were subjected to caesium chloride density gradient ultracentrifugation to separate the large high buoyant density (rho > 1.5 g/mL) proteoglycans from the SPI proteins of low buoyant density (rho < 1.33 g/mL). The top two ultracentrifuge fractions containing the SPIs of interest were subjected to enzyme linked immunosorbent analysis (ELISA) and also examined by Western and Affinity blotting using an antibody to bovine pancreatic trypsin inhibitor and biotinylated trypsin respectively for detection and an alkaline phosphatase 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium system for visualisation. The major SPI proteins present in the Western and Affinity blots were 34-36 kDa species, minor 12 and 16, and 85 and 120 kDa species were also present. Qualitatively similar results were obtained for each respective tissue zone of the lumbar and lumbosacral disc specimens examined. Densitometric analysis of the major 34-36 kDa SPI bands visualised on Western and Affinity blots using NIH 1.61.1 image analysis software indicated that lumbar IVD samples contained higher levels of this SPI species than lumbosacral IVD samples. ELISA confirmed that lumbar IVD extracts contained quantitatively higher levels of BPTI equivalents per g of tissue extracted than lumbosacral IVDs. This study therefore has demonstrated that the ovine disc contains a range of SPI species which share some homology with bovine pancreatic trypsin inhibitor and in this respect are similar to SPIs previously demonstrated in canine IVDs.

The biosynthetic gene cluster for the anticancer drug bleomycin from Streptomyces verticillus ATCC15003 as a model for hybrid peptide-polyketide natural product biosynthesis

The hybrid peptide-polyketide backbone of bleomycin (BLM) is assembled by the BLM megasynthetase that consists of both nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) modules. BlmIX/BlmVIII/BlmVII constitute a natural hybrid NRPS/PKS/NRPS system, serving as a model for both hybrid NRPS/PKS and PKS/NRPS systems. Sequence analysis and functional comparison of domains and modules of BlmIX/BlmVIII/BlmVII with those of nonhybrid NRPS and PKS systems suggest that (1) the same catalytic sites appear to be conserved in both hybrid NRPS-PKS and nonhybrid NRPS or PKS systems, with the exception of the KS domains in the hybrid NRPS/PKS systems that are unique; (2) specific interpolypeptide linkers may play a critical role in intermodular communication to facilitate transfer of the growing intermediates between the interacting NRPS and/or PKS modules; and (3) posttranslational modification of the BLM megasynthetase has been accomplished by a single PPTase with a broad substrate specificity toward the apo forms of both acyl carrier proteins (ACPs) and peptidyl carrier proteins (PCPs).

The ocular albinism type 1 gene product is an N-glycoprotein but glycosylation is not required for its subcellular distribution

The ocular albinism type 1 (OA1) gene product is a membrane glycoprotein that may play a role in controlling melanosome growth and maturation. A number of mutations in the OA1 gene lead to ocular albinism due at least in part to retention of the aberrant protein in the endoplasmic reticulum. To examine whether N-glycosylation plays a role in the post-translational trafficking of the Oa1 protein, we constructed a series of mutant mouse Oa1 cDNAs encoding an Oa1-green fluorescent protein fusion in which some or all of the potential glycosylation sites were eliminated by site-directed mutagenesis. Biochemical studies in transfected cells treated with tunicamycin and peptide:N-glycosidase F suggest that asparagine at amino acid 106 is essential for N-glycosylation of the protein. Mutation at amino acid 106 that eliminated glycosylation did not affect the endo/lysosomal distribution of the Oa1 protein in either COS cells or cultured murine melanocytes.

Transparency of an overdense plasma layer

The transition from opacity to transparency of overdense plasma layers for the propagation of high-intensity laser pulses of circular polarization is investigated theoretically and by simulation. We discuss in detail the regions where stationary solutions exist and therefore the plasma layer is opaque. We find that the opacity depends not only on the electron density and the laser intensity but also on the thickness of the plasma layer. We also discuss the overlap region where both transparency and opacity are possible and how it depends on the history. Ion acceleration is studied in both the opacity region and the transparency region.

A randomized clinical trial of ciprofloxacin and metronidazole to treat acute pouchitis

Metronidazole is effective for the treatment of acute pouchitis after ileal pouch-anal anastomosis, but it has not been directly compared with other antibiotics. This randomized clinical trial was designed to compare the effectiveness and side effects of ciprofloxacin and metronidazole for treating acute pouchitis. Acute pouchitis was defined as a score of 7 or higher on the 18-point Pouchitis Disease Activity Index (PDAI) and symptom duration of 4 weeks or less. Sixteen patients were randomized to a 2-week course of ciprofloxacin 1,000 mg/d (n = 7) or metronidazole 20 mg/kg/d (n = 9). Clinical symptoms, endoscopic findings, and histologic features were assessed before and after therapy. Both ciprofloxacin and metronidazole produced a significant reduction in the total PDAI score as well as in the symptom, endoscopy, and histology subscores. Ciprofloxacin lowered the PDAI score from 10.1+/-2.3 to 3.3+/-1.7 (p = 0.0001), whereas metronidazole reduced the PDAI score from 9.7+/-2.3 to 5.8+/-1.7 (p = 0.0002). There was a significantly greater reduction in the ciprofloxacin group than in the metronidazole group in terms of the total PDAI (6.9+/-1.2 versus 3.8+/-1.7; p = 0.002), symptom score (2.4+/-0.9 versus 1.3+/-0.9; p = 0.03), and endoscopic score (3.6+/-1.3 versus 1.9+/-1.5; p = 0.03). None of patients in the ciprofloxacin group experienced adverse effects, whereas three patients in the metronidazole group (33%) developed vomiting, dysgeusia, or transient peripheral neuropathy. Both ciprofloxacin and metronidazole are effective in treating acute pouchitis with significant reduction of the PDAI scores. Ciprofloxacin produces a greater reduction in the PDAI and a greater improvement in symptom and endoscopy scores, and is better tolerated than metronidazole. Ciprofloxacin should be considered as one of the first-line therapies for acute pouchitis.

[The status and prospects of X-ray photographs marking technology]

This article introduces three different marking technologies used in clinical radiation photography at present and their respective theories, their advantages and disadvantages, analyzes the space-time and technology conditionality of different marking technologies in selecting mark messages. In the future, new marking technology will be fused with the cassette into one and will contain message as much as possible on photograph marks in order to satisfy the need of technicians and doctors.

Independent dose calculations for the PEACOCK System

An independent dose calculation method has been developed to validate intensity-modulated radiation therapy (IMRT) plans from the NOMOS PEACOCK System. After the plan is generated on the CORVUS planning system, the beam parameters are imported into an independent workstation. The beam parameters consist of intensity maps at each gantry angle and each arc position. In addition, CT scans of the patient are imported into the independent workstation to obtain the external contour of the patient. The coordinate system is defined relative to the alignment point chosen in the CORVUS plan. The independent calculation uses the pencil beam data viz tissue maximum ratio (TMR) and beam profiles for a single 1 x 0.8-cm beamlet formed by the NOMOS multileaf intensity-modulating collimator (MIMiC) leaf. The pencil beam data were measured for the 6-MV photon beam from Siemens PRIMUS linear accelerator using film dosimetry. The dose at a point is calculated using the depth and off-axis distance from a given pencil beam, corrected for its beam intensity. Isodose distributions are generated using the independent dose calculations and compared to the CORVUS plans. Isodose distributions show good agreement with the CORVUS plans for a number of clinical cases. The independent dose calculation algorithm is described in this paper.

Comparative study between IMRT with NOMOS BEAK and linac-based radiosurgery in the treatment of intracranial lesions

A comparative study was undertaken to examine intracranial irradiation using intensity-modulation radiation therapy (IMRT) and linear accelerator-based radiosurgery. The IMRT was examined using the Peacock system with a BEAK attachment. A clinical case involving a metastatic brain lesion, treated with 3 radiosurgery isocenters, was planned for IMRT. The radiosurgery was planned using the Leibinger planning system. The IMRT was planned using the CORVUS planning system. The CORVUS planning system uses an inverse planning algorithm, a recent development in radiotherapy. Isodose distributions and dose volume histograms were generated and compared. Analysis of the dosimetry shows that the dose conformity and homogeneity within the target using the RTOG guidelines are superior for IMRT. The advantages of IMRT using inverse planning system include the ease of planning and execution of treatment, especially for cases that involve concave targets that require multiple isocenters using radiosurgery.