The genome of the natural genetic engineer Agrobacterium tumefaciens C58

The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence. Their similarities include metabolic, transport, and regulatory systems that promote survival in the highly competitive rhizosphere; differences are apparent in their genome structure and virulence gene complement. Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.

Genome-wide, large-scale production of mutant mice by ENU mutagenesis

In the post-genome era, the mouse will have a major role as a model system for functional genome analysis. This requires a large number of mutants similar to the collections available from other model organisms such as Drosophila melanogaster and Caenorhabditis elegans. Here we report on a systematic, genome-wide, mutagenesis screen in mice. As part of the German Human Genome Project, we have undertaken a large-scale ENU-mutagenesis screen for dominant mutations and a limited screen for recessive mutations. In screening over 14,000 mice for a large number of clinically relevant parameters, we recovered 182 mouse mutants for a variety of phenotypes. In addition, 247 variant mouse mutants are currently in genetic confirmation testing and will result in additional new mutant lines. This mutagenesis screen, along with the screen described in the accompanying paper, leads to a significant increase in the number of mouse models available to the scientific community. Our mutant lines are freely accessible to non-commercial users (for information, see http://www.gsf.de/ieg/groups/enu-mouse.html).

A genome-wide search for linkage to asthma. German Asthma Genetics Group

Asthma is among the most frequent chronic diseases in childhood. Although numerous environmental risk factors have already been identified, the basis for familial occurrence of asthma remains unclear. Previous genome screens for atopy in British/Australian families and for asthma in different American populations showed inconsistent results. We report a sib pair study of a sample of 97 families, including 415 persons and 156 sib pairs. Following an extensive clinical evaluation, all participants were genotyped for 351 polymorphic dinucleotide markers. Linkage analysis for asthma identified four chromosomal regions that could to be linked to asthma: chromosome 2 (at marker D2S2298, P = 0.007), chromosome 6 (around D6S291, lowest P = 0.008), chromosome 9 (proximal to D9S1784, P = 0.007), and chromosome 12 (D12S351, P = 0.010). These linkage regions could be reproduced for all loci by analysis of total or specific immunoglobulin E (minimum P values at these regions were 0. 003, 0.001, 0.010, and 0.015, respectively).

Lines of murine oligodendroglial precursor cells immortalized by an activated neu tyrosine kinase show distinct degrees of interaction with axons in vitro and in vivo

Replication-defective retroviruses expressing the t-neu oncogene, or a hybrid protein with the neu tyrosine kinase linked to the external region of the human epidermal growth factor receptor (egfr-neu), were used to establish lines of murine oligodendroglial precursor cells. Differentiation of the t-neu lines into myelin-associated glycoprotein (MAG)-positive oligodendrocytes was induced by dibutyryl cAMP, and the egfr-neu line showed limited differentiation in vitro upon withdrawal of epidermal growth factor. Cerebellar granule cell neurons expressed mitogens for the cell lines. Upon transplantation into demyelinated lesions, t-neu line cells engaged with the demyelinated axons whereas the egfr-neu line cells differentiated further and ensheathed the axons. These cell lines thus interact with neurons in vitro and in vivo and can be used as tools to define the molecules involved in different stages of neuron-glia interaction.

Identification of reggie-1 and reggie-2 as plasmamembrane-associated proteins which cocluster with activated GPI-anchored cell adhesion molecules in non-caveolar micropatches in neurons

Neurons are believed to possess plasmalemmal microdomains and proteins analogous to the caveolae and caveolin of nonneuronal cells. Caveolae are plasmalemmal invaginations where activated glycosyl-phosphatidylinositol (GPI)-anchored proteins preferentially assemble and where transmembrane signaling may occur. Molecular cloning of rat reggie-1 and -2 (80% identical to goldfish reggie proteins) shows that reggie-2 is practically identical to mouse flotillin-1. Flotillin-1 and epidermal surface antigen (ESA) (flotillin-2) are suggested to represent possible membrane proteins in caveolae. Rat reggie-1 is 99% homologous to ESA in overlapping sequences but has a 49-amino-acid N-terminus not present in ESA. Antibodies (ABs) which recognize reggie-1 or -2 reveal that both proteins cluster at the plasmamembrane and occur in micropatches in neurons [dorsal root ganglia (DRGs), retinal ganglion, and PC-12 cells] and in nonneuronal cells. In neurons, reggie micropatches occur along the axon and in lamellipodia and filopodia of growth cones, but they do not occur in caveolae. By quantitative electronmicroscopic analysis we demonstrate the absence of caveolae in (anti-caveolin negative) neurons and show anti-reggie-1 immunogold-labeled clusters at the plasmamembrane of DRGs. When ABs against the GPI-anchored cell adhesion molecules (CAMs) F3 and Thy-1 are applied to live DRGs, the GPI-linked CAMs sequester into micropatches. Double immunofluorescence shows a colocalization of the CAMs with micropatches of anti-reggie antibodies. Thus, reggie-1 and reggie-2 identify sites where activated GPI-linked CAMs preferentially accumulate and which may represent noncaveolar micropatches (domains).

Inhibitors of histone deacetylase as new anticancer agents

Inhibitors of histone deacetylase (HDAC) are an emerging class of anticancer agents. They induce hyperacetylation in chromatin usually resulting in activation of certain genes. They induce terminal cell differentiation and/or apoptosis in cancer cells. Histone deacetylase activity is recruited by co-repressor proteins to certain regions of the chromatin and aberrant histone acetylation caused by that recruitment is responsible for the pathogenesis of certain cancers on a molecular level. Inhibitors of HDAC have been identified in natural sources and also synthetic inhibitors are available. The best studied inhibitor is trichostatin A, a hydroxamic acid that exerts its activity by complexation of a zinc ion that is supposed to mediate the acetamide cleavage at the catalytic site. There are several synthetic hydroxamic acids that bear resemblance to trichostatin. Another class of potent inhibitors are naturally occurring and synthetic cyclotetrapeptides that all contain an unusual amino acid with an epoxyketone, ketone or hydroxamic acid function in the side chain. Phenylacetate, phenylbutyrate, butyrate and similar short chain fatty acids are also weak inhibitors. Further inhibitors from natural sources are the epoxide depudecin and depsipeptide FR 901228. The benzamide MS-275 belongs to a new class of synthetic HDAC inhibitors and displays oral activity in animal models. First clinical studies have shown that histone hyperacetylation can be achieved safely in humans and that treatment of cancer is possible. Thus, inhibitors of HDAC are one of the most promising class of new anticancer agents. New screening assays are useful tools that will facilitate identification of further inhibitors.

Chromoendoscopy with indigocarmine improves the detection of adenomatous and nonadenomatous lesions in the colon

BACKGROUND AND STUDY AIMS

Depressed early cancers and flat adenomas have a high potential for malignancy with possible infiltrating growth, despite the small size of the lesion. Japanese investigators have shown that early diagnosis and classification of these lesions is possible with the help of chromoendoscopy. The aim of this study, therefore, was to evaluate the usefulness of chromoendoscopy during routine colonoscopy.

PATIENTS AND METHODS

During routine colonoscopy, vital staining with indigocarmine solution (0.4 %, 1 - 10 ml) was performed on all visible lesions in 100 consecutive patients without visible inflammatory changes. If findings on macroscopic examination were unremarkable, the sigmoid colon and rectum were stained with indigocarmine over a defined segment (0 - 30 cm ab ano) and inspected for lesions visible only after staining. Each lesion was classified with regard to type (polypoid, flat, or depressed), position and size. The staining pattern was classified according to the pit pattern classification.

RESULTS

A total of 52 patients had 105 visible lesions (89 polypoid, 14 flat and two depressed). The mean size of the lesions was 1.4 cm. Among the 48 patients with mucosa of normal appearance, 27 showed 178 lesions after staining (176 flat, two depressed) with a mean size of 3 mm. On histological investigation, 210 lesions showed hyperplastic or inflammatory changes, 67 were adenomas and six were cancers. Use of the pit pattern system to classify lesions (adenomatous, pit patterns III-V; nonadenomatous, pit patterns I-II) was possible, with a sensitivity of 92 % and a specificity of 93 %. Lesions with pit patterns III - V showed higher rates of dysplasia.

CONCLUSIONS

Chromoendoscopy allows easy detection of mucosal lesions in the colon and facilitates visualization of the margins of flat lesions. This technique unmasks multiple mucosal lesions which are not identified by routine video colonoscopy. The pit pattern seen after staining allows differentiation between hyperplastic and adenomatous lesions which may have consequences with regard to the endoscopic interventions needed.

OCO-2 advances photosynthesis observation from space via solar-induced chlorophyll fluorescence

Quantifying gross primary production (GPP) remains a major challenge in global carbon cycle research. Spaceborne monitoring of solar-induced chlorophyll fluorescence (SIF), an integrative photosynthetic signal of molecular origin, can assist in terrestrial GPP monitoring. However, the extent to which SIF tracks spatiotemporal variations in GPP remains unresolved. Orbiting Carbon Observatory-2 (OCO-2)'s SIF data acquisition and fine spatial resolution permit direct validation against ground and airborne observations. Empirical orthogonal function analysis shows consistent spatiotemporal correspondence between OCO-2 SIF and GPP globally. A linear SIF-GPP relationship is also obtained at eddy-flux sites covering diverse biomes, setting the stage for future investigations of the robustness of such a relationship across more biomes. Our findings support the central importance of high-quality satellite SIF for studying terrestrial carbon cycle dynamics.

Immunoreactive elastase I: clinical evaluation of a new noninvasive test of pancreatic function

We have evaluated the diagnostic value of the fecal elastase test in comparison with the secretin-pancreozymin test in the diagnosis of exocrine pancreatic insufficiency. Pancreatic elastase was measured immunologically. Immunoreactive elastase activity in spot stools from controls ranged from 136 to 4440 microgram/g; 95% of all values were within 175 to 1500 microgram/g. The elastase assay CVs ranged from 3.3% to 6.3% (intraassay) and from 4.1% to 10.2% (interassay). The output of elastase correlated well with those of amylase, lipase, and trypsin, yielding respective correlation coefficients of 0.83, 0.82, and 0.84 in controls and 0.86, 0.91, and 0.91 in patients with impaired pancreatic function. In contrast to fecal chymotrypsin, the test results were unaffected by pancreatic enzyme replacement therapy. These results indicate that fecal immunoreactive elastase may be recommended as a new, noninvasive tubeless test of pancreatic function.

Correction of radiation sensitivity in ataxia telangiectasia cells by a truncated I kappa B-alpha

Cells from patients with ataxia telangiectasia (AT) are hypersensitive to ionizing radiation and are defective in the regulation of DNA synthesis. A complementary DNA that corrects the radiation sensitivity and DNA synthesis defects in fibroblasts from an AT group D patient was isolated by expression cloning and shown to encode a truncated form of I kappa B-alpha, an inhibitor of the nuclear factor kappa B (NF-kappa B) transcriptional activator. The parental AT fibroblasts expressed large amounts of the I kappa B-alpha transcript and showed constitutive activation of NF-kappa B. The AT fibroblasts transfected with the truncated I kappa B-alpha expressed normal amounts of the I kappa B-alpha transcript and showed regulated activation of NF-kappa B. These results suggest that aberrant regulation of NF-kappa B and I kappa B-alpha contribute to the cellular defect in AT.

Improved sedation in diagnostic and therapeutic ERCP: propofol is an alternative to midazolam

BACKGROUND AND STUDY AIMS

Adequate sedation of the patient is required for diagnostic and therapeutic endoscopic retrograde cholangiopancreatography (ERCP). The anesthetic propofol, with its shorter half-life, affording better control, offers an alternative to the benzodiazepine midazolam. The aim of this randomized, controlled, unblinded study was to compare prospectively the quality of sedation under propofol and midazolam in patients undergoing ERCP.

PATIENTS AND METHODS

A total of 80 patients were randomized to sedation with propofol alone (n = 40) or midazolam alone (n = 40). Blood pressure, pulse, and oxygen saturation were measured. Midazolam was given by the endoscopist and titrated to the patients' response during ERCP, to a maximum dose of 15 mg per patient. In the propofol group an anesthetist was present to administer the propofol and to observe the patient. Standardized testing procedures (Steward score, Trieger test) were used to determine the length of postendoscopy recovery time. Efficacy of sedation was assessed by investigators and patients, using scoring systems.

RESULTS

Complete ERCP and adequate sedation was possible in 80% of patients (32 out of 40) with midazolam, and in 97.5% of patients (39 out of 40) with propofol (P<0.01). The average propofol induction dose was 1.24 mg/kg body weight, with maintenance requiring a mean dose of 9 mg/kg body weight per hour, or the equivalent of 354 mg in total. The average dose of midazolam administered was 0.12 mg/kg body weight; the total dose averaged 8 mg. Recovery time in the propofol patients was significantly shorter (P<0.01). The investigators (P<0.01) and the patients (P<0.05) both judged the quality of sedation to be better in the propofol group. There were no differences in blood pressure, pulse, or oxygen saturation between the two groups. One patient in the propofol group (79 years old) suffered a protracted apneic phase accompanied by hypotension that was managed by manual ventilation and drug therapy, and led to no complications.

CONCLUSIONS

Propofol proves to be an excellent sedative for ERCP and shows a shorter recovery time than midazolam. Because of the narrow therapeutic window, we recommend close patient monitoring.

Increased risk of bullous pemphigoid in male and very old patients: A population-based study on incidence

No data are available on gender- and age-specific incidences for bullous pemphigoid (BP). The aim of this study was to calculate incidences for different gender- and age-strata and to assess risk differences between these strata in BP. A retrospective population-based cohort was recruited from all patients diagnosed with BP in 2 well-defined regions of Germany. The average population number was 1.7 million, and the observation period was 9 years (1989-1997). Incidences were calculated as newly diagnosed cases for a population of 1 million per year. Confidence intervals (CI) were estimated based on a Poisson distribution. For evaluation of risk between different age and gender strata a Poisson regression analysis was used. The highest incidence was calculated for individuals older than 90 years, with 398 (CI: 360, 439) new cases of BP per 1 million residents for men, and 87 (CI: 70, 108) new cases per 1 million residents for women. Risk (95% CI) was 1.9 (1.3, 2.9) fold higher in men than in women. In addition, the risk for BP was increased for patients above the age of 60 years. The highest risk was found for patients older than 90 years. For this age group, the risk was 297 (CI: 107, 826) fold higher than in patients 60 years of age and younger. Men are affected by BP almost twice as often as women. The risk for BP increases rapidly beyond the age of 60 years. Because the structure of the European population is shifting towards the aged, more people are expected to suffer from BP in the coming decades.

Amide analogues of trichostatin A as inhibitors of histone deacetylase and inducers of terminal cell differentiation

Inhibitors of histone deacetylase (HD) bear great potential as new drugs due to their ability to modulate transcription and to induce apoptosis or differentiation in cancer cells. We have described previously analogues of the complex natural HD inhibitors trapoxin B and trichostatin A with activities in the submicromolar range. Here we report structure-activity relationship analyses of further analogues of trichostatin A with respect to in vitro inhibition of maize HD-2 and their ability to induce terminal cell differentiation in Friend leukemic cells. This is the first report that shows the correlation between HD inhibitory activity and action on cancer cells on a larger series of similar compounds. Only the compounds that inhibit HD induce differentiation and/or exert antiproliferative activities in cell culture. Our studies support the use of in vitro systems as screening tools and provide structure-activity relationships that merit further investigation of this interesting target.

The imaging of root canal obturation using micro-CT

AIM

To examine the potential and accuracy of micro-computed tomography (micro-CT) for imaging of filled root canals.

METHODOLOGY

The root canals of five extracted maxillary teeth were shaped manually with K-files. After irrigation and drying, the root canals were filled by lateral condensation using gutta-percha cones and AH plus (Dentsply Maillefer, Ballaigues, Switzerland) as sealer. The filled root canals were examined by micro-CT at resolutions <11 microm. Three-dimensional reconstructions of the root canal fillings were made. The roots were sectioned histologically and standard photographs of the sectioned surfaces were taken. Digitized photographic images and the corresponding micro-CT sections were correlated qualitatively by superimposition. Quantitative morphometric data were obtained with respect to the surface area of the root canal filling and the individual gutta-percha points of the histological and the micro-CT sections. Pearson correlation coefficients were calculated.

RESULTS

There was a good qualitative correlation between the images from the histological and the micro-CT sections. The fillings were clearly differentiated from the root canal walls. Individual gutta-percha cones and sealer were discernable. Pearson correlation coefficients showed a highly significant correlation between the two methods (P < 0.001) with respect to the area of the complete root canal filling (r = 0.992) and the gutta-percha cones (r = 0.968).

CONCLUSIONS

The micro-CT technique was a highly accurate and nondestructive method for the evaluation of root canal fillings and its constituents. Qualitative and quantitative correlation between histological and micro-CT examination of root canal fillings was high.

Mullerian inhibiting substance inhibits breast cancer cell growth through an NFkappa B-mediated pathway

Müllerian inhibiting substance (MIS), a member of the transforming growth factor-beta superfamily, induces regression of the Müllerian duct in male embryos. In this report, we demonstrate MIS type II receptor expression in normal breast tissue and in human breast cancer cell lines, breast fibroadenoma, and ductal adenocarcinomas. MIS inhibited the growth of both estrogen receptor (ER)-positive T47D and ER-negative MDA-MB-231 breast cancer cell lines, suggesting a broader range of target tissues for MIS action. Inhibition of growth was manifested by an increase in the fraction of cells in the G(1) phase of the cell cycle and induction of apoptosis. Treatment of breast cancer cells with MIS activated the NFkappaB pathway and selectively up-regulated the immediate early gene IEX-1S, which, when overexpressed, inhibited breast cancer cell growth. Dominant negative IkappaBalpha expression ablated both MIS-mediated induction of IEX-1S and inhibition of growth, indicating that activation of the NFkappaB signaling pathway was required for these processes. These results identify the NFkappaB-mediated signaling pathway and a target gene for MIS action and suggest a putative role for the MIS ligand and its downstream interactors in the treatment of ER-positive as well as negative breast cancers.

Linkage of the gene for the triple A syndrome to chromosome 12q13 near the type II keratin gene cluster

The triple A or Allgrove's syndrome (MIM*231550) is an autosomal recessive disease characterized by the triad of adrenocorticotropic hormone (ACTH) resistant adrenal insufficiency, achalasia and alacrima. Since its first description by Allgrove et al. (1978) more than 70 cases from all over the world have been reported. The syndrome manifests itself during the first decade of life with severe hypoglycaemic episodes which can cause sudden death. The frequent association with neurological disorders presenting as a mixed pattern of upper and lower motor neuropathy, sensory impairment, autonomic neuropathy and mental retardation may result in a severely disabling disease. As an additional feature some patients have hyperkeratosis of their palms and soles. We have performed a systematic genome linkage scan in eight triple A families of which three were consanguineous [including the large highly inbred kindred described by Moore et al. (1991)]. We obtained conclusive evidence for linkage of the triple A syndrome locus to markers on chromosome 12q13 (D12S368, theta max = 0, Zmax = 10.81) with no indication of genetic heterogeneity. Haplotype and multipoint analyses suggest that the gene is located on a chromosomal segment flanked by the markers D12S1629 and D12S312 which are 6 cM apart. This region harbors the type II keratin gene cluster, and potential candidate genes include SCN8A and HOXC genes.

Macrophage involvement in the kidney repair phase after ischaemia/reperfusion injury

Macrophage infiltration is a common feature of the early phase of renal ischaemia/reperfusion injury. Indeed, it is generally regarded as the cause of tissue injury in this phase, although it is also clear that it can lead to tissue repair in other phases. In order to ascertain whether macrophages are directly involved in the repair/late phase, which follows the pro-inflammatory and injury process of renal ischaemia/reperfusion, we used two different approaches based on macrophage depletion. Firstly, we produced renal ischaemia in mice that were previously treated with clodronate liposome. Secondly, during reperfusion we re-injected RAW 264.7 to macrophage-depleted mice 24 h prior to sacrifice. The results showed that regeneration, as evaluated by stathmin and PCNA markers, was macrophage-dependent: it was blocked when macrophage depletion was provoked and recovered with macrophage re-injection. The cytokine profile revealed the influence of the inflammatory environment on kidney repair: pro-inflammatory cytokines (MCP-1, MIP-1alpha) increased during the early stages of reperfusion, coinciding with low regeneration, and the anti-inflammatory cytokine IL-10 increased during the longer periods of reperfusion when regeneration was more evident. We conclude that macrophages induce renal regeneration after ischaemia/reperfusion, depending on the inflammatory milieu.

A novel ionizing radiation-induced signaling pathway that activates the transcription factor NF-kappaB

The signaling pathway through which ionizing radiation induces NF-kappaB activation is not fully understood. IkappaB-alpha, an inhibitory protein of NF-kappaB mediates the activation of NF-kappaB in response to various stimuli, including cytokines, mitogens, oxidants and other stresses. We have now identified an ionizing radiation-induced signaling pathway that is independent of TNF-alpha. IkappaB-alpha degradation is rapid in response to TNF-alpha induction, but it is absent in response to ionizing radiation exposure in cells from individuals with ataxia-telangiectasia (AT). Overexpression of wild-type ATM, the product of the gene defective in AT patients, restores radiation-induced degradation of IkappaB-alpha. Furthermore, phosphorylation of IkappaB-alpha by immunoprecipitated ATM kinase is increased in control fibroblasts and transfected AT cells following ionizing radiation exposure. These data provide support for a novel ionizing radiation-induced signaling pathway for activation of NF-kappaB and a molecular basis for the sensitivity of AT patients to oxidative stresses.