From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies

We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different transposable elements. We show that an interval between bands 3A2 and 3C2, believed in the 1970s to show a correlation between the number of bands on the polytene chromosomes and the 20 genes identified by conventional genetics, is predicted to contain 45 genes from its DNA sequence. We have determined the insertion sites of P-elements from 111 mutant lines, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis. We compare the European Drosophila Genome Project sequence with the corresponding part of the independently assembled and annotated Joint Sequence determined through "shotgun" sequencing. Discounting differences in the distribution of known transposable elements between the strains sequenced in the two projects, we detected three major sequence differences, two of which are probably explained by errors in assembly; the origin of the third major difference is unclear. In addition there are eight sequence gaps within the Joint Sequence. At least six of these eight gaps are likely to be sites of transposable elements; the other two are complex. Of the 275 genes in common to both projects, 60% are identical within 1% of their predicted amino-acid sequence and 31% show minor differences such as in choice of translation initiation or termination codons; the remaining 9% show major differences in interpretation.

Some diminutive colorectal polyps can be removed and discarded without pathological examination

BACKGROUND AND STUDY AIMS

Pathological examination of colorectal polyps is useful if clinical management is affected (i. e. when invasive carcinoma is detected or postpolypectomy surveillance interval is guided). Our aim was to assess whether the pathological examination of some diminutive (measuring ≤ 5 mm) polyps can be omitted.

PATIENTS AND METHODS

Consecutive patients undergoing a colonoscopy at Pasteur Hospital (Colmar, France) between January and August 2008 were included in this prospective study. Six senior gastroenterologists predicted the future surveillance interval without referring to the result of pathological examination.

RESULTS

In all, 350 polyps from 175 patients were removed and analyzed. The endoscopist was able to predict the correct surveillance interval without referring to the result of pathological examination in 118 patients (67.4 %; 95 % confidence interval [CI] 60.5 - 74.4). The pathological examination of 18.4 % (95 % CI 13.7 - 23.1) of diminutive polyps either associated with a cancer or a polyp measuring ≥ 10 mm or removed in very old or frail patients could be omitted without any consequence for the patient. If diminutive polyps one or two in number were discarded without pathological examination in patients with a personal history of colorectal neoplasm, three patients out of 43 would have a 5-year instead of a 3-year surveillance interval. As a whole, if 44.1 % (95 % CI 38.0 - 50.1) of diminutive polyps were discarded, the surveillance interval would remain identical in 98.3 % (95 % CI 96.4 - 100) of patients.

CONCLUSIONS

The pathological examination of up to 44 % of diminutive polyps (i. e. 33 % of all polyps), can be safely omitted. The pathological examination would be required only for those with suspicious gross appearance, those three or more in number, and those isolated one or two in number that are removed from people without personal history of colorectal neoplasm.

Age-dependent association of serum prolactin with glycaemia and insulin sensitivity in humans

The dopamine agonist bromocriptine has been approved for the treatment of type 2 diabetes in the United States. Bromocriptine inhibits prolactin secretion, and patients with hyperprolactinaemia display impaired insulin sensitivity. We therefore hypothesized that low prolactin levels are associated with lower glycaemia and higher insulin sensitivity in healthy subjects. Prolactin levels were determined from fasting serum in participants without diabetes from the cross-sectional Tübingen family study for type 2 diabetes (m/f = 562/1,121, age = 40 ± 13 years, BMI = 30 ± 9 kg/m(2)). A 75 g oral glucose tolerance test was performed, and the area under the glucose curve (AUC(0-120)Glucose) and insulin sensitivity index were calculated. A subgroup (n = 494) underwent hyperinsulinaemic-euglycaemic clamp tests. Prolactin associated positively with insulin sensitivity (p = 0.001, adjusted for gender, age, and BMI). Age strongly interacted (p < 0.0001) with the effect of prolactin on insulin sensitivity, inverting the positive relationship to a negative one in younger participants. Glycated haemoglobin (HbA1c) and AUC(0-120)Glucose correlated negatively with prolactin, and an interaction with age was found as well. Higher prolactin levels are associated with improved insulin sensitivity and lower glucose in individuals without diabetes. This relationship turns to its opposite in younger persons. As prolactin is a proxy for the dopaminergic tone in the central nervous system, these associations may indicate an age-dependent influence of the brain on peripheral insulin sensitivity.

Development of diabetes mellitus in aging transgenic mice following suppression of pancreatic homeoprotein IDX-1

Monogenic forms of diabetes can result from mutations in genes encoding transcription factors. Mutations in the homeodomain transcription factor IDX-1, a critical regulator of pancreas development and insulin gene transcription, confer a strong predisposition to the development of diabetes mellitus in humans. To investigate the role of IDX-1 expression in the pathogenesis of diabetes, we developed a model for the inducible impairment of IDX-1 expression in pancreatic beta cells in vivo by engineering an antisense ribozyme specific for mouse IDX-1 mRNA under control of the reverse tetracycline transactivator (rtTA). Doxycycline-induced impairment of IDX-1 expression reduced activation of the Insulin promoter but activated the Idx-1 promoter, suggesting that pancreatic beta cells regulate IDX-1 transcription to maintain IDX-1 levels within a narrow range. In transgenic mice that express both rtTA and the antisense ribozyme construct, impaired IDX-1 expression elevated glycated hemoglobin levels, diminished glucose tolerance, and decreased insulin/glucose ratios. Metabolic phenotypes induced by IDX-1 deficiency were observed predominantly in male mice over 18 months of age, suggesting that cellular mechanisms to protect IDX-1 levels in pancreatic beta cells decline with aging. We propose that even in the absence of Idx-1 gene mutations, pathophysiological processes that decrease IDX-1 levels are likely to impair glucose tolerance. Therapeutic strategies to attain normal glucose homeostasis by restoring normal IDX-1 levels may be of particular importance for older individuals with diabetes mellitus.

Assessing microbial degradation of o-xylene at field-scale from the reduction in mass flow rate combined with compound-specific isotope analyses

In recent years, natural attenuation (NA) has evolved into a possible remediation alternative, especially in the case of BTEX spills. In order to be approved by the regulators, biodegradation needs to be demonstrated which requires efficient site investigation and monitoring tools. Three methods--the Integral Groundwater Investigation method, the compound-specific isotope analysis (CSIA) and a newly developed combination of both--were used in this work to quantify at field scale the biodegradation of o-xylene at a former gasworks site which is heavily contaminated with BTEX and PAHs. First, the Integral Groundwater Investigation method [Schwarz, R., Ptak, T., Holder, T., Teutsch, G., 1998. Groundwater risk assessment at contaminated sites: a new investigation approach. In: Herbert, M. and Kovar, K. (Editors), GQ'98 Groundwater Quality: Remediation and Protection. IAHS Publication 250, pp. 68-71; COH 4 (2000) 170] was applied, which allows the determination of mass flow rates of o-xylene by integral pumping tests. Concentration time series obtained during pumping at two wells were used to calculate inversely contaminant mass flow rates at the two control planes that are defined by the diameter of the maximum isochrone. A reactive transport model was used within a Monte Carlo approach to identify biodegradation as the dominant process for reduction in the contaminant mass flow rate between the two consecutive control planes. Secondly, compound-specific carbon isotope analyses of o-xylene were performed on the basis of point-scale samples from the same two wells. The Rayleigh equation was used to quantify the degree of biodegradation that occurred between the wells. Thirdly, a combination of the Integral Groundwater Investigation method and the compound-specific isotope analysis was developed and applied. It comprises isotope measurements during the integral pumping tests and the evaluation of delta13C time series by an inversion algorithm to obtain spatially integrated mean isotope values at the control planes. It was shown that the Rayleigh equation is applicable to spatially integrated mean isotope values in order to obtain the mean biodegradation between the consecutive control planes. All three approaches yielded consistently a 98-99% degradation of o-xylene.

T cell receptor alpha-chain tail is required for protein kinase C-mediated down-regulation, but not for signaling

Antigen stimulation through the T cell receptor (TCR) induces phosphorylation of the associated CD3 gamma delta epsilon- and zeta-chain cytoplasmic tails. These events lead to the induction of the intracellular signaling pathways with concomitant receptor down-regulation. The TCR is down-regulated from the cell surface by the activation of protein kinase, C (PKC) and subsequent serine phosphorylation of the CD3 gamma-chain. We report here that the TCR alpha-chain cytoplasmic tail is also necessary for PKC-mediated internalization of the TCR complex. The requirement for the TCR alpha-chain cytoplasmic tail is specific for internalization of the TCR complex, since down-regulation of CD4 is still intact in hybridoma cells expressing a tailless TCR alpha-chain. The absence of TCR internalization directly correlates with defective PKC-mediated phosphorylation of the CD3 gamma-chain. Despite deficient PKC-mediated TCR down-regulation, the tailless alpha beta TCR still transduces antigenic signals resulting in the production of interleukin-2. Although the TCR tails are not obviously required for signal transduction, the TCR alpha-tail may serve as a targeting domain for PKC-mediated down-regulation of the TCR complex.

The role of volume-sensitive Cl- channels in the stimulation of chloride absorption by short-chain fatty acids in the rat colon

The short-chain fatty acids acetate, propionate and butyrate induced a concentration-dependent decrease in short-circuit current (Isc) of the rat colon in vitro. The decrease in Isc, being more pronounced in the distal than in the proximal colon, was dependent on the presence of Cl- ions and partly on the presence of HCO3-. In the distal colon, the fall in Isc could be inhibited by amiloride, indicating that the activity of the Na+/H+ exchanger is necessary for the induction of this response. The decrease in Isc was diminished by the Cl- channel blocker, 5-nitro-2-(3-phenylpropylamino)-benzoate, and the lipoxygenase inhibitor, nordihydroguaiaretic acid. In contrast, inhibitors of the leukotriene pathway or a Cl- channel blocker did not affect the Isc response in the proximal colon. Measurements of unidirectional fluxes revealed that butyrate caused a stimulation of the mucosa to serosa fluxes (Fms) of Na+ and Cl- in the distal, but only of FNams in the proximal colon. Unidirectional Rb+ fluxes were not altered. The stimulation of Fclms correlated with the degree of metabolism of the short-chain fatty acid. The increase in FClms was most pronounced for butyrate, smaller for acetate and not observed with the poorly metabolizable short-chain fatty acid, isobutyrate. Consequently, two factors seem to be responsible for the stimulation of Cl- absorption by short-chain fatty acids in the distal colon: (1) the intracellular production of HCO3- during the oxidation of short-chain fatty acids as substrate for the apical Cl-/HCO3- exchanger, and (2) the activation of volume-sensitive basolateral Cl- channels.

Apelin serum levels are not associated with early atherosclerosis or fat distribution in young subjects with increased risk for type 2 diabetes

Apelin is proposed to possess protective cardiovascular properties and may furthermore promote favorable effects on glucose metabolism. First data in humans seem to support this hypothesis. Therefore we aimed to assess the meaning of apelin as an early risk indicator in young subjects prone to atherosclerosis and type 2 diabetes. Furthermore we examined the association of apelin serum levels with insulin sensitivity/resistance and body fat distribution as probably dependent cardiovascular risk factors. We examined 344 individuals (f/m=216/128, mean age 46±1 years) with an increased risk for type 2 diabetes. Apelin-36 serum levels were measured via ELISA. Endothelial dysfunction and intima media thickness (IMT) were assessed using high resolution ultrasound. Visceral adipose tissue (VAT) was measured with an axial T1-weighted fast spin echo technique with a 1.5 T whole-body imager. According to the study population's age, FMD (6.4±0.2%) and IMT (0.56±0.01 mm) were within the expected ranges. Gender or age had no influence on serum apelin levels. When looked at early stages of atherosclerosis, we could not detect a significant correlation between apelin serum levels and FMD or IMT. Blood pressure as well was unaffected by serum apelin levels. Furthermore, neither parameters of insulin sensitivity like insulin sensitivity index (ISI), nor fat distribution like BMI, grade of adiposity, total adipose tissue or VAT were associated with apelin serum levels. We conclude that apelin serum levels do not add further information on the cardiovascular-, or diabetes risk pattern in a diabetes prone population.

Lessons learned implementing a province-wide smoking cessation initiative in Ontario's cancer centres

PURPOSE

A large body of evidence clearly shows that cancer patients experience significant health benefits with smoking cessation. Cancer Care Ontario, the provincial agency responsible for the quality of cancer services in Ontario, has undertaken a province-wide smoking cessation initiative. The strategies used, the results achieved, and the lessons learned are the subject of the present article.

METHODS

Evidence related to the health benefits of smoking cessation in cancer patients was reviewed. A steering committee developed a vision statement for the initiative, created a framework for implementation, and made recommendations for the key elements of the initiative and for smoking cessation best practices.

RESULTS

New ambulatory cancer patients are being screened for their smoking status in each of Ontario's 14 regional cancer centres. Current or recent smokers are advised of the benefits of cessation and are directed to smoking cessation resources as appropriate. Performance metrics are captured and used to drive improvement through quarterly performance reviews and provincial rankings of the regional cancer centres.

CONCLUSIONS

Regional smoking cessation champions, commitment from Cancer Care Ontario senior leadership, a provincial secretariat, and guidance from smoking cessation experts have been important enablers of early success. Data capture has been difficult because of the variety of information systems in use and non-standardized administrative and clinical processes. Numerous challenges remain, including increasing physician engagement; obtaining funding for key program elements, including in-house resources to support smoking cessation; and overcoming financial barriers to access nicotine replacement therapy. Future efforts will focus on standardizing processes to the extent possible, while tailoring the approaches to the populations served and the resources available within the individual regional cancer programs.

Apoptosis induced by gamma-irradiation, but not CD4 ligation, of peripheral T lymphocytes in vivo is p53-dependent

Mice generated by homologous recombination which carry a large deletion of the p53 tumour suppressor gene have a high incidence of spontaneous Thy1-positive thymic lymphoma. Extra-thymic lymphomas are rare. Apoptosis following gamma-irradiation in thymocytes from these animals in vitro is p53-dependent and there is a marked gene dose effect: heterozygotes show partial resistance to irradiation-induced cell death. Apoptosis in the T-cell zones of lymph nodes following in vivo gamma-irradiation was p53-dependent, but the gene dosage effect was less marked than that noted for thymocytes. Apoptosis was induced in vivo by ligation of CD4 on the cell surface following intravenous injection of anti-CD4 monoclonal antibody. Apoptosis was counted in lymph node sections using a semi-automated morphometric system. This showed no evidence of p53 dependency. In contrast to a previous report, which used a different line of p53-deficient mice, splenocytes from p53-null mice did not differ significantly from wild-type cells with respect to in vitro proliferative activity and response to mitogenic stimulation by concanavalin A. This may be due to strain differences. Therefore, whilst p53 has a role in the deletion of lymphocytes which have acquired pathological DNA strand breaks which may lead to mutations, the results of this study imply that p53 is not involved in the control of apoptosis following engagement of surface receptors, nor in response to physiological DNA breaks and normal recombination events during T-cell ontogeny.

Endothelial NO-synthase intron 4 polymorphism is associated with disturbed in vivo nitric oxide production in individuals prone to type 2 diabetes

Insulin resistance, as well as vascular disease, both share a relevant genetic background taking the influence of a positive family history of these disorders. On the other hand, insulin resistance is associated with a proatherosclerotic disturbance in nitric oxide dependent vasodilation, probably contributing to the link between these two disorders. We examined the association between nitric oxide dependent vasodilation (measured with high resolution ultrasound at 13 MHz) and three relevant NO-synthase (eNOS)-polymorphisms in 200 insulin resistant subjects participating in the Tuebinger Lifestyle Intervention Program (TULIP). This study revealed that carriers of the eNOS intron 4 polymorphism (aa 2.16%; ab 24.2%; bb 73.2%) show significantly worse endothelial, and thereby eNOS dependent vasodilation (p=0.03, multivariate ANOVA), as compared to wildtype carriers. The 5' UTR T-786C and the G894 T polymorphism did not show any influence on eNOS-activity. In subjects at increased risk to develop type 2 diabetes, the eNOS intron 4 polymorphism is independently associated with endothelial function as indicated by disturbed endothelial NO production. Due to the high prevalence and the relatively strong effect, this polymorphism might help to identify subjects at increased risk for atherosclerosis associated with overweight and insulin resistance.

mCCDcl1 cells show plasticity consistent with the ability to transition between principal and intercalated cells

The cortical collecting duct of the mammalian kidney plays a critical role in the regulation of body volume, sodium pH, and osmolarity and is composed of two distinct cells types, principal cells and intercalated cells. Each cell type is detectable in the kidney by the localization of specific transport proteins such as aquaporin 2 (Aqp2) and epithelial sodium channel (ENaC) in principal cells and V-ATPase B1 and connexin 30 (Cx30) in intercalated cells. mCCD_cl1 cells have been widely used as a mouse principal cell line on the basis of their physiological characteristics. In this study, the mCCD_cl1 parental cell line and three sublines cloned from isolated single cells (Ed1, Ed2, and Ed3) were grown on filters to assess their transepithelial resistance, transepithelial voltage, equivalent short circuit current and expression of the cell-specific markers Aqp2, ENaC, V-ATPaseB1, and Cx30. The parental mCCD_cl1 cell line presented amiloride-sensitive electrogenic sodium transport indicative of principal cell function; however, immunocytochemistry and RT-PCR showed that some cells expressed the intercalated cell-specific markers V-ATPase B1 and Cx30, including a subset of cells also positive for Aqp2 and ENaC. The three subclonal lines contained cells that were positive for both intercalated and principal cell-specific markers. The vertical transmission of both principal and intercalated cell characteristics via single cell cloning reveals the plasticity of mCCD_cl1 cells and a direct lineage relationship between these two physiologically important cell types and is consistent with mCCD_cl1 cells being precursor cells.

Defective signaling to Fyn by a T cell antigen receptor lacking the alpha -chain connecting peptide motif

A key role in the communication between the alphabetaTCR and the CD3/zeta complex is played by a specific motif within the connecting peptide domain of the TCR alpha chain (alpha-CPM). T cell hybridomas expressing an alpha-CPM-mutated TCR show a dramatic impairment in antigen-driven interleukin-2 production. This defect can be complemented by a calcium ionophore, indicating that activation of the calcium pathway is impaired. Several lines of evidence implicate Fyn in the regulation of calcium mobilization, at least in part through the activation of phospholipase Cgamma. Here we have investigated the potential involvement of Fyn in the TCR alpha-CPM signaling defect. Using T cell hybridomas expressing either a wild-type TCR or an alpha-CPM mutant, we show that Fyn fails to be activated by the mutant receptor following SEB binding and fails to generate tyrosine-phosphorylated Pyk2, a member of the focal adhesion kinase family. This defect correlated with an impairment in phospholipase Cgamma phosphorylation. Production of interlukin-2 and activation of the transcription factor NF-AT in response to triggering of the TCR alpha-CPM mutant with SEB were fully restored in the presence of constitutively active Fyn. Hence the signaling defect generated by the TCR alpha-CPM mutation results at least in part from an impaired coupling of the TCR.CD3 complex to Fyn activation.

Characterization of antibodies to prostate-specific antigen

Antibodies submitted to the ISOBM TD-3 PSA Workshop were tested for reactivity with free prostate-specific antigen (PSA) and the PSA alpha1-antichymotrypsin (ACT) complex, inhibition of proteolytic activity, recognition of continuous epitopes, and epitope specificity based on complete cross-inhibition studies. The antibodies could be separated into two categories: those recognizing hidden epitopes specific for free PSA, and those recognizing epitopes in both free PSA and the PSA-ACT complex. A large number of distinct antigenic domains were identified both in free PSA and the PSA-ACT complex.

Lethal Waterhouse-Friderichsen syndrome in posttraumatic asplenia

We herein report a case of fulminant lethal Waterhouse-Friderichsen syndrome in an elderly female patient seven years after posttraumatic splenectomy. In contrast to various reports, this patient had not been vaccinated against Streptococcus pneumoniae, Neisseria meningitidis, or Haemophilus influenzae, respectively, although infections with these microorganisms are known to cause the main lethal diseases in asplenic patients. Again, we recommend obligatory vaccinations against the mentioned bacteria for it is known that this decreases the risk of fatal septic events in these patients. To optimize prevention, it is imperative to vaccinate patients undergoing splenectomy before discharge from hospital.

Moving targets, long-lived infrastructure, and increasing needs for integration and adaptation in water management: an illustration from Switzerland

Switzerland provides an example of successful management of water infrastructure and water resources that was accomplished largely without integration across sectors. Limitations in this approach have become apparent; decisions that were formerly based only on technical and economic feasibility must now incorporate broader objectives such as ecological impact. In addition, current and emerging challenges relate to increasingly complex problems that are likely to demand more integrated approaches. If such integration is to be of benefit, it must be possible to redirect resources across sectors, and the synergies derived from integration must outweigh the additional cost of increased complexity.

Spectroscopic investigation of the deeply buried Cu(In,Ga)(S,Se)2∕Mo interface in thin-film solar cells

The Cu(In,Ga)(S,Se)(2)Mo interface in thin-film solar cells has been investigated by surface-sensitive photoelectron spectroscopy, bulk-sensitive x-ray emission spectroscopy, and atomic force microscopy. It is possible to access this deeply buried interface by using a suitable lift-off technique, which allows us to investigate the back side of the absorber layer as well as the front side of the Mo back contact. We find a layer of Mo(S,Se)(2) on the surface of the Mo back contact and a copper-poor stoichiometry at the back side of the Cu(In,Ga)(S,Se)(2) absorber. Furthermore, we observe that the Na content at the Cu(In,Ga)(S,Se)(2)Mo interface as well as at the inner grain boundaries in the back contact region is significantly lower than at the absorber front surface.

Osteoarthritis of the scaphoidtrapezium joint: an early sign of calcium pyrophosphate dihydrate disease

The aim of this study was to determine the value of scaphoidtrapezium osteoarthritis (ST osteoarthritis) as an early sign of calcium pyrophosphate dihydrate disease (CPDD) in a cohort of patients undergoing surgery for osteoarthritis of the first carpometacarpal joint. We examined whether patients with cartilage calcification of the wrist at the time of operation had ST osteoarthritis, indicating CPDD at an earlier time (retrospective study), and whether patients with ST osteoarthritis but without cartilage calcification at the time of surgery develop radiological or clinical signs of CPDD at a later time (prospective study). From 1 January 1989 to 31 December 1995 a total of 169 patients (from an orthopaedic clinic) with a diagnosis of osteoarthritis of the first carpometacarpal joint were included in the study; 167 underwent surgery and two were treated without. Of the 16 patients showing calcification on surgery and therefore included in the retrospective study, 12 had prior radiographs, of which eight showed ST osteoarthritis. Among these, four had no concomitant cartilage calcification in the prior radiographs. Of the 32 patients in the prospective group having ST osteoarthritis but no calcifications at the time of surgery, 27 could be clinically examined. Of these, two showed cartilage calcifications on the follow-up radiographs of the hands. The presence of ST osteoarthritis is a helpful diagnostic finding for the diagnosis of CPDD, especially in cases without radiographic cartilage or fibrocartilage calcification of the wrist. ST osteoarthritis may then point to the correct diagnosis.