Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR

Our abilities to detect and enumerate pollutant-biodegrading microorganisms in the environment are rapidly advancing with the development of molecular genetic techniques. Techniques based on multiplex and real-time PCR amplification of aromatic oxygenase genes were developed to detect and quantify aromatic catabolic pathways, respectively. PCR primer sets were identified for the large subunits of aromatic oxygenases from alignments of known gene sequences and tested with genetically well-characterized strains. In all, primer sets which allowed amplification of naphthalene dioxygenase, biphenyl dioxygenase, toluene dioxygenase, xylene monooxygenase, phenol monooxygenase, and ring-hydroxylating toluene monooxygenase genes were identified. For each primer set, the length of the observed amplification product matched the length predicted from published sequences, and specificity was confirmed by hybridization. Primer sets were grouped according to the annealing temperature for multiplex PCR permitting simultaneous detection of various genotypes responsible for aromatic hydrocarbon biodegradation. Real-time PCR using SYBR green I was employed with the individual primer sets to determine the gene copy number. Optimum polymerization temperatures for real-time PCR were determined on the basis of the observed melting temperatures of the desired products. When a polymerization temperature of 4 to 5 degrees C below the melting temperature was used, background fluorescence signals were greatly reduced, allowing detection limits of 2 x 10(2) copies per reaction mixture. Improved in situ microbial characterization will provide more accurate assessment of pollutant biodegradation, enhance studies of the ecology of contaminated sites, and facilitate assessment of the impact of remediation technologies on indigenous microbial populations.     

Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice

A comprehensive assessment of bacterial diversity and community composition in arctic and antarctic pack ice was conducted through cultivation and cultivation-independent molecular techniques. We sequenced 16S rRNA genes from 115 and 87 pure cultures of bacteria isolated from arctic and antarctic pack ice, respectively. Most of the 33 arctic phylotypes were >97% identical to previously described antarctic species or to our own antarctic isolates. At both poles, the alpha- and gamma-proteobacteria and the Cytophaga-Flavobacterium group were the dominant taxonomic bacterial groups identified by cultivation as well as by molecular methods. The analysis of 16S rRNA gene clone libraries from multiple arctic and antarctic pack ice samples revealed a high incidence of closely overlapping 16S rRNA gene clone and isolate sequences. Simultaneous analysis of environmental samples with fluorescence in situ hybridization (FISH) showed that approximately 95% of 4',6'-diamidino-2-phenylindole (DAPI)-stained cells hybridized with the general bacterial probe EUB338. More than 90% of those were further assignable. Approximately 50 and 36% were identified as gamma-proteobacteria in arctic and antarctic samples,respectively. Approximately 25% were identified as alpha-proteobacteria, and 25% were identified as belonging to the Cytophaga-Flavobacterium group. For the quantification of specific members of the sea ice community, new oligonucleotide probes were developed which target the genera Octadecabacter, Glaciecola, Psychrobacter, Marinobacter, Shewanella, and Polaribacter: High FISH detection rates of these groups as well as high viable counts corroborated the overlap of clone and isolate sequences. A terrestrial influence on the arctic pack ice community was suggested by the presence of limnic phylotypes.     

Ankle-arm index versus angiography for the preassessment of the fibula free flap

Peripheral arterial occlusive disease or congenital anomalies of the major crural arteries may limit the use of the fibula free flap and should be detected preoperatively. Conventional selective angiography is the definitive standard imaging method for making this diagnosis, but it has drawbacks. A safer, cheaper, more accurate, and noninvasive alternative is desirable. The authors sought to test the hypothesis that the ankle-arm index of each of the three crural arteries, combined with pencil Doppler examination of the peroneal skin perforators, would provide adequate information to restrict the use of angiography to cases in which the outcomes of either or both of these options are insufficient. The ankle-arm index data of each of the three crural arteries, as well as pencil Doppler examination of the peroneal skin perforators of both legs of nine prospectively included patients and the nonoperated legs of 13 retrospectively included patients, were compared statistically in four different ways with the preoperative angiographic findings. A combined ankle-arm index and pencil Doppler examination is not accurate enough to detect legs or arteries with subclinical peripheral arterial occlusive disease or vascular variation and, hence, is not a sufficient basis on which to develop the surgical plan for a fibula free flap.     

Oxygenation and microcirculation during skin stretching in undermined and nonundermined skin

The aim of this experimental study was to assess the skin microcirculation of undermined and nonundermined wound edges closed with a skin-stretching device. In eight piglets, 9 x 9-cm wounds were created on both flanks by excision of the skin and the subcutaneous layer down to the muscular fascia, with general anesthesia. On one flank, the surrounding skin was completely undermined. For a period of 30 minutes, wound closure was performed with a stretching device, using the principle of load cycling. The device stretched the skin and moved the opposing wound edges toward each other. During this period, laser Doppler flowmetry and transcutaneous oximetry were simultaneously used to monitor microcirculation and oxygenation in the stretched skin of both flanks. Undermining of the surrounding skin produced a 12 percent decrease in the laser Doppler flowmetry signal and a 21 percent decrease in the transcutaneous oximetry value. Skin stretching resulted in decreases in the laser Doppler flowmetry signals and the transcutaneous oximetry values, whether or not the skin was undermined. Releasing the stretching device resulted in rapid normalization of the laser Doppler flowmetry values in undermined and nonundermined skin and a slow return of the transcutaneous oximetry values to close to baseline levels in nonundermined skin. The transcutaneous oximetry values in undermined skin did not return to baseline levels; each period of skin stretching resulted in an additional decrease in the transcutaneous oximetry values. Stretching of undermined skin for 30 minutes produced a significant (p < 0.0001) decrease in skin oxygenation. As a result, 50 percent of the undermined stretched skin demonstrated skin necrosis at the wound edges, which was still present after 1 week. Wound healing in the nonundermined stretched skin proceeded without problems. It is concluded from these experiments that the viability of undermined skin becomes compromised as a result of significantly decreased oxygen availability in the skin during and after stretching. Consequently, it is recommended that skin stretching be performed on nonundermined skin, rather than undermined skin. In addition, when skin is stretched to close a large defect, it is logical to use cyclic loading, so that recuperation of the skin circulation can occur. Furthermore, laser Doppler flowmetry seemed to produce atypical signals in monitoring of skin viability of wound edges closed with a skin-stretching device.     

Four decades of teaching developmental biology in Germany

I have taught developmental biology in Essen for 30 years. Since my department is named Zoophysiologie (Zoophysiology), besides Developmental Biology, I also have to teach General Animal Physiology. This explains why the time for teaching developmental biology is restricted to a lecture course, a laboratory course and several seminar courses. However, I also try to demonstrate in the lecture courses on General Physiology the close relationship between developmental biology, physiology, morphology, anatomy, teratology, carcinogenesis, evolution and ecology (importance of environmental factors on embryogenesis). Students are informed that developmental biology is a core discipline of biology. In the last decade, knowledge about molecular mechanisms in different organisms has exponentially increased. The students are trained to understand the close relationship between conserved gene structure, gene function and signaling pathways, in addition to or as an extension of, classical concepts. Public reports about the human genome project and stem cell research (especially therapeutic and reproductive cloning) have shown that developmental biology, both in traditional view and at the molecular level, is essential for the understanding of these complex topics and for serious and non-emotional debate.     

The role of hydrophobic interactions in amyloidogenesis: example of prion-related polypeptides

Conversion of the non-infectious, cellular form of the prion protein (PrP(C)) to the infectious form (PrP(Sc)) is thought to be driven by an alpha-helical to beta-sheet conformational transition. To reveal the sequence determinants which encourage the transition to beta-fold, we study the synthetic peptides associated with hydrophobic conserved fragments of the N-terminal region of the prion protein. The structure of peptides in solution was probed under various thermodynamic conditions employing circular dichroism and steady state fluorescence spectroscopy as well as dye binding assays. The fluorescence methods utilized pyrene residues covalently attached to the end of the model peptides. In aqueous solutions, the structure assessments indicate the formation of metastable peptide aggregates; the molecular conformations within the peptide micelles are largely coiled. This stage in molecular assembly exists without significant beta-strand formation, i.e., before the appearance of any ordered secondary structure detectable by circular dichroism. At moderate concentrations of trifluoroethanol and/or acetonitrile, the conformational ensemble shifts towards beta-strand formation, and the population of the amorphous aggregates decreases significantly. Overall, the present data indicate that hydrophobic interactions between side chains of the peptide variants prevent, in fact, the formation of the rigid beta-sheet structures. Encouragement of beta-folds requires the destabilization of local interactions in the peptide chain, which in vivo might be possible within cell membranes as well as within partly folded molecular forms.     

Strict infection control measures do not prevent clonal spread of coagulase negative staphylococci colonizing central venous catheters in neutropenic hemato-oncologic patients

Coagulase negative staphylococci (CoNS) are a main cause of catheter related infections (CRI). Earlier studies (1994-1996) revealed a high incidence of CRI (6 per 1000 catheter days) among neutropenic hemato-oncologic patients in the Erasmus MC Hematology Department (Rotterdam, The Netherlands). This was mainly explained by expansion of two methicillin resistant Staphylococcus epidermidis (MRSE) clones (Nouwen et al., J. Clin. Microbiol. 36 (1998) 2696-2702). In a new, 16-bed unit in the same institution, we investigated the effect of strict clinical isolation measures on the incidence of CRI. During two 6-month screening periods (period I: April 1998-December 1998 and period II: April 1999-October 1999) all patients receiving a central venous catheter were prospectively monitored for the development of CRI. During period I every visitor of the cubicles had to wear hair caps, masks, gowns and gloves. During period II these procedures were abolished, but hands were cleansed using alcohol and masks were worn during both periods in case of coughing and sneezing. All CoNS strains isolated from blood cultures were genetically classifies by pulsed field gel electrophoresis (PFGE). The incidence of CRI during period I was 13.0 per 1000 catheter days, in comparison to 9.6 in period II (P=0.84). During this latter period, 19 CRI were diagnosed, 14 catheter related bacteremia episodes (CRB) and five local infections. Seventy-two percent (n=9) of CRB were due to a CoNS. The mean catheter survival until appearance of a CRI increased from 43 days during period I to 78 days in period II (P=0.39). The mean catheter survival until infection related removal was increased from 43 days to 133 days (P=0.12). During period I less experienced intervention radiologists introduced the catheters, which may have limited the efficacy of the strict hygiene measures. Thus, abolishing strict isolation precautions had no negative effect on the incidence of CRI. After genotyping of 38 MRSE strains isolated from blood and central venous catheter cultures of 12 patients in period II, eight PFGE types were found. Three types were found in more than one patient, but based on epidemiological data patient-to-patient spread could not be proven. No genotypic identity between patient and personnel CoNS isolates was shown and the two major clonal types that were present between 1994 and 1996 were not encountered. However, from December 1998 onwards new MRSE clones could be identified (types E and J). In conclusion, despite a constant rate of CRI and implementation of optimal patient care, clonal spread of MRSE strains was not prevented by strict hygiene measures.     

Insulinomimetic effects of kaempferitrin on glycaemia and on 14C-glucose uptake in rat soleus muscle

Bauhinia forficata is one of the Bauhinia species mostly used as an antidiabetic herbal remedy in Brazil. Kaempferitrin (kaempferol-3,7-O-(alpha)-L-dirhamnoside) is the predominant flavonol glycoside found in the B. forficata leaves. The aim of the present work was to study the long-term effect of kaempferitrin on glycaemia in diabetic rats, as well as the in vitro effect of this compound on 14C-D-glucose uptake and 14C-leucine incorporation into protein in normal rat soleus muscle. Kaempferitrin was found to have an acute lowering effect on blood glucose in diabetic rats and to stimulate the glucose uptake percentile, as efficiently as insulin in muscle from normal rats. This compound did not have any effect on glucosuria or on protein synthesis in muscle from normal and diabetic animals. However, the protein synthesis in the kaempferitrin-treated groups was maintained at the same level as the respective controls. Thus, the hypoglycaemic effect and the prompt efficiency of the kaempferitrin in stimulating [U-14C]-2-deoxi-D-glucose uptake in muscle -constitute the first evidence to indicate that the acute effect of this compound on blood glucose lowering may occur as a consequence of the altered intrinsic activity of the glucose transporter (Vmax or glucose transporters translocation?) not involving directly the synthesis of new carriers.     

Chronic nicotine inhibits inflammation and promotes influenza infection

Epidemiological data suggest an association between smoking, respiratory infections, and impaired wound healing. Inflammation is critical in the body's defense against pathogens and in the wound-healing process. Although nicotine is used to treat some inflammatory conditions, the mechanism of this action is largely unknown. To determine how nicotine affects inflammation, rats and mice were exposed to nicotine via miniosmotic pumps, and the inflammatory response to turpentine or influenza virus was assessed. Results showed that while nicotine suppressed the migration of leukocytes to the inflammation/infection site, it increased the influenza titer in the lung. The decreased inflammation correlated with lower chemotaxis/chemokinesis of peripheral blood mononuclear cells (PBMC) toward formyl-methionyl-leucyl-phenylalanine and monocyte chemoattractant protein-1 without affecting the density of their respective receptors. However, nicotine suppressed the chemokine-induced Ca(2+) response in PBMC, indicating impaired chemokine signaling. Thus, because nicotine suppresses leukocyte migration, it might contribute to the delayed wound healing and increased incidence of respiratory infections among smokers.     

Association of socioeconomic status and receipt of colorectal cancer investigations: a population- based retrospective cohort study

Background

Although the Canadian health care system was designed to ensure equal access, inequities persist. It is not known if inequities exist for receipt of investigations used to screen for colorectal cancer (CRC). We examined the association between socioeconomic status and receipt of colorectal investigation in Ontario.

Methods

People aged 50 to 70 years living in Ontario on Jan. 1, 1997, who did not have a history of CRC, inflammatory bowel disease or colorectal investigation within the previous 5 years were followed until death or Dec. 31, 2001. Receipt of any colorectal investigation between 1997 and 2001 inclusive was determined by means of linked administrative databases. Income was imputed as the mean household income of the person''s census enumeration area. Multivariate analysis was performed to evaluate the relationship between the receipt of any colorectal investigation and income.

Results

Of the study cohort of 1 664 188 people, 21.2% received a colorectal investigation in 1997–2001. Multivariate analysis demonstrated a significant association between receipt of any colorectal investigation and income (p < 0.001); people in the highest-income quintile had higher odds of receiving any colorectal investigation (adjusted odds ratio [OR] 1.38; 95% confidence interval [CI] 1.36–1.40) and of receiving colonoscopy (adjusted OR 1.50; 95% CI 1.48–1.53).

Interpretation

Socioeconomic status is associated with receipt of colorectal investigations in Ontario. Only one-fifth of people in the screening-eligible age group received any colorectal investigation. Further work is needed to determine the reason for this low rate and to explore whether it affects CRC mortality.Colorectal cancer (CRC) is the most common cause of cancer-related death among nonsmokers in North America. In 2004 an estimated 19 200 Canadians will receive a diagnosis of CRC and 8400 will die from the disease.¹ Although the age-standardized incidence and mortality of CRC have been decreasing, the number of new cases is increasing because of the growing size of the elderly population.CRC screening reduces the incidence and disease-specific mortality,^2,3,4,5,6 is cost-effective^7,8 and is endorsed by many professional societies.^{9,10,11,12,13,14,15} In 1994 the Canadian Task Force on the Periodic Health Examination (now the Canadian Task Force on Preventive Health Care) concluded that there was insufficient evidence to support CRC screening in asymptomatic people over the age of 40 years.¹⁶ In the 2001 update of these guidelines⁹ fecal occult blood testing (FOBT) every 1 or 2 years or flexible sigmoidoscopy every 5 years was recommended for screening average-risk people 50 years of age or older; there was judged to be insufficient evidence to support colonoscopy as the initial screening test. Despite these endorsements the use of CRC screening remains suboptimal.^17,18,19The Canadian health care system covers all medically necessary services without user fees. Although equity has been achieved in certain areas,^20,21 low socioeconomic status (SES) is associated with a lower rate of use of cardiovascular procedures^22,23 and screening tests for breast and cervical cancer.^24,25,26 It is unknown whether SES affects the receipt of CRC screening investigations. This study assessed the association of neighbourhood income (a marker of SES) with the receipt of colorectal investigations in people eligible for screening who lived in Ontario.