Evaluation of loop-mediated isothermal amplification for the rapid identification of bacteria and resistance determinants in positive blood cultures.

The use of molecular assays to rapidly identify pathogens and resistance genes directly from positive blood cultures (BCs) contribute to shortening the time required for the diagnosis of bloodstream infections. In this work, loop-mediated isothermal amplification (LAMP) assays have been examined for their potential use in BC diagnosis. Three different assays were applied. The commercially available eazyplex® MRSA test detects Staphylococcus aureus, S. epidermidis, mecA, and mecC. Two in-house assays [Gram-positive (GP) and Gram-negative (GN)] have been developed for the detection of streptococci, enterococci, vanA, vanB, Pseudomonas spp., Enterobacteriaceae, and the bla CTX-M family. A total of 370 positive BCs were analyzed. LAMP test results were obtained within 30 min, including sample preparation. Amplification was measured by real-time fluorescence detection. The threshold time for fluorescence intensity values ranged from 6.25 to 13.75 min. The specificity and sensitivity of the assays varied depending on the target. Overall, from 87.7% of BCs, true-positive results were obtained, compared to routine standard diagnosis. Twenty-one tests were true-negative because of the lack of an appropriate target (5.7%). The concordance of positive test results for resistance genes with subsequent antibiotic susceptibility testing was 100%. From 15 BC bottles with mixed cultures, eazyplex® assays produced correct results in 73% of the cases. This study shows that LAMP assays are fast and cost-saving tools for rapid BC testing in order to expedite the diagnostic report and improve the antibiotic stewardship for sepsis patients.

FOXM1 allows human keratinocytes to bypass the oncogene-induced differentiation checkpoint in response to gain of MYC or loss of p53.

Tumour suppressor p53 or proto-oncogene MYC is frequently altered in squamous carcinomas, but this is insufficient to drive carcinogenesis. We have shown that overactivation of MYC or loss of p53 via DNA damage triggers an anti-oncogenic differentiation-mitosis checkpoint in human epidermal keratinocytes, resulting in impaired cell division and squamous differentiation. Forkhead box M1 (FOXM1) is a transcription factor recently proposed to govern the expression of a set of mitotic genes. Deregulation of FOXM1 occurs in a wide variety of epithelial malignancies. We have ectopically expressed FOXM1 in keratinocytes of the skin after overexpression of MYC or inactivation of endogenous p53. Ectopic FOXM1 rescues the proliferative capacity of MYC- or p53-mutant cells in spite of higher genetic damage and a larger cell size typical of differentiation. As a consequence, differentiation induced by loss of p53 or MYC is converted into increased proliferation and keratinocytes displaying genomic instability are maintained within the proliferative compartment. The results demonstrate that keratinocyte oncogene-induced differentiation is caused by mitosis control and provide new insight into the mechanisms driving malignant progression in squamous cancer.

Psoriasin (S100A7) promotes stress-induced angiogenesis.

BACKGROUND: Vascular modifications occur early in the development of psoriasis, and angiogenesis is one of the key features in the pathogenesis of the disease. OBJECTIVES: To identify the role of the S100 protein psoriasin in psoriasis-associated angiogenesis. METHODS: The role of psoriasin in mediating angiogenesis was investigated by silencing psoriasin with small interfering RNA (siRNA) and measuring psoriasis-associated angiogenic factors in human epidermal keratinocytes. The secretion of psoriasin and the effect of psoriasin on general regulators of angiogenesis in keratinocytes, and on endothelial cell migration, proliferation, tube formation and production of angiogenic mediators, was evaluated. RESULTS: Reactive oxygen species (ROS) and hypoxia induced the expression of psoriasin. Downregulation of psoriasin in keratinocytes using siRNA altered the ROS-induced expression of the psoriasis-associated angiogenic factors vascular endothelial growth factor (VEGF), heparin-binding epidermal growth factor-like growth factor, matrix metalloproteinase 1 and thrombospondin 1. Overexpression of psoriasin altered several regulators of angiogenesis and led to the secretion of psoriasin. Treatment with extracellular psoriasin induced proliferation, migration and tube formation in dermal-derived endothelial cells to a similar extent as VEGF and interleukin-17, and induced the expression and release of proangiogenic mediators. These effects were suggested to be mediated by the PI3K and nuclear factor kappa B pathways. CONCLUSIONS: These findings suggest that psoriasin expression is promoted by oxidative stress in keratinocytes and amplifies the ROS-induced expression of angiogenic factors relevant to psoriasis. Moreover, extracellularly secreted psoriasin may act on dermal endothelial cells to contribute to key features angiogenesis.

The EGF receptor ligand amphiregulin controls cell division via FoxM1.

Epidermal growth factor receptor (EGFR) is central to epithelial cell physiology, and deregulated EGFR signaling has an important role in a variety of human carcinomas. Here we show that silencing of the EGF-related factor amphiregulin (AREG) markedly inhibits the expansion of human keratinocytes through mitotic failure and accumulation of cells with ⩾ 4n DNA content. RNA-sequencing-based transcriptome analysis revealed that tetracycline-mediated AREG silencing significantly altered the expression of 2331 genes, 623 of which were not normalized by treatment with EGF. Interestingly, genes irreversibly upregulated by suppression of AREG overlapped with genes involved in keratinocyte differentiation. Moreover, a significant proportion of the irreversibly downregulated genes featured upstream binding sites recognized by forkhead box protein M1 (FoxM1), a key transcription factor in the control of mitosis that is widely dysregulated in cancer. The downregulation of FoxM1 and its target genes preceded mitotic arrest. Constitutive expression of FoxM1 in AREG knockdown cells normalized cell proliferation, reduced the number of cells with ⩾ 4n DNA content and rescued expression of FoxM1 target genes. These results demonstrate that AREG controls G2/M progression and cytokinesis in keratinocytes via activation of a FoxM1-dependent transcriptional program, suggesting new avenues for treatment of epithelial cancer.

Evaluation of a shortened QIAsymphony DNA extraction protocol for stool samples using a multiplex real-time PCR for the detection of enteric pathogens.

A shortened DNA extraction protocol for the QIAsymphony SP was evaluated by quantitative and qualitative comparison of real-time PCR results of 150 co-extracted stool samples. The average ∆Cycle threshold value for positive pathogenic targets was 0.28 Ct. A consensus of 96.91%, with a correlation coefficient of 0.9880 was recorded.

Comparison of the QIAsymphony automated nucleic acid extraction and PCR setup platforms with NucliSens easyMAG and Corbett CAS-1200 liquid handling station for the detection of enteric pathogens in fecal samples.

In this study we compared the QIAsymphony Sample Preparation and Assay Setup modules (Qiagen), which provide automated nucleic acid extraction and PCR setup, to the NucliSens easyMAG (bioMérieux) and CAS-1200 liquid handling station (Corbett) for a molecular screening approach of enteric pathogens in fecal samples using multiplex real-time PCR. The relative DNA recovery of both platforms, within- and between-run reproducibility and a prospective study, including 510 clinical fecal samples, were performed. The results demonstrated that the QIAsymphony Sample Preparation and Assay Setup modules were highly reproducible and achieve equal performance, quantitative and qualitative, when compared with the NucliSens easyMAG and CAS-1200 systems for the molecular screening analysis of enteric pathogens in fecal samples.

Effect of wave exposure dynamics on gut content mass and growth of young-of-the-year fishes in the littoral zone of lakes.

Total length, body mass and gut content mass of young-of-the-year (YOY) perch Perca fluviatilis, dace Leuciscus leuciscus and bleak Alburnus alburnus were recorded over the summer of 2006 at three littoral sites at Upper Lake Constance. In P. fluviatilis and L. leuciscus, gut content mass correlated positively with wave-induced energy flux (E(F)) of the respective site and sampling day, while no correlation of gut content mass with E(F) was found in A. alburnus. It was assumed that benthivorous P. fluviatilis and L. leuciscus profited from suspended or uncovered benthic food items generated by wave action at sites and periods with high E(F). Alburnus alburnus, in contrast, feeding mainly on zooplankton in upper parts of the water column, could not profit from increased E(F). In P. fluviatilis, increased gut content mass during periods of high E(F) resulted in higher growth rates. For L. leuciscus, no real growth rates in local fish populations could be determined, as individuals were less sedentary, and when increased growth occurred at sites during the periods of high E(F), migration of fish levelled out the resulting size differences within few days. The results of this study show that dynamic habitat variables affect site profitability in the littoral zone of lakes, especially in benthivorous fishes. Therefore, dynamic habitat variables should be considered in addition to fixed habitat properties in analyses of habitat choice of fishes in the littoral zone of lakes.

5- and 6-pulse electron spin echo envelope modulation (ESEEM) of multi-nuclear spin systems.

In 3-pulse ESEEM and the original 4-pulse HYSCORE, nuclei with large modulation depth (k approximately 1) suppress spectral peaks from nuclei with weak modulations (k approximately 0). This cross suppression can impede the detection of the latter nuclei, which are often the ones of interest. We show that two extended pulse sequences, 5-pulse ESEEM and 6-pulse HYSCORE, can be used as experimental alternatives that suffer less strongly from the cross suppression and allow to recover signals of k approximately 0 nuclei in the presence of k approximately 1 nuclei. In the extended sequences, modulations from k approximately 0 nuclei are strongly enhanced. In addition, multi-quantum transitions are absent which simplifies the spectra. General analytical expressions for the modulation signals in these sequences are derived and discussed. Numerical simulations and experimental spectra that demonstrate the higher sensitivity of the extended pulse sequences are presented.

Ligand protons in a frozen solution of copper histidine relax via a T1e -driven three-spin mechanism.

Davies electron-nuclear double resonance spectra can exhibit strong asymmetries for long mixing times, short repetition times, and large thermal polarizations. These asymmetries can be used to determine nuclear relaxation rates in paramagnetic systems. Measurements of frozen solutions of copper(L-histidine)(2) reveal a strong field dependence of the relaxation rates of the protons in the histidine ligand, increasing from low (g( parallel)) to high (g( perpendicular)) field. It is shown that this can be attributed to a concentration-dependent T(1e)-driven relaxation process involving strongly mixed states of three spins: the histidine proton, the Cu(II) electron spin of the same complex, and another distant electron spin with a resonance frequency differing from the spectrometer frequency approximately by the proton Larmor frequency. The protons relax more efficiently in the g( perpendicular) region, since the number of distant electrons able to participate in this relaxation mechanism is higher than in the g( parallel) region. Analytical expressions for the associated nuclear polarization decay rate Tau(een) (-1) are developed and Monte Carlo simulations are carried out, reproducing both the field and the concentration dependences of the nuclear relaxation.

Twenty-three novel HLA-B alleles identified during intermediate-resolution testing.

Twenty-three novel human leukocyte antigen-B alleles are described: B*070204, *0738, *0742, *0821, *130202, *1312, *1575, *1598, *1599, *270507, *2728, *350104, *3558, *3811, *3931, *3932, *4045, *4107, *420501, *4812, *510106, *5520, and *5616. Thirteen of the variants are single-nucleotide substitutions from their most homologous allele, eight resulting in amino acid changes (B*0742, *1312, *1598, *1599, *3558, *3931, *4107, and *5616) and five with silent substitutions (B*070204, *130202, *270507, *350104, and *510106). Three alleles (B*0738, *4812, and *5520) differ by five nucleotide changes, altering four amino acids. The remaining seven alleles differ from their most similar alleles by two to three nucleotides, altering from one to two amino acids.

[Is there a German history of evidence-based medicine? Methodic standards of therapeutic research in the early 20th century and Paul Martini's "Methodology of therapeutic investigation" (1932)]. / Gibt es eine deutsche Vorgeschichte der Evidenz-basierten Medizin? Methodische Standards therapeutischer Forschung im beginnenden 20. Jahrhundert und Paul Martinis "Methodenlehre der therapeutischen Untersuchung"(1932).

The article addresses the history of evidence-based medicine in Germany. Its aim was to reconstruct the standard of clinical-therapeutic investigation in Germany at the beginning of the 20 (th) century. By a historical investigation of five important German general medical journals for the time between 1918 and 1932 an overview of the situation of clinical investigation is given. 268 clinical trails are identified, and are analysed in view of their methodological design. Heterogeneous results are found: While few examples of sophisticated methodology exist, the design of the majority of the studies is poor. A response to the situation described can be seen in Paul Martini's book "Methodology of Therapeutic Investigation", first published in 1932. Paul Martini's biography, his criticism of the situation of clinical-therapeutic investigation of his time, the major points of his methodology and the reception of the book in Germany and abroad are described.

Off-lattice Monte Carlo simulations of irreversible and reversible aggregation processes.

Monte Carlo simulations are used to get an insight into the formation of fractal aggregates from diluted to concentrated colloidal particle dispersions. Using irreversible conditions, we investigate the aggregation size distribution, architecture of the resulting fractal aggregates, possible transitions from simple aggregation to percolation and from percolation to the homogeneous aggregation regime, and discuss the fractal dimension determination from the radial distribution function. In particular the effects of the particle concentration on the aggregate fractal dimensions are considered. Reversibility is also introduced in the model so as to consider more realistic systems. The effects of aggregate fragmentation and internal reorganization are then investigated by adjusting the interparticle interaction potential. Important results dealing with the concomitant effect of aggregate break-up and internal reorganization on the aggregate local structure and stability with regards to phase separation are discussed.

Anti-interleukin 2 receptor antibodies and mycophenolate mofetil for treatment of steroid-resistant rejection in adult liver transplantation.

BACKGROUND: Steroid-resistant rejection (SRR) results in significant morbidity and mortality from the adverse effects of rescue therapy and in graft loss from chronic rejection. In our knowledge, the efficacy and safety of anti-interleukin (IL) 2r antibodies (daclizumab and basiliximab) for the treatment of SRR in adult liver transplantation has not previously been evaluated. METHODS: Twenty-five patients received either daclizumab or basiliximab as rescue therapy for SRR. Outcome and biochemical parameters were recorded before and after treatment with an anti-IL-2r antibody. RESULTS: The median time from transplantation to SRR was 25 days. Secondary immunosuppression included mycophenolate mofetil in 18 patients. Twelve patients (48%) had complete resolution of SRR. Aspartate transaminase levels normalized at a median of 37 days (range, 1-168 days). In 13 patients (52%) progressive hepatic dysfunction developed. Four of these patients received another transplant, and 6 patients had chronic rejection. Three patients died with graft failure. Of 16 patients with acute cellular rejection, 12 (75%) had resolution, 2 had chronic rejection, 1 required a repeat transplantation, and 1 died with graft failure. In contrast, all 9 patients with established chronic rejection in their pretreatment biopsy continued to have significant graft dysfunction, with 4 having persistent chronic graft dysfunction, 3 requiring repeat transplantation, and 2 dying with graft failure. CONCLUSION: Twelve (48%) of 25 patients who received an anti-IL-2r antibody because of SRR were successfully treated. All successfully treated patients had ongoing acute cellular rejection at liver biopsy (75%), whereas patients with histologic evidence of chronic rejection responded poorly.

An improved OPLS-AA force field for carbohydrates.

This work describes an improved version of the original OPLS-all atom (OPLS-AA) force field for carbohydrates (Damm et al., J Comp Chem 1997, 18, 1955). The improvement is achieved by applying additional scaling factors for the electrostatic interactions between 1,5- and 1,6-interactions. This new model is tested first for improving the conformational energetics of 1,2-ethanediol, the smallest polyol. With a 1,5-scaling factor of 1.25 the force field calculated relative energies are in excellent agreement with the ab initio-derived data. Applying the new 1,5-scaling makes it also necessary to use a 1,6-scaling factor for the interactions between the C4 and C6 atoms in hexopyranoses. After torsional parameter fitting, this improves the conformational energetics in comparison to the OPLS-AA force field. The set of hexopyranoses included in the torsional parameter derivation consists of the two anomers of D-glucose, D-mannose, and D-galactose, as well as of the methyl-pyranosides of D-glucose, D-mannose. Rotational profiles for the rotation of the exocyclic group and of different hydroxyl groups are also compared for the two force fields and at the ab initio level of theory. The new force field reduces the overly high barriers calculated using the OPLS-AA force field. This leads to better sampling, which was shown to produce more realistic conformational behavior for hexopyranoses in liquid simulation. From 10-ns molecular dynamics (MD) simulations of alpha-D-glucose and alpha-D-galactose the ratios for the three different conformations of the hydroxymethylene group and the average (3)J(H,H) coupling constants are derived and compared to experimental values. The results obtained for OPLS-AA-SEI force field are in good agreement with experiment whereas the properties derived for the OPLS-AA force field suffer from sampling problems. The undertaken investigations show that the newly derived OPLS-AA-SEI force field will allow simulating larger carbohydrates or polysaccharides with improved sampling of the hydroxyl groups.

Isolation of total-RNA from formalin-fixed rat retina.

The aim of this project was to establish a method for the purification of total-RNA from fixed rat-retina. Two different established methods were used for RNA purification, and successful isolation was verified with RT-PCR for amplification of beta-actin (two different product-lengths) and subsequent gel-electrophoresis. Total-RNA was successfully isolated from fixed rat-retina. The house keeping gene, beta-actin could be detected after fixing the retina either with 1% formalin or with 4% paraformaldehyde (PFA). Hexamer-primer based RT-PCR gave better results than the oligo-d(T)-primer based RT-PCR method. Both the 698 and 225 bp beta-actin-fragments could be successfully amplified, where amplification of the latter was more efficient. This approach shows that tissue fixation prior to RNA-isolation facilitates the rapid isolation of undamaged RNAs in tissues such as the retina, which are known to yield low levels of RNA and are vulnerable to RNases.

Heterogeneity and persistence length in human ocular mucins.

Atomic force microscopy (AFM) has been used to investigate the heterogeneity and flexibility of human ocular mucins and their subunits. We have paid particular attention, in terms of theory and experiment, to the problem of inducing the polymers to assume equilibrium conformations at a surface. Mucins deposited from a buffer containing Ni(2+) ions adopt extended conformations on mica akin to those observed for DNA under similar conditions. The heterogeneity of the intracellular native mucins is evident from a histogram of contour lengths, reflecting, in part, the diversity of mucin gene products expressed. Reduction of the native mucin with dithiothreitol, thereby breaking the S==S bonds between cysteine residues, causes a marked reduction in polymer length. These results reflect the modes of transport and assembly of newly synthesized mucins in vivo. By modifying the worm-like chain model for applicability to two dimensions, we have confirmed that under the conditions employed mucin adsorbs to mica in an equilibrated conformation. The determined persistence length of the native mucin, 36 nm, is consistent with that of an extended, flexible polymer; such characteristics will influence the properties of the gels formed in vivo.

The effect of the menstrual cycle on acne.

Acne is a common disease with an underlying hormonal basis; however, there has never been a study to determine the ways in which the different stages of the menstrual cycle affect acne in women. Four hundred female participants, aged 12 to 52 years, were questioned whether their acne got worse before, during, or after their menstrual period and also asked whether it was unrelated to the menstrual period. Their age, severity of acne, ethnicity, and oral contraceptive use were also recorded. Overall 177 of 400 (44%) of those interviewed experienced premenstrual flares of their acne. Severity of acne, ethnicity, and oral contraceptive use did not affect the premenstrual flare rate. Women older than 33 years had a higher rate of premenstrual flares relative to women aged 20 to 33 years (P =.03 by chi(2) analysis). We concluded that almost half of all women experience premenstrual flares of their acne. Premenstrual flares may be more common in older women.

Differential utilization and localization of ErbB receptor tyrosine kinases in skin compared to normal and malignant keratinocytes.

Induction of heparin-binding epidermal growth factor-like growth factor (HB-EGF) mRNA in mouse skin organ culture was blocked by two pan-ErbB receptor tyrosine kinase (RTK) inhibitors but not by genetic ablation of ErbB1, suggesting involvement of multiple ErbB species in skin physiology. Human skin, cultured normal keratinocytes, and A431 skin carcinoma cells expressed ErbB1, ErbB2, and ErbB3, but not ErbB4. Skin and A431 cells expressed more ErbB3 than did keratinocytes. Despite strong expression of ErbB2 and ErbB3, heregulin was inactive in stimulating tyrosine phosphorylation in A431 cells. In contrast, it was highly active in MDA-MB-453 breast carcinoma cells. ErbB2 displayed punctate cytoplasmic staining in A431 and keratinocytes, compared to strong cell surface staining in MDA-MB-453. In skin, ErbB2 was cytoplasmic in basal keratinocytes, assuming a cell surface pattern in the upper suprabasal layers. In contrast, ErbB1 retained a cell surface distribution in all epidermal layers. Keratinocyte proliferation in culture was found to be ErbB1-RTK-dependent, using a selective inhibitor. These results suggest that in skin keratinocytes, ErbB2 transduces ligand-dependent differentiation signals, whereas ErbB1 transduces ligand-dependent proliferation/survival signals. Intracellular sequestration of ErbB2 may contribute to the malignant phenotype of A431 cells, by allowing them to respond to ErbB1-dependent growth/survival signals, while evading ErbB2-dependent differentiation signals.

Epstein-Barr virus/human vector provides high-level, long-term expression of alpha1-antitrypsin in mice.

We have constructed plasmid DNA vectors that contain Epstein-Barr virus (EBV) sequences and the human gene (SERPINA1) encoding alpha1-Antitrypsin (AAT). We demonstrate that a plasmid carrying the full SERPINA1 on a 19-kb genomic fragment and the EBV gene EBNA1 and its family of repeats binding sites undergoes efficient extrachromosomal replication in dividing mammalian tissue culture cells. Therefore, use of a whole genomic therapeutic gene to provide both replication and gene expression may be an effective gene therapy vector design, if the target cells are dividing. The efficacy of this same vector for expression of AAT in vivo in the nondividing cells of mouse liver was determined by hydrodynamic injection of naked plasmid DNA by means of the tail vein. A single injection of an EBV/genomic SERPINA1 vector provided >300 microg/ml of AAT, which approached normal plasma levels and persisted for the >9-month duration of the experiment. These data exceed most previously reported values, probably due to sequences in the genomic DNA that resist silencing of gene expression, possibly in combination with favorable effects on expression provided by the EBV sequences. These results demonstrate that plasmid DNA with the correct cis-acting sequences can provide in vivo long-term expression of protein at high levels that are therapeutically relevant for gene therapy.