Fast DNA serotyping of Escherichia coli by use of an oligonucleotide microarray

Classical antibody-based serotyping of Escherichia coli is an important method in diagnostic microbiology for epidemiological purposes, as well as for a rough virulence assessment. However, serotyping is so tedious that its use is restricted to a few reference laboratories. To improve this situation we developed and validated a genetic approach for serotyping based on the microarray technology. The genes encoding the O-antigen flippase (wzx) and the O-antigen polymerase (wzy) were selected as target sequences for the O antigen, whereas fliC and related genes, which code for the flagellar monomer, were chosen as representatives for the H phenotype. Starting with a detailed bioinformatic analysis and oligonucleotide design, an ArrayTube-based assay was established: a fast and robust DNA extraction method was coupled with a site-specific, linear multiplex labeling procedure and hybridization analysis of the biotinylated amplicons. The microarray contained oligonucleotide DNA probes, each in duplicate, representing 24 of the epidemiologically most relevant of the over 180 known O antigens (O antigens 4, 6 to 9, 15, 26, 52, 53, 55, 79, 86, 91, 101, 103, 104, 111, 113, 114, 121, 128, 145, 157, and 172) as well as 47 of the 53 different H antigens (H antigens 1 to 12, 14 to 16, 18 to 21, 23 to 34, 37 to 43, 45, 46, 48, 49, 51 to 54, and 56). Evaluation of the microarray with a set of defined strains representing all O and H serotypes covered revealed that it has a high sensitivity and a high specificity. All of the conventionally typed 24 O groups and all of the 47 H serotypes were correctly identified. Moreover, strains which were nonmotile or nontypeable by previous serotyping assays yielded unequivocal results with the novel ArrayTube assay, which proved to be a valuable alternative to classical serotyping, allowing processing of single colonies within a single working day.

HCV-related advanced fibrosis/cirrhosis: randomized controlled trial of pegylated interferon alpha-2a and ribavirin

In patients with hepatitis C virus (HCV)-related advanced fibrosis/cirrhosis, 30% of sustained HCV clearance has been reported with pegylated interferon alpha-2a (PEG-IFN) alone, but the efficacy and tolerability of the PEG-IFN/ribavirin (RBV) combination remain poorly defined. A total of 124 treatment-naïve patients with biopsy proved HCV-related advanced fibrosis/cirrhosis (Ishak score F4-F6, Child-Pugh score < or =7) were randomized to 48 weeks of PEG-IFN (180 microg sc weekly) and standard dose of RBV (1000/1200 mg po daily, STD) or PEG-IFN (180 microg sc weekly) and low-dose of RBV (600/800 mg po daily, LOW). Sustained virologic response (SVR) rates with PEG-IFN/STD RBV (52%) were higher--albeit not significantly--than that with PEG-IFN/LOW RBV (38%, P = 0.153). In multivariate analysis, genotype 2/3 and a baseline platelet count > or =150 x 10(9)/L were independently associated with SVR. The likelihood of SVR was < 7% if viraemia had not declined by > or =2 log or to undetectable levels after 12 weeks. Nine adverse events in the STD RBV and 15 in the LOW RBV group were classified as severe (including two deaths); dose reductions for intolerance were required in 78% and 57% (P = 0.013), and treatment was terminated early in 23% and 27% of patients (P = n.s.). The benefit/risk ratio of treating compensated HCV-cirrhotics with STD PEG-IFN/RBV is favourable.

Self-assembly of sensory neurons into ganglia-like microtissues

Unraveling intra- and inter-cellular signaling networks managing cell-fate control, coordinating complex differentiation regulatory circuits and shaping tissues and organs in living systems remain major challenges in the post-genomic era. Resting on the laurels of past-century monolayer culture technologies, the cell culture community has only recently begun to appreciate the potential of three-dimensional mammalian cell culture systems to reveal the full scope of mechanisms orchestrating the tissue-like cell quorum in space and time. Capitalizing on gravity-enforced self-assembly of monodispersed primary embryonic mouse cells in hanging drops, we designed and characterized a three-dimensional cell culture model for ganglion-like structures. Within 24h, a mixture of mouse embryonic fibroblasts (MEF) and cells, derived from the dorsal root ganglion (DRG) (sensory neurons and Schwann cells) grown in hanging drops, assembled to coherent spherical microtissues characterized by a MEF feeder core and a peripheral layer of DRG-derived cells. In a time-dependent manner, sensory neurons formed a polar ganglion-like cap structure, which coordinated guided axonal outgrowth and innervation of the distal pole of the MEF feeder spheroid. Schwann cells, present in embryonic DRG isolates, tended to align along axonal structures and myelinate them in an in vivo-like manner. Whenever cultivation exceeded 10 days, DRG:MEF-based microtissues disintegrated due to an as yet unknown mechanism. Using a transgenic MEF feeder spheroid, engineered for gaseous acetaldehyde-inducible interferon-beta (ifn-beta) production by cotransduction of retro-/ lenti-viral particles, a short 6-h ifn-beta induction was sufficient to rescue the integrity of DRG:MEF spheroids and enable long-term cultivation of these microtissues. In hanging drops, such microtissues fused to higher-order macrotissue-like structures, which may pave the way for sophisticated bottom-up tissue engineering strategies. DRG:MEF-based artificial micro- and macrotissue design demonstrated accurate key morphological aspects of ganglions and exemplified the potential of self-assembled scaffold-free multicellular micro-/macrotissues to provide new insight into organogenesis.

The metastatic T-cell hybridoma antigen/P-selectin glycoprotein ligand 1 is required for hematogenous metastasis of lymphomas

Using variants of the murine BW5147 lymphoma cell-line, we have previously identified 3 monoclonal antibodies (MAbs) that discriminate between metastatic and nonmetastatic BW5147-derived T-cell hybridomas and lymphomas, as well as BW5147-unrelated T-lymphomas. These MAbs were reported to recognize an identical membrane-associated sialoglycoprotein, termed "metastatic T-cell hybridoma antigen" (MTH-Ag). Here, we document that the expression pattern of the MTH-Ag on metastatic and nonmetastatic BW5147 variants correlates with that of the P-selectin glycoprotein ligand 1 (PSGL-1), a sialomucin involved in leukocyte recruitment to sites of inflammation. Moreover, the MAbs against the MTH-Ag recognize PSGL-1 when it is transfected in MTH-Ag-negative BW5147 variants, suggesting that the MTH-Ag is PSGL-1. Overexpression of MTH-Ag/PSGL-1 in MTH-Ag-negative BW5147 variants did not affect their in vivo malignancy. Yet, down-regulation of MTH-Ag/PSGL-1 expression on metastatic, MTH-Ag-positive BW5147 variants, using an RNA interference (RNAi) approach, resulted, in a dose-dependent manner, in a significant reduction of liver and spleen colonization and a delay in mortality of the recipient mice upon intravenous inoculation. Collectively, these results demonstrate that, although MTH-Ag/PSGL-1 overexpression alone may not be sufficient for successful dissemination and organ colonization, MTH-Ag/PSGL-1 plays a critical role in hematogenous metastasis of lymphoid cancer cells.

A randomized clinical trial of mupirocin in the eradication of Staphylococcus aureus nasal carriage in human immunodeficiency virus disease

Seventy-six human immunodeficiency virus (HIV)-infected patients with Staphylococcus aureus nasal carriage were randomized to treatment groups receiving intranasal mupirocin or placebo twice daily for 5 days. Nasal cultures for S. aureus were obtained at 1, 2, 6, and 10 weeks after therapy. At 1 week, 88% of mupirocin-treated patients had negative nasal cultures compared with 8% in placebo patients (P<.001). The percentage of mupirocin-treated patients with persistently negative nasal cultures decreased over time (63%, 45%, and 29% at 2, 6, and 10 weeks, respectively) but remained significantly greater than the placebo group (3% at 2, 6, and 10 weeks). In mupirocin-treated patients, most (16/19) instances of nasal recolonization were with pretreatment strains (determined by means of by pulsed field gel electrophoresis); mupirocin resistance was not observed. Five days of treatment with mupirocin eliminated S. aureus nasal carriage in HIV-infected patients for several weeks; however, since the effect waned over time, intermittent dosing regimens should be considered for long-term eradication.

Impact of changing definitions for myocardial infarction: a report from the AMIS registry

BACKGROUND: To assess the impact of the new definitions of myocardial infarction, we retrospectively analyzed 9190 patients from 63 hospitals with reported peak troponin values included between 2001 and 2007 in the Swiss AMIS (Acute Myocardial Infarction in Switzerland) Plus registry. METHODS: Patients were classified as belonging to the "classic" myocardial infarction group (peak total CK or CK-MB above the upper limit of normal, or troponin T [TnT] >0.1 microg/L or troponin I [TnI] >0.1-0.8 microg/L [depending on the assay]) or "new" myocardial infarction group (TnT >0.01 microg/L or TnI >0.01-0.07 microg/L). RESULTS: There were 489 patients in the "new" group who were similar to the 8701 "classic" patients in terms of age, sex, and prevalence of both diabetes and renal failure, but more frequently had a history of prior coronary artery disease, hypertension, and hyperlipidemia. At admission, they less frequently had ST elevation on their electrocardiogram, were more frequently in Killip class I, and received less primary percutaneous coronary intervention. Hospital mortality was 3.5% in the "new" and 6.7% in the "classic" myocardial infarction group (P=.004). In a subset of patients with a longer follow-up, mortality at 3 and 12 months was 1% and 5.6%, respectively, for "new" and 1.6% and 4%, respectively, for "classic" myocardial infarction (NS). CONCLUSIONS: Patients with minimal elevation of serum troponin have smaller infarctions, less aggressive treatment, fewer early complications, and a better early prognosis than patients with higher serum biomarker levels. After discharge, however, their prognosis currently appears no different from that of patients with a "classic" myocardial infarction event.

Plurality of tree species responses to drought perturbation in Bornean tropical rain forest

Drought perturbation driven by the El Niño Southern Oscillation (ENSO) is a principal stochastic variable determining the dynamics of lowland rain forest in S.E. Asia. Mortality, recruitment and stem growth rates at Danum in Sabah (Malaysian Borneo) were recorded in two 4-ha plots (trees ≥ 10 cm gbh) for two periods, 1986–1996 and 1996–2001. Mortality and growth were also recorded in a sample of subplots for small trees (10 to <50 cm gbh) in two sub-periods, 1996–1999 and 1999–2001. Dynamics variables were employed to build indices of drought response for each of the 34 most abundant plot-level species (22 at the subplot level), these being interval-weighted percentage changes between periods and sub-periods. A significant yet complex effect of the strong 1997/1998 drought at the forest community level was shown by randomization procedures followed by multiple hypothesis testing. Despite a general resistance of the forest to drought, large and significant differences in short-term responses were apparent for several species. Using a diagrammatic form of stability analysis, different species showed immediate or lagged effects, high or low degrees of resilience or even oscillatory dynamics. In the context of the local topographic gradient, species’ responses define the newly termed perturbation response niche. The largest responses, particularly for recruitment and growth, were among the small trees, many of which are members of understorey taxa. The results bring with them a novel approach to understanding community dynamics: the kaleidoscopic complexity of idiosyncratic responses to stochastic perturbations suggests that plurality, rather than neutrality, of responses may be essential to understanding these tropical forests. The basis to the various responses lies with the mechanisms of tree-soil water relations which are physiologically predictable: the timing and intensity of the next drought, however, is not. To date, environmental stochasticity has been insufficiently incorporated into models of tropical forest dynamics, a step that might considerably improve the reality of theories about these globally important ecosystems.

Allocentric visual cues influence mental transformation of bodies

Identifying a human body stimulus involves mentally rotating an embodied spatial representation of one's body (motoric embodiment) and projecting it onto the stimulus (spatial embodiment). Interactions between these two processes (spatial and motoric embodiment) may thus reveal cues about the underlying reference frames. The allocentric visual reference frame, and hence the perceived orientation of the body relative to gravity, was modulated using the York Tumbling Room, a fully furnished cubic room with strong directional cues that can be rotated around a participant's roll axis. Sixteen participants were seated upright (relative to gravity) in the Tumbling Room and made judgments about body and hand stimuli that were presented in the frontal plane at orientations of 0°, 90°, 180° (upside down), or 270° relative to them. Body stimuli have an intrinsic visual polarity relative to the environment whereas hands do not. Simultaneously the room was oriented 0°, 90°, 180° (upside down), or 270° relative to gravity resulting in sixteen combinations of orientations. Body stimuli were more accurately identified when room and body stimuli were aligned. However, such congruency did not facilitate identifying hand stimuli. We conclude that static allocentric visual cues can affect embodiment and hence performance in an egocentric mental transformation task. Reaction times to identify either hands or bodies showed no dependence on room orientation.

Armenians

The history of Armenia during Late Antiquity, just as in the Classical period, was largely influenced by its geographical position as a land located between the empires of Rome and Persia.

Prescriptions of Chinese medicinal herbs in Switzerland: the example of suan zao ren (Ziziphi Spinosae Semen)

Introduction According to the Swiss Health Survey 2007, 1.7% of the adult population use traditional Chinese medicine (including Chinese herbal medicine, but excluding acupuncture). In contrast to conventional drugs, that contain single chemically defined substances, prescriptions of Chinese herbs are mixtures of up to 40 ingredients (parts of plants, fungi, animal substances and minerals). Originally they were taken in the form of decoctions, but nowadays granules are more popular. Medium daily dosages of granules range between 8 to 12g. In a recent work we identified the most commonly used Chinese herbs (all ingredients are referred to as herbs for reasons of simplicity) and classical formulas (mixtures). Here we present a short overview and the example of suan zao ren (Ziziphi Spinosae Semen), which is used in the treatment of insomnia and anxiety and contains saponins that have been shown to increase sleep in animal studies. Material and Methods A random sample of 1,053 prescriptions was drawn from the database of Lian Chinaherb AG, Switzerland, and analysed according to the most frequently used individual herbs and classical formulas. Cluster analysis (Jaccard similarity coefficient, complete linkage method) was applied to identify common combinations of herbs. Results The most frequently used herbs were dang gui (Angelicae Sinensis Radix), fu ling (Poria), bai shao (Paeoniae Radix Alba), and gan cao (Glycyrrhizae Radix et Rhizoma); the most frequently used classical formulas were gui pi tang (Restore the Spleen Decoction) and xiao yao san (Rambling Powder). The average number of herbs per prescription was 12.0, and the average daily dosage of granules was 8.7g. 74.3% of the prescriptions were for female, 24.8% for male patients. Suan zao ren was present in 14.2% of all prescriptions. These prescriptions contained on average 13.7 herbs, and the daily dosage of granules was 8.9g. Suan zao ren was more frequently prescribed by practitioners of non-Asian than of Asian origin but equally often for female and male patients. Cluster analysis grouped suan zao ren with yuan zhi (Polygalae Radix), bai zi ren (Platycladi Semen), sheng di huang (Rehmanniae Radix) and dan shen (Salviae Miltiorrhizae Radix et Rhizoma). Discussion Prescriptions including suan zao ren contained on average slightly more herbs than other prescriptions. This might be due to the fact that two of the three most popular classical formulas with suan zao ren are composed of 13 and 12 herbs with the possibility of adding more ingredients when necessary. Cluster analysis resulted in the clustering of suan zao ren with other herbs of the classical formula tian wang bu xin dan (Emperor of Heaven’s Special Pill to Tonify the Heart), indicating the use of suan zao ren for the treatment of insomnia and irritability. Unfortunately, the diagnoses of the patients were unavailable and thus correlations between use of suan zao ren and diseases could not be analysed.

Resistance of a lowland rain forest to increasing drought intensity in Sabah, Borneo

Occasional strong droughts are an important feature of the climatic environment of tropical rain forest in much of Borneo. This paper compares the response of a lowland dipterocarp forest at Danum, Sabah, in a period of low (LDI) and a period of high (HDI) drought intensity (1986-96, 9.98 y;1996-99, 2.62 y). Mean annual drought intensity was two-fold higher in the HDI than LDI period (1997 v. 976 mm), and each period had one moderately strong main drought (viz. 1992, 1998). Mortality of `all' trees greater than or equal to 10 cm gbh (girth at breast height) and stem growth rates of `small' trees 10less than or equal to50 cm gbh were measured in sixteen 0.16-ha subplots (half on ridge, half on lower slope sites) within two 4-ha plots. These 10-50-cm trees were composed largely of true understorey species. A new procedure was developed to correct for the effect of differences in length of census interval when comparing tree mortality rates. Mortality rates of small trees declined slightly but not significantly between the LDI and HDI periods (1.53 to 1.48% y(-1)): mortality of all trees showed a similar pattern. Relative growth rates declined significantly by 23% from LDI to HDI periods (11.1 to 8.6 mm m(-1) y(-1)): for absolute growth rates the decrease was 28% (2.45 to 1.77 mm y(-1)). Neither mortality nor growth rates were significantly influenced by topography. For small trees, across subplots, absolute growth rate was positively correlated in the LDI period, but negatively correlated in the HDI period, with mortality rate. There was no consistent pattern in the responses among the 19 most abundant species (n greater than or equal to 50 trees) which included a proposed drought-tolerant guild. In terms of tree survival, the forest at Danum was resistant to increasing drought intensity, but showed decreased stem growth attributable to increasing water stress.