Application of Sequence-Specific Labeled 16S rRNA Gene Oligonucleotide Probes for Genetic Profiling of Cyanobacterial Abundance and Diversity by Array Hybridization

DNA sequence information for the small-subunit rRNA gene (16S rDNA) obtained from cyanobacterial cultures was used to investigate the presence of cyanobacteria and their abundance in natural habitats. Eight planktonic communities developing in lakes characterized by relatively low algal biomass (mesotrophic) and in lakes with correspondingly high biomass (eutrophic) were selected for the study. The organismal compositions of the water samples were analyzed genetically, using multiplex sequence-specific labeling of oligonucleotide probes targeted to 16S rDNA and subsequent hybridization of the labeled probes to their respective complements spotted onto a solid support (DNA array). Ten probes were established to determine the relative abundances of the discernible cyanobacteria encountered in the selected lakes. The probes were generally specific for their targets, as determined through analyses of clone cultures. Reproducible abundance profiles were established for the lakes investigated in the subsequent analyses of natural cyanobacterial communities. The results from the genetic analyses were then compared with information obtained from standard hydrobiological and hydrochemical analyses. Qualitatively, there were relatively good correlations among the groups of organisms (Nostoc, Microcystis, and Planktothrix species) found in the different lakes. The levels of correlation were lower for the quantitative data. This may, however, be due to differences in sample processing technique. The conclusions from these comparisons are that the genetic abundance profiles may provide a foundation for separating and quantifying genetically distinct groups of cyanobacteria in their natural habitats.     

Okadaic acid,cAMP, and selected nutrients inhibit hepatocyte proliferation at different stages in G1: Modulation of the cAMP effect by phosphatase inhibitors and nutrients

The protein phosphatase inhibitor okadaic acid (> 100 nM) caused an abrupt and complete cessation of primary rat hepatocyte cell cycle progression at the restriction point in late G₁. A decline in the G₁/S transition rate was observed in response to elevated cAMP, excess selected nutrients, and okadaic acid (< 100 nM). Excess nutrients (40 mM glucose ± 5 mM dihydroxyacetone) acted by imposing an incomplete block in early G₁. The cAMP action was potentiated by the phosphatase inhibitor microcystin, which in itself did not affect DNA replication. This suggests that cAMP acted by phosphorylating substrate(s) that is dephosphorylated by a microcystin-sensitive phosphatase. The additive effects of submaximal concentrations of okadaic acid and cAMP analogs indicated that okadaic acid and cAMP acted via different pathways. In conclusion, okadaic acid, cAMP, and excess nutrients, acting through distinct pathways, inhibited hepatocytes in different parts of the G₁ phase. © 1995 Wiley-Liss, Inc.     

Hypsography, meteorology and hydrology of the Øvre Heimdalen catchment

The Lake Øvre Heimdalsvatn is greatly affected by wind. Precipitation, especially heavy rainfall, has probably a good possibility of eroding and leaching material into the lake. The mean annual temperature is −1.2°C, and the estimated mean annual evapo-transpiration is about 200 mm. The lake is covered by ice from late October to the beginning of June. Run-off, lake level and precipitation are well correlated, indicating that the influence of the catchment is large and rapid.     

Causality in Scale Space as an Approach to Change Detection

Kernel density estimation and kernel regression are useful ways to visualize and assess the structure of data. Using these techniques we define a temporal scale space as the vector space spanned by bandwidth and a temporal variable. In this space significance regions that reflect a significant derivative in the kernel smooth similar to those of SiZer (Significant Zero-crossings of derivatives) are indicated. Significance regions are established by hypothesis tests for significant gradient at every point in scale space. Causality is imposed onto the space by restricting to kernels with left-bounded or finite support and shifting kernels forward. We show that these adjustments to the methodology enable early detection of changes in time series constituting live surveillance systems of either count data or unevenly sampled measurements. Warning delays are comparable to standard techniques though comparison shows that other techniques may be better suited for single-scale problems. Our method reliably detects change points even with little to no knowledge about the relevant scale of the problem. Hence the technique will be applicable for a large variety of sources without tailoring. Furthermore this technique enables us to obtain a retrospective reliable interval estimate of the time of a change point rather than a point estimate. We apply the technique to disease outbreak detection based on laboratory confirmed cases for pertussis and influenza as well as blood glucose concentration obtained from patients with diabetes type 1.     

Prevalence and Risk Factors of Violence by Psychiatric Acute Inpatients: A Systematic Review and Meta-Analysis

Background

Violence in acute psychiatric wards affects the safety of other patients and the effectiveness of treatment. However, there is a wide variation in reported rates of violence in acute psychiatric wards.

Objectives

To use meta-analysis to estimate the pooled rate of violence in published studies, and examine the characteristics of the participants, and aspects of the studies themselves that might explain the variation in the reported rates of violence (moderators).

Method

Systematic meta-analysis of studies published between January 1995 and December 2014, which reported rates of violence in acute psychiatric wards of general or psychiatric hospitals in high-income countries.

Results

Of the 23,972 inpatients described in 35 studies, the pooled proportion of patients who committed at least one act of violence was 17% (95% confidence interval (CI) 14–20%). Studies with higher proportions of male patients, involuntary patients, patients with schizophrenia and patients with alcohol use disorder reported higher rates of inpatient violence.

Conclusion

The findings of this study suggest that almost 1 in 5 patients admitted to acute psychiatric units may commit an act of violence. Factors associated with levels of violence in psychiatric units are similar to factors that are associated with violence among individual patients (male gender, diagnosis of schizophrenia, substance use and lifetime history of violence).     

Albumin Kinetics in Patients Undergoing Major Abdominal Surgery

Background

The drop in plasma albumin concentration following surgical trauma is well known, but the temporal pattern of the detailed mechanisms behind are less well described. The aim of this explorative study was to assess changes in albumin synthesis and transcapillary escape rate (TER) following major surgical trauma, at the time of peak elevations in two well-recognized markers of inflammation.

Methods

This was a clinical trial of radiolabeled human serum albumin for the study of TER and plasma volume. Ten patients were studied immediately preoperatively and on the 2nd postoperative day after major pancreatic surgery. Albumin synthesis rate was measured by the flooding dose technique employing incorporation of isotopically labelled phenylalanine.

Results

Fractional synthesis rate of albumin increased from 11.7 (95% CI: 8.9, 14.5) to 15.0 (11.7, 18.4) %/day (p = 0.027), whereas the corresponding absolute synthesis rate was unchanged, 175 (138, 212) versus 150 (107, 192) mg/kg/day (p = 0.21). TER was unchanged, 4.9 (3.1, 6.8) %/hour versus 5.5 (3.9, 7.2) (p = 0.63). Plasma volume was unchanged but plasma albumin decreased from 33.5 (30.9, 36.2) to 22.1 (19.8, 24.3) g/L. (p<0.001).

Conclusion

Two days after major abdominal surgery, at the time-point when two biomarkers of generalised inflammation were at their peak and the plasma albumin concentration had decreased by 33%, we were unable to show any difference in the absolute synthesis rate of albumin, TER and plasma volume as compared with values obtained immediately pre-operatively. This suggests that capillary leakage, if elevated postoperatively, had ceased at that time-point. The temporal relations between albumin kinetics, capillary leakage and generalised inflammation need to be further explored.

Trial Registration

clinicaltrialsregister.eu: EudraCT 2010-08529-21 ClinicalTrials.gov NCT01194492     

Scientific workflow optimization for improved peptide and protein identification

Background

Peptide-spectrum matching is a common step in most data processing workflows for mass spectrometry-based proteomics. Many algorithms and software packages, both free and commercial, have been developed to address this task. However, these algorithms typically require the user to select instrument- and sample-dependent parameters, such as mass measurement error tolerances and number of missed enzymatic cleavages. In order to select the best algorithm and parameter set for a particular dataset, in-depth knowledge about the data as well as the algorithms themselves is needed. Most researchers therefore tend to use default parameters, which are not necessarily optimal.

Results

We have applied a new optimization framework for the Taverna scientific workflow management system (http://ms-utils.org/Taverna_Optimization.pdf) to find the best combination of parameters for a given scientific workflow to perform peptide-spectrum matching. The optimizations themselves are non-trivial, as demonstrated by several phenomena that can be observed when allowing for larger mass measurement errors in sequence database searches. On-the-fly parameter optimization embedded in scientific workflow management systems enables experts and non-experts alike to extract the maximum amount of information from the data. The same workflows could be used for exploring the parameter space and compare algorithms, not only for peptide-spectrum matching, but also for other tasks, such as retention time prediction.

Conclusion

Using the optimization framework, we were able to learn about how the data was acquired as well as the explored algorithms. We observed a phenomenon identifying many ammonia-loss b-ion spectra as peptides with N-terminal pyroglutamate and a large precursor mass measurement error. These insights could only be gained with the extension of the common range for the mass measurement error tolerance parameters explored by the optimization framework.     

Increased WD-repeat containing protein 1 in interstitial fluid from ovarian carcinomas shown by comparative proteomic analysis of malignant and healthy gynecological tissue

We aimed to identify differentially expressed proteins in interstitial fluid from ovarian cancer employing multiple fractioning and high resolution mass spectrometry-based proteomic analysis, and asked whether specific proteins that may serve as biomarker candidates or therapeutic targets could be identified. High throughput proteomics was conducted on immunodepleted and fractioned interstitial fluid from pooled samples of ovarian carcinomas, using endometrial carcinomas and healthy ovarian tissue as controls. Differential analysis revealed the up-regulation of extracellular proteasomes in tumor interstitial fluid compared to the healthy control. Moreover, a number of differentially expressed proteins in interstitial fluid from ovarian carcinomas compared with control tissues were identified. Detection of proteasome 20S related proteins in TIF compared to IF from healthy tissue indicates that the 20S proteasome can have a role in the tumor microenvironment. Six selected proteins, CEACAM5, FREM2, MUC5AC, TFF3, PYCARD and WDR1, were independently validated in individual tumor lysates from ovarian carcinomas by multiple reaction monitoring initiated detection and sequence analysis, Western blot and/or selected reaction monitoring. Quantification of specific proteins revealed substantial heterogeneity between individual samples. Nevertheless, WD repeat-containing protein 1 was confirmed as being significantly overexpressed in interstitial fluid from ovarian carcinomas compared to healthy ovarian tissue by Orbitrap analysis of individual native interstitial fluid from ovarian and endometrial carcinomas and healthy ovarian tissue. We suggest that this protein should be explored as a therapeutic target in ovarian carcinomas. This article is part of a Special Issue entitled: An Updated Secretome.