Lipopolysaccharides of polymyxin B-resistant mutants of Escherichia coii are extensively substituted by 2-aminoethyl pyrophosphate and contain aminoarabinose in lipid A

Lipopolysaccharides (LPS) of two polymyxin-resistant (pmr) mutants and the corresponding parent strain of Escherichia Coli were chemically analysed for composition and subjected to ³¹P-NMR (nuclear magnetic resonance) for assessment of phosphate substitution. Whereas the saccharide portions, fatty acids, and phosphate contents were similar in wild-type and pmr LPS, the latter contained two- to threefold higher amounts of 2-aminoethanol. The pmr LPS also contained 4-amino-4-deoxy-l -arabinopyranose (l -Ara_p4N), which is normally not a component of E. coli LPS. This aminopentose has been assigned to be linked to the 4′-phosphate of lipid A. Comparative ³¹P-NMR analysis of the de-O-acylated LPS of the wild-type and pmr strains revealed that phosphate groups of the pmr LPS were mainly (71-79%) diphosphate diesters, which accounted for only 20% in the wild-type LPS. Diphosphate monoesters were virtually nonexistent in the pmr LPS, whereas they accounted for 42% of all phosphates in wild-type LPS. In the lipid A of the pmr strains, the 4′-phosphate was to a significant degree (35%) substituted by l -Ara_p4N, whereas in the wild-type LPS the l -Ara_pN was absent. In the pmr lipid A₁ 2-aminoethanol was completely substituting the glycosidic pyrophosphate but not the glycosidic monophosphate, forming a diphosphate diester linkage at this position in 40% of lipid A molecules. In the wild-type LPS the glycosidic position of lipid A carried mostly unsubstituted monophosphate and pyrophosphate. Thus the polymyxin resistance was shown to be associated, along with the esterification of the lipid A 4′-monophosphate by aminoarabinose, with extensive esterification of diphosphates in LPS by 2-aminoethanol.     

A Novel Fibrosis Index Comprising a Non-Cholesterol Sterol Accurately Predicts HCV-Related Liver Cirrhosis

Diagnosis of liver cirrhosis is essential in the management of chronic hepatitis C virus (HCV) infection. Liver biopsy is invasive and thus entails a risk of complications as well as a potential risk of sampling error. Therefore, non-invasive diagnostic tools are preferential. The aim of the present study was to create a model for accurate prediction of liver cirrhosis based on patient characteristics and biomarkers of liver fibrosis, including a panel of non-cholesterol sterols reflecting cholesterol synthesis and absorption and secretion. We evaluated variables with potential predictive significance for liver fibrosis in 278 patients originally included in a multicenter phase III treatment trial for chronic HCV infection. A stepwise multivariate logistic model selection was performed with liver cirrhosis, defined as Ishak fibrosis stage 5–6, as the outcome variable. A new index, referred to as Nordic Liver Index (NoLI) in the paper, was based on the model: Log-odds (predicting cirrhosis) = −12.17+ (age×0.11) + (BMI (kg/m²)×0.23) + (D₇-lathosterol (μg/100 mg cholesterol)×(−0.013)) + (Platelet count (x10⁹/L)×(−0.018)) + (Prothrombin-INR×3.69). The area under the ROC curve (AUROC) for prediction of cirrhosis was 0.91 (95% CI 0.86–0.96). The index was validated in a separate cohort of 83 patients and the AUROC for this cohort was similar (0.90; 95% CI: 0.82–0.98). In conclusion, the new index may complement other methods in diagnosing cirrhosis in patients with chronic HCV infection.     

Acidification affects the perch,Perca fluviatilis,populations in small lakes,of southern Finland

Synopsis Characteristics of perch were studied in 4 recently acidified lakes in southern Finland. The densities of the populations were 0–250 ha^–1 compared with 1400–3300 ha^–1 in two circumneutral reference lakes. The perch were close to extinction in one acidic lake and dominated by 7 year old fish in two other acidic lakes, suggesting decreased reproduction. Individual fecundity was not reduced by the acidity, but high mortality (close to 100%) of eggs in two acidic lakes indicated recruitment failure. In one of the acidified lakes reproduction had continued resulting in a population dominated by younger fish. However, increased egg mortality, low density, and the resulting high growth rate of perch in this lake were considered to be consequences of the acidity. These findings are the first documentation on the possible decrease of fish populations in Finland due to acid precipitation.     

Endogenous IL-17 as a mediator of neutrophil recruitment caused by endotoxin exposure in mouse airways

We have previously demonstrated that administration of the recently described cytokine IL-17 in rat airways in vivo recruits and activates neutrophils locally. In the current study, we examined whether endogenous IL-17 is involved in mediating neutrophil recruitment caused by endotoxin exposure in mouse airways. Our in vivo data show that local endotoxin exposure causes the release of free, soluble IL-17 protein 6 h later. Systemic pretreatment with a neutralizing anti-IL-17 Ab almost completely inhibits neutrophil recruitment 24 h, but not 6 h, after endotoxin exposure in the airways. Pretreatment with neutralizing anti-IL-6 and anti-macrophage inflammatory protein (MIP)-2 Abs inhibits neutrophil recruitment caused by local endotoxin exposure and IL-17, respectively. Our in vitro data show that endotoxin exposure stimulates the release of soluble IL-17 protein in T lymphocytes harvested from lung and spleen, respectively, and that this cytokine release requires coculture with airway macrophages. Intracellular IL-17 protein is detected in T lymphocytes from spleen but not in airway macrophages after coculture and stimulation of these two cell types. Finally, anti-IL-17 does not alter endotoxin-induced release of IL-6 and MIP-2 from T lymphocytes and airway macrophages in coculture. In conclusion, our results indicate that endotoxin exposure causes the release of IL-17 from T lymphocytes and that this cytokine release requires the presence of macrophages. Once released, endogenous IL-17 acts in part by inducing local release of neutrophil-mobilizing cytokines such as IL-6 and MIP-2, from nonlymphocyte, nonmacrophage cells, and this contributes to recruitment of neutrophils in the airways. These IL-17-related mechanisms constitute potential targets for pharmacotherapy against exaggerated neutrophil recruitment in airway disease.     

Soluble IL-1RII and IL-18 are associated with incipient upper extremity soft tissue disorders

Previous studies suggest a role for IL-1β in the pathophysiology of upper extremity soft tissue disorders (UESTDs). We studied the levels of interleukin-1 family members in patients with incipient UESTDs and compared them with healthy controls. In this case control study, we included 163 patients with UESTDs and symptom duration shorter than 1 month and 42 healthy controls matched for age and gender at the group level. Serum levels of cytokines IL-1α, IL-1β, IL-1Ra, IL-6, IL-8, IL-18, IL-33, TNFα and sensitized C-reactive protein as well as IL-1 family soluble receptors sIL-1RII and sST2 were assessed. We used unconditional logistic regression models to study the associations between cytokines and UESTDs. After adjustment for potential confounders, the serum levels of sIL-1RII (p<0.001) and sST2 (p=0.014) were higher in the patients than the controls. The level of IL-18 was lower in the patients than the controls (p=0.005). There were no significant differences between the patients and controls regarding the levels of IL-1α, IL-1β, IL-1Ra, IL-33, IL-6, IL-8, TNFα, or sensitized C-reactive protein. The levels of circulating sIL-1RII and IL-18 are associated with incipient UESTDs, suggesting an important role for these IL-1 family members in the early course of UESTDs.     

Chemical anoxia delays germ cell apoptosis in the human testis

An understanding of testicular physiology and pathology requires knowledge of the regulation of cell death. Previous observation of suppression of apoptosis by hypoxia suggested a role for ATP in germ cell death. However, the exact effects of ATP production on germ cell death and of apoptosis on the levels of ATP and other adenine nucleotides (ANs) have remained unclear. We investigated the levels of ANs during human testicular apoptosis (analyzed by HPLC) and the role of chemical anoxia in germ cell death (detected by Southern blot analysis of DNA fragmentation, in situ end labeling of DNA, and electron microscopy). Incubation of seminiferous tubule segments under serum-free conditions induced apoptosis and concomitantly decreased the levels of ANs. Chemical anoxia, induced with potassium cyanide (KCN), an inhibitor of mitochondrial respiration, dropped ATP levels further and suppressed apoptosis at 4 h. After 24 h, many of the testicular cells underwent delayed apoptosis despite ATP depletion. Some cells showed signs of necrosis or toxicity. The addition of 2-deoxyglucose, an antimetabolite of glycolysis, did not alter the results obtained with KCN alone, whereas a toxic concentration of hydrogen peroxide switched apoptosis to necrosis. In most of the testicular cells, mitochondrial respiration appears to play a crucial role in controlling primary cell death cascades. In the human testis, there seem to be secondary apoptotic pathways that do not require functional respiration (or ATP).     

Population responses of perch (Perca fluviatilis) and roach (Rutilus rutilus) to recovery from acidification in small Finnish lakes

Decreasing trends in atmospheric emissions and acidic deposition during the 1990s have resulted in chemical recovery from acidification in the sensitive surface water systems of southern Finland. Responses of perch and roach populations to the improved water quality were studied in 30 small lakes with the aid of water chemistry monitoring data gathered in 1987–2002 and the data collected from two consecutive periods of gillnet test fishing, 1985–1988 and 2001–2002. In the most acidified lakes, alkalinity and ANC have increased and sulphate and labile aluminium concentrations decreasæed markedly. The response of perch populations to the improved water quality is seen in improved reproduction success, indicated by a higher CPUE in numbers and a lower mean weight. The growth rate of perch has declined as the population density has increased. Roach populations have not recovered in the same way as perch, there being no major changes in NPUE or mean weight. Lower growth rates were, however, observed in the roach populations of all study lakes. The increased perch population density as an obstacle to the recovery of roach populations is discussed. Despite the chemical and biological recovery of the study lakes, the buffer capacity of many headwater lakes is low and the lakes will be sensitive to any increases in acidic deposition in the future.     

Function-valued adaptive dynamics and the calculus of variations

Adaptive dynamics has been widely used to study the evolution of scalar-valued, and occasionally vector-valued, strategies in ecologically realistic models. In many ecological situations, however, evolving strategies are best described as function-valued, and thus infinite-dimensional, traits. So far, such evolution has only been studied sporadically, mostly based on quantitative genetics models with limited ecological realism. In this article we show how to apply the calculus of variations to find evolutionarily singular strategies of function-valued adaptive dynamics: such a strategy has to satisfy Euler's equation with environmental feedback. We also demonstrate how second-order derivatives can be used to investigate whether or not a function-valued singular strategy is evolutionarily stable. We illustrate our approach by presenting several worked examples.     

Correcting errors in shotgun sequences

Sequencing errors in combination with repeated regions cause major problems in shotgun sequencing, mainly due to the failure of assembly programs to distinguish single base differences between repeat copies from erroneous base calls. In this paper, a new strategy designed to correct errors in shotgun sequence data using defined nucleotide positions, DNPs, is presented. The method distinguishes single base differences from sequencing errors by analyzing multiple alignments consisting of a read and all its overlaps with other reads. The construction of multiple alignments is performed using a novel pattern matching algorithm, which takes advantage of the symmetry between indices that can be computed for similar words of the same length. This allows for rapid construction of multiple alignments, with no previous pair-wise matching of sequence reads required. Results from a C++ implementation of this method show that up to 99% of sequencing errors can be corrected, while up to 87% of the single base differences remain and up to 80% of the corrected reads contain at most one error. The results also show that the method outperforms the error correction method used in the EULER assembler. The prototype software, MisEd, is freely available from the authors for academic use.