Genome sequence of the edible cyanobacterium Arthrospira sp. PCC 8005.

We determined the genome sequence of Arthrospira sp. PCC 8005, a cyanobacterial strain of great interest to the European Space Agency for its nutritive value and oxygenic properties in the Micro-Ecological Life Support System Alternative (MELiSSA) biological life support system for long-term manned missions into space.

The surgical treatment of stage III empyema: the effect on lung function.

AIM: The aim of this study was to evaluate the surgical treatment of stage III empyema. METHODS: Between 2002 and 2005, 30 patients underwent surgery for treatment of diagnosed stage III empyema preoperatively. Patients were referred for spirometry to evaluate lung function postoperatively. RESULTS: Twenty nine patients underwent primary thoracotomy because of an extended stage III empyema, 1 patient video-assisted thoracoscopic surgery (VATS). Mean age was 62 years. Mean period from onset of symptoms until hospital admission was 29 days and mean time interval between admission and surgery was 11 days. Intraoperative complication happened in one patient (3%), in whom a phrenic nerve lesion was diagnosed. Overall mortality rate was 3%. In 17 patients postoperative spirometry was performed, showing normal vital capacity in 59% of the patients. CONCLUSION: There was no reluctance in performing primary thoracotomy in our population with a stage III empyema. Decortication by means of thoracotomy restored the complete expansion of the lung; the authors claim that vital capacity returned to normal values, as it was shown by the spirometry results postoperatively. Early referral to the respiratory department in case of a non-responding pneumonia and early surgical consultation in case of a parapneumonic effusion, will prevent progression to an extensive organized stage III empyema requiring decortication by thoracotomy.

Strain-specific genes of Helicobacter pylori: distribution, function and dynamics.

Whole-genome clustering of the two available genome sequences of Helicobacter pylori strains 26695 and J99 allows the detection of 110 and 52 strain-specific genes, respectively. This set of strain-specific genes was compared with the sets obtained with other computational approaches of direct genome comparison as well as experimental data from microarray analysis. A considerable number of novel function assignments is possible using database-driven sequence annotation, although the function of the majority of the identified genes remains unknown. Using whole-genome clustering, it is also possible to detect species-specific genes by comparing the two H.pylori strains against the genome sequence of Campylobacter jejuni. It is interesting that the majority of strain-specific genes appear to be species specific. Finally, we introduce a novel approach to gene position analysis by employing measures from directional statistics. We show that although the two strains exhibit differences with respect to strain-specific gene distributions, this is due to the extensive genome rearrangements. If these are taken into account, a common pattern for the genome dynamics of the two Helicobacter strains emerges, suggestive of certain spatial constraints that may act as control mechanisms of gene flux.

The product of the NF2 tumour suppressor gene localizes near the plasma membrane and is highly expressed in muscle cells.

Neurofibromatosis type 2 (NF2) is a disease resulting in the formation of schwannomas of the eighth cranial nerve, and other central nervous system tumours. A tumour suppressor gene has been found to be responsible for this disorder. The 595 amino acid NF2 protein shows a great deal of homology to a superfamily of membrane organizing proteins. To generate antibodies against the NF2 protein four synthetic peptides (SP) were injected in rabbits. COS cells transfected with an NF2 cDNA construct in an expression vector were used for immunocytochemical staining experiments; lysates of transfected COS cells were used for Western blotting experiments, as were lysates of E. coli cultures transformed with an NF2 cDNA construct subcloned in a prokaryotic expression vector. In western blots all sera detected a band indicating the appropriate molecular weight in lysates of transfected COS cells and E. coli. Immunocytochemical staining experiments indicate that the NF2 protein localizes in or near the cell membrane. Immunohistochemical staining of human tissue sections demonstrated the presence of the NF2 protein in muscle-, and Schwann cells. These results support the hypothesis that the NF2 protein functions as a membrane organizing element.

Studies on Clostridium acetobutylicum ginA promoters and antisense RNA.

The Clostridium acetobutylicum glnA gene has two transcript start sites under the control of promoters P1 and p2 . Initiation of transcription was regulated by nitrogen and a downstream region was implicated in the regulation of transcript initiation by nitrogen in Escherichia coli. Putative antisense RNA was produced from a single downstream transcript start site under the control of P3. An up-promoter mutation in P3 resulted in lower levels of glutamine synthetase (GS) activity. Putative antisense RNA had a role in down-regulating GS expression but was not involved in regulation by nitrogen. Deletion of downstream inverted repeat sequences resulted in very low levels of GS activity.

Immunohistochemical detection of the androgen receptor with monoclonal antibody F39.4 in routinely processed, paraffin-embedded human tissues after microwave pre-treatment.

We describe the immunohistochemical detection of the human androgen receptor (AR) in routinely processed, paraffin-embedded tissue with the monoclonal antibody (MAb) F39.4. Deparaffinized sections were heated in a microwave oven for antigen retrieval. A panel of human male- and female-derived tissues was investigated. We observed a nuclear staining pattern consistent with previous results on frozen sections. Moreover, we studied the possibility of detecting AR in prolonged formalin-fixed tissue and in paraffin-embedded archival material. After prolonged fixation times or long-term storage of paraffin-embedded tissue, the staining intensity for the AR did not deteriorate. Blocking experiments with the specific synthetic peptides demonstrated the specificity of this technique. We conclude that this method is specific, allows retrospective AR studies, and offers optimally preserved morphology.

Mechanisms contributing to the differential haemodynamic effects of bombesin and cholecystokinin in conscious, Long Evans rats.

1. Long Evans rats were chronically instrumented with intravascular catheters and pulsed Doppler probes to assess changes in renal, mesenteric and hindquarters blood flows and vascular conductances in response to bombesin (2.5 micrograms kg-1, i.v.) and cholecystokinin (CCK) (0.5 and 5.0 micrograms kg-1, i.v.). 2. Bombesin caused an increase in heart rate and blood pressure, together with a transient renal vasoconstriction and prolonged mesenteric vasodilatation; there was an early hindquarters vasodilatation followed by vasoconstriction. 3. In the presence of phentolamine, bombesin caused a fall in blood pressure due to enhanced hindquarters vasodilatation; these effects were reversed by propranolol and hence were possibly due to circulating adrenaline acting on vasodilator beta 2-adrenoceptors. 4. During concurrent administration of phentolamine, propranolol and atropine, bombesin caused prolonged tachycardia and a rise in blood pressure. The renal vasoconstrictor and mesenteric vasodilator effects of bombesin were not reduced under these conditions and thus probably were direct and/or indirect non-adrenergic, non-cholinergic (NANC) effects. 5. CCK caused dose-dependent increases in blood pressure accompanied by renal, mesenteric and hindquarters vasoconstriction followed, after the higher dose, by vasodilatations. The lower dose of CCK increased heart rate but there was a bradycardia followed by a tachycardia after the higher dose. 6. Experiments with antagonists as described above indicated the pressor effect of CCK was mediated largely through alpha-adrenoceptors, as were the mesenteric and hindquarters vasoconstrictor effects; CCK exerted NANC negative chronotropic effects. 7. All the effects of CCK were markedly inhibited by L364,718. This observation, and the finding that L364,718 had no effect on the responses to bombesin, together with the dissimilarities in the regional haemodynamic effects of exogenous CCK and bombesin, indicate that the cardiovascular actions of the latter were not dependent on the release of endogenous CCK.

Universal Linkage System: versatile nucleic acid labeling technique.

Over the last two decades nonradioactive nucleic acid labeling and detection systems have overcome the safety, disposal, stability and cost problems that are associated with radioactive techniques. Besides traditional, enzyme-mediated, nonradioactive labeling methods (e.g., random priming, nick translation or labeling by PCR), several chemical labeling systems have been developed (e.g., ULS, psoralen, alkylating agents). These methods provide fluorescent (or hapten) labeled probes for fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH) and microarray-based techniques. In this review the DNA-based molecular diagnostic applications and perspectives of the Universal Linkage System (ULS) technology will be described.

Aspartame: review of recent experimental and observational data.

In this report the neurotoxicity of aspartame and its constituent amino acids aspartic acid and phenylalanine is reviewed. The adverse reactions ascribed to the consumption of aspartame-containing products, as reported in the U.S.A., are discussed and placed in perspective with the results of recent behavioural studies in humans and animals. The issue of common intake levels associated with proposed uses of aspartame is addressed. In brief, the following conclusions can be drawn: When aspartame is consumed at levels within the ADI-limit of 40 mg/kg body wt, there is no significant risk for an aspartate-induced neurotoxic effect in the brain. When aspartame is consumed at levels within the ADI-limit by normal subjects or persons heterozygous for phenylketonuria (PKU) the resultant plasma phenylalanine concentrations are practically always within the normal postprandial range; elevation to plasma concentrations commonly associated with adverse effects has not been observed. Persons suffering from phenylketonuria (PKU-homozygotes) on a phenylalanine-restricted diet should avoid consumption of aspartame. PKU-homozygotes on the (less strict) phenylalanine-liberalized diet should be made aware of the phenylalanine content of aspartame. In the available behavioural studies in humans with acute dosing, no adverse effects were observed. Long-term studies on behaviour and cognitive function in (sensitive) humans are lacking. Analyses of adverse reaction reports made by consumers in the U.S.A. have not yielded a specific constellation of symptoms clearly related to aspartame that would suggest a widespread public health hazard associated with aspartame use. Focussed clinical studies are now being carried out in the U.S.A.; the results should provide additional evidence concerning the interpretation of the reports on adverse reactions ascribed to aspartame. In the regulation of admitted uses for aspartame the possibility of intake levels exceeding the ADI-limit in some groups of consumers should be a point of attention.

Toxicology of gallates: a review and evaluation.

The propyl, octyl and dodecyl esters of gallic acid have been studied extensively in a large number of animal experiments involving oral dosing. Experimental data on general toxicity and studies on reproduction, teratogenicity and mutagenicity are also available. Most of the key toxicity studies, however, date back to the 1950s, do not meet current standards of toxicity testing and do not provide evidence for carcinogenic or mutagenic action of the gallates. Mutagenicity studies with octyl gallate and dodecyl gallate are lacking. The biokinetics of propyl gallate apparently differ from those of octyl and dodecyl gallate, the octyl and dodecyl esters being absorbed and hydrolysed to a lesser degree than the propyl ester. In toxicity studies with propyl gallate, growth retardation, anaemia, kidney and liver changes and hyperplasia of the forestomach were the most prominent effects at dose levels above 10,000 mg/kg feed. At 5000 mg/kg feed, liver enzyme induction was seen. In the available studies with octyl gallate or dodecyl gallate as the test compound, effects were found at 3000 mg/kg feed or higher levels. In studies performed with the various gallates, no effects were observed at a dose level of 1000 mg/kg feed, a level that was adopted as the no-effect level by the FAO/WHO Joint Expert Committee on Food Additives (JECFA) in 1976. This committee established an acceptable daily intake (ADI) for man of 0.2 mg/kg body weight (as a sum of propyl, octyl and dodecyl gallates). A re-evaluation of the toxicity of gallates indicates that a 'classic' long-term toxicity study of propyl gallate meeting current standards is required. As yet, the available toxicological evidence indicates that gallates may be used safely as antioxidants.

The relationship between education and ethical behavior of nursing students.

Based on the cognitive theory of moral development of Kohlberg, refined by the addition of the dimension "ethics of care" and the educational theory of Janssen, the relationship of education and ethical behavior of nursing students was examined. Ethical behavior referred not only to the ethical reasoning of students but also to the relationship between this reasoning and their behavior. This study examined the responses of 2,624 nursing students to five ethical nursing dilemmas included in the Ethical Behavior Test by relating them to four educational variables: students' level of education, level of enrollment, school, and students' perceptions of the educational process. A significant relationship between education and ethical behavior was found.

State of the art of contaminated site management in The Netherlands: policy framework and risk assessment tools.

This paper presents the policy framework of contaminated site management in The Netherlands and the corresponding risk assessment tools, including innovations that have taken place since an overview was published in 1999. According to the Dutch Soil Protection Act assessment framework, soils are subdivided into three quality classes: clean, slightly contaminated and seriously contaminated. Historic cases of slightly contaminated soils are managed in a sustainable way by re-use of soil material within a region on the basis of risk-based and land use specific Maximal Values and Background Values. In case of serious soil contamination remediation is in principle necessary and the urgency of remediation has to be determined based on site-specific risks for human health, the ecosystem and groundwater. The major risk assessment tools in The Netherlands are the CSOIL exposure model (human health risks and food safety), Species Sensitivity Distributions and the Soil Quality Triad (ecological risks), along with a procedure to assess the risks due to contaminant spreading to and in the groundwater. Following the principle 'simple if possible, complex when necessary', tiered approaches are used. Contaminated site practices are supported with web-based decision support systems.

Coexistence of tight and loose bundled states in a model of bacterial flagellar dynamics.

Many microorganisms propel themselves through their fluid environment by means of multiple rotating flagella that self-organize to form bundles, a process that is complex and poorly understood. In the present work, the bundling behavior of a pair of flexible flagella, each driven by a constant torque motor, is investigated, using a mathematical model incorporating the fluid motion generated by each flagellum as well as the finite flexibility of the flagella. The initial stage of bundling is driven purely by hydrodynamics but the final state of the bundle is determined by a nontrivial balance between hydrodynamics and elasticity. As the flexibility of the flagella increases a regime is found where, depending on initial conditions, one finds bundles that are either tight, with the flagella in mechanical contact, or loose, with the flagella intertwined but not touching. That is, multiple coexisting states of bundling are found. The parameter regime (in terms of flexibility and distance between motors) at which this multiplicity occurs is comparable to the parameters for a number of bacteria.

A simple method of diverting anaesthetic waste gases and vapours from the Engström ECS-2000 ventilator.

A simple method of diverting anaesthetic waste gases from the Engström ECS-2000 ventilator is described. Unless special precautions are taken the digital volume measurement may be influenced; the simple solution of this problem is given.

Sites required for GltC-dependent regulation of Bacillus subtilis glutamate synthase expression.

The Bacillus subtilis gltAB genes, coding for the two subunits of glutamate synthase, are transcribed divergently from the gltC gene, encoding a LysR-type transcriptional activator of gltAB. The predicted gltA and gltC transcription start sites are separated by 51 to 52 bp. A 15-bp, consensus binding site (Box I) for LysR-type proteins was found centered at position -64 with respect to the gltA transcription start. This site was shown by mutational analysis to be required both for GltC-mediated activation of gltA and for autorepression of gltC. Box II, which is similar to Box I, is centered 22 bp downstream of Box I and overlaps the -35 region of the gltA promoter. Box II was found to be essential for activation of gltA but not for gltC autoregulation. Introduction of approximately one additional helical turn of DNA between Box I and Box II enhanced gltA expression 7- to 40-fold under nonactivating conditions and about 2-fold under activating conditions. Expression of gltA was dramatically decreased when the distance between Box I and Box II was altered by a nonintegral number of helical turns of DNA. gltC autorepression was abolished by most of the inserts between Box I and Box II but was augmented by adding one helical turn.

Studies on Clostridium acetobutylicum glnA promoters and antisense RNA.

The Clostridium acetobutylicum glnA gene has two transcript start sites under the control of promoters p1 and p2. Initiation of transcription was regulated by nitrogen and a downstream region was implicated in the regulation of transcript initiation by nitrogen in Escherichia coli. Putative antisense RNA was produced from a single downstream transcript start site under the control of p3. An up-promoter mutation in p3 resulted in lower levels of glutamine synthetase (GS) activity. Putative antisense RNA had a role in down-regulating GS expression but was not involved in regulation by nitrogen. Deletion of downstream inverted repeat sequences resulted in very low levels of GS activity.

Molecular analysis and regulation of the glnA gene of the gram-positive anaerobe Clostridium acetobutylicum.

The nucleotide sequence of a 2.0-kilobase DNA segment containing the Clostridium acetobutylicum glnA gene was determined. The upstream region of the glnA gene contained two putative extended promoter consensus sequences (p1 and p2), characteristic of gram-positive bacteria. A third putative extended gram-positive promoter consensus sequence (p3), oriented towards the glnA gene, was detected downstream of the structural gene. The sequences containing the proposed promoter regions p1 and p2 or p3 were shown to have promoter activity by subcloning into promoter probe vectors. The complete amino acid sequence (444 residues) of the C. acetobutylicum glutamine synthetase (GS) was deduced, and comparisons were made with the reported amino acid sequences of GS from other organisms. To determine whether the putative promoter p3 and a downstream region with an extensive stretch of inverted repeat sequences were involved in regulation of C. acetobutylicum glnA gene expression by nitrogen in Escherichia coli, deletion plasmids were constructed lacking p3 and various downstream sequences. Deletion of the putative promoter p3 and downstream inverted repeat sequences affected the regulation of GS and reduced the levels of GS approximately fivefold under nitrogen-limiting conditions but did not affect the repression of GS levels in cells grown under nitrogen-excess conditions.