The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments

Desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is able to grow at in situ temperatures below 0 degrees C. As abundant members of the microbial community in permanently cold marine sediments, D. psychrophila-like bacteria contribute to the global cycles of carbon and sulfur. Here, we describe the genome sequence of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 663 bp. Analysis of the genome gave insight into the metabolic properties of the organism, e.g. the presence of TRAP-T systems as a major route for the uptake of C(4)-dicarboxylates, the unexpected presence of genes from the TCA cycle, a TAT secretion system, the lack of a beta-oxidation complex and typical Desulfovibrio cytochromes, such as c(553), c(3) and ncc. D. psychrophila encodes more than 30 two-component regulatory systems, including a new Ntr subcluster of hybrid kinases, nine putative cold shock proteins and nine potentially cold shock-inducible proteins. A comparison of D. psychrophila's genome features with those of the only other published genome from a sulfate reducer, the hyperthermophilic archaeon Archaeoglobus fulgidus, revealed many striking differences, but only a few shared features.

Erregerdetektion und -identifikation bei einem Hirnabszess durch molekulargenetische Methoden

Brain abscesses are life-threatening and detection and identification of the causative pathogens are crucial for substantiating the diagnosis and for selecting the optimal antibiotic regimen. In approximately 20% of the patients microbiological cultures of abscess material remain sterile. The polymerase chain reaction (PCR) provides a methodological alternative, but data about the use of broad spectrum PCR assays to detect the causative pathogens in brain abscesses are rare. We report on the case of a 65-years-old patient with a brain abscess caused by Fusobacterium spp., which was only diagnosed by broad spectrum PCR. To our knowledge this is the second report about a brain abscess, where Fusobacterium spp. was identified only by broad spectrum PCR and subsequent DNA sequencing.

Ocular melanoma is not associated with CDKN2A or MC1R variants--a population-based study

Germline variants in the melanocortin 1 receptor gene (MC1R) and the p16 gene (CDKN2A) are associated with an increased risk of cutaneous melanoma. The frequency of these germline variants was examined in a population-based, incident series of 62 ocular melanoma cases and ethnicity-matched population controls. In both cases and controls, 59% of individuals carried at least one MC1R variant and there were no significant differences in the frequency of any of the five most common variants of MC1R. We also found no significant differences between cases and controls in the frequency of any of the four most common variants of CDKN2A, and no melanoma case carried a deleterious germline CDKN2A mutation. Our findings argue against an important predisposing effect of the MC1R and CDKN2A genes for ocular melanoma.

The uninsured and Medicaid Oregon tobacco user experience in a real world, phone based cessation programme

OBJECTIVE

To describe the experience of uninsured and Medicaid Oregon tobacco users who registered in Free & Clear (F&C), a telephone based cessation programme including five scheduled outbound calls.

DESIGN AND SETTING

Using a retrospective cohort design, 1334 (423 uninsured, 806 Medicaid, and 105 commercially insured) Oregon tobacco users who registered in F&C between 18 November 1998 and 28 February 2000 were identified and followed for 12 months post-registration; 648 (48.6%) were successfully contacted at 12 months. Information was collected from the F&C database. Unconditional logistic regression, adjusted for race and education, was used.

RESULTS

The seven day quit rate at 12 months, assuming non-respondents were smokers, was 14.8% (95% confidence interval (CI) 13.0 to 16.9). This rate was significantly higher among commercially insured participants (v Medicaid but not uninsured) and among participants who completed > or = 5 calls (v < 5 calls). The quit rate for those contacted at 12 months was 30.6% (95% CI 27.0% to 34.3%) and varied, however not significantly, by insurance and number of calls. After adjustment, respondents who completed > or = 5 calls were 60% more likely to quit tobacco (odds ratio (OR) 1.6, 95% CI 0.9 to 3.1), and uninsured respondents who completed > or = 5 calls were 70% more likely to quit tobacco (OR 1.7, 95% CI 0.9 to 3.5), relative to those who completed < 5 calls, but the difference was not significant.

CONCLUSIONS

The quit rates are similar to those reported in efficacy trials. The observed variation in quitting tobacco for respondents by number of calls completed and by insurance merits further investigation concentrating on increasing compliance with the call schedule, particularly for the uninsured.

Experimental prostate epithelial morphogenesis in response to stroma and three-dimensional matrigel culture

To reproduce the structural and functional differentiation of human prostatic acini in vivo, prostatic epithelial and stromal cells derived from human primary cultures were cocultured in Matrigel. In the absence of stroma and serum, epithelial spheroids composed of solid masses of stratified and cuboidal cells formed. Outer cells of the spheroid expressed cytokeratins 1, 5, 10, and 14, whereas the inner cells expressed cytokeratin 18. The addition of 2% serum induced formation of a lumen surrounded by a layer of one or two cuboidal and columnar epithelial cells. The further addition of stromal cultures, dihydrotestosterone, and estrogen induced polarization of the epithelium and increased spheroid-forming efficiency. Epithelium expressed either cytokeratin 18 alone or additionally cytokeratins 1, 5, 14, and 10. All spheroid epithelium expressed prostate-specific antigen and prostate-specific membrane antigen. Androgen receptor was only detected in the presence of stroma, serum, and hormones. Thus, development of a functional and morphologically correct prostate gland in vitro is dependent on extracellular matrix, steroid hormones, and factors from stromal cells and serum.

From images to interactions: high-resolution phase imaging in tapping-mode atomic force microscopy

In tapping-mode atomic force microscopy, the phase shift between excitation and response of the cantilever is used as a material-dependent signal complementary to topography. The localization of information in the phase signal is demonstrated with 1.4-nm lateral resolution on purple membrane of Halobacterium salinarum in buffer solution. In a first-order approximation, the phase signal is found to correlate with modulations of the tip oscillation amplitude, induced by topography. Extending the analysis to contributions of the tip-sample interaction area as a second-order approximation, a method is proposed to extract information about the interaction from the phase signal for surfaces with a roughness in the order of the tip radius.

Prostate epithelial cell lines form spheroids with evidence of glandular differentiation in three-dimensional Matrigel cultures

Normal (PNT2-C2) and metastatic (PC-3) prostate cell lines were grown in Matrigel to observe the effects on morphology and phenotype in comparison to monolayer culture. In monolayer cultures, PNT2-C2 showed typical round/cuboidal epithelial morphology, with tight cell associations, whereas in Matrigel they formed smooth spheroids, tightly packed with cells. In both monolayer and Matrigel, PNT2-C2 had a differentiated luminal epithelial phenotype with high expression of cytokeratin 8, prostate specific antigen (PSA), prostate specific membrane antigen (PSMA), E-cadherin and desmoglein. In contrast, PC-3 cells possessed an epithelial/mesenchyme morphology in monolayer with loose cell to cell contact and pseudopodial extensions. Immunohistochemical phenotyping indicated the cells were undifferentiated, expressing high levels of vimentin, beta1 integrin, CD44 and low expression of cytokeratin 8. In Matrigel they formed smooth and irregular spheroids, which had a lumen surrounded by a single cell layer. Matrigel also influenced the expression of PSA, PSMA and CD44. These results indicate that Matrigel culture can induce morphological differentiation of prostate cancer cells which initially had a basal phenotype.

Functional T lymphocytes infiltrate implanted polyvinyl alcohol foams during surgical wound closure therapy

Vacuum-assisted closure involving the implantation of polyvinyl alcohol foam is a technique recently developed for the treatment of patients suffering from either wound infection or chronic wounds. This method has been shown to improve and accelerate wound healing. However, little is known about the cell populations that infiltrate the foam, and their potential role in resolving the infection and promoting granulation tissue formation. Our study demonstrates that wound-implanted foams are mainly infiltrated with granulocytes, but that mononuclear cells, including macrophages and minor populations of T, B and natural killer lymphocytes, are also present. We show that foam-infiltrating T cells, especially CD4(+) T cells, constitute a phenotypically and functionally heterogeneous population influenced by wound-infecting bacteria. Thus, T lymphocytes could play a role in wound cleansing. In addition, our data indicate that implanted polyvinyl alcohol foams might be suitable microenvironments for manipulating T cell-mediated immune responses in patients.

Reduction potential of microbial, odour and ammonia emissions from a pig facility by biofilters

The intention of this study was the determination of the potential to reduce specific microbial bioaerosol (cultivable bacteria and fungi, total cell counts of microbes, airborne endotoxins and microbial volatile organic compounds, MVOC), odour and ammonia emissions from a pig facility by biofilters. Five identical biofilter units in half technical scale were filled with different filter materials (Biochips, coconut-peat, wood-bark, pellets + bark and compost) and connected in parallel to a piggery. The results showed obvious differences between the filter materials. Numbers of airborne cultivable bacteria were decreased by ca. 70 to 95% and the total counts of bacterial cells from ca. 25 to (>) 90%. The total amount of fungal cells was reduced by at least 60%, although the percentage of cultivable moulds in the air after passing the filters was sometimes higher than before. Airborne endotoxins and MVOC were effectively reduced by all filter materials to at least 90%. Regarding odour, the average reduction was between 40 and 83%, whereas only one of the filters proved to be capable of slightly reducing the ammonia emissions. No relationships between odour/ammonia and microbial bioaerosols with regard to the reduction efficiency of the different filter materials or the total load of the emitted air could be established. A tendency could be shown, that biofilters best capable to reduce odour emitted slightly more airborne bacteria, both cultivable and total cell counts.

The Edinburgh Mouse Atlas: using the CD

This paper provides a simple introduction to the reconstructions and data-handling tools stored on the Edinburgh Mouse Atlas CD, together with some of the ways in which the viewers and software can be used to understand mouse development and analyse data. The key aspect of the Mouse Atlas is that the underlying models are a complete representation of the histology, which has not been constrained to a particular interpretation. This means, for example, that the current anatomy domains can be further subdivided as required to any resolution up to the resolution of the models (2-7 microm). In the CD of the early embryos described here, virtually all tissues that can be usefully distinguished either by the histology or morphologically have been delineated.

Peptide repertoire of human cerebrospinal fluid: novel proteolytic fragments of neuroendocrine proteins

Polypeptides in human cerebrospinal fluid (CSF), isolated by phase separation in chloroform-methanol-water and reversed-phase HPLC, were characterised by sequence analysis and mass spectrometry. This identified the presence of peptide fragments of testican, neuroendocrine specific protein VGF, neuroendocrine protein 7B2, chromogranin B/secretogranin I, chromogranin A, osteopontin, IGF-II E-peptide and proenkephalin. The majority of these fragments were generated by proteolysis at dibasic sites, suggesting that they are derived by activities related to prohormone convertase(s). Several of the fragments have previously not been detected, and their functions in CSF or elsewhere are unknown. A characteristic feature of all these fragments is a very high content of acidic residues, in particular glutamic acid. In addition to the fragments of neuroendocrine proteins, endothelin-binding receptor-like protein 2, ribonuclease 1, IGF-binding protein 6, albumin, alpha1-acid glycoprotein 1, prostaglandin-H2 D-isomerase, apolipoprotein A1, transthyretin, beta2-microglobulin, ubiquitin, fibrinopeptide A, and C4A anaphylatoxin were found.

Comparison of apraxia in corticobasal degeneration and progressive supranuclear palsy

OBJECTIVE

To describe ideomotor apraxia in patients with corticobasal degeneration and those with progressive supranuclear palsy, two parkinsonian disorders that are often misdiagnosed due to the overlap in their clinical features, and to determine whether systematic apraxia testing is useful for differential diagnosis.

METHODS

Fourteen patients fulfilling National Institute of Neurological Disorders and Stroke-Society for Progressive Supranuclear Palsy clinical criteria for progressive supranuclear palsy, 13 patients fulfilling modified Lang criteria for corticobasal degeneration, and 12 normal healthy control subjects were given the Test of Oral and Limb Apraxia, which was scored according to the Florida Apraxia Battery for occurrence of various types of apraxic errors.

RESULTS

Both patients with progressive supranuclear palsy and corticobasal degeneration committed a greater number of apraxic errors than normal healthy control subjects on both transitive and intransitive tasks (p < 0.001 in both cases), but apraxia was much more severe in patients with corticobasal degeneration than progressive supranuclear palsy (p < 0.001). The index of apraxia severity, in combination with the assessment of the two key features of progressive supranuclear palsy (falls and vertical gaze palsy), correctly classified all patients.

CONCLUSIONS

Patients with corticobasal degeneration show more severe ideomotor apraxia than patients with progressive supranuclear palsy, and systematic assessment of ideomotor apraxia facilitates the differential diagnosis between patients with progressive supranuclear palsy and those with corticobasal degeneration.

Morphoea is neither associated with features of Borrelia burgdorferi infection, nor is this agent detectable in lesional skin by polymerase chain reaction

BACKGROUND

The aetiology of morphoea is still unknown. Borrelia burgdorferi as a causative agent of morphoea has been discussed since 1985, but the relationship remains uncertain.

OBJECTIVES

We aimed to find evidence for infection with B. burgdorferi by combined evaluation of different clinical and laboratory data in a group of 54 patients with morphoea.

METHODS

In each patient, an evaluation of the case history was performed with regard to infection with B. burgdorferi, using a standardized questionnaire. Questions focused on previous tick bites and skin changes suspicious for erythema migrans (EM). The case history data of 52 patients were compared with those of 104 matched control subjects and of 25 patients with acrodermatitis chronica atrophicans (ACA). Serological examinations were performed in 53 patients with morphoea. Furthermore, lesional skin was examined for borrelial DNA in 33 patients, using nested polymerase chain reaction (PCR) for the ospA and the borrelial rRNA gene.

RESULTS

Results of the questionnaire showed no differences between patients with morphoea and matched controls. In contrast, patients with ACA showed a much higher prevalence of tick bites and skin changes suspicious for EM as compared with patients with morphoea. Serological examination was positive in only one patient with morphoea alone and in two additional patients with coexistent ACA. No borrelial DNA was detected by PCR in lesional skin of 33 patients with morphoea.

CONCLUSIONS

No evidence was found for B. burgdorferi infection in patients with morphoea.

Pin1-dependent prolyl isomerization regulates dephosphorylation of Cdc25C and tau proteins

The reversible protein phosphorylation on serine or threonine residues that precede proline (pSer/Thr-Pro) is a key signaling mechanism for the control of various cellular processes, including cell division. The pSer/Thr-Pro moiety in peptides exists in the two completely distinct cis and trans conformations whose conversion is catalyzed specifically by the essential prolyl isomerase Pin1. Previous results suggest that Pin1 might regulate the conformation and dephosphorylation of its substrates. However, it is not known whether phosphorylation-dependent prolyl isomerization occurs in a native protein and/or affects dephosphorylation of pSer/Thr-Pro motifs. Here we show that the major Pro-directed phosphatase PP2A is conformation-specific and effectively dephosphorylates only the trans pSer/Thr-Pro isomer. Furthermore, Pin1 catalyzes prolyl isomerization of specific pSer/Thr-Pro motifs both in Cdc25C and tau to facilitate their dephosphorylation by PP2A. Moreover, Pin1 and PP2A show reciprocal genetic interactions, and prolyl isomerase activity of Pin1 is essential for cell division in vivo. Thus, phosphorylation-specific prolyl isomerization catalyzed by Pin1 is a novel mechanism essential for regulating dephosphorylation of certain pSer/Thr-Pro motifs.

Lipopeptide preparation and analysis

Lipophilic peptides and proteins present specific problems during preparation and analysis which require the use of modified methodology. This chapter discusses some of the methods that have been employed in the isolation and structural studies of the pulmonary surfactant-associated proteins B and C (SP-B and SP-C), other proteins with lipid-like physicochemical properties, and the SP-B precursor. In particular, methods for separation and analysis of peptide/lipid mixtures, high-resolution separation of lipopeptides, analysis of fatty acylated peptides, and secondary and tertiary structure analysis of lipopeptides are discussed.

[Placenta accreta with placenta previa after previous cesarean sections--a growing danger in modern obstetrics]

The increased rate of cesarean sections in recent decades has brought with it an increase in the frequency of placenta accreta. There are direct correlations between previous cesarean deliveries and also maternal age, with the risk of placenta accreta. There is also a direct correlation between placenta accreta and placenta previa. The risk of placenta accreta in women who have had placenta previa is 2% for those younger than 35 years and with no history of uterine surgery. The risk increases to 39% for those over 35 who have had 2 or more cesarean sections. We present 3 cases of placenta accreta admitted in 15 months, all of whom had a history of cesarean sections. The frequency of placenta accreta in our hospital is 1:1,579 deliveries, in line with the 1:1,420 in the literature. We consider hysterectomy the treatment of choice for this serious complication. When performing a cesarean in cases of placenta previa with a history of cesarean sections, the possibility of placenta accreta should be considered.

HIV infection and patterns of risk among women drug injectors and crack users in low and high sero-prevalence sites

As AIDS cases among US women continue to increase, a better understanding of women's behavioural risk patterns is needed to inform intervention efforts. Data were from 2,945 women drug injectors and crack users. Statistical analyses compared sociodemographic variables, lifetime behavioural risk patterns, HIV sero-prevalence and history of sexually transmitted diseases, and determined predictors of HIV infection separately in 16 low and four high sero-prevalence sites. Based on risk patterns, four behaviourally-defined sub-groups were constructed, and rates of HIV sero-prevalence were compared. In comparisons between low and high sero-prevalence sites, there were significant differences on most variables examined, and in the relative importance of the sociodemographic characteristics and risk patterns predicting HIV. Drug injection and sex exchange were each independent, significant, behavioural predictors of infection, with no significant difference between the odds ratios attributed to each predictor. HIV sero-prevalence was significantly different among four sub-groups. Interventions must be tailored to address observed differences among women in low and high sero-prevalence sites. Injection drug use and exchanging sex each play a major role in the transmission of HIV infection to US women. Prevention efforts targeted at women should address differences in behavioural risk patterns. Aggressive and innovative interventions are needed for women who exchange sex. AIDS research must investigate how socioeconomic factors impact women's risk for HIV infection.

A community-level HIV prevention intervention for inner-city women: results of the women and infants demonstration projects

OBJECTIVES

This study examined the effects of a multisite community-level HIV prevention intervention on women's condom-use behaviors.

METHODS

The theory-based behavioral intervention was implemented with low-income, primarily African American women in 4 urban communities. It was evaluated with data from pre- and postintervention cross-sectional surveys in matched intervention and comparison communities.

RESULTS

At baseline, 68% of the women had no intention of using condoms with their main partners and 70% were not using condoms consistently with other partners. After 2 years of intervention activities, increases in rates of talking with main partners about condoms were significantly larger in intervention communities than in comparison communities (P = .03). Intervention communities also had significant increases in the proportion of women who had tried to get their main partners to use condoms (P = .01). The trends for condom use with other partners were similar but nonsignificant.

CONCLUSIONS

Many women at risk for HIV infection are still not using condoms. Community-level interventions may be an effective way to reach large numbers of women and change their condom-use behaviors, particularly their behaviors with regard to communication with main sex partners.

A three-dimensional model of the mouse at embryonic day 9

This paper describes a digital, three-dimensional model of the mouse embryo at E9. The model was made by reconstruction from images of serial histological sections digitally warped to remove distortions and has a resolution of approximately 9 microns. The model can be digitally resectioned in any plane to provide images which resemble conventional histological sections. The main tissues have been identified and delineated by digital painting so that the anatomical components can be visualized and manipulated in 3-D surface- and volume-rendered views. This provides a three-dimensional definition of anatomy that will provide a useful tool for interpreting and understanding spatial data in mouse embryos. The anatomy of the model is discussed where it provides landmarks for interpretation and navigation or where it is unexpected in light of existing descriptions of the E9 mouse embryo. The complete anatomy is not presented in this paper but will be available on CD-ROM. A detailed description of the technical aspects of the construction of the model is included in an appendix. The model is the first of a series that will form the basis for an atlas/database of mouse development. This reconstruction and its associated anatomy are available in a variety of data formats with some supporting software from http:@genex.hgu.mrc.ac.uk/.

Isolation and characterization of hydrophobic polypeptides in human bile

Polypeptides were isolated from human bile by extraction with chloroform/methanol, followed by reversed-phase chromatography in methanol/ethylene chloride and gel filtration in chloroform/methanol. Peptides were characterized by SDS/PAGE, sequence analysis and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry. This identified haemoglobin alpha chain, ATP synthase lipid-binding protein subunit 9, an N-terminal fragment of mac25/insulin-like growth factor-binding protein 7 and an internal fragment of monocyte differentiation antigen CD14, all not described previously in bile. In addition, alpha1-antitrypsin, known in bile from previous work, was also identified. The hydrophobic character of haemoglobin alpha chain is not apparent from its amino acid sequence, but the other polypeptides all have major hydrophobic segments. These results show that several proteins are removed upon organic solvent extraction used for delipidation during the preparation of samples for proteome analysis. Several of the polypeptides found are unexpectedly present in bile, suggesting that specific excretion mechanisms may be involved.

Pregnancy and laparoscopic surgery

We reviewed the English literature regarding laparoscopic surgery during pregnancy and found that of 518 reported procedures, the most common was cholecystectomy (45%), followed by adnexal surgery (34%), appendectomy (15%), and other operations (6%). We add six cases to this list; three cholecystectomies, an adnexal procedure, and two for abdominal pain. Thirty-three percent were performed in the first trimester, 56% in the second, and 11% in the third trimester. This review demonstrates a definite trend, indicating that laparoscopy in pregnancy appears to be safe when performed by experienced practitioners. (J Am Assoc Gynecol Laparosc 6(3):347-351, 1999)