Pseudomonas fluorescens' view of the periodic table

Growth in a biofilm modulates microbial metal susceptibility, sometimes increasing the ability of microorganisms to withstand toxic metal species by several orders of magnitude. In this study, a high-throughput metal toxicity screen was initiated with the aim of correlating biological toxicity data in planktonic and biofilm cells to the physiochemical properties of metal ions. To this end, Pseudomonas fluorescens ATCC 13525 was grown in the Calgary Biofilm Device (CBD) and biofilms and planktonic cells of this microorganism were exposed to gradient arrays of different metal ions. These arrays included 44 different metals with representative compounds that spanned every group of the periodic table (except for the halogens and noble gases). The minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and minimum biofilm eradication concentration (MBEC) values were obtained after exposing the biofilms to metal ions for 4 h. Using these values, metal ion toxicity was correlated to the following ion-specific physicochemical parameters: standard reduction-oxidation potential, electronegativity, the solubility product of the corresponding metal–sulfide complex, the Pearson softness index, electron density and the covalent index. When the ions were grouped according to outer shell electron structure, we found that heavy metal ions gave the strongest correlations to these parameters and were more toxic on average than the other classes of the ions. Correlations were different for biofilms than for planktonic cells, indicating that chemical mechanisms of metal ion toxicity differ between the two modes of growth. We suggest that biofilms can specifically counter the toxic effects of certain physicochemical parameters, which may contribute to the increased ability of biofilms to withstand metal toxicity.     

Expression of the calcitonin receptor, calcitonin receptor-like receptor, and receptor activity modifying proteins during osteoclast differentiation

The expressions of the calcitonin receptor (CTR), the calcitonin receptor-like receptor (CLR), the receptor activity-modifying proteins (RAMP) 1-3, and of the receptor component protein (RCP) have been studied in mouse bone marrow macrophages (BMM) during osteoclast differentiation, induced by treatment with M-CSF and RANKL. Analyses of mRNA showed that CLR and RAMP1-3, but not CTR, were expressed in M-CSF stimulated BMM. RANKL gradually increased CTR mRNA, transiently enhanced CLR and transiently decreased RAMP1 mRNA, but did not affect RAMP2, RAMP3, or RCP mRNA. However, RANKL did not affect protein levels of CLR or RAMP1-3 as assessed by Western blots or FACS analyses, whereas immunocytochemistry showed enhanced CTR protein. Analyses of cAMP production showed that BMM cells expressed functional receptors for calcitonin gene-related peptide (CGRP), amylin, adrenomedullin, and intermedin, but not for calcitonin and calcitonin receptor stimulating peptide (CRSP), but that RANKL induced the expression of receptors for calcitonin and CRSP as well. Calcitonin, CGRP, amylin, adrenomedullin, intermedin, and CRSP all down regulated the CTR mRNA, but none of the peptides caused any effects on the expression of CLR or any of the RAMPs. Our data show that BMM cells express receptors for CGRP, amylin, adrenomedullin, and intermedin and that RANKL induces the formation of receptors for calcitonin and CRSP in these cells. We also show, for the first time, that the CTR is not only down regulated by signaling through the CTR but also by the peptides signaling through CLR/RAMPs.     

Amino acid residues in the GIY-YIG endonuclease II of phage T4 affecting sequence recognition and binding as well as catalysis

Phage T4 endonuclease II (EndoII), a GIY-YIG endonuclease lacking a carboxy-terminal DNA-binding domain, was subjected to site-directed mutagenesis to investigate roles of individual amino acids in substrate recognition, binding, and catalysis. The structure of EndoII was modeled on that of UvrC. We found catalytic roles for residues in the putative catalytic surface (G49, R57, E118, and N130) similar to those described for I-TevI and UvrC; in addition, these residues were found to be important for substrate recognition and binding. The conserved glycine (G49) and arginine (R57) were essential for normal sequence recognition. Our results are in agreement with a role for these residues in forming the DNA-binding surface and exposing the substrate scissile bond at the active site. The conserved asparagine (N130) and an adjacent proline (P127) likely contribute to positioning the catalytic domain correctly. Enzymes in the EndoII subfamily of GIY-YIG endonucleases share a strongly conserved middle region (MR, residues 72 to 93, likely helical and possibly substituting for heterologous helices in I-TevI and UvrC) and a less strongly conserved N-terminal region (residues 12 to 24). Most of the conserved residues in these two regions appeared to contribute to binding strength without affecting the mode of substrate binding at the catalytic surface. EndoII K76, part of a conserved NUMOD3 DNA-binding motif of homing endonucleases found to overlap the MR, affected both sequence recognition and catalysis, suggesting a more direct involvement in positioning the substrate. Our data thus suggest roles for the MR and residues conserved in GIY-YIG enzymes in recognizing and binding the substrate.     

Stable oxygen and carbon isotope information on the establishment of a new, opportunistic foraminiferal fauna in a Swedish Skagerrak fjord basin, in 1979/1980

Significant faunal changes reported from recent, coastal environments, which are not directly influenced by urban and industrial impact, are rarely seen. In Gullmar Fjord on the Swedish west coast, a significant foraminiferal fauna change occurred in connection with severe low-oxygen conditions that evolved in the winter of 1979/1980. A foraminiferal fauna marked by common Skagerrak–Kattegat species, which had previously characterised the deep fjord basin, was replaced by the opportunistic, low-oxygen tolerant species Stainforthia fusiformis (Williamsson).To study this phenomenon further we performed stable oxygen and carbon isotope analyses on the indicator species itself, S. fusiformis, both on specimens from sediment cores representing approximately the last 85 years and on living (stained) individuals taken from a transect across the deep fjord basin. Our purpose was to detail how and why S. fusiformis, came to dominate the fauna.The oxygen isotope results suggest that salinities and temperatures in the deep basin have been relatively constant over the last c. 85 years, while the carbon isotopes show a significant change towards more negative values in association with the faunal shift of 1979/1980. The combined results from both the cores and the surface sediments suggest that S. fusiformis did not inhabit the deep basin until 1980. Before then, almost all specimens of S. fusiformis were small sized and their carbon isotope values suggest they were re-deposited shallow-water specimens that had been transported down to the central, deep basin as part of a suspension load. After a major faunal extinction in 1979–1980, S. fusiformis of all sizes suddenly appeared in large numbers and their carbon isotopic values were similar to the signal from registered in the recent, living fauna within the deep basin. This suggests that the opportunistic S. fusiformis established itself in the deep basin as a consequence of the severe low-oxygen event and the faunal crash of the previously dominating Skagerrak–Kattegat fauna.     

Different HLA-DRB1 allele distributions in distinct clinical subgroups of sarcoidosis patients

Background

A strong genetic influence by the MHC class II region has been reported in sarcoidosis, however in many studies with different results. This may possibly be caused by actual differences between distinct ethnic groups, too small sample sizes, or because of lack of accurate clinical subgrouping.

Subjects and methods

In this study we HLA typed a large patient population (n = 754) recruited from one single centre. Patients were sub-grouped into those with Löfgren''s syndrome (LS) (n = 302) and those without (non-Löfgren''s) (n = 452), and the majority of them were clinically classified into those with recovery within two years (resolving) and those with signs of disease for more than two years (non-resolving). PCR was used for determination of HLA-DRB1 alleles. Swedish healthy blood donors (n = 1366) served as controls.

Results

There was a dramatic difference in the distribution of HLA alleles in LS compared to non-LS patients (p = 4 × 10^-36). Most notably, DRB1*01, DRB1*03 and DRB1*14, clearly differed in LS and non-LS patients. In relation to disease course, DRB1*07, DRB1*14 and DRB1*15 generally associated with, while DRB1*01 and DRB1*03 protected against, a non-resolving disease. Interestingly, the clinical influence of DRB1*03 (good prognosis) dominated over that of DRB1*15 (bad prognosis).

Conclusions

We found several significant differences between LS and non-LS patients and we therefore suggest that genetic association studies in sarcoidosis should include a careful clinical characterisation and sub-grouping of patients, in order to reveal true genetic associations. This may be particularly accurate to do in the heterogeneous non-LS group of patients.     

Structure of the natural transgene PgiC2 in the common grass Festuca ovina

Background

A horizontal gene transfer has brought an active nuclear gene, PgiC2, from a polyploid Poa species (P. palustris or a close relative) into the common grass sheep''s fescue (Festuca ovina). The donor and the receptor species are strictly reproductively separated, and PgiC2 occurs in a polymorphic state within F. ovina. The active gene copy is normally closely linked to a very similar pseudogene.

Methodology/Principal Findings

By genome walking we have obtained the up- and downstream sequences of PgiC2 and of corresponding genes in the donor and recipient species. Comparisons of these sequences show that the complete upstream region necessary for the gene''s expression is included in the transferred segment. About 1 kb upstream of PgiC2 a fragment with transposition associated properties has been found (TAF). It is present in P. palustris and its polyploid relatives, though not at the homologous position, and is absent from many other grasses, including non-transgenic F. ovina plants. It is possible that it is a part of a transposing element involved in getting the gene into a transferring agent and/or into the recipient chromosome.

Conclusions/Significance

The close similarity of the up- and downstream regions with the corresponding regions in P. palustris excludes all suggestions that PgiC2 is not a HGT but the result of a duplication within the F. ovina lineage. The small size of the genetic material transferred, the complex nature of the PgiC2 locus, and the associated fragment with transposition associated properties suggest that the horizontal transfer occurred via a vector and not via illegitimate pollination.     

Caveolae-mediated endocytosis of the glucosaminoglycan-interacting adipokine tartrate resistant acid phosphatase 5a in adipocyte progenitor lineage cells

Adipogenesis depends on growth factors controlling proliferation/differentiation of mesenchymal stem cells (MSCs). Membrane binding and endocytosis of growth factors are often coupled to receptor activation and downstream signaling leading to specific cellular responses. The novel adipokine tartrate-resistant acid phosphatase (TRAP) 5a exhibits a growth factor-like effect on MSCs and pre-adipocytes and induces hyperplastic obesity in vivo. However its molecular interaction with pre-adipocytes remains unknown. Therefore, this study aimed to investigate membrane interaction of TRAP and its endocytosis routes in pre-adipocytes. Confocal and/or electron microscopy were used to detect TRAP in untreated or TRAP 5a/b treated pre-adipocytes under conditions that allow or inhibit endocytosis in combination with co-staining of endocytotic vesicles. TRAP interaction with heparin/heparan sulfate was verified by gel filtration. It could be shown that TRAP 5a, but not 5b, binds to the membrane of pre-adipocytes where it co-localizes with heparin-sulfate proteoglycan glypican-4. Also in vitro, TRAP 5a exhibited affinity for both heparin and heparan sulfate with heparin inhibiting its enzyme activity. Upon caveolae-mediated endocytosis of saturating levels of TRAP 5a, TRAP 5a co-localized intracellularly with glypican-4 and late endosomal marker Rab-7 positive vesicles. The protein was also located in multivesicular bodies (MVBs) but did not co-localize with lysosomal marker LAMP-1. TRAP 5a endocytosis was also detectable in pre-osteoblasts, but not fibroblasts, embryonic MSCs or mature adipocytes. These results indicate that TRAP 5a exhibits binding to cell surface, endocytosis and affinity to glucosaminoglycans (GAGs) in pre-adipocyte and pre-osteoblast lineage cells in a manner similar to other heparin-binding growth factors.     

Viewing the Body after Bereavement Due to Suicide: A Population-Based Survey in Sweden

Background

Research on the assumed, positive and negative, psychological effects of viewing the body after a suicide loss is sparse. We hypothesized that suicide-bereaved parents that viewed their childs body in a formal setting seldom regretted the experience, and that viewing the body was associated with lower levels of psychological morbidity two to five years after the loss.

Methods and Findings

We identified 915 suicide-bereaved parents by linkage of nationwide population-based registries and collected data by a questionnaire. The outcome measures included the Patient Health Questionnaire (PHQ-9). In total, 666 (73%) parents participated. Of the 460 parents (69%) that viewed the body, 96% answered that they did not regret the experience. The viewing was associated with a higher risk of reliving the child''s death through nightmares (RR 1.61, 95% CI 1.13 to 2.32) and intrusive memories (RR 1.20, 95% CI 1.04 to 1.38), but not with anxiety (RR 1.02, 95% CI 0.74 to 1.40) and depression (RR 1.25, 95% CI 0.85 to 1.83). One limitation of our study is that we lack data on the informants'' personality and coping strategies.

Conclusions

In this Swedish population-based survey of suicide-bereaved parents, we found that by and large everyone that had viewed their deceased child in a formal setting did not report regretting the viewing when asked two to five years after the loss. Our findings suggest that most bereaved parents are capable of deciding if they want to view the body or not. Officials may assist by giving careful information about the child''s appearance and other details concerning the viewing, thus facilitating mental preparation for the bereaved person. This is the first large-scale study on the effects of viewing the body after a suicide and additional studies are needed before clinical recommendations can be made.     

Prostate Tumor-Derived Exosomes Down-Regulate NKG2D Expression on Natural Killer Cells and CD8+ T Cells: Mechanism of Immune Evasion

Tumor-derived exosomes, which are nanometer-sized extracellular vesicles of endosomal origin, have emerged as promoters of tumor immune evasion but their role in prostate cancer (PC) progression is poorly understood. In this study, we investigated the ability of prostate tumor-derived exosomes to downregulate NKG2D expression on natural killer (NK) and CD8⁺ T cells. NKG2D is an activating cytotoxicity receptor whose aberrant loss in cancer plays an important role in immune suppression. Using flow cytometry, we found that exosomes produced by human PC cells express ligands for NKG2D on their surface. The NKG2D ligand-expressing prostate tumor-derived exosomes selectively induced downregulation of NKG2D on NK and CD8⁺ T cells in a dose-dependent manner, leading to impaired cytotoxic function in vitro. Consistent with these findings, patients with castration-resistant PC (CRPC) showed a significant decrease in surface NKG2D expression on circulating NK and CD8⁺ T cells compared to healthy individuals. Tumor-derived exosomes are likely involved in this NKG2D downregulation, since incubation of healthy lymphocytes with exosomes isolated from serum or plasma of CRPC patients triggered downregulation of NKG2D expression in effector lymphocytes. These data suggest prostate tumor-derived exosomes as down-regulators of the NKG2D-mediated cytotoxic response in PC patients, thus promoting immune suppression and tumor escape.