Showing papers by "University of Lausanne published in 2001"
TL;DR: A new mechanism for bacterial uptake in the mucosa tissues that is mediated by dendritic cells (DCs) is reported, which open the tight junctions between epithelial cells, send dendrites outside the epithelium and directly sample bacteria.
Abstract: Penetration of the gut mucosa by pathogens expressing invasion genes is believed to occur mainly through specialized epithelial cells, called M cells, that are located in Peyer's patches. However, Salmonella typhimurium that are deficient in invasion genes encoded by Salmonella pathogenicity island 1 (SPI1) are still able to reach the spleen after oral administration. This suggests the existence of an alternative route for bacterial invasion, one that is independent of M cells. We report here a new mechanism for bacterial uptake in the mucosa tissues that is mediated by dendritic cells (DCs). DCs open the tight junctions between epithelial cells, send dendrites outside the epithelium and directly sample bacteria. In addition, because DCs express tight-junction proteins such as occludin, claudin 1 and zonula occludens 1, the integrity of the epithelial barrier is preserved.
2,463 citations
TL;DR: BAFF-R appears to be the principal receptor for BAFF-mediated mature B cell survival and is disrupted in A/WySnJ mice, which display a B cell phenotype qualitatively similar to that of the BAff-deficient mice.
Abstract: B cell homeostasis has been shown to critically depend on BAFF, the B cell activation factor from the tumor necrosis factor (TNF) family Although BAFF is already known to bind two receptors, BCMA and TACI, we have identified a third receptor for BAFF that we have termed BAFF-R BAFF-R binding appears to be highly specific for BAFF, suggesting a unique role for this ligand-receptor interaction Consistent with this, the BAFF-R locus is disrupted in A/WySnJ mice, which display a B cell phenotype qualitatively similar to that of the BAFF-deficient mice Thus, BAFF-R appears to be the principal receptor for BAFF-mediated mature B cell survival
942 citations
TL;DR: A survey of blood pressure measuring devices for which there is published evidence of independent validation using the BHS and AAMI protocols found that only a fraction of the many devices available have been surveyed.
Abstract: There is a large market for blood pressure measuring devices not only in clinical medicine but also among the public where the demand for self measurement of blood pressure is growing rapidly. For consumers, whether medical or lay, accuracy should be of prime importance when selecting a device to measure blood pressure. However, most devices have not been evaluated for accuracy independently using the two most widely used protocols: the British Hypertension Society (BHS) protocol and the standard set by the US Association for the Advancement of Medical Instrumentation (AAMI). 1 2 The Working Group on Blood Pressure Monitoring of the European Society of Hypertension has decided to review blood pressure measuring devices regularly to guide purchasers.3 For this first report devices for which there is published evidence of independent validation using these protocols have been surveyed. Because most blood pressure devices have not been independently validated, only a fraction of the many devices available have been surveyed. Devices that have been validated recently for which results have not yet been published were not included, but this shortcoming should be addressed in future.
#### Summary points
Two manual sphygmomanometers have been validated, one is recommended
Five devices for clinical use in hospitals have been validated, two are recommended
23 devices for self measurement of blood pressure have been validated, five are recommended
24 devices for ambulatory measurement of blood pressure have been validated, 16 are recommended
Validations and recommendations will be updated on the BMJ 's website
### Validation standards
In 1987, the American Association for the Advancement of Medical Instrumentation published a standard for sphygmomanometers which included a protocol for evaluating the accuracy of devices.4 In 1990 a protocol was devised by the British Hypertension Society.5 Both protocols have since been revised. 1 2 Since the two protocols can be reconciled the …
870 citations
TL;DR: It is shown that NF-κB activation upregulates the caspase 8 inhibitor FLIP, resulting in increased resistance to Fas ligand (FasL) or TNF, and suggest that FLIP is an important mediator of NF-σκB-controlled antiapoptotic signals.
Abstract: Activation of the transcription factor NF-κB is a major effector of the inducible resistance to death receptor-mediated apoptosis. Previous evidence indicates that the combined transcriptional activation of TRAF-1, TRAF-2, IAP-1, and IAP-2 is required to suppress cell death by tumor necrosis factor (TNF). Here we show that NF-κB activation upregulates the caspase 8 inhibitor FLIP, resulting in increased resistance to Fas ligand (FasL) or TNF. Restoration of either the full-length 55-kDa long form of FLIP or an alternatively spliced short form of FLIP in NF-κB null cells inhibits TNF- and FasL-induced cell death efficiently, whereas the expression of IAP or TRAF family members only partially rescues cells from death. Resistance to either FasL- or TNF-induced apoptosis is overcome when cells are incubated in the presence of the protein synthesis inhibitor cycloheximide. This treatment leads to the rapid downregulation of FLIP but not to that of TRAF2. Our findings suggest that FLIP is an important mediator of NF-κB-controlled antiapoptotic signals.
808 citations
Imperial College London1, The Royal Marsden NHS Foundation Trust2, University of Western Australia3, Queensland University of Technology4, St. Vincent's Health System5, University of New South Wales6, Charles University in Prague7, University of Paris8, French Institute of Health and Medical Research9, Max Planck Society10, Ludwig Maximilian University of Munich11, National and Kapodistrian University of Athens12, University of Massachusetts Boston13, University of Hong Kong14, Royal College of Surgeons in Ireland15, University of Palermo16, Kanazawa University17, University of Fukui18, Tokyo Medical and Dental University19, Dokkyo Medical University20, Maastricht University21, Rikshospitalet–Radiumhospitalet22, Tan Tock Seng Hospital23, Autonomous University of Barcelona24, Linköping University25, University of Lausanne26, National Cheng Kung University27, University of Leeds28, University of Edinburgh29, University of Birmingham30, AstraZeneca31, University of Glasgow32, University of Manchester33, Cancer Research UK34, Yale University35, Brown University36, University of Pittsburgh37, Vanderbilt University38, Yeshiva University39, Military Medical Academy40
TL;DR: In this paper, the effect of the Kirsten ras (Ki-ras) tumour genotype and outcome of patients with colorectal cancer was investigated using a multivariate analysis.
Abstract: Researchers worldwide with information about the Kirsten ras (Ki-ras) tumour genotype and outcome of patients with colorectal cancer were invited to provide that data in a schematized format for inclusion in a collaborative database called RASCAL (The Kirsten ras incolorectal-cancer collaborative group). Our results from 2721 such patients have been presented previously and for the first time in any common cancer, showed conclusively that different gene mutations have different impacts on outcome, even when the mutations occur at the same site on the genome. To explore the effect of Ki-ras mutations at different stages of colorectal cancer, more patients were recruited to the database, which was reanalysed when information on 4268 patients from 42 centres in 21 countries had been entered. After predetermined exclusion criteria were applied, data on 3439 patients were entered into a multivariate analysis. This found that of the 12 possible mutations on codons 12 and 13 of Kirsten ras, only one mutation on codon 12, glycine to valine, found in 8.6% of all patients, had a statistically significant impact on failure-free survival (P=0.004, HR 1.3) and overall survival (P=0.008, HR 1.29). This mutation appeared to have a greater impact on outcome in Dukes' C cancers (failure-free survival, P=0.008, HR 1.5, overall survival P=0.02, HR 1.45) than in Dukes' B tumours (failure-free survival, P=0.46, HR 1.12, overall survival P=0.36, HR 1.15). Ki-ras mutations may occur early in the development of pre-cancerous adenomas in the colon and rectum. However, this collaborative study suggests that not only is the presence of a codon 12 glycine to valine mutation important for cancer progression but also that it may predispose to more aggressive biological behaviour in patients with advanced colorectal cancer. ⌐ 2001 Cancer Research Campaign.
753 citations
TL;DR: The members of the extended GLUT family exhibit a surprisingly diverse substrate specificity, and the definition of sequence elements determining this substrate specificity will require a full functional characterization of all members.
Abstract: During the last 2 years, several novel genes that encode glucose transporter-like proteins have been identified and characterized. Because of their sequence similarity with GLUT1, these genes appear to belong to the family of solute carriers 2A ( SLC2A, protein symbol GLUT). Sequence comparisons of all 13 family members allow the definition of characteristic sugar/polyol transporter signatures: (1) the presence of 12 membrane-spanning helices, (2) seven conserved glycine residues in the helices, (3) several basic and acidic residues at the intracellular surface of the proteins, (4) two conserved tryptophan residues, and (5) two conserved tyrosine residues. On the basis of sequence similarities and characteristic elements, the extended GLUTfamily can be divided intothree subfamilies, namely class I (the previously known glucose transporters GLUT1-4), class II (the previously known fructose transporter GLUT5, the GLUT7, GLUT9 and GLUT11), and class III (GLUT6, 8, 10, 12, and the myoinositol transporter HMIT...
716 citations
TL;DR: It is shown that phosphorylation of an enzyme involved in the ubiquitylation cascade (Nedd4‐2) controls cell surface density of ENaC and a paradigm for the control of ion channels is proposed.
Abstract: The epithelial Na+ channel (ENaC) plays an essential role in the regulation of whole body Na+ balance and blood pressure. The cell surface expression of this channel, a complex of three subunits (α, β and γENaC), has been shown to be regulated by hormones such as aldosterone and vasopressin and by intracellular signaling, including ubiquitylation and/or phosphorylation. However, the molecular mechanisms involving phosphorylation in the regulation of ENaC are unclear. Here we show by expression studies in Xenopus laevis oocytes that the aldosterone-induced Sgk1 kinase interacts with the ubiquitin protein ligase Nedd4-2 in a PY motif-dependent manner and phosphorylates Nedd4-2 on Ser444 and, to a lesser extent, Ser338. Such phosphorylation reduces the interaction between Nedd4-2 and ENaC, leading to elevated ENaC cell surface expression. These data show that phosphorylation of an enzyme involved in the ubiquitylation cascade (Nedd4-2) controls cell surface density of ENaC and propose a paradigm for the control of ion channels. Moreover, they suggest a novel and complete signaling cascade for aldosterone-dependent regulation of ENaC.
700 citations
TL;DR: The microfabrication and characterisation of an on-chip flow-cytometer is described as the first building block of a complete cell-sorting device and the signal conditioning technique and impedance measurements of cells and particles of different sizes and types are discussed to demonstrate the differentiation of subpopulations in a mixed sample.
Abstract: A new cytological tool, based on the micro Coulter particle counter (μCPC) principle, aimed at diagnostic applications for cell counting and separation in haematology, oncology or toxicology is described. The device measures the spectral impedance of individual cells or particles and allows screening rates over 100 samples s−1 on a single-cell basis. This analyzer is intended to drive a sorting actuator producing a subsequent cell separation. Size reduction and integration of functions are essential in achieving precise measurements and high throughput. 3D finite element simulations are presented to compare various electrode geometries and their influence on cell parameters estimation. The device is based on a glass-polyimide microfluidic chip with integrated channels and electrodes microfabricated at the length scale of the particles to be investigated (1–20 μm). A laminar liquid flow carries the suspended particles through the measurement area.
Each particle’s impedance signal is recorded by a differential pair of microelectrodes using the cell surrounding media as a reference. The micromachined chip and processing electronic circuit allow simultaneous impedance measurements at multiple frequencies, ranging from 100 kHz to 15 MHz. In this paper, we describe the microfabrication and characterisation of an on-chip flow-cytometer as the first building block of a complete cell-sorting device. We then discuss the signal conditioning technique and finally impedance measurements of cells and particles of different sizes and types to demonstrate the differentiation of subpopulations in a mixed sample.
694 citations
TL;DR: It is shown that BRCA2 plays a dual role in regulating the actions of RAD51, a protein essential for homologous recombination and DNA repair, which may be a key event leading to genomic instability and tumorigenesis in patients predisposed to breast and ovarian cancers.
685 citations
TL;DR: In this article, the authors reported that activation of poly(ADP-ribose) polymerase (PARP) is an important factor in the pathogenesis of endothelial dysfunction in diabetes.
Abstract: Diabetic patients frequently suffer from retinopathy, nephropathy, neuropathy and accelerated atherosclerosis. The loss of endothelial function precedes these vascular alterations. Here we report that activation of poly(ADP-ribose) polymerase (PARP) is an important factor in the pathogenesis of endothelial dysfunction in diabetes. Destruction of islet cells with streptozotocin in mice induced hyperglycemia, intravascular oxidant production, DNA strand breakage, PARP activation and a selective loss of endothelium-dependent vasodilation. Treatment with a novel potent PARP inhibitor, starting after the time of islet destruction, maintained normal vascular responsiveness, despite the persistence of severe hyperglycemia. Endothelial cells incubated in high glucose exhibited production of reactive nitrogen and oxygen species, consequent single-strand DNA breakage, PARP activation and associated metabolic and functional impairment. Basal and high-glucose-induced nuclear factor-kappaB activation were suppressed in the PARP-deficient cells. Our results indicate that PARP may be a novel drug target for the therapy of diabetic endothelial dysfunction.
601 citations
TL;DR: Determination of the earliest cellular interactions that occur in and under the follicle-associated epithelium could greatly facilitate the design of effective mucosal vaccines in the future.
Abstract: Immune surveillance of mucosal surfaces requires the delivery of intact macromolecules and microorganisms across epithelial barriers to organized mucosal lymphoid tissues. Transport, processing and presentation of foreign antigens, as well as local induction and clonal expansion of antigen-specific effector lymphocytes, involves a close collaboration between organized lymphoid tissues and the specialized follicle-associated epithelium. M cells in the follicle-associated epithelium transport foreign macromolecules and microorganisms to antigen-presenting cells within and under the epithelial barrier. Determination of the earliest cellular interactions that occur in and under the follicle-associated epithelium could greatly facilitate the design of effective mucosal vaccines in the future.
TL;DR: In this article, the authors compare the performance of ENFA and generalized linear models (GLM) in three different scenarios: spreading, at equilibrium, and overabundant species.
TL;DR: Fasting can strongly influence PPAR expression, but in only a few selected tissues, including liver, kidney, heart, diaphragm, and esophagus.
Abstract: PPARs are members of the nuclear hormone receptor superfamily and are primarily involved in lipid metabolism. The expression patterns of all 3 PPAR isotypes in 22 adult rat organs were analyzed by a quantitative ribonuclease protection assay. The data obtained allowed comparison of the expression of each isotype to the others and provided new insight into the less studied PPAR beta (NR1C2) expression and function. This isotype shows a ubiquitous expression pattern and is the most abundant of the three PPARs in all analyzed tissues except adipose tissue. Its expression is especially high in the digestive tract, in addition to kidney, heart, diaphragm, and esophagus. After an overnight fast, PPAR beta mRNA levels are dramatically down-regulated in liver and kidney by up to 80% and are rapidly restored to control levels upon refeeding. This tight nutritional regulation is independent of the circulating glucocorticoid levels and the presence of PPAR alpha, whose activity is markedly up-regulated in the liver and small intestine during fasting. Finally, PPAR gamma 2 mRNA levels are decreased by 50% during fasting in both white and brown adipose tissue. In conclusion, fasting can strongly influence PPAR expression, but in only a few selected tissues.
TL;DR: It is demonstrated that activation of the RXR/PPARγ heterodimer protects against colon inflammation and suggested that combination therapy with both RXR and PPARγ ligands might hold promise in the clinic due to their synergistic effects.
Abstract: The peroxisome proliferator-activated receptor gamma (PPARgamma) is highly expressed in the colon mucosa and its activation has been reported to protect against colitis. We studied the involvement of PPARgamma and its heterodimeric partner, the retinoid X receptor (RXR) in intestinal inflammatory responses. PPARgamma(1/)- and RXRalpha(1/)- mice both displayed a significantly enhanced susceptibility to 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis compared with their wild-type littermates. A role for the RXR/PPARgamma heterodimer in the protection against colon inflammation was explored by the use of selective RXR and PPARgamma agonists. TNBS-induced colitis was significantly reduced by the administration of both PPARgamma and RXR agonists. This beneficial effect was reflected by increased survival rates, an improvement of macroscopic and histologic scores, a decrease in tumor necrosis factor alpha and interleukin 1beta mRNA levels, a diminished myeloperoxidase concentration, and reduction of nuclear factor kappaB DNA binding activity, c-Jun NH(2)-terminal kinase, and p38 activities in the colon. When coadministered, a significant synergistic effect of PPARgamma and RXR ligands was observed. In combination, these data demonstrate that activation of the RXR/PPARgamma heterodimer protects against colon inflammation and suggest that combination therapy with both RXR and PPARgamma ligands might hold promise in the clinic due to their synergistic effects.
TL;DR: It is suggested that the GacS/GacA system operates a switch between primary and secondary metabolism, with a major involvement of posttranscriptional control mechanisms.
Abstract: The sensor kinase GacS and the response regulator GacA are members of a two-component system that is present in a wide variety of gram-negative bacteria and has been studied mainly in enteric bacteria and fluorescent pseudomonads. The GacS/GacA system controls the production of secondary metabolites and extracellular enzymes involved in pathogenicity to plants and animals, biocontrol of soilborne plant diseases, ecological fitness, or tolerance to stress. A current model proposes that GacS senses a still-unknown signal and activates, via a phosphorelay mechanism, the GacA transcription regulator, which in turn triggers the expression of target genes. The GacS protein belongs to the unorthodox sensor kinases, characterized by an autophosphorylation, a receiver, and an output domain. The periplasmic loop domain of GacS is poorly conserved in diverse bacteria. Thus, a common signal interacting with this domain would be unexpected. Based on a comparison with the transcriptional regulator NarL, a secondary structure can be predicted for the GacA sensor kinases. Certain genes whose expression is regulated by the GacS/GacA system are regulated in parallel by the small RNA binding protein RsmA (CsrA) at a posttranscriptional level. It is suggested that the GacS/GacA system operates a switch between primary and secondary metabolism, with a major involvement of posttranscriptional control mechanisms.
TL;DR: In this article, the authors present a simple model of currency crises which is driven by the interplay between the credit constraints of private domestic firms and the existence of nominal price rigidities.
TL;DR: The findings presented here reveal unpredicted roles for PPARα and β in adult mouse epidermal repair and PPARβ mutant primary keratinocytes show impaired adhesion and migration properties.
Abstract: We show here that the alpha, beta, and gamma isotypes of peroxisome proliferator-activated receptor (PPAR) are expressed in the mouse epidermis during fetal development and that they disappear progressively from the interfollicular epithelium after birth. Interestingly, PPARalpha and beta expression is reactivated in the adult epidermis after various stimuli, resulting in keratinocyte proliferation and differentiation such as tetradecanoylphorbol acetate topical application, hair plucking, or skin wound healing. Using PPARalpha, beta, and gamma mutant mice, we demonstrate that PPARalpha and beta are important for the rapid epithelialization of a skin wound and that each of them plays a specific role in this process. PPARalpha is mainly involved in the early inflammation phase of the healing, whereas PPARbeta is implicated in the control of keratinocyte proliferation. In addition and very interestingly, PPARbeta mutant primary keratinocytes show impaired adhesion and migration properties. Thus, the findings presented here reveal unpredicted roles for PPARalpha and beta in adult mouse epidermal repair.
TL;DR: It is shown, by use of cultures of primary keratinocytes from wild-type and PPAR/ �/� mice, that such signals including TNF- and IFN-, induce keratinocyte differentiation and this effect is also observed in vivo during wound healing after an injury.
Abstract: The immediate response to skin injury is the release of inflammatory signals. It is shown here, by use of cultures of primary keratinocytes from wild-type and PPAR/ �/� mice, that such signals including TNF- and IFN-, induce keratinocyte differentiation. This cytokine-dependent cell differentiation pathway requires up-regulation of the PPAR/ gene via the stress-associated kinase cascade, which targets an AP-1 site in the PPAR/ promoter. In addition, the pro-inflammatory cytokines also initiate the production of endogenous PPAR/ ligands, which are essential for PPAR/ activation and action. Activated PPAR/ regulates the expression of genes associated with apoptosis resulting in an increased resistance of cultured keratinocytes to cell death. This effect is also observed in vivo during wound healing after an injury, as shown in dorsal skin of PPAR/ +/+ and PPAR/ +/� mice.
TL;DR: It is shown that Escherichia coli cells preadapted to high salinity contain increased levels of glycine betaine that prevent protein aggregation under thermal stress, and cells can specifically control protein stability and chaperone-mediated disaggregation and refolding by modulating the intracellular levels of different osmolytes.
TL;DR: In this article, the authors found that anti-apoptotic proteins, such as FLIP (also known as FLICE/caspase-8 inhibitory protein) have been found to be tightly regulated in T cells and might be involved in the control of both T-cell activation and death.
Abstract: Lymphocyte homeostasis is a balance between lymphocyte proliferation and lymphocyte death Tight control of apoptosis is essential for immune function, because its altered regulation can result in cancer and autoimmunity Signals from members of the tumour-necrosis-factor receptor (TNF-R) family, such as Fas and TNF-R1, activate the caspase cascade and result in lymphocyte death by apoptosis Anti-apoptotic proteins, such as FLIP (also known as FLICE/caspase-8 inhibitory protein) have recently been identified FLIP expression is tightly regulated in T cells and might be involved in the control of both T-cell activation and death Abnormal expression of FLIP might have a role not only in autoimmune diseases, but also in tumour development and cardiovascular disorders
TL;DR: In this paper, the authors show that capping of Fas is essential for optimal function and capping is ceramide-dependent, and they show that the presence of intact sphingolipid-enriched membrane domains may be essential for Fas capping since their disruption with cholesterol-depleting agents abrogated capping.
TL;DR: Fluoroquinolones appear to be the therapy of choice for bacterial keratitis, but, based upon these in vitro studies, some strains may be resistant.
Abstract: AIM To define the clinical and microbiological profile of bacterial keratitis at the Jules Gonin Eye Hospital and to test the in vitro bacterial resistance. METHODS Patients presenting with bacterial keratitis were prospectively followed; clinical features (age, risk factors, visual acuity) and response to therapy were analysed. Bacteriological profile was determined and the sensitivity/resistance of isolated strains were tested towards 12 ocular antibiotics (NCCLS disc diffusion test). RESULTS 85 consecutive patients (mean age 44.3 (SD 20.7) years) were prospectively enrolled from 1 March 1997 to 30 November 1998. The following risk factors were identified: contact lens wear, 36%; blepharitis, 21%; trauma, 20%; xerophthalmia, 15%; keratopathies, 8%; and eyelid abnormalities, 6%. The most commonly isolated bacteria were Staphylococcus epidermidis , 40%; Staphylococcus aureus , 22%; Streptococcus pneumoniae , 8%; others Streptococcus species, 5%; Pseudomonas , 9%; Moraxella and Serratia marcescens , 5% each; Bacillus , Corynebacterium , Alcaligenes xyloxidans , Morganella morganii , and Haemophilus influenza , 1% each. 1–15% of strains were resistant to fluoroquinolones, 13–22% to aminoglycosides, 37% to cefazolin, 18% to chloramphenicol, 54% to polymyxin B, 51% to fusidic acid, and 45% to bacitracin. Five of the 85 patients (5.8%) had a poor clinical outcome with a visual loss of one or more lines of visual acuity. CONCLUSION Fluoroquinolones appear to be the therapy of choice for bacterial keratitis, but, based upon these in vitro studies, some strains may be resistant.
TL;DR: It is shown by real-time RT-PCR and immunofluorescence that an aldosterone injection in adrenalectomized rats induces alpha-ENaC subunit expression along the entire ASDN within 2 h, whereas beta- and gamma- ENaC are constitutively expressed.
Abstract: Aldosterone controls sodium reabsorption and potassium secretion in the aldosterone-sensitive distal nephron (ASDN). Although clearance measurements have shown that aldosterone induces these transp...
TL;DR: RsmA was shown to exert an additional negative effect on cyanogenesis posttranscriptionally by acting on a region surrounding the hcnA ribosome-binding site, which suggests that, in P. aeruginosa, RsmA functions as a pleiotropic post transcriptional regulator of secondary metabolites directly and also indirectly by modulating the quorum-sensing circuitry.
Abstract: Posttranscriptional control is known to contribute to the regulation of secondary metabolism and virulence determinants in certain gram-negative bacteria. Here we report the isolation of a Pseudomonas aeruginosa gene which encodes a global translational regulatory protein, RsmA (regulator of secondary metabolites). Overexpression of rsmA resulted in a substantial reduction in the levels of extracellular products, including protease, elastase, and staphylolytic (LasA protease) activity as well as the PA-IL lectin, hydrogen cyanide (HCN), and the phenazine pigment pyocyanin. While inactivation of rsmA in P. aeruginosa had only minor effects on the extracellular enzymes and the PA-IL lectin, the production of HCN and pyocyanin was enhanced during the exponential phase. The influence of RsmA on N-acylhomoserine lactone-mediated quorum sensing was determined by assaying the levels of N-(3-oxododecanoyl)homoserine lactone (3-oxo-C12-HSL) and N-butanoylhomoserine lactone (C4-HSL) produced by the rsmA mutant and the rsmA-overexpressing strain. RsmA exerted a negative effect on the synthesis of both 3-oxo-C12-HSL and C4-HSL, which was confirmed by using lasI and rhlI translational fusions. These data also highlighted the temporal expression control of the lasI gene, which was induced much earlier and to a higher level during the exponential growth phase in an rsmA mutant. To investigate whether RsmA modulates HCN production solely via quorum-sensing control, hcn translational fusions were employed to monitor the regulation of the cyanide biosynthesis genes (hcnABC). RsmA was shown to exert an additional negative effect on cyanogenesis posttranscriptionally by acting on a region surrounding the hcnA ribosome-binding site. This suggests that, in P. aeruginosa, RsmA functions as a pleiotropic posttranscriptional regulator of secondary metabolites directly and also indirectly by modulating the quorum-sensing circuitry.
TL;DR: It is shown that the diversity of the training sets rather than the design of the methods is the main factor determining their prediction ability for new data, and the ALOGPS method provided better prediction ability than the other tested methods.
Abstract: A new method, ALOGPS v 2.0 (http://www.lnh.unil.ch/~itetko/logp/), for the assessment of n-octanol/water partition coefficient, log P, was developed on the basis of neural network ensemble analysis of 12 908 organic compounds available from PHYSPROP database of Syracuse Research Corporation. The atom and bond-type E-state indices as well as the number of hydrogen and non-hydrogen atoms were used to represent the molecular structures. A preliminary selection of indices was performed by multiple linear regression analysis, and 75 input parameters were chosen. Some of the parameters combined several atom-type or bond-type indices with similar physicochemical properties. The neural network ensemble training was performed by efficient partition algorithm developed by the authors. The ensemble contained 50 neural networks, and each neural network had 10 neurons in one hidden layer. The prediction ability of the developed approach was estimated using both leave-one-out (LOO) technique and training/test protocol. In case of interseries predictions, i.e., when molecules in the test and in the training subsets were selected by chance from the same set of compounds, both approaches provided similar results. ALOGPS performance was significantly better than the results obtained by other tested methods. For a subset of 12 777 molecules the LOO results, namely correlation coefficient r(2)= 0.95, root mean squared error, RMSE = 0.39, and an absolute mean error, MAE = 0.29, were calculated. For two cross-series predictions, i.e., when molecules in the training and in the test sets belong to different series of compounds, all analyzed methods performed less efficiently. The decrease in the performance could be explained by a different diversity of molecules in the training and in the test sets. However, even for such difficult cases the ALOGPS method provided better prediction ability than the other tested methods. We have shown that the diversity of the training sets rather than the design of the methods is the main factor determining their prediction ability for new data. A comparative performance of the methods as well as a dependence on the number of non-hydrogen atoms in a molecule is also presented.
TL;DR: The structure of the hydrated Cu(II) complex is determined by both neutron diffraction and first-principles molecular dynamics and it is argued that this picture is also consistent with experimental data obtained previously by visible near-infrared absorption, x-ray absorption near-edge structure, and nuclear magnetic resonance methods.
Abstract: We determined the structure of the hydrated Cu(II) complex by both neutron diffraction and first-principles molecular dynamics. In contrast with the generally accepted picture, which assumes an octahedrally solvated Cu(II) ion, our experimental and theoretical results favor fivefold coordination. The simulation reveals that the solvated complex undergoes frequent transformations between square pyramidal and trigonal bipyramidal configurations. We argue that this picture is also consistent with experimental data obtained previously by visible near-infrared absorption, x-ray absorption near-edge structure, and nuclear magnetic resonance methods. The preference of the Cu(II) ion for fivefold instead of sixfold coordination, which occurs for other cations of comparable charge and size, results from a Jahn-Teller destabilization of the octahedral complex.
TL;DR: A comparative geochemical, mineralogical, and microbiological study of three mine tailings impoundments from the La Andina, El Teniente, and El Salvador porphyry copper deposits, Chile is presented in this paper.
TL;DR: The results indicate that the study of adult multipotent precursors is a new platform to study adult human neurogenesis, potentially generate neural cells for transplantation, and design protocols for in vivo stimulation.
TL;DR: Splenic accumulation of prion infectivity and PrPSc was delayed, indicating that activation of specific complement components is involved in the initial trapping of prions in lymphoreticular organs early after infection.
Abstract: New-variant Creutzfeldt-Jakob disease and scrapie are typically initiated by extracerebral exposure to the causative agent, and exhibit early prion replication in lymphoid organs. In mouse scrapie, depletion of B-lymphocytes prevents neuropathogenesis after intraperitoneal inoculation, probably due to impaired lymphotoxin-dependent maturation of follicular dendritic cells (FDCs), which are a major extracerebral prion reservoir. FDCs trap immune complexes with Fc-gamma receptors and C3d/C4b-opsonized antigens with CD21/CD35 complement receptors. We examined whether these mechanisms participate in peripheral prion pathogenesis. Depletion of circulating immunoglobulins or of individual Fc-gamma receptors had no effect on scrapie pathogenesis if B-cell maturation was unaffected. However, mice deficient in C3, C1q, Bf/C2, combinations thereof or complement receptors were partially or fully protected against spongiform encephalopathy upon intraperitoneal exposure to limiting amounts of prions. Splenic accumulation of prion infectivity and PrPSc was delayed, indicating that activation of specific complement components is involved in the initial trapping of prions in lymphoreticular organs early after infection.
TL;DR: It is concluded that mycorrhizal fungi have evolved to be multi-genomic, through accumulation of mutations in an essentially clonal genome, with some infrequent recombination events.
Abstract: Ancient asexuals directly contradict the evolutionary theories that explain why organisms should evolve a sexual life history. The mutualistic, arbuscular mycorrhizal fungi are thought to have been asexual for approximately 400 million years. In the absence of sex, highly divergent descendants of formerly allelic nucleotide sequences are thought to evolve in a genome. In mycorrhizal fungi, where individual offspring receive hundreds of nuclei from the parent, it has been hypothesized that a population of genetically different nuclei should evolve within one individual. Here we use DNA-DNA fluorescent in situ hybridization to show that genetically different nuclei co-exist in individual arbuscular mycorrhizal fungi. We also show that the population genetics techniques used in other organisms are unsuitable for detecting recombination because the assumptions and underlying processes do not fit the fungal genomic structure shown here. Instead we used a phylogenetic approach to show that the within-individual genetic variation that occurs in arbuscular mycorrhizal fungi probably evolved through accumulation of mutations in an essentially clonal genome, with some infrequent recombination events. We conclude that mycorrhizal fungi have evolved to be multi-genomic.