Changing the epidemiology of carbapenem-resistant Pseudomonas aeruginosa in a Brazilian teaching hospital: the replacement of São Paulo metallo-β-lactamase-producing isolates

In Brazil, carbapenem-resistant Pseudomonas aeruginosa isolates are closely related to the S?o Paulo metallo-β-lactamase (SPM) Brazilian clone. In this study, imipenem-resistant isolates were divided in two sets, 2002/2003 and 2008/2009, analysed by pulsed field gel electrophoresis and tested for the Ambler class B metallo-β-lactamase (MBL) genes blaSPM-1, blaIMP and blaVIM. The results show a prevalence of one clone related to the SPM Brazilian clone in 2002/2003. In 2008/2009, P. aeruginosa isolates were mostly MBL negative, genetically diverse and unrelated to those that had been detected earlier. These findings suggest that the resistance to carbapenems by these recent P. aeruginosa isolates was not due to the spread of MBL-positive SPM-related clones, as often observed in Brazilian hospitals.     

Data integration technologies: an unfulfilled revolution in the drug discovery process?

Successful life science data integration is a complex feat facing today's researchers and bioinformaticians. It demands the seamless access, integration and query of unprecedented amounts of disparate biological data to advance the pace and effectiveness of new drug discovery. This article outlines the current state of technologies available to help achieve this feat. It explores the evolutionary processes that created these challenges, and the underpinnings of several technological innovations working to overcome them. Together, these technologies aim to change the face of drug R&D through an enhanced understanding and interpretation of life sciences data.     

Pouring Salt on a Wound: Pseudomonas aeruginosa Virulence Factors Alter Na+ and Cl? Flux in the Lung

Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen with multiple niches in the human body, including the lung. P. aeruginosa infections are particularly damaging or fatal for patients with ventilator-associated pneumonia, chronic obstructive pulmonary disease, and cystic fibrosis (CF). To establish an infection, P. aeruginosa relies on a suite of virulence factors, including lipopolysaccharide, phospholipases, exoproteases, phenazines, outer membrane vesicles, type III secreted effectors, flagella, and pili. These factors not only damage the epithelial cell lining but also induce changes in cell physiology and function such as cell shape, membrane permeability, and protein synthesis. While such virulence factors are important in initial infection, many become dysregulated or nonfunctional during the course of chronic infection. Recent work on the virulence factors alkaline protease (AprA) and CF transmembrane conductance regulator inhibitory factor (Cif) show that P. aeruginosa also perturbs epithelial ion transport and osmosis, which may be important for the long-term survival of this microbe in the lung. Here we discuss the literature regarding host physiology-altering virulence factors with a focus on Cif and AprA and their potential roles in chronic infection and immune evasion.     

Drug metabolism by cultured human hepatocytes: how far are we from the in vivo reality?

The investigation of metabolism is an important milestone in the course of drug development. Drug metabolism is a determinant of drug pharmacokinetics variability in human beings. Fundamental to this are phenotypic differences, as well as genotypic differences, in the expression of the enzymes involved in drug metabolism. Genotypic variability is easy to identify by means of polymerase chain reaction-based or DNA chip-based methods, whereas phenotypic variability requires direct measurement of enzyme activities in liver, or, indirectly, measurement of the rate of metabolism of a given compound in vivo. There is a great deal of phenotypic variability in human beings, only a minor part being attributable to gene polymorphisms. Thus, enzyme activity measurements in a series of human livers, as well as in vivo studies with human volunteers, show that phenotypic variability is, by far, much greater than genotypic variability. In vitro models are currently used to investigate the hepatic metabolism of new compounds. Cultured human hepatocytes are considered to be the closest model to the human liver. However, the fact that hepatocytes are placed in a microenvironment that differs from that of the cells in the liver raises the question of to what extent drug metabolism variability observed in vitro actually reflects that in the liver in vivo. This issue has been examined by investigating the metabolism of the model compound, aceclofenac (an approved analgesic/anti-inflammatory drug), both in vitro and in vivo. Hepatocytes isolated from programmed liver biopsies were incubated with aceclofenac, and the metabolites formed were investigated by HPLC. The patients were given the drug during the course of clinical recovery, and the metabolites, largely present in urine, were analysed. In vitro and in vivo data from the same individual were compared. There was a good correlation between the in vitro and in vivo relative abundance of oxidised metabolites (4'-OH-aceclofenac + 4'-OH-diclofenac; Spearman's rho = 0.855), and the hydrolysis of aceclofenac (diclofenac + 4'-OH-aceclofenac + 4'-OH-diclofenac; rho = 0.691), while the conjugation of the drug in vitro was somewhat lower than in vivo. Globally, the metabolism of aceclofenac in vitro correlated with the amount of metabolites excreted in urine after 16 hours (rho = 0.95). Overall, although differing among assays, the in vitro/in vivo metabolism data for each patient were surprisingly similar. Thus, the variability observed in vitro appears to reflect genuine phenotypic variability among the donors.     

Acetate synthesis from 2 CO2 in acetogenic bacteria: is carbon monoxide an intermediate?

Cultures of Acetobacterium woodii and Clostridium thermoaceticum growing on fructose or glucose, respectively, were found to produce small, but significant amounts of carbon monoxide. In the gas phase of the cultures up to 53 ppm CO were determined. The carbon monoxide production was completely inhibited by 1 mM cyanide. Cultures and cell suspensions of both acetogens incorporated ¹⁴CO specifically into the carboxyl group of acetate. This CO fixation into C₁ of acetate was unaffected by cyanide (1 mM). The findings are taken to indicate that CO (in a bound form) is the physiological precursor of the C₁ of acetate in acetate synthesis from CO₂. The cyanide inhibition experiments support the hypothesis that the cyanide-sensitive carbon monoxide dehydrogenase may serve to reduce CO₂ to CO rather than to incorporate the carbonyl into C₁ of acetate.     

Structural characterization of a Δ3, Δ2-enoyl-CoA isomerase from Pseudomonas aeruginosa: implications for its involvement in unsaturated fatty acid metabolism

Gene PA4980 from Pseudomonas aeruginosa encodes a putative enoyl-coenzyme A hydratase/isomerase that is associated with the function of the biofilm dispersion-inducing signal molecule cis-2-decenoic acid. To elucidate the role of PA4980 in cis-2-decenoic acid biosynthesis, we reported the crystal structure of its protein product at 2.39 Å. The structural analysis and substrate binding prediction suggest that it acts as a monofunctional enoyl-coenzyme A isomerase, implicating an alternative pathway of the cis-2-decenoic acid synthesis.     

Outlook on sponge reproduction science in the last ten years: are we far from where we should be?

To comprehend the state of the art of sponge reproduction science (SRS), we quantified and analyzed the trends in SRS in the last decade, aiming to answer three questions: (i) Were there fewer SRS works presented during the last sponge conference? (ii) Did the number of SRS publications decline in the last decade? (iii) Does the number of abstracts at sponge conferences influence overall SRS publications? In addition, we checked whether the SRS community has answered Ereskovsky’s ‘five important questions’, enabling us to advance SRS enough to be considered as a fourth period of this scientific field. We found that SRS was less represented at the last sponge conference, despite an increase in the number of publications during the last decade. Moreover, the number of abstracts presented at sponge conferences contributed to a small portion (25%) of the published works in this area during the last decade. In addition, we found that two of the five Ereskovsky’s questions are still mostly not answered. Thus, we conclude that SRS is healthy and advancing steadily, especially in some subareas (e.g. developmental biology and life history). There are still much to advance, but this is still a strong field of biological science research.     

Increasing dissolved silica trends in the Rhine River: an effect of recovery from high P loads?

The development of river dams and further human activities (causing increased nitrogen (N) and phosphorus (P) nutrient loads), are responsible for a decline in dissolved silica concentrations (DSi) in many river systems. Here, the impact of the reduction of N- and P-concentrations on DSi is examined for the Rhine River. During the last decade of the twentieth century, annual average DSi concentrations increased by ~70% in the Rhine at Bimmen/Lobith, whereas nitrate (NO₃) and phosphate (PO₄) concentrations decreased by approximately one third. Accordingly, decadal changes in nutrient elemental ratios shifted the river system from DSi-limitation to P-limitation. Specifically, a seasonal DSi-concentration increase is observed from May to December for the Rhine River (with exception of June). Observed increases in DSi concentration are probably due to improvements in water-basin and land-use management, specifically a reduction in point-source P discharge, leading to P-limiting conditions for diatom growth. Data of the warm season suggest that as the system is moving through the transition from P-excess to P-limitation conditions, P-limitation according to the elemental ratio DSi/total phosphorus (TP) is occurring later than for the ratio DSi/PO₄-P. Latter ratio will be buffered around ~16:1 during growing season. Reduction of N fertilization is less relevant, as N-limitation with respect to DSi is not achieved, even at the end of the analyzed period, but N-limitation may be reached in the future. Analysis of discharge–DSi relationship supports the hypothesis that DSi increase is affected by increasing P-limitation during the warm period and not only due to hydrological reasons. Results suggest, however, that the influence of hydrological parameters needs to be addressed in research for DSi concentration changes due to changed nutrient loads. Despite an overall increase in water temperature of 3°C over a 50-year period, no correlation with temperature was found for the last two decades of the twentieth century, for which DSi-data were available. In conclusion, in case of eutrophied river systems with excess of P, P-reduction may lead to an increase of DSi concentrations under certain conditions. This in turn is expected to impact not only DSi-sensitive coastal-zone ecosystems impacted by eutrophication but the carbon cycle as well.     

The peri-urban interface and house infestation with Triatoma infestans in the Argentine Chaco: an underreported process?

Peri-urban infestations with triatomine bugs, their sources and their dynamics haverarely been investigated. Here, we corroborated the reported occurrence ofTriatoma infestans in a peri-urban area and in neighbouring ruralhouses in Pampa del Indio, in the Argentine Chaco, and identified its putativesources using spatial analysis and demographic questionnaires. Peri-urbanhouseholders reported that 10% of their premises had triatomines, whereas T.infestans was collected by timed manual searches or community-basedsurveillance in only nine (3%) houses. Trypanosoma cruzi-infectedT. infestans and Triatoma sordida were collectedindoors only in peri-urban houses and were infected with TcVand TcI, respectively. The triatomines fed on chickens,cats and humans. Peri-urban infestations were most frequent in a squatter settlementand particularly within the recently built mud houses of rural immigrants, withlarge-sized households, more dogs and cats and more crowding. Several of the observedinfestations were most likely associated with passive bug transport from othersources and with active bug dispersal from neighbouring foci. Thus, the households inthe squatter settlement were at a greater risk of bug invasion and colonisation. Insum, the incipient process of domestic colonisation and transmission, along withpersistent rural-to-urban migratory flows and unplanned urbanisation, indicate theneed for active vector surveillance and control actions at the peri-urban interfaceof the Gran Chaco.     

Cyclopentane-nucleobase coupling in the synthesis of carbocyclic L-nucleosides: is a SN2-reaction an alternative to the Mitsunobu-reaction?

Several carbocyclic L-nucleosides have been synthesized by coupling a cyclopentane-system with heterocycles according to a modified Mitsunobu-protocol. This reaction gave two regioisomers, the N1-alkylated product and an unwanted O(2)-product. A simple S(N)2-reaction has been investigated as an alternative for such couplings.     

C-to-U conversion in the intercistronic ndhI/ndhG RNA of plastids from monocot plants: conventional editing in an unconventional small reading frame?

Editing of plastid RNAs proceeds by C-to-U, in hornwort species also by extensive U-to-C, transitions, which predominantly lead to the restoration of codons for structurally and/or functionally important, conserved amino acid residues. So far, only one instance of editing outside coding regions has been reported - in the psbL/ psbF intergenic region of Ginkgo biloba. This site was proposed to have no functional importance. Here we present an evaluation of an editing site in the ndhI/ ndhG intergenic region in a related group of monocot plants. Efficient editing of this site, as well as the phylogenetic conservation of the resulting uridine residue, point at an important role for the sequence restored by editing. Two potential functions can be envisaged. (1) RNA secondary structure predictions suggest that the C-to-U conversion at this site can lead to a modified stem/loop structure of the ndhG 5' UTR, which could influence ndhG expression. (2) Alternatively, editing of the ndhI/ ndhG intergenic region may tag a so far unidentified small (12-codon) ORF, and lead to the restoration of a conserved phenylalanine codon. A screen with specific antibodies elicited against the putative peptide failed to detect such a peptide in chloroplast fractions. However, this failure may be attributable to its low and/or development-specific expression.     

Why is grouper larval rearing difficult?: an approach from the development of the feeding apparatus in early stage larvae of the grouper,Epinephelus coioides

The osteological development of elements forming the oral cavity was examined in early stage larvae of the grouper,Epinephelus coioides, from hatching to 242.5 hours after hatching. By the time of initial mouth opening, at 54 hours after hatching, the fundamental elements, composed of the trabecula, some components of the lower branchial and hyoid arches, the quadrate and symplectic-hyomandibular cartilages, maxilla and Meckel's cartilage, had appeared. No further elements were observed until 165 hours after initial mouth opening, except some components in the lower branchial arch and head region. The appearance of new elements and initial ossification of existing cartilage occurred thereafter, but all elements related to feeding either had not appeared or had not started ossifying until 188.5 hours after initial mouth opening. Based on the morphology and developmental modes of these elements, the feeding mode of grouper larvae was considered to be “sucking/grasping.” However, the appearance and ossification of elements occurred slowly, with no transitional phase from sucking to grasping modes of feeding being observed during the study; such delayed development of the feeding-related bony elements was considered to be a cause of the difficulty in rearing early stage grouper larvae.     

Impaired TCA cycle flux in mitochondria in skeletal muscle from type 2 diabetic subjects: marker or maker of the diabetic phenotype?

The diabetic phenotype is complex, requiring elucidation of key initiating defects. Recent research has shown that diabetic myotubes express a primary reduced tricarboxylic acid (TCA) cycle flux. A reduced TCA cycle flux has also been shown both in insulin resistant offspring of T2D patients and exercising T2D patients in vivo. This review will discuss the latest advances in the understanding of the molecular mechanisms regulating the TCA cycle with focus on possible underlying mechanism which could explain the impaired TCA flux in insulin resistant human skeletal muscle in type 2 diabetes. A reduced TCA is both a marker and a maker of the diabetic phenotype.     

The structure of the 2[4Fe–4S] ferredoxin from Pseudomonas aeruginosa at 1.32-Å resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values

The structure of the 2[4Fe–4S] ferredoxin (PaFd) from Pseudomonas aeruginosa, which belongs to the Allochromatium vinosum (Alvin) subfamily, has been determined by X-ray crystallography at 1.32-Å resolution, which is the highest up to now for a member of this subfamily of Fds. The main structural features of PaFd are similar to those of AlvinFd. However, the significantly higher resolution of the PaFd structure makes possible a reliable comparison with available high-resolution structures of [4Fe–4S]-containing Fds, in an effort to rationalize the unusual electrochemical properties of Alvin-like Fds. Three major factors contributing to the reduction potential values of [4Fe–4S]^2+/+ clusters of Fds, namely, the surface accessibility of the clusters, the N–H···S hydrogen-bonding network, and the volume of the cavities hosting the clusters, are extensively discussed. The volume of the cavities is introduced in the present work for the first time, and can in part explain the very negative potential of cluster I of Alvin-like Fds.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

MEK mediates in vitro neural transdifferentiation of the adult newt retinal pigment epithelium cells: Is FGF2 an induction factor?

Adult newts can regenerate their entire retinas through transdifferentiation of the retinal pigment epithelium (RPE) cells. As yet, however, underlying molecular mechanisms remain virtually unknown. On the other hand, in embryonic/larval vertebrates, an MEK [mitogen‐activated protein kinase (MAPK)/extracellular signal‐regulated kinase (ERK) kinase] pathway activated by fibroblast growth factor‐2 (FGF2) is suggested to be involved in the induction of transdifferentiation of the RPE into a neural retina. Therefore, we examined using culture systems whether the FGF2/MEK pathway is also involved in the adult newt RPE transdifferentiation. Here we show that the adult newt RPE cells can switch to neural cells expressing pan‐retinal‐neuron (PRN) markers such as acetylated tubulin, and that an MEK pathway is essential for the induction of this process, whereas FGF2 seems an unlikely primary induction factor. In addition, we show by immunohistochemistry that the PRN markers are not expressed until the 1–3 cells thick regenerating retina, which contains retinal progenitor cells, appears. Our current results suggest that the activation of an MEK pathway in RPE cells might be involved in the induction process of retinal regeneration in the adult newt, however if this is the case, we must assume complementary mechanisms that repress the MEK‐mediated misexpression of PRN markers in the initial process of transdifferentiation.     

MEK mediates in vitro neural transdifferentiation of the adult newt retinal pigment epithelium cells: Is FGF2 an induction factor?

Adult newts can regenerate their entire retinas through transdifferentiation of the retinal pigment epithelium (RPE) cells. As yet, however, underlying molecular mechanisms remain virtually unknown. On the other hand, in embryonic/larval vertebrates, an MEK [mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) kinase] pathway activated by fibroblast growth factor-2 (FGF2) is suggested to be involved in the induction of transdifferentiation of the RPE into a neural retina. Therefore, we examined using culture systems whether the FGF2/MEK pathway is also involved in the adult newt RPE transdifferentiation. Here we show that the adult newt RPE cells can switch to neural cells expressing pan-retinal-neuron (PRN) markers such as acetylated tubulin, and that an MEK pathway is essential for the induction of this process, whereas FGF2 seems an unlikely primary induction factor. In addition, we show by immunohistochemistry that the PRN markers are not expressed until the 1-3 cells thick regenerating retina, which contains retinal progenitor cells, appears. Our current results suggest that the activation of an MEK pathway in RPE cells might be involved in the induction process of retinal regeneration in the adult newt, however if this is the case, we must assume complementary mechanisms that repress the MEK-mediated misexpression of PRN markers in the initial process of transdifferentiation.