Life in an unusual intracellular niche: a bacterial symbiont infecting the nucleus of amoebae

Amoebae serve as hosts for various intracellular bacteria, including human pathogens. These microbes are able to overcome amoebal defense mechanisms and successfully establish a niche for replication, which is usually the cytoplasm. Here, we report on the discovery of a bacterial symbiont that is located inside the nucleus of its Hartmannella sp. host. This symbiont, tentatively named ‘Candidatus Nucleicultrix amoebiphila'', is only moderately related to known bacteria (∼90% 16S and 23S rRNA sequence similarity) and member of a novel clade of protist symbionts affiliated with the Rickettsiales and Rhodospirillales. Screening of 16S rRNA amplicon data sets revealed a broad distribution of these bacteria in freshwater and soil habitats. ‘Candidatus Nucleicultrix amoebiphila'' traffics within 6 h post infection to the host nucleus. Maximum infection levels are reached after 96–120 h, at which time point the nucleus is pronouncedly enlarged and filled with bacteria. Transmission of the symbionts occurs vertically upon host cell division but may also occur horizontally through host cell lysis. Although we observed no impact on the fitness of the original Hartmannella sp. host, the bacteria are rather lytic for Acanthamoeba castellanii. Intranuclear symbiosis is an exceptional phenomenon, and amoebae represent an ideal model system to further investigate evolution and underlying molecular mechanisms of these unique microbial associations.     

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database

Background  

The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally used for illustration purposes, KEGG Pathways through KGML (KEGG Markup Language) files, can provide complete reaction sets and introduce species versioning, which offers advantages for the scope of cellular metabolism simulation modelling. In this project, KEGGconverter is described, implemented also as a web-based application, which uses as source KGML files, in order to construct integrated pathway SBML models fully functional for simulation purposes.     

The "open" and "closed" structures of the type-C inorganic pyrophosphatases from Bacillus subtilis and Streptococcus gordonii.

Recently, a new class of soluble inorganic pyrophosphatase (type-C PPase) has been described that is not homologous in amino acid sequence or kinetic properties to the well-studied PPases (types A and B) found in many organisms from bacteria to humans and thought to be essential to the cell. Structural studies of the type-C PPases from Streptococcus gordonii and Bacillus subtilis reveal a homodimeric structure, with each polypeptide folding into two domains joined by a flexible hinge. The active site, formed at the interface between the N and C-terminal domains, binds two manganese ions approximately 3.6 A apart in a conformation resembling binuclear metal centres found in other hydrolytic enzymes. An activated water molecule bridging the two metal ions is likely poised for nucleophilic attack of the substrate. Importantly, the S. gordonii and B. subtilis enzymes have crystallised in strikingly different conformations. In both subunits of the S. gordonii crystal structure (1.5 A resolution) the C-terminal domain is positioned such that the active site is occluded, with a sulphate ion bound in the active site. In contrast, in the B. subtilis structure (3.0 A resolution) the C-terminal domain is rotated by about 90 degrees, leaving the active site wide open and accessible for substrate binding.     

Herbivory in global climate change research: direct effects of rising temperature on insect herbivores

This review examines the direct effects of climate change on insect herbivores. Temperature is identified as the dominant abiotic factor directly affecting herbivorous insects. There is little evidence of any direct effects of CO₂ or UVB. Direct impacts of precipitation have been largely neglected in current research on climate change. Temperature directly affects development, survival, range and abundance. Species with a large geographical range will tend to be less affected. The main effect of temperature in temperate regions is to influence winter survival; at more northerly latitudes, higher temperatures extend the summer season, increasing the available thermal budget for growth and reproduction. Photoperiod is the dominant cue for the seasonal synchrony of temperate insects, but their thermal requirements may differ at different times of year. Interactions between photoperiod and temperature determine phenology; the two factors do not necessarily operate in tandem. Insect herbivores show a number of distinct life‐history strategies to exploit plants with different growth forms and strategies, which will be differentially affected by climate warming. There are still many challenges facing biologists in predicting and monitoring the impacts of climate change. Future research needs to consider insect herbivore phenotypic and genotypic flexibility, their responses to global change parameters operating in concert, and awareness that some patterns may only become apparent in the longer term.     

Differential effect of recruitment maneuvres on pulmonary blood flow and oxygenation during HFOV in preterm lambs.

The effects of lung volume recruitment manouvres on pulmonary blood flow (PBF) during high-frequency oscillatory ventilation (HFOV) in preterm neonates are unknown. Since increased airway pressure adversely affects PBF, we compared the effects of two HFOV recruitment strategies on PBF and oxygenation index (OI). Preterm lambs (128+/-1 day gestation; term approximately 150 days) were anesthetized and ventilated using HFOV (10 Hz, 33% tI) with a mean airway pressure (Pao) of 15 cmH2O. Lung volume was recruited by either increasing Pao to 25 cmH2O for 1 min, repeated five times at 5-min intervals (Sigh group; n=5) or stepwise (5 cmH2O) changes in Pao at 5-min intervals incrementing up to 30 cmH2O then decrementing back to 15 cmH2O (Ramp group; n=6). Controls (n=5) received constant HFOV at 15 cmH2O. PBF progressively decreased (by 45+/-4%) and OI increased (by 15+/-6%, indicating reduced oxygenation) in controls during HFOV, which was similar to the changes observed in the Sigh group of lambs. In the Ramp group, PBF fell (by 54+/-10%) as airway pressure increased (r2=0.99), although the PBF did not increase again as the Pao was subsequently reduced. The OI decreased (by 47+/-9%), reflecting improved oxygenation at high Pao levels during HFOV in the Ramp group. However, high Pao restored retrograde PBF during diastole in four of six lambs, indicating the restoration of right-to-left shunting through the ductus arteriosus. Thus the choice of volume recruitment maneuvre influences the magnitude of change in OI and PBF that occurs during HFOV. Despite significantly improving OI, the ramp recruitment approach causes sustained changes in PBF.     

The need for co-product allocation in the life cycle assessment of agricultural systems—is “biophysical” allocation progress?

Purpose

Several new “biophysical” co-product allocation methodologies have been developed for LCA studies of agricultural systems based on proposed physical or causal relationships between inputs and outputs (i.e. co-products). These methodologies are thus meant to be preferable to established allocation methodologies such as economic allocation under the ISO 14044 standard. The aim here was to examine whether these methodologies really represent underlying physical relationships between the material and energy flows and the co-products in such systems, and hence are of value.

Methods

Two key components of agricultural LCAs which involve co-product allocation were used to provide examples of the methodological challenges which arise from adopting biophysical allocation in agricultural LCA: (1) the crop production chain and (2) the multiple co-products produced by animals. The actual “causal” relationships in these two systems were illustrated, the energy flows within them detailed, and the existing biophysical allocation methods, as found in literature, were critically evaluated in the context of such relationships.

Results and discussion

The premise of many biophysical allocation methodologies has been to define relationships which describe how the energy input to agricultural systems is partitioned between co-products. However, we described why none of the functional outputs from animal or crop production can be considered independently from the rest on the basis of the inputs to the system. Using the example of manure in livestock systems, we also showed why biophysical allocation methodologies are still sensitive to whether a system output has economic value or not. This sensitivity is a longstanding criticism of economic allocation which is not resolved by adopting a biophysical approach.

Conclusions

The biophysical allocation methodologies for various aspects of agricultural systems proposed to date have not adequately explained how the physical parameters chosen in each case represent causal physical mechanisms in these systems. Allocation methodologies which are based on shared (but not causal) physical properties between co-products are not preferable to allocation based on non-physical properties within the ISO hierarchy on allocation methodologies and should not be presented as such.

     

The dietary flavonoid kaempferol effectively inhibits HIF-1 activity and hepatoma cancer cell viability under hypoxic conditions

Hepatocellular carcinoma (HCC) is characterized by high mortality rates and resistance to conventional treatment. HCC tumors usually develop local hypoxia, which stimulates proliferation of cancer cells and renders them resilient to chemotherapy. Adaptation of tumor cells to the hypoxic conditions depends on the hypoxia-inducible factor 1 (HIF-1). Over-expression of its regulated HIF-1α subunit, an important target of anti-cancer therapy, is observed in many cancers including HCC and is associated with severity of tumor growth and poor patient prognosis. In this report we investigate the effect of the dietary flavonoid kaempferol on activity, expression levels and localization of HIF-1α as well as viability of human hepatoma (Huh7) cancer cells. Treatment of Huh7 cells with kaempferol under hypoxic conditions (1% oxygen) effectively inhibited HIF-1 activity in a dose-dependent manner (IC₅₀ = 5.16 μM). The mechanism of this inhibition did not involve suppression of HIF-1α protein levels but rather its mislocalization into the cytoplasm due to inactivation of p44/42 MAPK by kaempferol (IC₅₀ = 4.75 μM). Exposure of Huh7 cells to 10 μΜ kaempferol caused significant reduction of their viability, which was remarkably more evident under hypoxic conditions. In conclusion, kaempferol, a non-toxic natural food component, inhibits both MAPK and HIF-1 activity at physiologically relevant concentrations (5-10 μM) and suppresses hepatocarcinoma cell survival more efficiently under hypoxia. It has, therefore, potential as a therapeutic or chemopreventive anti-HCC agent.     

Intra-amniotic LPS and antenatal betamethasone: inflammation and maturation in preterm lamb lungs

The proinflammatory stimulus of chorioamnionitis is commonly associated with preterm delivery. Women at risk of preterm delivery receive antenatal glucocorticoids to functionally mature the fetal lung. However, the effects of the combined exposures of chorioamnionitis and antenatal glucocorticoids on the fetus are poorly understood. Time-mated ewes with singleton fetuses received an intra-amniotic injection of lipopolysaccharide (LPS) either preceding or following maternal intramuscular betamethasone 7 or 14 days before delivery, and the fetuses were delivered at 120 days gestational age (GA) (term = 150 days GA). Gestation matched controls received intra-amniotic and maternal intramuscular saline. Compared with saline controls, intra-amniotic LPS increased inflammatory cells in the bronchoalveolar lavage and myeloperoxidase, Toll-like receptor 2 and 4 mRNA, PU.1, CD3, and Foxp3-positive cells in the fetal lung. LPS-induced lung maturation measured as increased airway surfactant and improved lung gas volumes. Intra-amniotic LPS-induced inflammation persisted until 14 days after exposure. Betamethasone treatment alone induced modest lung maturation but, when administered before intra-amniotic LPS, suppressed lung inflammation. Interestingly, betamethasone treatment after LPS did not counteract inflammation but enhanced lung maturation. We conclude that the order of exposures of intra-amniotic LPS or maternal betamethasone had large effects on fetal lung inflammation and maturation.     

Protein Disorder and Short Conserved Motifs in Disordered Regions Are Enriched near the Cytoplasmic Side of Single-Pass Transmembrane Proteins

Intracellular juxtamembrane regions of transmembrane proteins play pivotal roles in cell signalling, mediated by protein-protein interactions. Disordered protein regions, and short conserved motifs within them, are emerging as key determinants of many such interactions. Here, we investigated whether disorder and conserved motifs are enriched in the juxtamembrane area of human single-pass transmembrane proteins. Conserved motifs were defined as short disordered regions that were much more conserved than the adjacent disordered residues. Human single-pass proteins had higher mean disorder in their cytoplasmic segments than their extracellular parts. Some, but not all, of this effect reflected the shorter length of the cytoplasmic tail. A peak of cytoplasmic disorder was seen at around 30 residues from the membrane. We noted a significant increase in the incidence of conserved motifs within the disordered regions at the same location, even after correcting for the extent of disorder. We conclude that elevated disorder within the cytoplasmic tail of many transmembrane proteins is likely to be associated with enrichment for signalling interactions mediated by conserved short motifs.     

Tectonic epikeratoplasty with ethanol-stored donor corneas

To evaluate the efficacy and outcomes of tectonic epikeratoplasty with use of ethanol-preserved corneal grafts for the management of perforated corneal melts. The present retrospective case series includes 10 eyes which underwent tectonic epikeratoplasty for perforated corneal melts. The stromal remainders of Descemet membrane endothelial keratoplasty (DMEK) and Descemet stripping automated endothelial keratoplasty (DSAEK) graft preparation were stored in 95% ethanol and used as emergency tectonic grafts for restoring globe integrity after sterile and infectious perforated corneal melts. In 6 cases with subtotal corneal melt, DMEK remainders (endothelium-denuded corneoscleral buttons) were used for ‘limbus to limbus’ tectonic epikeratoplasty and in 4 cases DSAEK remainders (anterior stroma) were used to seal focal perforated melts. Graft storage time was 5.1?±?4.9 (ranging from 0.5 to 17) months. The surgeries were successful in all cases with restitution of the globe integrity. During the postoperative course 4 cases developed a graft melt (corneoscleral button for limbus to limbus tectonic epikeratoplasty, n?=?3; lamellar patch, n?=?1) within 2–6 months after the initial procedure. Three patients underwent successful repeat tectonic epikeratoplasty. In the fourth case of graft melt the globe was enucleated due to underlying expulsive haemorrhage and severe pain. The short-term results of the present case series suggest that the use of ethanol-stored stromal remainder of donor corneas after endothelial keratoplasty is an efficient temporary measure for tectonic restoration of perforated corneas.