Microbe Profile: Aquifex aeolicus: an extreme heat-loving bacterium that feeds on gases and inorganic chemicals.

The bacterium 'Aquifex aeolicus' is the model organism for the deeply rooted phylum Aquificae. This 'water-maker' is an H2-oxidizing microaerophile that flourishes in extremely hot marine habitats, and it also thrives on the sulphur compounds commonly found in volcanic environments. 'A. aeolicus' has hyper-stable proteins and a fully sequenced genome, with some of its essential metabolic pathways deciphered (including energy conservation). Many of its proteins have also been characterized (especially structurally), including many of the enzymes involved in replication, transcription, RNA processing and cell envelope biosynthesis. Enzymes that are of promise for biotechnological applications have been widely investigated in this species. 'A. aeolicus' has also added to our understanding of the origins of life and evolution.

Stereospecific interactions between chiral inorganic nanomaterials and biological systems.

Chirality is ubiquitous in nature and plays mysterious and essential roles in maintaining key biological and physiological processes. As biological systems display high selectivity for chiral biomolecules, chiral bio-nanoscience has become a popular research field during the last decade. Homochirality, as an essential attribute of natural compounds (l-amino acids, d-sugars, etc.), inspired the emergence of synthetic chiral nanomaterials, which in turn impacted their biological functions and fates. This review is a comprehensive overview of the interactions between chiral inorganic nanostructures and biosystems. We start with the recent progress in biocompatible chiral nanomaterials and focus on stereospecific biological interactions ranging from enantioselective reactions in applications such as sensing and catalysis to chirality-dependent controllable manipulation of cell behaviours and finally to enantiopure nanoplatforms for improved disease therapy. We also discuss the current challenges and future potential of these chiral nanotechnologies in biomedicine and bioengineering, provide strategies to overcome these barriers and offer a future perspective.

Biodegradable Inorganic Nanoparticles for Cancer Theranostics: Insights into the Degradation Behavior.

Inorganic nanoparticles as a versatile nanoplatform have been broadly applied in the diagnosis and treatment of cancers due to their inherent superior physicochemical properties (including magnetic, thermal, optical, and catalytic performance) and excellent functions (e.g., imaging, targeted delivery, and controlled release of drugs) through surface functional modification or ingredient dopant. However, in practical biological applications, inorganic nanomaterials are relatively difficult to degrade and excrete, which induces a long residence time in living organisms and thus may cause adverse effects, such as inflammation and tissue cysts. Therefore, the development of biodegradable inorganic nanomaterials is of great significance for their biomedical application. This Review will focus on the recent advances of degradable inorganic nanoparticles for cancer theranostics with highlight on the degradation mechanism, aiming to offer an in-depth understanding of degradation behavior and related biomedical applications. Finally, key challenges and guidelines will be discussed to explore biodegradable inorganic nanomaterials with minimized toxicity issues, facilitating their potential clinical translation in cancer diagnosis and treatment.

Inorganic nitrate, hypoxia, and the regulation of cardiac mitochondrial respiration-probing the role of PPARα.

Dietary inorganic nitrate prevents aspects of cardiac mitochondrial dysfunction induced by hypoxia, although the mechanism is not completely understood. In both heart and skeletal muscle, nitrate increases fatty acid oxidation capacity, and in the latter case, this involves up-regulation of peroxisome proliferator-activated receptor (PPAR)α expression. Here, we investigated whether dietary nitrate modifies mitochondrial function in the hypoxic heart in a PPARα-dependent manner. Wild-type (WT) mice and mice without PPARα (Ppara-/-) were given water containing 0.7 mM NaCl (control) or 0.7 mM NaNO3 for 35 d. After 7 d, mice were exposed to normoxia or hypoxia (10% O2) for the remainder of the study. Mitochondrial respiratory function and metabolism were assessed in saponin-permeabilized cardiac muscle fibers. Environmental hypoxia suppressed mass-specific mitochondrial respiration and additionally lowered the proportion of respiration supported by fatty acid oxidation by 18% (P < 0.001). This switch away from fatty acid oxidation was reversed by nitrate treatment in hypoxic WT but not Ppara-/- mice, indicating a PPARα-dependent effect. Hypoxia increased hexokinase activity by 33% in all mice, whereas lactate dehydrogenase activity increased by 71% in hypoxic WT but not Ppara-/- mice. Our findings indicate that PPARα plays a key role in mediating cardiac metabolic remodeling in response to both hypoxia and dietary nitrate supplementation.-Horscroft, J. A., O'Brien, K. A., Clark, A. D., Lindsay, R. T., Steel, A. S., Procter, N. E. K., Devaux, J., Frenneaux, M., Harridge, S. D. R., Murray, A. J. Inorganic nitrate, hypoxia, and the regulation of cardiac mitochondrial respiration-probing the role of PPARα.

Moulds on cementitious building materials-problems, prevention and future perspectives.

Materials rich in organic and inorganic compounds, such as building materials or paints, represent an excellent substrate for the development of moulds. Several conditions affect mould's growth on cementitious materials, such as nutrient and water availability, temperature, pH and moisture. Microorganisms, and especially moulds, attack these surfaces and contribute to their erosion, thereby reducing the life of the structure itself and negatively affecting human health through inhalation, ingestion and dermal contact with spores. Interventions are based on The European Communities Council Directive 89/106/EEC, that obliges the use of materials, products and building elements that are resistant to fungi and other forms of degradation, and that do not constitute a health risk for users and the environment. This mini-review summarises the current state of problems related to mould growth on cementitious building materials, emphasising new innovative approaches for limiting or contrasting their growth. In particular, the use of nanoparticles and the related nanomaterials as well as the potential use of new "biocides" from natural sources is discussed.

In situ analyses of inorganic nutrient distribution in sweetcorn and maize kernels using synchrotron-based X-ray fluorescence microscopy.

BACKGROUND AND AIMS: Understanding the spatial distribution of inorganic nutrients within edible parts of plant products helps biofortification efforts to identify and focus on specific uptake pathways and storage mechanisms. METHODS: Kernels of sweetcorn (Zea mays) variety 'High zeaxanthin 103146' and maize inbred line 'Thai Floury 2' were harvested at two different maturity stages, and the distributions of K, P, S, Ca, Zn, Fe and Mn were examined in situ using synchrotron-based X-ray fluorescence microscopy. KEY RESULTS: The distribution of inorganic nutrients was largely similar between maize and sweetcorn, but differed markedly depending upon the maturity stage after further embryonic development. The micronutrients Zn, Fe and Mn accumulated primarily in the scutellum of the embryo during early kernel development, while trace amounts of these were found in the aleurone layer at the mature stage. Although P accumulated in the scutellum, there was no direct relationship between the concentrations of P and those of the micronutrients, compared with the linear trend between Zn and Fe concentrations. CONCLUSIONS: This study highlights the important role of the embryo as a micronutrient reserve for sweetcorn and maize kernels, and the need to understand how biofortification efforts can further increase the inorganic nutrient concentration of the embryo for human consumption.

Limited carbon source retards inorganic arsenic release during roxarsone degradation in Shewanella oneidensis microbial fuel cells.

Directly relevant to the toxicity, mobility, and fate of arsenic, the biotransformation of inorganic and organic arsenicals has been extensively concerned, including roxarsone, a widely applied organoarsenical feed additive in poultry industry. Yet, little is known about the transformation details of roxarsone in microbial fuel cells (MFC). In this study, a two-chambered Shewanella oneidensis MR-1 microbial fuel cell was employed to investigate the transformation processes of roxarsone at various carbon source levels. Results show that limited carbon source remarkably inhibited inorganic arsenic release along roxarsone transformation, whereas numerous arsenical species were detected to be released into systems with sufficient carbon source supply, including trivalent and pentavalent inorganic arsenics, monomethylarsonous acid (MMA), and 4-hydroxy-3-aminobenzene arsonic acid (HAPA). Shewanella oneidensis MR-1 was able to cleave the C-As bond of trivalent HAPA yielding inorganic arsenics and MMA, even in the absence of the arsI gene encoding ArsI C-As lyase. We proposed a two-step nitro- and pentavalent-arsenate group reduction pathway for the roxarsone bioelectrochemical transformation. In addition, results indicated that the attached cells onto the electrode surface played a key function in the two-step reduction of roxarsone to trivalent HAPA, whereas planktonic cells were most likely responsible for the C-As bond breakage and the following dearylation. With these qualitative and quantitative estimations, it provides new insights into the mechanistic understanding of the roxarsone biotransformation process in microbial fuel cells, which is important for the biogeochemical cycling of arsenic.

A computational method for selecting short peptide sequences for inorganic material binding.

Discovering or designing biofunctionalized materials with improved quality highly depends on the ability to manipulate and control the peptide-inorganic interaction. Various peptides can be used as assemblers, synthesizers, and linkers in the material syntheses. In another context, specific and selective material-binding peptides can be used as recognition blocks in mining applications. In this study, we propose a new in silico method to select short 4-mer peptides with high affinity and selectivity for a given target material. This method is illustrated with the calcite (104) surface as an example, which has been experimentally validated. A calcite binding peptide can play an important role in our understanding of biomineralization. A practical aspect of calcite is a need for it to be selectively depressed in mining sites.

In vivo degeneration and the fate of inorganic nanoparticles.

What happens to inorganic nanoparticles (NPs), such as plasmonic gold or silver, superparamagnetic iron oxide, or fluorescent quantum dot NPs after they have been administrated to a living being? This review discusses the integrity, biodistribution, and fate of NPs after in vivo administration. The hybrid nature of the NPs is described, conceptually divided into the inorganic core, the engineered surface coating comprising of the ligand shell and optionally also bio-conjugates, and the corona of adsorbed biological molecules. Empirical evidence shows that all of these three compounds may degrade individually in vivo and can drastically modify the life cycle and biodistribution of the whole heterostructure. Thus, the NPs may be decomposed into different parts, whose biodistribution and fate would need to be analyzed individually. Multiple labeling and quantification strategies for such a purpose will be discussed. All reviewed data indicate that NPs in vivo should no longer be considered as homogeneous entities, but should be seen as inorganic/organic/biological nano-hybrids with complex and intricately linked distribution and degradation pathways.

Photosynthetic use of inorganic carbon in deep-water kelps from the Strait of Gibraltar.

Mechanisms of inorganic carbon assimilation were investigated in the four deep-water kelps inhabiting sea bottoms at the Strait of Gibraltar; these species are distributed at different depths (Saccorhiza polysiches at shallower waters, followed by Laminaria ochroleuca, then Phyllariopsis brevipes and, at the deepest bottoms, Phyllariopsis purpurascens). To elucidate the capacity to use HCO3(-) as a source of inorganic carbon for photosynthesis in the kelps, different experimental approaches were used. Specifically, we measured the irradiance-saturated gross photosynthetic rate versus pH at a constant dissolved inorganic carbon (DIC) concentration of 2 mM, the irradiance-saturated apparent photosynthesis (APS) rate versus DIC, the total and the extracellular carbonic anhydrase (CAext), the observed and the theoretical photosynthetic rates supported by the spontaneous dehydration of HCO3(-) to CO2, and the δ(13)C signature in tissues of the algae. While S. polyschides and L. ochroleuca showed photosynthetic activity at pH 9.5 (around 1.0 µmol O2 m(-2) s(-1)), the activity was close to zero in both species of Phyllariopsis. The APS versus DIC was almost saturated for the DIC values of natural seawater (2 mM) in S. polyschides and L. ochroleuca, but the relationship was linear in P. brevipes and P. purpurascens. The four species showed total and CAext activities but the inhibition of the CAext originated the observed photosynthetic rates at pH 8.0 to be similar to the theoretical rates that could be supported by the spontaneous dehydration of HCO3(-). The isotopic (13)C signatures ranged from -17.40 ± 1.81 to -21.11 ± 1.73 ‰ in the four species. Additionally, the δ(13)C signature was also measured in the deep-water Laminaria rodriguezii growing at 60-80 m, showing even a more negative value of -26.49 ± 1.25 ‰. All these results suggest that the four kelps can use HCO3(-) as external carbon source for photosynthesis mainly by the action of external CAext, but they also suggest that the species inhabiting shallower waters show a higher capacity than the smaller kelps living in deeper waters. In fact, the photosynthesis in the two Phyllariopsis species could be accomplished by the spontaneous dehydration of HCO3(-) to CO2. These differences in the capacity to use HCO3(-) in photosynthesis among species could be important considering the increasing levels of atmospheric CO2 predicted for the near future.

Comparison of Bioavailability and Biotransformation of Inorganic and Organic Arsenic to Two Marine Fish.

Dietary uptake could be the primary route of arsenic (As) bioaccumulation in marine fish, but the bioavailability of inorganic and organic As remains elusive. In this study, we investigated the trophic transfer and bioavailability of As in herbivorous rabbitfish Siganus fuscescens and carnivorous seabass Lateolabrax japonicus. Rabbitfish were fed with one artificial diet or three macroalgae, whereas seabass were fed with one artificial diet, one polychaete, or two bivalves for 28 days. The six spiked fresh prey diets contained different proportions of inorganic As [As(III) and As(V)] and organic As compounds [methylarsenate (MMA), dimethylarsenate (DMA), and arsenobetaine (AsB)], and the spiked artificial diet mainly contained As(III) or As(V). We demonstrated that the trophic transfer factors (TTF) of As in both fish were negatively correlated with the concentrations of inorganic As in the diets, while there was no relationship between TTF and the AsB concentrations in the diets. Positive correlation was observed between the accumulated As concentrations and the AsB concentrations in both fish, suggesting that organic As compounds (AsB) were more trophically available than inorganic As. Furthermore, the biotransformation ability of seabass was higher than that in rabbitfish, which resulted in higher As accumulation in seabass than in rabbitfish. Our study demonstrated that different prey with different inorganic/organic As proportions resulted in diverse bioaccumulation of total As in different marine fish.

Strains of the Harmful Cyanobacterium Microcystis aeruginosa Differ in Gene Expression and Activity of Inorganic Carbon Uptake Systems at Elevated CO2 Levels.

Cyanobacteria are generally assumed to be effective competitors at low CO2 levels because of their efficient CO2-concentrating mechanism (CCM), and yet how bloom-forming cyanobacteria respond to rising CO2 concentrations is less clear. Here, we investigate changes in CCM gene expression at ambient CO2 (400 ppm) and elevated CO2 (1,100 ppm) in six strains of the harmful cyanobacterium Microcystis. All strains downregulated cmpA encoding the high-affinity bicarbonate uptake system BCT1, whereas both the low- and high-affinity CO2 uptake genes were expressed constitutively. Four strains downregulated the bicarbonate uptake genes bicA and/or sbtA, whereas two strains showed constitutive expression of the bicA-sbtA operon. In one of the latter strains, a transposon insert in bicA caused low bicA and sbtA transcript levels, which made this strain solely dependent on BCT1 for bicarbonate uptake. Activity measurements of the inorganic carbon (Ci) uptake systems confirmed the CCM gene expression results. Interestingly, genes encoding the RuBisCO enzyme, structural carboxysome components, and carbonic anhydrases were not regulated. Hence, Microcystis mainly regulates the initial uptake of inorganic carbon, which might be an effective strategy for a species experiencing strongly fluctuating Ci concentrations. Our results show that CCM gene regulation of Microcystis varies among strains. The observed genetic and phenotypic variation in CCM responses may offer an important template for natural selection, leading to major changes in the genetic composition of harmful cyanobacterial blooms at elevated CO2.

Macroscopic modelling of bioethanol production from potato peel wastes in batch cultures supplemented with inorganic nitrogen.

Inorganic nitrogen supplementation is commonly used to boost fermentation metabolism in yeast cultures. However, an excessive addition can induce an opposite effect. Hence, it is important to ensure that the ammonia supplemented to the culture leads to an improvement of the ethanol production while avoiding undesirable inhibition effects. To this end, a macroscopic model describing the influence of ammonia addition on Saccharomyces cerevisiae metabolism during bioethanol production from potato peel wastes has been developed. The model parameters are obtained by a simplified identification methodology in five steps. It is validated with experimental data and successfully predicts the dynamics of growth, substrate consumption (ammonia and fermentable sugar sources) and bioethanol production, even in cross validation. The model is used to determine the optimal quantity of supplemented ammonia required for maximizing bioethanol production from potato peel wastes in batch cultures.

Detection of a variable intracellular acid-labile carbon pool in Thalassiosira weissflogii (Heterokontophyta) and Emiliania huxleyi (Haptophyta) in response to changes in the seawater carbon system.

Accumulation of an intracellular pool of carbon (C(i) pool) is one strategy by which marine algae overcome the low abundance of dissolved CO2 (CO2 (aq) ) in modern seawater. To identify the environmental conditions under which algae accumulate an acid-labile C(i) pool, we applied a (14) C pulse-chase method, used originally in dinoflagellates, to two new classes of algae, coccolithophorids and diatoms. This method measures the carbon accumulation inside the cells without altering the medium carbon chemistry or culture cell density. We found that the diatom Thalassiosira weissflogii [(Grunow) G. Fryxell & Hasle] and a calcifying strain of the coccolithophorid Emiliania huxleyi [(Lohmann) W. W. Hay & H. P. Mohler] develop significant acid-labile C(i) pools. C(i) pools are measureable in cells cultured in media with 2-30 µmol l(-1) CO2 (aq), corresponding to a medium pH of 8.6-7.9. The absolute C(i) pool was greater for the larger celled diatoms. For both algal classes, the C(i) pool became a negligible contributor to photosynthesis once CO2 (aq) exceeded 30 µmol l(-1) . Combining the (14) C pulse-chase method and (14) C disequilibrium method enabled us to assess whether E. huxleyi and T. weissflogii exhibited thresholds for foregoing accumulation of DIC or reduced the reliance on bicarbonate uptake with increasing CO2 (aq) . We showed that the C(i) pool decreases with higher CO2 :HCO3 (-) uptake rates.

Mineral and non-carbon nutrient utilization and recovery during sequential phototrophic-heterotrophic growth of lipid-rich algae.

A critical factor in implementing microalgal biofuels for mass production is the nutrient requirements. The current study investigated the fate of macro- and micronutrients and their availability in a sequential phototrophic-heterotrophic production process for the lipid rich microalga Auxenochlorella protothecoides. More than 99 % (by weight) of overall process nutrients were supplied during the initial photoautotrophic stage reflecting its significantly larger volume. Under photoautotrophic growth conditions only 9-35 % of supplied Mn, S, Fe, N, Mg, and Cu and less than 5 % of P, Mo, Co, B, Zn, and Ca were consumed by the algae. The rest of these nutrients remain in the spent growth media during the culture concentration-down from an 800 L phototrophic pond to a 5 L heterotrophic fermenter. In contrast, Zn, Mo, Mn, Mg, Ca, and N were exhausted (90-99 % removal) during the first 25 h of the heterotrophic growth stage. The depletion of these key nutrients may have ultimately limited the final biomass density and/or lipid productivity achieved. Approximately 10-20 % of the total supplied S, Mn, Fe, N, and Cu and 5 % of Ca and Zn were assimilated into algal biomass. Several elements including N, P, Mn, B, Cu, Ca, Mg, S, and Fe were released back into the liquid phase by anaerobic digestion (AD) of the residual biomass after lipid extraction. The nutrients recovered from the AD effluent and remaining in the spent medium should be recycled or their initial concentration to the phototrophic stage decreased to enhance process economics and sustainability for future commercialization of algal-derived biofuels.

Inorganic polyphosphates: biologically active biopolymers for biomedical applications.

Inorganic polyphosphate (polyP) is a widely occurring but only rarely investigated biopolymer which exists in both prokaryotic and eukaryotic organisms. Only in the last few years, this polymer has been identified to cause morphogenetic activity on cells involved in human bone formation. The calcium complex of polyP was found to display a dual effect on bone-forming osteoblasts and bone-resorbing osteoclasts. Exposure of these cells to polyP (Ca(2+) complex) elicits the expression of cytokines that promote the mineralization process by osteoblasts and suppress the differentiation of osteoclast precursor cells to the functionally active mature osteoclasts dissolving bone minerals. The effect of polyP on bone formation is associated with an increased release of the bone morphogenetic protein 2 (BMP-2), a key mediator that activates the anabolic processes leading to bone formation. In addition, polyP has been shown to act as a hemostatic regulator that displays various effects on blood coagulation and fibrinolysis and might play an important role in platelet-dependent proinflammatory and procoagulant disorders.

Impacts of labile organic carbon concentration on organic and inorganic nitrogen utilization by a stream biofilm bacterial community.

In aquatic ecosystems, carbon (C) availability strongly influences nitrogen (N) dynamics. One manifestation of this linkage is the importance in the dissolved organic matter (DOM) pool of dissolved organic nitrogen (DON), which can serve as both a C and an N source, yet our knowledge of how specific properties of DOM influence N dynamics are limited. To empirically examine the impact of labile DOM on the responses of bacteria to DON and dissolved inorganic nitrogen (DIN), bacterial abundance and community composition were examined in controlled laboratory microcosms subjected to various combinations of dissolved organic carbon (DOC), DON, and DIN treatments. Bacterial communities that had colonized glass beads incubated in a stream were treated with various glucose concentrations and combinations of inorganic and organic N (derived from algal exudate, bacterial protein, and humic matter). The results revealed a strong influence of C availability on bacterial utilization of DON and DIN, with preferential uptake of DON under low C concentrations. Bacterial DON uptake was affected by the concentration and by its chemical nature (labile versus recalcitrant). Labile organic N sources (algal exudate and bacterial protein) were utilized equally well as DIN as an N source, but this was not the case for the recalcitrant humic matter DON treatment. Clear differences in bacterial community composition among treatments were observed based on terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes. C, DIN, and DON treatments likely drove changes in bacterial community composition that in turn affected the rates of DON and DIN utilization under various C concentrations.

Efficiency of photosynthetic water oxidation at ambient and depleted levels of inorganic carbon.

Over 40 years ago, Joliot et al. (Photochem Photobiol 10:309-329, 1969) designed and employed an elegant and highly sensitive electrochemical technique capable of measuring O2 evolved by photosystem II (PSII) in response to trains of single turn-over light flashes. The measurement and analysis of flash-induced oxygen evolution patterns (FIOPs) has since proven to be a powerful method for probing the turnover efficiency of PSII. Stemler et al. (Proc Natl Acad Sci USA 71(12):4679-4683, 1974), in Govindjee's lab, were the first to study the effect of "bicarbonate" on FIOPs by adding the competitive inhibitor acetate. Here, we extend this earlier work by performing FIOPs experiments at various, strictly controlled inorganic carbon (Ci) levels without addition of any inhibitors. For this, we placed a Joliot-type bare platinum electrode inside a N2-filled glove-box (containing 10-20 ppm CO2) and reduced the Ci concentration simply by washing the samples in Ci-depleted media. FIOPs of spinach thylakoids were recorded either at 20-times reduced levels of Ci or at ambient Ci conditions (390 ppm CO2). Numerical analysis of the FIOPs within an extended Kok model reveals that under Ci-depleted conditions the miss probability is discernibly larger (by 2-3 %) than at ambient conditions, and that the addition of 5 mM HCO3 (-) to the Ci-depleted thylakoids largely restores the original miss parameter. Since a "mild" Ci-depletion procedure was employed, we discuss our data with respect to a possible function of free or weakly bound HCO3 (-) at the water-splitting side of PSII.

Ion and nutrient uptake by malaria parasite-infected erythrocytes.

Erythrocytes infected with malaria parasites have increased permeability to diverse organic and inorganic solutes. While these permeability changes have been known for decades, the molecular basis of transport was unknown and intensively debated. CLAG3, a parasite protein previously thought to function in cytoadherence, has recently been implicated in formation of the plasmodial surface anion channel (PSAC), an unusual small conductance ion channel that mediates uptake of most solutes. Consistent with transport studies, the clag genes are conserved in all plasmodia but are absent from other genera. The encoded protein is integral to the host membrane, as also predicted by electrophysiology. An important question is whether functional channels are formed by CLAG3 alone or through interactions with other proteins. In either case, gene identification should advance our understanding of parasite biology and may lead to new therapeutics.