A Minimal Model of Metabolism Based Chemotaxis

Since the pioneering work by Julius Adler in the 1960's, bacterial chemotaxis has been predominantly studied as metabolism-independent. All available simulation models of bacterial chemotaxis endorse this assumption. Recent studies have shown, however, that many metabolism-dependent chemotactic patterns occur in bacteria. We hereby present the simplest artificial protocell model capable of performing metabolism-based chemotaxis. The model serves as a proof of concept to show how even the simplest metabolism can sustain chemotactic patterns of varying sophistication. It also reproduces a set of phenomena that have recently attracted attention on bacterial chemotaxis and provides insights about alternative mechanisms that could instantiate them. We conclude that relaxing the metabolism-independent assumption provides important theoretical advances, forces us to rethink some established pre-conceptions and may help us better understand unexplored and poorly understood aspects of bacterial chemotaxis

Engineered hexavalent Fc proteins with enhanced Fc-gamma receptor avidity provide insights into immune-complex interactions

Tania Rowley et al. present multivalent Fc molecules with enhanced avidity for Fc gamma receptors in order to improve the treatment of autoantibody-mediated human diseases. They found several key amino acids involved in Fc receptor binding interactions

Chemical and structural analysis of an antibody folding intermediate trapped during glycan biosynthesis

Human IgG Fc glycosylation modulates immunological effector functions such as antibody-dependent cellular cytotoxicity and phagocytosis. Engineering of Fc glycans therefore enables fine-tuning of the therapeutic properties of monoclonal antibodies. The N-linked glycans of Fc are typically complex-type, forming a network of noncovalent interactions along the protein surface of the Cγ2 domain. Here, we manipulate the mammalian glycan-processing pathway to trap IgG1 Fc at sequential stages of maturation, from oligomannose- to hybrid- to complex-type glycans, and show that the Fc is structurally stabilized following the transition of glycans from their hybrid- to complex-type state. X-ray crystallographic analysis of this hybrid-type intermediate reveals that N-linked glycans undergo conformational changes upon maturation, including a flip within the trimannosyl core. Our crystal structure of this intermediate reveals a molecular basis for antibody biogenesis and provides a template for the structure-guided engineering of the protein-glycan interface of therapeutic antibodies

Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing

© 2016, Springer Science+Business Media New York. Understanding how minerals affect bacterial communities and their in situ activities in relation to environmental conditions are central issues in soil microbial ecology, as minerals represent essential reservoirs of inorganic nutrients for the biosphere. To determine the impact of mineral type and solution chemistry on soil bacterial communities, we compared the diversity, composition, and functional abilities of a soil bacterial community incubated in presence/absence of different mineral types (apatite, biotite, obsidian). Microcosms were prepared containing different liquid culture media devoid of particular essential nutrients, the nutrients provided only in the introduced minerals and therefore only available to the microbial community through mineral dissolution by biotic and/or abiotic processes. By combining functional screening of bacterial isolates and community analysis by bromodeoxyuridine DNA immunocapture and 16S rRNA gene pyrosequencing, we demonstrated that bacterial communities were mainly impacted by the solution chemistry at the taxonomic level and by the mineral type at the functional level. Metabolically active bacterial communities varied with solution chemistry and mineral type. Burkholderia were significantly enriched in the obsidian treatment compared to the biotite treatment and were the most effective isolates at solubilizing phosphorous or mobilizing iron, in all the treatments. A detailed analysis revealed that the 16S rRNA gene sequences of the OTUs or isolated strains assigned as Burkholderia in our study showed high homology with effective mineral-weathering bacteria previously recovered from the same experimental site

Copper and tin isotopic analysis of ancient bronzes for archaeological investigation: development and validation of a suitable analytical methodology

Although in many cases Pb isotopic analysis can be relied on for provenance determination of ancient bronzes, sometimes the use of “non-traditional” isotopic systems, such as those of Cu and Sn, is required. The work reported on in this paper aimed at revising the methodology for Cu and Sn isotope ratio measurements in archaeological bronzes via optimization of the analytical procedures in terms of sample pre-treatment, measurement protocol, precision, and analytical uncertainty. For Cu isotopic analysis, both Zn and Ni were investigated for their merit as internal standard (IS) relied on for mass bias correction. The use of Ni as IS seems to be the most robust approach as Ni is less prone to contamination, has a lower abundance in bronzes and an ionization potential similar to that of Cu, and provides slightly better reproducibility values when applied to NIST SRM 976 Cu isotopic reference material. The possibility of carrying out direct isotopic analysis without prior Cu isolation (with AG-MP-1 anion exchange resin) was investigated by analysis of CRM IARM 91D bronze reference material, synthetic solutions, and archaeological bronzes. Both procedures (Cu isolation/no Cu isolation) provide similar δ 65Cu results with similar uncertainty budgets in all cases (±0.02–0.04 per mil in delta units, k = 2, n = 4). Direct isotopic analysis of Cu therefore seems feasible, without evidence of spectral interference or matrix-induced effect on the extent of mass bias. For Sn, a separation protocol relying on TRU-Spec anion exchange resin was optimized, providing a recovery close to 100 % without on-column fractionation. Cu was recovered quantitatively together with the bronze matrix with this isolation protocol. Isotopic analysis of this Cu fraction provides δ 65Cu results similar to those obtained upon isolation using AG-MP-1 resin. This means that Cu and Sn isotopic analysis of bronze alloys can therefore be carried out after a single chromatographic separation using TRU-Spec resin. Tin isotopic analysis was performed relying on Sb as an internal standard used for mass bias correction. The reproducibility over a period of 1 month (n = 42) for the mass bias-corrected Sn isotope ratios is in the range of 0.06–0.16 per mil (2 s), for all the ratios monitored

Bioleaching of Ilmenite and Basalt in the Presence of Iron-oxidizing and Iron-Scavenging Bacteria

Bioleaching has been suggested as an alternative to traditional mining techniques in extraterrestrial environments because it does not require extensive infrastructure and bulky hardware. In situ bioleaching of silicate minerals, such as those found on the moon or Mars, has been proposed as a feasible alternative to traditional extraction techniques that require either extreme heat and/or substantial chemical treatment. In this study, we investigated the biotic and abiotic leaching of basaltic rocks (analogues to those found on the moon and Mars) and the mineral ilmenite (FeTiO3) in aqueous environments under acidic (pH ~ 2.5) and circumneutral pH conditions. The biological leaching experiments were conducted using Acidithiobacillus ferrooxidans, an iron (Fe)-oxidizing bacteria, and Pseudomonas mendocina, an Fe-scavenging bacteria. We found that both strains were able to grow using the Fe(II) derived from the tested basaltic rocks and ilmenite. Although silica leaching rates were the same or slightly less in the bacterial systems with A. ferrooxidans than in the abiotic control systems, the extent of Fe, Al and Ti released (and re-precipitated in new solid phases) was actually greater in the biotic systems. This is likely because the Fe(II) leached from the basalt was immediately oxidized by A. ferrooxidans, and precipitated into Fe(III) phases which causes a change in the equilibrium of the system, i.e. Le Chatelier\u27s principle. Iron(II) in the abiotic experiment was allowed to build up in solution which led to a decrease in its overall release rate. For example, the percentage of Fe, Al and Ti leached (dissolved + reactive mineral precipitates) from the Mars simulant in the A. ferrooxidans experimental system was 34, 41 and 13% of the total Fe, Al and Ti in the basalt, respectively, while the abiotic experimental system released totals of only 11, 25 and 2%. There was, however, no measurable difference in the amounts of Fe and Ti released from ilmenite in the experiments with A. ferrooxidans versus the abiotic controls. P. mendocina scavenged some Fe from the rock/mineral substrates, but the overall amount of leaching was small (\u3c2% of total Fe in rocks) when compared with the acidophilic systems. Although the mineralogy of the tested basaltic rocks was roughly similar, the surface areas of the lunar and Mars simulants varied greatly and thus were possible factors in the overall amount of metals released. Overall, our results indicate that the presence of bacteria does not increase the overall silica leaching rates of basaltic rocks; however, the presence of A. ferrooxidans does lead to enhanced release of Fe, Al and Ti and subsequent sequestration of Fe (and other metals) in Fe(III)-precipitates

The Vergenoeg Magnetite-Fluorite Deposit, South Africa: Support for a Hydrothermal Model for Massive Iron Oxide Deposits

Vergenoeg is a fluorite-bearing massive iron oxide deposit that is genetically related to granites of the Bushveld Complex. It consists of a pipe-shaped body containing primary fayalite, fluorite, apatite, ilmenite, and magnetite that cuts Rooiberg rhyolites and is surrounded by stratiform bodies of felsite and fragmental hematite-fluorite debris. With the exception of its abundant fluorite, Vergenoeg is similar to massive iron oxide deposits such as Kiruna, Pea Ridge, and Cerro Mercado, all of which are related to felsic magmatism. Models suggested for the origin of these deposits can be divided into those invoking separation of an immiscible iron oxide magma from the parent felsic magma and those invoking a hydrothermal solution. Vergenoeg is an excellent place to try to resolve this controversy because the primary fluorite permits study of inclusions of the fluid or magma that formed the ore. Fluorite at Vergenoeg lacks inclusions that might represent an immiscible iron-rich melt but contains abundant aqueous inclusions. Inclusion petrography, heating-freezing measurements, and gas analyses indicate that the primary mineral assemblage at Vergenoeg formed from a high-temperature (\u3e500°C), high-salinity (\u3e67 wt % NaCl equiv) fluid that coexisted with a vapor phase rich in CO2 . Stable isotope analyses of primary fayalite and titanian magnetite from deep in the Vergenoeg pipe yield calculated water compositions for these temperatures that are typical of magmatic water (δ 18O (H2O) = 7-8ppm at 500°C). Alteration of the primary fayalite-fluorite-ilmenite assemblage is widespread in the Vergenoeg pipe. It consists of an early assemblage containing ferroactinolite, grunerite, and titanian magnetite, and later assemblages containing various combinations of siderite, hematite, magnetite, ferropyrosmalite, stilpnomelane, biotite, sphene, quartz, and apatite, which are most common in the upper part of the pipe. Fluid inclusions related to these alteration assemblages homogenize at 150° to 500°C and have salinities of 1 to 35 wt percent NaCl equiv. Stable isotope analyses of hematite and inclusion waters in fluorite suggest that these fluids consist of a mixture of magmatic and meteoric water.These observations suggest that Vergenoeg mineralization formed from hydrothermal fluids of magmatic origin. Comparison of the fluid inclusion record at Vergenoeg to the more fragmentary record at other massive iron oxide deposits supports a magmatic hydrothermal model for this class of deposit