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

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

General Base Catalysis in the Urate Oxidase Reaction: Evidence for a Novel Thr−Lys Catalytic Diad

Urate oxidase catalyzes the oxidation of urate without the involvement of any cofactors. The gene encoding urate oxidase from Bacillus subtilis has been cloned and expressed, and the enzyme was purified and characterized. Formation of the urate dianion is believed to be a key step in the oxidative reaction. Rapid-mixing chemical quench studies provide evidence that the dianion is indeed an intermediate; at 15 °C the dianion forms within the mixing time of the rapid-quench instrument, and it disappears with a rate constant of 8 s-1. Steady-state kinetic studies indicate that an ionizable group on the enzyme with a pK of 6.4 must be unprotonated for catalysis, and it is presumed that the role of this group is to abstract a proton from the substrate. Surprisingly, examination of the active site provided by the previously reported crystal structure does not reveal any obvious candidates to act as the general base. However, Thr 69 is hydrogen-bonded to the ligand at the active site, and Lys 9, which does not contact the ligand, is hydrogen-bonded to Thr 69. The T69A mutant enzyme has a Vmax that is 3% of wild type, and the K9M mutant enzyme has a Vmax that is 0.4% of wild type. The ionization at pH 6.4 that is observed with wild-type enzyme is absent in both of these mutants. It is proposed that these residues form a catalytic diad in which K9 deprotonates T69 to allow it to abstract the proton from the N9 position of the substrate to generate the dianion

Dolomite Fronts and Associated Zinc-Lead Mineralization, USA

This paper provides previously unpublished drill core and mapping evidence of the spatial relationship between regional dolomitization and Mississippi Valley-type (MVT) mineralization in the midcontinent of the United States. Dolomitization is discussed for several key carbonate units and their contained MVT mineralization. This more complete picture of the relationship between regional dolomitization and mineralization provides constraints on models for MVT mineralization and serves as an exploration guide for new deposits

Experimental Determination of Equilibrium Fe Isotopic Fractionation between Pyrite and Dissolved Fe under Hydrothermal Conditions

Fe isotope fractionation between pyrite (FeS2) and dissolved Fe in NaCl- and sulfur-bearing aqueous fluids was determined under hydrothermal conditions (300-350 °C, 500 bars). The data were collected using two different, but complementary, experimental approaches, one involving classical Fe isotope exchange between Fe in pyrite and dissolved Fe in coexisting fluid, while the other involved homogenous precipitation of pyrite in a redox and pH buffered chemical system. Results from these experiments indicate equilibrium Fe isotopic fractionation between pyrite and fluid, Δ56FePyr-Fe(aq), of 0.99 ± 0.29‰ (2σ), in 56Fe/54Fe. The experimentally determined equilibrium pyrite-fluid Fe isotopic fractionation agrees with theoretical and spectrally-based predictions. The second series of experiments were conducted to better constrain the effect of precipitation rate on the temporal evolution of the Fe isotopic composition of pyrite and Fe bearing fluids in dynamic mixing environments, such as hydrothermal vent sites at mid-ocean ridges. Rapid homogenous precipitation of pyrite at 300 and 350 °C indicates that δ56Fe of dissolved Fe is significantly greater than pyrite that formed during the earliest stage of the experiment, possibly facilitated by either equilibrium or kinetic isotope effects involving FeS as a reactant during pyrite formation. Subsequent recrystallization of pyrite results in a Fe isotopic fractionation with dissolved Fe that moves towards the experimentally determined equilibrium Fe isotopic fractionation with reaction progress. The experimental data reported here may help to decipher the complex kinetic and thermodynamic processes involved in pyrite formation at deep sea vents, while also providing constraints for the rapidly developing theoretical models used to estimate equilibrium Fe isotope fractionation between pyrite and fluid at elevated temperatures and pressures