The magnetosome model: insights into the mechanisms of bacterial biomineralization.

Though the most ready example of biomineralization is the calcium phosphate of vertebrate bones and teeth, many bacteria are capable of creating biominerals inside their cells. Because of the diversity of these organisms and the minerals they produce, their study may reveal aspects of the fundamental mechanisms of biomineralization in more complex organisms. The best-studied case of intracellular biomineralization in bacteria is the magnetosome, an organelle produced by a diverse group of aquatic bacteria that contains single-domain crystals of the iron oxide magnetite (Fe3O4) or the iron sulfide greigite (Fe3S4). Here, recent advances in our understanding of the mechanisms of bacterial magnetite biomineralization are discussed and used as a framework for understanding less-well studied examples, including the bacterial intracellular biomineralization of cadmium, selenium, silver, nickel, uranium, and calcium carbonate. Understanding the molecular mechanisms underlying the biological formation of these minerals will have important implications for technologies such as the fabrication of nanomaterials and the bioremediation of toxic compounds

Genome Editing Method for the Anaerobic Magnetotactic Bacterium Desulfovibrio magneticus RS-1.

Magnetosomes are complex bacterial organelles that serve as model systems for studying bacterial cell biology, biomineralization, and global iron cycling. Magnetosome biogenesis is primarily studied in two closely related Alphaproteobacteria of the genus Magnetospirillum that form cubooctahedral-shaped magnetite crystals within a lipid membrane. However, chemically and structurally distinct magnetic particles have been found in physiologically and phylogenetically diverse bacteria. Due to a lack of molecular genetic tools, the mechanistic diversity of magnetosome formation remains poorly understood. Desulfovibrio magneticus RS-1 is an anaerobic sulfate-reducing deltaproteobacterium that forms bullet-shaped magnetite crystals. A recent forward genetic screen identified 10 genes in the conserved magnetosome gene island of D. magneticus that are essential for its magnetic phenotype. However, this screen likely missed mutants with defects in crystal size, shape, and arrangement. Reverse genetics to target the remaining putative magnetosome genes using standard genetic methods of suicide vector integration have not been feasible due to the low transconjugation efficiency. Here, we present a reverse genetic method for targeted mutagenesis in D. magneticus using a replicative plasmid. To test this method, we generated a mutant resistant to 5-fluorouracil by making a markerless deletion of the upp gene that encodes uracil phosphoribosyltransferase. We also used this method for targeted marker exchange mutagenesis by replacing kupM, a gene identified in our previous screen as a magnetosome formation factor, with a streptomycin resistance cassette. Overall, our results show that targeted mutagenesis using a replicative plasmid is effective in D. magneticus and may also be applied to other genetically recalcitrant bacteria.IMPORTANCE Magnetotactic bacteria (MTB) are a group of organisms that form intracellular nanometer-scale magnetic crystals though a complex process involving lipid and protein scaffolds. These magnetic crystals and their lipid membranes, termed magnetosomes, are model systems for studying bacterial cell biology and biomineralization and are potential platforms for biotechnological applications. Due to a lack of genetic tools and unculturable representatives, the mechanisms of magnetosome formation in phylogenetically deeply branching MTB remain unknown. These MTB contain elongated bullet-/tooth-shaped magnetite and greigite crystals that likely form in a manner distinct from that of the cubooctahedral-shaped magnetite crystals of the genetically tractable MTB within the Alphaproteobacteria Here, we present a method for genome editing in Desulfovibrio magneticus RS-1, a cultured representative of the deeply branching MTB of the class Deltaproteobacteria This marks a crucial step in developing D. magneticus as a model for studying diverse mechanisms of magnetic particle formation by MTB

Systematic design of single-mode coupled-resonator optical waveguides in photonic crystals

By establishing a direct relation between the dispersion and the field profile of a coupled-resonator optical waveguide (CROW) and those of its constituent cavities, we present a systematic method for the design of a single-mode CROW and for control of its dispersion. The procedure includes the design of a single-mode cavity and control of its frequency by engineering its structure. Then, by chaining these cavities in the proper direction and at an appropriate distance, we achieve the desired dispersion for the CROW

Uncertainty quantification for CO2 sequestration and enhanced oil recovery

This study develops a statistical method to perform uncertainty quantification for understanding CO2 storage potential within an enhanced oil recovery (EOR) environment at the Farnsworth Unit of the Anadarko Basin in northern Texas. A set of geostatistical-based Monte Carlo simulations of CO2-oil-water flow and reactive transport in the Morrow formation are conducted for global sensitivity and statistical analysis of the major uncertainty metrics: net CO2 injection, cumulative oil production, cumulative gas (CH4) production, and net water injection. A global sensitivity and response surface analysis indicates that reservoir permeability, porosity, and thickness are the major intrinsic reservoir parameters that control net CO2 injection/storage and oil/gas recovery rates. The well spacing and the initial water saturation also have large impact on the oil/gas recovery rates. Further, this study has revealed key insights into the potential behavior and the operational parameters of CO2 sequestration at CO2-EOR sites, including the impact of reservoir characterization uncertainty; understanding this uncertainty is critical in terms of economic decision making and the cost-effectiveness of CO2 storage through EOR.Comment: 9 pages, 6 figures, in press, Energy Procedia, 201

A Genetic Strategy for Probing the Functional Diversity of Magnetosome Formation

Model genetic systems are invaluable, but limit us to understanding only a few organisms in detail, missing the variations in biological processes that are performed by related organisms. One such diverse process is the formation of magnetosome organelles by magnetotactic bacteria. Studies of model magnetotactic α-proteobacteria have demonstrated that magnetosomes are cubo-octahedral magnetite crystals that are synthesized within pre-existing membrane compartments derived from the inner membrane and orchestrated by a specific set of genes encoded within a genomic island. However, this model cannot explain all magnetosome formation, which is phenotypically and genetically diverse. For example, Desulfovibrio magneticus RS-1, a δ-proteobacterium for which we lack genetic tools, produces tooth-shaped magnetite crystals that may or may not be encased by a membrane with a magnetosome gene island that diverges significantly from those of the α-proteobacteria. To probe the functional diversity of magnetosome formation, we used modern sequencing technology to identify hits in RS-1 mutated with UV or chemical mutagens. We isolated and characterized mutant alleles of 10 magnetosome genes in RS-1, 7 of which are not found in the α-proteobacterial models. These findings have implications for our understanding of magnetosome formation in general and demonstrate the feasibility of applying a modern genetic approach to an organism for which classic genetic tools are not available

Control of the replication initiator DnaA by an anti-cooperativity factor

Proper coordination of DNA replication with cell growth and division is critical for production of viable progeny. In bacteria, coordination of DNA replication with cell growth is generally achieved by controlling activity of the replication initiator DnaA and its access to the chromosomal origin of replication, oriC. Here we describe a previously unknown mechanism for regulation of DnaA. YabA, a negative regulator of replication initiation in Bacillus subtilis, interacts with DnaA and DnaN, the sliding (processivity) clamp of DNA polymerase. We found that in vivo, YabA associated with the oriC region in a DnaA-dependent manner and limited the amount of DnaA at oriC. In vitro, purified YabA altered binding of DnaA to DNA by inhibiting cooperativity. Although previously undescribed, proteins that directly inhibit cooperativity may be a common mechanism for regulating replication initiation. Conditions that cause release of DnaN from the replisome, or overproduction of DnaN, caused decreased association of YabA and increased association of DnaA with oriC. This effect of DnaN, either directly or indirectly, is likely responsible, in part, for enabling initiation of a new round of replication following completion of a previous round.United States. Public Health Service (grant GM41934)National Institutes of Health (U.S.) (NIH Kirschstein NRSA postdoctoral fellowship F32GM093408

Optical magnetic imaging of living cells

Magnetic imaging is a powerful tool for probing biological and physical systems. However, existing techniques either have poor spatial resolution compared to optical microscopy and are hence not generally applicable to imaging of sub-cellular structure (e.g., magnetic resonance imaging [MRI]1), or entail operating conditions that preclude application to living biological samples while providing sub-micron resolution (e.g., scanning superconducting quantum interference device [SQUID] microscopy2, electron holography3, and magnetic resonance force microscopy [MRFM]4). Here we demonstrate magnetic imaging of living cells (magnetotactic bacteria) under ambient laboratory conditions and with sub-cellular spatial resolution (400 nm), using an optically-detected magnetic field imaging array consisting of a nanoscale layer of nitrogen-vacancy (NV) colour centres implanted at the surface of a diamond chip. With the bacteria placed on the diamond surface, we optically probe the NV quantum spin states and rapidly reconstruct images of the vector components of the magnetic field created by chains of magnetic nanoparticles (magnetosomes) produced in the bacteria, and spatially correlate these magnetic field maps with optical images acquired in the same apparatus. Wide-field sCMOS acquisition allows parallel optical and magnetic imaging of multiple cells in a population with sub-micron resolution and >100 micron field-of-view. Scanning electron microscope (SEM) images of the bacteria confirm that the correlated optical and magnetic images can be used to locate and characterize the magnetosomes in each bacterium. The results provide a new capability for imaging bio-magnetic structures in living cells under ambient conditions with high spatial resolution, and will enable the mapping of a wide range of magnetic signals within cells and cellular networks5, 6

Extensional faulting on Tinos island, Aegean sea, Greece: How many detachments?

Zircon and apatite fission track (ZFT and AFT) and (U-Th)/He, 40Ar/39Ar hornblende, and U-Pb zircon ages from the granites of Tinos Island in the Aegean Sea, Greece, suggest, together with published ZFT data, that there are three extensional detachments on Tinos. The Tinos granites crosscut the Tinos detachment. Cooling of the granites was controlled by the Livadi detachment, which occurs structurally above the Tinos detachment. Our U-Pb zircon age is 14.6 ± 0.2 Ma and two 40Ar/39Ar hornblende ages are 14.4 ± 0.4 and 13.7 ± 0.4 Ma. ZFT and AFT ages go from 14.4 ± 1.2 to 12.2 ± 1.0 Ma and 12.8 ± 2.4 to 11.9 ± 2.0 Ma. (U-Th)/He ages are from 10.4 ± 0.2 to 9.9 ± 0.2 Ma (zircon) and 11.9 ± 0.5 to 10.0 ± 0.3 Ma (apatite). All ages decrease northeastward in the direction of hanging wall transport on the Livadi detachment and age-distance relationships yield a slip rate of 2.6 (+3.3 / −1.0) km Ma−1. This rate is smaller than a published slip rate of 6.5 km Ma−1 for the Vari detachment, which is another detachment structurally above the Tinos detachment. Because of the different rates and because published ZFT ages from the footwall of the Vari detachment are ∼10 Ma, we propose that the Vari detachment has to be distinguished from the older Livadi detachment. We discuss various models of how the extensional detachments may have evolved and prefer a scenario in which the Vari detachment cut down into the footwall of the Livadi detachment successively exhuming deeper structural units. The thermochronologic ages demonstrate the importance of quantitative data for constraining localization processes during extensional deformation