Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Thermal Control on the Location of the Volcanic Arc at Subduction Zones

At subduction zones, where oceanic plates are recycled into the Earth’s interior, water released by the subducting plate initiates partial melts that form volcanic arcs. Partial melts can be present in a broad melting zone below a narrow volcanic arc. The second melting zone can be formed by mantle upwelling induced by active extension behind the arc and subsequent decompression melting. In this dissertation, I explain the locations of the arc in global using a temperature-dependent melt focusing mechanism. I present a simple geometrical model to explain the observed correlation between the location of the arc and the back-arc spreading center (BASC) at five subduction zones. Lastly, I discuss the thermal influence of the BASC on the arc location. The melts rise vertically through the pore spaces in the mantle rock until they encounter a low permeability barrier formed at a temperature where the crystallization rate is maximum. As the melt trajectory is deflected laterally, the melts are focused at the apex of the permeability barrier and the volcano is more likely to form immediately above the magma pool. In the subduction zones without back-arc spreading, the projection of the apex of the barrier-forming isotherm shows good agreement with the observed arc locations. The arc and the BASC location are negatively correlated with the slab dip at five subduction zones. The decoupling depth between the slab and the overlying mantle defines the closest approach of the nose of the isotherm. The horizontal distance from the trench to the decoupling depth is controlled by the slab dip, which produces the negative correlation. The back-arc extension is related to the trench retreat and the slab anchoring at 660 km discontinuity, which results in a decrease in the slab dip. The relation between the slab anchoring depth and the slab dip generates the observed negative correlation. When the BASC develops near the trench, the thermal structure is disrupted by the mantle upwelling and thereby the predicted arc location moves toward the spreading center

Numerical subduction zone models with back-arc spreading center

This is a supplementary dataset for chapter 5 of Goeun Ha's Ph.D. dissertation

Geometrical Relations Between Slab Dip and the Location of Volcanic Arcs and Back‐Arc Spreading Centers

Abstract A global study of subduction zone dynamics indicates that the thermal structure of the overriding plate may control arc location. A fast convergence rate and a steep slab dip bring a hotter mantle further into the wedge corner, forming arc volcanoes closer to the trench. Separately, laboratory and numerical experiments showed that the development of a back‐arc spreading center (BASC) is driven by the migration of the subducting hinge, especially following changes in the slab geometry. As both arc location and the deformation regime of the overriding plate depend on slab kinematics and geometry, we investigate the possible correlations between BASC, the position of volcanic arcs, and slab dip at the scale of individual subduction zones. To do this, we compare the distance from trench to arc and trench to BASC at the Mariana, Scotia, Vanuatu, Tonga, and Kermadec subduction zones. In most cases, the arc and BASC are closer to the trench when the slab is dipping steeply. The correlation could result from an interplay between progressive changes in slab geometry and overriding plate deformation. This assumes, on the one hand, that the isotherm at the apex of which the arc forms is tied to a constant slab decoupling depth and, on the other hand, that back‐arc opening accommodates a change in slab dip. As slab dip decreases, both the BASC and the apex of the isotherm controlling the melt focusing move further from the trench. The observed trends are consistent with a slab anchored at 660 km depth

Melt Focusing Along Permeability Barriers at Subduction Zones and the Location of Volcanic Arcs

Abstract Fluids released from dehydration reactions occurring in subducting slabs trigger partial melting in the mantle wedge. The resulting magma rises through the overlying mantle wedge and lithosphere and forms arc volcanoes at subduction zones. In general, the location of the volcanic arc is narrowly defined even though the melting region in the mantle wedge can be broad. We propose here that a thermally controlled low permeability barrier at the base of lithosphere is able to focus melts to the place where the volcanic arc is actually observed. As the melt ascends, the permeability of the mantle rock decreases as a result of melt crystallization. A low permeability barrier may form in the cooler lithosphere and can trap ascending melt and redirect it laterally according to the slope of the permeability barrier, so that the ascending melt is focused at the apex of the permeability barrier. We model the location and shape of isotherms that approximate the permeability barriers in the mantle wedge based in two‐dimensional numerical subduction models that follow the specific geometry of various subduction zones. In 28 of 31 globally distributed test regions, the arc locations estimated from our model show good agreement with the actual arc locations. The modeling results indicate that volcanic arcs can be explained as the surface projection of the apex of the permeability barrier, regardless of the distribution of melt deeper in the mantle wedge

Clinical utility of immature reticulocyte fraction for identifying early red blood cell regeneration in anemic dogs

Abstract Background Evaluating regeneration is essential for the classification and differential diagnosis of anemia in dogs. Early detection of regeneration is challenging in anemic dogs. Objectives This study assessed the value of immature reticulocyte fraction (IRF) in differentiating preregenerative anemia (PRA) from nonregenerative anemia (NRA) in dogs. Animals Ninety‐four dogs: 49 controls and 45 with anemia. Methods Case‐control study. Fractions of low‐, medium‐ (MFR), and high‐fluorescence reticulocytes (HFR), were measured using the ADVIA 2120i hematology analyzer. The IRF was calculated as the sum of percentages of MFR and HFR. Data from dogs with regenerative anemia (RA, n = 19), PRA (n = 11), and NRA (n = 15) were retrospectively analyzed. The value of IRF was compared with reticulocyte production index (RPI) using the receiver operating characteristic (ROC) curve. Results The median of IRF was significantly higher in dogs with RA (46.5%; range, 40.9‐53.6%; P  .99) but was higher than dogs with NRA (18.7%; range, 8.8‐24%; P = .00). The area under the ROC curve of IRF was superior to that of RPI (0.897 vs 0.818, P = .00) in differentiating dogs with PRA from NRA. Conclusions and Clinical Importance The IRF is a reliable variable for detecting early regeneration in anemic dogs without reticulocytosis. The study suggests that the measurement of IRF could be useful in classifying anemic dogs