Otolith shape analysis of Lethrinus lentjan (Lacepède, 1802) and L. microdon (Valenciennes, 1830) from the Red Sea

Otolith shape and morphology are used to identify fish species and population stocks. The aim of this study was to distinguish the Lethrinus lentjan (Lacepède, 1802) and L. microdon (Valenciennes, 1830) (family: Lethrinidae) using otolith shape. The analyses apply the ShapeR package in R which enables to extract the outline and otolith morphology from images and for statistical examining of individual variation. Otoliths of 165 individuals from the two Lethrinus species were collected during 2019 and 2020. The wavelet levels were examined by using 6 wavelets to collect 63 coefficients. The regression between width and fish length were b = -0.03 (t = 2.6, P = 0.01) for L. lentjan and was significantly different (t = 2.120, P = 0.036) for L. microdon (b = 0.018)

Consistent and High Rates of Gene Transfer Can Be Obtained Using Flow-Through Transduction over a Wide Range of Retroviral Titers

Overview summary Flow-through transduction provides a means by which high rates of gene transfer can occur without using high titers of virus vector. Reproducibly high numbers of transduced cells can be obtained with a wide range of virus titers, thus relaxing the requirement of set (high) titers within a transduction protocol. Incorporating flow-through transductions within clinical applications of gene therapy may also obviate the need for large volumes of high-titer virus produced by vector producer cell line cultures.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63214/1/hum.1996.7.6-743.pd

Modelling variable glacier lapse rates using ERA-Interim reanalysis climatology: an evaluation at Vestari- Hagafellsjökull, Langjökull, Iceland

The near-surface air temperature lapse rate is an important tool for spatially distributing temperatures in snow- and ice-melt models, but is difficult to parameterize, as it is not simply correlated with boundary-layer meteorological variables, such as temperature itself. This contribution quantifies spring-autumn lapse rate variability over 5 years at Vestari-Hagafellsjökull, a southerly outlet of Langjökull in Iceland. It is observed that summer lapse rates (0.57 °C 100 m) are significantly lower than non-summer rates, and are also lower than the Saturated Adiabatic Lapse Rate (SALR), which is often adopted in melt models. This is consistent with reduced near-surface temperature sensitivity to free-atmosphere temperature change during the occurrence of melting. A Variable Lapse Rate (VLR) regression model is calibrated with standardized, 750 hPa temperature anomalies derived from ERA-Interim climatology, which is shown to be highly significantly correlated with near-surface temperatures. The modelled VLR overestimates cumulative June-September Positive Degree Days (PDDs) by 3% when used to extrapolate temperatures from 1100 to 500 m a.s.l. on the glacier, whereas the SALR overestimates cumulative PDDs by 14%. ERA-Interim data therefore appear to offer a good representation of free-atmosphere temperature variability over Vestari-Hagafellsjökull, and the modelling approach offers a simple means of improving lapse rate parameterizations in melt models. © 2012 Royal Meteorological Society

An optimization model for metabolic pathways

This article is available open access through the publisher’s website through the link below. Copyright @ The Author 2009.Motivation: Different mathematical methods have emerged in the post-genomic era to determine metabolic pathways. These methods can be divided into stoichiometric methods and path finding methods. In this paper we detail a novel optimization model, based upon integer linear programming, to determine metabolic pathways. Our model links reaction stoichiometry with path finding in a single approach. We test the ability of our model to determine 40 annotated Escherichia coli metabolic pathways. We show that our model is able to determine 36 of these 40 pathways in a computationally effective manner. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online (http://bioinformatics.oxfordjournals.org/cgi/content/full/btp441/DC1)

Hard X-ray standing-wave photoemission insights into the structure of an epitaxial Fe/MgO multilayer magnetic tunnel junction

The Fe/MgO magnetic tunnel junction is a classic spintronic system, with current importance technologically and interest for future innovation. The key magnetic properties are linked directly to the structure of hard-to-access buried interfaces, and the Fe and MgO components near the surface are unstable when exposed to air, making a deeper probing, nondestructive, in-situ measurement ideal for this system. We have thus applied hard X-ray photoemission spectroscopy (HXPS) and standing-wave (SW) HXPS in the few kilo-electron-volt energy range to probe the structure of an epitaxially grown MgO/Fe superlattice. The superlattice consists of 9 repeats of MgO grown on Fe by magnetron sputtering on an MgO(001) substrate, with a protective Al2O3 capping layer. We determine through SW-HXPS that 8 of the 9 repeats are similar and ordered, with a period of 33 ± 4 Å, with the minor presence of FeO at the interfaces and a significantly distorted top bilayer with ca. 3 times the oxidation of the lower layers at the top MgO/Fe interface. There is evidence of asymmetrical oxidation on the top and bottom of the Fe layers. We find agreement with dark-field scanning transmission electron microscope (STEM) and X-ray reflectivity measurements. Through the STEM measurements, we confirm an overall epitaxial stack with dislocations and warping at the interfaces of ca. 5 Å. We also note a distinct difference in the top bilayer, especially MgO, with possible Fe inclusions. We thus demonstrate that SW-HXPS can be used to probe deep buried interfaces of novel magnetic devices with few-angstrom precision

The Inverse Gamma Distribution and Benford's Law

According to Benford's Law, many data sets have a bias towards lower leading digits (about 30% are 1's). The applications of Benford's Law vary: from detecting tax, voter and image fraud to determining the possibility of match-fixing in competitive sports. There are many common distributions that exhibit such bias, i.e. they are almost Benford. These include the exponential and the Weibull distributions. Motivated by these examples and the fact that the underlying distribution of factors in protein structure follows an inverse gamma distribution, we determine the closeness of this distribution to a Benford distribution as its parameters change

Stochastic Analysis of Dimerization Systems

The process of dimerization, in which two monomers bind to each other and form a dimer, is common in nature. This process can be modeled using rate equations, from which the average copy numbers of the reacting monomers and of the product dimers can then be obtained. However, the rate equations apply only when these copy numbers are large. In the limit of small copy numbers the system becomes dominated by fluctuations, which are not accounted for by the rate equations. In this limit one must use stochastic methods such as direct integration of the master equation or Monte Carlo simulations. These methods are computationally intensive and rarely succumb to analytical solutions. Here we use the recently introduced moment equations which provide a highly simplified stochastic treatment of the dimerization process. Using this approach, we obtain an analytical solution for the copy numbers and reaction rates both under steady state conditions and in the time-dependent case. We analyze three different dimerization processes: dimerization without dissociation, dimerization with dissociation and hetero-dimer formation. To validate the results we compare them with the results obtained from the master equation in the stochastic limit and with those obtained from the rate equations in the deterministic limit. Potential applications of the results in different physical contexts are discussed.Comment: 10 figure

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

BackgroundThe mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question.ResultsIn this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations.ConclusionsOverall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches

Kinetics of retroviral production from the amphotropic ΨCRIP murine producer cell line

Rapidly expanding development and practice of gene therapy requires the availability of large quantities of high titer retroviral supernatants. One way to achieve high retroviral titers is through improved understanding of the kinetics of retroviral production and decay, and the subsequent development of improved cell culture methods. In the present study we investigated the effects of different operational modes on the retroviral production of the NIH 3T3 fibroblast derived amphotropic murine retroviral producing cell line pMFG/ΨCRIP. Semi-continuous culture (exchange of 50% of medium volume daily) was found to promote cell growth and enhance retroviral production. The rapid medium exchange resulted in significantly larger amounts of high titer supernatants and an extended production phase as compared to the batch control cultures. The specific viral productivity of the pMFG/ΨCRIP cells was in the range of 10 to 40 infectious viruses produced per thousand producer cells per day. The CV-1 African Green Monkey kidney cell line was used as the infection target. Lowering the serum level form 20% to 10% improved retroviral production slightly. However, at lower serum levels (1%, 5% and 10% (v/v)) growth of the producer cell line, and thus retroviral production, was directly proportional to the serum level. The half-life of the virus at 37°C was found to be 5.5 hours. Promoting the growth of producer cell lines can improve retroviral vectors titers and viral production. High cell density systems that allow for rapid cell growth and waste product removal are likely to be used to generate high-titer retroviral supernatants.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42618/1/10616_2004_Article_BF00353938.pd

High Pressure Insulator-Metal Transition in Molecular Fluid Oxygen

We report the first experimental evidence for a metallic phase in fluid molecular oxygen. Our electrical conductivity measurements of fluid oxygen under dynamic quasi-isentropic compression show that a non-metal/metal transition occurs at 3.4 fold compression, 4500 K and 1.2 Mbar. We discuss the main features of the electrical conductivity dependence on density and temperature and give an interpretation of the nature of the electrical transport mechanisms in fluid oxygen at these extreme conditions.Comment: RevTeX, 4 figure