Simulation of the inhibition of microbial sulfate reduction in a two-compartment upflow bioreactor subjected to molybdate injection

Souring of oil fields during secondary oil recovery by water injection occurs mainly due to the action of sulfate-reducing bacteria (SRB) adhered to the rock surface in the vicinity of injection wells. Upflow packed-bed bioreactors have been used in petroleum microbiology because of its similarity to the oil field near the injection wells or production. However, these reactors do not realistically describe the regions near the injection wells, which are characterized by the presence of a saturated zone and a void region close to the well. In this study, the hydrodynamics of the two-compartment packing-free/packed-bed pilot bioreactor that mimics an oil reservoir was studied. The packed-free compartment was modeled using a continuous stirred tank model with mass exchange between active and stagnant zones, whereas the packed-bed compartment was modeled using a piston-dispersion-exchange model. The proposed model adequately represents the hydrodynamic of the packed-free/packed-bed bioreactor while the simulations provide important information about the characteristics of the residence time distribution (RTD) curves for different sets of model parameters. Simulations were performed to represent the control of the sulfate-reducing bacteria activity in the bioreactor with the use of molybdate in different scenarios. The simulations show that increased amounts of molybdate cause an effective inhibition of the souring sulfate-reducing bacteria activity.     

Quantitative assessment of methyl‐esterification and other side reactions in a standard propionylation protocol for detection of histone modifications

Histone modifications play an important role in regulating chromatin stability and gene expression, but to date, investigating them remains challenging. In order to obtain peptides suitable for MS‐based analysis, chemical derivatization of N‐terminus and lysine residues by propionic anhydride is commonly performed. Several side reactions (methyl‐esterification, amidation, solvolysis, overpropionylation, and missed propionylation) during propionylation protocols have been described, yet their relative abundances remain vague. Because methyl‐esterification could interfere with correct interpretation of the modification pattern, it is essential to take measures to avoid it. Here we present in‐depth quantitative analyses of methyl‐esterification and the other side reactions in a standard propionylation protocol containing methanol, and when replacing methanol with isopropanol or acetonitrile. We show that the use of alternative solvents can eliminate methyl‐esterification and that even though other side reactions are not prevented, their contribution can be kept relatively small. We also show that replacing methanol can be of importance also in other proteomics methods, such as mixed cation exchange, using methanol under acidic conditions.     

Poromicromechanics reveals that physiological bone strains induce osteocyte-stimulating lacunar pressure

Mechanical loads which are macroscopically acting onto bony organs, are known to influence the activities of biological cells located in the pore spaces of bone, in particular so the signaling and production processes mediated by osteocytes. The exact mechanisms by which osteocytes are actually able to “feel” the mechanical loading and changes thereof, has been the subject of numerous studies, and, while several hypotheses have been brought forth over time, this topic has remained a matter of debate. Relaxation times reported in a recent experimental study of Gardinier et al. (Bone 46(4):1075–1081, 2010) strongly suggest that the lacunar pores are likely to experience, during typical physiological load cycles, not only fluid transport, but also undrained conditions. The latter entail the buildup of lacunar pore pressures, which we here quantify by means of a thorough multiscale modeling approach. In particular, the proposed model is based on classical poroelasticity theory, and able to account for multiple pore spaces. First, the model reveals distinct nonlinear dependencies of the resulting lacunar (and vascular) pore pressures on the underlying bone composition, highlighting the importance of a rigorous multiscale approach for appropriate computation of the aforementioned pore pressures. Then, the derived equations are evaluated for macroscopic (uniaxial as well as hydrostatic) mechanical loading of physiological magnitude. The resulting model-predicted pore pressures agree very well with the pressures that have been revealed, by means of in vitro studies, to be of adequate magnitude for modulating the responses of biological cells, including osteocytes. This underlines that osteocytes may respond to many types of loading stimuli at the same time, in particular so to fluid flow and hydrostatic pressure.     

A lumped parameter model of mechanically mediated acute and long-term adaptations of contractility and geometry in lymphatics for characterization of lymphedema

A primary purpose of the lymphatic system is to transport fluid from peripheral tissues to the central venous system in order to maintain tissue–fluid balance. Failure to perform this task results in lymphedema marked by swelling of the affected limb as well as geometric remodeling and reduced contractility of the affected lymphatic vessels. The mechanical environment has been implicated in the regulation of lymphatic contractility, but it is unknown how changes in the mechanical environment are related to loss of contractile function and remodeling of the tissue. The purpose of this paper was to introduce a new theoretical framework for acute and long-term adaptations of lymphatic vessels to changes in mechanical loading. This theoretical framework combines a simplified version of a published lumped parameter model for lymphangion function and lymph transport, a published microstructurally motivated constitutive model for the active and passive mechanical behavior of isolated rat thoracic ducts, and novel models for acute mechanically mediated vasoreactive adaptations and long-term volumetric growth to simulate changes in muscle contractility and geometry of a single isolated rat thoracic duct in response to a sustained elevation in afterload. The illustrative examples highlight the potential role of the mechanical environment in the acute maintenance of contractility and long-term geometric remodeling, presumably aimed at meeting fluid flow demands while also maintaining mechanical homeostasis. Results demonstrate that contractility may adapt in response to shear stress to meet fluid flow demands and show that pressure-induced long-term geometric remodeling may attenuate these adaptations and reduce fluid flow. The modeling framework and illustrative simulations help suggest relevant experiments that are necessary to accurately quantify and predict the acute and long-term adaptations of lymphangions to altered mechanical loading.     

<Emphasis Type="Italic">In silico</Emphasis> coronary wave intensity analysis: application of an integrated one-dimensional and poromechanical model of cardiac perfusion

Coronary wave intensity analysis (cWIA) is a diagnostic technique based on invasive measurement of coronary pressure and velocity waveforms. The theory of WIA allows the forward- and backward-propagating coronary waves to be separated and attributed to their origin and timing, thus serving as a sensitive and specific cardiac functional indicator. In recent years, an increasing number of clinical studies have begun to establish associations between changes in specific waves and various diseases of myocardium and perfusion. These studies are, however, currently confined to a trial-and-error approach and are subject to technological limitations which may confound accurate interpretations. In this work, we have developed a biophysically based cardiac perfusion model which incorporates full ventricular–aortic–coronary coupling. This was achieved by integrating our previous work on one-dimensional modelling of vascular flow and poroelastic perfusion within an active myocardial mechanics framework. Extensive parameterisation was performed, yielding a close agreement with physiological levels of global coronary and myocardial function as well as experimentally observed cumulative wave intensity magnitudes. Results indicate a strong dependence of the backward suction wave on QRS duration and vascular resistance, the forward pushing wave on the rate of myocyte tension development, and the late forward pushing wave on the aortic valve dynamics. These findings are not only consistent with experimental observations, but offer a greater specificity to the wave-originating mechanisms, thus demonstrating the value of the integrated model as a tool for clinical investigation.     

Computational modeling of the arterial wall based on layer-specific histological data

Arterial walls typically have a heterogeneous structure with three different layers (intima, media, and adventitia). Each layer can be modeled as a fiber-reinforced material with two families of relatively stiff collagenous fibers symmetrically arranged within an isotropic soft ground matrix. In this paper, we present two different modeling approaches, the embedded fiber (EF) approach and the angular integration (AI) approach, to simulate the anisotropic behavior of individual arterial wall layers involving layer-specific data. The EF approach directly incorporates the microscopic arrangement of fibers that are synthetically generated from a random walk algorithm and captures material anisotropy at the element level of the finite element formulation. The AI approach smears fibers in the ground matrix and treats the material as homogeneous, with material anisotropy introduced at the constitutive level by enhancing the isotropic strain energy with two anisotropic terms. Both approaches include the influence of fiber dispersion introduced by fiber angular distribution (departure of individual fibers from the mean orientation) and take into consideration the dispersion caused by fiber waviness, which has not been previously considered. By comparing the numerical results with the published experimental data of different layers of a human aorta, we show that by using histological data both approaches can successfully capture the anisotropic behavior of individual arterial wall layers. Furthermore, through a comprehensive parametric study, we establish the connections between the AI phenomenological material parameters and the EF parameters having straightforward physical or geometrical interpretations. This study provides valuable insight for the calibration of phenomenological parameters used in the homogenized modeling based on the fiber microscopic arrangement. Moreover, it facilitates a better understanding of individual arterial wall layers, which will eventually advance the study of the structure–function relationship of arterial walls as a whole.     

Low diversity and abundance of root endophytes prevail throughout the life cycle of an annual halophyte

Plants growing in highly saline soils harbor unique communities of fungal root endophytes. We aimed to gain insight into how these communities are established in natural plant populations. We used cultivation-based and molecular approaches to examine root-endophytic colonization in the annual halophyte Salicornia patula at three time points over a 5-month period, from establishment to flowering. At the last sampling, the endophytic community of S. patula was compared to that in the related but perennial halophyte Arthrocnemum macrostachyum. The presence of root endophytes in S. patula was negligible at the first two sampling times, and remained low at the last sampling compared to A. macrostachyum. The latter species showed a well-established endophytic community in its roots that differed from that in S. patula, which was dominated by members of Pleosporales. Although such differences could be partially due to the host lifestyle, the possibility of a strong effect of the substratum could not be excluded. Altogether, our data indicate that the fungal endophytic colonization of roots is a slow process under salt stress. Therefore, we suggest that, in contrast to what is proposed for other systems, endophyte symbioses are unlikely to impact the development of the short-life-cycled S. patula living in these environments.     

Alkaline-sulfite pretreatment and use of surfactants during enzymatic hydrolysis to enhance ethanol production from sugarcane bagasse

Sugarcane bagasse is a by-product from the sugar and ethanol industry which contains approximately 70 % of its dry mass composed by polysaccharides. To convert these polysaccharides into fuel ethanol it is necessary a pretreatment step to increase the enzymatic digestibility of the recalcitrant raw material. In this work, sugarcane bagasse was pretreated by an alkaline-sulfite chemithermomechanical process for increasing its enzymatic digestibility. Na₂SO₃ and NaOH ratios were fixed at 2:1, and three increasing chemical loads, varying from 4 to 8 % m/m Na₂SO₃, were used to prepare the pretreated materials. The increase in the alkaline-sulfite load decreased the lignin content in the pretreated material up to 35.5 % at the highest chemical load. The pretreated samples presented enhanced glucose yields during enzymatic hydrolysis as a function of the pretreatment severity. The maximum glucose yield (64 %) was observed for the samples pretreated with the highest chemical load. The use of 2.5 g l^?1 Tween 20 in the hydrolysis step further increased the glucose yield to 75 %. Semi-simultaneous hydrolysis and fermentation of the pretreated materials indicated that the ethanol yield was also enhanced as a function of the pretreatment severity. The maximum ethanol yield was 56 ± 2 % for the sample pretreated with the highest chemical load. For the sample pretreated with the lowest chemical load (2 % m/m NaOH and 4 % m/m Na₂SO₃), adding Tween 20 during the hydrolysis process increased the ethanol yield from 25 ± 3 to 39.5 ± 1 %.     

Characterization of the biochemical properties of recombinant Xyn10C from a marine bacterium, <Emphasis Type="Italic">Saccharophagus degradans</Emphasis> 2-40

Endo-1,4-β-xylanases are mostly classified into glycoside hydrolase (GH) family 10 or 11. In this study, we examined the catalytic functions of a recombinant endo-1,4-β-xylanase belonging to GH10 (Xyn10C) from a marine bacterium, Saccharophagus degradans 2-40. Optimal activity of this enzyme was evident at 30 °C and pH 7.0, but activity remained even at low temperatures, indicating its adaptation to cold. With respect to other xylanases known to be active in cold temperatures, Xyn10C is unique in that it showed maximal activity in the presence of 2 M of NaCl. The action patterns of recombinant Xyn10C on xylans from hardwood and softwood differed in part, but the enzyme hydrolyzed polysaccharidic substrates primarily to xylobiose and xylotriose through xylo-oligosaccharides, releasing a small amount of xylose. The K _m and V _max values on birchwood xylan were 10.4 mg mL^?1 and 253 µmol mg^?1 min^?1, respectively. The efficient catalytic function of Xyn10C on short-length xylo-oligosaccharide chains was similar to the typical function of other known GH10 xylanases.