A multiscale model for multiple platelet aggregation in shear flow

Biomechanics and Modeling in Mechanobiology - We developed a multiscale model for simulating aggregation of multiple, free-flowing platelets in low–intermediate shear viscous flow, in which...     

Biochemical and Physiological Responses of Cucumis sativus Cultivars to Different Combinations of Low-Temperature and High Humidity

Low-temperature and high humidity are typical environmental factors in the plastic tunnel and solar greenhouse during the cold season that restricts plant growth and development. Herein, we investigated the impact of different combinations of low-temperature and high humidity (day/night: T1 15/10 °C?+?95%, T2 12/8 °C?+?95%, and T3 9/5 °C?+?95%) along with a control (CK 25/18 °C?+?80%) on cucumber cultivars viz: Zhongnong37 (ZN37: resistant) and Shuyanbailv (SYB: sensitive). The low-temperature and high humidity stresses increased electrolyte leakage (EL), malondialdehyde (MDA), hydrogen peroxide (H₂O₂) and intercellular concentration of carbon dioxide (Ci), and reduced morphological indices, relative water content (RWC), net photosynthesis rate (Pn), stomatal conductance (Gs), transpiration rate (E) and leaf pigments in both cultivars as compared to control (CK). Superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), and glutathione reductase (GR) were decreased in cv. SYB under stress conditions as compared to cv. ZN37. Low-temperature and high humidity treatments showed an increase in proline and soluble protein content in cv. ZN37 as compared to cv. SYB. Abscisic acid (ABA) and jasmonic acid (JA) were augmented while indole-3-acetic acid (IAA), zeatin (ZT), zeatin riboside (ZR), and gibberellic acid (GA) were decreased in both cultivars. Under T3 (9/5 °C?+?95%), Pn, protoporphyrin, and ZT were extremely decreased by 71.3%, 74.3%, and 82.4%, respectively, in cv. SYB compared to control. Moreover, principal component analysis (PCA) based on physiochemical traits confirmed that cv. ZN37 had the strongest correlation with antioxidant enzymes, proline, and soluble protein content than cv. SYB under low-temperature and high humidity treatments. Our results suggest that a stress-tolerant cultivar mitigates stress damage in cucumber transplants by regulating photosynthetic efficiency, antioxidant capacity and hormonal profile when compared to a stress-sensitive cultivar.

     

Two simple and rapid methods for the detection of polymer-degrading enzymes on high-resolution, alkaline, cold, in situ-native (HiRACIN)-PAGE and high-resolution, in situ-inhibited native (HiRISIN)-PAGE

Two sensitive, high-resolution and exceedingly versatile methods for the detection of isoenzymes of polymer-degrading enzymes on high-resolution, alkaline, cold, in situ-native (HiRACIN)-PAGE and high-resolution in situ-inhibited, native (HiRISIN)-PAGE are described. Extracellular crude extracts containing xylanases and carboxymethylcellulases from Scopulariopsis sp. and glucoamylases from Aspergillus niger were subjected to non-denaturing PAGE containing substrates in the resolving gel. In case of HiRACIN-PAGE, the enzymes were prevented from degrading their respective substrates during run by carrying out electrophoresis at 4°C and the pH of running and resolving gel buffer systems were increased from 8.5 to 10.6. In case of HiRISIN-PAGE, adding competitive inhibitor of the enzyme, cellobiose, in the resolving gel prevents the degradation of polymer during the run. These techniques were successfully applied, for the first time, to visualize four, three and four sharp and distinct bands of xylanases, glucoamylases and CMCases, respectively.     

A novel thermodynamic relationship based on Kramers Theory for studying enzyme kinetics under high viscosity

In most studies of enzyme kinetics it has been found sufficient to use the classical Transition State Theory (TST) of Eyring and others. This theory was based on the solvent being an ideal dilute substance treated as a heat bath. However, enzymes found in organisms adapted to very low (psychrophiles) and very high (thermophiles) temperatures are also subjected to variable solute concentrations and viscosities. Therefore, the TST may not always be applicable to enzyme reactions carried out in various solvents with viscosities ranging from moderate to very high. There have been numerous advances in the theory of chemical reactions in realistic non-ideal solvents such as Kramers Theory. In this paper we wish to propose a modified thermodynamic equation, which have contributions from kcat, Km and the viscosity of the medium in which the enzyme reaction is occurring. These could be very useful for determining the thermodynamics of enzymes catalyzing reactions at temperature extremes in the presence of substrate solutions of different compositions and viscosities.     

A novel mathematical model of activation and sensitization of platelets subjected to dynamic stress histories

Blood recirculating devices, such as ventricular assist devices and prosthetic heart valves, are burdened by thromboembolic complications requiring complex and lifelong anticoagulant therapy with its inherent hemorrhagic risks. Pathologic flow patterns occurring in such devices chronically activate platelets, and the optimization of their thrombogenic performance requires the development of flow-induced platelet activation models. However, existing models are based on empirical correlations using the well-established power law paradigm of constant levels of shear stress during certain exposure times as factors for mechanical platelet activation. These models are limited by their range of application and do not account for other relevant phenomena, such as loading rate dependence and platelet sensitization to high stress conditions, which characterize the dynamic flow conditions in devices. These limitations were addressed by developing a new class of phenomenological stress-induced platelet activation models that specifies the rate of platelet activation as a function of the entire stress history and results in a differential equation that can be directly integrated to calculate the cumulative levels of activation. The proposed model reverts to the power law under constant shear stress conditions and is able to describe experimental results in response to a diverse range of highly dynamic stress conditions found in blood recirculating devices. The model was tested in vitro under emulated device flow conditions and correlates well with experimental results. This new model provides a reliable and robust mathematical tool that can be incorporated into computational fluid dynamic studies in order to optimize design, with the goal of improving the thrombogenic performance of blood recirculating devices.     

Computational evaluation of the thrombogenic potential of a hollow-fiber oxygenator with integrated heat exchanger during extracorporeal circulation

The onset of thromboembolic phenomena in blood oxygenators, even in the presence of adequate anticoagulant strategies, is a relevant concern during extracorporeal circulation (ECC). For this reason, the evaluation of the thrombogenic potential associated with extracorporeal membrane oxygenators should play a critical role into the preclinical design process of these devices. This study extends the use of computational fluid dynamics simulations to guide the hemodynamic design optimization of oxygenators and evaluate their thrombogenic potential during ECC. The computational analysis accounted for both macro- (i.e., vortex formation) and micro-scale (i.e., flow-induced platelet activation) phenomena affecting the performances of a hollow-fiber membrane oxygenator with integrated heat exchanger. A multiscale Lagrangian approach was adopted to infer the trajectory and loading history experienced by platelet-like particles in the entire device and in a repetitive subunit of the fiber bundles. The loading history was incorporated into a damage accumulation model in order to estimate the platelet activation state (PAS) associated with repeated passes of the blood within the device. Our results highlighted the presence of blood stagnation areas in the inlet section that significantly increased the platelet activation levels in particles remaining trapped in this region. The order of magnitude of PAS in the device was the same as the one calculated for the components of the ECC tubing system, chosen as a term of comparison for their extensive diffusion. Interpolating the mean PAS values with respect to the number of passes, we obtained a straightforward prediction of the thrombogenic potential as a function of the duration of ECC.     

Coupling of surface carboxyls of carboxymethylcellulase with aniline via chemical modification: extreme thermostabilization in aqueous and water-miscible organic mixtures

We wish to report the attainment of the highest ever T(opt) by introducing approximately two aromatic rings through chemical modification of surface carboxyl groups in carboxymethylcellulase from Scopulariopsis sp. with concomitant decrease in V(max), K(m), and optimum pH! This extraordinary enhancement in thermophilicity of aniline-coupled CMCase (T(opt) = 122 degrees C) by a margin of 73 degrees C as compared with the native enzyme (T(opt) = 49 degrees C) is the highest reported for any mesophilic enzyme that has been modified either through chemical modification or site-directed mutagenesis. It is also reported for the first time that aniline coupled CMCase (ACC) is simultaneously thermostable in aqueous as well as water-miscible organic solvents. The T(opt) of native CMCase and ACC were 25 and 90 degrees C, respectively, in 40% (v/v) aqueous dioxan. The modified enzyme was also stabilized against irreversible thermal denaturation. Therefore, at 55 degrees C, ACC had a half-life of 136 min as compared with native CMCase whose half-life was only 5 min. We believe that the reasons for this elevated thermostability and thermophilicity are surface aromatic-aromatic interactions and aromatic interactions with the sugar backbone of the substrate, respectively.     

The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean

The composite map of soybean shared among Soybase, LIS and SoyGD (March 2006) contained 3,073 DNA markers in the "Locus" class. Among the markers were 1,019 class I microsatellite markers with 2-3 bp simple sequence repeats (SSRs) of >10 iterations (BARC-SSR markers). However, there were few class II SSRs (2-5 bp repeats with <10 iterations; mostly SIUC-Satt markers). The aims here were to increase the number of classes I and II SSR markers and to integrate bacterial artificial chromosome (BAC) clones onto the soybean physical map using the markers. Used was 10 Mb of BAC-end sequence (BES) derived from 13,473 reads from 7,050 clones constituting minimum tile path 2 of the soybean physical map ( http://www.soybeangenome.siu.edu ; SoyGD). Identified were 1,053 1-6 bp motif, repeat sequences, 333 from class I (>10 repeats) and 720 from class II (<10 repeats). Potential markers were shown on the MTP_SSR track at Gbrowse. Primers were designed as 20-24 bp oligomers that had Tm of 55 +/- 1 C that would generate 100-500 bp amplicons. About 853 useful primer pairs were established. Motifs were not randomly distributed with biases toward AT rich motifs. Strong biases against the GC motif and all tetra-nucleotide repeats were found. The markers discovered were useful. Among the first 135 targeted for use in genetic map improvement about 60% of class II markers and 75% of class I markers were polymorphic among on the parents of four recombinant inbred line (RIL) populations. Many of the BES-based SSRs were located on the soybean genetic map in regions with few BARC-SSR markers. Therefore, BES-based SSRs represent useful tools for genetic map development in soybean. New members of a consortium to map the markers in additional populations are invited.