Stabilizing Control for a Pulsatile Cardiovascular Mathematical Model

In this paper, we develop a pulsatile model for the cardiovascular system which describes the reaction of this system to a submaximal constant workload imposed on a person at a bicycle ergometer test after a period of rest. Furthermore, the model should allow to use measurements for the pulsatile pressure in fingertips which provide information on the diastolic and the systolic pressure for parameter estimation. Based on the assumption that the baroreceptor loop is the essential control loop in this case, we design a stabilizing feedback control for the pulsatile model which is obtained by solving a linear-quadratic regulator problem for the linearization of a non-pulsatile counterpart of the pulsatile model. We also investigate the behavior of the model with respect to changes in the weight of the term in the cost functional for the linear-quadratic regulator problem which penalizes the deviation of the momentary pressure in the aorta from the pressure at the stationary situation which should be obtained.     

An Uncultivated Nitrate-Reducing Member of the Genus Herminiimonas Degrades Toluene

Stable isotope probing (SIP) is a cultivation-free methodology that provides information about the identity of microorganisms participating in assimilatory processes in complex communities. In this study, a Herminiimonas-related bacterium was identified as the dominant member of a denitrifying microcosm fed [¹³C]toluene. The genome of the uncultivated toluene-degrading bacterium was obtained by applying pyrosequencing to the heavy DNA fraction. The draft genome comprised ∼3.8 Mb, in 131 assembled contigs. Metabolic reconstruction of aromatic hydrocarbon (toluene, benzoate, p-cresol, 4-hydroxybenzoate, phenylacetate, and cyclohexane carboxylate) degradation indicated that the bacterium might specialize in anaerobic hydrocarbon degradation. This characteristic is novel for the order Burkholderiales within the class Betaproteobacteria. Under aerobic conditions, the benzoate oxidation gene cluster (BOX) system is likely involved in the degradation of benzoate via benzoyl coenzyme A. Many putative genes for aromatic hydrocarbon degradation were closely related to those in the Rhodocyclaceae (particularly Aromatoleum aromaticum EbN1) with respect to organization and sequence similarity. Putative mobile genetic elements associated with these catabolic genes were highly abundant, suggesting gene acquisition by Herminiimonas via horizontal gene transfer.     

Elevational patterns of plant richness and their drivers on an Asian mountain

We examined the elevational patterns of plant species along two transects on Mt Seorak, South Korea, and calculated four richness indices from field survey data: total number of species per 100 m elevational band; mean number of species per plot in each elevational band; total estimated number of species per elevational band; and beta diversity of each elevational band. We evaluated the effects of area, mean distance between plots, climatic variables (mean annual temperature and precipitation), and productivity on the richness patterns along the two transects. In total, 235 plant species belonging to 72 families and 161 genera were recorded from 130 plots along the two transects. The analyses revealed different patterns including monotonic decline, and unimodal and multimodal shapes for richness indices of total, woody, and herbaceous plants with the change in elevation along the two transects. The proportion of suitable area (as opposed to rocky areas) was the best predictor for total number of species per elevational band, mean number of species per plot, and total estimated number of species per elevational band of total and herbaceous plants along the two transects. Mean distance between plots was the most important variable for beta diversity of all plant groups. Although regional area, climatic variables, and productivity were important variables for predicting woody plant richness patterns, the effects were not consistent between the two transects. Our study suggests that elevational species richness patterns may differ not only among different plant groups, but also between nearby elevational transects, and that these differences are explained by differences in the underlying mechanisms shaping these patterns.     

Synthesis of Flavonoid O-Pentosides by Escherichia coli through Engineering of Nucleotide Sugar Pathways and Glycosyltransferase

Plants produce two flavonoid O-pentoses, flavonoid O-xyloside and flavonoid O-arabinoside. However, analyzing their biological properties is difficult because flavonoids are not naturally produced in sufficient quantities. In this study, Escherichia coli was used to synthesize the plant-specific flavonoid O-pentosides quercetin 3-O-xyloside and quercetin 3-O-arabinoside. Two strategies were used. First, E. coli was engineered to express components of the biosynthetic pathways for UDP-xylose and UDP-arabinose. For UDP-xylose biosynthesis, two genes, UXS (UDP-xylose synthase) from Arabidopsis thaliana and ugd (UDP-glucose dehydrogenase) from E. coli, were overexpressed. In addition, the gene encoding ArnA (UDP-l-Ara4N formyltransferase/UDP-GlcA C-4″-decarboxylase), which competes with UXS for UDP-glucuronic acid, was deleted. For UDP-arabinose biosynthesis, UXE (UDP-xylose epimerase) was overexpressed. Next, we engineered UDP-dependent glycosyltransferases (UGTs) to ensure specificity for UDP-xylose and UDP-arabinose. The E. coli strains thus obtained synthesized approximately 160 mg/liter of quercetin 3-O-xyloside and quercetin 3-O-arabinoside.     

Microfluidics-assisted rapid generation of tubular cell-laden microgel inside glass capillaries

Drug screening using engineered blood vessels (EBVs) faces considerable barriers in approximating the conditions of an in vivo environment. To address this issue, we have introduced a microfluidic system for cell-laden tubular microgels. N-Carboxyethyl chitosan crosslinked with oxidized dextran was used for in situ gelable tubular scaffolds. The microfluidic system consisted of four glass capillaries that generated a coaxial flow of pre-polymer and phosphate buffered solutions. It rapidly produced cell-laden tubular microgels inside glass capillaries. The mechanical strength of the tubular microgels was suitable for their application as EBVs, with a maximum Young’s modulus of 12.2 ± 1.9 kPa. In vitro cell studies using human umbilical vein endothelial cells verified the biocompatibility and non-cytotoxicity of the gelation and fabrication process. Thus, in situ gelable cell-laden tubular microgels can be a potential platform for screening drugs to treat blood vessel diseases.     

Enhancing the processivity of a family B-type DNA polymerase of Thermococcus onnurineus and application to long PCR

Mechanisms that allow replicative DNA polymerases to attain high processivity are often specific to a given polymerase and cannot be generalised to others. Amplification efficiency is lower in family B-type DNA polymerases than in family A-type (Taq) polymerases because of their strong 3′–5′ exonuclease-activity. Here, we have red the exonuclease domain of the Thermococcus onnurineus NA1 (TNA1) DNA polymerase, especially Asn210 to Asp215 residues in Exo II motif (NXXXFD), to improve the processivity. N213D mutant protein had higher processivity and extension rate than the wild-type TNA1 DNA polymerase, retaining a lower mutation frequency than recombinant Taq DNA polymerase. Consequently, the N213D mutant could amplify target DNA up to 13.5 kb in length from human genomic DNA and 16.2 kb in length from human mitochondrial DNA while wild-type TNA1 amplified target DNA of 2.7 kb in length from human genomic DNA.     

Increased expression of Fe-chelatase leads to increased metabolic flux into heme and confers protection against photodynamically induced oxidative stress

Fe-chelatase (FeCh, EC 4.99.1.1) inserts Fe²⁺ into protoporphyrin IX (Proto IX) to form heme, which influences the flux through the tetrapyrrole biosynthetic pathway as well as fundamental cellular processes. In transgenic rice (Oryza sativa), the ectopic expression of Bradyrhizobium japonicum FeCh protein in cytosol results in a substantial increase of FeCh activity compared to wild-type (WT) rice and an increasing level of heme. Interestingly, the transgenic rice plants showed resistance to oxidative stress caused not only by the peroxidizing herbicide acifluorfen (AF) as indicated by a reduced formation of leaf necrosis, a lower conductivity, lower malondialdehyde and H₂O₂ contents as well as sustained F_v/F_m compared to WT plants, but also by norflurazon, paraquat, salt, and polyethylene glycol. Moreover, the transgenic plants responded to AF treatment with markedly increasing FeCh activity. The accompanying increases in heme content and heme oxygenase activity demonstrate that increased heme metabolism attenuates effects of oxidative stress caused by accumulating porphyrins. These findings suggest that increases in heme levels and porphyrin scavenging capacity support a detoxification mechanism serving against porphyrin-induced oxidative stress. This study also implicates heme as possibly being a positive signal in plant stress responses.