The PDZ-binding motif of the avian NS1 protein affects transmission of the 2009 influenza A(H1N1) virus

By nature of their segmented RNA genome, influenza A viruses (IAVs) have the potential to generate variants through a reassortment process. The influenza nonstructural (NS) gene is critical for a virus to counteract the antiviral responses of the host. Therefore, a newly acquired NS segment potentially determines the replication efficiency of the reassortant virus in a range of different hosts. In addition, the C-terminal PDZ-binding motif (PBM) has been suggested as a pathogenic determinant of IAVs. To gauge the pandemic potential from human and avian IAV reassortment, we assessed the replication properties of NS-reassorted viruses in cultured cells and in the lungs of mice and determined their transmissibility in guinea pigs. Compared with the recombinant A/Korea/01/2009 virus (rK09; 2009 pandemic H1N1 strain), the rK09/VN:NS virus, in which the NS gene was adopted from the A/Vietnam/1203/2004 virus (a human isolate of the highly pathogenic avian influenza H5N1 virus strains), exhibited attenuated virulence and reduced transmissibility. However, the rK09/VN:NS-PBM virus, harboring the PBM in the C-terminus of the NS1 protein, recovered the attenuated virulence of the rK09/VN:NS virus. In a guinea pig model, the rK09/VN:NS-PBM virus showed even greater transmission efficiency than the rK/09 virus. These results suggest that the PBM in the NS1 protein may determine viral persistence in the human and avian IAV interface.     

The Validity of Quasi-Steady-State Approximations in Discrete Stochastic Simulations

In biochemical networks, reactions often occur on disparate timescales and can be characterized as either fast or slow. The quasi-steady-state approximation (QSSA) utilizes timescale separation to project models of biochemical networks onto lower-dimensional slow manifolds. As a result, fast elementary reactions are not modeled explicitly, and their effect is captured by nonelementary reaction-rate functions (e.g., Hill functions). The accuracy of the QSSA applied to deterministic systems depends on how well timescales are separated. Recently, it has been proposed to use the nonelementary rate functions obtained via the deterministic QSSA to define propensity functions in stochastic simulations of biochemical networks. In this approach, termed the stochastic QSSA, fast reactions that are part of nonelementary reactions are not simulated, greatly reducing computation time. However, it is unclear when the stochastic QSSA provides an accurate approximation of the original stochastic simulation. We show that, unlike the deterministic QSSA, the validity of the stochastic QSSA does not follow from timescale separation alone, but also depends on the sensitivity of the nonelementary reaction rate functions to changes in the slow species. The stochastic QSSA becomes more accurate when this sensitivity is small. Different types of QSSAs result in nonelementary functions with different sensitivities, and the total QSSA results in less sensitive functions than the standard or the prefactor QSSA. We prove that, as a result, the stochastic QSSA becomes more accurate when nonelementary reaction functions are obtained using the total QSSA. Our work provides an apparently novel condition for the validity of the QSSA in stochastic simulations of biochemical reaction networks with disparate timescales.     

Tensile properties of the medial patellofemoral ligament: The effect of specimen orientation

For recurrent patellar dislocation, reconstruction of the medial patellofemoral ligament (MPFL) with replacement autografts has often been performed but with only little data on the tensile properties of the MPFL to guide graft selection. With its complex anatomy and geometry, these properties are difficult to obtain. In this study, we showed how the orientation of the femur-MPFL-patella complex (FMPC) during uniaxial tensile testing can have a significant effect on its structural properties. Twenty two FMPCs were isolated from porcine stifle joints and randomly assigned to two groups of 11 each. For the first group, the specimens were loaded to failure with the patella oriented 30 degrees away from the direction of the applied load to mimic its orientation in situ, called natural orientation. In the second group, the patella was aligned in the direction of the tensile load, called non-natural orientation. The stiffness for the natural orientation group was 65±13 N/mm, 32% higher than that for the non-natural orientation group (50±17 N/mm; p<0.05). The ultimate loads were 438±128 N and 386±136 N, respectively (p>0.05). Ten out of 11 specimens in the natural orientation group failed at the femoral attachment (the narrowest portion of the MPFL) compared to 6 out of 11 in the non-natural orientation group. Our findings suggest that the specimen orientation that mimics the in-situ loading conditions of the MPFL should be used to obtain more representative data for the structural properties of the FMPC.     

Effects of various chemical agents and early ethylene production on floral senescence of Hibiscus syriacus L.

To understand the factors that induce floral senescence in Hibiscus syriacus L., we have investigated the effects of various chemical agents on flower senescence at two different flowering stages, before and after full bloom, as well as the relationship between flower longevity and endogenous ethylene production before full bloom. Treatments with ethylene, 1-aminocyclopropane-1-carboxylic acid (ACC), and ethephon enhanced floral senescence, while aminoethoxyvinylglycine (AVG) promoted flower longevity regardless of treatment timing. Although ethanol slightly extended flower longevity, abscisic acid (ABA), nitric oxide, boric acid and sucrose, which have been reported to affect flower longevity or senescence, had no effect on H. syriacus floral senescence. The polyamine spermine (SPM), methylglyoxal-bis(guanylhydrazone) (MGBG), an inhibitor of SPM biosynthesis, and cycloheximide (CHI) accelerated flower senescence when applied before full bloom, but had no effect when applied after full bloom. SPM, MGBG and CHI treatments resulted in enhanced ethylene production during flower opening, and the promotion of flower senescence is mediated by ethylene production prior to full bloom. Furthermore, endogenous ethylene, spontaneously produced before blooming, was closely associated with floral senescence. These results suggest that ethylene production during flower opening plays a key role in determining the timing of Hibiscus flower senescence.     

A TGF‐β‐induced gene, βig‐h3, is crucial for the apoptotic disappearance of the medial edge epithelium in palate fusion

TGF‐β3, TβR‐I, and TGF‐β‐activated Smad2 has been suggested to be a series of signaling molecules for secondary palate fusion. In this article, we show that a gene induced by TGF‐β, βig‐h3, is coincidentally expressed with TGF‐β3 in medial edge epithelial (MEE) cells undergoing apoptosis during normal palatal fusion. βig‐h3 was also highly expressed in the areas of post‐weaning mammary gland cells and developing phalangeal joints in which TGF‐β3 or BMP‐4‐induced apoptosis occurs, respectively. Blocking of βig‐h3 expression in E12.5 embryos with antisense oligodeoxynucleotides (ODN) resulted in cleft of the secondary palate in 84% of the treated mice that were born. Moreover, the antisense ODN treatment resulted in a failure of apoptosis in the MEE between palatal shelves in physical contact in organ culture. We conclude that βig‐h3 expression in the MEE is stimulated by TGF‐β3, causes cell death, and consequently results in complete fusion of the apposed palatal shelves. J. Cell. Biochem. 107: 818–825, 2009. © 2009 Wiley‐Liss, Inc.     

Synthesis,initial SAR and biological evaluation of 1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridin-4-amine derived inhibitors of IκB kinase

A new series of tricyclic-based inhibitors of IKK have been derived from an earlier lead compound. The synthesis and structure–activity relationships (SAR) are described. Compound 4k inhibited TNF production in rats stimulated with LPS.     

Functional expression of Coprinus cinereus peroxidase in Pichia pastoris

A Coprinus cinereus peroxidase (CiP) was successfully expressed by the methylotrophic yeast Pichia pastoris. The 1095-bp gene encoding peroxidase from C. cinereus was cloned with a highly inducible alcohol oxidase (AOX1) promoter and integrated into the genome of P. pastoris. The recombinant CiP (rCiP) fused with the α-mating factor pre-pro leader sequence derived from Saccharomyces cerevisiae accumulated neither inside the cell nor within the wall, and were efficiently secreted into the culture medium. SDS-PAGE and immunoblot analysis revealed that the rCiP was not hyper-glycosylated and its α-factor signal sequence was correctly processed. It was also found that the kinetic properties of rCiP were similar to those of native CiP. In order to produce large amounts of rCiP, the high cell density cultivation of recombinant P. pastoris was carried out in a fermentor with fed-batch mode. The peroxidase activity obtained in a 5 l fermentor cultivation became about 6 times (1200 U/ml) higher than that in shake-flask cultures (200 U/ml).     

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

Driven by advancements in high-throughput biological technologies and the growing number of sequenced genomes, the construction of in silico models at the genome scale has provided powerful tools to investigate a vast array of biological systems and applications. Here, we review comprehensively the uses of such models in industrial and medical biotechnology, including biofuel generation, food production, and drug development. While the use of in silico models is still in its early stages for delivering to industry, significant initial successes have been achieved. For the cases presented here, genome-scale models predict engineering strategies to enhance properties of interest in an organism or to inhibit harmful mechanisms of pathogens. Going forward, genome-scale in silico models promise to extend their application and analysis scope to become a transformative tool in biotechnology.     

Effects of UCP2 and UCP3 Variants on the Manifestation of Overweight in Korean Children

To investigate the associations of uncoupling protein (UCP)2 and UCP3 gene variants with overweight and related traits, we genotyped UCP2−866G>A, UCP2Ala55Val, and UCP3−55C>T in 737 Korean children and 732 adults and collected data regarding anthropometric status and blood biochemistry. Information concerning the children's lifestyles and dietary habits was collected. The UCP2−866G>A and UCP3−55C>T gene variants showed significant associations with BMI level, waist circumference, and body weight in the children but not in the adults. Compared with −866GG carriers, the −866GA and AA carriers showed a strong decreasing trend in the risk for overweight (odds ratio (OR), 0.67; 95% confidence interval (CI), 0.45–1.01; P = 0.053). In comparison with UCP3−55CC carriers, children carrying −55CT and TT showed a significant reduction in the risk of overweight (OR, 0.67; 95% CI, 0.46–0.98; P = 0.039). There was also evidence of interactions between the effects of the combined UCP2−UCP3 genotype and obesity‐related metabolic traits. The greatest protective effect against overweight was seen in those with the combined genotype non‐UCP2−866GG and non‐UCP3−55CC, as compared with those carrying both UCP2−866GG and UCP3−55CC (OR, 0.60; 95% CI, 0.38–0.95; P = 0.030). In the subgroup with a low level of physical activity, UCP3−55CC carriers had higher BMI values than UCP3−55T carriers (16.6 ± 2.3 kg/m² vs. 16.1 ± 1.9 kg/m², P = 0.016). Low physical activity may aggravate the susceptibility to overweight in UCP2−866GG and UCP3−55CC carriers.