A neural network study on the dynamic identification of a fermentation system

The objective of this paper is to propose neural networks for the study of dynamic identification and prediction of a fermentation system which produces mainly 2,3-butanediol (2,3-BDL). The metabolic products of the fermentation, acetic acid, acetoin, ethanol, and 2,3-BDL were measured on-line via a mass spectrometer modified by the insertion of a dimethylvinylsilicone membrane probe. The measured data at different sampling times were included as the input and output nodes, at different learning batches, of the network. A fermentation system is usually nonlinear and dynamic in nature. Measured fermentation data obtained from the complex metabolic pathways are often difficult to be entirely included in a static process model, therefore, a dynamic model was suggested instead. In this work, neural networks were provided by a dynamic learning and prediction process that moved along the time sequence batchwise. In other words, a scheme of two-dimensional moving window (number of input nodes by the number of training data) was proposed for reading in new data while forgetting part of the old data. Proper size of the network including proper number of input/output nodes were determined by trained with the real-time fermentation data. Different number of hidden nodes under the consideration of both learning performance and computation efficiency were tested. The data size for each learning batch was determined. The performance of the learning factors such as the learning coefficient η and the momentum term coefficient α were also discussed. The effect of different dynamic learning intervals, with different starting points and the same ending point, both on the learning and prediction performance were studied. On the other hand, the effect of different dynamic learning intervals, with the same starting point and different ending points, was also investigated. The size of data sampling interval was also discussed. The performance from four different types of transfer functions, x/(1+|x|), sgn(x)·x ²/(1+x ²), 2/(1+e ^{? x} )?1, and 1/(1+e ^{? x} ) was compared. A scaling factor b was added to the transfer function and the effect of this factor on the learning was also evaluated. The prediction results from the time-delayed neural networks were also studied.     

The nucleolar phosphoprotein B23 interacts with hepatitis delta antigens and modulates the hepatitis delta virus RNA replication

Hepatitis delta virus (HDV) encodes two isoforms of delta antigens (HDAgs). The small form of HDAg is required for HDV RNA replication, while the large form of HDAg inhibits the viral replication and is required for virion assembly. In this study, we found that the expression of B23, a nucleolar phosphoprotein involved in disparate functions including nuclear transport, cellular proliferation, and ribosome biogenesis, is up-regulated by these two HDAgs. Using in vivo and in vitro experimental approaches, we have demonstrated that both isoforms of HDAg can interact with B23 and their interaction domains were identified as the NH(2)-terminal fragment of each molecule encompassing the nuclear localization signal but not the coiled-coil region of HDAg. Sucrose gradient centrifugation analysis indicated that the majority of small HDAg, but a lesser amount of the large HDAg, co-sedimented with B23 and nucleolin in the large nuclear complex. Transient transfection experiments also indicated that introducing exogenous full-length B23, but not a mutated B23 defective in HDAg binding, enhanced HDV RNA replication. All together, our results reveal that HDAg has two distinct effects on nucleolar B23, up-regulation of its gene expression and the complex formation, which in turn regulates HDV RNA replication. Therefore, this work demonstrates the important role of nucleolar protein in regulating the HDV RNA replication through the complex formation with the key positive regulator being small HDAg.     

Antimicrobial and cytotoxic activities of neolignans from Magnolia officinalis

In the light of the steady increase of infections related to vancomycin-resistant enterococci (VRE) and methicillin-resistant Staphylococcus aureus (MRSA), the medicinal plant Magnolia officinalis was subjected to bioassay-directed fractionation, which led to the isolation of the known neolignans piperitylmagnolol (1), magnolol (2), and honokiol (3) from the MeOH extract. In broth-microdilution assays, 1-3 exhibited antibacterial activities against VRE and MRSA at minimum-inhibitory concentrations (MIC) in the range of 6.25-25 microg/ml, compound 1 being the most-potent antibiotic. The ratio of MBC/MIC (MBC = minimum bactericidal concentration) was < or = 2 for all compounds. The kinetics of the antibacterial action of 1 and 3 were studied by means of time-kill assays; both compounds were bactericidal against VRE and MRSA, their actions being time dependent, or both time and concentration dependent. Magnolol (2) was acetylated to magnolol monoacetate (4) and magnolol diacetate (5) (partial or full masking of the phenolic OH functions). The cytotoxic properties of 1-5 against human OVCAR-3 (ovarian adenocarcinoma), HepG2 (hepatocellular carcinoma), and HeLa (cervical epitheloid carcinoma) cell lines were evaluated. The CD50 values for compounds 1-3 were in the range of 3.3-13.3 microg/ml, derivatives 4 and 5 being much less potent. This study indicates that piperitylmagnolol (= 3-[(1S,6S)-6-isopropyl-3-methylcyclohex-2-enyl]-5,5'-di(prop-2-enyl)[1,1'-biphenyl]-2,2'-diol; 1) possesses both significant anti-VRE activity and moderate cytotoxicity against the above cancer cell lines.     

Free oxygen radicals are generated at the time of aspiration of oocytes from ovaries that have been stored for a long time

In ischaemic tissues, reperfusion induces acute injury and functional changes. In this work, ovaries were stored for various times, and superoxide dismutase (SOD) and dimethylthiourea (DTMU) were used at the time of oocyte aspiration. We then attempted to determine whether free oxygen radicals are generated at oocyte aspiration and whether they impair the developmental competence of oocytes. Over 2 mM of DMTU and 1000 U/ml of SOD significantly improved the rate of blastulation 8 days after insemination. For ovaries that were preserved for 3 and 7 h, using antioxidants also significantly improved the rate of blastulation 8 days after insemination. However, no effect was observed on oocytes from ovaries preserved for 1 h. We examined how the antioxidants affected the presence of germinal vesicles, chromatin configuration, and polar body extrusion 6 or 21 h after culture. Chromatin configuration was classified into three groups according to the amount of chromatin condensation (group 1, strong condensation; group 2, moderate; group 3, slight). Storing ovaries for a long time decreased the frequency of occurrence of group 2, but increased groups 1 and 3. However, using antioxidants at oocyte aspiration decreased the frequency of group 3 and increased group 1. Moreover, there was no difference in the rate of germinal vesicle breakdown and polar body extrusion. Our results show that preserving ovaries for a long time induces the generation of free oxygen radicals and that these chemicals impair oocyte viability. Using antioxidants at oocyte aspiration was beneficial for embryo production.     

Biological production of 2,3-butanediol

2,3-Butanediol (2,3-BDL), which is very important for a variety of chemical feedstocks and liquid fuels, can be derived from the bioconversion of natural resources. One of its well known applications is the formation of methyl ethyl ketone, by dehydration, which can be used as a liquid fuel additive. This article briefly reviews the basic properties of 2,3-BDL and the metabolic pathway for the microbial formation of 2,3-BDL. Both the biological production of 2,3-BDL and the variety of strains being used are introduced. Genetically improved strains for BDL production which follow either the original mechanisms or new mechanisms are also described. Studies on fermentation conditions are briefly reviewed. On-line analysis, modeling, and control of BDL fermentation are discussed. In addition, downstream recovery of 2,3-BDL and the integrated process (being important issues of BDL production) are also introduced.     

Characterization of the distal tail fiber locus and determination of the receptor for phage AR1, which specifically infects Escherichia coli O157:H7

Phage AR1 is similar to phage T4 in several essential genes but differs in host range. AR1 infects various isolates of Escherichia coli O157:H7 but does not infect K-12 strains that are commonly infected by T4. We report here the determinants that confer this infection specificity. In T-even phages, gp37 and gp38 are components of the tail fiber that are critical for phage-host interaction. The counterparts in AR1 may be similarly important and, therefore, were characterized. The AR1 gp37 has a sequence that differs totally from those of T2 and T4, except for a short stretch at the N terminus. The gp38 sequence, however, has some conservation between AR1 and T2 but not between AR1 and T4. The sequences that are most closely related to the AR1 gp37 and gp38 are those of phage Ac3 in the T2 family. To identify the AR1-specific receptor, E. coli O157:H7 was mutated by Tn10 insertion and selected for an AR1-resistant phenotype. A mutant so obtained has an insertion occurring at ompC that encodes an outer membrane porin. To confirm the role of OmpC in the AR1 infection, homologous replacement was used to create an ompC disruption mutant (RM). When RM was complemented with OmpC originated from an O157:H7 strain, but not from K-12, its AR1 susceptibility was fully restored. Our results suggest that the host specificity of AR1 is mediated at least in part through the OmpC molecule.     

Severe exercise and exercise training exert opposite effects on human neutrophil apoptosis via altering the redox status

Neutrophil spontaneous apoptosis, a process crucial for immune regulation, is mainly controlled by alterations in reactive oxygen species (ROS) and mitochondria integrity. Exercise has been proposed to be a physiological way to modulate immunity; while acute severe exercise (ASE) usually impedes immunity, chronic moderate exercise (CME) improves it. This study aimed to investigate whether and how ASE and CME oppositely regulate human neutrophil apoptosis. Thirteen sedentary young males underwent an initial ASE and were subsequently divided into exercise and control groups. The exercise group (n = 8) underwent 2 months of CME followed by 2 months of detraining. Additional ASE paradigms were performed at the end of each month. Neutrophils were isolated from blood specimens drawn at rest and immediately after each ASE for assaying neutrophil spontaneous apoptosis (annexin-V binding on the outer surface) along with redox-related parameters and mitochondria-related parameters. Our results showed that i) the initial ASE immediately increased the oxidative stress (cytosolic ROS and glutathione oxidation), and sequentially accelerated the reduction of mitochondrial membrane potential, the surface binding of annexin-V, and the generation of mitochondrial ROS; ii) CME upregulated glutathione level, retarded spontaneous apoptosis and delayed mitochondria deterioration; iii) most effects of CME were unchanged after detraining; and iv) CME blocked ASE effects and this capability remained intact even after detraining. Furthermore, the ASE effects on neutrophil spontaneous apoptosis were mimicked by adding exogenous H₂O₂, but not by suppressing mitochondrial membrane potential. In conclusion, while ASE induced an oxidative state and resulted in acceleration of human neutrophil apoptosis, CME delayed neutrophil apoptosis by maintaining a reduced state for long periods of time even after detraining.     

Interaction and replication activation of genotype I and II hepatitis delta antigens

The nucleotide sequences of hepatitis D viruses (HDV) vary 5 to 14% among isolates of the same genotype and 23 to 34% among different genotypes. The only viral-genome-encoded antigen, hepatitis delta antigen (HDAg), has two forms that differ in size. The small HDAg (HDAg-S) trans-activates viral replication, while the large form (HDAg-L) is essential for viral assembly. Previously, it has been shown that the packaging efficiency of HDAg-L is higher for genotype I than for genotype II. In this study, the question of whether other functional properties of the HDAgs are affected by genotype differences is addressed. By coexpression of the two antigens in HuH-7 cells followed by specific antibody precipitation, it was found that HDAgs of different origins interacted without genotypic discrimination. Moreover, in the presence of hepatitis B virus surface antigen, HDAg-S was incorporated into virion-like particles through interaction with HDAg-L without genotype restriction. As to the differences in replication activation of genotype I HDV RNA, all HDAg-S clones tested had some trans-activation activity, and this activity varied greatly among isolates. As to the support of HDV genotype II replication, only clones of HDAg-S from genotype II showed trans-activation activity, and this activity also varied among isolates. In conclusion, genotype has no effect on HDAg interaction and genotype per se only partly predicts how much the HDAg-S of an HDV isolate affects the replication of a second HDV isolate.