Apoptotic process of porcine intestinal M cells

Membranous (M) cells of the follicle-associated epithelium (FAE) are believed to sample antigens from the gut lumen. However, the origin, differentiation mechanism, and cell death of M cells are still a matter of controversy. Therefore, we investigated the process of M cell differentiation and determined their fate in the intestine of three-way crossbred female pigs. We used anti-cytokeratin 18 and anti-PCNA antibodies to distinguish M cells and proliferative cells and performed immunohistochemistry, enzyme histochemistry, and scanning electron microscopy on fresh ileal Peyer’s patches. Cell migration and apoptotic cells were detected by BrdU labeling and the TUNEL method, respectively. The turnover of the FAE was similar to that of the villi. M cells were mostly observed from the FAE crypt to the FAE periphery, but not in the FAE apex. As proliferative M cells (cytokeratin 18⁺/PCNA⁺ cells) have previously been detected in the FAE crypt, porcine M cells may be directly derived from intestinal epithelial stem cells and committed as a distinct cell lineage in the crypts. M cells from the FAE periphery were unstained or only weakly stained for alkaline phosphatase, whereas cytokeratin 18⁺/alkaline phosphatase⁺ cells lying near to the FAE apex showed a columnar shape similar to that of adjacent enterocytes. These data suggest that the committed M cells differentiate to mature M cells by contact with lymphocytes at the FAE periphery, and that they trans-differentiate to enterocytes and are finally excluded near the FAE apex. This investigation was supported by a Grant-in-Aid for Scientific Research (16658107) from the Ministry of Education, Culture, Sports, Science and Technology, by two grants (Prion Project and Secure and Healthy Livestock Farming Project) from the Ministry of Agriculture, Forestry and Fisheries, and by a grant from the Naito Foundation.     

Investigation of the early stages of human γD-crystallin aggregation process

Cataract, a major cause of visual impairment worldwide, is a common disease of the eye lens related to protein aggregation. Several factors including the exposure of ultraviolet irradiation and possibly acidic condition may induce the unfolding and subsequent aggregation of the crystallin proteins leading to crystalline lens opacification. Human γD-crystallin (HγDC), a 173 residue monomeric protein, abundant in the nucleus of the human eye lens, has been shown to aggregate and form amyloid fibrils under acidic conditions and that this aggregation route is thought to be a potential initiation pathway for the onset of age-related nuclear cataract. However, the underlying mechanism of fibril formation remains elusive. This report is aimed at examining the structural changes and possible amyloid fibril formation pathway of HγDC using molecular dynamics and molecular docking simulations. Our findings demonstrated that incubation of HγDC under the acidic condition redistributes the protein surface charges and affects the protein interaction with its surrounding solvent environment. This brings about a twist motion in the overall tertiary structure that gives rise to newly formed anti-parallel β-strands in the C-terminal flexible loop regions. The change in protein structural conformation also involves an alteration in specific salt-bridge interactions. Altogether, these findings revealed a plausible mechanism for amyloid fibril formation of HγDC that is important to the early stages of HγDC aggregation involved in cataractogenesis.     

Safety of the production process of SURFACEN® to inactivate and remove virus

SURFACEN^® is a biological product produced from pig lungs. Since these animals can be potential sources of microbial pathogens such as viruses, the manufacturing process of this product should guarantee safety from health hazards. The SURFACEN^® production procedure is capable of effective viral clearance (inactivation/removal) by involving two stages of organic solvent extraction followed by acetone precipitation and heat treatment. In this study, we evaluated the clearance capacity of these four stages for a wide range of viruses by performing spiking experiments. Residual contamination was assessed using a Tissue Culture Infectious Dose assay (log₁₀ TCID₅₀). The validation study demonstrated that, for all viruses tested, the TCID₅₀ titers were reduced by more than 2 log₁₀ in each stage. Total log reduction values achieved were between ≥17.82 log₁₀ and ≥27.93 log₁₀, depending on the virus physical properties, titer, and the number of processing stages applied. Results indicated that the production procedure of SURFACEN^® can inactivate or remove contaminant viruses from the raw material.     

Is aggregation of beta-amyloid peptides a mis-functioning of a current interaction process?

In a previous study, Hughes et al. [Proc. Natl. Acad. Sci. USA 93 (1996) 2065-2070] demonstrated that the amyloid peptide is able to interact with itself in a two-hybrid system and that interaction is specific. They further supported that the method could be used to define the sequences that might be important in nucleation-dependent aggregation. The sequence of the amyloid peptide can be split into four clusters, two hydrophilic (1-16 and 22-28) and two hydrophobic (17-21 and 29-42). We designed by molecular modeling and tested by the two-hybrid approach, series of mutations spread all over the sequence and changing the distribution of hydrophobicity and/or the spatial hindrance. In the two-hybrid assay, interaction of native Abeta is reproduced. Screening of mutations demonstrates that the C-domain (residues 29-40 (42)), the median domain (residues 17-22) and the N-domain (1-16) are all crucial for interaction. This demonstrates that almost all fragments of the amyloid peptide but a loop (residues 23-28) and the C-term amino acid are important for the native interaction. We support that the folded three-dimensional (3D) structure is the Abeta-Abeta interacting species, that the whole sequence is involved in that 3D fold which has a low secondary structure propensity and a high susceptibility to mutations and thus should have a low stability. The native fold of Abeta could be stabilized in Abeta-Abeta complexes which could in other circumstances facilitate the nucleation event of aggregation that leads to the formation of stable senile plaques.     

Oxidation of proteins: is it a programmed process?

Proteins represent extremely susceptible targets for oxidants. Oxidative modifications of proteins may bring about violation of their structure and functionality. It implies that the structures of proteins are not infallible in terms of their antioxidant defence. The protection mechanisms in preventing oxidative damages for proteins within cells are mainly related to a large variety of antioxidant enzymatic systems. In contrast, plasma proteins are scarcely protected by these systems, so the mechanism that provides their functioning in the conditions of generating reactive oxygen species (ROS) seems to be much more complicated. Oxidation of many proteins was long considered as a random process. However, the highly site-specific oxidation processes was convincingly demonstrated for some proteins, indicating that protein structure could be adapted to oxidation. According to our hypothesis, some of the structural elements present in proteins are capable of scavenging ROS to protect other protein structures against ROS toxicity. Various antioxidant elements (distinct subdomains, domains, regions, and polypeptide chains) may act as ROS interceptors, thus mitigating the ROS action on functionally crucial amino acid residues of proteins. In the review, the oxidative modifications of certain plasma proteins, such as α₂-macroglobulin, serum human albumin, fibrinogen, and fibrin-stabilising factor, which differ drastically in their spatial structures and functions, are analysed. The arguments that demonstrate the possibility of existing hypothetical antioxidant structures are presented. For the first time, the emphasis is being placed on the programmed mechanism of protein oxidation.     

α-Amylase immobilization on gelatin: Optimization of process variables

α-Amylase was extracted and purified from soybean seeds to apparent homogeneity by affinity precipitation. The homogeneous enzyme preparation was immobilized on gelatin matrix using glutaraldehyde as an organic hardener. Response surface methodology (RSM) and 3-level-3-factor Box–Behnken design was employed to evaluate the effects of immobilization parameters, such as gelatin concentration, glutaraldehyde concentration and hardening time on the activity of immobilized α-amylase. The results showed that 20% gelatin (w/v), 10% glutaraldehyde (v/v) and 1 h hardening time yielded an optimum immobilization of 82.5%.     

Trickle or clumped infection process? A stochastic model for the infection process of the parasitic roundworm of humans, Ascaris lumbricoides

The importance of the mode of acquisition of infectious stages of directly-transmitted parasitic helminths has been acknowledged in population dynamics models; hosts may acquire eggs/larvae singly in a “trickle” type manner or in “clumps”. Such models have shown that the mode of acquisition influences the distribution and dynamics of parasite loads, the stability of host-parasite systems and the rate of emergence of anthelmintic resistance, yet very few field studies have allowed these questions to be explored with empirical data. We have analysed individual worm weight data for the parasitic roundworm of humans, Ascaris lumbricoides, collected from a three-round chemo-expulsion study in Dhaka, Bangladesh, with the aim of discerning whether a trickle or a clumped infection process predominates. We found that hosts tend to harbour female worms of a similar weight, indicative of a clumped infection process, but acknowledged that unmeasured host heterogeneities (random effects) could not be completely excluded as a cause. Here, we complement our previous statistical analyses using a stochastic infection model to simulate sizes of individual A. lumbricoides infecting a population of humans. We use the intraclass correlation coefficient (ICC) as a quantitative measure of similarity among simulated worm sizes and explore the behaviour of this statistic under assumptions corresponding to trickle or clumped infections and unmeasured host heterogeneities. We confirm that both mechanisms are capable of generating aggregates of similar-sized worms, but that the particular pattern of ICCs described pre- and post-anthelmintic treatment in the data is more consistent with aggregation generated by clumped infections than by host heterogeneities alone. This provides support to the notion that worms may be acquired in clumps. We discuss our results in terms of the population biology of A. lumbricoides and highlight the significance of our modelling approach for the study of the population dynamics of helminth parasites.     

Quantum mechanical study of the inclusion process of adamantanol isomers by l-tryptophan-modified-β-cyclodextrin

The complexation processes of 1 and 2-adamantanol with l-tryptophan-β-cyclodextrin have been studied using ab initio Hartree–Fock and density functional theory levels. For the host: guest inclusion processes, the up mode with the OH group of the alcohol oriented towards the secondary rim, is found to be in qualitative agreement with the experimental finding. A molecular recognition mechanism is proposed based on the host: guest relative dipole orientation. For the complex with the 2-Ada isomer the host and guest the dipoles are parallels favoring the interaction energy and. This mechanism can explain the small energy difference for the processes involving the adamantanol isomers and modified cyclodextrins.     

μ-Synthesis of dissimilation process of glycerol to 1,3-propanediol in microbial continuous culture

In this paper, robust control problem using μ-synthesis in microbial continuous culture is studied. The dissimilation process of glycerol to 1,3-propanediol cannot avoid the disturbances caused by uncertain factors. Based on the biodynamical model, a control system with the initial glycerol concentration as input control is proposed to simplify the controller design. μ-synthesis method is applied to find a feedback controller to assure both of robust stability and robust performance of the closed-loop system simultaneously. To solve the corresponding structured singular value optimization problem, a converged result is obtained through D–K iteration method. The μ-synthesis system is also compared with the corresponding $H_\infty$ system. The simulation results indicate that the μ-controller might be more feasible for the continuous bioprocess controlling.     

Why is the denaturation process of super-helical DNA so uncooperative?

A theoretical model is proposed for the helix-coil transition in circular covalently closed DNA. In the melting interval the topological constrains for such a molecule are considered to affect both the inner state of the melted regions and the spatial configuration of the whole molecule ("writhing"). A good agreement is achieved between the theoretically calculated and experimentally obtained parameters of the denaturation process. A conclusion is drawn, that at the early stages of thermodenaturation (approximately till the transition midpoint) the effect of topological constrains is realised mainly through the writhing of the molecule. The denatured regions exist in the form of relaxed loops.     

Assembly of phagocyte NADPH oxidase: A concerted binding process?

Background

The phagocyte NADPH-oxidase is a multicomponent enzyme that generates superoxide anions. It comprises a membrane redox component flavocytochrome b₅₅₈ and four cytosolic proteins (p67^phox, p47^phox, p40^phox and Rac) that must assemble to produce an active system. In this work we focused on the spatio-temporal control of the activation process of phagocyte NADPH oxidase.

Methods

A wide range of techniques including fast kinetics with a stopped-flow apparatus and various combinations of the activating factors was used to test the order of assembly and the role of the p47^phox–p67^phox complex.

Results

The data presented here are consistent with the absence of a catalytic role of the p47^phox–p67^phox interacting state and support the idea of independent binding sites for the cytosolic proteins on the flavocytochrome b₅₅₈ allowing random binding order. However, the formation of the active complex appears to involve a synergistic process of binding of the activated cytosolic subunits to cytochrome b₅₅₈. All partners should be in the vicinity for optimal assembly, a delay or the absence of one of the partners in this process seems to lead to a decrease in the efficiency of the catalytic core.

Conclusion and general significance

The activation and assembly of the NADPH oxidase components have to be achieved simultaneously for the formation of an efficient and optimal enzyme complex. This mechanism appears to be incompatible with continuous fast exchanges of the cytosolic proteins during the production of superoxide ion in the phagosome.     

Advantages of a two-step enzymatic process for cotton–polyester blends

Cotton fabric samples were treated with a formulation of a total crude Trichoderma reesei cellulase in a two-step procedure. In the first step, samples were treated at a low liquor ratio by padding through the enzyme formulation at 21°C and 55°C with a wet pickup of 100% and batched for 12 h. The samples were then treated at a high liquor ratio (1:25) with an identical enzyme formulation at 55°C, with intensive agitation. The pre-treatment influenced the overall weight loss and rate of hydrolysis in samples, and the protein concentration in the liquor of the second step. The overall weight loss was 25–28% (w/w) in the two-step procedure compared to a weight loss of 22% (w/w) in the one-step batch hydrolysis.     

Treatment of metal-contaminated wastes: why select a biological process?

Nature has demonstrated some subtle and intricate mechanisms for selectively controlling the mobility of metal pollutants in the environment. However, the application of this science to technology has been disappointing. A small number of pilot-plant studies have been carried out to investigate the potential of microorganisms (primarily bacteria) to remove metals from liquid wastes but only one system in the past 15 years has been commercialized. In order to explain this lack of application, it is important to understand the effectiveness, robustness and reliability of biological processes involving metals and their ability to compete with proven physicochemical technologies.     

The real face of HIF1α in the tumor process

It is well known that the hypoxia-inducible factor 1 α (HIF1α) is detectable as adaptive metabolic response to hypoxia. However, HIF1/HIF1α is detectable even under normoxic conditions, if the metabolism is altered, e.g., high proliferation index. Importantly, both hypoxic metabolism and the Warburg effect have in common a decrease of the intracellular pH value.

In our interpretation, HIF1α is not directly accumulated by hypoxia, but by a process which occurs always under hypoxic conditions, a decrease of the intracellular pH value because of metabolic imbalances. We assume that HIF1α is a sensitive controller of the intracellular pH value independently of the oxygen concentration. Moreover, HIF1α has its major role in activating genes to eliminate toxic metabolic waste products (e.g., NH₃/NH₄+) generated by the tumor-specific metabolism called glutaminolysis, which occur during hypoxia, or the Warburg effect. For that reason, HIF1α appears as a potential target for tumor therapy to disturb the pH balance and to inhibit the elimination of toxic metabolic waste products in the tumor cells.     

The inhibitory effect of ginsan on TGF-β mediated fibrotic process

Transforming growth factor-beta (TGF-β) plays a central role in the development of fibrosis by stimulating extracellular matrix accumulation, and signals either directly or indirectly through types I, II, and III (TβRI, II, and III) TGF-β receptor complexes. Ginsan, a polysaccharide extracted from Panax ginseng, has multiple immunomodulatory effects. Here, we examine whether ginsan regulates the fibrogenic process by interfering with TGF-β signaling pathways. TGF-β treatment of murine or human normal lung fibroblasts enhanced the levels of several fibrotic markers, including smooth muscle alpha actin (α-SMA), collagen-1, and fibronectin. Interestingly, ginsan treatment either before or after TGF-β administration led to significant reductions in all of α-SMA, collagen-1, and fibronectin expression levels. Ginsan not only inhibited phosphorylation of Smad2 and Smad3, but also attenuated pERK and pAKT signaling induced by TGF-β. Moreover, ginsan restored TβRIII protein expression, which was significantly downregulated by TGF-β, but reduced TβRI and TβRII protein levels. In a murine model of bleomycin (BLM)-induced pulmonary fibrosis, ginsan significantly suppressed accumulation of collagen, α-SMA, and TGF-β. These data collectively suggest that ginsan acts as an effective anti-fibrotic agent in the treatment of pulmonary fibrosis by blocking multiple TGF-β signaling pathways.     

The influence of the blood handling process on the measurement of circulating TGF-β1

In order to evaluate the impact of blood sample handling processes on circulating TGF-β1 levels, blood specimens were obtained from 13 healthy volunteers using different handling processes (kept at room temperature (RT) or on ice before centrifugation, using different centrifugal forces). TGF-β1 levels were measured using an enzyme-linked immunosorbent assay. A paired-T test was used for statistical analysis. The TGF-β1 level in on-ice serum was significantly lower than that in room-temperature serum (P<0.001), and both were significantly higher than that found in on-ice plasma (P<0.001). Compared with on-ice plasma samples, the longer the samples were kept at RT, the higher the levels of TGF-β1 in plasma (P=0.268, 0.040, and 0.0015 for 5 min, 30 min, and 60 min in RT, respectively). Compared with plasma centrifuged at 2,500×g for 30?min, the TGF-β1 levels were much lower than those found in plasma centrifuged at 1,200×g for 10?min (P=0.003); and a double centrifugation before TGF-β1 detection, significantly decreased the level (P<0.001). It is suggested that the optimal sampling conditions for the detection of TGF-β1 should be plasma prepared on ice and spun down at a higher centrifugal force.     

Evaluation of the hydrolytic–acidogenic step of a two-stage mesophilic anaerobic digestion process of sunflower oil cake

The influence of the hydraulic retention time (HRT) and organic loading rate (OLR) on the performance of the hydrolytic–acidogenic step of a two-stage anaerobic digestion process of sunflower oil cake (SuOC) were assessed. The experiments were performed in laboratory-scale completely stirred tank reactors at mesophilic (35 °C) temperature. Six OLR (ranging from 4 to 9 g VS L⁻¹ d⁻¹) for four HRTs (8, 10, 12 and 15 days) were tested to check the effect of each operational variable. Based on the results obtained, it can be concluded that the hydrolysis yields obtained for all HRTs and OLRs assayed were in the range of 20.5–30.1%. In addition, the acidification degree of the substrate was mainly influenced by the OLR but not by the HRTs, the highest value (83.8%) being achieved for an HRT of 10 days and an OLR of 6 g VS L⁻¹ d⁻¹.     

Large-scale production of diesel-like biofuels – process design as an inherent part of microorganism development

Industrial biotechnology is playing an important role in the transition to a bio-based economy. Currently, however, industrial implementation is still modest, despite the advances made in microorganism development. Given that the fuels and commodity chemicals sectors are characterized by tight economic margins, we propose to address overall process design and efficiency at the start of bioprocess development. While current microorganism development is targeted at product formation and product yield, addressing process design at the start of bioprocess development means that microorganism selection can also be extended to other critical targets for process technology and process scale implementation, such as enhancing cell separation or increasing cell robustness at operating conditions that favor the overall process. In this paper we follow this approach for the microbial production of diesel-like biofuels. We review current microbial routes with both oleaginous and engineered microorganisms. For the routes leading to extracellular production, we identify the process conditions for large scale operation. The process conditions identified are finally translated to microorganism development targets. We show that microorganism development should be directed at anaerobic production, increasing robustness at extreme process conditions and tailoring cell surface properties. All the same time, novel process configurations integrating fermentation and product recovery, cell reuse and low-cost technologies for product separation are mandatory. This review provides a state-of-the-art summary of the latest challenges in large-scale production of diesel-like biofuels.