The zebrafish genome encodes the largest vertebrate repertoire of functional aquaporins with dual paralogy and substrate specificities similar to mammals

Background  

Aquaporins are integral membrane proteins that facilitate the transport of water and small solutes across cell membranes. These proteins are vital for maintaining water homeostasis in living organisms. In mammals, thirteen aquaporins (AQP0-12) have been characterized, but in lower vertebrates, such as fish, the diversity, structure and substrate specificity of these membrane channel proteins are largely unknown.     

Engineering of zinc finger and MHC motifs to locked-in tertiary folds

Summary The assembly of helical and β-sheet peptide blocks containing reactive chain ends results in highly branched chain architectures (‘locked-in folds’) mimicking native tertiary structures. This molecular kit strategy allows to bypass the protein folding problem in protein de novo design and gives access to protein mimetics of high thermodynamic stability. The validity of this concept is exemplified for the design and synthesis of locked-in folds mimicking the zinc finger and MHC folding motifs.     

Extracellular ATP signaling during differentiation of C2C12 skeletal muscle cells: role in proliferation

Evidence shows that extracellular ATP signals influence myogenesis, regeneration and physiology of skeletal muscle. Present work was aimed at characterizing the extracellular ATP signaling system of skeletal muscle C2C12 cells during differentiation. We show that mechanical and electrical stimulation produces substantial release of ATP from differentiated myotubes, but not from proliferating myoblasts. Extracellular ATP-hydrolyzing activity is low in myoblasts and high in myotubes, consistent with the increased expression of extracellular enzymes during differentiation. Stimulation of cells with extracellular nucleotides produces substantial Ca(2+) transients, whose amplitude and shape changed during differentiation. Consistently, C2C12 cells express several P2X and P2Y receptors, whose level changes along with maturation stages. Supplementation with either ATP or UTP stimulates proliferation of C2C12 myoblasts, whereas excessive doses were cytotoxic. The data indicate that skeletal muscle development is accompanied by major functional changes in extracellular ATP signaling.     

Improved expression of kinases in Baculovirus-infected insect cells upon addition of specific kinase inhibitors to the culture helpful for structural studies

As exemplified by three cases, we show that the addition of a small molecular weight inhibitor to the culture of Baculovirus-infected insect cells can dramatically improve the expression of a recombinant kinase. The expression of the tyrosine kinase KDR was sevenfold higher and mainly in a soluble form, when the KDR inhibitor PTK/ZK was added to the culture at the time of Baculovirus infection. The expression of the catalytic domain of the serine/threonine kinase PKCtheta, which is otherwise not possible with the Baculovirus expression system, was expressed mainly soluble at 120mg/L by the addition of the PKC inhibitor BIM XI to the culture of Baculovirus-infected insect cells. For Abl kinase, the expression could also be significantly increased by the addition of the Abl kinase inhibitor STI571 to the culture. For all three kinases, this method had previously been applied by us for the improved production of kinase/inhibitor complex protein, leading to the co-crystal structures. It is shown here at the cases KDR-PTK/ZK and PKCtheta-BIM XI, that the stimulatory effect of an inhibitor on kinase expression is applicable under many culture conditions. The presented method represents a valuable tool to obtain structural knowledge on kinase-inhibitor complexes.     

Role of the reticuloendothelial system in the catabolism of low density lipoprotein in the rat

The role of the reticuloendothelial system (RES) in receptor-independent catabolism of human low density lipoprotein (h-LDL) was evaluated in the rat in vivo after blockade of its phagocytic activity with gadolinium chloride (GaCl3). After blockade of the RES with GaCl3, the recovery of [125I] h-LDL in the liver of 17 alpha-ethinyl oestradiol-treated rats (EE-rats), was decreased by 37 and 16%, 15 and 60 min after h-LDL injection, respectively. This decrease did not result in a decreased LDL degradation which represented 14 and 55% of the injected dose in the two groups of rats after 15 and 60 min respectively, both on GaCl3 and control rats. Contrasting with EE-rats, the catabolism of h-LDL in untreated rats is much slower and takes place essentially through a receptor-independent mechanism. Six hours after the injection of [125I] h-LDL, 64% of the dose was degraded. This proportion decreased to 45% after blockade of the RES phagocytic activity. This 30 percent difference represents the proportion of h-LDL catabolized by receptor-independent mechanisms present in the Küpffer and endothelial cells. We conclude from our study that in the normal rat, the parenchymal cells of the liver on the one hand and the Küpffer and endothelial cells on the other hand contribute 70 and 30% respectively to the receptor-independent catabolism of low density lipoproteins in vivo.     

Life cycle assessment of vitamin D3 synthesis: from batch to photo-high p,T

Purpose

Novel process windows allow the development of faster, flexible, and greener processes. Therefore, novel process windows were applied to develop a greener process for the synthesis of vitamin D₃. In this study the environmental impacts of several batch pathways to obtain vitamin D₃ are benchmarked against the continuous microflow process, where novel process windows such as high temperature and pressure were applied. To evaluate the environmental impact of these processes, life cycle assessments were conducted.

Methods

A new process concept was developed to optimize and simplify the synthesis of crystalline vitamin D₃. This process was conducted in microflow by combining UV photoirradiation and high-p,T (photo-high-p,T) processing. Microreactors allow a high photon flux and enable the harsh conditions, respectively. The process was coupled with an integrated continuous crystallization, and its feasibility has been proven and reported before. The potential environmental impacts were assessed from a cradle-to-gate perspective. Both processes, continuous and batch, were modeled in Aspen Plus using foreground data from the experimental continuous setup, and background data from different patents. The assessment was performed in the software Umberto NXL LCA using the ReCiPe Midpoint 2008 method.

Results and discussion

The continuous process has a significantly lower environmental impact than the batch processes. This lower impact is largely due to the fact that fewer amounts of material, particularly solvents, are used. Moreover, the continuous process is faster and has fewer steps, i.e., process-simplified. Among the industrial processes, the synthesis conducted in isopropanol has the lowest environmental impact, although, even in this case, the impact is between 20 and 30 times higher—depending on the conditions—compared with the continuous process. When the batch process is conducted in benzene, the worst environmental impact is obtained. Finally, recycle of the solvent for the best batch case was assessed. This improved the batch process to make it comparable with the continuous process.

Conclusions

The continuous production of vitamin D₃ leads to an interesting alternative to the industrial process. Continuous manufacturing of vitamin D₃ is faster, requires fewer steps, and uses less solvents compared with the industrial synthesis. However, although the environmental impact of this continuous process is already lower than that of the batch processes, the continuous process can still benefit from further optimization, particularly the introduction of a recycle loops for the solvents methyl tert-butyl ether and acetonitrile.

     

Tree growth,mortality, and above-ground biomass accumulation in a holm oak forest under a five-year experimental field drought

A holm oak forest was exposed to an experimental drought during 5 years to elucidate the growth responses of the dominant species Quercus ilex, Arbutus unedo and Phillyrea latifolia. Soil water availability was partially reduced, about 15% as predicted for this area for the next decades by GCM and ecophysiological models, by plastic strips intercepting rainfall and by ditch exclusion of water runoff. The stem diameter increment was highly correlated with annual rainfall in all species, and drought treatment strongly reduced the diameter increment of Q. ilex (41%) and specially of A. unedo (63%), the species showing higher growth rates. Stem mortality rates were highly correlated with previous stem density, but drought treatment increased mortality rates in all species. Q. ilex showed the highest mortality rates (9% and 18% in control and drought plots, respectively), and P. latifolia experienced the lowest mortality rates (1% and 3% in control and drought plots, respectively). Drought strongly reduced the increment of live aboveground biomass during these 5 years (83%). A. unedo and Q. ilex experienced a high reduction in biomass increment by drought, whereas P. latifolia biomass increment was insensitive to drought. The different sensitivity to drought of the dominant species of the holm oak forest may be very important determining their future development and distribution in a drier environment as expected in Mediterranean areas for the next decades. These drier conditions could thus have strong effects on structure (species composition) and functioning (carbon uptake and biomass accumulation) of these Mediterranean forests.     

Metabolic response to ethanol and isopropanol in D. funebris and D. immigrans

Ethanol at low concentration increases larval viability in D. funebris and D. melanogaster and decreases it in D. immigrans. Isopropanol decreases viability in all three species. Isopropanol depresses alcohol dehydrogenase activity. This is accompanied by a change in the relative proportion of electrophoretic forms of the enzyme. Acetone appears in the medium when larvae of D. funebris and D. immigrans develop in the presence of isopropanol. It can be transformed again into isopropanol on reaching a threshold value. It seems that this transformation cannot be carried out by alcohol dehydrogenase alone.     

Pre-Analytical Sample Quality: Metabolite Ratios as an Intrinsic Marker for Prolonged Room Temperature Exposure of Serum Samples

Advances in the “omics” field bring about the need for a high number of good quality samples. Many omics studies take advantage of biobanked samples to meet this need. Most of the laboratory errors occur in the pre-analytical phase. Therefore evidence-based standard operating procedures for the pre-analytical phase as well as markers to distinguish between ‘good’ and ‘bad’ quality samples taking into account the desired downstream analysis are urgently needed. We studied concentration changes of metabolites in serum samples due to pre-storage handling conditions as well as due to repeated freeze-thaw cycles. We collected fasting serum samples and subjected aliquots to up to four freeze-thaw cycles and to pre-storage handling delays of 12, 24 and 36 hours at room temperature (RT) and on wet and dry ice. For each treated aliquot, we quantified 127 metabolites through a targeted metabolomics approach. We found a clear signature of degradation in samples kept at RT. Storage on wet ice led to less pronounced concentration changes. 24 metabolites showed significant concentration changes at RT. In 22 of these, changes were already visible after only 12 hours of storage delay. Especially pronounced were increases in lysophosphatidylcholines and decreases in phosphatidylcholines. We showed that the ratio between the concentrations of these molecule classes could serve as a measure to distinguish between ‘good’ and ‘bad’ quality samples in our study. In contrast, we found quite stable metabolite concentrations during up to four freeze-thaw cycles. We concluded that pre-analytical RT handling of serum samples should be strictly avoided and serum samples should always be handled on wet ice or in cooling devices after centrifugation. Moreover, serum samples should be frozen at or below -80°C as soon as possible after centrifugation.     

Estimation of the physiological mechanical conditioning in vascular tissue engineering by a predictive fluid-structure interaction approach

The in vitro replication of physiological mechanical conditioning through bioreactors plays a crucial role in the development of functional Small-Caliber Tissue-Engineered Blood Vessels. An in silico scaffold-specific model under pulsatile perfusion provided by a bioreactor was implemented using a fluid-structure interaction (FSI) approach for viscoelastic tubular scaffolds (e.g. decellularized swine arteries, DSA). Results of working pressures, circumferential deformations, and wall shear stress on DSA fell within the desired physiological range and indicated the ability of this model to correctly predict the mechanical conditioning acting on the cells-scaffold system. Consequently, the FSI model allowed us to a priori define the stimulation pattern, driving in vitro physiological maturation of scaffolds, especially with viscoelastic properties.