Root cause analysis during process development using Joint-Y PLS

The original purpose of the JYPLS model was to aid product transfer and scale-up. This work demonstrates that the JYPLS model is also well suited to analyze data from a process in development where the number and type of sensors and sensor locations are also being decided. The specific application in this case was to determine the root cause for a bias found during the development of a multivariate calibration model for a Near Infrared (NIR) instrument. The calibration model was built in parallel with the development of the manufacturing process itself. Each time the calibration model was tested with data from a new batch run, a non-explained bias was observed. Laboratory results on samples gathered from the process show that the NIR signal itself was biased and not the actual concentration of the constituent. Data on the processing conditions were collected for all the batches and included in the JYPLS model along with NIR and lab results. The loadings and scores from the JYPLS model were interpreted to isolate the root cause of the observed drift in the calibration model. This work discusses the general approach and presents the sequence of diagnostics used to analyze the different campaigns during process development. This should be applicable to other scenarios in process development where the data has the same architecture.     

The total quasi-steady-state approximation for complex enzyme reactions

Biochemistry in general and enzyme kinetics in particular have been heavily influenced by the model of biochemical reactions known as Michaelis–Menten kinetics. Assuming that the complex concentration is approximately constant after a short transient phase leads to the usual Michaelis–Menten (MM) approximation (or standard quasi-steady-state approximation (sQSSA)), which is valid when the enzyme concentration is sufficiently small. This condition is usually fulfilled for in vitro experiments, but often breaks down in vivo. The total QSSA (tQSSA), which is valid for a broader range of parameters covering both high and low enzyme concentrations, has been introduced in the last two decades. We extend the tQSSA to more complex reaction schemes, like fully competitive reactions, double phosphorylation, Goldbeter–Koshland switch and we show that for a very large range of parameters our tQSSA provides excellent fitting to the solutions of the full system, better than the sQSSA and the single reaction tQSSA. Finally, we discuss the need for a correct model formulation when doing “reverse engineering”, which aims at finding unknown parameters by fitting the model to experimentally obtained data. We show that the estimated parameters are much closer to the real values when using the tQSSA rather than the sQSSA, which overestimates the parameter values greatly.     

Molecular-Level Characterization of Heterogeneous Catalytic Systems by Algorithmic Time Dependent Monte Carlo

Monte Carlo algorithms and codes, used to study heterogeneous catalytic systems in the frame of the computational section of the NANOCAT project, are presented along with some exemplifying applications and results. In particular, time dependent Monte Carlo methods supported by high level quantum chemical information employed in the field of heterogeneous catalysis are focused. Technical details of the present algorithmic Monte Carlo development as well as possible evolution aimed at a deeper interrelationship of quantum and stochastic methods are discussed, pointing to two different aspects: the thermal-effect involvement and the three-dimensional catalytic matrix simulation. As topical applications, (i) the isothermal and isobaric adsorption of CO on Group 10 metal surfaces, (ii) the hydrogenation on metal supported catalysts of organic substrates in two-phase and three-phase reactors, and (iii) the isomerization of but-2-ene species in three-dimensional supported and unsupported zeolite models are presented.     

Mechanical Gradient Cues for Guided Cell Motility and Control of Cell Behavior on Uniform Substrates

A novel method for the fabrication and the use of simple uniform poly(dimethylsiloxane) PDMS substrates for controlling cell motility by a mechanical gradient is reported. The substrate is fabricated in PDMS using soft lithography and consists of a soft membrane suspended on top of a patterned PDMS substrate. The difference in the gradient stiffness is related to the underlying pattern. It is shown experimentally that these uniform substrates can modulate the response of cell motility, thus enabling patterning on the surfaces with precise cell motility. Because of the uniformity of the substrate, cells can spread equally and a directional movement to stiffer regions is clearly observed. Varying the geometry underlying the membrane, cell patterning and movement can be quantitatively characterized. This procedure is capable of controlling cell motility with high fidelity over large substrate areas. The most significant advance embodied in this method is that it offers the use of mechanical features to control cell adhesion and not topographical or chemical variations, which has not been reported so far. This modulation of the response of cell motility will be useful for the design and fabrication of advanced planar and 3D biological assemblies suitable for applications in the field of biotechnology and for tissue‐engineering purposes.     

Early hormonal and surgical treatment of cryptorchidism

PURPOSE: We investigated the efficacy of early gonadotropin treatment of cryptorchidism for promoting testicular descent and ameliorating testicular histology. MATERIALS AND METHODS: We treated 319 cryptorchid testes in 281 boys 4 months to 3 years old with luteinizing hormone-releasing hormone and human chorionic gonadotropin sequential therapy. Surgery was done on the 207 testes that did not respond to medical treatment. Microscopic biopsies were performed in 134 of these 207 testes. Histological findings were compared to those of 30 cryptorchid testes in boys younger than 1 year who underwent surgery without previous hormonal treatment. RESULTS: Combined luteinizing hormone-releasing hormone and human chorionic gonadotropin treatment induced scrotal descent of a percentage of cryptorchid testes depending on clinical position. Therapeutic success was greater when testes were in a lower position and results were not age dependent. Hormonal treatment of cryptorchidism during the first year of life stimulated spermatogonia maturation. CONCLUSIONS: When administered at the end of age 6 months, hormonal treatment can be considered an effective and timely substitution for gonadotropin and testosterone insufficiency in cryptorchid infants. Therefore, we recommend this therapeutic procedure combined with surgery in the first year of life.     

Quantitative Analysis of Plant Cytosolic Calcium Signals in Response to Water Activated by Low-Power Non-Thermal Plasma

Non-thermal plasma technology is increasingly being applied in the plant biology field. Despite the variety of beneficial effects of plasma-activated water (PAW) on plants, information about the mechanisms of PAW sensing by plants is still limited. In this study, in order to link PAW perception to the positive downstream responses of plants, transgenic Arabidopsis thaliana seedlings expressing the Ca²⁺-sensitive photoprotein aequorin in the cytosol were challenged with water activated by low-power non-thermal plasma generated by a dielectric barrier discharge (DBD) source. PAW sensing by plants resulted in the occurrence of cytosolic Ca²⁺ signals, whose kinetic parameters were found to strictly depend on the operational conditions of the plasma device and thus on the corresponding mixture of chemical species contained in the PAW. In particular, we highlighted the effect on the intracellular Ca²⁺ signals of low doses of DBD-PAW chemicals and also presented the effects of consecutive plant treatments. The results were discussed in terms of the possibility of using PAW-triggered Ca²⁺ signatures as benchmarks to accurately modulate the chemical composition of PAW in order to induce environmental stress resilience in plants, thus paving the way for further applications in agriculture.     

Codon-based mutagenesis using dimer-phosphoramidites

A new approach for the synthesis of randomized DNA sequences containing the 20 codons corresponding to all natural amino acids is described. The strategy is based on the use of dinucleotide phosphoramidite building blocks within a resin-splitting procedure. Through this protocol, a minimal number of seven dimers is sufficient to encode all 20 natural amino acids. This synthesis procedure is extremely flexible and allows codon usage from different hosts to be accommodated.     

Multiple conformations of physiological membrane-bound cytochrome c

One-tenth of cytochrome c (cyt c) remains bound to the inner mitochondrial membrane (IMM) at physiological ionic strength (I; i.e. , I approximately 150 mM), exhibiting decreased electron transport (ET) activity. We now show that this form of membrane-bound cyt c (MB-cyt c) can be obtained in vitro and that binding to membranes at low I generates an additional conformation with higher ET activity. This low I bound form of MB-cyt c (MBL-cyt c) exhibited intrinsic ET rates similar to those of electrostatically bound cyt c (EB-cyt c). The ET activity of IMM-bound MB-cyt c approached slowly that of MBL-cyt c or EB-cyt c, suggesting that MB-cyt c converts to MBL-cyt c while bound to IMM. When maintained at physiological I, both forms of MB-cyt c were released from the membrane, indicating that they convert to an EB-cyt c-like form. This process may be very dynamic in cellular mitochondria, as binding and release for both MB-cyt c forms increased considerably with temperature. I-Dependent binding of MB-cyt c does not require IMM, and it can be reproduced using large or small unilamellar vesicles (SUV). Using SUV-cyt c complexes, we characterized the secondary structure of MB-cyt c and MBL-cyt c by circular dichroism. Conformational analysis revealed that cyt c binding as MB-cyt c decreases its alpha-helical content (70-79%) and increases its beta-sheet up to 135%. The secondary structure of MBL-cyt c was similar to that of EB-cyt c and soluble cyt c, with a modest increase in beta-sheet. Taken together, our experiments suggest that physiological cyt c exists in soluble and membrane-bound conformations with similar ET activity, which may exchange very rapidly, and that soluble hydrophilic proteins can bind transiently to biomembranes.     

Identification of peptides specific for cerebrospinal fluid antibodies in multiple sclerosis by using phage libraries

The study of the origin and pathogenetic relevance of the oligoclonal antibodies present in the cerebrospinal fluid (CSF) of multiple sclerosis (MS) patients has been hampered by a lack of specific ligands. We recently reported a general strategy, based on phage-displayed random peptide libraries, to identify ligands for disease-specific antibodies even in the absence of any information on the nature of the pathologic antigen. With this procedure, we identified several peptides specifically recognized by antibodies present in the CSF of MS patients. Using these peptides as reagents, we demonstrated that they mimic different natural epitopes and react with antibodies enriched in the CSF of MS patients. Antibodies recognizing the selected peptides are commonly found with equal frequency in the sera of MS patients and of normal individuals. In contrast, the repertoire of CSF antibodies appears to be individual-specific and is probably the result of a nonspecific immunodysregulation rather than a stereotyped response to a single antigen/agent.