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Geostatistical and morphological methods applied to three-dimensional microscopy.

Three-dimensional (3-D) images of osteocyte lacunae were examined on a confocal microscope. Both geostatistical and morphological processing techniques were used to improve and to analyse them. By a geostastical approach, this study aims at improving 3-D confocal images before any further image processing. Optimized linear filters, which take account of the second-order statistics and the 3-D structure of the data, allow for the removal of imperfections such as noise and/or blur due to the axial convolution, and interpolate voxels on a face-centred cubic grid from an initial cubic grid. An application of this technique to 3-D biological images is demonstrated. In a second step, a 3-D binary image is digitized and cleaned with 3-D morphological filters. The standard 3-D measurements cannot be applied in this case, since all osteocytes cut the border of the field. For this reason a 3-D Boolean model has been adjusted, from which it is possible to derive all useful information on the repartition and the morphology of the osteocytes.

Humans

Engineering the Vero Cell Lineage: Toward a Programmable Vaccine Manufacturing Platform.

Vero cells remain an indispensable continuous substrate for human viral vaccine manufacturing. Despite decades of empirical process optimization, intrinsic genomic instability, including segmental aneuploidy and dynamic chromatin rearrangements, continues to limit the durability of engineered phenotypes under sustained viral burden and bioreactor stress. Here, we review the expanding engineering toolkit for the Vero lineage across a three-layered functional framework: the membrane interface, cytoplasmic foundry, and nuclear blueprint, evaluating translational prospects at each level. Receptor transplantation and morphological reprogramming have broadened viral entry range and enabled suspension-adapted culture formats, while metabolic flux management and temporally controlled apoptosis modulation have addressed intracellular production bottlenecks, albeit often with trade-offs between productivity, biosafety, and long-term population stability. At the genomic level, targeted perturbations of transcriptional regulators and emerging epigenetic interventions offer more durable gains, yet expression drift, clonal heterogeneity, and karyotypic instability during extended passaging highlight the need for locus-level precision rather than constitutive trait installation. Looking forward, infection-responsive dynamic logic circuits and the systematic identification of Vero-specific genomic safe harbors could shift the paradigm toward a conditionally responsive manufacturing architecture. Collectively, these advances suggest a pathway for transitioning the Vero lineage from a passive, empirically optimized biological substrate into a conditionally responsive, genomically stable, and programmable platform for modern vaccine preparedness.

Vero cells

Promoter recognition and promoter strength in the Escherichia coli system.

The strength of Escherichia coli promoters in vivo as well as the rates of association between RNA polymerase and promoter sequences differ by more than an order of magnitude. Since efficient promoter recognition and rapid binding of the enzyme might be a prerequisite for exceptional promoter strength we have determined the forward rate constants kon (as well as koff) for nine promoters including PL, PA1, and PN25 from phages lambda, T7, and T5, respectively as well as Pbla and PlacUV5 from E. coli. The second order forward rate constants span a 30-fold range from 1 X 10(7) M-1 s-1 for Pbla and PL up to 2.9 X 10(8) M-1 S-1 for PN25. Little correlation between 'promoter recognition' as defined by the rate of complex formation of a promoter sequence with RNA polymerase and its strength in vivo as defined by the rate of RNA synthesis has been found. This adds to the evidence that the complex functional pathway encoded in a promoter sequence can be limited at various levels and that promoter strength in vivo is the result of an optimization process involving more than just one functional parameter.

Bacteriophage lambda

The effects of a biosurfactant on oxygen transfer in a cyclone column reactor.

A laboratory-scale cyclone column reactor was tested to determine how its oxygen transfer characteristics were affected by surfactants in the liquid medium. The volumetric oxygen transfer coefficient was greatly decreased by small quantities of the synthetic surfactants dodecyltrimethylammonium bromide and sodium dodecylsulfate, and the biosurfactant surfactin produced by Bacillus subtilis (ATCC 21332). Since the gas holdup fraction was generally increased due to foaming, the effectiveness of the surfactants was probably due to an increase in the interfacial film resistance. B. subtilis was grown in the cyclone column to 0.6 g dm-3 with a significant level of surfactin produced while maintaining at least 75% oxygen saturation in the broth. Process optimization and scale-up of surfactin production will have to consider oxygen transfer as a key parameter.

Bacillus subtilis

Quantitative magnetic resonance spectroscopy by optimized numerical curve fitting.

A technique is reported for generating the quantitative area under selected peaks within a 31P NMR spectrum. A numerical iterative method generates the fitted curve so as to minimize the RMS deviation between the fit and the experimental data. The curve is constructed from elemental grains of spectral density ('spexels'), each of which represents an elemental Lorentzian distribution, where the centre frequency and line width of the spexel may be varied within predetermined limits. This provides a fit that in principle is not restricted to a Lorentzian model. The method allows peak areas to be estimated, including the case of overlapping peaks. The method has been tested using simulated spectra containing six overlapping spectral lines each of known amplitude (ranging from 367 to 661 mV) and area; together with additional Gaussian noise with a standard deviation ranging from 30 to 646 mV. The results of fitting both unfiltered and filtered spectra were compared. The variation of quality of fit with spectral noise and filtering has been evaluated. In all cases, the method fitted the peak amplitudes to within 1% of the simulated value. The optimization processes provide an excellent non-linear spectrum filtering algorithm. Provided the noise in the spectra did not exceed ca 400 mV, prefiltered data could be adequately fitted.

Computer Simulation

A multicomponent, random walk model of transport and metabolism inside a neuron.

A model of multicomponent transport, consumption, and production of metabolites inside a neuron containing discrete mitochondria and glycolytic enzymes is developed using a random walk model of molecular transport. The ratio of anaerobic to aerobic metabolism which maximizes ATP production under normal, ischemic, and anoxic conditions is calculated. The ratio of the number of mitochondria to glycolytic enzymes which maximizes ATP under normal conditions is also calculated. Because the volume of the neuron is fixed, the sum of the number of mitochondria and glycolytic enzymes is fixed. This constraint is incorporated in the optimization process as an interior penalty function. Some of the advantages of employing the random walk technique are simple stoichiometry can be used to model consumption and production of metabolites, the geometry of the enzyme system and their active sites can be easily included in the model, and saturation of enzymes can be more easily modeled.

Animals

Parameter optimization model of learning in stepping motion.

In this study we combine the representation of motion by a finite number of hardwired functions with parameter optimization to model learning during a stepping motion. Representation of experimental kinematic data by a finite number of predetermined functions and undetermined coefficients was analyzed. Least squares approximation was used to represent experimental data of stepping motions over obstacles of different heights. Functional relationships between coefficients and obstacles heights were also obtained. Learning of stepping over an obstacle was then formulated as a finite dimensional optimization problem. The pattern of foot path, and joint angles trajectories obtained by this learning model, were then compared to the experimental data. The results of the data fitting analysis and of the optimization process as a model for motion learning, indicate that motion can be adequately represented by a set of hardwired functions, and a finite number of task dependent coefficients.

Humans

On visual orientation of dot patterns.

Two-dimensional normally distributed random dot patterns were used in two experiments on visual orientation estimation. In the first experiment the patterns differed in their sample correlation and in dot number. In the second one the number of dots was maintained constant but the patterns were generated as a superposition of two normally distributed orthogonal sets composed of different number of dots. In both experiments the estimated orientation depended on stimuli correlation - with increasing correlation the estimated orientation gets closer to the orientation of the least square distance axis of the pattern. Even at very low unsignificant correlations there still remained a hint about stimulus orientation which was not estimated at random. Equalizing consecutively the number of dots in the two orthogonal dot patterns during the second experiment did not result in chance performance either. The bimodal angular distributions of the obtained responses permitted to approach the problem of orientation ambiguity. The results are discussed in terms of optimization processes taking place in the visual system.

Cybernetics

Some factors influencing the proportion of periplasmic hepatitis B virus pre-S2 antigen in the recombinant yeast Hansenula polymorpha.

A central composite design (CCD) was used to evaluate, for the purpose of future process optimization, the influence of pH, yeast extract and ammonium chloride concentrations on the proportion of periplasmic hepatitis B pre-S2 antigen in the recombinant yeast Hansenula polymorpha. Each factor was tested at five levels, and a second order polynomial model for the proportion of periplasmic antigen was fitted to the treatment combinations. pH showed the greatest effect: the proportion of periplasmic antigen was greatly increased at the higher pH levels. At the higher pH levels used, the proportion of periplasmic antigen was enhanced by a high concentration of ammonium chloride. Additional experiments have confirmed both the validity of the selected model and the optimal conditions found. A significant correlation was found between the proportion of periplasmic antigen and the total yield of antigen. These results indicated that it should be possible to modulate the distribution of the pre-S2 antigen between the periplasm and the cytoplasm of the yeast.

Ammonium Chloride

The use of particle concentration fluorescence immunoassay technology for the analysis of rDNA products.

The electrophoretic and immunological techniques typically used to detect potentially useful biopharmaceutical proteins are sensitive with detection limits in the nanogram range. However, quantitation of a recombinant protein can be cumbersome, and involve large numbers of samples throughout process optimization schemes. Although electrophoretic methods (i.e., SDS-PAGE and Western blots) now avail themselves to quantitation by densitometry, these techniques are time consuming because of the lack of appropriate automated systems. Biological activity assays, when available, often require relatively pure material and are not suitable for analyzing and quantitating impure or semi-purified samples, typical of the fermentation milieu. The optimization of several rDNA-derived protein systems from both prokaryotic and eukaryotic hosts has been completed using PCFIA, a rapid, sensitive system with high throughput. The development of Particle Concentration Fluorescence Immunoassay (CFIA) procedures for several of these rDNA-derived proteins of interest as potential biopharmaceuticals (e.g., alpha-1-antitrypsin, tPA, soluble CD4, and a malaria vaccine candidate) are discussed.

Binding, Competitive

Optimization of cultivation and nutrition conditions and substrate pretreatment for solid-substrate fermentation of wheat straw by Coriolus versicolor.

Bioconversion of wheat straw by solid-substrate fermentation (SSF) with Coriolus versicolor was optimized by varying its physiological parameters. Selective delignification (more lignin than holocellulose degradation) and increases in crude protein (CP) content and in vitro dry matter digestibility (IVDMD) were taken as the criteria to select optimum levels of these parameters. The fungus behaved optimally under the following set of cultural and nutritional conditions: pH 5.5, moisture level 55%, temperature 30 degrees C, duration of fermentation 21 d, form of inoculum--grain culture, turning frequency--once at mid-incubation, urea (nitrogen source) 1.5% (sterile) or 3.0% (nonsterile), single superphosphate (phosphorus + sulfur source) 1.0%, no addition of free polysaccharides (as whey or molasses). A maximum of 17.5% increase in IVDMD involving 4.3% degradation of lignin, was attained in the optimized SSF under laboratory conditions. The digestibility improvement could be further increased by using a substrate pretreatment (physical/chemical/biological) in the following order of preference: NaOH treatment, urea or urine treatment, ensiling, steaming, grinding. For practical farm applications, urea treatment and ensiling appeared most feasible. The laboratory optimized process was also scaled up to 4 kg (sterile and unsterile) and 50 kg (unsterile) fermentations.

Animal Feed

Three-dimensional determination of an oblique osteotomy in the hip by mathematical optimization fulfilling some anatomical demands.

The present paper describes a nonlinear optimization process to estimate the single cutting plane of an oblique osteotomy in the hip. This kind of osteotomy was introduced and practised by Charit (Research report 81, University of Witwaters brand, Johannesburg, 1981). We calculate the cutting plane in such a way that the postoperative coverage of the resulting two parts of the femur are as great as possible whereby some anatomical constraint conditions are fulfilled. Additionally a simplified preoperative planning is described by using a sphere lying on the femoral head and determined by a least-squares method.

Biomechanical Phenomena

High-performance liquid chromatographic determination of metabolic products for fermentation control of mammalian cell culture: analysis of carbohydrates, organic acids and orthophosphate using refractive index and ultraviolet detectors.

A method for the determination of carbohydrate substrates and excreted metabolic end-products of cell culture supernatants using a strong cation-exchange column in the H+ form has been developed. Organic acids and carbohydrates can be determined in addition to orthophosphoric acid. Pyrrolidone carboxylic acid, resulting from chemical conversion of the amino acid glutamine during the incubation of fresh medium and during the fermentation process, can be determined. The chromatographic method allows the correction of glutamine uptake values for physiological studies. Measured values of pyrrolidone carboxylic acid in supernatants of human hybridoma cell line show that it cannot be consumed by the cells. This technique allows the separation of major metabolites used in process optimization. Peak homogeneity is proved by on-line monitoring of the effluent with an ultraviolet (214 nm) and a refractive index detector connected in series.

Acids

Enhanced chemiluminescence for the detection of membrane-bound nucleic acid sequences: advantages of the Amersham system.

A range of nonradioactive nucleic acid labeling and detection systems have been developed that enable the user to label probes directly with enzyme molecules or indirectly with hapten-derivatized nucleotides. Horseradish peroxidase is used for the direct labeling procedures due to the ease of chemical modification and the relative thermal and chemical stability of this enzyme. Horseradish peroxidase has also been conjugated to a high-specificity antifluorescein antibody for detection of hapten (fluorescein)-labeled hybrids. Enhanced chemiluminescence is a light-emitting process optimized for the detection of low levels of horseradish peroxidase on membrane supports. Results are obtained as hard copy images on x-ray film.

Base Composition

Comparative profiling of microbial community structure, enzyme potential, metabolic features, and volatile composition in craft and Jiafan Huangjiu processes.

Craft Huangjiu and Jiafan Huangjiu represent two distinct industrial Huangjiu product outcomes with contrasting volatile profiles. This study compared craft Huangjiu (L70) and Jiafan Huangjiu (L79) to characterize their physicochemical, microbial, gene-level functional, metabolic, and volatile features. Because L70 involved mid-fermentation addition of finished Huangjiu, this comparison was not intended to isolate the sole effect of fermentation interruption versus continued fermentation. L79 showed more extensive carbon and nitrogen utilization, with lower residual substrates and higher ethanol and acetic acid contents than L70, whereas L70 retained a less complete fermentation state. At the volatile level, GC-MS and volatile metabolomics consistently showed an ester-enriched profile in L79 and a more alcohol-dominant profile in L70. FlavorDB-based putative annotation and threshold-based OAV analysis further indicated distinct database-assigned descriptor distributions and potential odor-active compounds, with more OAV > 1 ester-related compounds in L79. Metagenomic analysis showed that L70 was dominated by Lactobacillus acetotolerans, whereas L79 contained higher relative abundances of Saccharomyces cerevisiae, Aspergillus oryzae, Aspergillus flavus, and Fructilactobacillus fructivorans. Metagenomic functional annotation showed higher representation of hydrolysis-related CAZy genes and ester-related enzyme annotations in L79. KEGG-based pathway mapping further indicated greater gene-level potential for ethanol-, acetate-, and acetyl-CoA-related metabolism in L79. Accordingly, the L70 profile should be interpreted as the integrated final-product outcome of process intervention, exogenous input, and subsequent fermentation. The findings provide a comparative basis for future flavor regulation and process optimization in Huangjiu and other fermented alcoholic beverages.

Volatile Organic Compounds

Proteomic characterization of acidic aqueous extracts from Vicia faba L. pod valves identifies chitinase as a major co-extracted protein macromolecule.

Naturally acidic aqueous extracts from Vicia faba L. pod valves are being explored as sustainable, L-DOPA-oriented plant preparations. Pod valves represent an underutilized processing by-product reported to contain L-DOPA, a compound widely used in Parkinson's disease therapy, while acidic aqueous media may help preserve its physicochemical stability. However, the protein macromolecules co-extracted from V. faba pod valves under these conditions remain poorly characterized. This information is relevant because persistent plant proteins may influence extract composition, stability, susceptibility to degradation, and downstream processing requirements. Here, we characterized co-extracted V. faba protein macromolecules in aqueous pod-valve extracts prepared in ultrapure water or naturally acidic media, including 2% Phyllanthus emblica, 5% Punica granatum, and 2% Ribes rubrum. Protein profiles were first evaluated by SDS-PAGE and subsequently analyzed by nanoflow liquid chromatography coupled to high-resolution tandem mass spectrometry (nLC-MS/MS). Protein identifications were complemented with Gene Ontology annotation and a descriptive semi-quantitative assessment of relative protein representation across extraction media. Chitinase was the most represented V. faba-assigned protein macromolecule across the extracts, with additional highly represented proteins including glucan endo-1,3-beta-D-glucosidase, pathogenesis-related proteins, and polyphenol oxidase A1. These co-extracted proteins are mainly associated with plant defense, stress responses, cell-wall remodeling, and oxidative processing, suggesting that they may be relevant for extract quality attributes during handling and storage. This study provides a compositional proteomic reference for the co-extracted protein macromolecules present in acidic aqueous extracts from V. faba pod valves, supporting future studies on extract stability, processing optimization, and the development of standardized plant-based preparations.

Vicia faba

Selective monitoring of trace-level catechin and myricetin in herbal and aqueous matrices using magnetic MIP-DSPME: Optimization via design of experiments.

A novel dispersive solid-phase microextraction approach utilizing a magnetic molecularly imprinted polymer (MMIP) integrated with HPLC-UV detection was developed for the concurrent quantification of catechin and myricetin in herbal extracts and aqueous samples. The sorbent was engineered as a core-shell nanocomposite, consisting of a selective polymer layer deposited onto Fe3O4@SiO2-APTMS magnetic nanoparticles. Dual-template imprinting using catechin and myricetin generated complementary binding cavities within the polymer framework. Experimental variables influencing extraction were systematically screened and subsequently optimized. A Plackett-Burman design was first applied to identify the most influential factors, with pH and sorption time identified as the dominant variables. These parameters were subsequently fine-tuned using a central composite design, and the optimization process was completed in only 30 experimental runs. The sorption characteristics of the imprinted sorbent (MMIP) were compared with those of its non-imprinted counterpart (MNIP). The MMIP demonstrated markedly higher maximum binding capacities (Qmax), reaching 119.3 mg g-1 for myricetin and 112.1 mg g-1 for catechin, whereas the corresponding values for the MNIP were 32.55 and 32.08 mg g-1, respectively. Moreover, the affinity constants (KL = 0.760-0.950 L mg-1) were approximately 2.3-fold higher for the MMIP, confirming its stronger and more selective interactions with the target analytes. The selectivity coefficients for the targeted flavonoids relative to structurally related compounds, including ferulic acid, p-coumaric acid, melatonin, and curcumin, exceeded 3.5 for the MMIP, whereas the corresponding values for the MNIP were close to 1.1, demonstrating the high molecular recognition capability of the imprinted sorbent. Method validation demonstrated limits of detection (LODs) of 0.33-0.59 ng mL-1 and limits of quantification (LOQs) of 1.10-1.96 ng mL-1, and excellent linearity over the concentration range of 5.0-5500 ng mL-1 (R2 > 0.998). The method achieved recoveries of 93.96% to 105.69% with RSDs below 5.5%, while the preconcentration factors ranged from 209 to 229. Furthermore, the sorbent retained more than 95% of its extraction efficiency after four consecutive reuse cycles and more than 80% after six cycles, demonstrating excellent stability and reusability. The proposed method was successfully applied to the analysis of six medicinal plant extracts and water samples, showing negligible matrix interference and superior sensitivity, selectivity, and operational simplicity compared with conventional solid-phase extraction methods.

Flavonoids

The NK model of rugged fitness landscapes and its application to maturation of the immune response.

Adaptive evolution is, to a large extent, a complex combinatorial optimization process. Such processes can be characterized as "uphill walks on rugged fitness landscapes". Concrete examples of fitness landscapes include the distribution of any specific functional property such as the capacity to catalyze a specific reaction, or bind a specific ligand, in "protein space". In particular, the property might be the affinity of all possible antibody molecules for a specific antigenic determinant. That affinity landscape presumably plays a critical role in maturation of the immune response. In this process, hypermutation and clonal selection act to select antibody V region mutant variants with successively higher affinity for the immunizing antigen. The actual statistical structure of affinity landscapes, although knowable, is currently unknown. Here, we analyze a class of mathematical models we call NK models. We show that these models capture significant features of the maturation of the immune response, which is currently thought to share features with general protein evolution. The NK models have the important property that, as the parameter K increases, the "ruggedness" of the NK landscape varies from a single peaked "Fujiyama" landscape to a multi-peaked "badlands" landscape. Walks to local optima on such landscapes become shorter as K increases. This fact allows us to choose a value of K that corresponds to the experimentally observed number of mutational "steps", 6-8, taken as an antibody sequence matures. If the mature antibody is taken to correspond to a local optimum in the model, tuning the model requires that K be about 40, implying that the functional contribution of each amino acid in the V region is affected by about 40 others. Given this value of K, the model then predicts several features of "antibody space" that are in qualitative agreement with experiment: (1) The fraction of fitter variants of an initial "roughed in" germ line antibody amplified by clonal selection is about 1-2%. (2) Mutations at some sites of the mature antibody hardly affect antibody function at all, but mutations at other sites dramatically decrease function. (3) The same "roughed in" antibody sequence can "walk" to many mature antibody sequences. (4) Many adaptive walks can end on the same local optimum. (5) Comparison of different mature sequences derived from the same initial V region shows evolutionary hot spots and parallel mutations. All these predictions are open to detailed testing by obtaining monoclonal antibodies early in the immune response and carrying out in vitro mutagenesis and adaptive hill climbing with respect to affinity for the immunizing antigen.

Amino Acid Sequence