On the performances of noise filters in the restoration of oscillatory behavior in continuous yeast cultures

Continuous flow microbial fermentations under industrial conditions are subject to the influx of noise, mainly through the feed stream. Noise upsets the normal deterministic behavior. For continuous cultures of Saccharomyces cerevisiae exhibiting oscillatory responses, four kinds of commonly used noise filters, three algorithmic and one neural, have been compared for their ability to restore noise-free oscillations. An auto-associative neural filter was the best, similar to earlier observations for other organisms under non-oscillatory conditions. This enhances the general applicability of neural filters for industrial scale fermentations.     

Hybrid filtering to rescue stable oscillations from noise-induced chaos in continuous cultures of budding yeast

In large-scale fermentations with oscillating microbial cultures, noise is commonly present in the feed stream(s). As this can destabilize the oscillations and even generate chaotic behavior, noise filters are employed. Here three types of filters were compared by applying them to a noise-affected continuous culture of Saccharomyces cerevisiae with chaotic oscillations. The aim was to restore the original noise-free stable oscillations. An extended Kalman filter was found to be the least efficient, a neural filter was better and a combined hybrid filter was the best. In addition, better filtering of noise was achieved in the dilution rate than in the oxygen mass transfer coefficient. These results suggest the use of hybrid filters with the dilution rate as the manipulated variable for bioreactor control.     

Hybrid neural simulation of a fed-batch bioreactor for a nonideal recombinant fermentation

Fermentations employing genetically modified microbes under industrial conditions are difficult to monitor on line or to describe by simple, good mathematical models. So, a practically convenient approach is to combine mathematical models of some aspects with artificial neural networks of those aspects which are difficult to measure or model. Such hybrid models have been applied earlier to laboratory-scale bioreactors. In the present work, a model based on laboratory data for the synthesis of recombinant #-galactosidase was corrupted by adding imperfect mixing and noise in the feed stream to generate data mimicking a real nonideal operation. These data were used to train a recurrent Elman neural network and a hybrid neural network, and it was seen that a hybrid network provides more accurate estimates of both extra-cellular and intra-cellular variables. The benefit is enhanced by the hybrid network's superiority being more pronounced for the intra-cellular recombinant protein, #-galactosidase, which is the main product of interest.     

The microdistribution of mayflies (Ephemeroptera) in myriophyllum beds in Pennington Creek,Johnston County,Oklahoma

I studied the population densities and the microdistributions of the four most abundant mayfly (Ephemeroptera) nymphs in Myriophyllum heterophyllum beds in Pennington Creek, Johnston County, Oklahoma, from May to December, 1977. The section of the stream studied has relatively constant flow rates and temperatures throughout the year due to continuous inflow from groundwater. This uniform physical environment allows the plant beds to grow throughout the year and provide a permanent habitat. The four mayflies are Tricorythodes fictus (Tricorythidae), Caenis delicata (Caenidae), Baetis favistriga and B. quilleri (Baetidae). All four species are of similar size and feed by scraping periphyton from the surface of the Myriophyllum. T. fictus and the two species of Baetis have overlapping microdistributions in the leafy, upper one-half of the plant bed. T. fictus and C. delicata have overlapping microdistributions in the lower portion of the plant bed and roots. Each species has similar population densities where their distributions overlap. There is no significant selection for position with respect to current flow in the Myriophyllum for any of the species. Food and space are always abundant, especially in the top one-half of the Myriophyllum. There are no major changes in these trends over the year.     

A modification of tooth germ cultivation in vitro and in ovo

Mandibular molar anlages excised from 17-day mouse foetuses were cultured in vitro or in ovo (on the chorioallantoic membrane). In both cases, the explants were underlain either with a Millipore filter or with a piece of fibrin foam. Tooth germs were harvested after 7 days of cultivation and processed histologically. Spatial arrangement was highly preserved in the tooth germs cultured in vitro on fibrin foam. In vitro cultures on Millipore filters revealed significant flattening of tooth germs, caused especially by the collapse of enamel organ and the pulp. The cytodifferentiation of tooth germs cultured in vitro on both substrates (Millipore filter, fibrin foam) was characterized by the presence of odontoblasts, polarizing ameloblasts and predentine. The cytodifferentiation of tooth germs cultured in ovo on Millipore filters placed on chorioallantoic membrane was characterized by the presence of odontoblasts, ameloblasts, predentine, dentine and enamel. However, the flattening of these explants was identical with the changes of the explants cultured on Millipore filters in vitro. In ovo cultivation on the fibrin foam failed to bring satisfactory results.     

Development of simple fitness landscapes for peptides by artificial neural filter systems

The applicability of artificial neural filter systems as fitness functions for sequence-oriented peptide design was evaluated. Two example applications were selected: classification of dipeptides according to their hydrophobicity and classification of proteolytic cleavage-sites of protein precursor sequences according to their mean hydrophobicities and mean side-chain volumes. The cleavage-sites covered 12 residues. In the dipeptide experiments the objective was to separate a selected set of molecules from all other possible dipeptide sequences. Perceptrons, feedforward networks with one hidden layer, and a hybrid network were applied. The filters were trained by a (1,) evolution strategy. Two types of network units employing either a sigmoidal or a unimodal transfer function were used in the feedforward filters, and their influence on classification was investigated. The two-layer hybrid network employed gaussian activation functions. To analyze classification of the different filter systems, their output was plotted in the two-dimensional sequence space. The diagrams were interpreted as fitness landscapes qualifying the markedness of a characteristic peptide feature which can be used as a guide through sequence space for rational peptide design. It is demonstrated that the applicability of neural filter systems as a heuristic method for sequence optimization depends on both the appropriate network architecture and selection of representative sequence data. The networks with unimodal activation functions and the hybrid networks both led to a number of local optima. However, the hybrid networks produced the best prediction results. In contrast, the filters with sigmoidal activation produced good reclassification results leading to fitness landscapes lacking unreasonable local optima. Similar results were obtained for classification of both dipeptides and cleavage-site sequences.     

Fungal nitrilases as biocatalysts: Recent developments

Of the numerous putative fungal nitrilases available from protein databases only a few enzymes were purified and characterized. The purified nitrilases from Fusarium solani, Fusarium oxysporum f. sp. melonis and Aspergillus niger share a preference for (hetero)aromatic nitriles, temperature optima between 40 and 50 °C and pH optima in the slightly alkaline region. On the other hand, they differ in their chemoselectivity, i.e. their tendency to produce amides as by-products. The production of fungal nitrilases is increased by up to three orders of magnitude on the addition of 2-cyanopyridine to the culture media. The whole-cell and subcellular biocatalysts were immobilized by various methods (LentiKats®; adsorption on hydrophobic or ion exchange resins; cross-linked enzyme aggregates). Operational stability was examined using continuous stirred membrane bioreactors. Fungal nitrilases appear promising for biocatalytic applications and biodegradation of nitrile environmental contaminants.     

Seasonality of macrophytes and interaction with flow in a New Zealand lowland stream

Introduced submerged macrophytes have come to dominate many shallow water bodies in New Zealand, and are a common component of many lowland streams. We investigated the seasonal variation of macrophyte abundance, its influence on flow and channel volume, and the implications of this on stream habitat and functioning in Whakapipi Stream, a typical lowland stream draining a predominantly agricultural catchment.Abundance of macrophytes over the summer was primarily controlled by the phenological cycles of the two dominant species. Mean minimum total macrophyte biomass (36 g m^–2) and cover (7%) occurred in winter (June and August, respectively), and mean maximum biomass (324 g m^–2), and cover (79%) occurred in late summer (March and February respectively). Egeria densa comprised the majority of both cover and biomass during the study period, except early summer (December) when Potamogeton crispus was prevalent in the shallow stream reaches.Macrophyte beds had a major impact on summer stream velocities, reducing average velocities by an estimated 41%. Stream cross-sectional area was maintained at relatively stable levels similar to that recorded over winter, when stream discharge was in the order of seven times greater. The mean velocity distribution coefficient (), and Manning's roughness coefficient (n) were dependent on and displayed a positive linear relationship with macrophyte abundance. The velocity distribution coefficient is recommended as a better indicator of macrophyte effects on velocity in natural streams, as it does not assume uniform velocity, channel depth and slope within the stream reach.Our study shows that submerged macrophytes play an important structuring role within the stream during the summer period, where macrophyte beds act as semi-permeable dams, retarding flow velocities and increasing stream depth and cross-sectional area. This promotes habitat heterogeneity by creating a greater range of flow velocity variation, and also provides large stable low-flow areas. Other likely ecosystem effects resulting from macrophyte/velocity interactions include increased sedimentation, potential for nutrient processing and increased primary production, both by macrophytes and attached epiphyton. The complex architecture of submerged macrophytes and their influence on stream flow may also provide an increased diversity of habitat for other aquatic biota. We propose that management of degraded lowland streams such as the Whakapipi Stream to maintain stretches with moderate quantities of submerged macrophytes interspersed with shaded areas would optimise stream health during low summer flows.     

Cleavage of RNA in Hybrid Duplexes by E. coli Ribonuclease H: III. Substrate Properties of RNA Duplex Complexes with Oligodeoxyribonucleotides Containing a Bleomycin A5 Residue

The effect of bleomycin A₅ residue linked to four-, eight-, and twelve-mer oligodeoxyribonucleotides on the substrate properties of their tandem and continuous (with or without unmodified octanucleotide effectors) hybrid duplexes was studied using E. coli RNase H. The bleomycin derivatives of oligodeoxyribonucleotides were shown to form hybrid duplexes with practically the same thermostability as those formed by unmodified oligodeoxyribonucleotides. The RNA in the bleomycin-containing hybrid duplexes is cleaved by E. coli RNase H; however, the initial hydrolysis rate (v ₀) is 2.6–3.4-fold reduced for the continuous duplexes. In the case of tandem hybrid complexes, the effect of bleomycin on v ₀ was less pronounced. We hypothesized that steric factors play a key role in the bleomycin inhibition and effectors probably determine the substrate properties of such hybrid complexes. Of all the tandem systems studied, the RNA duplex with the bleomycin-containing tetranucleotide flanked with two effectors displayed the best substrate properties.     

Growth of Trichoderma reesei RUT C-30 in stirred tank and reciprocating plate bioreactors

A series of fed-batch experiments at different agitation speeds were performed using the industrially important strain Trichoderma reesei RUT C-30 in two different bioreactors to understand the close relationship that exists between the shear field within a bioreactor, the morphology of the microorganism, the rheology of cultivation broth, and the process performance. The two bioreactors, stirred tank bioreactor (STB) and reciprocating plate bioreactor (RPB), are characterized by a significantly different shear field to which microorganisms are exposed. Highest biomass concentration (ca. 15 g l⁻¹) was obtained at higher agitation rates in both bioreactors due to better oxygen supply. However, better filter paper activities per mg of protein were obtained at lower agitation in both bioreactors. In both bioreactors, young and healthier fungi in the batch phase were not affected by shear even at higher agitation rates. However, during the fed-batch phase, higher degree of fragmentation of clump morphology at high agitation intensity was confirmed by image analysis. Also, the rheological analysis showed an increase in apparent viscosity during the batch phase and early fed-batch phase due to the increase in the biomass concentration. During the late stages of cultivation, the apparent viscosity decreased due to cell lysis and spore formation.     

Intensive rotifer cultures using chemostats

Continuous production of the rotifer Brachionus plicatilis rotundiformis (S-type) in an intensive chemostat culture system has been investigated. The production dynamics of rotifers in relation to different flow rates and feed regimes show that the growth rate and production depends on the type of algal feed and flow rate utilized in the culture system. It was possible to achieve a mean production of up to 318.84 × 10⁶ rotifers m^–3 d^–1 at a flow rate of 6 1 h^–1 in 100 1 chemostats and up to 261.21 × 10⁶ rotifers m^–3 d^–1 at a flow rate of 40 1 h –1 while using 1 m³ capacity rotifer chemostats as production units. The 3 fatty acid composition of rotifers while using Chlorella and Nannochloropsis in the culture system has been described. The results of this investigation show that the rotifer productivity in the continuous culture system is considerably higher than in any of the conventional culture systems described to date for aquacultural purposes.This research was financed by the Kuwait Foundation for the Advancement of Sciences (KFAS), Kuwait, under a contract research project code 86-04-02.     

Acoustic feature extraction by cross-correlation in crickets?

Common concepts of acoustic feature extraction within the auditory pathway of vertebrates and insects assume temporal filters tuned to particular periodicities. Crickets respond selectively to the conspecific song pattern and reveal a bandpass characteristic, which is thought to arise from a matched filter for a restricted range of periods. Unexpectedly, females of the two sibling species Teleogryllus oceanicus and T. commodus differed in fundamental filter properties. While T. oceanicus revealed a period filter, T. commodus exhibited a pulse duration filter. This finding raises the question of how so distinct properties of homologous neuronal circuits for pattern analysis have evolved during speciation. Evidence is presented that signal analysis by cross-correlation offers a simple explanation for differences in pattern selectivity as well as for the evolutionary transition. By cross-correlation the similarity of an external pattern with an internal template is determined over a certain time window. A comparison of behavioural data and cross-correlation values suggested that both species have similar templates. However, time windows were significantly different between species (T. oceanicus: 180–400 ms, T. commodus: 90–160 ms). Consequently, solely a change in the evaluation time window is required to account for the observed differences in feature extraction that serve to maintain species isolation.Dedicated to Franz Huber, who enriched neuroethology both by his pioneering studies as well as his infectious enthusiasm     

Neural network models for biological waste-gas treatment systems

This paper outlines the procedure for developing artificial neural network (ANN) based models for three bioreactor configurations used for waste-gas treatment. The three bioreactor configurations chosen for this modelling work were: biofilter (BF), continuous stirred tank bioreactor (CSTB) and monolith bioreactor (MB). Using styrene as the model pollutant, this paper also serves as a general database of information pertaining to the bioreactor operation and important factors affecting gas-phase styrene removal in these biological systems. Biological waste-gas treatment systems are considered to be both advantageous and economically effective in treating a stream of polluted air containing low to moderate concentrations of the target contaminant, over a rather wide range of gas-flow rates. The bioreactors were inoculated with the fungus Sporothrix variecibatus, and their performances were evaluated at different empty bed residence times (EBRT), and at different inlet styrene concentrations (C(i)). The experimental data from these bioreactors were modelled to predict the bioreactors performance in terms of their removal efficiency (RE, %), by adequate training and testing of a three-layered back propagation neural network (input layer-hidden layer-output layer). Two models (BIOF1 and BIOF2) were developed for the BF with different combinations of easily measurable BF parameters as the inputs, that is concentration (gm(-3)), unit flow (h(-1)) and pressure drop (cm of H(2)O). The model developed for the CSTB used two inputs (concentration and unit flow), while the model for the MB had three inputs (concentration, G/L (gas/liquid) ratio, and pressure drop). Sensitivity analysis in the form of absolute average sensitivity (AAS) was performed for all the developed ANN models to ascertain the importance of the different input parameters, and to assess their direct effect on the bioreactors performance. The performance of the models was estimated by the regression coefficient values (R(2)) for the test data set. The results obtained from this modelling work can be useful for obtaining important relationships between different bioreactor parameters and for estimating their safe operating regimes.     

Application of flow cytometry to differentiating Exophiala dermatitidis E. moniliae and E. jeanselmei from each other

We applied a flow cytometry apparatus (FCM) to differenciating Exophiala dermatitidis, E. moniliae and E. jeanselmei from each other. The wavelength of the argon laser emitted from the FCM was 488 nm and the aperture of nozzle from which the stream of fluid containing single cells was blown out was 100 m. By irradiating the stream with laser by either the forward light scatter (FLS) or by the perpendicular light scattr (PLS), we were able to get two pieces of informations. Histograms displayed by the FLS indicate the cell size, while dot displays by the PLS reflect the cell structure. As a result, E. dermatitidis was clearly differenciated from either E. moniliae or E. jeanselmei by their histograms by FLS. In addition, dot displays by the PLS differenciated E. moniliae from E. jeanselmei.In conclusion, flow cytometry is available for differenciating E. dermatitidis, E. moniliae and E. jeanselmei from each other.     

Continuous production of fructose syrup and ethanol from hydrolysed Jerusalem artichoke juice

Summary The results from this study showed that Jerusalem artichoke juice can be used for the production of very enriched fructose syrup by selective conversion of glucose to ethanol in a continuous process using immobilized cells ofSaccharomyces cerevisiae ATCC 36859. The product contained up to 99% of the total carbohydrates as fructose compared to 76% in the feed. Using Jerusalem artichoke juice supplemented with some glucose a product was obtained with 7.5% w/v ethanol which made ethanol recovery economically favourable. It was found that some fructose was consumed in these continuous processes; the glucose/fructose conversion rate ratio was regulated by the glucose concentration in the product stream.     

Will alewives (Alosa pseudoharengus) feed in the dark?

Synopsis Results of a laboratory experiment indicate that alewives (Alosa pseudoharengus) can feed in the dark onDaphnia and that this feeding is not size selective. It is presumed that the fish filter feed. Observations on small alewives (ca 50 to 70 mm) confirm that they will filter feed in Lake Michigan and filtering activity increases as it gets dark.     

Megafauna associations with deepwater corals (Primnoa spp.) in the Gulf of Alaska

Our study showed that one species of water strider (Aquarius najas) dominated the insect fauna (>90% of the biomass) on and near the surface of a small stream in southern Sweden, but the diet of Daubenton's bats (Myotis daubentonii), regularly feeding over the same stream, contained <1% of these insects. To explain why the bats did not eat water striders in proportion to the apparent abundance of these insects, we tested three hypotheses, with the following results: (1) The water striders did not respond to artificial bat calls and therefore their defence against bats is not based on ultrasonic hearing. (2) Water striders hand-fed to the bats were eaten with similar frequency as palatable controls (caddis flies), so there is no evidence that water striders are unpalatable to bats. (3) Attempted prey-captures by the bats occurred less often than expected within 1 m of the bank of the stream (the bank consisted of a stone wall), indicating that the bats' flight or, alternatively, their detection or capture of insects, was difficult within that area, possibly constrained by clutter. At dusk and just before the bats emerged to feed, the water striders moved away from the open water. They remained motionless close to the bank for as long as the bats were active.     

Negative dietary effects of Colorado potato beetle eggs for the larvae of native and introduced ladybird beetles

Aphidophagous ladybird beetles (Coleoptera: Coccinellidae) are attracted to and feed heavily on aphids, but many species will also feed opportunistically on other prey that they encounter. In potatoes (Solanum tuberosum L.) in Washington State, USA, coccinellids feed on both green peach aphids (“GPA,” Myzus persicae Sulzer) and eggs of the Colorado potato beetle (“CPB,” Leptinotarsa decemlineata Say). The guild of aphidophagous ladybirds includes two native species, Hippodamia convergens Guérin-Méneville and Coccinella transversoguttata Brown. Recently, an introduced species, Coccinella septempunctata L., has invaded and apparently displaced its native congener. A second exotic, Harmonia axyridis Pallas, has colonized the area and is becoming more abundant. We compared larval development of each species on a monotypic diet of GPA, a monotypic diet of CPB eggs, or a mixed diet of both GPA and CPB eggs. Our goal was to answer two questions: (1) do larvae of the four ladybird species benefit from including CPB eggs in their diet and (2) do the four ladybird species differ in their ability to utilize CPB eggs as prey? No larva of any species completed development on a pure diet of CPB eggs, and survivorship was highest for all species when they fed on a pure diet of GPA. One native species, H. convergens, and one exotic species, H. axyridis, exhibited significantly lower survivorship on a mixed diet of both CPB eggs and GPA, compared to a pure GPA diet; H. axyridis also took longer to develop from egg to adult when both prey were provided. Survivorship of the two Coccinella spp. was not altered by the inclusion of CPB eggs with GPA, although CPB eggs lengthened the development time of C. transversoguttata. Adult size was not consistently affected by diet for any of the coccinellids. Overall, no ladybird species benefited from the inclusion of potato beetle eggs in its diet. The two Coccinella species responded similarly to the inclusion of CPB eggs, and so we would not expect any difference in the success of coccinellid larval development in potato fields following the replacement of C. transversoguttata by C. septempunctata. Hippodamia convergens and H. axyridis, the two species whose survivorship was depressed by combining CPB egg and aphid prey, were also the two species that consumed the greatest number of CPB eggs during successful larval development. A comparison of total egg consumption by each species cohort suggested that displacement of the other species by H. axyridis would not alter CPB biological control, because the higher per capita feeding rate by H. axyridis larvae compensated for individuals’ greater mortality risk on a diet including CPB eggs.     

Host preference in Pseudacteon phorid flies: response of P. tricuspis and P. curvatus to black, red and hybrid imported Solenopsis fire ants in multiple choice bioassays

Host preferences in both sexes of Pseudacteon tricuspis Borgmeier (Jaguariuna biotype) and Pseudacteon curvatus Borgmeier (Formosa biotype) and their relative attraction to the imported fire ants (IFA), Solenopsis invicta Buren (red IFA), Solenopsis richteri Forel (black IFA) and S. invicta × S. richteri hybrids (hybrid IFA) were investigated in two separate experiments utilizing multiple choice flight bioassays. The results of both experiments clearly showed that both sexes of the Jaguariuna biotype of P. tricuspis could distinguish among the three IFA species and demonstrated greater preference for hybrid IFA and red IFA. This conclusion is supported by a variety of data collected on the number of fly visits, attack rate, and hovering duration (Experiment 1), and on the number of trapped flies (Experiment 2), which showed that black IFA is the least preferred of the three species. Similar results were recorded for the Formosan biotype of P. curvatus, although the data were not as strongly conclusive. Females of this biotype spent a significantly greater amount of time in hovering mode over red IFA and hybrid IFA compared to black IFA, but the other data were not significant. The red IFA is the natural host of both phorid fly biotypes and our results suggest that both biotypes may have evolved a specialized relationship with red IFA including an ability to discriminate it from related fire ants. These results are discussed in relation to the possible role of fire ant chemicals in mediating host preferences in phorid flies, contributions of male phorid flies to fire ant biocontrol, and the practical implications of the key findings.     

Herbivory and tree mortality across a pinyon pine hybrid zone

We examined the abundances of three common insect herbivores on pure and hybrid pinyon pines along a 250-km transect in west-central Arizona, United States. Using six morphological traits, we developed a hybrid index to classify trees as pure Pinus californiarum, hybrid, or pure Pinus edulis. The insects (the stem-boring moth, Dioryctria albovittella, the scale insect, Matsucoccus acalyptus, and several species of pitch moths that produce wounds on the trunk and branches) exhibited different distributional patterns across tree types. Stem-boring moths were significantly more abundant on trees at hybrid sites compared to trees at pure sites. In addition, within hybrid sites, hybrids supported significantly more moth larvae than pure trees of either species. These two patterns support the hybrid susceptibility hypothesis in which hybrid breakdown results in increased susceptibility to herbivory. In contrast to stem-borers, there were significantly more pitch moth wounds on trees at pure P. californiarum sites than at hybrid and pure P. edulis sites. Within the hybrid zone, pitch moth abundance was equal on pure P. californiarum and hybrids, and both were significantly greater than on pure P. edulis. These within-site comparisons support the dominance hypothesis where hybrid resistance differs from one tree species, but not the other. Scale insects exhibited the most restricted distribution; over the 250 km transect they were found only in the hybrid zone. This supports the hybrid susceptibility and/or the stress hypothesis (i.e., species at the edge of their range suffer greater stress and are more susceptible to herbivory). We summed the mean numbers of these three common herbivores across sites and found that hybrid sites supported 2.1 and 3.9 times more herbivores than pure P. californiarum and P. edulis sites, respectively. Furthermore, tree mortality was on average, 35 times greater within the hybrid zone compared to pure zones of each species and was associated with the cumulative abundance of herbivores (r ²=0.646). Regardless of whether this mortality is due to insect infestation, stress or a combination of both, these results suggest that hybrid zones are important arenas of natural selection.