The chloroplast and mitochondrial genomes of two Gomphonema parvulum (Bacillariophyta) environmental isolates from South Carolina (United States) and Virginia (United States)

Gomphonema parvulum is a cosmopolitan freshwater diatom that is used as an indicator in water quality biomonitoring. In this study, we report the culturing of two geographically separated isolates from southeastern North America, their morphology, and the sequencing and assembly of their mitochondrial and chloroplast genomes. Morphologically, both strains fit G. parvulum sensu lato, but the frustules from a protected habitat in South Carolina were smaller than those cited in the historic data of this species from the same location as well as a second culture from Virginia. Phylogenetic analyses using the rbcL gene placed both within a clade with G. parvulum. Genetic markers, including full chloroplast and mitochondrial genomes and the nuclear small subunit rRNA gene region were assembled from each isolate. The organellar genomes of the two strains varied slightly in size due to small differences in intergenic regions with chloroplast genomes of 121,035 bp and 121,482 bp and mitochondrial genomes of 34,639 bp and 34,654 bp. The intraspecific pairwise identities of the chloroplast and mitochondrial genomes of these two isolates were 97.9% and 95.4%, respectively. Multigene phylogenetic analysis demonstrated a close relationship between G. parvulum, Gomphoneis minuta, and Didymosphenia geminata.     

Effects of moderate ammonium enrichment on three submersed macrophytes under contrasting light availability

1. Increased ammonium concentrations and decreased light availability in a water column have been reported to adversely affect submersed vegetation in eutrophic waters worldwide. 2. We studied the chronic effects of moderate enrichment (NH₄–N: 0.16–0.25 mg L^?1) on the growth and carbon and nitrogen metabolism of three macrophytes (Ceratophyllum demersum, Myriophyllum spicatum and Vallisneria natans) under contrasting light availability in a 2‐month experiment. 3. The enrichment greatly increased the contents of free amino acids and nitrogen in the shoot / leaf of the macrophytes. This indicates that was the dominant N source for the macrophytes. 4. Soluble carbohydrate contents remained relatively stable in the shoot / leaf of the macrophytes irrespective of the treatments. Under ambient light, the starch contents in the shoot / leaf of C. demersum and M. spicatum increased with enrichment, whereas V. natans did not exhibit any change. The starch contents decreased in C. demersum, increased in M. spicatum and remained unchanged in V. natans after the combined treatment of enrichment and reduced light. 5. The enrichment did not affect the growth of the three macrophytes under the ambient light. However, it did suppress the growth of C. demersum and M. spicatum under the reduced light. The results indicate that a moderate enrichment was not directly toxic to the macrophytes although it might change their viability in eutrophic lakes in terms of the carbon and nitrogen metabolism.     

Studies supporting the use of mechanical mixing in large scale beer fermentations

Brewing fermentations have traditionally been undertaken without the use of mechanical agitation, with mixing being provided only by the fluid motion induced by the CO₂ evolved during the batch process. This approach has largely been maintained because of the belief in industry that rotating agitators would damage the yeast. Recent studies have questioned this view. At the bench scale, brewer’s yeast is very robust and withstands intense mechanical agitation under aerobic conditions without observable damage as measured by flow cytometry and other parameters. Much less intense mechanical agitation also decreases batch fermentation time for anaerobic beer production by about 25% compared to mixing by CO₂ evolution alone with a small change in the concentration of the different flavour compounds. These changes probably arise for two reasons. Firstly, the agitation increases the relative velocity and the area of contact between the cells and the wort, thereby enhancing the rate of mass transfer to and from the cells. Secondly, the agitation eliminates spatial variations in both yeast concentration and temperature, thus ensuring that the cells are maintained close to the optimum temperature profile during the whole of the fermentation time. These bench scale studies have recently been supported by results at the commercial scale from mixing by an impeller or by a rotary jet head, giving more consistent production without changes in final flavour. It is suggested that this reluctance of the brewing industry to use (adequate) mechanical agitation is another example where the myth of shear damage has had a detrimental effect on the optimal operation of commercial bioprocessing.     

Dependence of mycelial morphology on impeller type and agitation intensity

The influence of the agitation conditions on the morphology of Penicillium chrysogenum (freely dispersed and aggregated forms) was examined using radial (Rushton turbines and paddles), axial (pitched blades, propeller, and Prochem Maxflow T), and counterflow impellers (Intermig). Culture broth was taken from a continuous fermentation at steady state and was agitated for 30 min in an ungassed vessel of 1.4-L working volume. The power inputs per unit volume of liquid in the tank, P/V(L), ranged from 0.6 to 6 kW/m(3). Image analysis was used to measure mycelial morphology. To characterize the intensity of the damage caused by different impellers, the mean total hyphal length (freely dispersed form) and the mean projected area (all dispersed types, i.e., also including aggregates) were used. [In this study, breakage of aggregates was taken into account quantitatively for the first time.]At 1.4-L scale and a given P/V(L), changes in the morphology depended significantly on the impeller geometry. However, the morphological data (obtained with different geometries and various P/V(L)) could be correlated on the basis of equal tip speed and two other, less simple, mixing parameters. One is based on the specific energy dissipation rate in the impeller region, which is simply related to P/V(L) and particular impeller geometrical parameters. The other which is developed in this study is based on a combination of the specific energy dissipation rate in the impeller swept volume and the frequency of mycelial circulation through that volume. For convenience, the function arising from this concept is called the "energy dissipation/circulation" function.To test the broader validity of these correlations, scale-up experiments were carried out in mixing tanks of 1.4, 20, and 180 L using a Rushton turbine and broth from a fed-batch fermentation. The energy dissipation/circulation function was a reasonable correlating parameter for hyphal damage over this range of scales, whereas tip speed, P/V(L), and specific energy dissipation rate in the impeller region were poor. Two forms of the energy dissipation/circulation function were considered, one of which additionally allowed for the numbers of vortices behind the blades of each impeller type. Although both forms were successful at correlating the data for the standard impeller designs considered here, there was preliminary evidence that allowing for the vortices would be valuable. (c) 1996 John Wiley & Sons, Inc.     

Systematic microcarrier screening and agitated culture conditions improves human mesenchymal stem cell yield in bioreactors

Production of human mesenchymal stem cells for allogeneic cell therapies requires scalable, cost‐effective manufacturing processes. Microcarriers enable the culture of anchorage‐dependent cells in stirred‐tank bioreactors. However, no robust, transferable methodology for microcarrier selection exists, with studies providing little or no reason explaining why a microcarrier was employed. We systematically evaluated 13 microcarriers for human bone marrow‐derived MSC (hBM‐MSCs) expansion from three donors to establish a reproducible and transferable methodology for microcarrier selection. Monolayer studies demonstrated input cell line variability with respect to growth kinetics and metabolite flux. HBM‐MSC1 underwent more cumulative population doublings over three passages in comparison to hBM‐MSC2 and hBM‐MSC3. In 100 mL spinner flasks, agitated conditions were significantly better than static conditions, irrespective of donor, and relative microcarrier performance was identical where the same microcarriers outperformed others with respect to growth kinetics and metabolite flux. Relative growth kinetics between donor cells on the microcarriers were the same as the monolayer study. Plastic microcarriers were selected as the optimal microcarrier for hBM‐MSC expansion. HBM‐MSCs were successfully harvested and characterised, demonstrating hBM‐MSC immunophenotype and differentiation capacity. This approach provides a systematic method for microcarrier selection, and the findings identify potentially significant bioprocessing implications for microcarrier‐based allogeneic cell therapy manufacture.     

The cryptoendolithic microbial environment in the Ross Desert of Antarctica: Satellite-transmitted continuous nanoclimate data, 1984 to 1986

Summary A satellite mediated station for monitoring nanoclimate (climate in the millimeter range) data, suitable for use in polar regions is described. The station, located in the Ross desert of Antarctica, has been in operation for more than 3 years, measuring rock temperatures, air temperature, light, snow, wind, and moisture. The data indicate that biological activity in the cryptoendolithic microbial ecosystem is limited to the period from mid November to mid February. The total number of hours of biological activity, based on assumptions of the minimum light, temperature and moisture requirements of the community, is less than 1000 h/year. The time above 0°C, representing more nearly optimal conditions, is between 50 and 550 h/year, depending on the orientation of the surface.Ross desert is an unofficial name for the ice-free region between 160° and 164°E and 76°30 and 78°30S. This area is more generally referred to as the dry valleys     

Extending the rationale of combination therapy to unresponsive erectile dysfunction

Combination therapies aim to overcome the limitations of individual drugs by selecting diverse targets of action to enhance effectiveness synergistically. This article reviews the principles of combination therapy and its applications for benign prostatic hyperplasia and overactive bladder. It then examines pathophysiological, pharmacological, and clinical evidence for currently available drug and device combinations for erectile dysfunction that has not responded to first-line, single-agent therapy.     

Effects of agitation intensity on mycelial morphology and protein production in chemostat cultures of recombinant Aspergillus oryzae

The effects of agitation on fragmentation of a recombinant strain of Aspergillus oryzae and its consequential effects on protein production have been investigated. Constant mass, 5.3-L chemostat cultures at a dilution rate of 0.05 h-1 and a dissolved oxygen level of 75% air saturation, have been conducted at 550, 700, and 1000 rpm. These agitation speeds were chosen to cover a range of specific power inputs (2.2 to 12 kW m-3) from realistic industrial levels to much higher values. The use of a constant mass chemostat linked to a gas blender allowed variation of agitation speed and hence gas hold-up without affecting the dilution rate or the concentration of dissolved oxygen. The morphology of both the freely dispersed mycelia and clumps was characterized using image analysis. Statistical analysis showed that it was possible to obtain steady states with respect to morphology. The mean projected area at each steady state under growing conditions correlated well with the 'energy dissipation/circulation" function, [P/(kD3tc)], where P is the power input, D the impeller diameter, tc the mean circulation time, and k is a geometric constant for a given impeller. Rapid transients of morphological parameters in response to a speed change from 1000 to 550 rpm probably resulted from aggregation. Protein production (alpha-amylase and amyloglucosidase) was found to be independent of agitation speed in the range 550 to 1000 rpm (P/V = 2.2 and 12.6 kW m-3, respectively), although significant changes in mycelial morphology could be measured for similar changes in agitation conditions. This suggests that mycelial morphology does not directly affect protein production (at a constant dilution rate and, therefore, specific growth rate). An understanding of how agitation affects mycelial morphology and productivity would be valuable in optimizing the design and operation of large-scale fungal fermentations for the production of recombinant proteins. Copyright 1999 John Wiley & Sons, Inc.     

Measurement of strain-dependent toxicity in the indene bioconversion using multiparameter flow cytometry

The bionconversion of indene to cis-(1S,2R)-indandiol, a potential key intermediate in the synthesis of Merck's HIV protease inhibitor, CRIXIVAN trade mark, can be achieved using Rhodococcus, Pseudomonas putida, and Escherichia coli strains. This study reports on the application of multiparameter flow cytometry for the measurement of cytoplasmic membrane integrity and membrane depolarization as indicators of toxic effects of the substrate, product, and by-products using each of these strains. Measurements of oxygen uptake rate (OUR) and optical density (OD) as indicators of metabolic activity and biomass growth, respectively, were also made. Measurements of the cytoplasmic membrane potential, cell viability, and respiratory activity provided a sensitive set of parameters to assess toxicity in the indene bioconversion and provided the basis for process improvements and strain selection. The toxic concentrations of the substrate, product, and by-products for each strain have been determined. The results show that it is possible to accumulate cis-(1S,2R)-indandiol and cis-1-amino-2-indanol up to 20 g/L without significant negative effects on cell physiology using any of the strains tested. The Gram-negative P. putida (421-5 and GM 730) and E. coli strains were more resistant to indene and the isolated chemicals of the biotransformation than the Gram-positive Rhodoccoccus I24 strain, possibly due to the presence of the outer membrane and efflux pump mechanisms. P. putida GM 730 and the E. coli TDO 123 strains responded similarly to toxic effects, and the E. coli TDO 123 strain was more resistant than the P. putida 421-5 strain. In addition to the recommendations for strain selection, the identified targets for bioprocess improvement include a combination of genetic as well as process engineering approaches.