Dynamic flux balance analysis (DFBA) is an extension of classical flux balance analysis that allows the dynamic effects of the extracellular environment on microbial metabolism to be predicted and optimised. Recently this computational framework has been extended to microbial communities for which the individual species are known and genome-scale metabolic reconstructions are available. In this review, the authors provide an overview of the emerging DFBA approach with a focus on two case studies involving the conversion of mixed hexose/pentose sugar mixtures by synthetic microbial co-culture systems. These case studies illustrate the key requirements of the DFBA approach, including the incorporation of individual species metabolic reconstructions, formulation of extracellular mass balances, identification of substrate uptake kinetics, numerical solution of the coupled linear program/differential equations and model adaptation for common, suboptimal growth conditions and identified species interactions. The review concludes with a summary of progress to date and possible directions for future research.
Second generation lipid systems for the delivery of bioactive compounds have been developed by mixing a liquid carrier oil with a solid lipid to form so-called nanostructured lipid carriers (NLCs). In this study, we investigated the effect of different liquid carrier oils on the crystallization and aggregation behavior of tristearin NLC dispersions. We found that NLC suspension stability was strongly affected by the type and amount of the carrier oil. As the oil concentration was increased, the crystallization and melting temperatures decreased, the polymorphic transformation rate increased, the particles became more spherical, and suspension stability was enhanced. These results suggest that oil trapped within the growing crystal matrix accelerated polymorphic transformation but retarded the large shape change normally associated with the transformation. We also found that considerably less surfactant was necessary to produce stable NLC suspensions than was required to stabilize solid lipid nanoparticle (SLN) suspensions without a carrier oil. Based on preliminary simulation results, we hypothesized that improved NLC suspension stability was attributable to both reduced particle shape change, which created less new surface area to be covered by surfactant, and increased mobility of surfactant molecules, which resulted in available surfactant being more efficient at covering created surface area.
Kidney disease is an important cause of morbidity and mortality in patients with sickle cell anemia (SCA). The factors that affect progression of renal disease are unknown, especially in children and adolescents. Alterations in blood pressure, including hypertension and lack of the normal nocturnal dip in blood pressure, are important determinants of diabetic nephropathy and other renal diseases and may play a role in sickle cell nephropathy. Our primary hypothesis was that children with SCA who have microalbuminuria will demonstrate less nocturnal dipping of blood pressure compared to patients without microalbuminuria. We also investigated other potential factors associated with microalbuminuria.
Molecularly-guided trials (i.e. PMed) now seek to aid clinical decision-making by matching cancer targets with therapeutic options. Progress has been hampered by the lack of cancer models that account for individual-to-individual heterogeneity within and across cancer types. Naturally occurring cancers in pet animals are heterogeneous and thus provide an opportunity to answer questions about these PMed strategies and optimize translation to human patients. In order to realize this opportunity, it is now necessary to demonstrate the feasibility of conducting molecularly-guided analysis of tumors from dogs with naturally occurring cancer in a clinically relevant setting.
We performed a preliminary study involving 10 dogs to assess the applicability of body MRI for staging of canine diffuse hematopoietic neoplasia. T1-weighted (before and after intravenous gadolinium), T2-weighted, in-phase, out-of-phase, and short tau inversion recovery pulse sequences were used. By using digital region of interest (ROI) and visual comparison techniques, relative parenchymal organ (medial iliac lymph nodes, liver, spleen, kidney cortex, and kidney medulla) signal intensity was quantified as less than, equal to, or greater than that of skeletal muscle in 2 clinically normal young adult dogs and 10 dogs affected with either B-cell lymphoma (n = 7) or myelodysplastic syndrome (n = 3). Falciform fat and urinary bladder were evaluated to provide additional perspective regarding signal intensity from the pulse sequences. Dogs with nonfocal disease could be distinguished from normal dogs according to both the visual and ROI signal-intensity relationships. In normal dogs, liver signal intensity on the T2-weighted sequence was greater than that of skeletal muscle by using either the visual or ROI approach. However in affected dogs, T2-weighted liver signal intensity was less than that of skeletal muscle by using either the ROI approach (10 of 10 dogs) or the visual approach (9 of 10 dogs). These findings suggest that the comparison of relative signal intensity among organs may have merit as a research model for infiltrative parenchymal disease (ROI approach) or metabolic effects of disease; this comparison may have practical clinical applicability (visual comparison approach) as well.
A key step in any process that converts lignocellulose to biofuels is the efficient fermentation of both hexose and pentose sugars. The co-culture of respiratory-deficient Saccharomyces cerevisiae and wild-type Scheffersomyces stipitis has been identified as a promising system for microaerobic ethanol production because S. cerevisiae only consumes glucose while S. stipitis efficiently converts xylose to ethanol.
This association study of Eucalyptus pilularis populations provides empirical evidence for the role of Pectin Methylesterase (PME) in influencing solid wood characteristics of Eucalyptus. PME6 was primarily associated with the shrinkage and collapse of drying timber, which are phenotypic traits consistent with the role of pectin as a hydrophilic polysaccharide. PME7 was primarily associated with cellulose and pulp yield traits and had an inverse correlation with lignin content. Selection of specific alleles in these genes may be important for improving trees as sources of high-quality wood products. A heterozygote advantage was postulated for the PME7 loci and, in combination with haplotype blocks, may explain the absence of a homozygous class at all single-nucleotide polymorphisms investigated in this gene.
To evaluate and compare circulating concentrations of islet amyloid polypeptide (IAPP), insulin, and glucose in nondiabetic cats classified by body condition score (BCS) and in cats with naturally occurring diabetes mellitus.
The nature of plant cells to grow as multicellular aggregates in suspension culture has profound effects on bioprocess performance. Recent advances in the measurement of plant cell aggregate size allow for routine process monitoring of this property. We have exploited this capability to develop a conceptual model to describe changes in the aggregate size distribution that are observed over the course of a Taxus cell suspension batch culture. We utilized the population balance equation framework to describe plant cell aggregates as a particulate system, accounting for the relevant phenomenological processes underlying aggregation, such as growth and breakage. We compared model predictions to experimental data to select appropriate kernel functions, and found that larger aggregates had a higher breakage rate, biomass was partitioned asymmetrically following a breakage event, and aggregates grew exponentially. Our model was then validated against several datasets with different initial aggregate size distributions and was able to quantitatively predict changes in total biomass and mean aggregate size, as well as actual size distributions. We proposed a breakage mechanism where a fraction of biomass was lost upon each breakage event, and demonstrated that even though smaller aggregates have been shown to produce more paclitaxel, an optimum breakage rate was predicted for maximum paclitaxel accumulation. We believe this is the first model to use a segregated, corpuscular approach to describe changes in the size distribution of plant cell aggregates, and represents an important first step in the design of rational strategies to control aggregation and optimize process performance.
We developed a multicellular model of the mammalian circadian clock characterized by a high degree of heterogeneity with respect to single cell periodicity and behavior (intrinsic and driven oscillators), neurotransmitter release (VIP, GABA and glutamate synthesis) and spatial organization (core and shell regions), mimicking structural patterns within the suprachiasmatic nucleus (SCN) associated with distinct circadian functions. We simulated the SCN core and shell separately utilizing experimentally derived connectivity schemes for the two subdivisions as observed within the rat SCN. The core was modeled via a small world network characterized by VIP and GABA co-localization, whereas the shell was simulated as a nearest neighbor network promoting local GABAergic connections. To study the function of the axonal plexus extending from the densely innervated ventrolateral region to distal areas across the dorsomedial SCN, directed long range links from the core to the shell were gradually introduced via a probability p(cs) that ranged from 0 to 1. A probability value of 0 excluded core-shell interactions, whereas p(cs)=1 achieved maximal connectivity between the two regions. Our model exhibited a threshold in the number of core-to-shell links required for sufficient cell-to-cell coordination to maintain periodicity and rhythmic behavior across the entire model network (including both shell and core populations) in constant darkness as well as 12:12h light-dark cycles. By contrast, constant light was shown to increase phase synchronization across the shell while core populations remained poorly synchronized, suggesting differential light response across the two SCN compartments. We further simulated increasing percentages of intrinsic oscillators and demonstrated a negative correlation between the number of intrinsic oscillators distributed across the SCN and the ability of the system to produce synchronized signals. Simulations that differed with respect to the placement of intrinsic oscillators supported the hypothesis that improved synchronization is achieved with networks characterized by localized intrinsic oscillators placed exclusively within the shell versus networks containing uniformly distributed intrinsic oscillators in both SCN compartments. This study has successfully reproduced a number of spatiotemporal and behavioral attributes of the SCN, providing a useful computational tool to correlate observed circadian phenotypes with distinct chemoarchitectural properties of spatially localized neural populations.
Current researches into the production of biochemicals from lignocellulosic feedstocks are focused on the identification and engineering of individual microbes that utilize complex sugar mixtures. Microbial consortia represent an alternative approach that has the potential to better exploit individual species capabilities for substrate uptake and biochemical production. In this work, we construct and experimentally validate a dynamic flux balance model of a Saccharomyces cerevisiae and Escherichia coli co-culture designed for efficient aerobic consumption of glucose/xylose mixtures. Each microbe is a substrate specialist, with wild-type S. cerevisiae consuming only glucose and engineered E. coli strain ZSC113 consuming only xylose, to avoid diauxic growth commonly observed in individual microbes. Following experimental identification of a common pH and temperature for optimal co-culture batch growth, we demonstrate that pure culture models developed for optimal growth conditions can be adapted to the suboptimal, common growth condition by adjustment of the non-growth associated ATP maintenance of each microbe. By comparing pure culture model predictions to co-culture experimental data, the inhibitory effect of ethanol produced by S. cerevisiae on E. coli growth was found to be the only interaction necessary to include in the co-culture model to generate accurate batch profile predictions. Co-culture model utility was demonstrated by predicting initial cell concentrations that yield simultaneous glucose and xylose exhaustion for different sugar mixtures. Successful experimental validation of the model predictions demonstrated that steady-state metabolic reconstructions developed for individual microbes can be adapted to develop dynamic flux balance models of microbial consortia for the production of renewable chemicals.
Sequential uptake of pentose and hexose sugars that compose lignocellulosic biomass limits the ability of pure microbial cultures to efficiently produce value-added bioproducts. In this work, we used dynamic flux balance modeling to examine the capability of mixed cultures of substrate-selective microbes to improve the utilization of glucose/xylose mixtures and to convert these mixed substrates into products. Co-culture simulations of Escherichia coli strains ALS1008 and ZSC113, engineered for glucose and xylose only uptake respectively, indicated that improvements in batch substrate consumption observed in previous experimental studies resulted primarily from an increase in ZSC113 xylose uptake relative to wild-type E. coli. The E. coli strain ZSC113 engineered for the elimination of glucose uptake was computationally co-cultured with wild-type Saccharomyces cerevisiae, which can only metabolize glucose, to determine if the co-culture was capable of enhanced ethanol production compared to pure cultures of wild-type E. coli and the S. cerevisiae strain RWB218 engineered for combined glucose and xylose uptake. Under the simplifying assumption that both microbes grow optimally under common environmental conditions, optimization of the strain inoculum and the aerobic to anaerobic switching time produced an almost twofold increase in ethanol productivity over the pure cultures. To examine the effect of reduced strain growth rates at non-optimal pH and temperature values, a break even analysis was performed to determine possible reductions in individual strain substrate uptake rates that resulted in the same predicted ethanol productivity as the best pure culture.
We developed a multicellular model characterized by a high degree of heterogeneity to investigate possible mechanisms that underlie circadian network synchronization and rhythmicity in the suprachiasmatic nucleus (SCN). We populated a two-dimensional grid with 400 model neurons coupled via ?-aminobutyric acid (GABA) and vasoactive intestinal polypeptide (VIP) neurotransmitters through a putative Ca(2+) mediated signaling cascade to investigate their roles in gene expression and electrical firing activity of cell populations. As observed experimentally, our model predicted that GABA would affect the amplitude of circadian oscillations but not synchrony among individual oscillators. Our model recapitulated experimental findings of decreased synchrony and average periods, loss of rhythmicity, and reduced circadian amplitudes as VIP signaling was eliminated. In addition, simulated increases of VIP reduced periodicity and synchrony. We therefore postulated a physiological range of VIP within which the system is able to produce sustained and synchronized oscillations. Our model recapitulated experimental findings of diminished amplitudes and periodicity with decreasing intracellular Ca(2+) concentrations, suggesting that such behavior could be due to simultaneous decrease of individual oscillation amplitudes and population synchrony. Simulated increases in Cl(-) levels resulted in increased Cl(-) influx into the cytosol, a decrease of inhibitory postsynaptic currents, and ultimately a shift of GABA-elicited responses from inhibitory to excitatory. The simultaneous reduction of IPSCs and increase in membrane resting potential produced GABA dose-dependent increases in firing rates across the population, as has been observed experimentally. By integrating circadian gene regulation and electrophysiology with intracellular and intercellular signaling, we were able to develop the first (to our knowledge) multicellular model that allows the effects of clock genes, electrical firing, Ca(2+), GABA, and VIP on circadian system behavior to be predicted.
Plant cell aggregates have long been implicated in affecting cellular metabolism in suspension culture, yet the rigorous characterization of aggregate size as a process variable and its effect on bioprocess performance has not been demonstrated. Aggregate fractionation and analysis of biomass-associated product is commonly used to assess the effect of aggregation, but we establish that this method is flawed under certain conditions and does not necessarily agree with comprehensive studies of total culture performance. Leveraging recent advances to routinely measure aggregate size distributions, we developed a simple method to manipulate aggregate size and evaluate its effect on the culture as a whole, and found that Taxus suspension cultures with smaller aggregates produced significantly more paclitaxel than cultures with larger aggregates in two cell lines over a range of aggregate sizes, and where biomass accumulation was equivalent before elicitation with methyl jasmonate. Taxus cuspidata (T. cuspidata) P93AF cultures with mean aggregate sizes of 690 and 1,100 ?m produced 22 and 11 mg/L paclitaxel, respectively, a twofold increase for smaller aggregates, and T. cuspidata P991 cultures with mean aggregate sizes of 400 and 840 ?m produced 6 and 0.3 mg/L paclitaxel, respectively, an increase of 20-fold for smaller aggregates. These results demonstrate the importance of validating experiments aimed at a specific phenomenon with total process studies, and provide a basis for treating aggregate size as a targeted process variable for rational control strategies.
Plant cells grow as aggregates in suspension culture, but little is known about the dynamics of aggregation, and no routine methodology exists to measure aggregate size. In this study, we evaluate several different methods to characterize aggregate size in Taxus suspension cultures, in which aggregate diameters range from 50 to 2,000 microm, including filtration and image analysis, and develop a novel method using a specially equipped Coulter counter system. We demonstrate the suitability of this technology to measure plant cell culture aggregates, and show that it can be reliably used to measure total biomass accumulation compared to standard methods such as dry weight. Furthermore, we demonstrate that all three methods can be used to measure an aggregate size distribution, but that the Coulter counter is more reliable and much faster, and also provides far better resolution. While absolute measurements of aggregate size differ based on the three evaluation techniques, we show that linear correlations are sufficient to account for these differences (R(2) > 0.99). We then demonstrate the utility of the novel Coulter counter methodology by monitoring the dynamics of a batch process and find that the mean aggregate size increases by 55% during the exponential growth phase, but decreases during stationary phase. The results indicate that the Coulter counter method can be routinely used for advanced process characterization, particularly to study the relationship between aggregate size and secondary metabolite production, as well as a source of reliable experimental data for modeling aggregation dynamics in plant cell culture.
The suprachiasmatic nucleus (SCN) of the hypothalamus is a multicellular system that drives daily rhythms in mammalian behavior and physiology. Although the gene regulatory network that produces daily oscillations within individual neurons is well characterized, less is known about the electrophysiology of the SCN cells and how firing rate correlates with circadian gene expression. We developed a firing rate code model to incorporate known electrophysiological properties of SCN pacemaker cells, including circadian dependent changes in membrane voltage and ion conductances. Calcium dynamics were included in the model as the putative link between electrical firing and gene expression. Individual ion currents exhibited oscillatory patterns matching experimental data both in current levels and phase relationships. VIP and GABA neurotransmitters, which encode synaptic signals across the SCN, were found to play critical roles in daily oscillations of membrane excitability and gene expression. Blocking various mechanisms of intracellular calcium accumulation by simulated pharmacological agents (nimodipine, IP3- and ryanodine-blockers) reproduced experimentally observed trends in firing rate dynamics and core-clock gene transcription. The intracellular calcium concentration was shown to regulate diverse circadian processes such as firing frequency, gene expression and system periodicity. The model predicted a direct relationship between firing frequency and gene expression amplitudes, demonstrated the importance of intracellular pathways for single cell behavior and provided a novel multiscale framework which captured characteristics of the SCN at both the electrophysiological and gene regulatory levels.
The suprachiasmatic nucleus (SCN) of the hypothalamus is a multioscillator system that drives daily rhythms in mammalian behavior and physiology. Based on recent data implicating vasoactive intestinal polypeptide (VIP) as the key intercellular synchronizing agent, we developed a multicellular SCN model to investigate the effects of cellular heterogeneity and intercellular connectivity on circadian behavior. A 2-dimensional grid was populated with 400 model cells that were heterogeneous with respect to their uncoupled rhythmic behavior (intrinsic and damped pacemakers with a range of oscillation periods) and VIP release characteristics (VIP producers and nonproducers). We constructed small-world network architectures in which local connections between VIP producing cells and their 4 nearest neighbors were augmented with random connections, resulting in long-range coupling across the grid. With only 10% of the total possible connections, the small-world network model was able to produce similar phase synchronization indices as a mean-field model with VIP producing cells connected to all other cells. Partial removal of random connections decreased the synchrony among neurons, the amplitude of VIP and cAMP response element binding protein oscillations, the mean period of intrinsic periods across the population, and the percentage of oscillating cells. These results indicate that small-world connectivity provides the optimal compromise between the number of connections and control of circadian amplitude and synchrony. This model predicts that small decreases in long-range VIP connections in the SCN could have dramatic effects on period and amplitude of daily rhythms, features commonly described with aging.
The conversion of sustainable energy crops using microbiological fermentation to biofuels and bioproducts typically uses submerged-state processes. Alternatively, solid-state fermentation processes have several advantages when compared to the typical submerged-state processes. This study compares the use of solid-state versus submerged-state fermentation using the mesophilic anaerobic bacterium Clostridium phytofermentans in the conversion of switchgrass to the end products of ethanol, acetate, and hydrogen. A shift in the ratio of metabolic products towards more acetate and hydrogen production than ethanol production was observed when C. phytofermentans was grown under solid-state conditions as compared to submerged-state conditions. Results indicated that the end product concentrations (in millimolar) obtained using solid-state fermentation were higher than using submerged-state fermentation. In contrast, the total fermentation products (in weight of product per weight of carbohydrates consumed) and switchgrass conversion were higher for submerged-state fermentation. The conversion of xylan was greater than glucan conversion under both fermentation conditions. An initial pH of 7 and moisture content of 80 % resulted in maximum end products formation. Scanning electron microscopy study showed the presence of biofilm formed by C. phytofermentans growing on switchgrass under submerged-state fermentation whereas bacterial cells attached to surface and no apparent biofilm was observed when grown under solid-state fermentation. To our knowledge, this is the first study reporting consolidated bioprocessing of a lignocellulosic substrate by a mesophilic anaerobic bacterium under solid-state fermentation conditions.
The detection of environmental enterococci has been determined primarily by using culture-based techniques that might exclude some enterococcal species as well as those that are nonculturable. To address this, the relative abundances of enterococci were examined by challenging fecal and water samples against a currently available genus-specific assay (Entero1). To determine the diversity of enterococcal species, 16S rRNA gene-based group-specific quantitative PCR (qPCR) assays were developed and evaluated against eight of the most common environmental enterococcal species. Partial 16S rRNA gene sequences of 439 presumptive environmental enterococcal strains were analyzed to study further the diversity of enterococci and to confirm the specificities of group-specific assays. The group-specific qPCR assays showed relatively high amplification rates with targeted species (>98%), although some assays cross-amplified with nontargeted species (1.3 to 6.5%). The results with the group-specific assays also showed that different enterococcal species co-occurred in most fecal samples. The most abundant enterococci in water and fecal samples were Enterococcus faecalis and Enterococcus faecium, although we identified more water isolates as Enterococcus casseliflavus than as any of the other species. The prevalence of the Entero1 marker was in agreement with the combined number of positive signals determined by the group-specific assays in most fecal samples, except in gull feces. On the other hand, the number of group-specific assay signals was lower in all water samples tested, suggesting that other enterococcal species are present in these samples. While the results highlight the value of genus- and group-specific assays for detecting the major enterococcal groups in environmental water samples, additional studies are needed to determine further the diversity, distributions, and relative abundances of all enterococcal species found in water.
The demand for biofuel ethanol made from clean, renewable nonfood sources is growing. Cellulosic biomass, such as switch grass (Panicum virgatum L.), is an alternative feedstock for ethanol production; however, cellulosic feedstock hydrolysates contain high levels of xylose, which needs to be converted to ethanol to meet economic feasibility. In this study, the effects of xylose isomerase on cell growth and ethanol production from biomass sugars representative of switch grass were investigated using low cell density cultures. The lager yeast species Saccharomyces pastorianus was grown with immobilized xylose isomerase in the fermentation step to determine the impact of the glucose and xylose concentrations on the ethanol production rates. Ethanol production rates were improved due to xylose isomerase; however, the positive effect was not due solely to the conversion of xylose to xylulose. Xylose isomerase also has glucose isomerase activity, so to better understand the impact of the xylose isomerase on S. pastorianus, growth and ethanol production were examined in cultures provided fructose as the sole carbon. It was observed that growth and ethanol production rates were higher for the fructose cultures with xylose isomerase even in the absence of xylose. To determine whether the positive effects of xylose isomerase extended to other yeast species, a side-by-side comparison of S. pastorianus and Saccharomyces cerevisiae was conducted. These comparisons demonstrated that the xylose isomerase increased ethanol productivity for both the yeast species by increasing the glucose consumption rate. These results suggest that xylose isomerase can contribute to improved ethanol productivity, even without significant xylose conversion.
Solid lipid nanoparticles (SLNs) have applications in drug delivery and the encapsulation of bioactive, lipophilic compounds. However, SLNs tend to aggregate when stored due to the lipid crystals undergoing a polymorphic transformation from the unstable ? form to the stable ? form. We developed a population balance equation (PBE) model for prediction of average polymorph content and aggregate size distribution to better understand this undesirable behavior. Experiments with SLNs stored at room temperature showed that polymorphic transformation was the rate determining step for our system, SLNs with smaller initial size distributions aggregated more rapidly, and aggregates contained particles with both ? and ? crystals. Using parameter values estimated from our data, the PBE model was able to capture the bimodal nature of aggregate size distributions, the ?-to-? polymorph ratio, and the faster aggregation dynamics of SLNs with smaller initial size distributions. However, the model was unable to adequately capture the fast disappearance rate of primary particles, the broad size distributions of formed aggregates, and the significant ? content of aggregating particles. These discrepancies suggest that a PBE model which accounts for polymorph content as an internal variable along with aggregate size may be required to better reproduce experimental observations.
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