Thermal analysis of bacteria by differential scanning calorimetry: relationship of protein denaturation in situ to maximum growth temperature

3D bioprinting optimization of human mesenchymal stromal cell laden gelatin-alginate-collagen bioink

3D bioprinting technology has gained increased attention in the regenerative medicine and tissue engineering communities over the past decade with their attempts to create functional living tissues and organsde novo. While tissues such as skin, bone, and cartilage have been successfully fabricated using 3D bioprinting, there are still many technical and process driven challenges that must be overcome before a complete tissue engineered solution is realized. Although there may never be a single adopted bioprinting process in the scientific community, adherence to optimized bioprinting protocols could reduce variability and improve precision with the goal of ensuring high quality printed constructs. Here, we report on the bioprinting of a gelatin-alginate-collagen bioink containing human mesenchymal stromal cells (hMSCs) which has been optimized to ensure printing consistency and reliability. The study consists of three phases: a pre-printing phase which focuses on bioink characterization; a printing phase which focuses on bioink extrudability/printability, construct stability, and printing accuracy; and a post-processing phase which focuses on the homogeneity and bioactivity of the encapsulated hMSC printed constructs. The results showed that eight identical constructs containing hMSCs could be reliably and accurately printed into stable cross-hatched structures with a single material preparation, and that batch-to-batch consistency was accurately maintained across all preparations. Analysis of the proliferation, morphology, and differentiation of encapsulated hMSCs within the printed constructs showed that cells were able to form large,interconnected colonies and were capable of robust adipogenic differentiation within 14 d of culturing.

Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations

Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in nonmesophilic organisms, however, is currently missing. In this study, thermodynamically constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (Δ_rG'), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures. IMPORTANCE Metabolic flexibility is a central component of any organism's ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to various temperatures. The models predicted differences in metabolic efficiency that were attributed to changes in metabolic pathway utilization and metabolite concentration during growth under optimal and nonoptimal temperatures. Experimental growth measurements were used for model calibration, and temperature-dependent transcriptomic changes corroborated the model-predicted rearrangement of metabolic fluxes. Overall, this study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of an extremophilic organism.

In-depth interrogation of protein thermal unfolding data with MoltenProt

Protein stability is a key factor in successful structural and biochemical research. However, the approaches for systematic comparison of protein stability are limited by sample consumption or compatibility with sample buffer components. Here we describe how miniaturized measurement of intrinsic tryptophan fluorescence (NanoDSF assay) in combination with a simplified description of protein unfolding can be used to interrogate the stability of a protein sample. We demonstrate that improved protein stability measures, such as apparent Gibbs free energy of unfolding, rather than melting temperature Tm , should be used to rank the results of thermostability screens. The assay is compatible with protein samples of any composition, including protein complexes and membrane proteins. Our data analysis software, MoltenProt, provides an easy and robust way to perform characterization of multiple samples. Potential applications of MoltenProt and NanoDSF include buffer and construct optimization for X-ray crystallography and cryo-electron microscopy, screening for small-molecule binding partners and comparison of effects of point mutations.

Differential scanning calorimetry of whole Escherichia coli treated with the antimicrobial peptide MSI-78 indicate a multi-hit mechanism with ribosomes as a novel target

Differential Scanning Calorimetry (DSC) of intact Escherichia coli (E. coli) was used to identify non-lipidic targets of the antimicrobial peptide (AMP) MSI-78. The DSC thermograms revealed that, in addition to its known lytic properties, MSI-78 also has a striking effect on ribosomes. MSI-78’s effect on DSC scans of bacteria was similar to that of kanamycin, an antibiotic drug known to target the 30S small ribosomal subunit. An in vitro transcription/translation assay helped confirm MSI-78’s targeting of ribosomes. The scrambled version of MSI-78 also affected the ribosome peak of the DSC scans, but required greater amounts of peptide to cause a similar effect to the unscrambled peptide. Furthermore, the effect of the scrambled peptide was not specific to the ribosomes; other regions of the DSC thermogram were also affected. These results suggest that MSI-78’s effects on E. coli are at least somewhat dependent on its particular structural features, rather than a sole function of its overall charge and hydrophobicity. When considered along with earlier work detailing MSI-78’s membrane lytic properties, it appears that MSI-78 operates via a multi-hit mechanism with multiple targets.

Nanomaterial transformation and association with fresh and freeze-dried wastewater activated sludge: implications for testing protocol and environmental fate

Engineered nanomaterials (ENMs) are an emerging class of contaminants entering wastewater treatment plants (WWTPs), and standardized testing protocols are needed by industry and regulators to assess the potential removal of ENMs during wastewater treatment. A United States Environmental Protection Agency (USEPA) standard method (OPPTS 835.1110) for estimating soluble pollutant removal during wastewater treatment using freeze-dried, heat-treated (FDH) activated sludge (AS) has been recently proposed for predicting ENM fate in WWTPs. This study is the first to evaluate the use of FDH AS in batch experiments for quantifying ENM removal from wastewater. While soluble pollutants sorbed equally to fresh and FDH AS, fullerene, silver, gold, and polystyrene nanoparticles' removals with FDH AS were approximately 60-100% less than their removals with fresh AS. Unlike fresh AS, FDH AS had a high concentration of proteins and other soluble organics in the liquid phase, an indication of bacterial membrane disintegration due to freeze-drying and heat exposure. This cellular matter stabilized ENMs such that they were poorly removed by FDH AS. Therefore, FDH AS is not a suitable sorbent for estimating nanoparticle removal in WWTPs, whereas fresh AS has been shown to reasonably predict full-scale performance for titanium removal. This study indicates that natural or engineered processes (e.g., anaerobic digestion, biosolids decomposition in soils) that result in cellular degradation and matrices rich in surfactant-like materials (natural organic matter, proteins, phospholipids, etc.) may transform nanoparticle surfaces and significantly alter their fate in the environment.

In vivo characterization of thermal stabilities of Aeropyrum pernix cellular components by differential scanning calorimetry

Revival studies of Aeropyrum pernix show that the viability of cells and cell recovery after heat treatment depends on the temperature of treatment. Differential scanning calorimetry (DSC) is used to analyze the relative thermal stabilities of cellular components of A. pernix and to identify the cellular components responsible for the observed lag phase and reduced maximum growth following a heat treatment. DSC thermograms show 5 visible endothermic transitions with 2 major transitions. DSC analysis of isolated crude ribosomes aids the assignment of the 2 major peaks observed in whole-cell thermograms to denaturation of ribosomal structures. A comparison of partial and immediate full rescan thermograms of A. pernix whole cells indicates that both major peaks represent irreversible thermal transitions. A DNA peak is also identified in the whole-cell thermogram by comparison with the optical data of isolated pure DNA. DNA melting is shown to be irreversible in dilute solution, whereas it is partially reversible in whole cells, owing at least in part, to restricted volume effects. In contrast to mesophilic organisms, hyperthermophilic A. pernix ribosomes are more thermally stable than DNA, but in both organisms, irreversible changes leading to cell death occur owing to ribosomal denaturation.

Chaperones in preventing protein denaturation in living cells and protecting against cellular stress

A variety of cellular internal and external stress conditions can be classified as proteotoxic stresses. Proteotoxic stresses can be defined as stresses that increase the fraction of proteins that are in an unfolded state, thereby enhancing the probability of the formation of intracellular aggregates. These aggregates, if not disposed, can lead to cell death. In response to the appearance of damaged proteins, cells induce the expression of heat shock proteins. These can function as molecular chaperones to prevent protein aggregation and to keep proteins in a state competent for either refolding or degradation. Most knowledge of the function and regulation (by co-factors) of individual heat shock proteins comes from cell free studies on refolding of heat- or chemically denatured, purified proteins. Unlike the experimental situation in a test tube, cells contain multiple chaperones and co-factors often moving in and out different subcompartments that contain a variety of protein substrates at different folding states. Also, within cells folding competes with the degradative machinery. In this chapter, an overview will be provided on how the main cytosolic/nuclear chaperone Hsp70 is regulated, what is known about its interaction with other main cytosolic/nuclear chaperone families (Hsp27, Hsp90, and Hsp110), and how it may function as a molecular chaperone in living mammalian cells to protect against proteotoxic stresses.

Ribosome modulation factor protects Escherichia coli during heat stress, but this may not be dependent on ribosome dimerisation

The role of ribosome modulation factor (RMF) in protecting heat-stressed Escherichia coli cells was identified by the observation that cultures of a mutant strain lacking functional RMF (HMY15) were highly heat sensitive in stationary phase compared to those of the parent strain (W3110). No difference in heat sensitivity was observed between these strains in exponential phase, during which RMF is not synthesised. Studies by differential scanning calorimetry demonstrated that the ribosomes of stationary-phase cultures of the mutant strain had lower thermal stability than those of the parent strain in stationary phase, or exponential-phase ribosomes. More rapid breakdown of ribosomes in the mutant strain during heating was confirmed by rRNA analysis and sucrose density gradient centrifugation. Analyses of ribosome composition showed that the 100S dimers dissociated more rapidly during heating than 70S particles. While ribosome dimerisation is a consequence of the conformational changes caused by RMF binding, it may not therefore be essential for RMF-mediated ribosome stabilisation.

Evaluation of structural changes induced by high hydrostatic pressure in Leuconostoc mesenteroides

Scanning electron microcopy (SEM), transmission electron microscopy (TEM), and differential scanning calorimetry (DSC) were used to evaluate structural changes in Leuconostoc mesenteroides cells as a function of high-hydrostatic-pressure treatment. This bacterium usually grows in chains of cells, which were increasingly dechained at elevated pressures. High-pressure treatments at 250 and 500 MPa also caused changes in the external surface and internal structure of cells. Dechaining and blister formation on the surface of cells increased with pressure, as observed in SEM micrographs. TEM studies showed that cytoplasmic components of the cells were affected by high-pressure treatment. DSC studies of whole cells showed increasing denaturation of ribosomes with pressure, in keeping with dense compacted regions in the cytoplasm of pressure-treated cells observed in TEM micrographs. Apparent reduction of intact ribosomes observed in DSC thermograms was related to the reduction in number of viable cells. The results indicate that inactivation of L. mesenteroides cells is mainly due to ribosomal denaturation observed as a reduction of the corresponding peak in DSC thermograms and condensed interior regions of cytoplasm in TEM micrographs.

Evaluation of high hydrostatic pressure sensitivity of Staphylococcus aureus and Escherichia coli O157:H7 by differential scanning calorimetry

Differential scanning calorimetry (DSC) was used to evaluate the relative high hydrostatic pressure (HHP) resistances of bacterial strains from Staphylococcus aureus and Escherichia coli O157:H7 in vivo. The total apparent enthalpy change and thermal stability were two DSC parameters used to compare bacterial strains of untreated control and pressure-treated bacteria. DSC thermograms indicated that ribosomal denaturation appears to be a major factor in cell death by both thermal and high pressure treatments. However, the analysis of calorimetric data for control samples as well as pressure-treated samples clearly showed that the sensitivities of bacteria to various physical stresses can be different. While S. aureus 765 had a relatively higher resistance to thermal treatment in comparison to S. aureus 485, S. aureus 485 was determined to be more resistant to pressure than S. aureus 765. This information can be utilized in the design of processes specific to targeting certain cellular components by using different physical stresses.

Calorimetric determination of inactivation parameters of micro-organisms

AIMS

This study aimed to apply differential scanning calorimetry (DSC) to evaluate the thermal inactivation kinetics of bacteria.

METHODS AND RESULTS

The apparent enthalpy (DeltaH) of Escherichia coli cells was evaluated by a temperature scan in a DSC after thermal pretreatment in the calorimeter to various temperatures between 56 and 80 degrees C. Conventional semilogarithmic survival curve analysis was combined with a linearly increasing temperature protocol. Calorimetrically determined D and z values were compared to those obtained from plate count data collected under isothermal conditions to validate the new approach.

CONCLUSIONS

The calculated D values using both apparent enthalpy and viability data for cells heat treated in the DSC were similar to the D values obtained from isothermal treatment. Temperatures for 1 through 10-log microbial population reductions, calculated from plate count and enthalpy data, were in agreement within 0.5-2.4 degrees C at a 4 degrees C min-1 heating rate.

SIGNIFICANCE AND IMPACT OF THE STUDY

This novel calorimetric method provides an approach to obtain accurate and reproducible kinetic parameters for inactivation. The calorimetric method here described is time efficient and is conducted under conditions similar to food processing conditions.

Homeostasis of the membrane proton permeability in Bacillus subtilis grown at different temperatures

Bacillus subtilis was grown at its growth temperature limits and at various temperatures in between the lower and upper growth temperature boundary. Liposomes were made of the extracted membrane lipids derived from these cells. The headgroup composition of the cytoplasmic membrane lipids did not differ significantly at the lower (13 degrees C) and upper (50 degrees C) temperature boundary. The averaged lipid acyl chain length, degree of saturation, and ratio of iso- and anteiso-branched fatty acids increased with the temperature. At the temperature of growth, the membranes were in a liquid-crystalline phase, but liposomes derived from cells grown at 13 degrees C were almost threefold more viscous than those derived from 50 degrees C grown cells. The temperature dependence of the proton permeability of the liposomes was determined using the acid-pulse method with monitoring of the outside pH with the fluorescent probe pyranine. The proton permeability of each liposome preparation increased with the temperature. However, the proton permeability of the liposomes at the growth temperature of the cells from which the lipids were derived was almost constant. These data indicate that the growth temperature dependent variation in lipid acyl chain composition permits maintenance of the proton permeability of the cytoplasmic membrane. This 'homeo-proton permeability adaptation' precludes futile cycling of protons at higher growth temperatures and allows cells to sustain the proton motive force as a driving force for essential energy transducing processes.

Hsp70 and Hsp40 chaperone activities in the cytoplasm and the nucleus of mammalian cells

The existence and function of a Hsp40-Hsp70 chaperone machinery in mammalian cells in vivo was investigated. The rate of heat inactivation of firefly luciferase transiently expressed in hamster O23 fibroblasts was analyzed in cells co-transfected with the gene encoding the human Hsp40 (Ohtsuka, K. (1993) Biochem. Biophys. Res. Commun. 197, 235-240), the human inducible Hsp70 (Hunt, C., and Morimoto, R. I. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 6455-6459), or a combination of both. Whereas the expression of human Hsp70 alone in hamster cells was sufficient for the protection of firefly luciferase during heat shock, expression of the human Hsp40 alone was not. Rather, this led to a small but significant increase in the heat sensitivity of luciferase. The expression of the human Hsp40 only led to heat protection when the human Hsp70 was expressed as well. Under such conditions the rate of luciferase reactivation from the heat-inactivated state was increased, but the rate of inactivation during heat shock was not affected. Using constructs that direct firefly luciferase either to the cytoplasm or to the nucleus (Michels, A. A., Nguyen, V.-T., Konings, A. W. T., Kampinga, H. H., and Bensaude, O. (1995) Eur. J. Biochem. 234, 382-389), it was demonstrated that these chaperone functions are found in both compartments. Our data provide the first evidence on how the Hsp40/Hsp70 chaperone complex acts as heat protector in mammalian cells in vivo.

Thermotolerance and nuclear protein aggregation: protection against initial damage or better recovery?

Heat-induced nuclear protein aggregation and subsequent disaggregation were measured in nonpreheated and preheated (thermotolerant) HeLa S3 cells. The effect of thermotolerance on the formation of and recovery from heat-induced nuclear protein aggregates was related to the cellular levels of hsp27, hsp60, hsp70, hsc70, and hsp90. Cells heated at different time points after the thermotolerance trigger showed various levels of protection against heat-induced nuclear protein aggregation. This protection, however, did not parallel the development and decay of thermotolerance on cell survival. The protection was maximal when the thermotolerance level already had started to decay. The level of protection against nuclear protein aggregation did however parallel the cellular level of hsp70 indicating that hsp70 may be involved in this process. At all stages during the development and decay, thermotolerant cells showed a more rapid recovery (disaggregation) from the heat-induced nuclear protein aggregates than non-thermotolerant cells. The rates of disaggregation during development and decay of thermotolerance paralleled the cellular levels of hsp27 suggesting that hsp27 is somehow involved in this recovery process from heat-induced nuclear protein aggregates. The total cellular levels of none of the individual hsp's completely correlate with development and decay of thermotolerance, indicating that overexpression of any of these hsp's alone does not determine the level of thermotolerance. Clonogenic cell survival paralleled the rates of disaggregation, leading to the notion that recovery processes are the most important determinant for the thermotolerant state of HeLa S3 cells. The best correlation with clonogenic survival was found when both initial aggregation and subsequent disaggregation were taken into account, suggesting that the combined action of various hsp's in these two processes have to be included in thermotolerance development and decay.

In vitro transcription close to the melting point of DNA: analysis of Thermotoga maritima RNA polymerase-promoter complexes at 75 degrees C using chemical probes

The interaction of DNA dependent RNA polymerase of the extreme thermophile bacteria Thermotoga maritima with a promoter bearing DNA fragment was investigated in the temperature range from 20 to 85 degrees C. We show that the T. maritima RNA polymerase recognizes and utilizes the Escherichia coli T7 A1 promoter with an efficiency similar to that of the E. coli polymerase. We have investigated the interaction of both polymerases with the same promoter over a wide range of temperatures using hydroxyl radical foot-printing and osmium tetroxide probing. This study revealed that the T. maritima polymerase goes through a series of isomerisation events very similar to the E. coli polymerase, i.e. the closed, intermediate and open complexes, but the transitions themselves occur at radically different temperatures. This indicates that conformational changes in the DNA that accompany initiation of transcription such as promoter melting are determined by the polymerase rather than the DNA sequence.

Heat-induced intranuclear protein aggregation and thermal radiosensitization

In the current study, the hypothesis that thermal radiosensitization is (indirectly) caused by heat-induced denaturation and aggregation of nuclear proteins is further investigated. Thermotolerant rodent cells showed a reduced intranuclear protein aggregation as compared with non-tolerant cells immediately after a heat treatment. This was reflected in the extent of radiosensitization when the cells were X-irradiated immediately after a heat treatment. When heat and radiation were separated in time, a faster disaggregation was found in thermotolerant cells, which was paralleled by a more rapid decline of radiosensitization. Cells transfected with hsp72 showed protection against heat-induced nuclear protein aggregation and reduced thermal radiosensitization. Transfection with hsp27 resulted in an accelerated nuclear protein disaggregation and accelerated decline of thermal radiosensitization. Despite a significant overall correlation between TER and nuclear protein aggregation, the slopes of the correlation curves for the individual cell lines deviated significantly. Yet, the experiments support the hypothesis that radiosensitization is primarily caused by inhibition of DNA repair as a result of the presence of denatured and aggregated proteins in the cell nucleus. Expression of hsps (e.g. in thermotolerant cells), by affecting nuclear protein aggregation, can have an impact on thermal radiosensitization.

Hyperthermia (heat shock)-induced protein denaturation in liver, muscle and lens tissue as determined by differential scanning calorimetry

Protein denaturation has been shown to occur in cells during heat shock and is closely correlated with the cellular responses to hyperthermia; however, little is known about protein denaturation in tissue. This study describes an analysis of endothermic transitions in the hyperthermic region using differential scanning calorimetry (DSC) in liver, white muscle, and lens tissue from Wistar rat, New Zealand white rabbit, and Rainbow trout. Complex DSC profiles consisting of several transitions were obtained for each tissue. Evidence is given that these transitions are due primarily to protein denaturation. Onset temperatures of denaturation (Tl) for rat liver, muscle, and lens are about 38, 39 and 48 degrees C, respectively. Thus, significant protein denaturation occurs in liver and muscle during mild hyperthermia (40-45 degrees C) with lens considerably more stable. The values of Tl for the same tissue from the different animals correlates well with body temperature (rabbit 39.4, rat 38.2, and trout grown at 11 degrees C); Tl increased in the same order as the body temperature for each tissue. Thus, there is correlation between the onset temperature for protein denaturation in these tissues and body temperature.

Differential scanning calorimetric studies of superficial digital flexor tendon degeneration in the horse

Differential scanning calorimetry (DSC) of equine superficial digital flexor tendons revealed the presence of a small exothermic peak at 23 degrees C of unknown origin, and a large endothermic peak at 70 degrees C due to denaturation of cross-linked collagen fibres. In the central degenerated core of damaged tendons the denaturation temperature remained at 70 degrees C but the enthalpy decreased in relation to the extent of degeneration of the tendon. We suggest that this reduction in enthalpy is due to depolymerisation and denaturation of the collagen fibres. This contention is supported by the observed increased activity of the degradative enzyme cathepsin B secreted by the fibroblasts. DSC analysis of cultured porcine tendon fibroblasts revealed a multicomponent endotherm, denaturation beginning at 46 degrees C, a temperature capable of being achieved within the tendon during intensive exercise. DSC clearly has considerable potential in complementing morphological and biochemical studies to determine the aetiology and progress of equine tendon degeneration.

Thermotolerance in mammalian cells. Protein denaturation and aggregation, and stress proteins

Cells that have been pre-exposed to thermal stress can acquire a transient resistance against the killing effect of a subsequent thermal stress. The cause for this phenomenon, called thermotolerance, seems to be an enhanced resistance of proteins against thermal denaturation and aggregation. This resistance can be expressed as an attenuation of damage formation (less initial damage) or as a better repair of the protein damage (facilitated recovery). Heat Shock (or better, Stress) Proteins (HSPs) may play a role in and even be required for thermal resistance. However, rather than stress-induced enhanced synthesis and elevated total levels of HSPs per se, the concentration of, both constitutive and inducible, HSPs at and/or (re)distributed to specific subcellular sites may be the most important factor for the acquisition of thermotolerance. Specific HSPs may be involved either in damage protection or in damage repair.

Heat killing of bacterial spores analyzed by differential scanning calorimetry

Thermograms of the exosporium-lacking dormant spores of Bacillus megaterium ATCC 33729, obtained by differential scanning calorimetry, showed three major irreversible endothermic transitions with peaks at 56, 100, and 114 degrees C and a major irreversible exothermic transition with a peak at 119 degrees C. The 114 degrees C transition was identified with coat proteins, and the 56 degrees C transition was identified with heat inactivation. Thermograms of the germinated spores and vegetative cells were much alike, including an endothermic transition attributable to DNA. The ascending part of the main endothermic 100 degrees C transition in the dormant-spore thermograms corresponded to a first-order reaction and was correlated with spore death; i.e., greater than 99.9% of the spores were killed when the transition peak was reached. The maximum death rate of the dormant spores during calorimetry, calculated from separately measured D and z values, occurred at temperatures above the 73 degrees C onset of thermal denaturation and was equivalent to the maximum inactivation rate calculated for the critical target. Most of the spore killing occurred before the release of most of the dipicolinic acid and other intraprotoplast materials. The exothermic 119 degrees C transition was a consequence of the endothermic 100 degrees C transition and probably represented the aggregation of intraprotoplast spore components. Taken together with prior evidence, the results suggest that a crucial protein is the rate-limiting primary target in the heat killing of dormant bacterial spores.