Fourier analysis and systems identification of the p53 feedback loop

Cytosolic [Ca2+]i was measured using a microspectrofluorimetric technique. Prostaglandin F2 alpha (PGF2 alpha, 10(-6) M) transiently increased the concentration of free cytosolic Ca2+ ([Ca2+]i) in individual rat and human granulosa cells. In a study examining a total of 170 individual rat and human granulosa cells, approximately 100% of rat granulosa cells and 80% of human granulosa cells tested responded to PGF2 alpha (10(-6) M). In a dose-response trial, the magnitude of the [Ca2+]i response did not vary, although a decreasing number of cells responded to decreasing PGF2 alpha concentrations (10(-5) to 10(-9) M). PGE2 (10(-4) to 10(-6) M) did not affect [Ca2+]i in rat or human granulosa cells. GnRH (10(-6) M) increased [Ca2+]i in rat but not human granulosa cells. Over 90% of rat granulosa cells tested responded. Angiotensin II (ANG II, 10(-5) M) increased [Ca2+]i in approximately 25% of rat, but not human granulosa cells. Individual rat granulosa cells which responded to GnRH responded to PGF2 alpha and vice versa. Individual rat granulosa cells which responded to ANG II responded to PGF2 alpha and GnRH. Conversely, less than 30% of individual rat granulosa cells which responded to PGF2 alpha and GnRH responded to ANG II. Desensitization (pretreatment) of rat granulosa cells by continuous hormone perifusion suggested that effects of PGF2 alpha, GnRH, and ANG II on [Ca2+]i were receptor specific. However, the effects of combined hormone treatments on [Ca2+]i were not additive. The transient increase in [Ca2+]i in response to PGF2 alpha or GnRH, alone, may be maximal. Results of this study suggested that effects of PGF2 alpha, GnRH, and ANG II receptor-ligand interactions may be at least partially mediated by transient increases in [Ca2+]i in rat granulosa cells. Similarly, effects of PGF2 alpha, but not GnRH or ANG II, receptor-ligand interactions may be mediated by transient increases in [Ca2+]i in human granulosa cells.

Stochastic δN formalism is a powerful tool to calculate the cosmological correlators non-perturbatively. However, it requires the initial data for the amplitude of the noise on the initial flat hypersurface which for a free theory during inflation is fixed to be H/2π. In this work, we study the setups where the underlying theory involves interactions and the stochastic noises inherit these interactions. We extend the stochastic δN formalism to these setups and rewrite the corresponding Langevin and Fokker-Planck equations in which the QFT corrections in the amplitude of the noises are taken into account. As an example, in the three-phase SR-USR-SR setup which is employed for PBHs formation, the modification in the amplitude of noise is calculated from the one-loop corrections in power spectrum via in-in formalism. We show that in these setups the amplitude of the stochastic noise is modified to H/2π(1+ Δ𝒫ℛ/𝒫(0) ℛ)1/2 in which Δ𝒫ℛ/𝒫(0) ℛ is the fractional one-loop correction in power spectrum.

The p53 network is perhaps the most important pathway involved in preventing the initiation of cancer, p53 levels and activity are upregulated in response to various stresses including DNA damage, hypoxia, and oncogene activation. Active p53 initiates different transcriptional programs that result in cell cycle arrest, cellular senescence or apoptosis. p53 also activates the transcription of Mdm2, which in turns target p53 for degradation, therefore creating a negative feedback loop on p53. Previous studies showed that the level of p53 increased dramatically after exposure to damaging radiation, then declined in a series of damped oscillations. Recent quantitative studies examined p53 responses in individual living cells, using time-lapse fluorescent microscopy and showed that-on an individual cell level-the oscillations are not damped. Instead, one cell may have only one pulse of p53, while its neighbor may show several repeated pulses. As the amount of irradiation increased, the percentage of cells showing a high number of p53 pulses also increased. The mean height and width of the pulses was constant and did not depend on the damage level. These observations opened new questions regarding the mechanism and function of p53 oscillatory dynamics. In this chapter I will review the different models that have been suggested for p53 oscillations, including proposed reasons for variation between cells, and will discuss potential functions for oscillatory dynamics in the p53 signaling pathway and in stress responses in general.

Fluorescence digital imaging microscopy (FDIM) has been used to perform a cell cycle analysis of both the amount and the distribution of nuclear DNA topoisomerase I in individual CEM human leukemia cells. Cells were stained by indirect immunofluorescence methods using a polyclonal antiserum generated with a 21-amino-acid peptide representing amino acids 219-239 of human topoisomerase I. Immunohistochemical staining was followed by staining with Hoechst dye 33342, allowing DNA content to be determined in each cell. Cell cycle analysis showed that nuclear topoisomerase I content doubled (2.2-fold increase) as the cells progressed from G1 to G2/M phases of the cell cycle. However, when normalized for nuclear size, topoisomerase I content per nuclear area remained almost constant (1.3-fold increase). For comparison, we measured the amount of proliferating cell nuclear antigen (PCNA), a protein whose expression fluctuates during the cell cycle. Nuclear PCNA content increased 2.7-fold from G1 to S phase, then declined in G2/M- phases, whereas PCNA content per nuclear area increased 1.7-fold from G1 to S phase. We also measured topoisomerase I content in leucine-deprived cells to determine if altered growth conditions affect topoisomerase I protein expression. Compared to CEM cells in logarithmic growth, leucine-deprived CEM cells had 1.8-fold less topoisomerase I content per nuclear area. Subnuclear distribution studies of proliferating CEM cells showed topoisomerase I to be localized predominantly in the nucleoli throughout the cell cycle. In contrast, leucine-deprived cells exhibited a perinuclear distribution of topoisomerase I. Our results show that FDIM is a useful technique in determining the cell cycle position and both the content and the distribution of topoisomerase I as well as other nuclear proteins in individual cells.

There is a close relationship between the mechanical properties of cells and their physiological function. Non-invasive measurements of the physical properties of cells, especially of adherent cells, are challenging to perform. Through a non-contact optical interferometric technique, we measure and combine the phase, amplitude, and frequency of vibrating silicon pedestal micromechanical resonant sensors to quantify the “loss tangent” of individual adherent human colon cancer cells (HT-29). The loss tangent, a dimensionless ratio of viscoelastic energy loss and energy storage — a measure of the viscoelasticity of soft materials, obtained through an optical path length model, was found to be 1.88 0.08 for live cells and 4.32 0.13 for fixed cells, revealing significant changes (p < 0.001) in mechanical properties associated with estimated nanoscale cell membrane fluctuations of 3.86 0.2 nm for live cells and 2.87 0.1 nm for fixed cells. By combining these values with the corresponding two-degree-of-freedom Kelvin-Voigt model, we obtain the elastic stiffness and viscous loss associated with each individual cell rather than estimations from a population. The technique is unique as it decouples the heterogeneity of individual cells in our population and further refines the viscoelastic solution space.

H2AX phosphorylation at Ser139 (formation of γ-H2AX) is an indicator of double-strand breaks in DNA (DSBs) after the action of different genotoxic stresses, including ionizing radiation, environmental agents, and chemotherapy drugs. The sites of DSBs can be visualized as focal sites of γ-H2AX using antibodies and immunofluorescence microscopy. The microscopy technique is the most sensitive method of DSB detection in individual cells. It is useful for experimental research, radiation biodosimetry, and clinical practice. In this chapter, we provide an immunochemical protocol for γ-H2AX labeling and analysis by confocal microscopy. The advantage of the assay is that it enables the quantitation of γ-H2AX foci in individual cells in different phases of the cell cycle.

How can cells shape and utilize dynamic gene regulation to enable complex cellular behaviors? I study this question in natural and synthetic contexts. The first project studies how a natural genetic network can imbue cells with a sense of ‘time’. It has long been known that environmental signals induce diverse cellular differentiation programs. In certain systems, cells defer differentiation for extended time periods after the signal appears, proliferating through multiple rounds of cell division before committing to a new fate. How can cells set a deferral time much longer than the cell cycle? Here we study Bacillus subtilis cells that respond to sudden nutrient limitation with multiple rounds of growth and division before differentiating into spores. A well characterized genetic circuit controls the concentration and phosphorylation of the master regulator Spo0A, which rises to a critical concentration to initiate sporulation. However, it remains unclear how this circuit enables cells to defer sporulation for multiple cell cycles. Using quantitative time-lapse fluorescence microscopy of Spo0A dynamics in individual cells, we observed pulses of Spo0A phosphorylation at a characteristic cell cycle phase. Pulse amplitudes grew systematically and cell-autonomously over multiple cell cycles leading up to sporulation. This pulse growth required a key positive feedback loop involving the sporulation kinases, without which the deferral of sporulation became ultrasensitive to kinase expression. Thus, deferral is controlled by a pulsed positive feedback loop in which kinase expression is activated by pulses of Spo0A phosphorylation. This pulsed positive feedback architecture provides a more robust mechanism for setting deferral times than constitutive kinase expression. Finally, using mathematical modeling, we show how pulsing and time delays together enable ‘polyphasic’ positive feedback, in which different parts of a feedback loop are active at different times. Polyphasic feedback can enable more accurate tuning of long deferral times. Together, these results suggest that Bacillus subtilis uses a pulsed positive feedback loop to implement a timer that operates over time scales much longer than a cell cycle. The second project proposes a method to rapidly generate and test complex genetic network dynamics in living cells. Existing microorganisms have evolved genetic circuitry to meet diverse challenges and maximize their survival and fitness. These challenges arise from external environmental pressures, or internal evolved constraints. Furthermore, these challenges may be either static or dynamic in nature. While existing circuits have likely evolved to be ‘good enough’ to respond to historical challenges, it remains unclear if they can be improved upon, and whether they respond well to novel situations. Synthetic biology seeks to engineer organisms with complex novel phenotypes, both to harness these novel organisms for a function and to understand their underlying biology. Dynamic gene expression strategies may be necessary to successfully generate these phenotypes. Unfortunately, generating novel dynamic gene expression patterns with conventional genetic engineering remains a challenge. Here I propose and describe progress towards a computerized feedback control setup to enable the programming and rapid testing of dynamic gene regulatory patterns in living cells. Small sets of genes will be regulated optogenetically based on programmed control laws, and past and present cellular state. This setup will enable us to explore the functions and limits of engineered dynamic gene regulation, while hopefully, in the process, providing lessons about the underlying biology.

In situ (6-4)photoproduct determination by laser cytometry and autoradiography

Presented here are the methods used for detection of short, single-copy DNA sequences within human cells. These methods rely on (1) peptide nucleic acid (PNA) invasion of the target double-stranded DNA site to locally open a small single-stranded region within long DNA duplex, (2) site-specific formation of padlock probe, and (3) its rolling circle amplification for signal magnification. The signal detection is accomplished via either fluorescent in situ hybridization (FISH), flow cytometry (fluorescence-activated cell sorting, FACS), or droplet-based microfluidics. This methodology allows for sensitive and specific detection of DNA marker sequences without the need for DNA extraction and purification, making it possible to identify small genomic variations within individual human cells.

The tumor suppressor p53, one of the most intensely investigated proteins, is usually studied by experiments that are averaged over cell populations, potentially masking the dynamic behavior in individual cells. We present a system for following, in individual living cells, the dynamics of p53 and its negative regulator Mdm2 (refs. 1,4-7): this system uses functional p53-CFP and Mdm2-YFP fusion proteins and time-lapse fluorescence microscopy. We found that p53 was expressed in a series of discrete pulses after DNA damage. Genetically identical cells had different numbers of pulses: zero, one, two or more. The mean height and duration of each pulse were fixed and did not depend on the amount of DNA damage. The mean number of pulses, however, increased with DNA damage. This approach can be used to study other signaling systems and suggests that the p53-Mdm2 feedback loop generates a 'digital' clock that releases well-timed quanta of p53 until damage is repaired or the cell dies.

X-ray fluorescence (XRF) imaging is a highly sensitive non-invasive imaging method for detection of small element quantities in objects, from human-sized scales down to single-cell organelles, using various X-ray beam sizes. Our aim was to investigate the cellular uptake and distribution of Q10, a highly conserved coenzyme with antioxidant and bioenergetic properties. Q10 was labeled with iodine (I2-Q10) and individual primary human skin cells were scanned with nano-focused beams. Distribution of I2-Q10 molecules taken up inside the screened individual skin cells was measured, with a clear correlation between individual Q10 uptake and cell size. Experiments revealed that labeling Q10 with iodine causes no artificial side effects as a result of the labeling procedure itself, and thus is a perfect means of investigating bioavailability and distribution of Q10 in cells. In summary, individual cellular Q10 uptake was demonstrated by XRF, opening the path towards Q10 multi-scale tracking for biodistribution studies.

Mammalian cells are extremely vulnerable to external assaults compared with plant and microbial cells because of the weakness of cell membranes compared with cell walls. Construction of ultrathin and robust artificial shells on mammalian cells with biocompatible materials is a promising strategy for protecting single cells against harsh environmental conditions. Herein, layer-by-layer assembly combined with a transglutaminase-catalyzed cross-linking reaction was employed to prepare cross-linked and biocompatible gelatin nanoshells on individual human cervical carcinoma cell line (HeLa) cells and mouse insulinoma cell line 6 (MIN6) cells. The encapsulated HeLa and MIN6 cells showed high viability and a prolonged encapsulation period. Moreover, the nanoshells can protect encapsulated cells from cytotoxic enzymes (such as trypsin) and polycation (polyethylenimine) attacks and help cells resist high physical stress. We also investigated how nanoshells would affect the cell viability, proliferation, and cell cycle distribution of encapsulated and released cells. The approach presented here may provide a new and versatile method for nanoencapsulation of individual mammalian cells, which would help cells endure various environmental stresses and thereby expand the application field of isolated mammalian cells.

BackgroundThe tumor suppressor protein p53 is activated by cellular stress. DNA double strand breaks (DSBs) induce the activation of the kinase ATM, which stabilizes p53 and activates its transcriptional activity. Single cell analysis revealed that DSBs induced by gamma irradiation trigger p53 accumulation in a series of pulses that vary in number from cell to cell. Higher levels of irradiation increase the number of p53 pulses suggesting that they arise from periodic examination of the damage by ATM. If damage persists, additional pulses of p53 are triggered. The threshold of damage required for activating a p53 pulse is unclear. Previous studies that averaged the response across cell populations suggested that one or two DNA breaks are sufficient for activating ATM and p53. However, it is possible that by averaging over a population of cells important features of the dependency between DNA breaks and p53 dynamics are missed.ResultsUsing fluorescent reporters we developed a system for following in individual cells the number of DSBs, the kinetics of repair and the p53 response. We found a large variation in the initial number of DSBs and the rate of repair between individual cells. Cells with higher number of DSBs had higher probability of showing a p53 pulse. However, there was no distinct threshold number of breaks for inducing a p53 pulse. We present evidence that the decision to activate p53 given a specific number of breaks is not entirely stochastic, but instead is influenced by both cell-intrinsic factors and previous exposure to DNA damage. We also show that the natural variations in the initial amount of p53, rate of DSB repair and cell cycle phase do not affect the probability of activating p53 in response to DNA damage.ConclusionsThe use of fluorescent reporters to quantify DNA damage and p53 levels in live cells provided a quantitative analysis of the complex interrelationships between both processes. Our study shows that p53 activation differs even between cells that have a similar number of DNA breaks. Understanding the origin and consequences of such variability in normal and cancerous cells is crucial for developing efficient and selective therapeutic interventions.

This study was undertaken with the aim of identifying the different cell types found in human bone marrow by examining their surface morphology. In an attempt to obtain a homogeneous cell population, cells were both fractionated by discontinuous albumin density gradient centrifugation (DADGC) and selectively grown in nutrient agar. Both cell preparations underwent the critical point drying technique before examination under both the scanning electron microscope (SEM) and subsequently the light microscope (LM). When the SEM image of individual cells was compared with the corresponding LM image, it was not easy to identify the different cell types, because of the shrinkage and distortion that occurred during their preparation. The shrinkage observed under the SEM amounted to a 45% reduction in mean cell diameter. This shrinkage was confirmed by comparing the SEM and LM images of the same cell. Although shrinkage occurred throughout the dehydration sequence, critical point drying was responsible for a 25% reduction in mean cell diameter. Furthermore, direct observation under LM of fixed cells drying in air from ethanol, revealed visible contraction of the cell and distortion of the cell membrane. We assume that a similar morphological change occurred during critical point drying. We conclude that the shrinkage and distortion, caused by the dehydration process involved in SEM preparation, severely limit the value of a study of surface morphology by SEM in the identification of the different cell types found in human bone marrow.

miRNAs are small RNAs that regulate gene expression post‐transcriptionally. By repressing the translation and promoting the degradation of target mRNAs, miRNAs may reduce the cell‐to‐cell variability in protein expression, induce correlations between target expression levels, and provide a layer through which targets can influence each other's expression as “competing RNAs” (ceRNAs). However, experimental evidence for these behaviors is limited. Combining mathematical modeling with RNA sequencing of individual human embryonic kidney cells in which the expression of two distinct miRNAs was induced over a wide range, we have inferred parameters describing the response of hundreds of miRNA targets to miRNA induction. Individual targets have widely different response dynamics, and only a small proportion of predicted targets exhibit high sensitivity to miRNA induction. Our data reveal for the first time the response parameters of the entire network of endogenous miRNA targets to miRNA induction, demonstrating that miRNAs correlate target expression and at the same time increase the variability in expression of individual targets across cells. The approach is generalizable to other miRNAs and post‐transcriptional regulators to improve the understanding of gene expression dynamics in individual cell types.