Sphingolipids in Apoptosis

Forty years ago, the term “apoptosis” was introduced to describe a form of programmed cell death. Key players that mediate apoptosis at the molecular level such as caspases, death receptors, Bcl-2 family members have since been identified and their regulation remains a research focus of many laboratories. In 1993, approximately 20 years after the introduction of apoptosis, the sphingolipid ceramide was first linked to this form of cell death. Sphingolipids are bioactive components of cellular membranes that are involved in numerous physiological functions. In this paper, we discuss the inherent complexities of sphingolipid signaling and elaborate on how sphingolipids, primarily ceramide, influence apoptotic events such as death receptor aggregation in the plasma membrane and pore formation at the mitochondria. Possible roles of sphingolipids in other subcellular compartments, such as the nucleus, endoplasmic reticulum and lysosomes are also discussed. We conclude by summarizing the recent developments in sphingolipid based cancer therapy. This article is part of a Special Issue entitled “Apoptosis: Four Decades Later”

Evolutionary minority game with heterogeneous strategy distribution

We present detailed numerical results for a modified form of the so-called Minority Game, which provides a simplified model of a competitive market. Each agent has a limited set of strategies, and competes to be in a minority. An evolutionary rule for strategy modification is included to mimic simple learning. The results can be understood by considering crowd formation within the population.Comment: Revtex file + 4 figure

Theory of Phase Transition in the Evolutionary Minority Game

We discover the mechanism for the transition from self-segregation (into opposing groups) to clustering (towards cautious behaviors) in the evolutionary minority game (EMG). The mechanism is illustrated with a statistical mechanics analysis of a simplified EMG involving three groups of agents: two groups of opposing agents and one group of cautious agents. Two key factors affect the population distribution of the agents. One is the market impact (the self-interaction), which has been identified previously. The other is the market inefficiency due to the short-time imbalance in the number of agents using opposite strategies. Large market impact favors "extreme" players who choose fixed strategies, while large market inefficiency favors cautious players. The phase transition depends on the number of agents ($N$), the reward-to-fine ratio ($R$), as well as the wealth reduction threshold ($d$) for switching strategy. When the rate for switching strategy is large, there is strong clustering of cautious agents. On the other hand, when $N$ is small, the market impact becomes large, and the extreme behavior is favored.Comment: 5 pages and 3 figure

Temporal oscillations and phase transitions in the evolutionary minority game

The study of societies of adaptive agents seeking minority status is an active area of research. Recently, it has been demonstrated that such systems display an intriguing phase-transition: agents tend to {\it self-segregate} or to {\it cluster} according to the value of the prize-to-fine ratio, $R$. We show that such systems do {\it not} establish a true stationary distribution. The winning-probabilities of the agents display temporal oscillations. The amplitude and frequency of the oscillations depend on the value of $R$. The temporal oscillations which characterize the system explain the transition in the global behavior from self-segregation to clustering in the $R<1$ case.Comment: 5 pages, 5 figure

Strategy updating rules and strategy distributions in dynamical multiagent systems

In the evolutionary version of the minority game, agents update their strategies (gene-value $p$) in order to improve their performance. Motivated by recent intriguing results obtained for prize-to-fine ratios which are smaller than unity, we explore the system's dynamics with a strategy updating rule of the form $p \to p \pm \delta p$ ($0 \leq p \leq 1$). We find that the strategy distribution depends strongly on the values of the prize-to-fine ratio $R$, the length scale $\delta p$, and the type of boundary condition used. We show that these parameters determine the amplitude and frequency of the the temporal oscillations observed in the gene space. These regular oscillations are shown to be the main factor which determines the strategy distribution of the population. In addition, we find that agents characterized by $p={1 \over 2}$ (a coin-tossing strategy) have the best chances of survival at asymptotically long times, regardless of the value of $\delta p$ and the boundary conditions used.Comment: 4 pages, 7 figure

Multi-Choice Minority Game

The generalization of the problem of adaptive competition, known as the minority game, to the case of $K$ possible choices for each player is addressed, and applied to a system of interacting perceptrons with input and output units of the type of $K$-states Potts-spins. An optimal solution of this minority game as well as the dynamic evolution of the adaptive strategies of the players are solved analytically for a general $K$ and compared with numerical simulations.Comment: 5 pages, 2 figures, reorganized and clarifie

Design and application of genetically-encoded malonyl-CoA biosensors for metabolic engineering of microbial cell factories

Malonyl-CoA is the basic building block for synthesizing a range of important compounds including fatty acids, phenylpropanoids, flavonoids and non-ribosomal polyketides. Centering around malonyl-CoA, we summarized here the various metabolic engineering strategies employed recently to regulate and control malonyl-CoA metabolism and improve cellular productivity. Effective metabolic engineering of microorganisms requires the introduction of heterologous pathways and dynamically rerouting metabolic flux towards products of interest. Transcriptional factor-based biosensors translate an internal cellular signal to a transcriptional output and drive the expression of the designed genetic/biomolecular circuits to compensate the activity loss of the engineered biosystem. Recent development of genetically-encoded malonyl-CoA sensor has stood out as a classical example to dynamically reprogram cell metabolism for various biotechnological applications. Here, we reviewed the design principles of constructing a transcriptional factor-based malonyl-CoA sensor with superior detection limit, high sensitivity and broad dynamic range. We discussed various synthetic biology strategies to remove pathway bottleneck and how genetically-encoded metabolite sensor could be deployed to improve pathway efficiency. Particularly, we emphasized that integration of malonyl-CoA sensing capability with biocatalytic function would be critical to engineer efficient microbial cell factory. Biosensors have also advanced beyond its classical function of a sensor actuator for in situ monitoring of intracellular metabolite concentration. Applications of malonyl-CoA biosensors as a sensor-invertor for negative feedback regulation of metabolic flux, a metabolic switch for oscillatory balancing of malonyl-CoA sink pathway and source pathway and a screening tool for engineering more efficient biocatalyst are also presented in this review. We envision the genetically-encoded malonyl-CoA sensor will be an indispensable tool to optimize cell metabolism and cost-competitively manufacture malonyl-CoA-derived compounds

An engineered constitutive promoter set with broad activity range for Cupriavidus necator H16

Well-characterized promoters with variable strength form the foundation of heterologous pathway optimization. It is also a key element that bolsters the success of microbial engineering and facilitates the development of biological tools like biosensors. In comparison to microbial hosts such as Escherichia coli and Saccharomyces cerevisiae, the promoter repertoire of Cupriavidus necator H16 is highly limited. This limited number of characterized promoters poses a significant challenge during the engineering of C. necator H16 for biomanufacturing and biotechnological applications. In this article, we first examined the architecture and genetic elements of the four most widely used constitutive promoters of C. necator H16 (i.e., PphaC1, PrrsC, Pj5, and Pg25) and established a narrow 6-fold difference in their promoter activities. Next, using these four promoters as starting points and applying a range of genetic modifications (including point mutation, length alteration, incorporation of regulatory genetic element, promoter hybridization, and configuration alteration), we created a library of 42 constitutive promoters, all of which are functional in C. necator H16. Although these promoters are also functional in E. coli, they show different promoter strength and hierarchical rank of promoter activity. Subsequently, the activity of each promoter was individually characterized, using l-arabinose-inducible PBAD promoter as a benchmark. This study has extended the range of constitutive promoter activities to 137-fold, with some promoter variants exceeding the l-arabinose-inducible range of PBAD promoter. Not only has the work enhanced our flexibility in engineering C. necator H16, it presented novel strategies in adjusting promoter activity in C. necator H16 and highlighted similarities and differences in transcriptional activity between this organism and E. coli

Development of a unilateral ureteral obstruction model in cynomolgus monkeys

Background Chronic kidney disease (CKD) has a high global prevalence and large unmet need. Central to developing new CKD therapies are in vivo models in CKD. However, next-generation antibody, protein, and gene therapies are highly specific, meaning some do not cross-react with rodent targets. This complicates preclinical development, as established in vivo rodent models cannot be utilized unless tool therapeutics are also developed. Tool compounds can be difficult to develop and, if available, typically have different epitopes, sequences, and/or altered affinity, making it unclear how efficacious the lead therapeutic may be, or what dosing regimen to investigate. To address this, we aimed to develop a nonhuman primate model of CKD. Methods In vivo rodent unilateral ureteral obstruction (UUO) models kidney fibrosis and is commonly used due to its rapidity, consistency, and ease. We describe translation of this model to the cynomolgus monkey, specifically optimizing the model duration to allow adequate time for assessment of novel therapeutics prior to the fibrotic plateau. Results We demonstrated that disease developed more slowly in cynomolgus monkeys than in rodents post-UUO, with advanced fibrosis developing by 6 weeks. The tubulointerstitial fibrosis in cynomolgus monkeys was more consistent with human obstructive disease than in rodents, having a more aggressive tubular basement expansion and a higher fibroblast infiltration. The fibrosis was also associated with increased transglutaminase activity, consistent with that seen in patients with CKD. Conclusion This cynomolgus monkey UUO model can be used to test potential human-specific therapeutics in kidney fibrosis

A comparison of aerosol chemical and optical properties from the 1st and 2nd Aerosol Characterization Experiments

Shipboard measurements of aerosol chemical composition and optical properties were made during both ACE-1 and ACE-2. ACE-1 focused on remote marine aerosol minimally perturbed by continental sources. ACE-2 studied the outflow of European aerosol into the NE Atlantic atmosphere. A variety of air masses were sampled during ACE-2 including Atlantic, polar, Iberian Peninsula, Mediterranean, and Western European. Reported here are mass size distributions of non-sea salt (nss) sulfate, sea salt, and methanesulfonate and submicron and supermicron concentrations of black and organic carbon. Optical parameters include submicron and supermicron aerosol scattering and backscattering coefficients at 550 nm, the absorption coefficient at 550±20 nm, the Ångström exponent for the 550 and 700 nm wavelength pair, and single scattering albedo at 550 nm. All data are reported at the measurement relative humidity of 55%. Measured concentrations of nss sulfate aerosol indicate that, relative to ACE-1, ACE-2 aerosol during both marine and continental flow was impacted by continental sources. Thus, while sea salt controlled the aerosol chemical composition and optical properties of both the submicron and supermicron aerosol during ACE-1, it played a relatively smaller role in ACE-2. This is confirmed by the larger average Ångström exponent for ACE-2 continental aerosol of 1.2±0.26 compared to the ACE-1 average of -0.03±0.38. The depletion of chloride from sea salt aerosol in ACE-2 continental air masses averaged 55±25% over all particle sizes. This compares to the ACE-2 marine average of 4.8±18% and indicates the enhanced interaction of anthropogenic acids with sea salt as continental air masses are transported into the marine atmosphere. Single scattering albedos averaged 0.95±0.03 for ACE-2 continental air masses. Averages for ACE-2 and ACE-1 marine air masses were 0.98±0.01 and 0.99±0.01, respectively