Systems biology approaches to metabolic and cardiovascular disorders: network perspectives of cardiovascular metabolism

In this review, we examine cardiovascular metabolism from three different, but highly complementary, perspectives. First, from the abstract perspective of a metabolite network, composed of nodes and links. We present fundamental concepts in network theory, including emergence, to illustrate how nature has designed metabolism with a hierarchal modular scale-free topology to provide a robust system of energy delivery. Second, from the physical perspective of a modular spatially compartmentalized network. We review evidence that cardiovascular metabolism is functionally compartmentalized, such that oxidative phosphorylation, glycolysis, and glycogenolysis preferentially channel ATP to ATPases in different cellular compartments, using creatine kinase and adenylate kinase to maximize efficient energy delivery. Third, from the dynamics perspective, as a network of dynamically interactive metabolic modules capable of self-oscillation. Whereas normally, cardiac metabolism exists in a regime in which excitation-metabolism coupling closely matches energy supply and demand, we describe how under stressful conditions, the network can be pushed into a qualitatively new dynamic regime, manifested as cell-wide oscillations in ATP levels, in which the coordination between energy supply and demand is lost. We speculate how this state of "metabolic fibrillation" leads to cell death if not corrected and discuss the implications for cardioprotection.     

Single-molecule FRET reveals nucleotide-driven conformational changes in molecular machines and their link to RNA unwinding and DNA supercoiling

Many complex cellular processes in the cell are catalysed at the expense of ATP hydrolysis. The enzymes involved bind and hydrolyse ATP and couple ATP hydrolysis to the catalysed process via cycles of nucleotide-driven conformational changes. In this review, I illustrate how smFRET (single-molecule fluorescence resonance energy transfer) can define the underlying conformational changes that drive ATP-dependent molecular machines. The first example is a DEAD-box helicase that alternates between two different conformations in its catalytic cycle during RNA unwinding, and the second is DNA gyrase, a topoisomerase that undergoes a set of concerted conformational changes during negative supercoiling of DNA.     

Fostering Industrial Symbiosis With Agent-Based Simulation and Participatory Modeling

The sciences of industrial ecology, complex systems, and adaptive management are intimately related, since they deal with flows and dynamic interdependencies between system elements of various kinds. As such, the tool kit of complex systems science could enrich our understanding of how industrial ecosystems might evolve over time. In this article, I illustrate how an important tool of complex systems science— agent-based simulation —can help to identify those potential elements of an industrial ecosystem that could work together to achieve more eco-efficient outcomes. For example, I show how agent-based simulation can generate cost-efficient energy futures in which groups of firms behave more eco-efficiently by introducing strategically located clusters of renewable, low-emissions, distributed generation. I then explain how role-playing games and participatory modeling can build trust and reduce conflict about the sharing of common-pool resources such as water and energy among small clusters of evolving agents. Collective learning can encourage potential industrial partners to gradually cooperate by exchanging by-products and/or sharing common infrastructure by dint of their close proximity. This kind of coevolutionary learning, aided by participatory modeling, could help to bring about industrial symbiosis.     

Consequences of local Allee effects in spatially structured populations

The ideal free distribution model incorporating the Allee effect was published by Fretwell and Lucas (1970), but went almost unnoticed within the ecological literature. The model is relevant to populations distributed among patchy habitats. It predicts a sporadic but substantial decline in populations at high densities, which in turn induces the rapid growth of new populations. In this paper, I show that the simple process explained by this model can be used to change our view of several phenomena within the field of population ecology, behavioural ecology and conservation. The ecological consequences of the model are well known. A key feature of Fretwell and Lucas's model is what I call the "Allee paradox:" there is a range of local population densities at which local individual fitness is less than the potential mean gain that could be obtained in the environment; however, individuals cannot disperse. This paradox can be used to explain why helping appears before suitable breeding areas are fully occupied, and why breeding females aggregate when male coercion is a reproductive cost. The model also predicts high clustering between related populations, and, in conservation biology, it can identify unfounded concerns about the dangers of extinction, delays in recolonisation processes after human-induced population decline, and latency periods in the initial phases of expansion of invasive species.     

Animal egg as evolutionary innovation: a solution to the "embryonic hourglass" puzzle

The evolutionary origin of the egg stage of animal development presents several difficulties for conventional developmental and evolutionary narratives. If the egg's internal organization represents a template for key features of the developed organism, why can taxa within a given phylum exhibit very different egg types, pass through a common intermediate morphology (the so-called "phylotypic stage"), only to diverge again, thus exemplifying the embryonic "hourglass"? Moreover, if different egg types typically represent adaptations to different environmental conditions, why do birds and mammals, for example, have such vastly different eggs with respect to size, shape, and postfertilization dynamics, whereas all these features are more similar for ascidians and mammals? Here, I consider the possibility that different body plans had their origin in self-organizing physical processes in ancient clusters of cells, and suggest that eggs represented a set of independent evolutionary innovations subsequently inserted into the developmental trajectories of such aggregates. I first describe how "dynamical patterning modules" (DPMs) associations between components of the metazoan developmental-genetic toolkit and certain physical processes and effects may have organized primitive animal body plans independently of an egg stage. Next, I describe how adaptive specialization of cells released from such aggregates could have become "proto-eggs," which regenerated the parental cell clusters by cleavage, conserving the characteristic DPMs available to a lineage. Then, I show how known processes of cytoplasmic reorganization following fertilization are often based on spontaneous, self-organizing physical effects ("egg-patterning processes": EPPs). I suggest that rather than acting as developmental blueprints or prepatterns, the EPPs refine the phylotypic body plans determined by the DPMs by setting the boundary and initial conditions under which these multicellular patterning mechanisms operate. Finally, I describe how this new perspective provides a resolution to the embryonic hourglass puzzle.     

Proteogenomic approaches for the molecular characterization of natural microbial communities

At the present time we know little about how microbial communities function in their natural habitats. For example, how do microorganisms interact with each other and their physical and chemical surroundings and respond to environmental perturbations? We might begin to answer these questions if we could monitor the ways in which metabolic roles are partitioned amongst members as microbial communities assemble, determine how resources such as carbon, nitrogen, and energy are allocated into metabolic pathways, and understand the mechanisms by which organisms and communities respond to changes in their surroundings. Because many organisms cannot be cultivated, and given that the metabolisms of those growing in monoculture are likely to differ from those of organisms growing as part of consortia, it is vital to develop methods to study microbial communities in situ. Chemoautotrophic biofilms growing in mine tunnels hundreds of meters underground drive pyrite (FeS(2)) dissolution and acid and metal release, creating habitats that select for a small number of organism types. The geochemical and microbial simplicity of these systems, the significant biomass, and clearly defined biological-inorganic feedbacks make these ecosystem microcosms ideal for development of methods for the study of uncultivated microbial consortia. Our approach begins with the acquisition of genomic data from biofilms that are sampled over time and in different growth conditions. We have demonstrated that it is possible to assemble shotgun sequence data to reveal the gene complement of the dominant community members and to use these data to confidently identify a significant fraction of proteins from the dominant organisms by mass spectrometry (MS)-based proteomics. However, there are technical obstacles currently restricting this type of "proteogenomic" analysis. Composite genomic sequences assembled from environmental data from natural microbial communities do not capture the full range of genetic potential of the associated populations. Thus, it is necessary to develop bioinformatics approaches to generate relatively comprehensive gene inventories for each organism type. These inventories are critical for expression and functional analyses. In proteomic studies, for example, peptides that differ from those predicted from gene sequences can be measured, but they generally cannot be identified by database matching, even if the difference is only a single amino acid residue. Furthermore, many of the identified proteins have no known function. We propose that these challenges can be addressed by development of proteogenomic, biochemical, and geochemical methods that will be initially deployed in a simple, natural model ecosystem. The resulting approach should be broadly applicable and will enhance the utility and significance of genomic data from isolates and consortia for study of organisms in many habitats. Solutions draining pyrite-rich deposits are referred to as acid mine drainage (AMD). AMD is a very prevalent, international environmental problem associated with energy and metal resources. The biological-mineralogical interactions that define these systems can be harnessed for energy-efficient metal recovery and removal of sulfur from coal. The detailed understanding of microbial ecology and ecosystem dynamics resulting from the proposed work will provide a scientific foundation for dealing with the environmental challenges and technological opportunities, and yield new methods for analysis of more complex natural communities.     

Phylogenetic approaches for studying diversification

Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever‐accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non‐equilibrium theories recognising the crucial role of history.     

中国园林生态学发展综述

运用文献计量等方法对已有科研成果进行统计分析,结果表明:中国近50年园林生态学科领域科研发展经过了起步探索(1962-1981)、缓慢发展(1982-2001)、快速发展(2002-2011)3个时期,园林生态学作为生态学一个新的分支学科,于20世纪90年代末初见端倪,作为一门新兴独立的应用生态学分支学科于21世纪初已基本形成.中国园林生态学领域的研究包括园林生态系统中生物与环境相互作用关系问题、人与环境相互作用关系问题以及园林生态系统与其他生态系统之间相互作用关系问题.当代园林生态研究主要有生态效益研究、生物与环境研究、人的需求与行为研究、生态规划与生态管理研究4个方面,目前园林生态学研究主要侧重生物与环境研究和生态效益研究,两方面的研究成果占总体研究成果的76.3％.不同研究方面也有各自的侧重点,如生物与环境研究侧重对植物的研究,生态效益研究侧重净化环境、水土保持和防灾减灾,生态规划与生态管理研究则侧重生态规划与设计.对四个研究方面的论文主题词检索和高频主题关键词的分布进行统计,结果显示,研究的热点有多样性、群落、水土保持、防灾避险、净化环境、生态规划与设计等.对CNKI中4个研究方面成果中获基金资助项目论文进行统计(不排重),总体成果中基金项目论文所占比重为10.8％,国家和地方基金是园林生态学科研基金资助的主要来源,基金论文比例之和达到85.4％,且国家和地方基金资助论文较多的是“生态与环境研究”和“生态效益研究”,合计占基金论文79.1％.SCI-E中收录的文献基金论文率为47.1％,是CNKI数据库收录的文献基金论文率的4.3倍,且国际基金是基金论文的主要资助来源之一,说明中国园林生态学领域部分科研成果得到国际学界关注.基于CNKI相关主题词统计,“园林生态学”的研究成果只有“景观生态学”的1％,“城市生态学”的8.3％,“园林生态学”学科系统理论研究在相关生态学科研究中所占比重很低,其理论和方法研究还较薄弱.今后在进一步完善学科理论体系、持续开展生态效益和园林植物研究的同时,为更好地研究和解决人-自然复合生态系统问题,提供更多的科学理论支撑,还需拓展交叉生态心理学或环境心理学等其他相关理论,更多地关注人与环境互相作用关系以及生态规划与生态管理等方面的研究,既使环境更好地满足人的行为需求,也使人认识到改变一些行为能更好地保护环境.     

Deciphering the physiological response of Escherichia coli under high ATP demand

One long‐standing question in microbiology is how microbes buffer perturbations in energy metabolism. In this study, we systematically analyzed the impact of different levels of ATP demand in Escherichia coli under various conditions (aerobic and anaerobic, with and without cell growth). One key finding is that, under all conditions tested, the glucose uptake increases with rising ATP demand, but only to a critical level beyond which it drops markedly, even below wild‐type levels. Focusing on anaerobic growth and using metabolomics and proteomics data in combination with a kinetic model, we show that this biphasic behavior is induced by the dual dependency of the phosphofructokinase on ATP (substrate) and ADP (allosteric activator). This mechanism buffers increased ATP demands by a higher glycolytic flux but, as shown herein, it collapses under very low ATP concentrations. Model analysis also revealed two major rate‐controlling steps in the glycolysis under high ATP demand, which could be confirmed experimentally. Our results provide new insights on fundamental mechanisms of bacterial energy metabolism and guide the rational engineering of highly productive cell factories.     

Fish cognition: what can we learn, and what do they need to learn?

Fish provide a wonderful opportunity to explore processes that shape and select cognitive ability. In this presentation, I will illustrate three aspects of work that my colleagues and I have used to investigate fish learning and memory over the last decade. First, I will discuss how comparing different populations sampled from contrasting habitats allows differences in cognitive ability to be related to the evolutionary ecology of the fish. I will use examples that have investigated how differences in learning ability between populations of the same species can arise. Here, the examples will be taken from the ubiquitous three‐spined stickleback, and a Panamanian poecilid, Brachyraphis .
The second approach has used fish cognition as a tool to quantify behaviour to enable assessment of different aspects of fish welfare. For example, the recent work investigating pain perception in trout required the use of a learning task to quantify how fish behaviour was modified after noxious stimulation. Ways in which these, and similar, processes can be used in future studies of fish welfare will be discussed.
The final part of the presentation will consider recent work that addresses the problems of releasing hatchery‐reared fish for restocking purposes. Although a common practice, most of the hatchery‐reared fish die shortly after they are released. Much of the observed mortality apparently stems from the fishes' inexperience with a variable environment. Experiments with juvenile cod and brown trout suggest that both age, and the early rearing environment, have profound effects on fish learning and behaviour. I will discuss how simple modifications to current rearing practices may have large beneficial effects on the post‐release survival of hatchery‐reared fish.     

Matters Arising

Abstract: The possibility that neurofilaments could be involved in the transduction of chemical and mechanical energy in axons led us to investigate whether neurofilament proteins can hydrolyze ATP. We fractionated neurofilaments from rabbit spinal cord and found that preparations highly enriched for neurofilament proteins hydrolyzed ATP at a substantial rate (as high as 0.4 μmol/min/mg protein). However, the ATPase activity was neither inhibited by anti-neurofilament antibody, nor was it precipitated by the antibody under circumstances that precipitated most of the neurofilament polypeptides. We conclude that neurofilament proteins do not hydrolyze ATP at a significant rate under the conditions of our assay; if hydrolysis of ATP is a physiological function of neurofilaments, additional factors are required.     

The Effects of Biogeography and Biotic Interactions on Lemur Community Assembly

Geographic patterns of biodiversity result from broad-scale biogeographic and present-day ecological processes. The aim of this study was to investigate the relative importance of biogeographic history and ecology driving patterns of diversity in modern primate communities in Madagascar. I collected data on endemic lemur species co-occurrence from range maps and survey literature for 100 communities in protected areas. I quantified and compared taxonomic, phylogenetic, and functional dimensions of intra- and intersite diversity. I tested environmental and geographic predictors of diversity and endemism. I calculated deforestation rates within protected areas between the years 2000 and 2014, and tested if diversity is related to forest cover and loss. I found the phylogenetic structure of lemur communities could be explained primarily by remotely sensed plant productivity, supporting the hypothesis that there was ecological differentiation among ecoregions, while functional-trait disparity was not strongly related to environment. Taxonomic and phylogenetic diversity also increased with increasing topographic heterogeneity. Beta diversity was explained by both differences in ecology among localities and potential river barriers. Approximately 3000 km² were deforested in protected areas since the year 2000, threatening the most diverse communities (up to 31%/park). The strong positive association of plant productivity and topographic heterogeneity with lemur diversity indicates that high productivity, rugged landscapes support greater diversity. Both ecology and river barriers influenced lemur community ecology and biogeography. These results underscore the need for focused conservation efforts to slow the loss of irreplaceable evolutionary and ecological diversity.     

Some thoughts on the evolutionary basis for the prominent role of ATP and ADP in cellular energy metabolism

The predominance of the adenosine triphosphate/adenosine diphosphate (ATP/ADP) couple in cellular phosphorylation reactions, including those that form the basis for cellular energy metabolism, cannot be explained on thermodynamic grounds since a variety of "high energy phosphate" compounds (including ADP itself) found in the cell would, based on thermodynamic considerations, be at least as effective as ATP in serving as a phosphoryl donor. How then did present-day organisms come to rely on the ATP/ADP couple as the principal mediator of phosphorylation reactions? The early appearance of adenine compounds in the prebiotic environment is suggested by experiments indicating that, relative to other purine or pyridimine compounds, adenine derivatives are preferentially synthesized under simulated prebiotic conditions (Ponnamperuma et al., 1963). In addition to the roles of adenine nucleotides in phosphorylation reactions, other adenine derivatives (e.g. Coenzyme A, flavin adenine dinucleotide, puridine nucleotides) are employed in a variety of metabolic roles. The principal function of the adenine moiety in these latter cases is in the binding of these derivatives to the relevant enzyme. The capability for binding of the adenine moiety appears to have arisen early in evolution and been exploited in a multitude of contexts, a suggestion consistent with observed similarities between the binding sites of several enzymes employing adenine derivatives as substrate. The early availability of suitable adenine compounds in the biosphere and development of complementary binding sites on cellular proteins, coupled with the expected advantages in having a limited number of metabolites as central mediators of endergonic and exergonic metabolism could readily have led to the observed pre-eminence of adenine nucleotides in cellular energy metabolism.(ABSTRACT TRUNCATED AT 250 WORDS)     

The Response of Cyclic Electron Flow around Photosystem I to Changes in Photorespiration and Nitrate Assimilation

Photosynthesis captures light energy to produce ATP and NADPH. These molecules are consumed in the conversion of CO₂ to sugar, photorespiration, and NO₃⁻ assimilation. The production and consumption of ATP and NADPH must be balanced to prevent photoinhibition or photodamage. This balancing may occur via cyclic electron flow around photosystem I (CEF), which increases ATP/NADPH production during photosynthetic electron transport; however, it is not clear under what conditions CEF changes with ATP/NADPH demand. Measurements of chlorophyll fluorescence and dark interval relaxation kinetics were used to determine the contribution of CEF in balancing ATP/NADPH in hydroponically grown Arabidopsis (Arabidopsis thaliana) supplied different forms of nitrogen (nitrate versus ammonium) under changes in atmospheric CO₂ and oxygen. Measurements of CEF were made under low and high light and compared with ATP/NADPH demand estimated from CO₂ gas exchange. Under low light, contributions of CEF did not shift despite an up to 17% change in modeled ATP/NADPH demand. Under high light, CEF increased under photorespiratory conditions (high oxygen and low CO₂), consistent with a primary role in energy balancing. However, nitrogen form had little impact on rates of CEF under high or low light. We conclude that, according to modeled ATP/NADPH demand, CEF responded to energy demand under high light but not low light. These findings suggest that other mechanisms, such as the malate valve and the Mehler reaction, were able to maintain energy balance when electron flow was low but that CEF was required under higher flow.Photosynthesis must balance both the amount of energy harvested by the light reactions and how it is stored to match metabolic demands. Light energy is harvested by the photosynthetic antenna complexes and stored by the electron and proton transfer complexes as ATP and NADPH. It is used primarily to meet the energy demands for assimilating carbon (from CO₂) and nitrogen (from NO₃⁻ and NH₄⁺; Keeling et al., 1976; Edwards and Walker, 1983; Miller et al., 2007). These processes require different ratios of ATP and NADPH, requiring a finely balanced output of energy in these forms. For example, if ATP were to be consumed at a greater rate than NADPH, electron transport would rapidly become limiting by the lack of NADP⁺, decreasing rates of proton translocation and ATP regeneration. Alternatively, if NADPH were consumed faster than ATP, proton translocation through ATP synthase would be reduced due to limiting ADP and the difference in pH between lumen and stroma would increase, restricting plastoquinol oxidation at the cytochrome b₆f complex and initiating nonphotochemical quenching (Kanazawa and Kramer, 2002). The stoichiometric balancing of ATP and NADPH must occur rapidly, because pool sizes of ATP and NADPH are relatively small and fluxes through primary metabolism are large (Noctor and Foyer, 2000; Avenson et al., 2005; Cruz et al., 2005; Amthor, 2010).The balancing of ATP and NADPH supply is further complicated by the rigid nature of linear electron flow (LEF). In LEF, electrons are transferred from water to NADP⁺, oxidizing water to oxygen and reducing NADP⁺ to NADPH. This electron transfer is coupled to proton translocation and generates a proton motive force, which powers the regeneration of ATP. The stoichiometry of ATP/NADPH produced by these reactions is thought to be 1.29 based on the ratio of proton pumping and the requirement for ATP synthase in the thylakoid (Sacksteder et al., 2000; Seelert et al., 2000). However, under ambient CO₂, oxygen, and temperature, the ATP/NADPH required by CO₂ fixation, photorespiration, and NO₃⁻ assimilation is approximately 1.6 (Edwards and Walker, 1983). The ATP/NADPH demand from central metabolism changes significantly from 1.6 if the ratio of CO₂ or oxygen changes, driving different rates of photosynthesis and photorespiration (see “Theory”). Such changes in energy demand require a flexible mechanism to balance ATP/NADPH that responds to environmental conditions.The difference between ATP/NADPH supply from LEF and demand from primary metabolism could be balanced via cyclic electron flow around PSI (CEF; Avenson et al., 2005; Shikanai, 2007; Joliot and Johnson, 2011; Kramer and Evans, 2011). During CEF, electrons from either NADPH or ferredoxin are cycled around PSI into the plastoquinone pool and regenerate ATP without reducing NADP⁺ (Golbeck et al., 2006). Therefore, CEF has been suggested to be important for optimal photosynthesis and plant growth, but its physiological role in energy balancing is not clear (Munekage et al., 2002, 2004; Livingston et al., 2010). For example, there was no shift in CEF in Arabidopsis (Arabidopsis thaliana) measured under low light (less than 300 μmol m⁻² s⁻¹) and different oxygen partial pressures, which would significantly change the ATP/NADPH demand of primary metabolism (Avenson et al., 2005). Similar results were seen under low light in leaves of barley (Hordeum vulgare) and Hedera helix (Genty et al., 1990). While CEF did not shift with energy demand in steady-state photosynthesis under low light, it did increase with photorespiration as expected at high light (Miyake et al., 2004, 2005). These observations could be explained if CEF becomes more important for energy balancing under high irradiances when other mechanisms become saturated.To determine under which conditions CEF responded to ATP/NADPH demand, we used biochemical models of leaf CO₂ fixation to model ATP and NADPH demand under a variety of conditions (see “Theory”). We then used in vivo spectroscopy to measure the relative response of CEF to modeled ATP/NADPH demand from CO₂ fixation and NO₃⁻ assimilation in hydroponically grown Arabidopsis. Our findings indicate that CEF responded to modeled ATP/NADPH demand under high light but not under low light or nitrate availability.     

Metformin is synthetically lethal with glucose withdrawal in cancer cells

Comment on: Menendez JA, et al. Cell Cycle 2012; 11: 2782-92.In a recent issue of Cell Cycle, Menendez and colleagues proposed a novel concept, that metformin is synthetically lethal with glucose withdrawal in cancer cells.¹ Historically, synthetic lethality has focused on how tumor cells are responsive to certain agents that only harbor specific constitutive epigenetic or genetic lesions.² More recent data from several groups have uncovered that altered tumor microenvironment could be used to confer synthetic lethality to specific drugs, defined as “contextual synthetic lethality,” that is microenvironment-mediated. For example, hypoxia-induced HR (homologous repair) defect has been shown to be synthetically lethal to PARP inhibition, while PARP inhibition, per se, did not alter HR inhibition or function, thus providing a prime example of “contextual synthetic lethality.”³ In this report, Menendez et al. have elegantly connected the glucose-deprived tumor microenvironment in primary tumors as a synthetic lethal partner to metformin. Metformin is a FDA-approved drug to treat diabetic patients that is gaining momentum as a repurposing drug for cancer treatment.⁴ Using several different breast cancer cells with and without oncogenic activation, the authors have shown that the glucose-rich conditions of the in vitro experiments dictates the use of very high concentrations of metformin, which are not applicable to glucose-starved in vivo conditions. While other reports have alluded to the effect of glucose withdrawal in killing genetically compromised cells to therapeutic effect of metformin in vitro,⁵ Menendez et al have provided a logical explanation for the use of very high concentrations of metformin to achieve anticancer effects in vitro in the high glucose-rich environment used in these experiments, which are clinically not applicable in vivo in patients.Based on these findings, it can be envisaged that in the tumor microenvironment, where the cancer cells are under extreme nutritional and hypoxic stress (a niche for cancer stem cells), metformin treatment could favor synthetic lethality and hence effectively can attenuate tumor growth. The tumor microenvironment thus enables the bioenergetic switch in favor of glycolysis and dependence on glucose and glutamine as a rapid source of nutrition. While the authors’ data clearly depicts how metformin eliminates the tolerance of the breast cancer cells to fluctuations in glucose concentrations, it is important to understand how the availability of other dominant sources of energy, such as glutamine, might participate in this scenario. It is plausible that subtype of breast cancers, i.e., basal vs luminal, might depend on different energy sources, albeit to a different extent.⁶ This is important, because tumor cells often acquire metabolic adaptability toward available preferred energy source to adapt well to nutritional stress via autophagy and altered metabolism.⁷ Along these lines, the authors rationalize the therapeutic targeting of the cancer stem cells by metformin through its synthetic lethal activity to the hyperglycotic phenotype often seen in CSC to sustain their stemness.⁸ Further characterization of how metformin treatment alters the metabolic nodes in cancer stem cells and/or p53-null cells would explain the underpinning mechanisms for increased susceptibility of these indolent and aggressive cancer cells toward metformin.It is well documented that metformin, by inhibiting complex I of respiratory chain in mitochondria (ETCI), induces a decrease in the ATP levels, and that glucose depletion also decreases ATP levels, albeit to varying levels. Therefore, it is possible that simultaneous targeting of both pathways (glycolytic pathway and OXPHOS) caused ATP depletion below a critical threshold, resulting in cell death. This concept is supported by the elegant study⁹ highlighting the effectiveness of combination of glycolysis inhibition by 2-DG and metformin in several preclinical models exhibiting anti-tumor effects, including MB-MDA231 used in this study.Since recent studies indicate that inhibiting glucose uptake with small-molecule inhibitors led to a decline in cylcin E2 and p-RB levels,¹⁰ it is a possibility that cell cycle inhibitor levels are also regulated under glucose withdrawal conditions, sensitizing cells to cytotoxic effects of metformin in breast cancer cells.Considering data from several studies, a view that metformin treatment has pleotropic effects on several signaling pathways under glucose-free conditions seems a practical possibility. Overall, this work offers several new insights into glucose-dependent mechanisms underpinning the mode of action of metformin as a viable therapeutic strategy.     

Implicit frequency dependence and kin selection in fluctuating environments

Summary I consider a general model of a fluctuating environment in which the environmental state each year is drawn at random from some given distribution. Each year organisms must choose what action to perform before the environmental state for that year is known. There is no interaction with kin. In this scenario, natural selection will tend to produce organisms which maximize their geometric mean fitness. In this paper I introduce the idea of the profile of a strategy. This function quantifies how the strategy peforms for each environmental state. I show that there is a unique profile such that a strategy is optimal if and only if it has this profile. I then give a characterization of the optimal profile which generalizes previous work by others in this area. The characterization of the optimal profile has a game theoretical interpretation. Motivated by this I introduce a game in which individuals play the field in a constant environment. This game may be interpreted as a cooperative game between kin. The key result of this paper shows that a strategy maximizes geometric mean fitness in the original fluctuating environment problem if and only if it is an evolutionarily stable strategy of the deterministic environment game. It is well known that an optimal strategy in a fluctuating environment may be mixed, involving adaptive coin-flipping. Others have previously noted that this may result in some individuals sacrificing individual reproductive success for the good of the genotype. My analysis shows that one may regain the concept of individual optimization if the quantity maximized is suitably defined. Under an optimal strategy every action taken maximizes the expected number of offspring produced, where this expectation is not calculated using the true distribution of environmental states, but a distribution modified to take account of the actions of kin.     

A polyphosphate-lon protease complex in the adaptation of Escherichia coli to amino acid starvation

Cells must balance energy-efficient growth with the ability to adapt rapidly to sudden changes in their environment. For example, in an environment rich in amino acids, cells do not expend energy for making amino acid biosynthetic enzymes. However, if the environment becomes depleted of amino acids (nutritional downshift), cells will be exposed to a lack of both the amino acid biosynthetic enzymes and the amino acids required to make these enzymes. To solve this dilemma, cells must use their own proteins as sources of amino acids in response to the nutritional downshift. Once amino acid biosynthetic enzymes start to accumulate, the cell is able to produce its own amino acids, and a new growth phase begins. In Escherichia coli, amino acid starvation leads to the accumulation of an unusual molecule, polyphosphate (polyP), a linear polymer of many hundreds of orthophosphate residues. Protein degradation in this bacterium appears to be triggered by the accumulation of polyP. PolyP forms a complex with the ATP-dependent Lon protease. The formation of a complex then enables Lon to degrade free ribosomal proteins. Certain very abundant ribosomal proteins can be the sacrificial substrates targeted for degradation at the onset of the downshift. Here I propose to call the polyP-Lon complex the "stringent protease," and I discuss new insights of protein degradation control in bacteria.     

Is it possible to produce succinic acid at a low pH?

Bio-based succinate is still a matter of special emphasis in biotechnology and adjacent research areas. The vast majority of natural and engineered producers are bacterial strains that accumulate succinate under anaerobic conditions. Recently, we succeeded in obtaining an aerobic yeast strain capable of producing succinic acid at low pH. Herein, we discuss some difficulties and advantages of microbial pathways producing "succinic acid" rather than "succinate." It was concluded that the peculiar properties of the constructed yeast strain could be clarified in view of a distorted energy balance. There is evidence that in an acidic environment, the majority of the cellular energy available as ATP will be spent for proton and anion efflux. The decreased ATP:ADP ratio could essentially reduce the growth rate or even completely inhibit growth. In the same way, the preference of this elaborated strain for certain carbon sources could be explained in terms of energy balance. Nevertheless, the opportunity to exclude alkali and mineral acid waste from microbial succinate production seems environmentally friendly and cost-effective.     

Time-resolved measurements of intracellular ATP in the yeast Saccharomyces cerevisiae using a new type of nanobiosensor

Adenosine 5'-triphosphate is a universal molecule in all living cells, where it functions in bioenergetics and cell signaling. To understand how the concentration of ATP is regulated by cell metabolism and in turn how it regulates the activities of enzymes in the cell it would be beneficial if we could measure ATP concentration in the intact cell in real time. Using a novel aptamer-based ATP nanosensor, which can readily monitor intracellular ATP in eukaryotic cells with a time resolution of seconds, we have performed the first on-line measurements of the intracellular concentration of ATP in the yeast Saccharomyces cerevisiae. These ATP measurements show that the ATP concentration in the yeast cell is not stationary. In addition to an oscillating ATP concentration, we also observe that the concentration is high in the starved cells and starts to decrease when glycolysis is induced. The decrease in ATP concentration is shown to be caused by the activity of membrane-bound ATPases such as the mitochondrial F(0)F(1) ATPase-hydrolyzing ATP and the plasma membrane ATPase (PMA1). The activity of these two ATPases are under strict control by the glucose concentration in the cell. Finally, the measurements of intracellular ATP suggest that 2-deoxyglucose (2-DG) may have more complex function than just a catabolic block. Surprisingly, addition of 2-DG induces only a moderate decline in ATP. Furthermore, our results suggest that 2-DG may inhibit the activation of PMA1 after addition of glucose.     

Ser203在大鼠脑驱动蛋白水解ATP中重要作用的晶体学分析

鼠脑驱动蛋白（rat brain kinesin）是一种利用水解ATP所释放的能量在微管束上高速并且连续性运动的常规驱动蛋白. 它在神经突触的物质运输中起着重要作用. 研究驱动蛋白是如何将ATP中储藏的化学能转化为机械动能是理解其运动机能的重要课题. 本课题获得了鼠脑驱动蛋白单体与ATP结构类似物AMPPCP形成的复合物晶体结构. 将这个晶体结构与鼠脑驱动蛋白单体-另一种ATP结构类似物AMPPNP形成的复合物晶体结构以及鼠脑驱动蛋白单体-ATP水解产物ADP形成的复合物晶体结构进行相互比较,揭示了活性中心的开关区域I中丝氨酸203可能作为质子的供体,加速了ATP中gamma-磷酸和beta-磷酸的断裂,从而导致ATP的水解.