Do Trees Grow on Money? Auxin as the Currency of the Cellular Economy

Auxin plays a role in nearly every aspect of a plant''s life. Signals from the developmental program, physiological status, and encounters with other organisms all converge on the auxin pathway. The molecular mechanisms facilitating these interactions are diverse; yet, common themes emerge. Auxin can be regulated by modulating rates of biosynthesis, conjugation, and transport, as well as sensitivity of a cell to the auxin signal. In this article, we describe some well-studied examples of auxin''s interactions with other pathways.It has often been said—sometimes in joyful wonderment, sometimes in teeth-grinding frustration—auxin does everything. Although the major molecular details of the auxin pathway are largely known, many questions remain about how this one simple signaling molecule is responsible for directing so many diverse responses. The focus of this article is to try to illustrate several themes of how auxin acts in concert with other pathways to trigger specific cellular events in time and space.One potentially useful analogy in trying to understand auxin''s complicated roles is to think of it as money. Auxin does not have much intrinsic value—it stores very little energy or raw materials. However, like paper currency, it has great symbolic value, as an easily circulated means of facilitating transactions in the dynamic economy of plant life. As with currency, the amount, form, and location of auxin affects which transactions are possible. Other factors, such as what commodities are available in a given time and place, constrain which transactions auxin can facilitate. For instance, you cannot usually buy a goldfish at a shoe store, and it is quite challenging to purchase an ice cream sundae at 8 am.Here, we describe some of the ways in which the developmental program, the abiotic environment, the circadian clock, other hormones, and other organisms modify the auxin response. Auxin can be regulated by modulating rates of biosynthesis, conjugation, and transport, as well as sensitivity of a cell to the auxin signal. In addition, the dominant pathway of biosynthesis, the composition and levels of IAA conjugates, the direction of auxin transport, and the downstream consequences of sensing auxin can all be radically altered by the cellular milieu. These context-specific networks help shape the outcome (transactions) of cellular exposure to auxin. Each of the networks impinging on the cellular response to auxin could easily fill a long article (or entire collection) on their own. For brevity''s sake, only a handful of examples will be described highlighting some of the molecular mechanisms by which other signaling networks intersect with the auxin pathway.     

Do Changes in the Pace of Events Affect One-Off Judgments of Duration?

Five experiments examined whether changes in the pace of external events influence people’s judgments of duration. In Experiments 1a–1c, participants heard pieces of music whose tempo accelerated, decelerated, or remained constant. In Experiment 2, participants completed a visuo-motor task in which the rate of stimulus presentation accelerated, decelerated, or remained constant. In Experiment 3, participants completed a reading task in which facts appeared on-screen at accelerating, decelerating, or constant rates. In all experiments, the physical duration of the to-be-judged interval was the same across conditions. We found no significant effects of temporal structure on duration judgments in any of the experiments, either when participants knew that a time estimate would be required (prospective judgments) or when they did not (retrospective judgments). These results provide a starting point for the investigation of how temporal structure affects one-off judgments of duration like those typically made in natural settings.     

How Effective Are DNA Barcodes in the Identification of African Rainforest Trees?

Background

DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species.

Methodology/Principal Findings

We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95–100% success), but less for species identification (71–88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84–90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA.

Conclusions/Significance

Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.     

Do Correlation Patterns Reflect the Role of Development in Morphological Evolution?

Correlation patterns have been widely used in evolutionary studies for exploring the role of development in channelling morphological evolution. The approach was firstly introduced by Olson and Miller in the 1950s, but it did not gain prominence until the 1980s, due to some extent to Gould and Lewontin’s (Proc R Soc Lond B 205:581–598, 1979) assertion of the importance of considering organisms as integrated entities, where the internal organization of a structure, and not only the selective regime acting upon it, would play a fundamental role in its evolution. Here we show that this approach, mainly focused on the study of small, quantitative shape changes of existing structures, does not deal with a fundamental aspect of developmental systems, that is, their intrinsic capacity of originating morphological novelties. We show that only when the physicochemical processes underlying morphogenesis and pattern formation are taken into account, would the causal role of development be fully incorporated into the evolutionary view.     

The Chilling Effect: How Do Researchers React to Controversy?

Background

Can political controversy have a “chilling effect” on the production of new science? This is a timely concern, given how often American politicians are accused of undermining science for political purposes. Yet little is known about how scientists react to these kinds of controversies.

Methods and Findings

Drawing on interview (n = 30) and survey data (n = 82), this study examines the reactions of scientists whose National Institutes of Health (NIH)-funded grants were implicated in a highly publicized political controversy. Critics charged that these grants were “a waste of taxpayer money.” The NIH defended each grant and no funding was rescinded. Nevertheless, this study finds that many of the scientists whose grants were criticized now engage in self-censorship. About half of the sample said that they now remove potentially controversial words from their grant and a quarter reported eliminating entire topics from their research agendas. Four researchers reportedly chose to move into more secure positions entirely, either outside academia or in jobs that guaranteed salaries. About 10% of the group reported that this controversy strengthened their commitment to complete their research and disseminate it widely.

Conclusions

These findings provide evidence that political controversies can shape what scientists choose to study. Debates about the politics of science usually focus on the direct suppression, distortion, and manipulation of scientific results. This study suggests that scholars must also examine how scientists may self-censor in response to political events.     

Janus-Faced Autophagy: A Dual Role of Cellular Self-Eating in Neurodegeneration?

Autophagy is a highly regulated cellular pathway used by eukaryotic cells to consume parts of their constituents during development or starvation. It is associated with extensive rearrangements of intracellular membranes, and involves the cooperation of many gene products in the regulation and execution phase by largely unknown mechanisms. Recent results strongly indicate the role of autophagy in the degradation of damaged macromolecules, in particular misfolded, aberrant proteins, and in organelle turnover; in mutant mice with reduced autophagy, accumulation of abnormal cytosolic proteins as inclusion bodies and massive cell loss occur similarly to human neurodegenerative disorders. Thus, autophagy seems to prevent neurons from undergoing protein aggregation-induced degeneration. In contrast, we have shown that inactivation of genes involved in autophagosome formation suppresses neuronal demise induced by various hyperactivating ion channel mutations or by neurotoxins in the nematode Caenorhabditis elegans. These results raise the possibility that autophagy may also contribute to excitotoxic necrotic-like cell death. This way, autophagic degradation of cytoplasmic materials might have a dual role in the survival of neurons. Depending on the actual cellular milieu and insulting factor, it can act both as a protector and contributor to neuronal damage.

Addendum to:

Influence of Autophagy Genes on Ion Channel-Dependent Neuronal Degeneration in Caenorhabditis elegans

M.L. Tóth, P. Simon, A.L. Kovács,and T. Vellai

J Cell Sci 2007; 120:1134-41     

How Do Alien Plants Fit in the Space-Phylogeny Matrix?

Recent advances in the field of plant community phylogenetics and invasion phylogenetics are mostly based on plot-level data, which do not take into consideration the spatial arrangement of individual plants within the plot. Here we use within-plot plant coordinates to investigate the link between the physical distance separating plants, and their phylogenetic relatedness. We look at two vegetation types (forest and grassland, similar in species richness and in the proportion of alien invasive plants) in subtropical coastal KwaZulu-Natal, South Africa. The relationship between phylogenetic distance and physical distance is weak in grassland (characterised by higher plant densities and low phylogenetic diversity), and varies substantially in forest vegetation (variable plant density, higher phylogenetic diversity). There is no significant relationship between the proportion of alien plants in the plots and the strength of the physical-phylogenetic distance relationship, suggesting that alien plants are well integrated in the local spatial-phylogenetic landscape.     

To Grow or to Reproduce? The Role of Life-History Plasticity in Food Web Dynamics

The size of an individual is a key feature influencing and determined by a species' life history and ecology. Here, I consider how life-history plasticity within a single species can influence the outcome of food web interactions along a productivity gradient. An individual can either reproduce early but remain susceptible to predators throughout its life (strategy 1) or delay reproduction and grow to a predator-invulnerable size refuge (strategy 2). At low productivity, strategy 1 is favored because the probability of growing to a size refuge is low compared to the probability of being eaten. Here, the system is consumer controlled, and predators have large effects on the food web. At high productivity, strategy 2 is favored because high food availability increases the probability of prey attaining size refuge before being eaten. Consequently, the system becomes less consumer controlled, and predators have weaker effects on food web dynamics. At intermediate productivity, either strategy 1 or strategy 2 can be favored, depending on the initial conditions of the system. Field and laboratory experiments with a common freshwater snail Helisoma trivolis and its insect predator Belostoma flumineum support both the key assumptions and predictions of the models.     

How Old Do You Feel? The Role of Age Discrimination and Biological Aging in Subjective Age

Subjective age, or how young or old individuals experience themselves to be relative to their chronological age, is a crucial construct in gerontology. Subjective age is a significant predictor of important health outcomes, but little is known about the criteria by which individuals'' subjectively evaluate their age. To identify psychosocial and biomedical factors linked to the subjective evaluation of age, this study examined whether perceived age discrimination and markers of biological aging are associated with subjective age. Participants were 4776 adults (M _age = 68) from the 2008 and 2010 waves of the Health and Retirement Study (HRS) who completed measures of subjective age, age discrimination, demographic variables, self-rated health and depression, and had physical health measures, including peak expiratory flow, grip strength, waist circumference, systolic and diastolic blood pressure. Telomere length was available for a subset of participants in the 2008 wave (n = 2214). Regression analysis indicated that perceived age discrimination, lower peak expiratory flow, lower grip strength, and higher waist circumference were associated with an older subjective age, controlling for sociodemographic factors, self-rated health, and depression. In contrast, blood pressure and telomere length were not related to subjective age. These findings are consistent with the hypothesis that how old a person feels depends in part on psychosocial and biomedical factors, including the experiences of ageism and perceptible indices of fitness and biological age.     

How Much Do Metamemory Beliefs Contribute to the Font-Size Effect in Judgments of Learning?

Evidence shows that the font size of study items significantly influences judgments of learning (JOLs) and that people’s JOLs are generally higher for larger words than for smaller words. Previous studies have suggested that font size influences JOLs in a belief-based way. However, few studies have directly examined how much people’s beliefs contribute to the font-size effect in JOLs. This study investigated the degree to which font size influenced JOLs in a belief-based way. In Experiment 1, one group of participants (learners) studied words with different font sizes and made JOLs, whereas another group of participants (observers) viewed the learners'' study phase and made JOLs for the learners. In Experiment 2, participants made both JOLs and belief-based recall predictions for large and small words. Our results suggest that metamemory beliefs play an important role in the font-size effect in JOLs.     

Do Epigenetic Events Take Place in the Vastus Lateralis of Patients with Mild Chronic Obstructive Pulmonary Disease?

Muscle dysfunction is a major comorbidity in Chronic Obstructive Pulmonary Disease (COPD). Several biological mechanisms including epigenetic events regulate muscle mass and function in models of muscle atrophy. Investigations conducted so far have focused on the elucidation of biological mechanisms involved in muscle dysfunction in advanced COPD. We assessed whether the epigenetic profile may be altered in the vastus lateralis of patients with mild COPD, normal body composition, and mildly impaired muscle function and exercise capacity. In vastus lateralis (VL) of mild COPD patients with well-preserved body composition and in healthy age-matched controls, expression of DNA methylation, muscle-enriched microRNAs, histone acetyltransferases (HTAs) and deacetylases (HDACs), protein acetylation, small ubiquitin-related modifier (SUMO) ligases, and muscle structure were explored. All subjects were clinically evaluated. Compared to healthy controls, in the VL of mild COPD patients, muscle function and exercise capacity were moderately reduced, DNA methylation levels did not differ, miR-1 expression levels were increased and positively correlated with both forced expiratory volume in one second (FEV₁) and quadriceps force, HDAC4 protein levels were increased, and muscle fiber types and sizes were not different. Moderate skeletal muscle dysfunction is a relevant feature in patients with mild COPD and preserved body composition. Several epigenetic events are differentially expressed in the limb muscles of these patients, probably as an attempt to counterbalance the underlying mechanisms that alter muscle function and mass. The study of patients at early stages of their disease is of interest as they are a target for timely therapeutic interventions that may slow down the course of the disease and prevent the deleterious effects of major comorbidities.     

Do neurons in the vertebrate CNS migrate on laminin?

In adult rat brain the extracellular matrix glycoprotein, laminin, is found only in basement membranes, but is transiently expressed by astrocytes after brain injury. Here, I show that laminin also appears in immature brain cells during CNS development, and that its presence coincides with phases of neuronal migration. In early embryos, laminin is seen throughout the whole thickness of the forming brain, and is apparently synthesized by the cells, as judged by its intracytoplasmic localization. As development proceeds, intracellular laminin becomes restricted to the periventricular regions while punctate deposits of laminin follow the course of vimentin-positive radial glial fibers. In most brain regions, the adult pattern of laminin expression is achieved by birth. In the post-natal rat cerebellum, however, laminin is detected in external granule cells, in Purkinje cells, and in punctate deposits along the radial Bergmann glial fibers. By day 24 after birth, when the migration of external granule cells is complete, all laminin immunoreactivity disappears from these structures. The transient expression of laminin in regions where neurons are migrating raises the possibility that laminin plays a role in neuronal migration during CNS development.     

Role of the ubiquitin–proteasome system on macrophages in the tumor microenvironment

Tumor-associated macrophages (TAMs) are key components of the tumor microenvironment, and their different polarization states play multiple roles in tumors by secreting cytokines, chemokines, and so on, which are closely related to tumor development. In addition, the enrichment of TAMs is often associated with poor prognosis of tumors. Thus, targeting TAMs is a potential tumor treatment strategy, in which therapeutic approaches such as reducing TAMs numbers, remodeling TAMs phenotypes, and altering their functions are being extensively investigated. Meanwhile, the ubiquitin–proteasome system (UPS), an important mechanism of protein hydrolysis in eukaryotic cells, participates in cellular processes by regulating the activity and stability of key proteins. Interestingly, UPS plays a dual role in the process of tumor development, and its role in TAMs deserve to be investigated in depth. This review builds on this foundation to further explore the multiple roles of UPS on TAMs and identifies a promising approach to treat tumors by targeting TAMs with UPS.     

How Do Astrocytes Participate in Neural Plasticity?

Work over the past 20 years has implicated electrically nonexcitable astrocytes in complex neural functions. Despite controversies, it is increasingly clear that many, if not all, neural processes involve astrocytes. This review critically examines past work to identify the commonalities among the many published studies of neuroglia signaling. Although several studies have shown that astrocytes can impact short-term and long-term synaptic plasticity, further work is required to determine the requirement for astrocytic Ca²⁺ and other second messengers in these processes. One of the roadblocks to the field advancing at a rapid pace has been technical. We predict that the novel experimental tools that have emerged in recent years will accelerate the field and likely disclose an entirely novel path of neuroglia signaling within the near future.The year 2014 represents the 20th anniversary of a pair of papers published by the writers that provided the first indication that astrocytes actively signal to neurons, and that these glial cells have the potential to be participants in the control of neural circuit function and behavior (Nedergaard 1994; Parpura et al. 1994). Although we have taken independent paths, we come together on this anniversary to discuss what we have learned since 1994, where we see the field progressing, and, finally, to discuss some key steps that we believe should be taken in the next decade to begin to further clarify the diverse roles that astrocytes play in brain function in health and disease.Without knowledge of one another’s work, we published a pair of papers that provided the first demonstration that physiological changes in astrocytes influence neurons: stimulated Ca²⁺ changes in astrocytes led to delayed Ca²⁺ responses in neurons (Nedergaard 1994; Parpura et al. 1994). To set the backdrop to these studies, this was a period of explosive growth in Ca²⁺ imaging that resulted from the availability of fluorescent Ca²⁺ indicators and sensitive cameras to permit low-light-level imaging of intracellular biochemistry. As a consequence, there had been several recently published studies revealing that astrocytes show Ca²⁺ elevations in response to mechanical contact or even to the addition of neurotransmitters, such as glutamate (Cornell-Bell et al. 1990). However, the functional downstream consequences were unknown. In our studies, which used a combination of different stimuli—mechanical, optical, as well as a chemical transmitter bradykinin—we were able to show a robust impact of the astrocytic Ca²⁺ signal on the adjacent neurons (Nedergaard 1994; Parpura et al. 1994). Despite differences in mechanistic conclusions, these papers stimulated revised thinking about roles of astrocytes in the brain—perhaps these glial cells were actively signaling, albeit on a slower time scale, to modulate neurons, circuits, and, ultimately, behavior.The subsequent two decades have been spent examining the signaling of astrocytes to neurons in more intact systems. As a consequence of this work, it is clear that astrocytes play critical roles in actively modulating brain function, although we are still putting the pieces of the puzzle in place to understand where, when, and how this process occurs naturally in vivo and when dysfunction can lead to disorders of the brain.The field has gone through an explosive growth that has consisted of several phases. Initially, there was the dish phase in which the potential of the astrocyte was revealed in cell culture. These studies were essential as they captured our imagination and stimulated new thinking; however, they were limited by the fact that the properties of astrocytes can be different in vitro and in vivo. Next, we had the in situ phase, in which we asked whether similar processes could be detected in situ in acutely isolated brain slices. Then we began asking about roles in vivo through Ca²⁺ imaging together with two-photon microscopy as well as with molecular genetic alterations to permit the inhibition and stimulation of astrocytes. Each of these phases has offered unique insights, challenges, and opportunities for the field.Through all of these phases, an emergent picture is developing in which it is without doubt that astrocytes play important roles in vivo but that the mechanisms are so diverse and complex that an understanding is still to emerge.Some of the major challenges that we have faced and continue to face include: What are the endogenous signals of these glial cells? How can we stimulate astrocytes in a physiologically relevant manner? How can we inhibit astrocytes to determine when they are needed for brain function? And last, but by no means least, how diverse are astrocytes?We are still at the early days of understanding astrocytes, and patience regarding functional interpretation is required. We make this statement because there have been apparently contradictory conclusions drawn from different studies. The individual observations are important as they help provide a fuller picture of the biology of these complex cells. However, the jury still needs further evidence before definitive conclusions can be drawn. For example, a plethora of studies have shown that Ca²⁺ signals stimulate gliotransmission and the consequent modulation of neurons and synapses (see Agulhon et al. 2010), the field was rocked. We do not question the data of the study; instead, we believe this is an important piece of information that ultimately needs to be put in context. In contrast, additional studies have shown that IP₃ receptors are important for other aspects of astrocyte-induced synaptic modulation. A more recent study has shown that, in addition to Ca²⁺ release from internal stores, the influx of Ca²⁺ through transient receptor potential (TRP) channels is important for gliotransmission (Shigetomi et al. 2013). Clearly, such influx sites were unlikely to have been affected by the IP₃R₂ knockout and were shown to regulate d-serine release from the astrocyte. Another piece of the puzzle is added. Undoubtedly, there will be further twists and turns, but that is the joy of discovery, and it should be embraced.

Table 1.

Effect of Ca²⁺ signaling on excitatory or inhibitory potentials, slow inward current, synaptic failure, or neural bistability