The information, control, and value models of mobile health-driven empowerment.

Mobile health tools are often said to empower users by providing them with the information they need to exercise control over their health. We aim to bring clarity to this claim, and in doing so explore the relationship between empowerment and autonomy. We have identified three distinct models embedded in the empowerment rhetoric: empowerment as information, empowerment as control, and empowerment as values. Each distinct model of empowerment gives rise to an associated problem. These problems, the Problem of Interpretation, the Value Alignment Problem, and the Priority Problem, show that mobile health tools in their current form are either insufficient for empowerment or are self-defeating. These digital health technologies encourage users to adopt an individualized conception of autonomy, one that may weaken the doctor-patient relationship and undermine practices in shared decision making, and ultimately may not deliver on improving the health outcomes for those that need it the most.

Resolving the Dust Bowl paradox of grassland responses to extreme drought.

During the 1930s Dust Bowl drought in the central United States, species with the C3 photosynthetic pathway expanded throughout C4-dominated grasslands. This widespread increase in C3 grasses during a decade of low rainfall and high temperatures is inconsistent with well-known traits of C3 vs. C4 pathways. Indeed, water use efficiency is generally lower, and photosynthesis is more sensitive to high temperatures in C3 than C4 species, consistent with the predominant distribution of C3 grasslands in cooler environments and at higher latitudes globally. We experimentally imposed extreme drought for 4 y in mixed C3/C4 grasslands in Kansas and Wyoming and, similar to Dust Bowl observations, also documented three- to fivefold increases in C3/C4 biomass ratios. To explain these paradoxical responses, we first analyzed long-term climate records to show that under nominal conditions in the central United States, C4 grasses dominate where precipitation and air temperature are strongly related (warmest months are wettest months). In contrast, C3 grasses flourish where precipitation inputs are less strongly coupled to warm temperatures. We then show that during extreme drought years, precipitation-temperature relationships weaken, and the proportion of precipitation falling during cooler months increases. This shift in precipitation seasonality provides a mechanism for C3 grasses to respond positively to multiyear drought, resolving the Dust Bowl paradox. Grasslands are globally important biomes and increasingly vulnerable to direct effects of climate extremes. Our findings highlight how extreme drought can indirectly alter precipitation seasonality and shift ecosystem phenology, affecting function in ways not predictable from key traits of C3 and C4 species.

High-performance organic pseudocapacitors via molecular contortion.

Pseudocapacitors harness unique charge-storage mechanisms to enable high-capacity, rapidly cycling devices. Here we describe an organic system composed of perylene diimide and hexaazatrinaphthylene exhibiting a specific capacitance of 689 F g-1 at a rate of 0.5 A g-1, stability over 50,000 cycles, and unprecedented performance at rates as high as 75 A g-1. We incorporate the material into two-electrode devices for a practical demonstration of its potential in next-generation energy-storage systems. We identify the source of this exceptionally high rate charge storage as surface-mediated pseudocapacitance, through a combination of spectroscopic, computational and electrochemical measurements. By underscoring the importance of molecular contortion and complementary electronic attributes in the selection of molecular components, these results provide a general strategy for the creation of organic high-performance energy-storage materials.

Defining codominance in plant communities.

Species dominance and biodiversity in plant communities have received considerable attention and characterisation. However, species codominance, while often alleged, is seldom defined or quantified. Codominance is a common phenomenon and is likely to be an important driver of community structure, ecosystem function and the stability of both. Here we review the use of the term 'codominance' and find inconsistencies in its use, suggesting that the scientific community currently lacks a universal understanding of codominance. We address this issue by: (1) qualitatively defining codominance as mostly shared abundance that is distinctively isolated within a subset of a community, and (2) presenting a novel metric for quantifying the degree to which relative abundances are shared among a codominant subset of plant species, while also accounting for the remaining species within a plant community. Using both simulated and real-world data, we then demonstrate the process of applying the codominance metric to compare communities and to generate a quantitatively defensible subset of species to consider codominant within a community. We show that our metric effectively distinguishes the degree of codominance between four types of grassland ecosystems as well as simulated ecosystems with varying degrees of abundance sharing among community members. Overall, we make the case that increased research focusses on the conditions under which codominance occurs and the consequences for species coexistence, community structure and ecosystem function that would considerably advance the fields of community and ecosystem ecology.

Is a drought a drought in grasslands? Productivity responses to different types of drought.

Drought, defined as a marked deficiency of precipitation relative to normal, occurs as periods of below-average precipitation or complete failure of precipitation inputs, and can be limited to a single season or prolonged over multiple years. Grasslands are typically quite sensitive to drought, but there can be substantial variability in the magnitude of loss of ecosystem function. We hypothesized that differences in how drought occurs may contribute to this variability. In four native Great Plains grasslands (three C4- and one C3-dominated) spanning a ~ 500-mm precipitation gradient, we imposed drought for four consecutive years by (1) reducing each rainfall event by 66% during the growing season (chronic drought) or (2) completely excluding rainfall during a shorter portion of the growing season (intense drought). The drought treatments were similar in magnitude but differed in the following characteristics: event number, event size and length of dry periods. We observed consistent drought-induced reductions (28-37%) in aboveground net primary production (ANPP) only in the C4-dominated grasslands. In general, intense drought reduced ANPP more than chronic drought, with little evidence that drought duration altered this pattern. Conversely, belowground net primary production (BNPP) was reduced by drought in all grasslands (32-64%), with BNPP reductions greater in intense vs. chronic drought treatments in the most mesic grassland. We conclude that grassland productivity responses to drought did not strongly differ between these two types of drought, but when differences existed, intense drought consistently reduced function more than chronic drought.

A circuit mechanism for differentiating positive and negative associations.

The ability to differentiate stimuli predicting positive or negative outcomes is critical for survival, and perturbations of emotional processing underlie many psychiatric disease states. Synaptic plasticity in the basolateral amygdala complex (BLA) mediates the acquisition of associative memories, both positive and negative. Different populations of BLA neurons may encode fearful or rewarding associations, but the identifying features of these populations and the synaptic mechanisms of differentiating positive and negative emotional valence have remained unknown. Here we show that BLA neurons projecting to the nucleus accumbens (NAc projectors) or the centromedial amygdala (CeM projectors) undergo opposing synaptic changes following fear or reward conditioning. We find that photostimulation of NAc projectors supports positive reinforcement while photostimulation of CeM projectors mediates negative reinforcement. Photoinhibition of CeM projectors impairs fear conditioning and enhances reward conditioning. We characterize these functionally distinct neuronal populations by comparing their electrophysiological, morphological and genetic features. Overall, we provide a mechanistic explanation for the representation of positive and negative associations within the amygdala.

Firing Rate Homeostasis Can Occur in the Absence of Neuronal Activity-Regulated Transcription.

Despite dynamic inputs, neuronal circuits maintain relatively stable firing rates over long periods. This maintenance of firing rate, or firing rate homeostasis, is likely mediated by homeostatic mechanisms such as synaptic scaling and regulation of intrinsic excitability. Because some of these homeostatic mechanisms depend on transcription of activity-regulated genes, including Arc and Homer1a, we hypothesized that activity-regulated transcription would be required for firing rate homeostasis. Surprisingly, however, we found that cultured mouse cortical neurons from both sexes grown on multi-electrode arrays homeostatically adapt their firing rates to persistent pharmacological stimulation even when activity-regulated transcription is disrupted. Specifically, we observed firing rate homeostasis in Arc knock-out neurons, as well as knock-out neurons lacking the activity-regulated transcription factors AP1 and SRF. Firing rate homeostasis also occurred normally during acute pharmacological blockade of transcription. Thus, firing rate homeostasis in response to increased neuronal activity can occur in the absence of neuronal-activity-regulated transcription.SIGNIFICANCE STATEMENT Neuronal circuits maintain relatively stable firing rates even in the face of dynamic circuit inputs. Understanding the molecular mechanisms that enable this firing rate homeostasis could potentially provide insight into neuronal diseases that present with an imbalance of excitation and inhibition. It has long been proposed that activity-regulated transcription could underlie firing rate homeostasis because activity-regulated genes turn on when neurons are above their target firing rates and include many genes that could regulate firing rate. Surprisingly, despite this prediction, we found that cortical neurons can undergo firing rate homeostasis in the absence of activity-regulated transcription, indicating that firing rate homeostasis can be controlled by non-transcriptional mechanisms.

High-throughput functional comparison of promoter and enhancer activities.

Promoters initiate RNA synthesis, and enhancers stimulate promoter activity. Whether promoter and enhancer activities are encoded distinctly in DNA sequences is unknown. We measured the enhancer and promoter activities of thousands of DNA fragments transduced into mouse neurons. We focused on genomic loci bound by the neuronal activity-regulated coactivator CREBBP, and we measured enhancer and promoter activities both before and after neuronal activation. We find that the same sequences typically encode both enhancer and promoter activities. However, gene promoters generate more promoter activity than distal enhancers, despite generating similar enhancer activity. Surprisingly, the greater promoter activity of gene promoters is not due to conventional core promoter elements or splicing signals. Instead, we find that particular transcription factor binding motifs are intrinsically biased toward the generation of promoter activity, whereas others are not. Although the specific biases we observe may be dependent on experimental or cellular context, our results suggest that gene promoters are distinguished from distal enhancers by specific complements of transcriptional activators.

Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis.

Pharmacological perturbation is a powerful tool for understanding mRNA synthesis, but identification of the specific steps of this multi-step process that are targeted by small molecules remains challenging. Here we applied strand-specific total RNA sequencing (RNA-seq) to identify and distinguish specific pharmacological effects on transcription and pre-mRNA processing in human cells. We found unexpectedly that the natural product isoginkgetin, previously described as a splicing inhibitor, inhibits transcription elongation. Compared to well-characterized elongation inhibitors that target CDK9, isoginkgetin caused RNA polymerase accumulation within a broader promoter-proximal band, indicating that elongation inhibition by isoginkgetin occurs after release from promoter-proximal pause. RNA-seq distinguished isoginkgetin and CDK9 inhibitors from topoisomerase I inhibition, which alters elongation across gene bodies. We were able to detect these and other specific defects in mRNA synthesis at low sequencing depth using simple metagene-based metrics. These metrics now enable total-RNA-seq-based screening for high-throughput identification of pharmacological effects on individual stages of mRNA synthesis.

MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments.

MOTIVATION: With the rapid advances in DNA synthesis and sequencing technologies and the continuing decline in the associated costs, high-throughput experiments can be performed to investigate the regulatory role of thousands of oligonucleotide sequences simultaneously. Nevertheless, designing high-throughput reporter assay experiments such as massively parallel reporter assays (MPRAs) and similar methods remains challenging. RESULTS: We introduce MPRAnator, a set of tools that facilitate rapid design of MPRA experiments. With MPRA Motif design, a set of variables provides fine control of how motifs are placed into sequences, thereby allowing the investigation of the rules that govern transcription factor (TF) occupancy. MPRA single-nucleotide polymorphism design can be used to systematically examine the functional effects of single or combinations of single-nucleotide polymorphisms at regulatory sequences. Finally, the Transmutation tool allows for the design of negative controls by permitting scrambling, reversing, complementing or introducing multiple random mutations in the input sequences or motifs. AVAILABILITY AND IMPLEMENTATION: MPRAnator tool set is implemented in Python, Perl and Javascript and is freely available at www.genomegeek.com and www.sanger.ac.uk/science/tools/mpranator The source code is available on www.github.com/hemberg-lab/MPRAnator/ under the MIT license. The REST API allows programmatic access to MPRAnator using simple URLs. CONTACT: igs@sanger.ac.uk or mh26@sanger.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.

A reality check for climate change experiments: Do they reflect the real world?

Experiments are widely used in ecology, particularly for assessing global change impacts on ecosystem function. However, results from experiments often are inconsistent with observations made under natural conditions, suggesting the need for rigorous comparisons of experimental and observational studies. We conducted such a "reality check" for a grassland ecosystem by compiling results from nine independently conducted climate change experiments. Each experiment manipulated growing season precipitation (GSP) and measured responses in aboveground net primary production (ANPP). We compared results from experiments with long-term (33-yr) annual precipitation and ANPP records to ask if collectively (n = 44 experiment-years) experiments yielded estimates of ANPP, rain-use efficiency (RUE, grams per square meter ANPP per mm precipitation), and the relationship between GSP and ANPP comparable to observations. We found that mean ANPP and RUE from experiments did not deviate from observations. Experiments and observational data also yielded similar functional relationships between ANPP and GSP, but only within the range of historically observed GSP. Fewer experiments imposed extreme levels of GSP (outside the observed 33-yr record), but when these were included, they altered the GSP-ANPP relationship. This result underscores the need for more experiments imposing extreme precipitation levels to resolve how forecast changes in climate regimes will affect ecosystem function in the future.

Brain-wide maps of Fos expression during fear learning and recall.

Fos induction during learning labels neuronal ensembles in the hippocampus that encode a specific physical environment, revealing a memory trace. In the cortex and other regions, the extent to which Fos induction during learning reveals specific sensory representations is unknown. Here we generate high-quality brain-wide maps of Fos mRNA expression during auditory fear conditioning and recall in the setting of the home cage. These maps reveal a brain-wide pattern of Fos induction that is remarkably similar among fear conditioning, shock-only, tone-only, and fear recall conditions, casting doubt on the idea that Fos reveals auditory-specific sensory representations. Indeed, novel auditory tones lead to as much gene induction in visual as in auditory cortex, while familiar (nonconditioned) tones do not appreciably induce Fos anywhere in the brain. Fos expression levels do not correlate with physical activity, suggesting that they are not determined by behavioral activity-driven alterations in sensory experience. In the thalamus, Fos is induced more prominently in limbic than in sensory relay nuclei, suggesting that Fos may be most sensitive to emotional state. Thus, our data suggest that Fos expression during simple associative learning labels ensembles activated generally by arousal rather than specifically by a particular sensory cue.

Genomic Views of Transcriptional Enhancers: Essential Determinants of Cellular Identity and Activity-Dependent Responses in the CNS.

Sprinkled throughout the genome are a million regulatory sequences called transcriptional enhancers that activate gene promoters in the right cells, at the right time. Enhancers endow the brain with its incredible diversity of cell types and also translate neural activity into gene induction. Thanks to rapid advances in genomic technologies, it is now possible to identify thousands of enhancers rapidly, test their transcriptional function en masse, and address their neurobiological functions via genome editing. Enhancers also promise to be a great technological opportunity for neuroscience, offering the potential for cell-type-specific genetic labeling and manipulation without the need for transgenesis. The objective of this review and the accompanying 2015 SfN mini-symposium is to highlight the use of new and emerging genomic technologies to probe enhancer function in the nervous system. SIGNIFICANCE STATEMENT: Transcriptional enhancers turn on genes in the right cells, at the right time. Enhancers are also the genomic sequences that encode the incredible diversity of cell types in the brain and enable the brain to turn genes on in response to new experiences. New technology enables enhancers to be found and manipulated. The study of enhancers promises to inform our understanding of brain development and function. The application of enhancer technology holds promise in accelerating basic neuroscience research and enabling gene therapies to be targeted to specific cell types in the brain.

Underappreciated problems of low replication in ecological field studies.

The cost and difficulty of manipulative field studies makes low statistical power a pervasive issue throughout most ecological subdisciplines. Ecologists are already aware that small sample sizes increase the probability of committing Type II errors. In this article, we address a relatively unknown problem with low power: underpowered studies must overestimate small effect sizes in order to achieve statistical significance. First, we describe how low replication coupled with weak effect sizes leads to Type M errors, or exaggerated effect sizes. We then conduct a meta-analysis to determine the average statistical power and Type M error rate for manipulative field experiments that address important questions related to global change; global warming, biodiversity loss, and drought. Finally, we provide recommendations for avoiding Type M errors and constraining estimates of effect size from underpowered studies.

Widespread transcription at neuronal activity-regulated enhancers.

We used genome-wide sequencing methods to study stimulus-dependent enhancer function in mouse cortical neurons. We identified approximately 12,000 neuronal activity-regulated enhancers that are bound by the general transcriptional co-activator CBP in an activity-dependent manner. A function of CBP at enhancers may be to recruit RNA polymerase II (RNAPII), as we also observed activity-regulated RNAPII binding to thousands of enhancers. Notably, RNAPII at enhancers transcribes bi-directionally a novel class of enhancer RNAs (eRNAs) within enhancer domains defined by the presence of histone H3 monomethylated at lysine 4. The level of eRNA expression at neuronal enhancers positively correlates with the level of messenger RNA synthesis at nearby genes, suggesting that eRNA synthesis occurs specifically at enhancers that are actively engaged in promoting mRNA synthesis. These findings reveal that a widespread mechanism of enhancer activation involves RNAPII binding and eRNA synthesis.

Recent advances in functional assays of transcriptional enhancers.

In this special edition of Genomics, we present reviews of the current state of the field in identifying and functionally understanding transcriptional enhancers in cells and developing tissues. Typically several enhancers coordinate the expression of an individual target gene, each controlling that gene's expression in specific cell types at specific times. Until recently, identifying each gene's enhancers had been challenging because enhancers do not occupy prescribed locations relative to their target genes. Recently there have been powerful advances in DNA sequencing and other technologies that make it possible to identify the majority of enhancers in virtually any cell type of interest. The reviews in this edition of Genomics highlight some of these new and powerful approaches.

Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites.

More than 98% of a typical vertebrate genome does not code for proteins. Although non-coding regions are sprinkled with short (<200 bp) islands of evolutionarily conserved sequences, the function of most of these unannotated conserved islands remains unknown. One possibility is that unannotated conserved islands could encode non-coding RNAs (ncRNAs); alternatively, unannotated conserved islands could serve as promoter-distal regulatory factor binding sites (RFBSs) like enhancers. Here we assess these possibilities by comparing unannotated conserved islands in the human and mouse genomes to transcribed regions and to RFBSs, relying on a detailed case study of one human and one mouse cell type. We define transcribed regions by applying a novel transcript-calling algorithm to RNA-Seq data obtained from total cellular RNA, and we define RFBSs using ChIP-Seq and DNAse-hypersensitivity assays. We find that unannotated conserved islands are four times more likely to coincide with RFBSs than with unannotated ncRNAs. Thousands of conserved RFBSs can be categorized as insulators based on the presence of CTCF or as enhancers based on the presence of p300/CBP and H3K4me1. While many unannotated conserved RFBSs are transcriptionally active to some extent, the transcripts produced tend to be unspliced, non-polyadenylated and expressed at levels 10 to 100-fold lower than annotated coding or ncRNAs. Extending these findings across multiple cell types and tissues, we propose that most conserved non-coding genomic DNA in vertebrate genomes corresponds to promoter-distal regulatory elements.