Identification of a new hybrid serum response factor and myocyte enhancer factor 2-binding element in MyoD enhancer required for MyoD expression during myogenesis

MyoD is a critical myogenic factor induced rapidly upon activation of quiescent satellite cells, and required for their differentiation during muscle regeneration. One of the two enhancers of MyoD, the distal regulatory region, is essential for MyoD expression in postnatal muscle. This enhancer contains a functional divergent serum response factor (SRF)-binding CArG element required for MyoD expression during myoblast growth and muscle regeneration in vivo. Electrophoretic mobility shift assay, chromatin immunoprecipitation, and microinjection analyses show this element is a hybrid SRF- and MEF2 Binding (SMB) sequence where myocyte enhancer factor 2 (MEF2) complexes can compete out binding of SRF at the onset of differentiation. As cells differentiate into postmitotic myotubes, MyoD expression no longer requires SRF but instead MEF2 binding to this dual-specificity element. As such, the MyoD enhancer SMB element is the site for a molecular relay where MyoD expression is first initiated in activated satellite cells in an SRF-dependent manner and then increased and maintained by MEF2 binding in differentiated myotubes. Therefore, SMB is a DNA element with dual and stage-specific binding activity, which modulates the effects of regulatory proteins critical in controlling the balance between proliferation and differentiation.     

Northward displacement of optimal climate conditions for ecotypes of Eriophorum vaginatum L. across a latitudinal gradient in Alaska

Plants are often genetically specialized as ecotypes attuned to local environmental conditions. When conditions change, the optimal environment may be physically displaced from the local population, unless dispersal or in situ evolution keep pace, resulting in a phenomenon called adaptational lag. Using a 30‐year‐old reciprocal transplant study across a 475 km latitudinal gradient, we tested the adaptational lag hypothesis by measuring both short‐term (tiller population growth rates) and long‐term (17‐year survival) fitness components of Eriophorum vaginatum ecotypes in Alaska, where climate change may have already displaced the optimum. Analyzing the transplant study as a climate transfer experiment, we showed that the climate optimum for plant performance was displaced ca. 140 km north of home sites, although plants were not generally declining in size at home sites. Adaptational lag is expected to be widespread globally for long‐lived, ecotypically specialized plants, with disruptive consequences for communities and ecosystems.     

Tiller population dynamics of reciprocally transplanted Eriophorum vaginatum L. ecotypes in a changing climate

Moist tussock tundra, dominated by the sedge Eriophorum vaginatum L., covers approximately 3.36 × 10⁸ km² of arctic surface area along with large amounts of subarctic land area. Eriophorum vaginatum exhibits ecotypic differentiation along latitudinal gradients in Alaska. While ecotypic differentiation may be beneficial during periods of climate stability, it may be detrimental as climate changes, causing adaptational lag. Following harvest of a 30-year reciprocal transplant experiment, age-specific demographic data on E. vaginatum tillers were collected to parameterize a Leslie matrix. Yellow Taxi analysis, based on Tukey's Jackknife, was used to determine mean pseudovalues of tiller population growth rate () for four source populations of E. vaginatum tussocks that were transplanted to each of three gardens along a latitudinal gradient. Source populations responded differentially along the latitudinal gradient. Survival and daughter tiller production influenced differences seen at the mid-latitude garden, and the overall tiller population performance was generally improved by northward transplanting relative to southward transplanting. A comparison of home-source and away-source within the same transplant garden indicates no home-site advantage. Although populations were still growing when transplanted to home-sites ( = 1.056), tiller population growth rate increased as ΔGDD became more negative relative to the home site (i.e., as tussocks were transplanted north). These results imply that populations are affected by climate gradients in a manner consistent with adaptational lag. This study documenting the response of high-latitude ecotypes to climate gradients may be an indication of the possible future effects of climate shift in more southern latitudes.     

Insulin and wnt1 pathways cooperate to induce reserve cell activation in differentiation and myotube hypertrophy

During ex vivo myoblast differentiation, a pool of quiescent mononucleated myoblasts, reserve cells, arise alongside myotubes. Insulin/insulin-like growth factor (IGF) and PKB/Akt-dependent phosphorylation activates skeletal muscle differentiation and hypertrophy. We have investigated the role of glycogen synthase kinase 3 (GSK-3) inhibition by protein kinase B (PKB)/Akt and Wnt/beta-catenin pathways in reserve cell activation during myoblast differentiation and myotube hypertrophy. Inhibition of GSK-3 by LiCl or SB216763, restored insulin-dependent differentiation of C2ind myoblasts in low serum, and cooperated with insulin in serum-free medium to induce MyoD and myogenin expression in C2ind myoblasts, quiescent C2 or primary human reserve cells. We show that LiCl treatment induced nuclear accumulation of beta-catenin in C2 myoblasts, thus mimicking activation of canonical Wnt signaling. Similarly to the effect of GSK-3 inhibitors with insulin, coculturing C2 reserve cells with Wnt1-expressing fibroblasts enhanced insulin-stimulated induction of MyoD and myogenin in reserve cells. A similar cooperative effect of LiCl or Wnt1 with insulin was observed during late ex vivo differentiation and promoted increased size and fusion of myotubes. We show that this synergistic effect on myotube hypertrophy involved an increased fusion of reserve cells into preexisting myotubes. These data reveal insulin and Wnt/beta-catenin pathways cooperate in muscle cell differentiation through activation and recruitment of satellite cell-like reserve myoblasts.     

Are Socioeconomic Benefits of Restoration Adequately Quantified? A Meta‐analysis of Recent Papers (2000–2008) in Restoration Ecology and 12 Other Scientific Journals

Many ecosystems have been transformed, or degraded by human use, and restoration offers an opportunity to recover services and benefits, not to mention intrinsic values. We assessed whether restoration scientists and practitioners use their projects to demonstrate the benefits restoration can provide in their peer‐reviewed publications. We evaluated a sample of the academic literature to determine whether links are made explicit between ecological restoration, society, and public policy related to natural capital. We analyzed 1,582 peer‐reviewed papers dealing with ecological restoration published between 1 January 2000 and 30 September 2008 in 13 leading scientific journals. As selection criterion, we considered papers that contained either “restoration” or “rehabilitation” in their title, abstract, or keywords. Furthermore, as one‐third of the papers were published in Restoration Ecology, we used that journal as a reference for comparison with all the other journals. We readily acknowledge that aquatic ecosystems are under‐represented, and that the largely inaccessible gray literature was ignored. Within these constraints, we found clear evidence that restoration practitioners are failing to signal links between ecological restoration, society, and policy, and are underselling the evidence of benefits of restoration as a worthwhile investment for society. We discuss this assertion and illustrate it with samples of our findings—with regards to (1) the geographical and institutional affiliations of authors; (2) the choice of ecosystems studied, methods employed, monitoring schemes applied, and the spatial scale of studies; and (3) weak links to payments for ecosystem service setups, agriculture, and ramifications for public policy.     

Motif-pattern dependence of biomolecular phase separation driven by specific interactions

Eukaryotic cells partition a wide variety of important materials and processes into biomolecular condensates—phase-separated droplets that lack a membrane. In addition to nonspecific electrostatic or hydrophobic interactions, phase separation also depends on specific binding motifs that link together constituent molecules. Nevertheless, few rules have been established for how these ubiquitous specific, saturating, motif-motif interactions drive phase separation. By integrating Monte Carlo simulations of lattice-polymers with mean-field theory, we show that the sequence of heterotypic binding motifs strongly affects a polymer’s ability to phase separate, influencing both phase boundaries and condensate properties (e.g. viscosity and polymer diffusion). We find that sequences with large blocks of single motifs typically form more inter-polymer bonds, which promotes phase separation. Notably, the sequence of binding motifs influences phase separation primarily by determining the conformational entropy of self-bonding by single polymers. This contrasts with systems where the molecular architecture primarily affects the energy of the dense phase, providing a new entropy-based mechanism for the biological control of phase separation.     

Information processing and signal integration in bacterial quorum sensing

Bacteria communicate using secreted chemical signaling molecules called autoinducers in a process known as quorum sensing. The quorum‐sensing network of the marine bacterium Vibrio harveyi uses three autoinducers, each known to encode distinct ecological information. Yet how cells integrate and interpret the information contained within these three autoinducer signals remains a mystery. Here, we develop a new framework for analyzing signal integration on the basis of information theory and use it to analyze quorum sensing in V. harveyi. We quantify how much the cells can learn about individual autoinducers and explain the experimentally observed input–output relation of the V. harveyi quorum‐sensing circuit. Our results suggest that the need to limit interference between input signals places strong constraints on the architecture of bacterial signal‐integration networks, and that bacteria probably have evolved active strategies for minimizing this interference. Here, we analyze two such strategies: manipulation of autoinducer production and feedback on receptor number ratios.     

Precision and kinetics of adaptation in bacterial chemotaxis

The chemotaxis network of the bacterium Escherichia coli is perhaps the most studied model for adaptation of a signaling system to persistent stimuli. Although adaptation in this system is generally considered to be precise, there has been little effort to quantify this precision, or to understand how and when precision fails. Using a Förster resonance energy transfer-based reporter of signaling activity, we undertook a systematic study of adaptation kinetics and precision in E. coli cells expressing a single type of chemoreceptor (Tar). Quantifiable loss of precision of adaptation was observed at levels of the attractant MeAsp as low 10 μM, with pronounced differences in both kinetics and precision of adaptation between addition and removal of attractant. Quantitative modeling of the kinetic data suggests that loss of precise adaptation is due to a slowing of receptor methylation as available modification sites become scarce. Moreover, the observed kinetics of adaptation imply large cell-to-cell variation in adaptation rates—potentially providing genetically identical cells with the ability to “hedge their bets” by pursuing distinct chemotactic strategies.     

A highly sensitive method for analysis of 7-dehydrocholesterol for the study of Smith-Lemli-Opitz syndrome

We describe a highly sensitive method for the detection of 7-dehydrocholesterol (7-DHC), the biosynthetic precursor of cholesterol, based on its reactivity with 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD) in a Diels-Alder cycloaddition reaction. Samples of biological tissues and fluids with added deuterium-labeled internal standards were derivatized with PTAD and analyzed by LC-MS. This protocol permits fast processing of samples, short chromatography times, and high sensitivity. We applied this method to the analysis of cells, blood, and tissues from several sources, including human plasma. Another innovative aspect of this study is that it provides a reliable and highly reproducible measurement of 7-DHC in 7-dehydrocholesterol reductase (Dhcr7)-HET mouse (a model for Smith-Lemli-Opitz syndrome) samples, showing regional differences in the brain tissue. We found that the levels of 7-DHC are consistently higher in Dhcr7-HET mice than in controls, with the spinal cord and peripheral nerve showing the biggest differences. In addition to 7-DHC, sensitive analysis of desmosterol in tissues and blood was also accomplished with this PTAD method by assaying adducts formed from the PTAD “ene” reaction. The method reported here may provide a highly sensitive and high throughput way to identify at-risk populations having errors in cholesterol biosynthesis.     

Episodic secretion of opioid activity in human plasma and monkey CSF: Evidence for a diurnal rhythm

Using a radioreceptor assay, opioiod activity has been determined in human plasma and monkey CSF at two-hour intervals across a 24-hour period. In both human plasma and monkey CSF, opioid activity showed an episodic secretion and a significant variation over time, suggesting a diurnal rhythm with increased levels in the morning. This rhythm is similar to those of adrenocorticotropin and beta-lipotropin (LPH) and reciprocal to the diurnal rhythm of pain sensitivity.