bluuebunny/crossref_metadata_2025 huggingface dataset:
A coupled bubble plume–reservoir model for hypolimnetic oxygenation
Authors: Singleton V. L. , Rueda F. J. , Little J. C.
Published: December 2010

A model for a linear bubble plume used for hypolimnetic oxygenation was coupled with a three‐dimensional hydrodynamic model to simulate the complex interaction between bubble plumes and the large‐scale processes of transport and mixing. The coupled model accurately simulated the evolution of dissolved oxygen (DO) and temperature fields that occurred during two full‐scale diffuser tests in a water supply reservoir. The prediction of asymmetric circulation cells laterally and longitudinally on both sides of the linear diffuser was due to the uneven reservoir bathymetry. Simulation of diffuser operation resulted in baroclinic pressure gradients, which caused vertical oscillations above the hypolimnion and contributed to distribution of plume detrainment upstream and downstream of the diffuser. On the basis of a first‐order variance analysis, the largest source of uncertainty for both predicted DO and temperature was the model bathymetry, which accounted for about 90% of the overall uncertainty. Because the oxygen addition rate was 4 times the sediment oxygen uptake (SOU) rate, DO predictions were not sensitive to SOU. In addition to bathymetry, the momentum assigned to plume entrainment and detrainment is a significant source of uncertainty in the coupled model structure and appreciably affects the predicted intensity of mixing and lake circulation. For baseline runs, the entrainment and detrainment velocities were assumed to be half of the velocities through the flux face of the grid cells. Additional research on appropriate values of the plume detrainment momentum for the coupled model is required.
Global slab deformation and centroid moment tensor constraints on viscosity
Authors: Alpert L. A. , Becker T. W. , Bailey I. W.
Published: December 2010

We analyze moment tensor solutions from deep subduction zone earthquakes to determine global slab deformation patterns. Inferred strain rates are compared to predicted deformation patterns from fluid models to help constrain the first‐order radial and lateral viscosity structure of the Earth. While all slabs that reach the lower mantle are compressed at their tip, intermediate depth patterns are more complex. We compute 3‐D spherical flow with various slab rheologies and compare the angular misfit between the compressive eigenvectors of the resultant stress field and global centroid moment tensor (gCMT) solutions. We find that upper mantle slab viscosities of ∼10–100 and lower mantle viscosities of ∼30–100 times the upper mantle produce the best match to gCMTs. A 0.1 viscosity reduction in the asthenosphere seems preferred. Slab geometry and lower mantle viscosity exert significant control on deformation. Inclusion of the phase changes at 410 km and 660 km increases extensional deformation at intermediate depth and compressional deformation at the lower mantle, improving the match to gCMTs for strong slabs. Our conclusions are fairly insensitive to surface boundary conditions. However, models which include net rotations of the surface with respect to the lower mantle produce compression at intermediate depths for west directed slabs and extension for east directed slabs. Without allowing for regional variations, these models yield the best match to gCMTs. While significant deviations between model and seismicity remain, our results show that seismicity provides an underutilized constraint for slab dynamics.
Ring current dynamics in moderate and strong storms: Comparative analysis of TWINS and IMAGE/HENA data with the Comprehensive Ring Current Model
Authors: Buzulukova N. , Fok M.‐C. , Goldstein J. , Valek P. , McComas D. J. , Brandt P. C.
Published: December 2010

We present a comparative study of ring current dynamics during strong and moderate storms. The ring current during the strong storm is studied with IMAGE/HENA data near the solar cycle maximum in 2000. The ring current during the moderate storm is studied using energetic neutral atom (ENA) data from the Two Wide‐Angle Imaging Neutral‐Atom Spectrometers (TWINS) mission during the solar minimum in 2008. For both storms, the local time distributions of ENA emissions show signatures of postmidnight enhancement (PME) during the main phases. To model the ring current and ENA emissions, we use the Comprehensive Ring Current Model (CRCM). CRCM results show that the main‐phase ring current pressure peaks in the premidnight‐dusk sector, while the most intense CRCM‐simulated ENA emissions show PME signatures. We analyze two factors to explain this difference: the dependence of charge‐exchange cross section on energy and pitch angle distributions of ring current. We find that the IMF By effect (twisting of the convection pattern due to By) is not needed to form the PME. Additionally, the PME is more pronounced for the strong storm, although relative shielding and hence electric field skewing is well developed for both events.
Long‐term neutron monitor observations and the 2009 cosmic ray maximum
Authors: Moraal H. , Stoker P. H.
Published: December 2010

The solar minimum of 2009 was characterized by a prolonged increase toward the maximum cosmic ray intensity, which was higher than it was during the maxima of 22 and 44 years ago. In the previous two so‐called qA <0 (solar dipole moment facing South) magnetic cycles, these increases were more sharply peaked than in 2009. The observations of the Sanae, Hermanus, Potchefstroom, and Tsumeb neutron monitors are used to investigate this behavior in terms of propagation conditions due to solar activity, the heliospheric magnetic field, and the profile of the wavy current sheet in the field. This 2009 cosmic ray maximum can only be understood after an investigation of the long‐term cosmic ray record. This study is augmented by observations of eight other neutron monitors. During 2009, solar activity parameters were significantly different from previous solar minima: The sun was much quieter, and the the heliospheric magnetic field was more than 20% weaker than during other recent minima. Both of these parameters imply a higher cosmic ray diffusion coefficient, which provides a natural explanation for both the higher galactic cosmic ray intensities that were observed and the absence of such an effect for anomalous cosmic rays.
Will climate change drive 21st century burn rates in Canadian boreal forest outside of its natural variability: collating global climate model experiments with sedimentary charcoal data
Authors: Bergeron Yves , Cyr Dominic , Girardin Martin P. , Carcaillet Christopher
Published: December 2010

Natural ecosystems have developed within ranges of conditions that can serve as references for setting conservation targets or assessing the current ecological integrity of managed ecosystems. Because of their climate determinism, forest fires are likely to have consequences that could exacerbate biophysical and socioeconomical vulnerabilities in the context of climate change. We evaluated future trends in fire activity under climate change in the eastern Canadian boreal forest and investigated whether these changes were included in the variability observed during the last 7000 years from sedimentary charcoal records from three lakes. Prediction of future annual area burned was made using simulated Monthly Drought Code data collected from an ensemble of 19 global climate model experiments. The increase in burn rate that is predicted for the end of the 21st century (0.45% year–1 with 95% confidence interval (0.32, 0.59) falls well within the long‐term past variability (0.37 to 0.90% year–1). Although our results suggest that the predicted change in burn rates per se will not move this ecosystem to new conditions, the effects of increasing fire incidence cumulated with current rates of clear‐cutting or other low‐retention types of harvesting, which still prevail in this region, remain preoccupying.
Resilience of the boreal forest in response to Holocene fire-frequency changes assessed by pollen diversity and population dynamics
Authors: Carcaillet Christopher , Richard Pierre J. H. , Bergeron Yves , Fréchette Bianca , Ali Adam A.
Published: December 2010

The hypothesis that changes in fire frequency control the long-term dynamics of boreal forests is tested on the basis of paleodata. Sites with different wildfire histories at the regional scale should exhibit different vegetation trajectories. Mean fire intervals and vegetation reconstructions are based respectively on sedimentary charcoal and pollen from two small lakes, one in the Mixedwood boreal forests and the second in the Coniferous boreal forests. The pollen-inferred vegetation exhibits different trajectories of boreal forest dynamics after afforestation, whereas mean fire intervals have no significant or a delayed impact on the pollen data, either in terms of diversity or trajectories. These boreal forests appear resilient to changes in fire regimes, although subtle modifications can be highlighted. Vegetation compositions have converged during the last 1200 years with the decrease in mean fire intervals, owing to an increasing abundance of boreal species at the southern site (Mixedwood), whereas changes are less pronounced at the northern site (Coniferous). Although wildfire is a natural property of boreal ecosystems, this study does not support the hypothesis that changes in mean fire intervals are the key process controlling long-term vegetation transformation. Fluctuations in mean fire intervals alone do not explain the historical and current distribution of vegetation, but they may have accelerated the climatic process of borealisation, likely resulting from orbital forcing.
Variation in local weather explains differences in fire regimes within a Québec south-eastern boreal forest landscape
Authors: Drobyshev Igor , Flannigan Mike D. , Bergeron Yves , Girardin Martin P. , Suran Byambagere
Published: December 2010

Variation in natural disturbance regime within a landscape is important for species population dynamics, because it controls spatial arrangement of sites providing regeneration and survival opportunities. In this study, we examine the differences in fire regime and evaluate possible sources of its variation between the surrounding mainland and the islands of Lake Duparquet (44.5 km2), a typical boreal lake in north-western Quebec, Canada. Dendrochronological reconstructions suggest that fires were frequent and of variable intensity on the islands, whereas fires were less frequent on the adjacent mainland, but were usually large and intense. Islands were significantly drier and warmer than the mainland, and maximum values of Fire Weather Index were significantly higher on the islands during both the early part of the fire season (May–June) and the whole fire season (May–September). The lightning density within the lake perimeter was significantly higher than in the surrounding mainland (0.63 v. 0.48 year–1 km–2 respectively). This pattern was a result of the differences in lightning density during the first half of the lightning season. The study suggests that more fire-prone local weather and higher frequency of lightning strikes could cause a higher frequency of low-intensity fires on the islands, compared with the mainland.
Landscape composition influences local pattern of fire size in the eastern Canadian boreal forest: role of weather and landscape mosaic on fire size distribution in mixedwood boreal forest using the Prescribed Fire Analysis System
Authors: Hély Christelle , Fortin C. Marie-Josée , Anderson Kerry R. , Bergeron Yves
Published: December 2010

Wildfire simulations were carried out using the Prescribed Fire Analysis System (PFAS) to study the effect of landscape composition on fire sizes in eastern Canadian boreal forests. We used the Lake Duparquet forest as reference, plus 13 forest mosaic scenarios whose compositions reflected lengths of fire cycle. Three fire weather risks based on duff moisture were used. We performed 100 simulations per risk and mosaic, with topography and hydrology set constant for the reference. Results showed that both weather and landscape composition significantly influenced fire sizes. Weather related to fire propagation explained almost 79% of the variance, while landscape composition and weather conditions for ignition explained ∼14 and 2% respectively. In terms of landscape, burned area increased with increasing presence of shade-tolerant species, which are related to long fire cycles. Comparisons among the distributions of cumulated area burned from scenarios plus those from the Société de Protection des Forêts contre le Feu database archives showed that PFAS simulated realistic fire sizes using the 80–100% class of probable fire extent. Future analyses would best be performed on a larger region as the limited size of the study area could not capture fires larger than 11 000 ha, which represent 3% of fires but 65% of the total area burned at the provincial scale.
A 400-year history of fires on lake islands in south-east Sweden
Authors: Niklasson Mats , Drobyshev Igor , Zielonka Tomasz
Published: December 2010

Island-lake ecosystems are suitable for testing scale dependence in forests disturbance theories thanks to differences in the potential for fire spread on islands and the mainland. We investigated past fire regime on the mainland and on islands in a large lake in south-east Sweden. We used dendrochronological methods to reconstruct fire disturbances on 18 small islands (0.04–24.1 ha) and in 43 sites in the surrounding 75-km2 landscape over the last 400 years. In the past, fires were frequent on both islands and mainland but not synchronised on an annual scale. Significant temporal changes occurred around the middle of the 18th century. Before 1750, fires were less frequent on islands than on the mainland (median fire return interval 58 v. 25 years respectively). However, an inversion of this pattern was observed during 1750–1860: islands showed even shorter fire intervals than mainland locations, suggesting additional and likely human-related source of ignitions (median fire return interval 15 v. 29 years respectively). A substantial decrease in fire activity in both islands and mainland was apparent in 1860–1890. We suggest that the present fire regime (the last 100 years) on the small islands is largely natural as fire suppression is not present there. The dynamic nature of the fire regime on islands still requires further studies: islands may, at times, attract lightning, humans with fire, or both.
Potentially limited detectability of short-term changes in boreal fire regimes: a simulation study
Authors: Metsaranta Juha M.
Published: December 2010

Climate change is expected to increase area burned in the boreal plains ecozone of Canada in the early 21st century (2001–50). I examined the influence of inter-annual variability in area burned and short observed time series on the probability of detecting if an increase has occurred, using a null model of present and future fire regimes. A wide range of fire cycles are consistent with annual area burned in the late 20th century (1959–99). Fire cycles estimated from the reciprocal of the average annual burn fraction over a 50-year period are not very precise, and overestimate the fire cycle if years with large annual area burned have not recently occurred. Under the default assumptions, the probability of detecting a doubling of annual area burned during 2001–50 is 73% if it occurred instantaneously, but only 31% if it occurred gradually. Imprecise estimates and uncertainty in the ability to detect changes in fire cycles poses challenges for implementing aspects of sustainable forest management. Alternate empirical or model-based statistics, such as return periods for annual areas burned of a given magnitude, may be useful for inferring frequencies and magnitudes of large fire years that have not yet been observed.
Forest responses to increasing aridity and warmth in the southwestern United States
Authors: Williams A. Park , Allen Craig D. , Millar Constance I. , Swetnam Thomas W. , Michaelsen Joel , Still Christopher J. , Leavitt Steven W.
Published: December 2010

In recent decades, intense droughts, insect outbreaks, and wildfires have led to decreasing tree growth and increasing mortality in many temperate forests. We compared annual tree-ring width data from 1,097 populations in the coterminous United States to climate data and evaluated site-specific tree responses to climate variations throughout the 20th century. For each population, we developed a climate-driven growth equation by using climate records to predict annual ring widths. Forests within the southwestern United States appear particularly sensitive to drought and warmth. We input 21st century climate projections to the equations to predict growth responses. Our results suggest that if temperature and aridity rise as they are projected to, southwestern trees will experience substantially reduced growth during this century. As tree growth declines, mortality rates may increase at many sites. Increases in wildfires and bark-beetle outbreaks in the most recent decade are likely related to extreme drought and high temperatures during this period. Using satellite imagery and aerial survey data, we conservatively calculate that ≈2.7% of southwestern forest and woodland area experienced substantial mortality due to wildfires from 1984 to 2006, and ≈7.6% experienced mortality associated with bark beetles from 1997 to 2008. We estimate that up to ≈18% of southwestern forest area (excluding woodlands) experienced mortality due to bark beetles or wildfire during this period. Expected climatic changes will alter future forest productivity, disturbance regimes, and species ranges throughout the Southwest. Emerging knowledge of these impending transitions informs efforts to adaptively manage southwestern forests.
Switching of the core structures of glycosphingolipids from globo- and lacto- to ganglio-series upon human embryonic stem cell differentiation
Authors: Liang Yuh-Jin , Kuo Huan-Hsien , Lin Chi-Hung , Chen Yen-Ying , Yang Bei-Chia , Cheng Yuan-Yuan , Yu Alice L. , Khoo Kay-Hooi , Yu John
Published: December 2010

A systematic survey of expression profiles of glycosphingolipids (GSLs) in two hESC lines and their differentiated embryoid body (EB) outgrowth with three germ layers was carried out using immunofluorescence, flow cytometry, and MALDI-MS and MS/MS analyses. In addition to the well-known hESC-specific markers stage-specific embryonic antigen 3 (SSEA-3) and SSEA-4, we identified several globosides and lacto-series GSLs, previously unrevealed in hESCs, including Gb
4
Cer, Lc
4
Cer, fucosyl Lc
4
Cer, Globo H, and disialyl Gb
5
Cer. During hESC differentiation into EBs, MS analysis revealed a clear-cut switch in the core structures of GSLs from globo- and lacto- to ganglio-series, which was not as evident by immunostaining with antibodies against SSEA-3 and SSEA-4, owing to their cross-reactivities with various glycosphingolipids. Such a switch was attributable to altered expression of key glycosyltransferases (GTs) in the biosynthetic pathways by the up-regulation of ganglio-series–related GTs with simultaneous down-regulation of globo- and lacto-series–related GTs. Thus, these results provide insights into the unique stage-specific transition and mechanism for alterations of GSL core structures during hESC differentiation. In addition, unique glycan structures uncovered by MS analyses may serve as surface markers for further delineation of hESCs and help identify of their functional roles not only in hESCs but also in cancers.
Robust circadian clocks from coupled protein-modification and transcription–translation cycles
Authors: Zwicker David , Lubensky David K. , ten Wolde Pieter Rein
Published: December 2010

The cyanobacterium
Synechococcus elongatus
uses both a protein phosphorylation cycle and a transcription–translation cycle to generate circadian rhythms that are highly robust against biochemical noise. We use stochastic simulations to analyze how these cycles interact to generate stable rhythms in growing, dividing cells. We find that a protein phosphorylation cycle by itself is robust when protein turnover is low. For high decay or dilution rates (and compensating synthesis rates), however, the phosphorylation-based oscillator loses its integrity. Circadian rhythms thus cannot be generated with a phosphorylation cycle alone when the growth rate, and consequently the rate of protein dilution, is high enough; in practice, a purely posttranslational clock ceases to function well when the cell doubling time drops below the 24-h clock period. At higher growth rates, a transcription–translation cycle becomes essential for generating robust circadian rhythms. Interestingly, although a transcription–translation cycle is necessary to sustain a phosphorylation cycle at high growth rates, a phosphorylation cycle can dramatically enhance the robustness of a transcription–translation cycle at lower protein decay or dilution rates. In fact, the full oscillator built from these two tightly intertwined cycles far outperforms not just each of its two components individually, but also a hypothetical system in which the two parts are coupled as in textbook models of coupled phase oscillators. Our analysis thus predicts that both cycles are required to generate robust circadian rhythms over the full range of growth conditions.
ATP-binding cassette-like transporters are involved in the transport of lignin precursors across plasma and vacuolar membranes
Authors: Miao Yu-Chen , Liu Chang-Jun
Published: December 2010

Lignin is a complex biopolymer derived primarily from the condensation of three monomeric precursors, the monolignols. The synthesis of monolignols occurs in the cytoplasm. To reach the cell wall where they are oxidized and polymerized, they must be transported across the cell membrane. However, the molecular mechanisms underlying the transport process are unclear. There are conflicting views about whether the transport of these precursors occurs by passive diffusion or is an energized active process; further, we know little about what chemical forms are required. Using isolated plasma and vacuolar membrane vesicles prepared from
Arabidopsis
, together with applying different transporter inhibitors in the assays, we examined the uptake of monolignols and their derivatives by these native membrane vesicles. We demonstrate that the transport of lignin precursors across plasmalemma and their sequestration into vacuoles are ATP-dependent primary-transport processes, involving ATP-binding cassette-like transporters. Moreover, we show that both plasma and vacuolar membrane vesicles selectively transport different forms of lignin precursors. In the presence of ATP, the inverted plasma membrane vesicles preferentially take up monolignol aglycones, whereas the vacuolar vesicles are more specific for glucoconjugates, suggesting that the different ATP-binding cassette-like transporters recognize different chemical forms in conveying them to distinct sites, and that glucosylation of monolignols is necessary for their vacuolar storage but not required for direct transport into the cell wall in
Arabidopsis
.
Expression patterns of neural genes in
Euperipatoides kanangrensis
suggest divergent evolution of onychophoran and euarthropod neurogenesis
Authors: Eriksson Bo Joakim , Stollewerk Angelika
Published: December 2010

One of the controversial debates on euarthropod relationships centers on the question as to whether insects, crustaceans, and myriapods (Mandibulata) share a common ancestor or whether myriapods group with the chelicerates (Myriochelata). The debate was stimulated recently by studies in chelicerates and myriapods that show that neural precursor groups (NPGs) segregate from the neuroectoderm generating the nervous system, whereas in insects and crustaceans the nervous tissue is produced by stem cells. Do the shared neural characters of myriapods and chelicerates represent derived characters that support the Myriochelata grouping? Or do they rather reflect the ancestral pattern? Analyses of neurogenesis in a group closely related to euarthropods, the onychophorans, show that, similar to insects and crustaceans, single neural precursors are formed in the neuroectoderm, potentially supporting the Myriochelata hypothesis. Here we show that the nature and the selection of onychophoran neural precursors are distinct from euarthropods. The onychophoran nervous system is generated by the massive irregular segregation of single neural precursors, contrasting with the limited number and stereotyped arrangement of NPGs/stem cells in euarthropods. Furthermore, neural genes do not show the spatiotemporal pattern that sets up the precise position of neural precursors as in euarthropods. We conclude that neurogenesis in onychophorans largely does not reflect the ancestral pattern of euarthropod neurogenesis, but shows a mixture of derived characters and ancestral characters that have been modified in the euarthropod lineage. Based on these data and additional evidence, we suggest an evolutionary sequence of arthropod neurogenesis that is in line with the Mandibulata hypothesis.
IL-4/STAT6 immune axis regulates peripheral nutrient metabolism and insulin sensitivity
Authors: Ricardo-Gonzalez Roberto R. , Red Eagle Alex , Odegaard Justin I. , Jouihan Hani , Morel Christine R. , Heredia Jose E. , Mukundan Lata , Wu Davina , Locksley Richard M. , Chawla Ajay
Published: December 2010

Immune cells take residence in metabolic tissues, providing a framework for direct regulation of nutrient metabolism. Despite conservation of this anatomic relationship through evolution, the signals and mechanisms by which the immune system regulates nutrient homeostasis and insulin action remain poorly understood. Here, we demonstrate that the IL-4/STAT6 immune axis, a key pathway in helminth immunity and allergies, controls peripheral nutrient metabolism and insulin sensitivity. Disruption of signal transducer and activator of transcription 6 (STAT6) decreases insulin action and enhances a peroxisome proliferator-activated receptor α (PPARα) driven program of oxidative metabolism. Conversely, activation of STAT6 by IL-4 improves insulin action by inhibiting the PPARα-regulated program of nutrient catabolism and attenuating adipose tissue inflammation. These findings have thus identified an unexpected molecular link between the immune system and macronutrient metabolism, suggesting perhaps the coevolution of these pathways occurred to ensure access to glucose during times of helminth infection.
Reclaiming freshwater sustainability in the Cadillac Desert
Authors: Sabo John L. , Sinha Tushar , Bowling Laura C. , Schoups Gerrit H. W. , Wallender Wesley W. , Campana Michael E. , Cherkauer Keith A. , Fuller Pam L. , Graf William L. , Hopmans Jan W. , Kominoski John S. , Taylor Carissa , Trimble Stanley W. , Webb Robert H. , Wohl Ellen E.
Published: December 2010

Increasing human appropriation of freshwater resources presents a tangible limit to the sustainability of cities, agriculture, and ecosystems in the western United States. Marc Reisner tackles this theme in his 1986 classic
Cadillac Desert: The American West and Its Disappearing Water
. Reisner's analysis paints a portrait of region-wide hydrologic dysfunction in the western United States, suggesting that the storage capacity of reservoirs will be impaired by sediment infilling, croplands will be rendered infertile by salt, and water scarcity will pit growing desert cities against agribusiness in the face of dwindling water resources. Here we evaluate these claims using the best available data and scientific tools. Our analysis provides strong scientific support for many of Reisner's claims, except the notion that reservoir storage is imminently threatened by sediment. More broadly, we estimate that the equivalent of nearly 76% of streamflow in the Cadillac Desert region is currently appropriated by humans, and this figure could rise to nearly 86% under a doubling of the region's population. Thus, Reisner's incisive journalism led him to the same conclusions as those rendered by copious data, modern scientific tools, and the application of a more genuine scientific method. We close with a prospectus for reclaiming freshwater sustainability in the Cadillac Desert, including a suite of recommendations for reducing region-wide human appropriation of streamflow to a target level of 60%.
Lateral acquisition of genes is affected by the friendliness of their products
Authors: Gophna Uri , Ofran Yanay
Published: December 2010

A major factor in the evolution of microbial genomes is the lateral acquisition of genes that evolved under the functional constraints of other species. Integration of foreign genes into a genome that has different components and circuits poses an evolutionary challenge. Moreover, genes belonging to complex modules in the pretransfer species are unlikely to maintain their functionality when transferred alone to new species. Thus, it is widely accepted that lateral gene transfer favors proteins with only a few protein–protein interactions. The propensity of proteins to participate in protein–protein interactions can be assessed using computational methods that identify putative interaction sites on the protein. Here we report that laterally acquired proteins contain significantly more putative interaction sites than native proteins. Thus, genes encoding proteins with multiple protein–protein interactions may in fact be more prone to transfer than genes with fewer interactions. We suggest that these proteins have a greater chance of forming new interactions in new species, thus integrating into existing modules. These results reveal basic principles for the incorporation of novel genes into existing systems.
Structure of a core fragment of glycoprotein H from pseudorabies virus in complex with antibody
Authors: Backovic Marija , DuBois Rebecca M. , Cockburn Joseph J. , Sharff Andrew J. , Vaney Marie-Christine , Granzow Harald , Klupp Barbara G. , Bricogne Gerard , Mettenleiter Thomas C. , Rey Felix A.
Published: December 2010

Compared with many well-studied enveloped viruses, herpesviruses use a more sophisticated molecular machinery to induce fusion of viral and cellular membranes during cell invasion. This essential function is carried out by glycoprotein B (gB), a class III viral fusion protein, together with the heterodimer of glycoproteins H and L (gH/gL). In pseudorabies virus (PrV), a porcine herpesvirus, it was shown that gH/gL can be substituted by a chimeric fusion protein gDgH, containing the receptor binding domain (RBD) of glycoprotein D fused to a truncated version of gH lacking its N-terminal domain. We report here the 2.1-Å resolution structure of the core fragment of gH present in this chimera, bound to the Fab fragment of a PrV gH-specific monoclonal antibody. The structure strongly complements the information derived from the recently reported structure of gH/gL from herpes simplex virus type 2 (HSV-2). Together with the structure of Epstein-Barr virus (EBV) gH/gL reported in parallel, it provides insight into potentially functional conserved structural features. One feature is the presence of a syntaxin motif, and the other is an extended “flap” masking a conserved hydrophobic patch in the C-terminal domain, which is closest to the viral membrane. The negative electrostatic surface potential of this domain suggests repulsive interactions with the lipid heads. The structure indicates the possible unmasking of an extended hydrophobic patch by movement of the flap during a receptor-triggered conformational change of gH, exposing a hydrophobic surface to interact with the viral membrane during the fusion process.
Baseline intrinsic flammability of Earth’s ecosystems estimated from paleoatmospheric oxygen over the past 350 million years
Authors: Belcher Claire M. , Yearsley Jonathan M. , Hadden Rory M. , McElwain Jennifer C. , Rein Guillermo
Published: December 2010

Atmospheric oxygen (O
2
) is estimated to have varied greatly throughout Earth’s history and has been capable of influencing wildfire activity wherever fuel and ignition sources were present. Fires consume huge quantities of biomass in all ecosystems and play an important role in biogeochemical cycles. This means that understanding the influence of O
2
on past fire activity has far-reaching consequences for the evolution of life and Earth’s biodiversity over geological timescales. We have used a strong electrical ignition source to ignite smoldering fires, and we measured their self-sustaining propagation in atmospheres of different oxygen concentrations. These data have been used to build a model that we use to estimate the baseline intrinsic flammability of Earth’s ecosystems according to variations in O
2
over the past 350 million years (Ma). Our aim is to highlight times in Earth’s history when fire has been capable of influencing the Earth system. We reveal that fire activity would be greatly suppressed below 18.5% O
2
, entirely switched off below 16% O
2
, and rapidly enhanced between 19–22% O
2
. We show that fire activity and, therefore, its influence on the Earth system would have been high during the Carboniferous (350–300 Ma) and Cretaceous (145–65 Ma) periods; intermediate in the Permian (299–251 Ma), Late Triassic (285–201 Ma), and Jurassic (201–145 Ma) periods; and surprisingly low to lacking in the Early–Middle Triassic period between 250–240 Ma. These baseline variations in Earth’s flammability must be factored into our understanding of past vegetation, biodiversity, evolution, and biogeochemical cycles.
Follicle-stimulating hormone increases bone mass in female mice
Authors: Allan Charles M. , Kalak Robert , Dunstan Colin R. , McTavish Kirsten J. , Zhou Hong , Handelsman David J. , Seibel Markus J.
Published: December 2010

Elevated follicle-stimulating hormone (FSH) activity is proposed to directly cause bone loss independent of estradiol deficiency in aging women. Using transgenic female mice expressing human FSH (TgFSH), we now reveal that TgFSH dose-dependently increased bone mass, markedly elevating tibial and vertebral trabecular bone volume. Furthermore, TgFSH stimulated a striking accrual of bone mass in hypogonadal mice lacking endogenous FSH and luteinizing hormone (LH) function, showing that FSH-induced bone mass occurred independently of background LH or estradiol levels. Higher TgFSH levels increased osteoblast surfaces in trabecular bone and stimulated de novo bone formation, filling marrow spaces with woven rather than lamellar bone, reflective of a strong anabolic stimulus. Trabecular bone volume correlated positively with ovarian-derived serum inhibin A or testosterone levels in TgFSH mice, and ovariectomy abolished TgFSH-induced bone formation, proving that FSH effects on bone require an ovary-dependent pathway. No detectable FSH receptor mRNA in mouse bone or cultured osteoblasts or osteoclasts indicated that FSH did not directly stimulate bone. Therefore, contrary to proposed FSH-induced bone loss, our findings demonstrate that FSH has dose-dependent anabolic effects on bone via an ovary-dependent mechanism, which is independent of LH activity, and does not involve direct FSH actions on bone cells.
Hydraulic trade-offs and space filling enable better predictions of vascular structure and function in plants
Authors: Savage V. M. , Bentley L. P. , Enquist B. J. , Sperry J. S. , Smith D. D. , Reich P. B. , von Allmen E. I.
Published: December 2010

Plant vascular networks are central to botanical form, function, and diversity. Here, we develop a theory for plant network scaling that is based on optimal space filling by the vascular system along with trade-offs between hydraulic safety and efficiency. Including these evolutionary drivers leads to predictions for sap flow, the taper of the radii of xylem conduits from trunk to terminal twig, and how the frequency of xylem conduits varies with conduit radius. To test our predictions, we use comprehensive empirical measurements of maple, oak, and pine trees and complementary literature data that we obtained for a wide range of tree species. This robust intra- and interspecific assessment of our botanical network model indicates that the central tendency of observed scaling properties supports our predictions much better than the West, Brown, and Enquist (WBE) or pipe models. Consequently, our model is a more accurate description of vascular architecture than what is given by existing network models and should be used as a baseline to understand and to predict the scaling of individual plants to whole forests. In addition, our model is flexible enough to allow the quantification of species variation around rules for network design. These results suggest that the evolutionary drivers that we propose have been fundamental in determining how physiological processes scale within and across plant species.
Timing and completion of puberty in female mice depend on estrogen receptor α-signaling in kisspeptin neurons
Authors: Mayer Christian , Acosta-Martinez Maricedes , Dubois Sharon L. , Wolfe Andrew , Radovick Sally , Boehm Ulrich , Levine Jon E.
Published: December 2010

Puberty onset is initiated by activation of neurons that secrete gonadotropin-releasing hormone (GnRH). The timing and progression of puberty may depend upon temporal coordination of two opposing central mechanisms—a restraint of GnRH secretion before puberty onset, followed by enhanced stimulation of GnRH release to complete reproductive maturation during puberty. Neuronal estrogen receptor α (ERα) has been implicated in both controls; however, the underlying neural circuits are not well understood. Here we test whether these mechanisms are mediated by neurons that express kisspeptin, a neuropeptide that modulates GnRH neurosecretion. Strikingly, conditional ablation of ERα in kisspeptin neurons results in a dramatic advancement of puberty onset in female mice. Furthermore, subsequent pubertal maturation is arrested in these animals, as they fail to acquire normal ovulatory cyclicity. We show that the temporal coordination of juvenile restraint and subsequent pubertal activation is likely mediated by ERα in two separate kisspeptin neuronal populations in the hypothalamus.
CBP gene transfer increases BDNF levels and ameliorates learning and memory deficits in a mouse model of Alzheimer's disease
Authors: Caccamo Antonella , Maldonado Monica A. , Bokov Alex F. , Majumder Smita , Oddo Salvatore
Published: December 2010

Cognitive dysfunction and memory loss are common features of Alzheimer's disease (AD). Abnormalities in the expression profile of immediate early genes that play a critical role in memory formation, such as the cAMP-response element binding protein (CREB), have been reported in the brains of AD patients. Here we show that amyloid-β (Aβ) accumulation, which plays a primary role in the cognitive deficits of AD, interferes with CREB activity. We further show that restoring CREB function via brain viral delivery of the CREB-binding protein (CBP) improves learning and memory deficits in an animal model of AD. Notably, such improvements occur without changes in Aβ and tau pathology, and instead are linked to an increased level of brain-derived neurotrophic factor. The resulting data suggest that Aβ-induced learning and memory deficits are mediated by alterations in CREB function, based on the finding that restoring CREB activity by directly modulating CBP levels in the brains of adult mice is sufficient to ameliorate learning and memory. Therefore, increasing CBP expression in adult brains may be a valid therapeutic approach not only for AD, but also for various brain disorders characterized by alterations in immediate early genes, further supporting the concept that viral vector delivery may be a viable therapeutic approach in neurodegenerative diseases.
Structural basis of flocculin-mediated social behavior in yeast
Authors: Veelders Maik , Brückner Stefan , Ott Dimitri , Unverzagt Carlo , Mösch Hans-Ulrich , Essen Lars-Oliver
Published: December 2010

In the budding yeast
Saccharomyces cerevisiae
, self-recognition and the thereby promoted aggregation of thousands of cells into protective flocs is mediated by a family of cell-surface adhesins, the flocculins (Flo). Based on this social behavior
FLO
genes fulfill the definition of “greenbeard” genes, which direct cooperation toward other carriers of the same gene. The process of flocculation plays an eminent role in the food industry for the production of beer and wine. However, the precise mode of flocculin-mediated surface recognition and the exact structure of cognate ligands have remained elusive. Here, we present structures of the adhesion domain of a flocculin complexed to its cognate ligands derived from yeast high-mannose oligosaccharides at resolutions up to 0.95 Å. Besides a PA14-like architecture, the Flo5A domain reveals a previously undescribed lectin fold that utilizes a unique
DcisD
calcium-binding motif for carbohydrate binding and that is widely spread among pro- and eukaryotes. Given the high abundance of high-mannose oligosaccharides in yeast cell walls, the Flo5A structure suggests a model for recognition, where social non-self- instead of unsocial self-interactions are favored.
Whispering-gallery mode resonators for highly unidirectional laser action
Authors: Wang Qi Jie , Yan Changling , Yu Nanfang , Unterhinninghofen Julia , Wiersig Jan , Pflügl Christian , Diehl Laurent , Edamura Tadataka , Yamanishi Masamichi , Kan Hirofumi , Capasso Federico
Published: December 2010

Optical microcavities can be designed to take advantage of total internal reflection, which results in resonators supporting whispering-gallery modes (WGMs) with a high-quality factor (Q factor). One of the crucial problems of these devices for practical applications such as designing microcavity lasers, however, is that their emission is nondirectional due to their radial symmetry, in addition to their inefficient power output coupling. Here we report the design of elliptical resonators with a wavelength-size notch at the boundary, which support in-plane highly unidirectional laser emission from WGMs. The notch acts as a small scatterer such that the Q factor of the WGMs is still very high. Using midinfrared (
λ
 ∼ 10 μm) injection quantum cascade lasers as a model system, an in-plane beam divergence as small as 6 deg with a peak optical power of ∼5 mW at room temperature has been demonstrated. The beam divergence is insensitive to the pumping current and to the notch geometry, demonstrating the robustness of this resonator design. The latter is scalable to the visible and the near infrared, thus opening the door to very low-threshold, highly unidirectional microcavity diode lasers.
The happiness–income paradox revisited
Authors: Easterlin Richard A. , McVey Laura Angelescu , Switek Malgorzata , Sawangfa Onnicha , Zweig Jacqueline Smith
Published: December 2010

The striking thing about the happiness–income paradox is that over the long-term —usually a period of 10 y or more—happiness does not increase as a country's income rises. Heretofore the evidence for this was limited to developed countries. This article presents evidence that the long term nil relationship between happiness and income holds also for a number of developing countries, the eastern European countries transitioning from socialism to capitalism, and an even wider sample of developed countries than previously studied. It also finds that in the short-term in all three groups of countries, happiness and income go together, i.e., happiness tends to fall in economic contractions and rise in expansions. Recent critiques of the paradox, claiming the time series relationship between happiness and income is positive, are the result either of a statistical artifact or a confusion of the short-term relationship with the long-term one.
Visualizing key hinges and a potential major source of compliance in the lever arm of myosin
Authors: Brown Jerry H. , Senthil Kumar V. S. , O’Neall-Hennessey Elizabeth , Reshetnikova Ludmila , Robinson Howard , Nguyen-McCarty Michelle , Szent-Györgyi Andrew G. , Cohen Carolyn
Published: December 2010

We have determined the 2.3-Å-resolution crystal structure of a myosin light chain domain, corresponding to one type found in sea scallop catch (“smooth”) muscle. This structure reveals hinges that may function in the “on” and “off” states of myosin. The molecule adopts two different conformations about the heavy chain “hook” and regulatory light chain (RLC) helix D. This conformational change results in extended and compressed forms of the lever arm whose lengths differ by 10 Å. The heavy chain hook and RLC helix D hinges could thus serve as a potential major and localized source of cross-bridge compliance during the contractile cycle. In addition, in one of the molecules of the crystal, part of the RLC N-terminal extension is seen in atomic detail and forms a one-turn alpha-helix that interacts with RLC helix D. This extension, whose sequence is highly variable in different myosins, may thus modulate the flexibility of the lever arm. Moreover, the relative proximity of the phosphorylation site to the helix D hinge suggests a potential role for conformational changes about this hinge in the transition between the on and off states of regulated myosins.
Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6
Authors: Lardenois Aurélie , Liu Yuchen , Walther Thomas , Chalmel Frédéric , Evrard Bertrand , Granovskaia Marina , Chu Angela , Davis Ronald W. , Steinmetz Lars M. , Primig Michael
Published: December 2010

Budding yeast noncoding RNAs (ncRNAs) are pervasively transcribed during mitosis, and some regulate mitotic protein-coding genes. However, little is known about ncRNA expression during meiotic development. Using high-resolution profiling we identified an extensive meiotic ncRNA expression program interlaced with the protein-coding transcriptome via sense/antisense transcript pairs, bidirectional promoters, and ncRNAs that overlap the regulatory regions of genes. Meiotic unannotated transcripts (MUTs) are mitotic targets of the conserved exosome component Rrp6, which itself is degraded after the onset of meiosis when MUTs and other ncRNAs accumulate in successive waves. Diploid cells lacking Rrp6 fail to initiate premeiotic DNA replication normally and cannot undergo efficient meiotic development. The present study demonstrates a unique function for budding yeast Rrp6 in degrading distinct classes of meiotically induced ncRNAs during vegetative growth and the onset of meiosis and thus points to a critical role of differential ncRNA expression in the execution of a conserved developmental program.
Thalamocortical model for a propofol-induced α-rhythm associated with loss of consciousness
Authors: Ching ShiNung , Cimenser Aylin , Purdon Patrick L. , Brown Emery N. , Kopell Nancy J.
Published: December 2010

Recent data reveal that the general anesthetic propofol gives rise to a frontal α-rhythm at dose levels sufficient to induce loss of consciousness. In this work, a computational model is developed that suggests the network mechanisms responsible for such a rhythm. It is shown that propofol can alter the dynamics in thalamocortical loops, leading to persistent and synchronous α-activity. The synchrony that forms in the cortex by virtue of the involvement of the thalamus may impede responsiveness to external stimuli, thus providing a correlate for the unconscious state.