bluuebunny/crossref_metadata_2025 huggingface dataset:
Coupling the snow thermodynamic model SNOWPACK with the microwave emission model of layered snowpacks for subarctic and arctic snow water equivalent retrievals
Authors: Langlois A. , Royer A. , Derksen C. , Montpetit B. , Dupont F. , Goïta K.
Published: November 2012

Satellite‐passive microwave remote sensing has been extensively used to estimate snow water equivalent (SWE) in northern regions. Although passive microwave sensors operate independent of solar illumination and the lower frequencies are independent of atmospheric conditions, the coarse spatial resolution introduces uncertainties to SWE retrievals due to the surface heterogeneity within individual pixels. In this article, we investigate the coupling of a thermodynamic multilayered snow model with a passive microwave emission model. Results show that the snow model itself provides poor SWE simulations when compared to field measurements from two major field campaigns. Coupling the snow and microwave emission models with successive iterations to correct the influence of snow grain size and density significantly improves SWE simulations. This method was further validated using an additional independent data set, which also showed significant improvement using the two‐step iteration method compared to standalone simulations with the snow model.
Erratum: Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests
Authors: Hartmann Martin , Howes Charles G , VanInsberghe David , Yu Hang , Bachar Dipankar , Christen Richard , Henrik Nilsson Rolf , Hallam Steven J , Mohn William W
Published: November 2012

Correction to: The ISME Journal (2012) 6, 2199–2218; doi:10.1038/ismej.2012.84; published online 2 August 2012 Since the publication of this article, the authors have noticed errors in two sentences that appeared within the online version of their paper. The errors have now been rectified, and the correct article appears in this issue.
Metal insertion into the molybdenum cofactor: product–substrate channelling demonstrates the functional origin of domain fusion in gephyrin
Authors: Belaidi Abdel A. , Schwarz Guenter
Published: November 2012

The complexity of eukaryotic multicellular organisms relies on evolutionary developments that include compartmentalization, alternative splicing, protein domain fusion and post-translational modification. Mammalian gephyrin uniquely exemplifies these processes by combining two enzymatic functions within the biosynthesis of the Moco (molybdenum cofactor) in a multidomain protein. It also undergoes extensive alternative splicing, especially in neurons, where it also functions as a scaffold protein at inhibitory synapses. Two out of three gephyrin domains are homologous to bacterial Moco-synthetic proteins (G and E domain) while being fused by a third gephyrin-specific central C domain. In the present paper, we have established the in vitro Moco synthesis using purified components and demonstrated an over 300-fold increase in Moco synthesis for gephyrin compared with the isolated G domain, which synthesizes adenylylated molybdopterin, and E domain, which catalyses the metal insertion at physiological molybdate concentrations in an ATP-dependent manner. We show that the C domain impacts the catalytic efficacy of gephyrin, suggesting an important structural role in product–substrate channelling as depicted by a structural model that is in line with a face-to-face orientation of both active sites. Our functional studies demonstrate the evolutionary advantage of domain fusion in metabolic proteins, which can lead to the development of novel functions in higher eukaryotes.
Further Evidence of Auditory Extinction in Aphasia
Authors: Marshall Rebecca Shisler , Basilakos Alexandra , Love-Myers Kim
Published: November 2012

Purpose

Preliminary research (Shisler, 2005) suggests that auditory extinction in individuals with aphasia (IWA) may be connected to binding and attention. In this study, the authors expanded on previous findings on auditory extinction to determine the source of extinction deficits in IWA.

Method

Seventeen IWA (Mage= 53.19 years) and 17 neurologically intact controls (Mage= 55.18 years) participated. Auditory stimuli were spoken letters presented in a free-field listening environment. Stimuli were presented in single-stimulus stimulation (SSS) or double-simultaneous stimulation (DSS) trials across 5 conditions designed to determine whether extinction is related to binding, inefficient attention resource allocation, or overall deficits in attention. All participants completed all experimental conditions.

Results

Significant extinction was demonstrated only by IWA when sounds were different, providing further evidence of auditory extinction. However, binding requirements did not appear to influence the IWA’s performance.

Conclusions

Results indicate that, for IWA, auditory extinction may not be attributed to a binding deficit or inefficient attention resource allocation because of equivalent performance across all 5 conditions. Rather, overall attentional resources may be influential. Future research in aphasia should explore the effect of the stimulus presentation in addition to the continued study of attention treatment.
Pitch Variability in Patients With Parkinson’s Disease: Effects of Deep Brain Stimulation of Caudal Zona Incerta and Subthalamic Nucleus
Authors: Karlsson Fredrik , Olofsson Katarina , Blomstedt Patric , Linder Jan , van Doorn Jan
Published: November 2012

Purpose

The purpose of the present study was to examine the effect of deep brain stimulation (DBS) of the subthalamic nucleus (STN) and the caudal zona incerta (cZi) pitch characteristics of connected speech in patients with Parkinson’s disease (PD).

Method

The authors evaluated 16 patients preoperatively and 12 months after DBS surgery. Eight patients were implanted in the STN (ages 51–72 years;
M
= 63 years). Six received bilateral implantation and 2 unilateral (left) implantation. Eight patients were bilaterally implanted in the cZi (ages 49–71 years;
M
= 60.8 years). Preoperative assessments were made after a levodopa challenge (approximately 1.5 times the ordinary dose). All postoperative examinations were made off and on stimulation with a clinically optimized dose of levodopa. Measurements of pitch range and variability were obtained from each utterance in a recorded read speech passage.

Results

Pitch range and coefficient of variation showed an increase in patients under STN–DBS. Patients under cZi–DBS showed no significant effects of treatment on investigated pitch properties.

Conclusion

STN–DBS was shown to increase pitch variation and range. The results provided no evidence of cZi–DBS having a beneficial effect on PD patients' pitch variability.
Nanophotonic light trapping in solar cells
Authors: Mokkapati S. , Catchpole K. R.
Published: November 2012

Nanophotonic light trapping for solar cells is an exciting field that has seen exponential growth in the last few years. There has been a growing appreciation for solar energy as a major solution to the world’s energy problems, and the need to reduce materials costs by the use of thinner solar cells. At the same time, we have the newly developed ability to fabricate controlled structures on the nanoscale quickly and cheaply, and the computational power to optimize the structures and extract physical insights. In this paper, we review the theory of nanophotonic light trapping, with experimental examples given where possible. We focus particularly on periodic structures, since this is where physical understanding is most developed, and where theory and experiment can be most directly compared. We also provide a discussion on the parasitic losses and electrical effects that need to be considered when designing nanophotonic solar cells.
Experimental and theoretical study on Raman spectra of magnesium fluoride clusters and solids
Authors: Neelamraju S. , Bach A. , Schön J. C. , Fischer D. , Jansen M.
Published: November 2012

In this study, the Raman and IR spectra of a large number of isomers of MgF2 clusters and of possible bulk polymorphs of MgF2 are calculated and compared with experimental data observed using a low-temperature atom beam deposition. The bulk polymorphs were taken from earlier work, while the cluster modifications for the neutral (MgF2)n (n = 1−10) clusters and charged clusters (up to the trimer anion and cation, (Mg3F7)− and (Mg3F5)+, respectively) are determined in the present work by global energy landscape explorations using simulated annealing. These theoretical calculations are complemented by an experimental study on both the vapor phase and the deposited films of MgF2, which are generated in a low-temperature atom beam deposition setup for the synthesis of MgF2 bulk phases. The MgF2 vapor and film are characterized via Raman spectroscopy of the MgF2 gas phase species embedded in an Ar-matrix and of the MgF2-films deposited onto a cooled substrate, respectively. We find that, in the vapor phase, there are monomers and dimers and charged species to be present in our experimental setup. Furthermore, the results suggest that in the amorphous bulk MgF2, rutile-like domains are present and MgF2 clusters similar to those in the matrix. Finally, peaks at about 800 cm−1, which are in the same range as the Ag modes of clusters with dangling fluorine atoms connected to three-coordinated Mg atoms, indicate that such dangling bonds are also present in amorphous MgF2.
Optical and elastic properties of diamond-like carbon with metallic inclusions: A theoretical study
Authors: Tritsaris Georgios A. , Mathioudakis Christos , Kelires Pantelis C. , Kaxiras Efthimios
Published: November 2012

A tough material commonly used in coatings is diamond-like carbon (DLC), that is, amorphous carbon with content in four-fold coordinated C higher than ∼70%, and its composites with metal inclusions. This study aims to offer useful guidelines for the design and development of metal-containing DLC coatings for solar collectors, where the efficiency of the collector depends critically on the performance of the absorber coating. We use first-principles calculations based on density functional theory to study the structural, electronic, optical, and elastic properties of DLC and its composites with Ag and Cu inclusions at 1.5% and 3.0% atomic concentration, to evaluate their suitability for solar thermal energy harvesting. We find that with increasing metal concentration optical absorption is significantly enhanced while at the same time, the composite retains good mechanical strength: DLC with 70–80% content in four-fold coordinated C and small metal concentrations (<3 at. %) will show high absorption in the visible (absorption coefficients higher than 105 cm−1) and good mechanical strength (bulk and Young's modulus higher than 300 and 500 GPa, respectively).
Temperature dependent elastic constants and ultimate strength of graphene and graphyne
Authors: Shao Tianjiao , Wen Bin , Melnik Roderick , Yao Shan , Kawazoe Yoshiyuki , Tian Yongjun
Published: November 2012

Based on the first principles calculation combined with quasi-harmonic approximation in this work, we focus on the analysis of temperature dependent lattice geometries, thermal expansion coefficients, elastic constants, and ultimate strength of graphene and graphyne. For the linear thermal expansion coefficient, both graphene and graphyne show a negative region in the low temperature regime. This coefficient increases up to be positive at high temperatures. Graphene has superior mechanical properties with Young's modulus E = 350.01 N/m and ultimate tensile strength of 119.2 GPa at room temperature. Based on our analysis, it is found that graphene's mechanical properties have strong resistance against temperature increase up to 1000 K. Graphyne also shows good mechanical properties with Young's modulus E = 250.9 N/m and ultimate tensile strength of 81.2 GPa at room temperature, but graphyne's mechanical properties have a weaker resistance with respect to the increase of temperature than that of graphene.
Graded-size Si-nanocrystal-multilayer solar cells
Authors: Yeol Shin Dong , Hee Park Jae , Kim Sung , Choi Suk-Ho , Joong Kim Kyung
Published: November 2012

Four kinds of Si-nanocrystal (NC) multilayers (MLs) have been fabricated on n-type Si wafers by changing the optical bandgap gradually in the directions towards the Si substrate or towards the center of the MLs through the variation of the NC size in each layer. Photovoltaic behaviors of the graded-size p-type Si-NC MLs/n-type Si-wafer heterojunction solar cells are shown to strongly depend on the ML structure. The Si-NC ML solar cells with a stepwise increase in the bandgap towards the center of the MLs exhibit best energy-conversion efficiency at low doping levels. These results are discussed based on the radiative and nonradiative processes in the graded-size Si-NC MLs, as analyzed by continuous-wave and time-resolved photoluminescence measurements.
Exploration of precessional spin dynamics in magnetic multilayers
Authors: Buschhorn S. , Brüssing F. , Ewerlin M. , Salikhov R. , Abrudan R. , Zabel H.
Published: November 2012

In this article, we present magnetization dynamics studies on magnetic multilayers using time resolved resonant magnetic x-ray scattering, which accesses both the frequency and the damping of the free magnetization precession. Here, we compare two multilayers with ferromagnetic Py (Py=Ni0.8Fe0.2) layers separated by conducting Cu layers and by non-conducting AlOx layers. Magnetic Bragg peaks from the multilayer are excited by tuning the circular polarized x-ray energy to the L2,3 resonant absorption edges of Fe and Ni in Py. The coherent precessional dynamics follows then from an analysis of the time dependent Bragg peak intensity after field pulse excitation. We find coherent precession of all magnetic layers within both multilayers and also the same precessional frequency, independent of the interlayer material. At the same time, the precessional damping is considerably different for Cu and AlOx as interlayer materials. Reasons for the enhanced damping in Py/Cu multilayers are discussed. Additional depth dependent studies are presented using a single Py layer through variation of the angle of incidence.
Electronic energy transfer: Localized operator partitioning of electronic energy in composite quantum systems
Authors: Khan Yaser , Brumer Paul
Published: November 2012

A Hamiltonian based approach using spatially localized projection operators is introduced to give precise meaning to the chemically intuitive idea of the electronic energy on a quantum subsystem. This definition facilitates the study of electronic energy transfer in arbitrarily coupled quantum systems. In particular, the decomposition scheme can be applied to molecular components that are strongly interacting (with significant orbital overlap) as well as to isolated fragments. The result defines a consistent electronic energy at all internuclear distances, including the case of separated fragments, and reduces to the well-known Förster and Dexter results in their respective limits. Numerical calculations of coherent energy and charge transfer dynamics in simple model systems are presented and the effect of collisionally induced decoherence is examined.
1.55 μm direct bandgap electroluminescence from strained n-Ge quantum wells grown on Si substrates
Authors: Gallacher K. , Velha P. , Paul D. J. , Cecchi S. , Frigerio J. , Chrastina D. , Isella G.
Published: November 2012

Electroluminescence from strained n-Ge quantum well light emitting diodes grown on a silicon substrate are demonstrated at room temperature. Electroluminescence characterisation demonstrates two peaks around 1.55 μm and 1.8 μm, which correspond to recombination between the direct and indirect transitions, respectively. The emission wavelength can be tuned by around 4% through changing the current density through the device. The devices have potential applications in the fields of optical interconnects, gas sensing, and healthcare.
Cutting forces related with lattice orientations of graphene using an atomic force microscopy based nanorobot
Authors: Zhang Yu , Gao Yang , Liu Lianqing , Xi Ning , Wang Yuechao , Ma Laipeng , Dong Zaili , Wejinya Uchechukwu C.
Published: November 2012

The relationship between cutting forces and lattice orientations of monolayer graphene is investigated by using an atomic force microscopy (AFM) based nanorobot. In the beginning, the atomic resolution image of the graphene lattice is obtained by using an AFM. Then, graphene cutting experiments are performed with sample rotation method, which gets rid of the tip effect completely. The experimental results show that the cutting force along the armchair orientation is larger than the force along the zigzag orientation, and the cutting forces are almost identical every 60°, which corresponds well with the 60° symmetry in graphene honeycomb lattice structure. By using Poisson analysis method, the single cutting force along zigzag orientation is 3.9 nN, and the force along armchair is 20.5 nN. This work lays the experimental foundation to build a close-loop fabrication strategy with real-time force as a feedback sensor to control the cutting direction.
Air-stable π-conjugated amorphous copolymer field-effect transistors with high mobility of 0.3 cm2/Vs
Authors: Georgakopoulos S. , Gu Y. , Nielsen M. M. , Shkunov M.
Published: November 2012

We have fabricated organic bottom-contact top-gate field-effect transistors with an indenofluorene-phenanthrene co-polymer semiconductor, exhibiting ON/OFF ratio of 107 and uncommonly high mobility for an amorphous conjugated polymer of up to 0.3 cm2/Vs. Lack of crystallinity in this material is indicated by atomic force microscopy, grazing incidence wide angle X-ray scattering, and differential scanning calorimetry data. Nevertheless, fitting transistor data to the Gaussian disorder model gives low energetic disorder of σ = 48 meV and high prefactor mobility μ0 = 0.67 cm2/Vs. The measured transistor mobility is also exceptionally stable in ambient conditions, decreasing only by approximately 15% over two months.
Communication: Formation of slow electrons in the Auger decay of core-ionized water molecules
Authors: Hikosaka Y. , Yamamoto K. , Nakano M. , Odagiri T. , Soejima K. , Suzuki I. H. , Lablanquie P. , Penent F. , Ito K.
Published: November 2012

Double Auger decay of O1s−1 and its satellite states in H2O has been studied with a multi-electron coincidence method, and a process leading to autoionizing O* fragments has been revealed. The breaking of the two O–H bonds producing the autoionizing O* fragments occurs for highly excited H2O2+ populated by the initial Auger decay. The O* fragments are more favorably produced in the decay from the satellite states, resulting from the larger population of highly excited H2O2+ states inheriting the valence excitation in the initial state.
Accurate evaluation of subband structure in a carrier accumulation layer at an n-type InAs surface: LDF calculation combined with high-resolution photoelectron spectroscopy
Authors: Inaoka Takeshi , Sanuki Yoshihito , Shoji Masahiro
Published: November 2012

Adsorption on an n-type InAs surface often induces a gradual formation of a carrier-accumulation layer at the surface. By means of high-resolution photoelectron spectroscopy (PES), Betti et al. made a systematic observation of subbands in the accumulation layer in the formation process. Incorporating a highly nonparabolic (NP) dispersion of the conduction band into the local-density-functional (LDF) formalism, we examine the subband structure in the accumulation-layer formation process. Combining the LDF calculation with the PES experiment, we make an accurate evaluation of the accumulated-carrier density, the subband-edge energies, and the subband energy dispersion at each formation stage. Our theoretical calculation can reproduce the three observed subbands quantitatively. The subband dispersion, which deviates downward from that of the projected bulk conduction band with an increase in wave number, becomes significantly weaker in the formation process. Accurate evaluation of the NP subband dispersion at each formation stage is indispensable in making a quantitative analysis of collective electronic excitations and transport properties in the subbands.
Transcriptome identification of the resistance-associated genes (RAGs) to Aspergillus flavus infection in pre-harvested peanut (Arachis hypogaea)
Authors: Wang Tong , Chen Xiao-Ping , Li Hai-Fen , Liu Hai-Yan , Hong Yan-Bin , Yang Qing-Li , Chi Xiao-Yuan , Yang Zhen , Yu Shan-Lin , Li Ling , Liang Xuan-Qiang
Published: November 2012

Pre-harvest aflatoxin contamination caused by Aspergillus favus is a major concern in peanut. However, little is known about the resistance mechanism, so the incorporation of resistance into cultivars with commercially-acceptable genetic background has been slowed. To identify resistance-associated genes potentially underlying the resistance mechanism, we compared transcriptome profiles in resistant and susceptible peanut genotypes under three different treatments: well watered, drought stress and both A. flavus and drought stress using a customised NimbleGen microarray representing 36 158 unigenes. Results showed that the profile of differentially expressed genes (DEGs) displayed a similar pattern of distribution among the functional classes between resistant and susceptible peanuts in response to drought stress. Under A. flavus infection with drought stress, a total of 490 unigenes involved in 26 pathways were differentially expressed in the resistant genotype YJ1 uniquely responding to A. flavus infection, in which 96 DEGs were related to eight pathways: oxidation reduction, proteolysis metabolism, coenzyme A biosynthesis, defence response, signalling, oligopeptide transport, transmembrane transport and carbohydrate biosynthesis/metabolism. Pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database showed that eight networks were significantly associated with resistance to A. flavus infection in resistant genotype YJ1 compared with susceptible Yueyou7. To validate microarray analysis, 15 genes were randomly selected for real-time RT–PCR analysis. The results provided in this study may enhance our understanding of the pre-harvest peanut–A. flavus interaction and facilitate to develop aflatoxin resistant peanut lines in future breeding programs.
Long-term influence of normal variation in neonatal characteristics on human brain development
Authors: Walhovd Kristine B. , Fjell Anders M. , Brown Timothy T. , Kuperman Joshua M. , Chung Yoonho , Hagler Donald J. , Roddey J. Cooper , Erhart Matthew , McCabe Connor , Akshoomoff Natacha , Amaral David G. , Bloss Cinnamon S. , Libiger Ondrej , Schork Nicholas J. , Darst Burcu F. , Casey B. J. , Chang Linda , Ernst Thomas M. , Frazier Jean , Gruen Jeffrey R. , Kaufmann Walter E. , Murray Sarah S. , van Zijl Peter , Mostofsky Stewart , Dale Anders M. ,   for the Pediatric Imaging, Neurocognition, and Genetics Study, Jernigan Terry L. , McCabe Connor , Chang Linda , Akshoomoff Natacha , Newman Erik , Dale Anders M. , Ernst Thomas , Dale Anders M. , Van Zijl Peter , Kuperman Joshua , Murray Sarah , Bloss Cinnamon , Schork Nicholas J. , Appelbaum Mark , Gamst Anthony , Thompson Wesley , Bartsch Hauke , Jernigan Terry L. , Dale Anders M. , Akshoomoff Natacha , Chang Linda , Ernst Thomas , Keating Brian , Amaral David , Sowell Elizabeth , Kaufmann Walter , Van Zijl Peter , Mostofsky Stewart , Casey B.J. , Ruberry Erika J. , Powers Alisa , Rosen Bruce , Kenet Tal , Frazier Jean , Kennedy David , Gruen Jeffrey
Published: November 2012

It is now recognized that a number of cognitive, behavioral, and mental health outcomes across the lifespan can be traced to fetal development. Although the direct mediation is unknown, the substantial variance in fetal growth, most commonly indexed by birth weight, may affect lifespan brain development. We investigated effects of normal variance in birth weight on MRI-derived measures of brain development in 628 healthy children, adolescents, and young adults in the large-scale multicenter Pediatric Imaging, Neurocognition, and Genetics study. This heterogeneous sample was recruited through geographically dispersed sites in the United States. The influence of birth weight on cortical thickness, surface area, and striatal and total brain volumes was investigated, controlling for variance in age, sex, household income, and genetic ancestry factors. Birth weight was found to exert robust positive effects on regional cortical surface area in multiple regions as well as total brain and caudate volumes. These effects were continuous across birth weight ranges and ages and were not confined to subsets of the sample. The findings show that (
i
) aspects of later child and adolescent brain development are influenced at birth and (
ii
) relatively small differences in birth weight across groups and conditions typically compared in neuropsychiatric research (e.g., Attention Deficit Hyperactivity Disorder, schizophrenia, and personality disorders) may influence group differences observed in brain parameters of interest at a later stage in life. These findings should serve to increase our attention to early influences.
The dynamic pause-unpackaging state, an off-translocation recovery state of a DNA packaging motor from bacteriophage T4
Authors: Kottadiel Vishal I. , Rao Venigalla B. , Chemla Yann R.
Published: November 2012

Tailed bacteriophages and herpes viruses use powerful ATP-driven molecular motors to translocate their viral genomes into a preformed capsid shell. The bacteriophage T4 motor, a pentamer of the large terminase protein (gp17) assembled at the portal vertex of the prohead, is the fastest and most powerful known, consistent with the need to package a ∼170-kb viral genome in approximately 5 min. Although much is known about the mechanism of DNA translocation, very little is known about how ATP modulates motor–DNA interactions. Here, we report single-molecule measurements of the phage T4 gp17 motor by using dual-trap optical tweezers under different conditions of perturbation. Unexpectedly, the motor pauses randomly when ATP is limiting, for an average of 1 s, and then resumes translocation. During pausing, DNA is unpackaged, a phenomenon so far observed only in T4, where some of the packaged DNA is slowly released. We propose that the motor pauses whenever it encounters a subunit in the apo state with the DNA bound weakly and incorrectly. Pausing allows the subunit to capture ATP, whereas unpackaging allows scanning of DNA until a correct registry is established. Thus, the “pause-unpackaging” state is an off-translocation recovery state wherein the motor, sometimes by taking a few steps backward, can bypass the impediments encountered along the translocation path. These results lead to a four-state mechanochemical model that provides insights into the mechanisms of translocation of an intricately branched concatemeric viral genome.
Self-boosting vaccines and their implications for herd immunity
Authors: Arinaminpathy Nimalan , Lavine Jennie S. , Grenfell Bryan T.
Published: November 2012

Advances in vaccine technology over the past two centuries have facilitated far-reaching impact in the control of many infections, and today’s emerging vaccines could likewise open new opportunities in the control of several diseases. Here we consider the potential, population-level effects of a particular class of emerging vaccines that use specific viral vectors to establish long-term, intermittent antigen presentation within a vaccinated host: in essence, “self-boosting” vaccines. In particular, we use mathematical models to explore the potential role of such vaccines in situations where current immunization raises only relatively short-lived protection. Vaccination programs in such cases are generally limited in their ability to raise lasting herd immunity. Moreover, in certain cases mass vaccination can have the counterproductive effect of allowing an increase in severe disease, through reducing opportunities for immunity to be boosted through natural exposure to infection. Such dynamics have been proposed, for example, in relation to pertussis and varicella-zoster virus. In this context we show how self-boosting vaccines could open qualitatively new opportunities, for example by broadening the effective duration of herd immunity that can be achieved with currently used immunogens. At intermediate rates of self-boosting, these vaccines also alleviate the potential counterproductive effects of mass vaccination, through compensating for losses in natural boosting. Importantly, however, we also show how sufficiently high boosting rates may introduce a new regime of unintended consequences, wherein the unvaccinated bear an increased disease burden. Finally, we discuss important caveats and data needs arising from this work.
Transcription factor-dependent nuclear localization of a transcriptional repressor in jasmonate hormone signaling
Authors: Withers John , Yao Jian , Mecey Christy , Howe Gregg A. , Melotto Maeli , He Sheng Yang
Published: November 2012

The plant hormone jasmonate (JA) plays an important role in regulating growth, development and immunity. A key step in JA signaling is ligand-dependent assembly of a coreceptor complex consisting of the F-box protein COI1 and JAZ transcriptional repressors. Assembly of this receptor complex results in proteasome-mediated degradation of JAZ repressors, which at resting state bind to and repress the MYC transcription factors. Although the JA receptor complex is believed to function within the nucleus, how this receptor complex enters the nucleus and, more generally, the cell biology of jasmonate signaling are not well understood. In this study, we conducted mutational analysis of the C termini (containing the conserved Jas motif) of two JAZ repressors, JAZ1 and JAZ9. These analyses unexpectedly revealed different subcellular localization patterns of JAZ1ΔJas and JAZ9ΔJas, which were associated with differential interaction of JAZ1ΔJas and JAZ9ΔJas with MYC2 and differential repressor activity in vivo. Importantly, physical interaction with MYC2 appears to play an active role in the nuclear targeting of JAZ1 and JAZ9, and the nuclear localization of JAZ9 was compromised in
myc2
mutant plants. We identified a highly conserved arginine residue in the Jas motif that is critical for coupling MYC2 interaction with nuclear localization of JAZ9 and JAZ9 repressor function in vivo. Our results suggest a model for explaining why some JAZΔJas proteins, but not others, confer constitutive JA-insensitivity when overexpressed in plants. Results also provide evidence for a transcription factor-dependent mechanism for nuclear import of a cognate transcriptional repressor JAZ9 in plants.
The Miocene mammal
Necrolestes
demonstrates the survival of a Mesozoic nontherian lineage into the late Cenozoic of South America
Authors: Rougier Guillermo W. , Wible John R. , Beck Robin M. D. , Apesteguía Sebastian
Published: November 2012

The early Miocene mammal
Necrolestes patagonensis
from Patagonia, Argentina, was described in 1891 as the only known extinct placental “insectivore” from South America (SA). Since then, and despite the discovery of additional well-preserved material, the systematic status of
Necrolestes
has remained in flux, with earlier studies leaning toward placental affinities and more recent ones endorsing either therian or specifically metatherian relationships. We have further prepared the best-preserved specimens of
Necrolestes
and compared them with newly discovered nontribosphenic Mesozoic mammals from Argentina; based on this, we conclude that
Necrolestes
is related neither to marsupials nor placentals but is a late-surviving member of the recently recognized nontherian clade Meridiolestida, which is currently known only from SA. This conclusion is supported by a morphological phylogenetic analysis that includes a broad sampling of therian and nontherian taxa and that places
Necrolestes
within Meridiolestida. Thus,
Necrolestes
is a remnant of the highly endemic Mesozoic fauna of nontribosphenic mammals in SA and extends the known record of meridiolestidans by almost 45 million years. Together with other likely relictual mammals from earlier in the Cenozoic of SA and Antarctica,
Necrolestes
demonstrates the ecological diversity of mammals and the mosaic pattern of fauna replacement in SA during the Cenozoic. In contrast to northern continents, the Cenozoic faunal history of SA was characterized by a long period of interaction between endemic mammalian lineages of Mesozoic origin and metatherian and eutherian lineages that probably dispersed to SA during the latest Cretaceous or earliest Paleocene.
miR-155 targets histone deacetylase 4 (HDAC4) and impairs transcriptional activity of B-cell lymphoma 6 (BCL6) in the Eµ-miR-155 transgenic mouse model
Authors: Sandhu Sukhinder K. , Volinia Stefano , Costinean Stefan , Galasso Marco , Neinast Reid , Santhanam Ramasamy , Parthun Mark R. , Perrotti Danilo , Marcucci Guido , Garzon Ramiro , Croce Carlo M.
Published: November 2012

Multiple studies have established that microRNAs (miRNAs) are involved in the initiation and progression of cancer. Notably, miR-155 is one of the most overexpressed miRNAs in several solid and hematological malignancies. Ectopic miR-155 expression in mice B cells (Eμ-miR-155 transgenic mice) has been shown to induce pre–B-cell proliferation followed by high-grade lymphoma/leukemia. Loss of miR-155 in mice resulted in impaired immunity due to defective T-cell–mediated immune response. Here we provide a mechanistic insight into miR-155–induced leukemogenesis in the Eμ-miR-155 mouse model through genome-wide transcriptome analysis of naïve B cells and target studies. We found that a key transcriptional repressor and proto-oncogene,
Bcl6
is significantly down-regulated in Eμ-miR-155 mice. The reduction of
Bcl6
subsequently leads to de-repression of some of the known
Bcl6
targets like inhibitor of differentiation (
Id2
), interleukin-6 (
IL6
),
cMyc
,
Cyclin D1
, and
Mip1α/ccl3
, all of which promote cell survival and proliferation. We show that
Bcl6
is indirectly regulated by miR-155 through
Mxd1/Mad1
up-regulation. Interestingly, we found that miR-155 directly targets HDAC4, a corepressor partner of BCL6. Furthermore, ectopic expression of HDAC4 in human-activated B-cell–type diffuse large B-cell lymphoma (DLBCL) cells results in reduced miR-155–induced proliferation, clonogenic potential, and increased apoptosis. Meta-analysis of the diffuse large B-cell lymphoma patient microarray data showed that miR-155 expression is inversely correlated with
Bcl6
and
Hdac4
. Hence this study provides a better understanding of how miR-155 causes disruption of the BCL6 transcriptional machinery that leads to up-regulation of the survival and proliferation genes in miR-155–induced leukemias.
pH-triggered, activated-state conformations of the influenza hemagglutinin fusion peptide revealed by NMR
Authors: Lorieau Justin L. , Louis John M. , Schwieters Charles D. , Bax Adriaan
Published: November 2012

The highly conserved first 23 residues of the influenza hemagglutinin HA2 subunit constitute the fusion domain, which plays a pivotal role in fusing viral and host-cell membranes. At neutral pH, this peptide adopts a tight helical hairpin wedge structure, stabilized by aliphatic hydrogen bonding and charge–dipole interactions. We demonstrate that at low pH, where the fusion process is triggered, the native peptide transiently visits activated states that are very similar to those sampled by a G8A mutant. This mutant retains a small fraction of helical hairpin conformation, in rapid equilibrium with at least two open structures. The exchange rate between the closed and open conformations of the wild-type fusion peptide is ∼40 kHz, with a total open-state population of ∼20%. Transitions to these activated states are likely to play a crucial role in formation of the fusion pore, an essential structure required in the final stage of membrane fusion.
Ultrasensitivity of the
Bacillus subtilis
sporulation decision
Authors: Narula Jatin , Devi Seram N. , Fujita Masaya , Igoshin Oleg A.
Published: November 2012

Starving
Bacillus subtilis
cells execute a gene expression program resulting in the formation of stress-resistant spores. Sporulation master regulator, Spo0A, is activated by a phosphorelay and controls the expression of a multitude of genes, including the forespore-specific sigma factor σ
F
and the mother cell-specific sigma factor σ
E
. Identification of the system-level mechanism of the sporulation decision is hindered by a lack of direct control over Spo0A activity. This limitation can be overcome by using a synthetic system in which Spo0A activation is controlled by inducing expression of phosphorelay kinase KinA. This induction results in a switch-like increase in the number of sporulating cells at a threshold of KinA. Using a combination of mathematical modeling and single-cell microscopy, we investigate the origin and physiological significance of this ultrasensitive threshold. The results indicate that the phosphorelay is unable to achieve a sufficiently fast and ultrasensitive response via its positive feedback architecture, suggesting that the sporulation decision is made downstream. In contrast, activation of σ
F
in the forespore and of σ
E
in the mother cell compartments occurs via a cascade of coherent feed-forward loops, and thereby can produce fast and ultrasensitive responses as a result of KinA induction. Unlike σ
F
activation, σ
E
activation in the mother cell compartment only occurs above the KinA threshold, resulting in completion of sporulation. Thus, ultrasensitive σ
E
activation explains the KinA threshold for sporulation induction. We therefore infer that under uncertain conditions, cells initiate sporulation but postpone making the sporulation decision to average stochastic fluctuations and to achieve a robust population response.
Dual-acting riboswitch control of translation initiation and mRNA decay
Authors: Caron Marie-Pier , Bastet Laurène , Lussier Antony , Simoneau-Roy Maxime , Massé Eric , Lafontaine Daniel A.
Published: November 2012

Riboswitches are mRNA regulatory elements that control gene expression by altering their structure in response to specific metabolite binding. In bacteria, riboswitches consist of an aptamer that performs ligand recognition and an expression platform that regulates either transcription termination or translation initiation. Here, we describe a dual-acting riboswitch from
Escherichia coli
that, in addition to modulating translation initiation, also is directly involved in the control of initial mRNA decay. Upon lysine binding, the
lysC
riboswitch adopts a conformation that not only inhibits translation initiation but also exposes RNase E cleavage sites located in the riboswitch expression platform. However, in the absence of lysine, the riboswitch folds into an alternative conformation that simultaneously allows translation initiation and sequesters RNase E cleavage sites. Both regulatory activities can be individually inhibited, indicating that translation initiation and mRNA decay can be modulated independently using the same conformational switch. Because RNase E cleavage sites are located in the riboswitch sequence, this riboswitch provides a unique means for the riboswitch to modulate RNase E cleavage activity directly as a function of lysine. This dual inhibition is in contrast to other riboswitches, such as the thiamin pyrophosphate-sensing
thiM
riboswitch, which triggers mRNA decay only as a consequence of translation inhibition. The riboswitch control of RNase E cleavage activity is an example of a mechanism by which metabolite sensing is used to regulate gene expression of single genes or even large polycistronic mRNAs as a function of environmental changes.
Structural basis of mouse cytomegalovirus m152/gp40 interaction with RAE1γ reveals a paradigm for MHC/MHC interaction in immune evasion
Authors: Wang Rui , Natarajan Kannan , Revilleza Maria Jamela R. , Boyd Lisa F. , Zhi Li , Zhao Huaying , Robinson Howard , Margulies David H.
Published: November 2012

Natural killer (NK) cells are activated by engagement of the NKG2D receptor with ligands on target cells stressed by infection or tumorigenesis. Several human and rodent cytomegalovirus (CMV) immunoevasins down-regulate surface expression of NKG2D ligands. The mouse CMV MHC class I (MHC-I)–like m152/gp40 glycoprotein down-regulates retinoic acid early inducible-1 (RAE1) NKG2D ligands as well as host MHC-I. Here we describe the crystal structure of an m152/RAE1γ complex and confirm the intermolecular contacts by mutagenesis. m152 interacts in a pincer-like manner with two sites on the α1 and α2 helices of RAE1 reminiscent of the NKG2D interaction with RAE1. This structure of an MHC-I–like immunoevasin/MHC-I–like ligand complex explains the binding specificity of m152 for RAE1 and allows modeling of the interaction of m152 with classical MHC-I and of related viral immunoevasins.
Architectural switch in plant photosynthetic membranes induced by light stress
Authors: Herbstová Miroslava , Tietz Stefanie , Kinzel Christopher , Turkina Maria V. , Kirchhoff Helmut
Published: November 2012

Unavoidable side reactions of photosynthetic energy conversion can damage the water-splitting photosystem II (PSII) holocomplex embedded in the thylakoid membrane system inside chloroplasts. Plant survival is crucially dependent on an efficient molecular repair of damaged PSII realized by a multistep repair cycle. The PSII repair cycle requires a brisk lateral protein traffic between stacked grana thylakoids and unstacked stroma lamellae that is challenged by the tight stacking and low protein mobility in grana. We demonstrated that high light stress induced two main structural changes that work synergistically to improve the accessibility between damaged PSII in grana and its repair machinery in stroma lamellae: lateral shrinkage of grana diameter and increased protein mobility in grana thylakoids. It follows that high light stress triggers an architectural switch of the thylakoid network that is advantageous for swift protein repair. Studies of the thylakoid kinase mutant
stn8
and the double mutant
stn7/8
demonstrate the central role of protein phosphorylation for the structural alterations. These findings are based on the elaboration of mathematical tools for analyzing confocal laser-scanning microscopic images to study changes in the sophisticated thylakoid architecture in intact protoplasts.
Effects of sex and COMT genotype on environmentally modulated cognitive control in mice
Authors: Papaleo Francesco , Erickson Lucy , Liu Guangping , Chen Jingshan , Weinberger Daniel R.
Published: November 2012

Cognitive functioning differs between males and females, likely in part related to genetic dimorphisms. An example of a common genetic variation reported to have sexually dimorphic effects on cognition and temperament in humans is the Val/Met polymorphism in catechol-O-methyltransferase (COMT). We tested male and female wild-type mice (+/+) and theirCOMTknockout littermates (+/−and−/−) in the five-choice serial reaction time task (5CSRTT) to investigate the effects of sex,COMTgenotype, and their interactions with environmental manipulations of cognitive functions such as attention, impulsivity, compulsivity, motivation, and rule-reversal learning. No sex- or COMT-dependent differences were present in the basic acquisition of the five-choice serial reaction time task. In contrast, specific environmental manipulations revealed a variety of sex- and COMT-dependent effects. Following an experimental change to trigger impulsive responding, the sexes showed similar increases in impulsiveness, but males eventually habituated whereas females did not. Moreover,COMTknockout mice were more impulsive compared with wild-type littermates. Manipulations involving mild stress adversely affected cognitive performance in males, and particularlyCOMTknockout males, but not in females. In contrast, following amphetamine treatment, subtle sex by genotype and sex by treatment interactions emerged primarily limited to compulsive behavior. After repeated testing, female mice showed improved performance, working harder and eventually outperforming males. Finally, removing the food-restriction condition enhanced sex and COMT differences, revealing that overall, females outperform males and COMT knockout males outperform their wild-type littermates. These findings illuminate complex sex- and COMT-related effects and their interactions with environmental factors to influence specific executive cognitive domains.
TRIM28 mediates chromatin modifications at the TCRα enhancer and regulates the development of T and natural killer T cells
Authors: Zhou Xiao-Fei , Yu Jiayi , Chang Mikyoung , Zhang Minying , Zhou Dapeng , Cammas Florence , Sun Shao-Cong
Published: November 2012

T-cell receptor–α (TCRα) rearrangement in CD4
+
CD8
+
double-positive immature thymocytes is a prerequisite for production of αβ T cells and invariant natural killer T cells. This developmental event is regulated by the TCRα enhancer (Eα), which induces chromatin modification and recruitment of the recombination-activating proteins Rag1 and Rag2. However, the molecular mechanism underlying the activation and long-range action of Eα remains incompletely understood. We show here that the chromatin-modifying factor TRIM28 is highly expressed in double-positive thymocytes and persistently phosphorylated at serine 473. TRIM28 binds to Eα and induces histone 3 lysine 4 trimethylation in the Eα and distant regions of the TCRα locus, coupled with recruitment of Rag proteins. T-cell–conditional ablation of TRIM28 impaired TCRα gene rearrangement and compromised the development of αβ T cells and invariant natural killer T cells. These findings establish TRIM28 as a unique regulator of thymocyte development and highlight an epigenetic mechanism involving TRIM28-mediated active chromatin modification in the TCRα locus.
Mutual antagonism between IP3RII and miRNA-133a regulates calcium signals and cardiac hypertrophy
Authors: Drawnel Faye M. , Wachten Dagmar , Molkentin Jeffery D. , Maillet Marjorie , Aronsen Jan Magnus , Swift Fredrik , Sjaastad Ivar , Liu Ning , Catalucci Daniele , Mikoshiba Katsuhiko , Hisatsune Chihiro , Okkenhaug Hanneke , Andrews Simon R. , Bootman Martin D. , Roderick H. Llewelyn
Published: November 2012

Inositol 1,4,5′-triphosphate receptor II (IP3RII) calcium channel expression is increased in both hypertrophic failing human myocardium and experimentally induced models of the disease. The ectopic calcium released from these receptors induces pro-hypertrophic gene expression and may promote arrhythmias. Here, we show that IP3RII expression was constitutively restrained by the muscle-specific miRNA, miR-133a. During the hypertrophic response to pressure overload or neurohormonal stimuli, miR-133a down-regulation permitted IP3RII levels to increase, instigating pro-hypertrophic calcium signaling and concomitant pathological remodeling. Using a combination of in vivo and in vitro approaches, we demonstrated that IP3-induced calcium release (IICR) initiated the hypertrophy-associated decrease in miR-133a. In this manner, hypertrophic stimuli that engage IICR set a feed-forward mechanism in motion whereby IICR decreased miR-133a expression, further augmenting IP3RII levels and therefore pro-hypertrophic calcium release. Consequently, IICR can be considered as both an initiating event and a driving force for pathological remodeling.