bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of barley straw residues to avoid high erosion and runoff rates on persimmon plantations in Eastern Spain under low frequency–high magnitude simulated rainfall events
Authors: Cerdà Artemi , González-Pelayo Óscar , Giménez-Morera Antonio , Jordán Antonio , Pereira Paulo , Novara Agata , Brevik Eric C. , Prosdocimi Massimo , Mahmoodabadi Majid , Keesstra Saskia , Orenes Fuensanta García , Ritsema Coen J.
Published: March 2016

Soil and water losses due to agricultural mismanagement are high and non-sustainable in many orchards. An experiment was set up with rainfall simulation at 78 mm h–1 over 1 hour on 20 paired plots of 2 m2 (bare and straw covered) in new persimmon plantations in Eastern Spain. Effects of straw cover on the control of soil and water losses were assessed. An addition of 60% straw cover (75 g m–2) resulted in delayed ponding and runoff generation and consequently reduced water losses from 60% to 13% of total rainfall. The straw cover reduced raindrop impact and thus sediment detachment from 1014 to 47 g plot–1 h–1. The erosion rate was reduced from 5.1 to 0.2 Mg ha–1 h–1. The straw mulch was found to be extremely efficient in reducing soil erosion rates.
LSD1 modulates stress-evoked transcription of immediate early genes and emotional behavior
Authors: Rusconi Francesco , Grillo Barbara , Ponzoni Luisa , Bassani Silvia , Toffolo Emanuela , Paganini Leda , Mallei Alessandra , Braida Daniela , Passafaro Maria , Popoli Maurizio , Sala Mariaelvina , Battaglioli Elena
Published: March 2016

Significance

In mammals, different forms of stress, including psychosocial stress, can affect several aspects of health, fostering mood and anxiety disorders in humans. However, a lack of knowledge about the mechanisms underlying the brain physiology of the stress response hinders the development of new therapeutic strategies. We describe the role of the epigenetic enzyme Lysine-Specific Demethylase 1 (LSD1) in the transduction pathway that translates social stress into an altered transcriptional physiology of plasticity genes in hippocampus. In particular, we show that in the brain LSD1 is finely tuned by a mammal-restricted splicing-based mechanism, and its demethylase activity consistently affects anxiety-like behavior in mice. This work addresses a fundamental mechanism, explaining a brain-related phenotype as a result of genome–environment interactions mediated by the epigenome.
Optogenetic skeletal muscle-powered adaptive biological machines
Authors: Raman Ritu , Cvetkovic Caroline , Uzel Sebastien G. M. , Platt Randall J. , Sengupta Parijat , Kamm Roger D. , Bashir Rashid
Published: March 2016

Significance

Understanding the design rules that govern the structure and function of natural biological systems gives us the ability to forward engineer machines integrated with and powered by biological components. Such machines, or “bio-bots,” can sense, process, and respond to dynamic environmental signals in real time, enabling a variety of applications. Here we present a modular optogenetic muscle actuator used to power actuation and locomotion of 3D printed flexible skeletons. Observing and controlling the functional response of such muscle-powered machines helps replicate the complex adaptive functionality we observe in natural biological systems. This demonstration thus sets the stage for building the next generation of bio-integrated machines and systems targeted at a diverse array of functional tasks.
Galápagos hydroclimate of the Common Era from paired microalgal and mangrove biomarker
2
H/
1
H values
Authors: Nelson Daniel B. , Sachs Julian P.
Published: March 2016

Significance

The equatorial Pacific is centrally important in Earth’s climate system. Changes there cause disruptions to global economies and food and water security. Yet, projected tropical precipitation changes in response to higher greenhouse gas concentrations remain uncertain, due in part to a scarcity of paleoclimate records to validate models. We therefore applied a new method in Galápagos lakes for reconstructing rainfall and salinity using sedimentary lipids from microalgae and mangrove trees. Our data revise the understanding of changes over the Common Era to provide a spatially and temporally coherent view of tropical Pacific rainfall. We separate convergence zone from El Niño-driven changes and observe substantial fluctuations even in the absence of perturbations as large as current anthropogenic forcing.
Force-producing ADP state of myosin bound to actin
Authors: Wulf Sarah F. , Ropars Virginie , Fujita-Becker Setsuko , Oster Marco , Hofhaus Goetz , Trabuco Leonardo G. , Pylypenko Olena , Sweeney H. Lee , Houdusse Anne M. , Schröder Rasmus R.
Published: March 2016

Significance

The force-generating state of myosin bound to actin is a key state in the chemomechanical cycle of this motor, but the structural details of the force-generating state are unknown. CryoEM structures of myosin V bound to actin with and without nucleotide reveal a previously unidentified conformation of elements associated with nucleotide binding and, most importantly, of the β-sheet that controls the position of nucleotide-binding elements. These specific structural features explain how myosin can bind strongly to both actin and MgADP, allowing force to be developed. Thus, this structure provides fundamental insights into how myosin works. It also provides insights into how strain may prevent release of MgADP, which is a critical property for the cellular roles of many myosins, including myosin V.
High-seas fish wars generate marine reserves
Authors: Herrera Guillermo E. , Moeller Holly V. , Neubert Michael G.
Published: March 2016

Significance

Marine reserves—areas where fishing is prohibited—have been implemented to conserve fish stocks and their habitats. They have been established in near-shore fisheries, where a single state (or “sole owner”) regulates the distribution of fishing effort. Modeling has shown that, under some conditions, the sole owner may also use closed areas to maximize sustainable profit. Here, we show that reserves may also play a role in fisheries management on the high seas, where a limited number of states compete in a noncooperative fishing game. Our theoretical analysis complements recent empirical studies of high-seas protected areas and is relevant in other management contexts characterized by a limited number of harvesters.
Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold
Authors: Beeby Morgan , Ribardo Deborah A. , Brennan Caitlin A. , Ruby Edward G. , Jensen Grant J. , Hendrixson David R.
Published: March 2016

Significance

Many bacteria swim using helical propellers, flagella. Intriguingly, different bacteria show different swimming abilities, strikingly illustrated by the abilities of some to bore through viscous fluids (e.g., gastrointestinal mucus) in which others are completely immobilized. We used 3D electron microscopy to show that differences can be explained by the structures of the torque-generating motors: two diverse high-torque motors position additional torque-generating complexes at wider radii from the axial driveshaft than in the model enteric bacteria; this positioning is consistent with the exertion of greater leverage to rotate the flagellum and thus greater torque generation. Intriguingly, these torque-generating complexes are scaffolded at wider radii by a conserved but divergent family of structures, suggesting an ancient origin of reconfiguring torque output.
Phasic, suprathreshold excitation and sustained inhibition underlie neuronal selectivity for short-duration sounds
Authors: Alluri Rishi K. , Rose Gary J. , Hanson Jessica L. , Leary Christopher J. , Vasquez-Opazo Gustavo A. , Graham Jalina A. , Wilkerson Jeremy
Published: March 2016

Significance

Understanding how excitatory and inhibitory inputs are integrated to achieve sensory selectivity is an important, but elusive, goal in neuroscience. Whole-cell recordings in vivo have revealed excitation and inhibition, but the computational mechanisms are generally unclear. In the inferior colliculus, neurons exist that respond selectively to short-duration sounds; the mechanistic basis of this selectivity has long been debated. We combined whole-cell recordings, in vivo, with conductance extraction algorithms and focal pharmacological manipulations to show that duration selectivity results from an anticoincidence of suprathreshold excitation and inhibition. These results challenge the widely held view that postinhibitory rebound depolarization must coincide with subthreshold excitation to generate duration selectivity.
Stability of the human polymerase δ holoenzyme and its implications in lagging strand DNA synthesis
Authors: Hedglin Mark , Pandey Binod , Benkovic Stephen J.
Published: March 2016

Significance

The results from the reported studies indicate that the human lagging strand polymerase, pol δ, maintains a loose association with the sliding clamp, proliferating cell nuclear antigen (PCNA), while replicating and rapidly dissociates on stalling, leaving PCNA behind on the DNA. This behavior has profound implications on lagging strand synthesis as it limits the extent of processive DNA synthesis on undamaged DNA and promotes the rapid dissociation of pol δ on stalling at a replication-blocking lesion. This challenges the accepted models for polymerase recycling and exchange on the lagging strand and instead suggests passive mechanisms for the human system. These studies provide valuable insight for future experiments in the fields DNA replication, DNA repair, and DNA damage tolerance.
Spironolactone blocks Epstein–Barr virus production by inhibiting EBV SM protein function
Authors: Verma Dinesh , Thompson Jacob , Swaminathan Sankar
Published: March 2016

Significance

Epstein–Barr virus is a human herpesvirus associated with several types of malignancy. We show that spironolactone, a drug used to block mineralocorticoid activity, also has anti-EBV activity and that it acts by inhibiting the function of an essential EBV protein SM, which preferentially increases expression of specific EBV genes. We also show that the mineralocorticoid blocking activity is not the basis for spironolactone’s antiviral activity. Because the SM protein acts at steps of the viral life cycle distinct from those targeted by currently available therapies, this study paves the way for development of novel anti-EBV drugs to address emerging problems of drug resistance and toxicity.
A RhoA and Rnd3 cycle regulates actin reassembly during membrane blebbing
Authors: Aoki Kana , Maeda Fumiyo , Nagasako Tomoya , Mochizuki Yuki , Uchida Seiichi , Ikenouchi Junichi
Published: March 2016

Significance

The plasma membrane and the underlying actin cortex show dynamic interactions. When the plasma membrane detaches from the actin cortex, the plasma membrane protrudes. The protruded membrane is called a membrane bleb and is often observed during cell migration or cytokinesis. In the present study, we determined the molecular mechanisms involved in the reassembly of the actin cortex in membrane blebs using live-cell imaging.
Gene deficiency and pharmacological inhibition of soluble epoxide hydrolase confers resilience to repeated social defeat stress
Authors: Ren Qian , Ma Min , Ishima Tamaki , Morisseau Christophe , Yang Jun , Wagner Karen M. , Zhang Ji-chun , Yang Chun , Yao Wei , Dong Chao , Han Mei , Hammock Bruce D. , Hashimoto Kenji
Published: March 2016

Significance

Depression is the most common and debilitating psychiatric disorder in the world. However, the precise mechanisms underlying depression remain largely unknown. Recent evidence suggests that soluble epoxide hydrolase (sEH) plays a key role in inflammation, which is involved in depression. The sEH inhibitor, TPPU, showed antidepressant effects in animal models of depression. Expression of sEH protein was increased in the brain of chronically stressed (susceptible) mice and depressed patients. Prophylactic sEH inhibition or sEH-KO resulted in resilience to repeated social defeat stress, associated with increased BDNF-TrkB signaling in prefrontal cortex and hippocampus of KO mice. This study shows that sEH plays a key role in the pathophysiology of depression, and that its inhibitors could be potential therapeutic drugs for depression.
BRCA2 regulates DMC1-mediated recombination through the BRC repeats
Authors: Martinez Juan S. , von Nicolai Catharina , Kim Taeho , Ehlén Åsa , Mazin Alexander V. , Kowalczykowski Stephen C. , Carreira Aura
Published: March 2016

Significance

The function of BRCA2 (breast cancer susceptibility protein 2) in mitotic homologous recombination is well established; this role for BRCA2 includes promotion of RAD51 recombination function by regulating its assembly on DNA. However, loss of BRCA2 also leads to aberrant meiosis. Even though interaction of BRCA2 and the meiotic counterpart of RAD51, DMC1 (DNA meiotic recombinase 1), was reported, the specific role of BRCA2 in meiotic recombination is unknown. We demonstrate that the BRC repeats interact with DMC1 to stimulate both association with ssDNA and homologous DNA pairing. Furthermore, we demonstrate strong stimulation by BRCA2 of DNA strand exchange promoted by DMC1, even using ssDNA complexed with RPA (replication protein-A). These findings define BRCA2 as a mediator of meiotic recombination.
Four-dimensional maps of the human somatosensory system
Authors: Avanzini Pietro , Abdollahi Rouhollah O. , Sartori Ivana , Caruana Fausto , Pelliccia Veronica , Casaceli Giuseppe , Mai Roberto , Lo Russo Giorgio , Rizzolatti Giacomo , Orban Guy A.
Published: March 2016

Significance

Here, we show how anatomical and functional data recorded from patients undergoing stereo-EEG can be combined to generate highly resolved four-dimensional maps of human cortical processing. We used this technique, which provides spatial maps of the active cortical nodes at a millisecond scale, to depict the somatosensory processing following electrical stimulation of the median nerve in nearly 100 patients. The results showed that human somatosensory system encompasses a widespread cortical network including a phasic component, centered on primary somatosensory cortex and neighboring motor, premotor, and inferior parietal regions, as well as a tonic component, centered on the opercular and insular areas, lasting more than 200 ms.
Recombinant thiopeptides containing noncanonical amino acids
Authors: Luo Xiaozhou , Zambaldo Claudio , Liu Tao , Zhang Yuhan , Xuan Weimin , Wang Chen , Reed Sean A. , Yang Peng-Yu , Wang Rongsheng E. , Javahishvili Tsotne , Schultz Peter G. , Young Travis S.
Published: March 2016

Significance

Thiopeptides are a subclass of ribosomally synthesized natural products with complex structures and potent antimicrobial activities. Here we describe a general strategy that allows the incorporation of noncanonical amino acids into thiopeptides by introducing orthogonal amber suppressor aminoacyl-tRNA synthetase/tRNA pairs into a thiocillin-producing strain of
Bacillus cereus
. We show that thiocillin variants harboring a noncanonical amino acid with bioorthogonal chemical reactivity can be further modified to create probes for biological studies. This work should significantly enhance our ability to manipulate the structures and properties of ribosomally produced natural products by recombinant methods.
IL-12 drives functional plasticity of human group 2 innate lymphoid cells
Authors: Lim Ai Ing , Menegatti Silvia , Bustamante Jacinta , Le Bourhis Lionel , Allez Matthieu , Rogge Lars , Casanova Jean-Laurent , Yssel Hans , Di Santo James P.
Published: March 2016

Group 2 innate lymphoid cells (ILC2) include IL-5– and IL-13–producing CRTh2+CD127+ cells that are implicated in early protective immunity at mucosal surfaces. Whereas functional plasticity has been demonstrated for both human and mouse ILC3 subsets that can reversibly give rise to IFN-γ–producing ILC1, plasticity of human or mouse ILC2 has not been shown. Here, we analyze the phenotypic and functional heterogeneity of human peripheral blood ILC2. Although subsets of human CRTh2+ ILC2 differentially express CD117 (c-kit receptor), some ILC2 surface phenotypes are unstable and can be modulated in vitro. Surprisingly, human IL-13+ ILC2 can acquire the capacity to produce IFN-γ, thereby generating plastic ILC2. ILC2 cultures demonstrated that IFN-γ+ ILC2 clones could be derived and were stably associated with increased T-BET expression. The inductive mechanism for ILC2 plasticity was mapped to the IL-12–IL-12R signaling pathway and was confirmed through analysis of patients with Mendelian susceptibility to mycobacterial disease due to IL-12Rβ1 deficiencies that failed to generate plastic ILC2. We also detected IL-13+IFN-γ+ ILC2 ex vivo in intestinal samples from Crohn’s disease patients. These results demonstrate cytokine production plasticity for human ILC2 and further suggest that environmental cues can dictate ILC phenotype and function for these tissue-resident innate effector cells.
First international comparison of primary absorbed dose to water standards in the medium-energy X-ray range
Authors: Büermann Ludwig , Guerra Antonio Stefano , Pimpinella Maria , Pinto Massimo , Pooter Jacco de , Prez Leon de , Jansen Bartel , Denoziere Marc , Rapp Benjamin
Published: March 2016

This report presents the results of the first international comparison of primary measurement standards of absorbed dose to water for the medium-energy X-ray range. Three of the participants (VSL, PTB, LNE-LNHB) used their existing water calorimeter based standards and one participant (ENEA) recently developed a new standard based on a water-graphite calorimeter. The participants calibrated three transfer chambers of the same type in terms of absorbed dose to water (N

Dw) and in addition in terms of air kerma (NK
) using the CCRI radiation qualities in the range 100 kV to 250 kV. The additional NK values were intended to be used for a physical analysis of the ratios N

Dw/NK
.

All participants had previously participated in the BIPM.RI(I)-K3 key comparison of air kerma standards. Ratios of pairs of NMI's NK
results of the current comparison were found to be consistent with the corresponding key comparison results within the expanded uncertainties of 0.6 % - 1 %. The N

Dw results were analysed in terms of the degrees of equivalence with the comparison reference values which were calculated for each beam quality as the weighted means of all results. The participant's results were consistent with the reference value within the expanded uncertainties. However, these expanded uncertainties varied significantly and ranged between about 1-1.8 % for the water calorimeter based standards and were estimated at 3.7 % for the water-graphite calorimeter.

It was shown previously that the ratios N

Dw/NK
for the type of ionization chamber used as transfer chamber in this comparison were very close (within less than 1 %) to the calculated values of (μ̄en/ρ)w,a
d, the mean values of the water-to-air ratio of the mass-energy-absorption coefficients at the depth d in water. Some of the participant's results deviated significantly from the expected behavior.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Excess strain in the Echigo Plain sedimentary basin, NE Japan: evidence from coseismic deformation of the 2011 Tohoku-oki earthquake
Authors: Nishimura T. , Suito H. , Kobayashi T. , Dong Q. , Shibayama T.
Published: March 2016

Coseismic deformation depends on both the source fault and on the elastic properties of the crust. Large coseismic deformation associated with the 2011 Mw 9.0 Tohoku-oki earthquake enabled us to investigate strain anomalies from crustal inhomogeneity. Concentrated contractional strain was observed in the Echigo Plain (Niigata-Kobe Tectonic Zone) before the Tohoku-oki earthquake, whereas continuous and campaign global navigation satellite system measurements show a widespread distribution of coseismic extensional strain in and around the plain. A 1-D displacement profile shows high strain (7.2 ± 0.7 microstrain) in a 17 km long section across the Echigo Plain and low strain (3.3 ± 0.4 microstrain) along a 15 km long section east of the plain, despite the latter being closer to the megathrust fault source. We performed numerical modelling of coseismic deformation using a heterogeneous subsurface structure and successfully reproduced excess extension in the plain, which is filled by low-rigidity sediments. This study demonstrates the importance of considering heterogeneous crust in deformation modelling.
Automatic detection of social rhythms in bipolar disorder
Authors: Abdullah Saeed , Matthews Mark , Frank Ellen , Doherty Gavin , Gay Geri , Choudhury Tanzeem
Published: March 2016

Objective To evaluate the feasibility of automatically assessing the Social Rhythm Metric (SRM), a clinically-validated marker of stability and rhythmicity for individuals with bipolar disorder (BD), using passively-sensed data from smartphones.

Methods Seven patients with BD used smartphones for 4 weeks passively collecting sensor data including accelerometer, microphone, location, and communication information to infer behavioral and contextual patterns. Participants also completed SRM entries using a smartphone app.

Results We found that automated sensing can be used to infer the SRM score. Using location, distance traveled, conversation frequency, and non-stationary duration as inputs, our generalized model achieves root-mean-square-error of 1.40, a reasonable performance given the range of SRM score (0–7). Personalized models further improve performance with mean root-mean-square-error of 0.92 across users. Classifiers using sensor streams can predict stable (SRM score ≥3.5) and unstable (SRM score <3.5) states with high accuracy (precision: 0.85 and recall: 0.86).

Conclusions Automatic smartphone sensing is a feasible approach for inferring rhythmicity, a key marker of wellbeing for individuals with BD.
Precision medicine: opportunities, possibilities, and challenges for patients and providers
Authors: Adams Samantha A , Petersen Carolyn
Published: March 2016

Precision medicine approaches disease treatment and prevention by taking patients’ individual variability in genes, environment, and lifestyle into account. Although the ideas underlying precision medicine are not new, opportunities for its more widespread use in practice have been enhanced by the development of large-scale databases, new methods for categorizing and representing patients, and computational tools for analyzing large datasets. New research methods may create uncertainty for both healthcare professionals and patients. In such situations, frameworks that address ethical, legal, and social challenges can be instrumental for facilitating trust between patients and providers, but must protect patients while not stifling progress or overburdening healthcare professionals. In this perspective, we outline several ethical, legal, and social issues related to the Precision Medicine Initiative’s proposed changes to current institutions, values, and frameworks. This piece is not an exhaustive overview, but is intended to highlight areas meriting further study and action, so that precision medicine’s goal of facilitating systematic learning and research at the point of care does not overshadow healthcare’s goal of providing care to patients.
General relativistic considerations of the field shedding model of fast radio bursts
Authors: Punsly Brian , Bini Donato
Published: March 2016

Popular models of fast radio bursts (FRBs) involve the gravitational collapse of neutron star progenitors to black holes. It has been proposed that the shedding of the strong neutron star magnetic field (B) during the collapse is the power source for the radio emission. Previously, these models have utilized the simplicity of the Schwarzschild metric which has the restriction that the magnetic flux is magnetic ‘hair’ that must be shed before final collapse. But neutron stars have angular momentum and charge and a fully relativistic Kerr–Newman solution exists in which B has its source inside of the event horizon. In this Letter, we consider the magnetic flux to be shed as a consequence of the electric discharge of a metastable collapsed state of a Kerr–Newman black hole. It has also been argued that the shedding model will not operate due to pair creation. By considering the pulsar death line, we find that for a neutron star with B = 1011–1013 G and a long rotation period, >1s this is not a concern. We also discuss the observational evidence supporting the plausibility of magnetic flux shedding models of FRBs that are spawned from rapidly rotating progenitors.
Pre-existence and Persistence of Resistant Minority Hepatitis C Virus Variants in Genotype 1-Infected Patients Treated With Simeprevir/Peginterferon/Ribavirin
Authors: Fevery Bart , Thys Kim , Van Eygen Veerle , Verbinnen Thierry , Van Rossem Elizabeth , Buelens Annemie , Aerssens Jeroen , Witek James , Picchio Gaston , De Meyer Sandra , Lenz Oliver
Published: March 2016

Background.  The pre-existence of minority hepatitis C virus (HCV) variants and their impact on treatment outcome, as well as the persistence of emerging resistant variants posttreatment in patients failing treatment with simeprevir/peginterferon/ribavirin (SMV/PR), were assessed by deep sequencing (DS).

Methods.  Population sequencing (PS) and Illumina DS were performed on HCV genotype 1 isolates from patients treated with SMV/PR in Phase 2b (PILLAR [NCT00882908] and ASPIRE [NCT00980330]) and Phase 3 (QUEST-1 [NCT01289782], QUEST-2 [NCT01290679], and PROMISE [NCT01281839]) trials.

Results.  Minority polymorphisms (ie, detected pretreatment by DS only) reducing SMV activity in vitro were uncommon (3.6%, 19 of 534 patients). These SMV-resistant minority polymorphisms were detected in similar proportions of patients achieving (3.7%) and not achieving (3.3%) sustained virologic response with SMV/PR and generally did not emerge as major variants at time of failure. SMV-resistant variants emerging at time of failure were no longer detected at end of study in 69.3% and 52.0% of the patients by PS and DS, respectively.

Conclusions.  Minority polymorphisms did not impact outcome of SMV/PR treatment. The majority of emerging variants that became undetectable at end of study by PS were also undetectable by DS. These results suggest no added value of DS for clinical usage of SMV.
Use of Mycelium and Detached Leaves in Bioassays for Assessing Resistance to Boxwood Blight
Authors: Guo Yonghong , Olsen Richard T. , Kramer Matthew , Pooler Margaret
Published: March 2016

Boxwood blight caused by Calonectria pseudonaviculata is a newly emergent disease of boxwood (Buxus spp. L.) in the United States that causes leaf drop, stem lesions, and plant death. A rapid and reliable laboratory assay that enables screening hundreds of boxwood genotypes for resistance to boxwood blight is needed to enable breeding and selection of resistant cultivars. Using eight boxwood cultivars with differing susceptibilities, we examined parameters for a screening assay comparing whole plant inoculation with detached leaf inoculation, use of mycelium versus spores as the inoculum, comparison of times of the year for inoculation, and comparison of two leaf inoculation methods. Inoculation of detached leaves gave comparable results to inoculation of whole plants when compared across genotypes, although the detached leaf assay resulted in greater percentages of symptom expression. The time of year of plant inoculation (spring, summer, or winter) did not affect the relative expression of symptoms among the most resistant and susceptible genotypes. Inoculating plants with mycelium was as effective as spore inoculation for causing disease symptoms and allowed us to distinguish the more resistant genotypes, yet mycelium inoculation was much easier to prepare in large quantities for multiple assays.
Seasonal Susceptibility of Grapevine Pruning Wounds and Cane Colonization in Catalonia, Spain Following Artificial Infection withDiplodia seriataandPhaeomoniella chlamydospora
Authors: Elena Georgina , Luque Jordi
Published: March 2016

Diplodia seriata and Phaeomoniella chlamydospora are two fungal pathogens associated with grapevine trunk diseases worldwide. This study aimed to evaluate the period during which grapevine pruning wounds remain susceptible to fungal infection and to describe the colonization of canes artificially inoculated with these pathogens. In the first experiment, pruning wounds made in either fall or winter were separately inoculated with each pathogen at different times after pruning. Wound susceptibility to both pathogens decreased as the period between pruning and inoculation increased, from high percentages recorded in the first inoculation round (D. seriata, 97.5% and P. chlamydospora, 75%) down to approximately 10% 12 weeks after pruning. Pruning wounds remained more susceptible to D. seriata after a late pruning in winter whereas no overall seasonal changes in wound susceptibility were detected for P. chlamydospora. In the second experiment, canes were pruned by leaving two different lengths between the top node and the pruning wound before inoculations. Pathogens were recovered at different incubation periods and from different sites along the canes to estimate fungal cane colonization. A longer pruned internode made cane colonization by P. chlamydospora difficult, as indicated by fungal recoveries lower than 10% at the lowest recovery site, whereas D. seriata was less inhibited.
Understanding how biodiversity unfolds through time under neutral theory
Authors: Missa Olivier , Dytham Calvin , Morlon Hélène
Published: March 2016

Theoretical predictions for biodiversity patterns are typically derived under the assumption that ecological systems have reached a dynamic equilibrium. Yet, there is increasing evidence that various aspects of ecological systems, including (but not limited to) species richness, are not at equilibrium. Here, we use simulations to analyse how biodiversity patterns unfold through time. In particular, we focus on the relative time required for various biodiversity patterns (macroecological or phylogenetic) to reach equilibrium. We simulate spatially explicit metacommunities according to the Neutral Theory of Biodiversity (NTB) under three modes of speciation, which differ in how evenly a parent species is split between its two daughter species. We find that species richness stabilizes first, followed by species area relationships (SAR) and finally species abundance distributions (SAD). The difference in timing of equilibrium between these different macroecological patterns is the largest when the split of individuals between sibling species at speciation is the most uneven. Phylogenetic patterns of biodiversity take even longer to stabilize (tens to hundreds of times longer than species richness) so that equilibrium predictions from neutral theory for these patterns are unlikely to be relevant. Our results suggest that it may be unwise to assume that biodiversity patterns are at equilibrium and provide a first step in studying how these patterns unfold through time.
Towards a morphological metric of assemblage dynamics in the fossil record: a test case using planktonic foraminifera
Authors: Hsiang Allison Y. , Elder Leanne E. , Hull Pincelli M.
Published: March 2016

With a glance, even the novice naturalist can tell you something about the ecology of a given ecosystem. This is because the morphology of individuals reflects their evolutionary history and ecology, and imparts a distinct ‘look’ to communities—making it possible to immediately discern between deserts and forests, or coral reefs and abyssal plains. Once quantified, morphology can provide a common metric for characterizing communities across space and time and, if measured rapidly, serve as a powerful tool for quantifying biotic dynamics. Here, we present and test a new high-throughput approach for analysing community shape in the fossil record using semi-three-dimensional (3D) morphometrics from vertically stacked images (light microscopic or photogrammetric). We assess the potential informativeness of community morphology in a first analysis of the relationship between 3D morphology, ecology and phylogeny in 16 extant species of planktonic foraminifera—an abundant group in the marine fossil record—and in a preliminary comparison of four assemblages from the North Atlantic. In the species examined, phylogenetic relatedness was most closely correlated with ecology, with all three ecological traits examined (depth habitat, symbiont ecology and biogeography) showing significant phylogenetic signal. By contrast, morphological trees (based on 3D shape similarity) were relatively distantly related to both ecology and phylogeny. Although improvements are needed to realize the full utility of community morphometrics, our approach already provides robust volumetric measurements of assemblage size, a key ecological characteristic.
Building up the nucleus: nuclear organization in the establishment of totipotency and pluripotency during mammalian development
Authors: Borsos Máté , Torres-Padilla Maria-Elena
Published: March 2016

In mammals, epigenetic reprogramming, the acquisition and loss of totipotency, and the first cell fate decision all occur within a 3-d window after fertilization from the one-cell zygote to the formation of the blastocyst. These processes are poorly understood in molecular detail, yet this is an essential prerequisite to uncover principles of stem cells, chromatin biology, and thus regenerative medicine. A unique feature of preimplantation development is the drastic genome-wide changes occurring to nuclear architecture. From studying somatic and in vitro cultured embryonic stem cells (ESCs) it is becoming increasingly established that the three-dimensional (3D) positions of genomic loci relative to each other and to specific compartments of the nucleus can act on the regulation of gene expression, potentially driving cell fate. However, the functionality, mechanisms, and molecular characteristics of the changes in nuclear organization during preimplantation development are only now beginning to be unraveled. Here, we discuss the peculiarities of nuclear compartments and chromatin organization during mammalian preimplantation development in the context of the transition from totipotency to pluripotency.
Fan1 deficiency results in DNA interstrand cross-link repair defects, enhanced tissue karyomegaly, and organ dysfunction
Authors: Thongthip Supawat , Bellani Marina , Gregg Siobhan Q. , Sridhar Sunandini , Conti Brooke A. , Chen Yanglu , Seidman Michael M. , Smogorzewska Agata
Published: March 2016

Deficiency of FANCD2/FANCI-associated nuclease 1 (FAN1) in humans leads to karyomegalic interstitial nephritis (KIN), a rare hereditary kidney disease characterized by chronic renal fibrosis, tubular degeneration, and characteristic polyploid nuclei in multiple tissues. The mechanism of how FAN1 protects cells is largely unknown but is thought to involve FAN1's function in DNA interstrand cross-link (ICL) repair. Here, we describe a Fan1-deficient mouse and show that FAN1 is required for cellular and organismal resistance to ICLs. We show that the ubiquitin-binding zinc finger (UBZ) domain of FAN1, which is needed for interaction with FANCD2, is not required for the initial rapid recruitment of FAN1 to ICLs or for its role in DNA ICL resistance. Epistasis analyses reveal that FAN1 has cross-link repair activities that are independent of the Fanconi anemia proteins and that this activity is redundant with the 5′–3′ exonuclease SNM1A. Karyomegaly becomes prominent in kidneys and livers of Fan1-deficient mice with age, and mice develop liver dysfunction. Treatment of Fan1-deficient mice with ICL-inducing agents results in pronounced thymic and bone marrow hypocellularity and the disappearance of c-kit+ cells. Our results provide insight into the mechanism of FAN1 in ICL repair and demonstrate that the Fan1 mouse model effectively recapitulates the pathological features of human FAN1 deficiency.
Crystal structure of Na4Co7−xAl0.67x(As1−yPyO4)6(x = 1.60;y= 0.116)
Authors: Issaoui Chokri , Chebbi Hammouda , Guesmi Abderrahmen
Published: March 2016

The title compound, tetrasodium hepta(cobalt/aluminium) hexa(arsenate/phosphate), Na4Co5.40Al1.07(As0.883P0.116O4)6, was prepared by a solid-state reaction. It is a new member of the family of isostructural compounds with the general formulaA4M7(XO4)6(A: Na, K;M: Ni, Co;X: P, As) that is most similar to Na4Co5.63Al0.91(AsO4)6. The Co2+ions in the title compound are substituted by Al3+in a fully occupied octahedral site (site symmetry 2/m) and a partially occupied tetrahedral site (site symmetry 2). A third octahedral site is fully occupied by Co2+ions only. With regard to the P and As atoms, one site (site symmetrym) is simultaneously occupied by As and P, whereas in the second site there is only arsenic. The alkali cations are, as in the isostructural compounds, distributed over half-occupied crystallographic sites, with a positional disorder of one of them. The proposed structural model is based both on a careful investigation of the crystal data, as well as validation by means of bond-valence-sum (BVS) and charge-distribution (CHARDI) calculations. The correlation between the X-ray refinement and the validation results is discussed.
Crystal structure of diaquabis(N,N-diethylnicotinamide-κN1)bis(2,4,6-trimethylbenzoato-κO1)cobalt(II)
Authors: Aşkın Gülçin Şefiye , Necefoğlu Hacali , Özkaya Safiye , Çatak Çelik Raziye , Hökelek Tuncer
Published: March 2016

The centrosymmetric molecule in the monomeric title cobalt complex, [Co(C10H11O2)2(C10H14N2O)2(H2O)2], contains two water molecules, two 2,4,6-trimethylbenzoate (TMB) ligands and two diethylnicotinamide (DENA) ligands. All ligands coordinate to the CoIIatom in a monodentate fashion. The four O atoms around the CoIIatom form a slightly distorted square-planar arrangement, with the distorted octahedral coordination sphere completed by two pyridine N atoms of the DENA ligands. The dihedral angle between the planar carboxylate group and the adjacent benzene ring is 84.2 (4)°, while the benzene and pyridine rings are oriented at a dihedral angle of 38.87 (10)°. The water molecules exhibit both intramolecular (to the non-coordinating carboxylate O atom) and intermolecular (to the amide carbonyl O atom) O—H...O hydrogen bonds. The latter lead to the formation of layers parallel to (100), enclosingR44(32) ring motifs. These layers are further linkedviaweak C—H...O hydrogen bonds, resulting in a three-dimensional network. One of the two ethyl groups of the DENA ligand is disordered over two sets of sites with an occupancy ratio of 0.490 (13):0.510 (13).
Crystal structure oftrans-bis(diethanolamine-κ3O,N,O′)manganese(II) bis(3-aminobenzoate)
Authors: Ibragimov Aziz B. , Zakirov Bakhtiyar S. , Ashurov Jamshid M.
Published: March 2016

Reaction ofm-aminobenzoic acid (MABA), diethanolamine (DEA) and MnCl2·4H2O led to the formation of the title salt, [Mn(C4H11NO2)2](C7H6NO2)2. In the complex cation, the Mn2+ion is located on an inversion centre and is coordinated by two symmetry-related tridentate DEA molecules, leading to the formation of a slightly distorted MnN2O4octahedron. The MABA−counter-anions are connected to the complex ion by a pair of rather strong O—H...O hydrogen bonds, yielding a 1:2 supramolecular aggregate. Much weaker N—H...O hydrogen bonds connect neighbouring aggregates into a three-dimensional network structure.
Crystal structure of spinel-type Li0.64Fe2.15Ge0.21O4
Authors: Redhammer Günther J. , Tippelt Gerold
Published: March 2016

Spinel-type Li0.64Fe2.15Ge0.21O4, lithium diiron(III) germanium tetraoxide, has been formed as a by-product during flux growth of an Li–Fe–Ge pyroxene-type material. In the title compound, lithium is ordered on the octahedralBsites, while Ge4+orders onto the tetrahedralAsites, and iron distributes over both the octahedral and tetrahedral sites, and is in the trivalent state as determined from Mössbauer spectroscopy. The oxygen parameteruis 0.2543; thus, the spinel is close to having an ideal cubic closed packing of the O atoms. The title spinel is compared with other Li- and Ge-containing spinels.
“Learning to listen”: boys’ gender narratives – implications for theory and practice
Authors: Farrell Francis
Published: March 2016

Purpose

– The purpose of this paper is to critically investigate year 6 and year 9 boys’ constructions of masculinity in the light of theories of inclusive masculinity and to consider the implications of the findings for critical masculinities scholarship in educational research.

Design/methodology/approach

– Qualitative data was collected through fieldwork in school settings consisting of observations and semi-structured interviews. Data analysis draws upon pro-feminist and post-structuralist theories of the gendered subject.

Findings

– The data shows some evidence of inclusive forms of masculinity expressed by the boys’ rejection of a “boy code” (Pollack, 1999) and their narratives of caring and emotional experience. However, discourses of dominant masculinity persist and continue to shape the boys’ subjectivities. The most striking finding is the capacity of the educational gender work programme reported on in this study to provide boys with the resources to problematise the social construction of masculinity.

Research limitations/implications

– The data suggests analysis in binary terms of inclusive or dominant masculinity fails to recognise the fuzzy educational middle ground occupied by the “overlooked ordinary boys” (Brown, 1987; Roberts, 2012) of this study.

Practical implications

– Educational gender work programmes which provide boys with the resources to question dominant masculine practices enable boys to exceed the “symbolic order” and trouble dominant gender discourse.

Originality/value

– In order to develop nuanced theory and practice researchers need to listen to boys’ accounts of their experiences. Analysis of boys gender work in terms of binary adult constructs of masculinity run the risk of perpetuating the essentialism they purport to avoid rather than producing studies which provide an empirically robust foundation for developing an effective practical educational agenda. In a neo-liberal policy context the role of gender equity programmes with the capacity to produce more reflexive masculine subjects requires reassertion within the curriculum.
Systematic exploration of scenario spaces
Authors: Carlsen Henrik , Eriksson E. Anders , Dreborg Karl Henrik , Johansson Bengt , Bodin Örjan
Published: March 2016

Purpose

– Scenarios have become a vital methodological approach in business as well as in public policy. When scenarios are used to guide analysis and decision-making, the aim is typically robustness and in this context we argue that two main problems at scenario set level is conservatism, i.e. all scenarios are close to a perceived business-as-usual trajectory and lack of balance in the sense of arbitrarily mixing some conservative and some extreme scenarios. The purpose of this paper is to address these shortcomings by proposing a methodology for generating sets of scenarios which are in a mathematical sense maximally diverse.

Design/methodology/approach

– In this paper, we develop a systematic methodology, Scenario Diversity Analysis (SDA), which addresses the problems of broad span vs conservatism and imbalance. From a given set of variables with associated states, SDA generates scenario sets where the scenarios are in a quantifiable sense maximally different and therefore best span the whole set of feasible scenarios.

Findings

– The usefulness of the methodology is exemplified by applying it to sets of storylines of the emissions scenarios of the Intergovernmental Panel on Climate Change. This ex-post analysis shows that the storylines were not maximally diverse and given the challenges ahead with regard to emissions reduction and adaptation planning, we argue that it is important to strive for diversity when developing scenario sets for climate change research.

Originality/value

– The proposed methodology adds significant novel features to the field of systematic scenario generation, especially with regard to scenario diversity. The methodology also enables the combination of systematics with the distinct future logics of good intuitive logics scenarios.
Foresight and the third mission of universities: the case for innovation system foresight
Authors: Piirainen Kalle Artturi , Andersen Allan Dahl , Andersen Per Dannemand
Published: March 2016

Purpose

– This paper aims to argue that innovation system foresight (ISF) can significantly contribute to the third mission of universities by creating an active dialogue between universities, industry and society.

Design/methodology/approach

– This paper’s approach is conceptual. The authors analyse the third mission and relevant literature on innovation systems and foresight to explain how and why foresight contributes to the third mission.

Findings

– The authors propose that foresight contributes to the third mission of universities, particularly to the research and development and innovation dimensions through the development of joint understanding of the agendas and future needs of stakeholders. In addition, foresight enables education to be designed to address identified needs.

Research limitations/implications

– The findings are both conceptual and exploratory in nature. Thus, the argument needs further examination through a broader study on foresight in the university–industry context and/or longitudinal research on the outcomes and impact of foresight in this context.

Practical implications

– The findings highlight the importance of understanding the systemic nature of innovation and its role in economic development. Universities must understand their role within the larger innovation system to fulfil the potential of economic development and by extension, their third mission.

Originality/value

– The paper outlines a novel approach of using ISF to promote university–industry partnerships and the growth of innovation systems. The paper also contributes to the discussion of the third mission by outlining that mission in practical terms.