bluuebunny/crossref_metadata_2025 huggingface dataset:
LYM2-dependent chitin perception limits molecular flux via plasmodesmata
Authors: Faulkner Christine , Petutschnig Elena , Benitez-Alfonso Yoselin , Beck Martina , Robatzek Silke , Lipka Volker , Maule Andrew J.
Published: May 2013

Chitin acts as a pathogen-associated molecular pattern from fungal pathogens whose perception triggers a range of defense responses. We show that LYSIN MOTIF DOMAIN-CONTAINING GLYCOSYLPHOSPHATIDYLINOSITOL-ANCHORED PROTEIN 2 (LYM2), the
Arabidopsis
homolog of a rice chitin receptor-like protein, mediates a reduction in molecular flux via plasmodesmata in the presence of chitin. For this response,
lym2
-1
mutants are insensitive to the presence of chitin, but not to the flagellin derivative flg22. Surprisingly, the chitin-recognition receptor CHITIN ELCITOR RECEPTOR KINASE 1 (CERK1) is not required for chitin-induced changes to plasmodesmata flux, suggesting that there are at least two chitin-activated response pathways in
Arabidopsis
and that LYM2 is not required for CERK1-mediated chitin-triggered defense responses, indicating that these pathways are independent. In accordance with a role in the regulation of intercellular flux, LYM2 is resident at the plasma membrane and is enriched at plasmodesmata. Chitin-triggered regulation of molecular flux between cells is required for defense responses against the fungal pathogen
Botrytis cinerea,
and thus we conclude that the regulation of symplastic continuity and molecular flux between cells is a vital component of chitin-triggered immunity in
Arabidopsis
.
Addressing uncertainty in adaptation planning for agriculture
Authors: Vermeulen Sonja J. , Challinor Andrew J. , Thornton Philip K. , Campbell Bruce M. , Eriyagama Nishadi , Vervoort Joost M. , Kinyangi James , Jarvis Andy , Läderach Peter , Ramirez-Villegas Julian , Nicklin Kathryn J. , Hawkins Ed , Smith Daniel R.
Published: May 2013

We present a framework for prioritizing adaptation approaches at a range of timeframes. The framework is illustrated by four case studies from developing countries, each with associated characterization of uncertainty. Two cases on near-term adaptation planning in Sri Lanka and on stakeholder scenario exercises in East Africa show how the relative utility of capacity vs. impact approaches to adaptation planning differ with level of uncertainty and associated lead time. An additional two cases demonstrate that it is possible to identify uncertainties that are relevant to decision making in specific timeframes and circumstances. The case on coffee in Latin America identifies altitudinal thresholds at which incremental vs. transformative adaptation pathways are robust options. The final case uses three crop–climate simulation studies to demonstrate how uncertainty can be characterized at different time horizons to discriminate where robust adaptation options are possible. We find that impact approaches, which use predictive models, are increasingly useful over longer lead times and at higher levels of greenhouse gas emissions. We also find that extreme events are important in determining predictability across a broad range of timescales. The results demonstrate the potential for robust knowledge and actions in the face of uncertainty.
Role of aspartate 132 at the orifice of a proton pathway in cytochromecoxidase
Authors: Johansson Ann-Louise , Högbom Martin , Carlsson Jens , Gennis Robert B. , Brzezinski Peter
Published: May 2013

Proton transfer across biological membranes underpins central processes in biological systems, such as energy conservation and transport of ions and molecules. In the membrane proteins involved in these processes, proton transfer takes place through specific pathways connecting the two sides of the membrane via control elements within the protein. It is commonly believed that acidic residues are required near the orifice of such proton pathways to facilitate proton uptake. In cytochromecoxidase, one such pathway starts near a conserved Asp-132 residue. Results from earlier studies have shown that replacement of Asp-132 by, e.g., Asn, slows proton uptake by a factor of ∼5,000. Here, we show that proton uptake at full speed (∼104s−1) can be restored in the Asp-132–Asn oxidase upon introduction of a second structural modification further inside the pathway (Asn-139–Thr) without compensating for the loss of the negative charge. This proton-uptake rate was insensitive to Zn2+addition, which in the wild-type cytochromecoxidase slows the reaction, indicating that Asp-132 is required for Zn2+binding. Furthermore, in the absence of Asp-132 and with Thr at position 139, at high pH (>9), proton uptake was significantly accelerated. Thus, the data indicate that Asp-132 is not strictly required for maintaining rapid proton uptake. Furthermore, despite the rapid proton uptake in the Asn-139–Thr/Asp-132–Asn mutant cytochromecoxidase, proton pumping was impaired, which indicates that the segment around these residues is functionally linked to pumping.
Influence of organic films on the evaporation and condensation of water in aerosol
Authors: Davies James F. , Miles Rachael E. H. , Haddrell Allen E. , Reid Jonathan P.
Published: May 2013

Uncertainties in quantifying the kinetics of evaporation and condensation of water from atmospheric aerosol are a significant contributor to the uncertainty in predicting cloud droplet number and the indirect effect of aerosols on climate. The influence of aerosol particle surface composition, particularly the impact of surface active organic films, on the condensation and evaporation coefficients remains ambiguous. Here, we report measurements of the influence of organic films on the evaporation and condensation of water from aerosol particles. Significant reductions in the evaporation coefficient are shown to result when condensed films are formed by monolayers of long-chain alcohols [C

n

H

(2
n
+1)

OH], with the value decreasing from 2.4 × 10
−3
to 1.7 × 10
−5
as
n
increases from 12 to 17. Temperature-dependent measurements confirm that a condensed film of long-range order must be formed to suppress the evaporation coefficient below 0.05. The condensation of water on a droplet coated in a condensed film is shown to be fast, with strong coherence of the long-chain alcohol molecules leading to islanding as the water droplet grows, opening up broad areas of uncoated surface on which water can condense rapidly. We conclude that multicomponent composition of organic films on the surface of atmospheric aerosol particles is likely to preclude the formation of condensed films and that the kinetics of water condensation during the activation of aerosol to form cloud droplets is likely to remain rapid.
Intensifiers as stance markers
Authors: Lim Ni-Eng , Hong Huaqing
Published: May 2013

While the study of Mandarin Chinese intensifiers has been prolific, the methodologies used have been limited to comparative and grammaticalization studies, revealing little about the discourse-pragmatic usages of individual intensifiers. Utilizing a balanced corpus composed of 15 different prototypical genres, the associative strength of 12 commonly used intensifiers in each genre was statistically determined based on their frequency distribution. The results reveal a clear preference pattern of intensifiers across a range of “written” and “spoken”-based genres. Upon the premise that the genre preferences of intensifiers stem from matching dimensions of communicative intent/discourse context between genre and intensifier, genre-analysis was conducted to unveil the core “stances” each intensifier might possibly project. In conclusion, it is argued that genre-analysis based on empirical corpus data provides a valid alternative means to uncover seemingly “covert” aspects of language use.
A syntactic classification of the synchronic use of gěi in Beijing Mandarin
Authors: Sanders Robert Martin , Uehara Satoshi
Published: May 2013

This study fills a gap in the literature on the polyfunctional nature of the Chinese ditransitive verb gěi ‘to give’, which has undergone semantic and functional extensions. Our approach differs from previous studies by focusing on a narrowly defined location in time and space, i.e. contemporary Beijing oral language, and by basing our linguistic analysis on data obtained through the systematic sampling of a corpus of spontaneous casual discourse. Based on the existing literature we produce a taxonomy of five extended functions and structures 1) causative verb, 2) passive marker, 3) benefactive/malefactive/dative marker, 4) disposal marker and 5) ditransitive suffix. Of these, the first four share the common linear structure [NP1 gěi NP2 V]. Applying this taxonomy to our data we identified the relative productivity of each of these functions and created a synchronic constructional network of gěi, revealing its complex network of connections.
Constructing the ‘tellables’
Authors: Xiang Xuehua
Published: May 2013

Based on twelve celebrity interviews in Mandarin Chinese and American English, broadcast in a range of talk-radio/television programs in the U.S. and China, the current study is a comparative analysis of interviewers’ questioning practices and the cultural underpinnings of those questions. The analysis focuses on the interviewers’ question-word interrogatives in the discourse context of multiple Turn Construction Units (multi-TCUs). The study demonstrates similar interviewing strategies between two datasets including couching queries in partial knowledge of the guest’s “celebrity-induced experiences,” and using the presupposition function of question-word interrogatives to “control” responses. Significant differences exist: The English interviews primarily reference the guest’s behaviors/activities as context for query, and frame the interviewee’s first-person accounts as particularizations of commonly shared ‘tellables.’ The Chinese interviews tend to use external reference-points, particularly the behavior and sentiments of others, thus constructing a comparative/contrastive angle from which the guest relays first-person accounts.
UniTIE
Authors: Haapanen Paula , McAnsh Suzy , Braidwood Eva , Hollingsworth Robert
Published: May 2013

In its aspirations to enhance mobility within higher education and focus on the comparability and quality of university degrees, the Bologna Process has emphasised the need for transparency in describing students’ knowledge and abilities. In response, the project, “UniTIE: Curriculum planning in the Language Centres”, was initiated to improve the transparency with which English courses are described and assessed at university language centres in Finland. This article provides a brief overview of the project, discusses the work carried out within a community of practice to develop descriptors for university English courses, and reports on the outcomes of the project.
Gesture and imagination
Authors: Nemirovsky Ricardo , Kelton Molly L. , Rhodehamel Bohdan
Published: May 2013

This study examines the role of gesture in collective imagining, the embodied process of bringing objects and events into quasi-presence during social interaction. Drawing on the phenomenological tradition, we argue in favor of an alternative to the gestures-as-simulated-action account proposed by Hostetter and Alibali (2008). Specifically, we suggest viewing gestures as key constituents of phantasms, quasi-present objects that are produced through multi-modal utterances. This perspective highlights the ways in which gestures mark profound transformations of participants’ experiential histories, transformations that open up, for the speakers, new insights into the matters they strive to imagine. The study of these insights led us to emphasize not the simulative, but the creative roles of gestures. Our account of gesture in collective imagining is illustrated by a microanalysis of an episode from an interview with a mother-child dyad following their interaction with a mathematics exhibit in a science center.
The effects of multiculturalism and mechanistic disdain for robots in human-to-robot communication scenarios
Authors: Heo Hyun-Hee , Kim Min-Sun
Published: May 2013

This study investigates the effects of cultural orientation and the degree of disdain for robots on the preferred conversational styles in human-to-robot interactions. 203 participants self-reported on questionnaires through a computer-based online survey. The two requesting situations were intended to simulate the participants’ interactions with humanoid social robots through an Internet video-phone medium of communication. Structural equation modeling was performed to examine the mediating role of mechanistic disdain between multicultural orientation and conversational constraints. The findings reveal that between the two dimensions of multicultural orientation, only open-mindedness inversely influences mechanistic disdain. Mechanistic disdain, in turn, negatively affects three face-related conversational constraints, thereby leading to a lesser concern for robots’ feelings, for minimizing impositions on robots, and for avoiding robots’ negative evaluations. The implications of our findings on humans’ relations with virtual robot entities and on the future development of humanoid robots are discussed.
Evolutionary pressures promoting complexity in navigation and communication
Authors: Kazakov Dimitar , Bartlett Mark
Published: May 2013

This article presents results from simulations studying the hypothesis that mechanisms for landmark-based navigation could have served as preadaptations for compositional language. It is argued that sharing directions would significantly have helped bridge the gap between general and language-specific cognitive faculties. A number of different levels of navigational and communicative abilities are considered, resulting in a range of possible evolutionary paths. The selective pressures for, resp. against, increased complexity in either faculty are then evaluated for a range of environments. The study aims specifically to identify whether there is a viable evolutionary path leading to compositional language, and if so, under what circumstances. The results show that environmental conditions can render a step towards more complex communication either desirable or harmul, and suggest that very specific initial conditions and changes in the environment, resp. the ecological niche occupied, would have been needed to select for compositional language. Subject to these conditions, a (proto)language using order, but no hierarchical structure could evolve. This represents a middle ground, which brings closer hypotheses about syntax that have so far appeared difficult to reconcile.
Evidencing international threat
Authors: Chang Gordon C. , Lueck Kerstin , Mehan Hugh B.
Published: May 2013

By studying the discourse utilized by the Iraq Survey Group (ISG) and its chief officers during 2003–2004, we show the methods by which U.S. government-appointed experts helped to affirm the existence of an Iraqi threat even in the absence of physical evidence for weapons of mass destruction (WMD) stockpiles or active weapons programs found in Iraq during U.S. ground search. Their data collection and interpretation work illuminates the principle that the claims and calculations of international threat can be primarily constructed by language and discourse processes rather than by direct/concrete material referents. It also points to the need for institutions and a lay audience to apply a higher evidentiary threshold to ascertain the existence of an international threat.
The representation of handshape change in Taiwan Sign Language
Authors: Lee Hsin-Hsien
Published: May 2013

Handshape change is the change of handshape from one configuration to another. It is a unique and pervasive pattern attested in sign languages. The issue here is how to represent this change of handshape phonologically. Previous studies on handshape change were mostly done on American Sign Language (ASL) and two different ways of representing handshape change have been proposed. Some models (e.g. Liddell 1990; Uyechi 1996) propose that all surface handshapes are represented underlyingly, whereas others (e.g. Brentari 1998; Corina 1993; Sandler 1989) suggest representing only one handshape because the other handshape is predictable. Handshape change attested in monomorphemic signs in Taiwan Sign Language (TSL) will be described and analyzed in this paper. I argue that the TSL data support the latter view. In addition, a restrictive model is preferred if it can describe the data adequately and at the same time does not over-generate.
ASL ‘topics’ revisited
Authors: Todd Peyton
Published: May 2013

Sign linguists routinely parse ASL sentences using the category ‘topic’, by which is meant a constituent on the left edge of the main clause, structurally separate from it, and marked by a discrete formal symbolic event, more fully brow raise + backward head tilt + pause, although brow raise is sometimes considered sufficient. This paper provides evidence confirming suspicions that these left-detached constituents need not be marked by brow raise, and suggests that brow raise is better regarded as signaling a type of momentary focus — thus explaining why sign languages tend to employ it as they do — and that it belongs to a larger set of ‘topic-marking’ devices whose iconicity remains active in day-to-day signing.
Quantifying the consensus on anthropogenic global warming in the
scientific literature
Authors: Cook John , Nuccitelli Dana , Green Sarah A , Richardson Mark , Winkler Bärbel , Painting Rob , Way Robert , Jacobs Peter , Skuce Andrew
Published: May 2013

We analyze the evolution of the scientific consensus on anthropogenic global warming
(AGW) in the peer-reviewed scientific literature, examining 11 944 climate abstracts
from 1991–2011 matching the topics ‘global climate change’ or ‘global warming’. We
find that 66.4% of abstracts expressed no position on AGW, 32.6% endorsed AGW, 0.7%
rejected AGW and 0.3% were uncertain about the cause of global warming. Among
abstracts expressing a position on AGW, 97.1% endorsed the consensus position that
humans are causing global warming. In a second phase of this study, we invited
authors to rate their own papers. Compared to abstract ratings, a smaller percentage
of self-rated papers expressed no position on AGW (35.5%). Among self-rated papers
expressing a position on AGW, 97.2% endorsed the consensus. For both abstract ratings
and authors’ self-ratings, the percentage of endorsements among papers expressing a
position on AGW marginally increased over time. Our analysis indicates that the
number of papers rejecting the consensus on AGW is a vanishingly small proportion of
the published research.
How the Future Shaped the Past: The Case of the Cashless Society
Authors: Bátiz-Lazo Bernardo , Haigh Thomas , Stearns David L.
Published: May 2013

The future matters to business history, because the adoption of new technology and new organizational forms has often been driven by acceptance of a collective sense of what the future will be. Investments are made and strategies set on an industry-wide basis, influenced by the predictions of business consultants, industry groups, and futurists. To explore the part played by the future in shaping the past, we focus on the establishment and early acceptance of the idea of a rapid and inevitable transition to a “cashless society” in the US retail financial services industry during the 1960s and 1970s. Our aim is thus to advance a methodological point rather than to arrive at a definitive conclusion about the future of money.
Identification and Molecular Mapping of a Wheat Gene for Resistance to an Unadapted Isolate of Colletotrichum cereale
Authors: Inoue Yoshihiro , Mori Ryota , Takahashi Yujiro , Kiguchi So , Enomoto Takashi , Chuma Izumi , Tosa Yukio
Published: May 2013

To elucidate genetic mechanisms of host species specificity between graminicolous anthracnose fungi and gramineous plants, infection assays were performed with a Sorghum isolate (Colletotrichum sublineolum), a Digitaria isolate (C. hanaui), a Polypogon isolate (C. cereale), and an Avena isolate (C. cereale). They were specifically virulent on the plants from which they were isolated. When 72 wheat lines were inoculated with an unadapted isolate from Asia Minor bluegrass (Cgp29), however, some exceptional cultivars were recognized. Although most cultivars were resistant to Cgp29, ‘Hope’ was susceptible. In F2 populations derived from crosses between three resistant cultivars—‘Norin 4’ (N4), ‘Chinese Spring’ (CS), and ‘Shin-chunaga’ (Sch)—and the susceptible Hope, resistant and susceptible seedlings segregated in a 3:1 ratio, suggesting that a major gene is involved in the resistance of each cultivar to Cgp29. In F2 populations derived from crosses between the three resistant cultivars, all seedlings were resistant, suggesting that these three cultivars carry the same gene. This resistance gene was designated as “resistance to Colletotrichum cereale 1” (Rcc1). Analysis with the CS–Hope chromosome substitution lines and molecular mapping revealed that Rcc1 was located on the long arm of chromosome 5A. Cytologically, Rcc1 was mainly associated with hypersensitive reaction. These results suggest that major genes similar to those controlling cultivar specificity are involved in the resistance of wheat against the unadapted isolate of C. cereale.
Effect of Perioperative Intravenous Lidocaine Administration on Pain, Opioid Consumption, and Quality of Life after Complex Spine Surgery
Authors: Farag Ehab , Ghobrial Michael , Sessler Daniel I. , Dalton Jarrod E. , Liu Jinbo , Lee Jae H. , Zaky Sherif , Benzel Edward , Bingaman William , Kurz Andrea
Published: May 2013

Background:

The authors tested the primary hypothesis that perioperative IV lidocaine administration during spine surgery (and in the postanesthesia care unit for no more than 8 h) decreases pain and/or opioid requirements in the initial 48 postoperative hours. Secondary outcomes included major complications, postoperative nausea and vomiting, duration of hospitalization, and quality of life.

Methods:

One hundred sixteen adults having complex spine surgery were randomly assigned to perioperative IV lidocaine (2 mg·kg−1·h−1) or placebo during surgery and in the postanesthesia care unit. Pain was evaluated with a verbal response scale. Quality of life at 1 and 3 months was assessed using the Acute Short-form (SF) 12 health survey. The authors initially evaluated multivariable bidirectional noninferiority on both outcomes; superiority on either outcome was then evaluated only if noninferiority was established.

Results:

Lidocaine was significantly superior to placebo on mean verbal response scale pain scores (P < 0.001; adjusted mean [95% CI] of 4.4 [4.2-4.7] and 5.3 [5.0-5.5] points, respectively) and significantly noninferior on mean morphine equivalent dosage (P = 0.011; 55 [36-84] and 74 [49-111] mg, respectively). Postoperative nausea and vomiting and the duration of hospitalization did not differ significantly. Patients given lidocaine had slightly fewer 30-day complications than patients given placebo (odds ratio [95% CI] of 0.91 [0.84–1.00]; P = 0.049). Patients given lidocaine had significantly greater SF-12 physical composite scores than placebo at 1 (38 [31–47] vs. 33 [27–42]; P = 0.002) and 3 (39 [31–49] vs. 34 [28–44]; P = 0.04) months, postoperatively.

Conclusion:

IV lidocaine significantly improves postoperative pain after complex spine surgery.
Automated Alerting and Recommendations for the Management of Patients with Preexisting Hypoxia and Potential Acute Lung Injury
Authors: Blum James M. , Stentz Michael J. , Maile Michael D. , Jewell Elizabeth , Raghavendran Krishnan , Engoren Milo , Ehrenfeld Jesse M.
Published: May 2013

Background:

Acute lung injury (ALI) is associated with high mortality. Low tidal volume (Vt) ventilation has been shown to reduce mortality in ALI patients in the intensive care unit. Anesthesiologists do not routinely provide lung-protective ventilation strategies to patients with ALI in the operating room. The authors hypothesized that an alert, recommending lung-protective ventilation regarding patients with potential ALI, would result in lower Vt administration.

Methods:

The authors conducted a randomized controlled trial on anesthesia providers caring for patients with potential ALI. Patients with an average or last collected ratio of partial pressure of arterial oxygen to inspired fraction of oxygen less than 300 were randomized to providers being sent an alert with a recommended Vt of 6 cc/kg predicted body weight or conventional care. Primary outcomes were Vt/kg predicted body weight administered to patients. Secondary outcomes included ventilator parameters, length of postoperative ventilation, and death.

Results:

The primary outcome was a clinically significant reduction in mean Vt from 508–458 cc (P = 0.033), with a reduction in Vt when measured in cc/kg predicted body weight from 8 to 7.2 cc/kg predicted body weight (P = 0.040). There were no statistically significant changes in other outcomes or adverse events associated with either arm.

Conclusions:

Automated alerts generated for patients at risk of having ALI resulted in a statistically significant reduction in Vt administered when compared with a control group. Further research is required to determine whether a reduction in Vt results in decreased mortality and/or postoperative duration of mechanical ventilation.
miR-21 Contributes to Xenon-conferred Amelioration of Renal Ischemia–Reperfusion Injury in Mice
Authors: Jia Ping , Teng Jie , Zou Jianzhou , Fang Yi , Zhang Xiaoyan , Bosnjak Zeljko J. , Liang Mingyu , Ding Xiaoqiang
Published: May 2013

Background:

MicroRNAs participate in the regulation of numerous physiological and disease processes. The in vivo role of microRNAs in anesthetics-conferred organoprotection is unknown.

Methods:

Mice were exposed for 2 h to either 70% xenon, or 70% nitrogen, 24 h before the induction of renal ischemia-reperfusion injury. The role of microRNA, miR-21, in renal protection conferred by the delayed xenon preconditioning was examined using in vivo knockdown of miR-21 and analysis of miR-21 target pathways.

Results:

Xenon preconditioning provided morphologic and functional protection against renal ischemia-reperfusion injury (n = 6), characterized by attenuation of renal tubular damage, apoptosis, and oxidative stress. Xenon preconditioning significantly increased the expression of miR-21 in the mouse kidney. A locked nucleic acid-modified anti–miR-21, given before xenon preconditioning, knocked down miR-21 effectively, and exacerbated subsequent renal ischemia-reperfusion injury. Mice treated with anti–miR-21 and ischemia-reperfusion injury showed significantly higher serum creatinine than antiscrambled oligonucleotides-treated mice, 24 h after ischemia-reperfusion (1.37 ± 0.28 vs. 0.81 ± 0.14 mg/dl; n = 5; P < 0.05). Knockdown of miR-21 induced significant up-regulation of programmed cell death protein 4 and phosphatase and tensin homolog deleted on chromosome 10, two proapoptotic target effectors of miR-21, and resulted in significant down-regulation of phosphorylated protein kinase B and increased tubular cell apoptosis. In addition, xenon preconditioning up-regulated hypoxia-inducible factor-1α and its downstream effector vascular endothelial growth factor in a time-dependent manner. Knockdown of miR-21 resulted in a significant decrease of hypoxia-inducible factor-1α.

Conclusions:

These results indicate that miR-21 contributes to the renoprotective effect of xenon preconditioning.
A basal thunnosaurian from Iraq reveals disparate phylogenetic origins for Cretaceous ichthyosaurs
Authors: Fischer Valentin , Appleby Robert M. , Naish Darren , Liston Jeff , Riding James B. , Brindley Stephen , Godefroit Pascal
Published: May 2013

Cretaceous ichthyosaurs have typically been considered a small, homogeneous assemblage sharing a common Late Jurassic ancestor. Their low diversity and disparity have been interpreted as indicative of a decline leading to their Cenomanian extinction. We describe the first post-Triassic ichthyosaur from the Middle East,
Malawania anachronus
gen. et sp. nov. from the Early Cretaceous of Iraq, and re-evaluate the evolutionary history of parvipelvian ichthyosaurs via phylogenetic and cladogenesis rate analyses.
Malawania
represents a basal grade in thunnosaurian evolution that arose during a major Late Triassic radiation event and was previously thought to have gone extinct during the Early Jurassic. Its pectoral morphology appears surprisingly archaic, retaining a forefin architecture similar to that of its Early Jurassic relatives. After the initial latest Triassic radiation of early thunnosaurians, two subsequent large radiations produced lineages with Cretaceous representatives, but the radiation events themselves are pre-Cretaceous. Cretaceous ichthyosaurs therefore include distantly related lineages, with contrasting evolutionary histories, and appear more diverse and disparate than previously supposed.
Relevance for food sciences of quantitative spatially resolved element profile investigations in wheat (
Triticum aestivum
) grain
Authors: Pongrac Paula , Kreft Ivan , Vogel-Mikuš Katarina , Regvar Marjana , Germ Mateja , Vavpetič Primož , Grlj Nataša , Jeromel Luka , Eichert Diane , Budič Bojan , Pelicon Primož
Published: May 2013

Bulk element concentrations of whole grain and element spatial distributions at the tissue level were investigated in wheat (
Triticum aestivum
) grain grown in Zn-enriched soil. Inductively coupled plasma mass spectrometry and inductively coupled plasma optical emission spectrometry were used for bulk analysis, whereas micro-proton-induced X-ray emission was used to resolve the two-dimensional localization of the elements. Soil Zn application did not significantly affect the grain yield, but did significantly increase the grain Ca, Fe and Zn concentrations, and decrease the grain Na, P and Mo concentrations; bulk Mg, S, K, Mn, Cu, Cd and Pb concentrations remained unchanged. These changes observed in bulk element concentrations are the reflection of tissue-specific variations within the grain, revealing that Zn application to soil can lead to considerable alterations in the element distributions within the grain, which might ultimately influence the quality of the milling fractions. Spatially resolved investigations into the partitioning of the element concentrations identified the tissues with the highest element concentrations, which is of utmost importance for accurate prediction of element losses during the grain milling and polishing processes.
A space–time variational approach to hydrodynamic stability theory
Authors: Yano Masayuki , Patera Anthony T.
Published: May 2013

We present a hydrodynamic stability theory for incompressible viscous fluid flows based on a space–time variational formulation and associated generalized singular value decomposition of the (linearized) Navier–Stokes equations. We first introduce a linear framework applicable to a wide variety of stationary- or time-dependent base flows: we consider arbitrary disturbances in both the initial condition and the dynamics measured in a ‘data’ space–time norm; the theory provides a rigorous, sharp (realizable) and efficiently computed bound for the velocity perturbation measured in a ‘solution’ space–time norm. We next present a generalization of the linear framework in which the disturbances and perturbation are now measured in respective selected space–time
semi-norms
; the semi-norm theory permits rigorous and sharp quantification of, for example, the growth of initial disturbances or functional outputs. We then develop a (Brezzi–Rappaz–Raviart) nonlinear theory which provides, for disturbances which satisfy a certain (rather stringent) amplitude condition, rigorous finite-amplitude bounds for the velocity and output perturbations. Finally, we demonstrate the application of our linear and nonlinear hydrodynamic stability theory to unsteady moderate Reynolds number flow in an eddy-promoter channel.
The effect of population structure on the rate of evolution
Authors: Frean Marcus , Rainey Paul B. , Traulsen Arne
Published: May 2013

Ecological factors exert a range of effects on the dynamics of the evolutionary process. A particularly marked effect comes from population structure, which can affect the probability that new mutations reach fixation. Our interest is in population structures, such as those depicted by ‘star graphs’, that amplify the effects of selection by further increasing the fixation probability of advantageous mutants and decreasing the fixation probability of disadvantageous mutants. The fact that star graphs increase the fixation probability of beneficial mutations has lead to the conclusion that evolution proceeds more rapidly in star-structured populations, compared with mixed (unstructured) populations. Here, we show that the effects of population structure on the rate of evolution are more complex and subtle than previously recognized and draw attention to the importance of fixation time. By comparing population structures that amplify selection with other population structures, both analytically and numerically, we show that evolution can slow down substantially even in populations where selection is amplified.
First report on chitinous holdfast in sponges (Porifera)
Authors: Ehrlich Hermann , Kaluzhnaya Oksana V. , Tsurkan Mikhail V. , Ereskovsky Alexander , Tabachnick Konstantin R. , Ilan Micha , Stelling Allison , Galli Roberta , Petrova Olga V. , Nekipelov Serguei V. , Sivkov Victor N. , Vyalikh Denis , Born René , Behm Thomas , Ehrlich Andre , Chernogor Lubov I. , Belikov Sergei , Janussen Dorte , Bazhenov Vasilii V. , Wörheide Gert
Published: May 2013

A holdfast is a root- or basal plate-like structure of principal importance that anchors aquatic sessile organisms, including sponges, to hard substrates. There is to date little information about the nature and origin of sponges’ holdfasts in both marine and freshwater environments. This work, to our knowledge, demonstrates for the first time that chitin is an important structural component within holdfasts of the endemic freshwater demosponge
Lubomirskia baicalensis
. Using a variety of techniques (near-edge X-ray absorption fine structure, Raman, electrospray ionization mas spectrometry, Morgan–Elson assay and Calcofluor White staining), we show that chitin from the sponge holdfast is much closer to α-chitin than to β-chitin. Most of the three-dimensional fibrous skeleton of this sponge consists of spicule-containing proteinaceous spongin. Intriguingly, the chitinous holdfast is not spongin-based, and is ontogenetically the oldest part of the sponge body. Sequencing revealed the presence of four previously undescribed genes encoding chitin synthases in the
L. baicalensis
sponge. This discovery of chitin within freshwater sponge holdfasts highlights the novel and specific functions of this biopolymer within these ancient sessile invertebrates.
Demographic loss, genetic structure and the conservation implications for Indian tigers
Authors: Mondol Samrat , Bruford Michael W. , Ramakrishnan Uma
Published: May 2013

India is home to approximately 60 per cent of the world's remaining wild tigers, a species that has declined in the last few centuries to occupy less than 7 per cent of its former geographical range. While Indian tiger numbers have somewhat stabilized in recent years, they remain low and populations are highly fragmented. Therefore, the application of evidence-based demographic and genetic management to enhance the remaining populations is a priority. In this context, and using genetic data from historical and modern tigers, we investigated anthropogenic impacts on genetic variation in Indian tigers using mitochondrial and nuclear genetic markers. We found a very high number of historical mitochondrial DNA variants, 93 per cent of which are not detected in modern populations. Population differentiation was higher in modern tigers. Simulations incorporating historical data support population decline, and suggest high population structure in extant populations. Decreased connectivity and habitat loss as a result of ongoing fragmentation in the Indian subcontinent has therefore resulted in a loss of genetic variants and increased genetic differentiation among tiger populations. These results highlight that anthropogenic fragmentation and species-specific demographic processes can interact to alter the partitioning of genetic variation over very short time scales. We conclude that ongoing strategies to maximize the size of some tiger populations, at the expense of losing others, is an inadequate conservation strategy, as it could result in a loss of genetic diversity that may be of adaptive significance for this emblematic species.
Genetic consequences of a century of protection: serial founder events and survival of the little spotted kiwi (Apteryx owenii)
Authors: Ramstad Kristina M. , Colbourne Rogan M. , Robertson Hugh A. , Allendorf Fred W. , Daugherty Charles H.
Published: May 2013

We present the outcome of a century of post-bottleneck isolation of a long-lived species, the little spotted kiwi (Apteryx owenii, LSK) and demonstrate that profound genetic consequences can result from protecting few individuals in isolation. LSK were saved from extinction by translocation of five birds from South Island, New Zealand to Kapiti Island 100 years ago. The Kapiti population now numbers some 1200 birds and provides founders for new populations. We used 15 microsatellite loci to compare genetic variation among Kapiti LSK and the populations of Red Mercury, Tiritiri Matangi and Long Islands that were founded with birds from Kapiti. Two LSK native to D'Urville Island were also placed on Long Island. We found extremely low genetic variation and signatures of acute and recent genetic bottleneck effects in all four populations, indicating that LSK have survived multiple genetic bottlenecks. The Long Island population appears to have arisen from a single mating pair from Kapiti, suggesting there is no genetic contribution from D'Urville birds among extant LSK. TheNe/NCratio of Kapiti Island LSK (0.03) is exceptionally low for terrestrial vertebrates and suggests that genetic diversity might still be eroding in this population, despite its large census size.
Grizzly bear predation links the loss of native trout to the demography of migratory elk in Yellowstone
Authors: Middleton Arthur D. , Morrison Thomas A. , Fortin Jennifer K. , Robbins Charles T. , Proffitt Kelly M. , White P. J. , McWhirter Douglas E. , Koel Todd M. , Brimeyer Douglas G. , Fairbanks W. Sue , Kauffman Matthew J.
Published: May 2013

The loss of aquatic subsidies such as spawning salmonids is known to threaten a number of terrestrial predators, but the effects on alternative prey species are poorly understood. At the heart of the Greater Yellowstone ecosystem, an invasion of lake trout has driven a dramatic decline of native cutthroat trout that migrate up the shallow tributaries of Yellowstone Lake to spawn each spring. We explore whether this decline has amplified the effect of a generalist consumer, the grizzly bear, on populations of migratory elk that summer inside Yellowstone National Park (YNP). Recent studies of bear diets and elk populations indicate that the decline in cutthroat trout has contributed to increased predation by grizzly bears on the calves of migratory elk. Additionally, a demographic model that incorporates the increase in predation suggests that the magnitude of this diet shift has been sufficient to reduce elk calf recruitment (4–16%) and population growth (2–11%). The disruption of this aquatic–terrestrial linkage could permanently alter native species interactions in YNP. Although many recent ecological changes in YNP have been attributed to the recovery of large carnivores—particularly wolves—our work highlights a growing role of human impacts on the foraging behaviour of grizzly bears.
Does seed mass drive the differences in relative growth rate between growth forms?
Authors: Houghton Jennie , Thompson Ken , Rees Mark
Published: May 2013

The idea that herbaceous plants have higher relative growth rates (RGRs) compared with woody plants is fundamental to many of the most influential theories in plant ecology. This difference in growth rate is thought to reflect systematic variation in physiology, allocation and leaf construction. Previous studies documenting this effect have, however, ignored differences in seed mass. As woody species often have larger seeds and RGR is negatively correlated with seed mass, it is entirely possible the lower RGRs observed in woody species is a consequence of having larger seeds rather than different growth strategies. Using a synthesis of the published literature, we explored the relationship between RGR and growth form, accounting for the effects of seed mass and study-specific effects (e.g. duration of study and pot volume), using a mixed-effects model. The model showed that herbaceous species do indeed have higher RGRs than woody species, and that the difference was independent of seed mass, thus at all seed masses, herbaceous species on average grow faster than woody ones.
Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies
Authors: Supple Megan A. , Hines Heather M. , Dasmahapatra Kanchon K. , Lewis James J. , Nielsen Dahlia M. , Lavoie Christine , Ray David A. , Salazar Camilo , McMillan W. Owen , Counterman Brian A.
Published: May 2013

Identifying the genetic changes driving adaptive variation in natural populations is key to understanding the origins of biodiversity. The mosaic of mimetic wing patterns in Heliconius butterflies makes an excellent system for exploring adaptive variation using next-generation sequencing. In this study, we use a combination of techniques to annotate the genomic interval modulating red color pattern variation, identify a narrow region responsible for adaptive divergence and convergence in Heliconius wing color patterns, and explore the evolutionary history of these adaptive alleles. We use whole genome resequencing from four hybrid zones between divergent color pattern races of Heliconius erato and two hybrid zones of the co-mimic Heliconius melpomene to examine genetic variation across 2.2 Mb of a partial reference sequence. In the intergenic region near optix, the gene previously shown to be responsible for the complex red pattern variation in Heliconius, population genetic analyses identify a shared 65-kb region of divergence that includes several sites perfectly associated with phenotype within each species. This region likely contains multiple cis-regulatory elements that control discrete expression domains of optix. The parallel signatures of genetic differentiation in H. erato and H. melpomene support a shared genetic architecture between the two distantly related co-mimics; however, phylogenetic analysis suggests mimetic patterns in each species evolved independently. Using a combination of next-generation sequencing analyses, we have refined our understanding of the genetic architecture of wing pattern variation in Heliconius and gained important insights into the evolution of novel adaptive phenotypes in natural populations.
Proteome-wide discovery of mislocated proteins in cancer
Authors: Lee KiYoung , Byun Kyunghee , Hong Wonpyo , Chuang Han-Yu , Pack Chan-Gi , Bayarsaikhan Enkhjargal , Paek Sun Ha , Kim Hyosil , Shin Hye Young , Ideker Trey , Lee Bonghee
Published: May 2013

Several studies have sought systematically to identify protein subcellular locations, but an even larger task is to map which of these proteins conditionally relocates in disease (the mislocalizome). Here, we report an integrative computational framework for mapping conditional location and mislocation of proteins on a proteome-wide scale, called a conditional location predictor (CoLP). Using CoLP, we mapped the locations of over 10,000 proteins in normal human brain and in glioma. The prediction showed 0.9 accuracy using 100 location tests of 20 randomly selected proteins. Of the 10,000 proteins, over 150 have a strong likelihood of mislocation under glioma, which is striking considering that few mislocation events have been identified in this disease previously. Using immunofluorescence and Western blotting in both primary cells and tissues, we successfully experimentally confirmed 15 mislocations. The most common type of mislocation occurs between the endoplasmic reticulum and the nucleus; for example, for RNF138, TLX3, and NFRKB. In particular, we found that the gene for the mislocating protein GFRA4 had a nonsynonymous point mutation in exon 2. Moreover, redirection of GFRA4 to its normal location, the plasma membrane, led to marked reductions in phospho-STAT3 and proliferation of glioma cells. This framework has the potential to track changes in protein location in many human diseases.
Inactivation of Plasma Membrane–Localized CDPK-RELATED KINASE5 Decelerates PIN2 Exocytosis and Root Gravitropic Response inArabidopsis
Authors: Rigó Gábor , Ayaydin Ferhan , Tietz Olaf , Zsigmond Laura , Kovács Hajnalka , Páy Anikó , Salchert Klaus , Darula Zsuzsanna , Medzihradszky Katalin F. , Szabados László , Palme Klaus , Koncz Csaba , Cséplő Ágnes
Published: May 2013

CRK5 is a member of the Arabidopsis thaliana Ca2+/calmodulin-dependent kinase-related kinase family. Here, we show that inactivation of CRK5 inhibits primary root elongation and delays gravitropic bending of shoots and roots. Reduced activity of the auxin-induced DR5–green fluorescent protein reporter suggests that auxin is depleted from crk5 root tips. However, no tip collapse is observed and the transcription of genes for auxin biosynthesis, AUXIN TRANSPORTER/AUXIN TRANSPORTER-LIKE PROTEIN (AUX/LAX) auxin influx, and PIN-FORMED (PIN) efflux carriers is unaffected by the crk5 mutation. Whereas AUX1, PIN1, PIN3, PIN4, and PIN7 display normal localization, PIN2 is depleted from apical membranes of epidermal cells and shows basal to apical relocalization in the cortex of the crk5 root transition zone. This, together with an increase in the number of crk5 lateral root primordia, suggests facilitated auxin efflux through the cortex toward the elongation zone. CRK5 is a plasma membrane–associated kinase that forms U-shaped patterns facing outer lateral walls of epidermis and cortex cells. Brefeldin inhibition of exocytosis stimulates CRK5 internalization into brefeldin bodies. CRK5 phosphorylates the hydrophilic loop of PIN2 in vitro, and PIN2 shows accelerated accumulation in brefeldin bodies in the crk5 mutant. Delayed gravitropic response of the crk5 mutant thus likely reflects defective phosphorylation of PIN2 and deceleration of its brefeldin-sensitive membrane recycling.