bluuebunny/crossref_metadata_2025 huggingface dataset:
Corrosion in low dielectric constant Si-O based thin films: Buffer concentration effects
Authors: Zeng F. W. , Gates S. M. , Lane M. W.
Published: May 2014

Organosilicate glass (OSG) is often used as an interlayer dielectric (ILD) in high performance integrated circuits. OSG is a brittle material and prone to stress-corrosion cracking reminiscent of that observed in bulk glasses. Of particular concern are chemical-mechanical planarization techniques and wet cleans involving solvents commonly encountered in microelectronics fabrication where the organosilicate film is exposed to aqueous environments. Previous work has focused on the effect of pH, surfactant, and peroxide concentration on the subcritical crack growth of these films. However, little or no attention has focused on the effect of the conjugate acid/base concentration in a buffer. Accordingly, this work examines the “strength” of the buffer solution in both acidic and basic environments. The concentration of the buffer components is varied keeping the ratio of acid/base and therefore pH constant. In addition, the pH was varied by altering the acid/base ratio to ascertain any additional effect of pH. Corrosion tests were conducted with double-cantilever beam fracture mechanics specimens and fracture paths were verified with ATR-FTIR. Shifts in the threshold fracture energy, the lowest energy required for bond rupture in the given environment, GTH, were found to shift to lower values as the concentration of the base in the buffer increased. This effect was found to be much larger than the effect of the hydroxide ion concentration in unbuffered solutions. The results are rationalized in terms of the salient chemical bond breaking process occurring at the crack tip and modeled in terms of the chemical potential of the reactive species.
‘If No Gasoline, No Water’: Privatizing Drinking Water Quality in South Texas Colonias
Authors: Jepson Wendy , Brown Heather Lee
Published: May 2014

Our study investigates why low-income Mexican-American residents living in rural and periurban subdivisions ( colonias) in South Texas, one of the poorest regions in the United States, are increasingly dependent upon water vending machines as the main source of drinking water despite continued water infrastructure development. We outline a relational framework that builds on current debates within nature–society scholarship to address this paradox. We demonstrate how institutional enclosure—the creation or repurposing of institutions that curtails public participation in water governance—paired with water quality discourses and daily practices, operate over time to enroll residents as neoliberal subjects. We focus our attention on the emergence of the ‘water consumer’, or the individual who purchases drinking water from the vending machine. This approach addresses the coproduction of political subjectivities in relation to institutional change and how subjectivity reconstitutes a new hydrosocial relationship mediated by the water vending machine. We argue for a relational approach that attends to the production of political subjectivities as central to, not as a result of, the neoliberalization of nature.
Persistence of central Australian aquatic invertebrate communities
Authors: Brim-Box J. , Davis J. , Strehlow K. , McBurnie G. , Duguid A. , Brock C. , McConnell K. , Day C. , Palmer C.
Published: May 2014

Central Australia supports a restricted but important range of freshwater systems, including small, permanent spring-fed streams and larger riverine pools ranging from permanent to ephemeral. These sites support a significant percentage of the aquatic and terrestrial biodiversity within the region. Comparison of records from the first exploratory scientific expedition to the area in 1894, and surveys conducted in 1986, 1994 and 2008, revealed the persistence of the aquatic invertebrate fauna, despite the recent impacts of European settlement. The presence of aquatic insects with Gondwanan origins suggests affinities with assemblages present in a much wetter era (~18 000 years ago). Persistence can be attributed to multiple environmental and social factors, including the role of local aquifers in sustaining permanent systems, the remote and inaccessible nature of the sites, and the protection and management afforded by reservation within national parks. Characterisation of the drivers and stressors that influence these ecosystems suggests that climate change could potentially result in a loss of endemic and relictual species. Hence, the relictual waterbodies of central Australia can be viewed as potential ‘sentinel’ sites for assessing the impacts of changing conditions.
A theoretical analysis of how strain-specific viruses can control microbial species diversity
Authors: Thingstad T. Frede , Våge Selina , Storesund Julia E. , Sandaa Ruth-Anne , Giske Jarl
Published: May 2014

Significance

This work presents the first detailed analysis to the authors’ knowledge of how species-level diversity is a property emerging from competitive and defensive abilities at the organism level in a microbial system where the diversity-generating mechanism is strain-specific viral lysis. The theoretical analysis constitutes a general case treatment of the important special case question of what properties may make SAR11, a subphylum within the Alphaproteobacteria, so dominant in the pelagic environment. The resulting conceptual framework connects differences in the molecular defense mechanism to ecosystem-level properties such as diversity and activity. It also suggests a reinterpretation of the concept of dormancy in aquatic microbial communities.
Blended particle filters for large-dimensional chaotic dynamical systems
Authors: Majda Andrew J. , Qi Di , Sapsis Themistoklis P.
Published: May 2014

Significance

Combining large uncertain computational models with big noisy datasets is a formidable problem throughout science and engineering. These are especially difficult issues when real-time state estimation and prediction are needed such as, for example, in weather forecasting. Thus, a major challenge in contemporary data science is the development of statistically accurate particle filters to capture non-Gaussian features in large-dimensional chaotic dynamical systems. New blended particle filters are developed in this paper. These algorithms exploit the physical structure of turbulent dynamical systems and capture non-Gaussian features in an adaptively evolving low-dimensional subspace through particles interacting with evolving Gaussian statistics on the remaining portion of the phase space.
Harvesting wild flax in the Galilee, Israel and extracting fibers  bearing on Near Eastern plant domestication
Authors: Abbo Shahal , Zezak Inbar , Lev-Yadun Simcha , Shamir Orit , Friedman Toni , Gopher Avi
Published: May 2014

Flax (Linum usitatissimum, 2n = 30) is considered as the first fiber and oil crop of Neolithic Near Eastern agriculture and is often mentioned as one of the Near Eastern Neolithic “founder crops” assemblage. Wild flax fibers were recovered from a 30,000-year-old Upper Paleolithic site in Georgia, suggesting that the utilization of wild flax by Old World hunter–gatherer societies pre-dates the Neolithic agricultural revolution. We examined the potential of a wild flax species (L.pubescens, 2n = 18), an abundant element in open plant formations in Israel, as a source of fibers. Whole plants were pulled by hand in two sites in the eastern Galilee, Israel, during May 2006 and May 2007. The roots, stems and inflorescences of the collected plants were separated, dried and weighed. Fibers were extracted by retting and hammering the stems, dried, weighed and yarn was spun. BecauseLinum pubescensis not the wild progenitor of domesticated flax but rather a distantly related wild relative, the results of our experimental flax harvest are discussed in the context of both Levantine hunter–gatherers’ subsistence and the Neolithic recruitment of species as potential candidates for domestication.
War rape survivors of the Second Congo War: A perspective from symbolic convergence theory
Authors: Simi Demi , Matusitz Jonathan
Published: May 2014

This paper examines actions and narratives of war rape survivors of the Second Congo War. The Second Congo War, which officially began in 1998, is an enduring armed struggle that involves more than fighting for mineral resources. It also involves massive attacks against women (i.e. by engaging in the systematic rape of women). The theoretical framework used in this analysis is symbolic convergence theory (SCT). Coined by Bormann [1972. “Fantasy and Rhetorical Vision: The Rhetorical Criticism of Social Reality.” Quarterly Journal of Speech 58: 396–407], SCT postulates that group consciousness is achieved when a group shares emotions, experiences, and stories. SCT regards group cohesion as a result of rhetorical visions by delivering a collective objective through fantasy themes, fantasy types, symbolic cues, and sagas. An important conclusion of this analysis is that, through various forms of symbolic convergence and fantasies, Congolese women are able to cope with the reality of war rape and ‘navigate’ (in the best way they can) in today’s society. In other words, SCT helps to explain how rape survivors find ways to mitigate their own suffering.
Perceptions of value: assessing the agent/commission model of UK higher education recruitment in Africa
Authors: Thomson Alex , Hulme Rob , Hulme Moira , Doughty Guy
Published: May 2014

The UK’s higher education relationship with Africa has changed in recent years. Past associations of developmental cooperation have been superseded by market-based student recruitment seeking income for UK universities. This paper is about assessing a form of recruitment that helps underpin this new relationship: the agent/commission model. It identifies the nature of this approach to recruitment, and the processes involved. The paper also asks who benefits from the agent/commission model. The research captured a ‘snapshot’ of opinion within a case study UK university, seeking the views of agents themselves and their service users. It was found that all these actors considered the work of agents to be of value. There are certainly flaws in the agent/commission model, and wider societal implications for African states and economies, but it is suggested that agents should be given more credit for the work that they do than is presently reflected in the current literature.
Dynactin integrity depends upon direct binding of dynamitin to Arp1
Authors: Cheong Frances Ka Yan , Feng Lijuan , Sarkeshik Ali , Yates John R. , Schroer Trina A.
Published: May 2014

Dynactin is a multiprotein complex that works with cytoplasmic dynein and other motors to support a wide range of cell functions. It serves as an adaptor that binds both dynein and cargoes and enhances single-motor processivity. The dynactin subunit dynamitin (also known as p50) is believed to be integral to dynactin structure because free dynamitin displaces the dynein-binding p150Glued subunit from the cargo-binding Arp1 filament. We show here that the intrinsically disordered dynamitin N-terminus binds to Arp1 directly. When expressed in cells, dynamitin amino acids (AA) 1–87 causes complete release of endogenous dynamitin, p150, and p24 from dynactin, leaving behind Arp1 filaments carrying the remaining dynactin subunits (CapZ, p62, Arp11, p27, and p25). Tandem-affinity purification–tagged dynamitin AA 1–87 binds the Arp filament specifically, and binding studies with purified native Arp1 reveal that this fragment binds Arp1 directly. Neither CapZ nor the p27/p25 dimer contributes to interactions between dynamitin and the Arp filament. This work demonstrates for the first time that Arp1 can directly bind any protein besides another Arp and provides important new insight into the underpinnings of dynactin structure.
PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition
Authors: Lancaster Alex K. , Nutter-Upham Andrew , Lindquist Susan , King Oliver D.
Published: May 2014

Summary: Prions are self-templating protein aggregates that stably perpetuate distinct biological states and are of keen interest to researchers in both evolutionary and biomedical science. The best understood prions are from yeast and have a prion-forming domain with strongly biased amino acid composition, most notably enriched for Q or N. PLAAC is a web application that scans protein sequences for domains with prion-like amino acid composition. Users can upload sequence files, or paste sequences directly into a textbox. PLAAC ranks the input sequences by several summary scores and allows scores along sequences to be visualized. Text output files can be downloaded for further analyses, and visualizations saved in PDF and PNG formats.

Availability and implementation:  http://plaac.wi.mit.edu/. The Ruby-based web framework and the command-line software (implemented in Java, with visualization routines in R) are available at http://github.com/whitehead/plaac under the MIT license. All software can be run under OS X, Windows and Unix.

Contact:  oliver.king@umassmed.edu or lindquist_admin@wi.mit.edu
Interplay between Mdm2 and HIPK2 in the DNA damage response
Authors: Zhang Xiao-Peng , Liu Feng , Wang Wei
Published: May 2014

The tumour suppressor p53 is activated to induce cell-cycle arrest or apoptosis in the DNA damage response (DDR). p53 phosphorylation at Ser46 by HIPK2 (homeodomain-interacting protein kinase 2) is a critical event in apoptosis induction. Interestingly, HIPK2 is degraded by Mdm2 (a negative regulator of p53), whereas Mdm2 is downregulated by HIPK2 through several mechanisms. Here, we develop a four-module network model for the p53 pathway to clarify the role of interplay between Mdm2 and HIPK2 in the DDR evoked by ultraviolet radiation. By numerical simulations, we reveal that Mdm2-dependent HIPK2 degradation promotes cell survival after mild DNA damage and that inhibition of HIPK2 degradation is sufficient to trigger apoptosis. In response to severe damage, p53 phosphorylation at Ser46 is promoted by the accumulation of HIPK2 due to downregulation of nuclear Mdm2 in the later phase of the response. Meanwhile, the concentration of p53 switches from moderate to high levels, contributing to apoptosis induction. We show that the presence of three mechanisms for Mdm2 downregulation, i.e. repression of
mdm2
expression, inhibition of its nuclear entry and HIPK2-induced degradation, guarantees the apoptosis of irreparably damaged cells. Our results agree well with multiple experimental observations, and testable predictions are also made. This work advances our understanding of the regulation of p53 activity in the DDR and suggests that HIPK2 should be a significant target for cancer therapy.
The effect of seasonal birth pulses on pathogen persistence in wild mammal populations
Authors: Peel A. J. , Pulliam J. R. C. , Luis A. D. , Plowright R. K. , O'Shea T. J. , Hayman D. T. S. , Wood J. L. N. , Webb C. T. , Restif O.
Published: May 2014

The notion of a critical community size (CCS), or population size that is likely to result in long-term persistence of a communicable disease, has been developed based on the empirical observations of acute immunizing infections in human populations, and extended for use in wildlife populations. Seasonal birth pulses are frequently observed in wildlife and are expected to impact infection dynamics, yet their effect on pathogen persistence and CCS have not been considered. To investigate this issue theoretically, we use stochastic epidemiological models to ask how host life-history traits and infection parameters interact to determine pathogen persistence within a closed population. We fit seasonal birth pulse models to data from diverse mammalian species in order to identify realistic parameter ranges. When varying the synchrony of the birth pulse with all other parameters being constant, our model predicted that the CCS can vary by more than two orders of magnitude. Tighter birth pulses tended to drive pathogen extinction by creating large amplitude oscillations in prevalence, especially with high demographic turnover and short infectious periods. Parameters affecting the relative timing of the epidemic and birth pulse peaks determined the intensity and direction of the effect of pre-existing immunity in the population on the pathogen's ability to persist beyond the initial epidemic following its introduction.
Subcellular preservation in giant ostracod sperm from an early Miocene cave deposit in Australia
Authors: Matzke-Karasz Renate , Neil John V. , Smith Robin J. , Symonová Radka , Mořkovský Libor , Archer Michael , Hand Suzanne J. , Cloetens Peter , Tafforeau Paul
Published: May 2014

Cypridoidean ostracods are one of a number of animal taxa that reproduce with giant sperm, up to 10 000 µm in length, but they are the only group to have aflagellate, filamentous giant sperm. The evolution and function of this highly unusual feature of reproduction with giant sperm are currently unknown. The hypothesis of long-term evolutionary persistence of this kind of reproduction has never been tested. We here report giant sperm discovered by propagation phase contrast X-ray synchrotron micro- and nanotomography, preserved in five Miocene ostracod specimens from Queensland, Australia. The specimens belong to the species
Heterocypris collaris
Matzke-Karasz
et al
. 2013 (one male and three females) and
Newnhamia mckenziana
Matzke-Karasz
et al
. 2013 (one female). The sperm are not only the oldest petrified gametes on record, but include three-dimensional subcellular preservation. We provide direct evidence that giant sperm have been a feature of this taxon for at least 16 Myr and provide an additional criterion (i.e. longevity) to test hypotheses relating to origin and function of giant sperm in the animal kingdom. We further argue that the highly resistant, most probably chitinous coats of giant ostracod sperm may play a role in delaying decay processes, favouring early mineralization of soft tissue.
Costs of mating competition limit male lifetime breeding success in polygynous mammals
Authors: Lukas Dieter , Clutton-Brock Tim
Published: May 2014

Although differences in breeding lifespan are an important source of variation in male fitness, the factors affecting the breeding tenure of males have seldom been explored. Here, we use cross-species comparisons to investigate the correlates of breeding lifespan in male mammals. Our results show that male breeding lifespan depends on the extent of polygyny, which reflects the relative intensity of competition for access to females. Males have relatively short breeding tenure in species where individuals have the potential to monopolize mating with multiple females, and longer ones where individuals defend one female at a time. Male breeding tenure is also shorter in species in which females breed frequently than in those where females breed less frequently, suggesting that the costs of guarding females may contribute to limiting tenure length. As a consequence of these relationships, estimates of skew in male breeding success within seasons overestimate skew calculated across the lifetime and, in several polygynous species, variance in lifetime breeding success is not substantially higher in males than in females.
What does not kill them makes them stronger: larval environment and infectious dose alter mosquito potential to transmit filarial worms
Authors: Breaux Jennifer A. , Schumacher Molly K. , Juliano Steven A.
Published: May 2014

For organisms with complex life cycles, larval environments can modify adult phenotypes. For mosquitoes and other vectors, when physiological impacts of stressors acting on larvae carry over into the adult stage they may interact with infectious dose of a vector-borne pathogen, producing a range of phenotypes for vector potential. Investigation of impacts of a common source of stress, larval crowding and intraspecific competition, on adult vector interactions with pathogens may increase our understanding of the dynamics of pathogen transmission by mosquito vectors. Using
Aedes aegypti
and the nematode parasite
Brugia pahangi
, we demonstrate dose dependency of fitness effects of
B. pahangi
infection on the mosquito, as well as interactions between competitive stress among larvae and infectious dose for resulting adults that affect the physiological and functional ability of mosquitoes to act as vectors. Contrary to results from studies on mosquito–arbovirus interactions, our results suggest that adults from crowded larvae may limit infection better than do adults from uncrowded controls, and that mosquitoes from high-quality larval environments are more physiologically and functionally capable vectors of
B. pahangi
. Our results provide another example of how the larval environment can have profound effects on vector potential of resulting adults.
Extreme cost of rivalry in a monandrous species: male–male interactions result in failure to acquire mates and reduced longevity
Authors: Lizé Anne , Price Thomas A. R. , Heys Chloe , Lewis Zenobia , Hurst Gregory D. D.
Published: May 2014

Mating system variation is profound in animals. In insects, female willingness to remate varies from mating with hundreds of males (extreme polyandry) to never remating (monandry). This variation in female behaviour is predicted to affect the pattern of selection on males, with intense pre-copulatory sexual selection under monandry compared to a mix of pre- and post-copulatory forces affecting fitness under polyandry. We tested the hypothesis that differences in female mating biology would be reflected in different costs of pre-copulatory competition between males. We observed that exposure to rival males early in life was highly costly for males of a monandrous species, but had lower costs in the polyandrous species. Males from the monandrous species housed with competitors showed reduced ability to obtain a mate and decreased longevity. These effects were specific to exposure to rivals compared with other types of social interactions (heterospecific male and mated female) and were either absent or weaker in males of the polyandrous species. We conclude that males in monandrous species suffer severe physiological costs from interactions with rivals and note the significance of male–male interactions as a source of stress in laboratory culture.
Mechanical limits to maximum weapon size in a giant rhinoceros beetle
Authors: McCullough Erin L.
Published: May 2014

The horns of giant rhinoceros beetles are a classic example of the elaborate morphologies that can result from sexual selection. Theory predicts that sexual traits will evolve to be increasingly exaggerated until survival costs balance the reproductive benefits of further trait elaboration. InTrypoxylus dichotomus, long horns confer a competitive advantage to males, yet previous studies have found that they do not incur survival costs. It is therefore unlikely that horn size is limited by the theoretical cost–benefit equilibrium. However, males sometimes fight vigorously enough to break their horns, so mechanical limits may set an upper bound on horn size. Here, I tested this mechanical limit hypothesis by measuring safety factors across the full range of horn sizes. Safety factors were calculated as the ratio between the force required to break a horn and the maximum force exerted on a horn during a typical fight. I found that safety factors decrease with increasing horn length, indicating that the risk of breakage is indeed highest for the longest horns. Structural failure of oversized horns may therefore oppose the continued exaggeration of horn length driven by male–male competition and set a mechanical limit on the maximum size of rhinoceros beetle horns.
Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium
Authors: Sizova Maria V. , Muller Paul A. , Stancyk David , Panikov Nicolai S. , Mandalakis Manolis , Hazen Amanda , Hohmann Tine , Doerfert Sebastian N. , Fowle William , Earl Ashlee M. , Nelson Karen E. , Epstein Slava S.
Published: May 2014

Three strictly anaerobic, Gram-positive, non-spore-forming, rod-shaped, motile bacteria, designated strains ACB1T, ACB7T and ACB8, were isolated from human subgingival dental plaque. All strains required yeast extract for growth. Strains ACB1T and ACB8 were able to grow on glucose, lactose, maltose, maltodextrin and raffinose; strain ACB7T grew weakly on sucrose only. The growth temperature range was 30–42 °C with optimum growth at 37 °C. Major metabolic fermentation end products of strain ACB1T were acetate and lactate; the only product of strains ACB7T and ACB8 was acetate. Major fatty acids of strain ACB1T were C14 : 0, C16 : 0, C16 : 1ω7c dimethyl aldehyde (DMA) and C18 : 1ω7c DMA. Major fatty acids of strain ACB7T were C12 : 0, C14 : 0, C16 : 0, C16 : 1ω7c and C16 : 1ω7c DMA. The hydrolysate of the peptidoglycan contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. Genomic DNA G+C content varied from 42 to 43.3 % between strains. According to 16S rRNA gene sequence phylogeny, strains ACB1T, ACB8 and ACB7T formed two separate branches within the genus

Oribacterium

, with 98.1–98.6 % sequence similarity to the type strain of the type species,

Oribacterium sinus

. Predicted DNA–DNA hybridization values between strains ACB1T, ACB8, ACB7T and

O. sinus

F0268 were <70 %. Based on distinct genotypic and phenotypic characteristics, strains ACB1T and ACB8, and strain ACB7T are considered to represent two distinct species of the genus

Oribacterium

, for which the names Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov. are proposed. The type strains are ACB1T ( = DSM 24637T = HM-481T = ATCC BAA-2638T) and ACB7T ( = DSM 24638T = HM-482T = ATCC BAA-2639T), respectively.
Boseongicola aestuarii gen. nov., sp. nov., isolated from a tidal flat sediment
Authors: Park Sooyeon , Park Ja-Min , Lee Keun-Chul , Bae Kyung Sook , Yoon Jung-Hoon
Published: May 2014

A Gram-stain-negative, aerobic, non-motile and pleomorphic (coccoid, ovoid or rod-shaped) bacterial strain, BS-W15T, isolated from a tidal flat sediment at Boseong in South Korea, was characterized taxonomically. Strain BS-W15T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0 % (w/v) NaCl. Neighbour-joining and maximum-likelihood phylogenetic trees, based on 16S rRNA gene sequences, revealed that strain BS-W15T joined the cluster comprising the type strains of

Profundibacterium mesophilum

,

Hwanghaeicola aestuarii

,

M. pelagius

and

M. salinus

, showing 93.5–96.4 % sequence similarities. Strain BS-W15T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The polar lipid profile of strain BS-W15T contained phosphatidylcholine and phosphatidylglycerol as major components, differentiating it from those of the type strains of

P. mesophilum

,

H. aestuarii

,

M. pelagius

and

M. salinus

. The DNA G+C content of strain BS-W15T was 58.7 mol%. The differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrate that strain BS-W15T is distinct from type strains of

P. mesophilum

,

H. aestuarii

,

M. pelagius

and

M. salinus

. On the basis of the data presented, strain BS-W15T is considered to represent a novel genus and species, for which the name Boseongicola aestuarii gen. nov., sp. nov. is proposed. The type strain is BS-W15T ( = KCTC 32576T = CECT 8489T).
Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari Zhu et al. 2013 as Kosakonia sacchari comb. nov.
Authors: Gu Chun Tao , Li Chun Yan , Yang Li Jie , Huo Gui Cheng
Published: May 2014

A Gram-stain-negative bacterial strain, 10-17T, was isolated from traditional sourdough in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, RNA polymerase β subunit (rpoB) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, ATP synthase β subunit (atpD) gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain 10-17T was phylogenetically related to

Enterobacter hormaechei

CIP 103441T,

Enterobacter cancerogenus

LMG 2693T,

Enterobacter asburiae

JCM 6051T,

Enterobacter mori

LMG 25706T,

Enterobacter ludwigii

EN-119T and

Leclercia adecarboxylata

LMG 2803T, having 99.5 %, 99.3 %, 98.7 %, 98.5 %, 98.4 % and 98.4 % 16S rRNA gene sequence similarity, respectively. On the basis of polyphasic characterization data obtained in the present study, a novel species, Enterobacter xiangfangensis sp. nov., is proposed and the type strain is 10-17T ( = LMG 27195T = NCIMB 14836T = CCUG 62994T).

Enterobacter sacchari

Zhu et al. 2013 was reclassified as Kosakonia sacchari comb. nov. on the basis of 16S rRNA, rpoB, gyrB, infB and atpD gene sequence analysis and the type strain is strain SP1T( = CGMCC 1.12102T = LMG 26783T).
Loktanella variabilis sp. nov., isolated from a tidal flat
Authors: Park Ja-Min , Park Sooyeon , Jung Yong-Taek , Cho Jae Yeol , Yoon Jung-Hoon
Published: May 2014

Two Gram-negative, aerobic and rod-shaped or ovoid bacterial strains with different colony colours (greyish yellow and moderate orange), designated J-MR2-YT and J-MR2-O, were isolated from a tidal flat in the South Sea of South Korea. The two novel strains grew optimally at 35–37 °C. Strains J-MR2-YT and J-MR2-O showed no difference in their 16S rRNA gene sequences, and the mean DNA–DNA relatedness between them was 94 %. Phylogenetic trees based on 16S rRNA gene sequences revealed that strains J-MR2-YT and J-MR2-O clustered consistently with the type strains of

Loktanella soesokkakensis

,

L. hongkongensis

and

L. cinnabarina

, with which it exhibited 97.83–99.06 % sequence similarity. Sequence similarities to the type strains of the other recognized species of the genus

Loktanella

were 94.01–96.26 %. Both strains contained Q-10 as the predominant ubiquinone, C18 : 1ω7c as the major fatty acid and phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and one unidentified aminolipid as the major polar lipids. The DNA G+C contents of strains J-MR2-YT and J-MR2-O were 68.1 and 68.4 mol%, respectively, and DNA–DNA relatedness values with the type strains of

L. soesokkakensis

,

L. hongkongensis

and

L. cinnabarina

were 19–37 %. Differential phenotypic properties, together with their phylogenetic and genetic distinctiveness, revealed that the two novel strains are separated from other species of the genus

Loktanella

. On the basis of the data presented, strains J-MR2-YT and J-MR2-O are proposed to represent a novel species of the genus

Loktanella

, for which the name Loktanella variabilis sp. nov. is proposed. The type strain is J-MR2-YT ( = KCTC 42074T = CECT 8572T).
Population genomics of parallel hybrid zones in the mimetic butterflies,H. melpomeneandH. erato
Authors: Nadeau Nicola J. , Ruiz Mayté , Salazar Patricio , Counterman Brian , Medina Jose Alejandro , Ortiz-Zuazaga Humberto , Morrison Anna , McMillan W. Owen , Jiggins Chris D. , Papa Riccardo
Published: May 2014

Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies ofHeliconiusbutterflies can be very narrow and are maintained by strong selection acting on color pattern. The comimetic species,H. eratoandH. melpomene,have parallel hybrid zones in which both species undergo a change from one color pattern form to another. We use restriction-associated DNA sequencing to obtain several thousand genome-wide sequence markers and use these to analyze patterns of population divergence across two pairs of parallel hybrid zones in Peru and Ecuador. We compare two approaches for analysis of this type of data—alignment to a reference genome and de novo assembly—and find that alignment gives the best results for species both closely (H. melpomene) and distantly (H. erato,∼15% divergent) related to the reference sequence. Our results confirm that the color pattern controlling loci account for the majority of divergent regions across the genome, but we also detect other divergent regions apparently unlinked to color pattern differences. We also use association mapping to identify previously unmapped color pattern loci, in particular theRolocus. Finally, we identify a new cryptic population ofH. timaretain Ecuador, which occurs at relatively low altitude and is mimetic withH. melpomene malleti.
HD-Zip Proteins GL2 and HDG11 Have Redundant Functions in Arabidopsis Trichomes, and GL2 Activates a Positive Feedback Loop via MYB23
Authors: Khosla Aashima , Paper Janet M. , Boehler Allison P. , Bradley Amanda M. , Neumann Titus R. , Schrick Kathrin
Published: May 2014

The class IV homeodomain leucine zipper transcription factor GLABRA2 (GL2) acts in a complex regulatory circuit that regulates the differentiation of trichomes in Arabidopsis thaliana. We describe a genetic interaction with HOMEODOMAIN GLABROUS11 (HDG11), previously identified as a negative regulator of trichome branching. gl2 hdg11 double mutants display enhanced trichome cell-type differentiation defects. Transgenic expression of HDG11 using the GL2 promoter partially suppresses gl2 trichome phenotypes. Vice versa, expression of GL2 under the control of its native promoter partially complements hdg11 ectopic branching. Since gl2 hdg11 and gl2 myb23 double mutants and the triple mutant display similar trichome differentiation defects, we investigated a connection to the R2R3-MYB transcription factor MYB23. We show that MYB23 transcript levels are significantly reduced in shoots from gl2 mutants and that GL2 can drive the expression of a MYB23-promoter fusion to green fluorescent protein. Yeast one-hybrid, chromatin immunoprecipitation, and in planta reporter gene experiments indicate that an L1-box in the MYB23 promoter acts as a GL2 binding site. Taken together, our findings reveal a functional redundancy between GL2 and HDG11, two homeodomain leucine zipper transcription factors previously thought to mediate opposing functions in trichome morphogenesis. A model is proposed in which GL2 transcript levels are maintained through a positive feedback loop involving GL2 activation of MYB23.
The Novel Nuclear Envelope Protein KAKU4 Modulates Nuclear Morphology inArabidopsis
Authors: Goto Chieko , Tamura Kentaro , Fukao Yoichiro , Shimada Tomoo , Hara-Nishimura Ikuko
Published: May 2014

In animals, the nuclear lamina is a fibrillar meshwork on the inner surface of the nuclear envelope, composed of coiled-coil lamin proteins and lamin binding membrane proteins. Plants also have a meshwork on the inner surface of the nuclear envelope, but little is known about its composition other than the presence of members of the CROWDED NUCLEI (CRWN) protein family, possible plant lamin analogs. Here, we describe a candidate lamina component, based on two Arabidopsis thaliana mutants (kaku2 and kaku4) with aberrant nuclear morphology. The responsible gene in kaku2 encodes CRWN1, and the responsible gene in kaku4 encodes a plant-specific protein of unknown function (KAKU4) that physically interacts with CRWN1 and its homolog CRWN4. Immunogold labeling revealed that KAKU4 localizes at the inner nuclear membrane. KAKU4 deforms the nuclear envelope in a dose-dependent manner, in association with nuclear membrane invagination and stack formation. The KAKU4-dependent nuclear envelope deformation was enhanced by overaccumulation of CRWN1, although KAKU4 can deform the nuclear envelope even in the absence of CRWN1 and/or CRWN4. Together, these results suggest that plants have evolved a unique lamina-like structure to modulate nuclear shape and size.
Modelling environmental and socio‐economic trade‐offs associated with land‐sparing and land‐sharing approaches to oil palm expansion
Authors: Lee Janice Ser Huay , Garcia‐Ulloa John , Ghazoul Jaboury , Obidzinski Krystof , Koh Lian Pin
Published: May 2014

The effectiveness of land‐sharing and land‐sparing approaches has been widely debated. Yet, few studies quantify the environmental and socio‐economic outcomes of these approaches within a real‐world landscape. Indonesia's plans to increase its palm oil production present an opportunity to investigate the potential environmental and socio‐economic implications of the land‐sharing and sparing approaches.

We developed a computer model to simulate the expansion of oil palm agriculture in Sumatra, Indonesia, under four different scenarios distinguishable by the dominance of scheme smallholders or industrial estates: business‐as‐usual, BAU (25 : 75, scheme smallholders:industrial estates); high‐yielding industry dominated, ESTATE (10 : 90); low‐yielding smallholder dominated, SMALLHOLDER (40 : 60), high‐yielding smallholder dominated, HYBRID (40 : 60; but with improved smallholder yields).

Our results reveal several trade‐offs associated with varying the proportion of scheme smallholders and productivity of oil palm plantations. The ESTATE scenario (reflecting land‐sparing) resulted in lowest environmental costs in terms of forest conversion, greenhouse gas emissions, biodiversity losses and nitrogen fertilizer usage. Additionally, infrastructural development and tax revenues were highest under the land‐sparing approach, though fewer jobs were created. The SMALLHOLDER scenario (indicating land‐sharing) resulted in highest environmental costs in terms of forest conversion, carbon dioxide emissions and biodiversity losses but involved more households in oil palm agriculture and thus created more employment opportunities. The HYBRID scenario ranked second best in terms of both minimizing forest loss and job creation. However, the drawbacks of this approach included high nitrogen fertilizer consumption, lower infrastructural development and lower tax revenues.

Synthesis and applications. From an environmental perspective, it is far more important to implement spatial restrictions on oil palm expansion over forests since increasing the productivity of smallholdings and industrial estates among the four scenarios examined show minimal differences to biodiversity loss and greenhouse gas emissions. The hybrid approach shows that increasing the proportion of scheme smallholders need not come at a great environmental cost for achieving Indonesia's palm oil production target. From a policy perspective, this hybrid approach requires a change in legislation to increase the minimum land area an industrial estate owner must allocate to scheme smallholders (40%), as well as increased support to improve productivity in oil palm smallholdings.
Implementing person‐environment approaches to prevent falls: A qualitative inquiry in applying the Westmead approach to occupational therapy home visits
Authors: Clemson Lindy , Donaldson Alex , Hill Keith , Day Lesley
Published: May 2014

Background/aims

Despite evidence of the effectiveness of home safety interventions for preventing falls, there is limited uptake of such interventions within community services. Therefore, as part of a broader translational project, we explored issues underlying the implementation of an evidence‐based home safety fall prevention intervention.

Method

We conducted in‐depth interviews with eight occupational therapists and two programme coordinators engaged to deliver a home safety fall prevention intervention. Six community health centres within two metropolitan regions of Melbourne, Australia participated. The RE‐AIM framework and Diffusion of Innovations theory underpinned the interviews which examine the enablers and barriers to implementing a home safety fall prevention intervention and integrating it into routine community preventive practice. Analysis involved thematic and content analysis.

Results

Investment in the home safety for fall prevention intervention was supported and valued by coordinators and therapists alike, and a number of themes emerged which influenced implementation of this intervention. These included issues of: compatibility with organisational processes, individual practitioner practices and skills, a prevention approach, and client expectations; relative advantage in terms of flexibility of the process, client engagement and regional capacity building; complexity of implementing the intervention; and observability related to the invisible nature of fall prevention outcomes.

Conclusion

Implementation of this home safety fall prevention intervention was influenced by a range of interrelated organisational, practitioner and client related factors. The findings from this project provide insights into, and opportunities to increase the sustainable implementation of the home safety fall prevention intervention into practice.
Effects of eNOS rs1799983 and ACE rs4646994 polymorphisms on the therapeutic efficacy of salvianolate injection in Chinese patients with coronary heart disease
Authors: Fang Chao , Ren Xian , Zhou Huan , Gong Zhi‐Cheng , Shen Li , Bai Jing , Yin Ji‐Ye , Qu Jian , Li Xiang‐Ping , Zhou Hong‐Hao , Liu Zhao‐Qian
Published: May 2014

The purpose of the present study was to clarify the association of eNOS 894G/T and ACE I/D genetic polymorphisms with the risk of coronary heart disease (CHD) and to explore the effects of these polymorphisms on the therapeutic efficacy of salvianolate injection in Chinese CHD patients. In all, 153 CHD patients and 198 healthy controls were enrolled in the study. We collected 5 mL peripheral blood for DNA extraction. Genetic diagnosis of eNOS 894G/T was determined by direct sequencing. Polymerase chain reaction–restriction fragment length polymorphism analysis was used to detect ACE I/D genotypes. We observed significant differences in the frequency distribution of eNOS and ACE polymorphisms between CHD patients and healthy controls (P < 0.05). Binary logistic regression stepwise analysis revealed that the genotypes had an additive and dominant effect on patients' therapeutic responses (P < 0.05). These data suggest that the genetic polymorphisms of ACE I/D and eNOS 894G/T probably play a role in the development of CHD and these genetic polymorphisms may affect the response to salvianolate injection in Chinese CHD patients.
The novel role and underlying mechanism of Wnt5a in regulating cellular cholesterol accumulation
Authors: Qin Li , Hu Rong , Zhu Neng , Yao Hai‐Lun , Lei Xiao‐Yong , Li Shun‐Xiang , Liao Duan‐Fang , Zheng Xi‐Long
Published: May 2014

Cholesterol accumulation is a critical step during the development and progression of atherosclerosis. Recently, Wnt5a expression has been found to be markedly upregulated in both murine and human atherosclerotic lesions. However, the effect and mechanism of Wnt5a in atherosclerosis is poorly understood. In the present study, we investigated the effects and potential mechanisms of Wnt5a on cholesterol accumulation during atherosclerosis. We used RAW264.7 and vascular smooth muscle cells (VSMC) treated with oxidized low‐density lipoprotein (oxLDL) as lipid‐loaded cell models. We found that expression of Wnt5a protein was increased in a concentration (25, 50, 75 and 100 μg/mL)‐ and time (24, 48 and 72 h)‐dependent manner by oxLDL treatment. To explore the underlying mechanism, we used Wnt5a short interference (si) RNA to knockdown Wnt5a expression in both RAW264.7 cells and VSMC, or applied recombinant Wnt5a (rWnt5a) to stimulate Wnt5a signalling. After Wnt5a knockdown, total cholesterol (TC) and free cholesterol (FC) content in both cell types increased significantly (P < 0.05) upon exposure to oxLDL. Conversely, the TC and FC content decreased markedly (P < 0.05) after treatment of cells with rWnt5a. More importantly, both protein and mRNA expression of Caveolin‐1 and ATP‐binding cassette transporter A1 (ABCA1) was significantly reduced after exposure of wnt5a siRNA‐treated cells to oxLDL, whereas rWnt5a treatment of cells resulted in increased Caveolin‐1 and ABCA1 protein expression after exposure of cells to oxLDL. Together, these findings demonstrate, for the first time, that Wnt5a reduces the accumulation of cholesterol in lipid‐loaded cells by regulating the mRNA expression of Caveolin‐1 and ABCA1, which are involved in reverse cholesterol transport. This may present a novel mechanism of Wnt5a‐mediated cholesterol transportation in macrophages and VSMC. Therefore, targeting the Wnt5a signalling pathway may have clinical implications in atherosclerosis.
A randomised controlled trial of outpatient compared with inpatient cervical ripening with prostaglandin E2 (OPRA study)
Authors: Wilkinson C , Bryce R , Adelson P , Turnbull D
Published: May 2014

Objective

To compare clinical outcomes from outpatient with inpatient cervical prostaglandin E2 ripening for low risk labour induction.

Design

Randomised controlled trial.

Setting

Two tertiary hospitals in Adelaide, Australia.

Population

Women with uncomplicated term pregnancies, scheduled for induction of labour for reasons of post‐dates or for social reasons.

Methods

Eight hundred and twenty‐seven women were randomised at induction decision to an outpatient or inpatient group. All women had CTG monitoring before and after vaginal PgE2 administration. The inpatient women were admitted and the outpatient group was discharged home overnight with instructions to return if labour established or rupture of membranes occurred. Next morning, outpatient women were admitted for rupture of membranes or further ripening. After membrane rupture, both groups received routine care.

Main outcome measures

Oxytocin use, maternal and fetal outcomes, and whether planned outpatient management was achievable.

Results

There were no significant differences in oxytocin use (2.5% difference, CI−4.3 to 9.4), caesarean sections (−0.59% difference, CI−6.3 to 5.1), epidural use (1.5% difference, CI−5.1 to 8.2), vaginal delivery within 24 hours (−8.2% difference, CI−17.6 to 1.3) or labour complications. More than half of the randomised women did not receive the intervention as they laboured spontaneously, or did not require ripening. The post‐hoc analysis of women who received ripening also indicated no statistically significant differences in the patterns or results, with the exception of outpatient women having a longer mean length of active labour (mean difference 66 minutes, CI 4–128 minutes). Outpatient women who received ripening were diagnosed more frequently with non‐reassuring CTG monitoring and hyperstimulation, with less than half of the women going home and remaining home overnight.

Conclusions

This study demonstrated no clinical advantage or disadvantage in prostaglandin E2 outpatient cervical ripening. Uterine stimulation following prostaglandins may preclude a woman from going home or remaining at home overnight and may not be the best agent for outpatient ripening.