bluuebunny/crossref_metadata_2025 huggingface dataset:
Communication: Vacuum ultraviolet photoabsorption of interstellar icy thiols
Authors: Bhuin Radha Gobinda , Sivaraman Bhalamurugan , Lo Jen-Iu , Sekhar B. N. Raja , Cheng Bing-Ming , Pradeep Thalappil , Mason Nigel John
Published: December 2014

Following the recent identification of ethanethiol in the interstellar medium (ISM) we have carried out Vacuum UltraViolet (VUV) spectroscopy studies of ethanethiol (CH3CH2SH) from 10 K until sublimation in an ultrahigh vacuum chamber simulating astrochemical conditions. These results are compared with those of methanethiol (CH3SH), the lower order thiol also reported to be present in the ISM. VUV spectra recorded at higher temperature reveal conformational changes in the ice and phase transitions whilst evidence for dimer production is also presented.
Sharp chemical interface in epitaxial Fe3O4 thin films
Authors: Gálvez S. , Rubio-Zuazo J. , Salas-Colera E. , Muñoz-Noval A. , Castro G. R.
Published: December 2014

Chemically sharp interface was obtained on single phase single oriented Fe3O4 (001) thin film (7 nm) grown on NiO (001) substrate using oxygen assisted molecular beam epitaxy. Refinement of the atomic structure, stoichiometry, and oxygen vacancies were determined by soft and hard x-ray photoelectron spectroscopy, low energy electron diffraction and synchrotron based X-ray reflectivity, and X-ray diffraction. Our results demonstrate an epitaxial growth of the magnetite layer, perfect iron stoichiometry, absence of oxygen vacancies, and the existence of an intermixing free interface. Consistent magnetic and electrical characterizations are also shown.
Interface correlated exchange bias effect in epitaxial Fe3O4 thin films grown on SrTiO3 substrates
Authors: Zhu Qiu-Xiang , Zheng Ming , Yang Ming-Min , Zheng Ren-Kui , Wang Yu , Li Xiao-Min , Shi Xun
Published: December 2014

We report exchange bias effect in Fe3O4 films epitaxially grown on SrTiO3 substrates. This effect is related to the formation of Ti3+-vacancy complexes at the surface of SrTiO3 in ultrahigh vacuum that in turn triggers the growth of a thin antiferromagnetic (AFM) FeO layer (∼5 nm) at the interface. The picture of antiferromagnetic FeO interacting with native ferrimagnetic Fe3O4 matrix reasonably accounts for this anomalous magnetic behavior. With increasing film thickness from 17 to 43 nm, the exchange bias effect and the magnetization anomaly associated with the AFM phase transition of the FeO layer are progressively weakened due to the increase in the volume fraction of the Fe3O4 phase, indicating the interfacial nature of the exchange coupling. Our results highlight the important role of interface engineering in controlling the magnetic properties of iron oxide thin films.
Conundrums in merging public policy into private dentistry: experiences from Australia’s recent past
Authors: Lam Raymond , Kruger Estie , Tennant Marc
Published: December 2014

Oral disease continues to be a major problem in Australia impacting quality of life, the economy and broader health system. Although the understanding of caries and periodontal disease has improved along with increased government support, oral diseases continue to be the most prevalent among all health conditions. This is despite unprecedented levels of funding in the Chronic Disease Dental Scheme and the Teen Dental Plan. Access to primary care dentistry in the private sector, where the majority of dental services are provided, remains a critical issue. Under the current system of dentistry, it cannot be assumed that the practice of dentistry represents a prioritised approach to combat disease patterns based on scientific evidence in primary health and prevention. Drawing on data in relation to these two programs, the present study highlights issues impacting dental service provision. This includes issues such as access and affordability to dental care, sustainability of policy and its unintended consequences, private practice pressures and the impact of remuneration on treatment. This paper argues that without structural reform there will continue to be barriers in implementing policies capable of improving oral health. What is known about the topic? The burden of oral diseases remains high and there continue to be problems in accessing and affording dental treatment. What does this paper add? This paper highlights factors impacting dental service provision and offers potential solutions to improve access to primary care dentistry. What are the implications for practitioners? A consideration of these factors may assist policy makers and governments in formulating effective policies.
Improving the feeding value of straws with Pleurotus ostreatus
Authors: Khan N. A. , Hussain S. , Ahmad N. , Alam S. , Bezabhi M. , Hendriks W. H. , Yu P. , Cone J. W.
Published: December 2014

The high content of lignin in cell walls is the major limiting factor in the digestion and utilisation of cereal crop residues by ruminants. The aim of this study was to evaluate the effectiveness of the white rot fungus, Pleurotus ostreatus (P. ostreatus), to degrade lignin and to enhance the rumen degradability of maize stover, rice straw, wheat straw and their mixture in equal proportion on a dry-matter (DM) basis. Four samples of each substrate were incubated aerobically in triplicate with P. ostreatus for 0 (Control), 21, 28 and 35 days under solid-state conditions (temperature, 24°C; humidity, 70 ± 5%). The changes in chemical composition, DM and nutrient losses, and rumen fermentation characteristics using in vitro DM digestibility (DMD) and the in vitro gas-production (GP) technique were measured. The results showed that incubation with P. ostreatus decreased (P < 0.001) the contents of neutral detergent fibre and lignin with a concomitant increase (P < 0.001) in the contents of ash and crude protein. The losses of nutrients differed (P < 0.001) among the straw types, with rice straw and maize stover showing the largest (P < 0.05) lignin degradation compared to wheat and mixed straws. The DMD and 72-h cumulative GP increased (P < 0.001) consistently with increasing fungal incubation period and for all substrates the highest values of DMD and GP were measured after 35 days of incubation with P. ostreatus. The lignin degradation was strongly associated with hemicellulose degradation (r = 0.71) across the various straws. Results of the present study demonstrated that incubation of low-quality crop residues with P. ostreatus under solid-state conditions upgrades their feeding value by reducing the content of lignin and increasing the content of crude protein and ruminal degradation.
Baseline and greenhouse-gas emissions in extensive livestock enterprises, with a case study of feeding lipid to beef cattle
Authors: Herd Robert M. , Oddy V. Hutton , Bray Steven
Published: December 2014

For accurate calculation of reductions in greenhouse-gas (GHG) emissions, methodologies under the Australian Government’s Carbon Farming Initiative (CFI) depend on a valid assessment of the baseline and project emissions. Life-cycle assessments (LCAs) clearly show that enteric methane emitted from the rumen of cattle and sheep is the major source of GHG emissions from livestock enterprises. Where a historic baseline for a CFI methodology for livestock is required, the use of simulated data for cow–calf enterprises at six sites in southern Australia demonstrated that a 5-year rolling emission average will provide an acceptable trade off in terms of accuracy and stability, but this is a much shorter time period than typically used for LCA. For many CFI livestock methodologies, comparative or pair-wise baselines are potentially more appropriate than historic baselines. A case study of lipid supplementation of beef cows over winter is presented. The case study of a control herd of 250 cows used a comparative baseline derived from simple data on livestock numbers and class of livestock to quantify the emission abatement. Compared with the control herd, lipid supplementation to cows over winter increased livestock productivity, total livestock production and enterprise GHG emissions from 990 t CO2-e to 1022 t CO2-e. Energy embodied in the supplement and extra diesel used in transporting the supplement diminished the enteric-methane abatement benefit of lipid supplementation. Reducing the cow herd to 238 cows maintained the level of livestock production of the control herd and reduced enterprise emissions to 938 t CO2-e, but was not cost effective under the assumptions of this case study.
A critical review of nanohybrids: synthesis, applications and environmental implications
Authors: Aich Nirupam , Plazas-Tuttle Jaime , Lead Jamie R. , Saleh Navid B.
Published: December 2014

Environmental context Recent developments in nanotechnology have focussed towards innovation and usage of multifunctional and superior hybrid nanomaterials. Possible exposure of these novel nanohybrids can lead to unpredicted environmental fate, transport, transformation and toxicity scenarios. Environmentally relevant emerging properties and potential environmental implications of these newer materials need to be systematically studied to prevent harmful effects towards the aquatic environment and ecology. Abstract Nanomaterial synthesis and modification for applications have progressed to a great extent in the last decades. Manipulation of the physicochemical properties of a material at the nanoscale has been extensively performed to produce materials for novel applications. Controlling the size, shape, surface functionality, etc. has been key to successful implementation of nanomaterials in multidimensional usage for electronics, optics, biomedicine, drug delivery and green fuel technology. Recently, a focus has been on the conjugation of two or more nanomaterials to achieve increased multifunctionality as well as creating opportunities for next generation materials with enhanced performance. With incremental production and potential usage of such nanohybrids come the concerns about their ecological and environmental effects, which will be dictated by their not-yet-understood physicochemical properties. While environmental implication studies concerning the single materials are yet to give an integrated mechanistic understanding and predictability of their environmental fate and transport, the importance of studying the novel nanohybrids with their multi-dimensional and complex behaviour in environmental and biological exposure systems are immense. This article critically reviews the literature of nanohybrids and identifies potential environmental uncertainties of these emerging ‘horizon materials’.
A comparison of biodiversity–ecosystem function relationships in alpine grasslands across a degradation gradient on the Qinghai–Tibetan Plateau
Authors: Wang Xuexia , Dong Shikui , Sherman Ruth , Liu Quanru , Liu Shiliang , Li Yuanyuan , Wu Yu
Published: December 2014

To examine biodiversity–ecosystem function relationships in alpine grasslands of the Qinghai–Tibetan Plateau, we compared differences in plant species and functional group diversity (sedges, grasses, legumes and non-leguminous forbs) to aboveground biomass, soil carbon (C) and nitrogen (N) pools and soil loss in five sites that ranged from healthy to severely degraded grasslands. Plant diversity decreased from 36 species in the healthy grassland to 15 species in the severely degraded grassland, and the plant functional groups changed from predominantly grasses and sedges to mostly forbs as the level of degradation increased. Plant biomass and soil pools of C and N decreased whereas soil loss and the amount of bare ground increased across the degradation gradient from healthy to severely degraded grasslands. Simple linear regressions showed strong positive relationships between species diversity and aboveground biomass of sedges, grasses and legumes and between soil C and N pools, but negative relationships between species diversity and non-leguminous forbs and soil loss. Our results provide strong evidence that plant diversity in grasslands on the Qinghai–Tibetan Plateau is positively related to primary productivity, C and N storage in soils and soil conservation, and that grassland degradation is impairing ecosystem function resulting in a loss in ecosystem services.
Nonrandom, diversifying processes are disproportionately strong in the smallest size classes of a tropical forest
Authors: Green Peter T. , Harms Kyle E. , Connell Joseph H.
Published: December 2014

Significance

A long-standing paradigm in forest ecology holds that patterns of relative abundance among a forest’s mature trees are largely set by biotic and abiotic processes that operate most strongly at the earliest life-cycle stages. Although support for this model is implicit in the vast body of research on tropical seedling dynamics, the paradigm has never formally been tested in any forest. Using multidecadal demographic data, we present quantitative evidence for the primacy of early-stage, nonrandom dynamics in forest ecology. This finding corroborates the importance that tropical ecologists have traditionally assigned to early-stage dynamics, and calls for greater and more widespread inclusion of the smallest size classes into large, plot-based tropical forest dynamics projects worldwide.
A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization
Authors: Qiu Chen , McCann Kathleen L. , Wine Robert N. , Baserga Susan J. , Hall Traci M. Tanaka
Published: December 2014

Significance

RNA regulation occurs at many levels including processing to mature forms, subcellular localization, and translation. RNA-binding proteins are crucial to direct and regulate these processes. Pumilio/feminization of XX and XO animals (fem)-3 mRNA-binding factor (PUF) proteins are RNA-binding proteins formed from eight α-helical repeats [Pumilio (PUM) repeats] that recognize specific mRNA sequences. Previous structural studies revealed characteristic curved structures and sequence specificity unique to these classical PUF proteins. We show here that PUM repeats also form different folds with 11 PUM repeats. Moreover, these proteins, exemplified by human Puf-A and yeast Puf6 proteins, recognize double-stranded RNA or DNA without sequence specificity. Interestingly, Puf-A and Puf6 PUM repeats lack specificity for RNA bases yet use residues at conserved positions on topologically equivalent protein surfaces for new nucleic acid recognition modes.
Forests, fields, and the edge of sustainability at the ancient Maya city of Tikal
Authors: Lentz David L. , Dunning Nicholas P. , Scarborough Vernon L. , Magee Kevin S. , Thompson Kim M. , Weaver Eric , Carr Christopher , Terry Richard E. , Islebe Gerald , Tankersley Kenneth B. , Grazioso Sierra Liwy , Jones John G. , Buttles Palma , Valdez Fred , Ramos Hernandez Carmen E.
Published: December 2014

Significance

The rise of complex societies and sustainable land use associated with urban centers has been a major focus for anthropologists, geographers, and ecologists. Here we present a quantitative assessment of the agricultural, agroforestry, and water management strategies of the inhabitants of the prominent ancient Maya city of Tikal, and how their land use practices effectively sustained a low-density urban population for many centuries. Our findings also reveal, however, that the productive landscape surrounding Tikal, managed to the brink of its carrying capacity during the Late Classic period, did not have the resilience to withstand the droughts of the 9th century. These results offer essential insights that address the question of why some cities thrive while others decline.
Genetic modifiers of EGFR dependence in non-small cell lung cancer
Authors: Sharifnia Tanaz , Rusu Victor , Piccioni Federica , Bagul Mukta , Imielinski Marcin , Cherniack Andrew D. , Pedamallu Chandra Sekhar , Wong Bang , Wilson Frederick H. , Garraway Levi A. , Altshuler David , Golub Todd R. , Root David E. , Subramanian Aravind , Meyerson Matthew
Published: December 2014

Significance

Non-small cell lung cancers (NSCLCs) harboring mutations in the epidermal growth factor receptor (
EGFR
) gene are often singularly reliant on EGFR activity for tumor cell survival, but the genetic basis for this dependence is not fully understood. In this study, we have performed a screen to identify a spectrum of kinase genes whose overexpression can overcome NSCLC cells’ reliance on EGFR. Using both unbiased and targeted approaches, we demonstrate that these genes commonly bypass dependence on EGFR through reactivation of downstream signaling pathways.
Economic optimization of a global strategy to address the pandemic threat
Authors: Pike Jamison , Bogich Tiffany , Elwood Sarah , Finnoff David C. , Daszak Peter
Published: December 2014

Significance

Emerging pandemics are increasing in frequency, threatening global health and economic growth. Global strategies to thwart pandemics can be classed as adaptive (reducing impact after a disease emerges) or mitigation (reducing the causes of pandemics). Our economic analysis shows that the optimal time to implement a globally coordinated adaptive policy is within 27 y and that given geopolitical challenges around pandemic control, these should be implemented urgently. Furthermore, we find that mitigation policies, those aimed at reducing the likelihood of an emerging disease originating, are more cost effective, saving between $344.0 billion and $360.8 billion over the next 100 y if implemented today.
Essential role for autophagy during invariant NKT cell development
Authors: Salio Mariolina , Puleston Daniel J. , Mathan Till S. M. , Shepherd Dawn , Stranks Amanda J. , Adamopoulou Eleni , Veerapen Natacha , Besra Gurdyal S. , Hollander Georg A. , Simon Anna Katharina , Cerundolo Vincenzo
Published: December 2014

Significance

Autophagy is an evolutionarily conserved catabolic process essential to maintaining cellular homeostasis through the breakdown and recycling of damaged organelles and long-lived proteins. We report that autophagy plays an essential cell-intrinsic role in maintaining the survival of a subset of innate-like cells known as invariant natural killer T (iNKT) cells. Autophagy deficiency prevents transition to a quiescent state after population expansion of thymic iNKT cells. Hence, autophagy-deficient iNKT cells accumulate mitochondria and oxygen radicals and subsequently die of apoptosis.
Topological sensitivity analysis for systems biology
Authors: Babtie Ann C. , Kirk Paul , Stumpf Michael P. H.
Published: December 2014

Significance

Mathematical models are widely used to study natural systems. They allow us to test and generate hypotheses, and help us to understand the processes underlying the observed behavior. However, such models are, by necessity, simplified representations of the true systems, so it is critical to understand the impact of assumptions made when using a particular model. Here we provide a method to assess how uncertainty about the structure of a natural system affects the conclusions we can draw from mathematical models of its dynamics. We use biological examples to illustrate the importance of considering uncertainty in both model structure and parameters. We show how solely considering the latter source of uncertainty can result in misleading conclusions and incorrect model inferences.
Occurrence of pristine aerosol environments on a polluted planet
Authors: Hamilton Douglas S. , Lee Lindsay A. , Pringle Kirsty J. , Reddington Carly L. , Spracklen Dominick V. , Carslaw Kenneth S.
Published: December 2014

Significance

Uncertainty in aerosol forcing of climate since the preindustrial era hampers efforts to quantify the sensitivity of global temperature to radiative perturbations caused by human activity. Because forcings are referenced to preindustrial conditions, a large part of the uncertainty will be reduced only by accurately defining pristine aerosol conditions before air pollution. We show that pristine conditions should still be observable on a few days per month in many regions of the Earth. However, pristine cloudy regions, which are of most importance for forcing uncertainty, occur almost entirely in the Southern Hemisphere. Reduction in uncertainty of predominantly Northern Hemisphere forcing may therefore have to rely on measurements from a different hemisphere, which will limit the extent to which uncertainties can be reduced.
A long noncoding RNA connects c-Myc to tumor metabolism
Authors: Hung Chiu-Lien , Wang Ling-Yu , Yu Yen-Ling , Chen Hong-Wu , Srivastava Shiv , Petrovics Gyorgy , Kung Hsing-Jien
Published: December 2014

Significance

Long noncoding RNA (lncRNA) has been implicated in carcinogenesis and regarded as an emerging alternative target for cancer therapy. This study provides, to our knowledge, the first case of lncRNA that serves as a coactivator of c-Myc and a master regulator of tumor metabolism. This lncRNA, prostate cancer gene expression marker 1 (
PCGEM1
), is overexpressed in prostate cancer and implicated in castration resistance. It also forms an independent complex with androgen receptor (AR). Being a dual coactivator for AR and c-Myc,
PCGEM1
reprograms the transcriptional network of metabolic genes and androgen-responsive genes, making it an ideal therapeutic target for prostate cancer. The present study provides significant insights into lncRNA’s role in c-Myc activation, tumor metabolism, and prostate carcinogenesis.
Detergent-free isolation, characterization, and functional reconstitution of a tetrameric K
+
channel: The power of native nanodiscs
Authors: Dörr Jonas M. , Koorengevel Martijn C. , Schäfer Marre , Prokofyev Alexander V. , Scheidelaar Stefan , van der Cruijsen Elwin A. W. , Dafforn Timothy R. , Baldus Marc , Killian J. Antoinette
Published: December 2014

Significance

The study of membrane proteins is often hampered by their tendency to misfold when extracted by detergent. Here, we explore a detergent-free approach to isolating membrane proteins while retaining their native lipid environment, making use of an amphipathic polymer that solubilizes intact membrane patches in the form of nanodiscs. Using a potassium channel as a model protein, we show that these “native nanodiscs” are highly thermostable particles that are suitable for spectroscopic studies, allowing structural characterization of the protein in its native environment and direct analysis of the lipids in its immediate surroundings. We also demonstrate that the channel can be reconstituted from nanodiscs into planar lipid bilayers for functional characterization, thus making native nanodiscs an excellent alternative to detergent solubilization.
Prehistoric genomes reveal the genetic foundation and cost of horse domestication
Authors: Schubert Mikkel , Jónsson Hákon , Chang Dan , Der Sarkissian Clio , Ermini Luca , Ginolhac Aurélien , Albrechtsen Anders , Dupanloup Isabelle , Foucal Adrien , Petersen Bent , Fumagalli Matteo , Raghavan Maanasa , Seguin-Orlando Andaine , Korneliussen Thorfinn S. , Velazquez Amhed M. V. , Stenderup Jesper , Hoover Cindi A. , Rubin Carl-Johan , Alfarhan Ahmed H. , Alquraishi Saleh A. , Al-Rasheid Khaled A. S. , MacHugh David E. , Kalbfleisch Ted , MacLeod James N. , Rubin Edward M. , Sicheritz-Ponten Thomas , Andersson Leif , Hofreiter Michael , Marques-Bonet Tomas , Gilbert M. Thomas P. , Nielsen Rasmus , Excoffier Laurent , Willerslev Eske , Shapiro Beth , Orlando Ludovic
Published: December 2014

Significance

The domestication of the horse revolutionized warfare, trade, and the exchange of people and ideas. This at least 5,500-y-long process, which ultimately transformed wild horses into the hundreds of breeds living today, is difficult to reconstruct from archeological data and modern genetics alone. We therefore sequenced two complete horse genomes, predating domestication by thousands of years, to characterize the genetic footprint of domestication. These ancient genomes reveal predomestic population structure and a significant fraction of genetic variation shared with the domestic breeds but absent from Przewalski’s horses. We find positive selection on genes involved in various aspects of locomotion, physiology, and cognition. Finally, we show that modern horse genomes contain an excess of deleterious mutations, likely representing the genetic cost of domestication.
Mechanical resilience and cementitious processes in Imperial Roman architectural mortar
Authors: Jackson Marie D. , Landis Eric N. , Brune Philip F. , Vitti Massimo , Chen Heng , Li Qinfei , Kunz Martin , Wenk Hans-Rudolf , Monteiro Paulo J. M. , Ingraffea Anthony R.
Published: December 2014

Significance

A volcanic ash–lime mortar has been regarded for centuries as the principal material constituent that provides long-term durability to ancient Roman architectural concrete. A reproduction of Imperial-age mortar based on Trajan’s Markets (110 CE) wall concrete resists microcracking through cohesion of calcium–aluminum–silicate–hydrate cementing binder and in situ crystallization of platey strätlingite, a durable calcium-aluminosilicate mineral that reinforces interfacial zones and the cementitious matrix. In the 1,900-y-old mortar dense intergrowths of the platey crystals obstruct crack propagation and preserve cohesion at the micron scale. Trajanic concrete provides a proven prototype for environmentally friendly conglomeratic concretes that contain ∼88 vol % volcanic rock yet maintain their chemical resilience and structural integrity in seismically active environments at the millenial scale.
Identification of S-nitroso-CoA reductases that regulate protein S-nitrosylation
Authors: Anand Puneet , Hausladen Alfred , Wang Ya-Juan , Zhang Guo-Fang , Stomberski Colin , Brunengraber Henri , Hess Douglas T. , Stamler Jonathan S.
Published: December 2014

Significance

Coenzyme A (CoA) is a small-molecular-weight thiol that plays a central role in cellular metabolism. We have discovered a novel, phylogenetically conserved class of enzymes that reduce S-nitroso-CoA (SNO-CoA) and thereby regulate protein S-nitrosylation. These denitrosylases, identified as alcohol dehydrogenase 6 (Adh6) in yeast and aldo-keto reductase 1A1 in mammals, may be analogized to deacetylases, which regulate CoA-mediated protein acetylation. In yeast, Adh6 (previously without ascribed cellular function) regulates endogenous protein S-nitrosylation (heretofore unknown) including function-altering S-nitrosylation that impacts CoA-related metabolism. Thus, our findings establish a novel role for CoA in protein S-nitrosylation (operating through SNO-CoA), which is governed by specific enzymes. This mechanism may regulate the influence of nitric oxide on cellular metabolism in health and disease.
TORC1 regulators Iml1/GATOR1 and GATOR2 control meiotic entry and oocyte development in
Drosophila
Authors: Wei Youheng , Reveal Brad , Reich John , Laursen Willem J. , Senger Stefania , Akbar Tanveer , Iida-Jones Takako , Cai Weili , Jarnik Michal , Lilly Mary A.
Published: December 2014

Significance

The target of rapamycin complex 1 (TORC1) promotes cell growth and anabolic metabolism. In yeast, entry into meiosis is contingent on the down-regulation of TORC1 activity by the increased minichromosome loss 1/GTPase-activating proteins toward Rags 1 (Iml1/GATOR1) complex in response to amino acid starvation. Here we define the developmental requirements for the TORC1 regulators Iml1/GATOR1 and GATOR2 during
Drosophila
oogenesis. We demonstrate that, as is observed in yeast, the Iml1/GATOR1 complex down-regulates TORC1 activity to facilitate the mitotic/meiotic transition in
Drosophila
ovarian cysts. Later in oogenesis, components of the GATOR2 complex oppose the activity of GATOR1 to enable a rise in TORC1 activity that drives oocyte development and growth. Thus, a conserved nutrient stress pathway has been incorporated into a developmental program that regulates meiotic progression in
Drosophila
.
Regulation of the Rhp26
ERCC6/CSB
chromatin remodeler by a novel conserved leucine latch motif
Authors: Wang Lanfeng , Limbo Oliver , Fei Jia , Chen Lu , Kim Bong , Luo Jie , Chong Jenny , Conaway Ronald C. , Conaway Joan W. , Ranish Jeff A. , Kadonaga James T. , Russell Paul , Wang Dong
Published: December 2014

Significance

Cockayne syndrome group B protein/excision repair cross-complementation group 6 (CSB/ERCC6) belongs to a subfamily of SWI2/SNF2 (SWItch/sucrose nonfermentable)-related chromatin-remodeling complexes. Defects in the CSB protein result in Cockayne syndrome, which is a rare autosomal-recessive neurologic disorder clinically characterized with progeriod features, growth failure, and photosensitivity. However, it remains poorly understood how the CSB enzymatic activity is regulated for CSB to perform its desired biological functions. Here, we reveal the molecular mechanism of autoinhibition of CSB enzymatic activities. We identify a novel conserved motif (leucine latch motif) that interacts with lobe 2 of the core ATPase domain and hinge region and locks the enzyme into an inactive conformation as a latch. This work provides important novel mechanistic insights into the autoregulation of CSB/ERCC6 proteins.
Correlated variation and population differentiation in satellite DNA abundance among lines of
Drosophila melanogaster
Authors: Wei Kevin H.-C. , Grenier Jennifer K. , Barbash Daniel A. , Clark Andrew G.
Published: December 2014

Significance

Most eukaryotic genomes harbor large amounts of highly repetitive satellite DNA primarily in centromeric regions. Closely related
Drosophila
species have nearly complete turnover of the types and quantities of simple sequence repeats. However, the detailed dynamics of turnover remains unclear, in part due to technical challenges in examining these highly repetitive sequences. We present a method (k-Seek) that identifies and quantifies simple sequence repeats from whole genome sequences. By characterizing natural variation in tandem repeats within
Drosophila melanogaster
, we identified many novel repeats and found that geographically isolated populations show differentiation patterns that are, unexpectedly, incongruous with demographic history. Moreover, repeats undergo correlated change in abundance, providing additional insight into the dynamics of satellite DNA and genome evolution.
Outward-facing conformers of LacY stabilized by nanobodies
Authors: Smirnova Irina , Kasho Vladimir , Jiang Xiaoxu , Pardon Els , Steyaert Jan , Kaback H. Ronald
Published: December 2014

Significance

LacY, a paradigm for the major facilitator superfamily (the largest family of transport proteins) catalyzes the coupled symport of a galactoside and an H
+
. Although a detailed mechanism has been postulated, to test its veracity stable conformers of different intermediates would be particularly informative. Camelid single-domain nanobodies (Nbs), which can stabilize specific conformers, are ∼15 kDa in size and have a unique structure that allows flexible antigen-binding loops to insert into clefts and cavities. Nbs prepared against an outward (periplasmic)-open LacY mutant are described herein. The Nbs bind effectively to WT LacY and inactivate transport by stabilizing the symporter in outward-open conformations with increased accessibility to the sugar-binding site. Moreover, several Nbs dramatically increase affinity for galactosides.
Treacher Collins syndrome TCOF1 protein cooperates with NBS1 in the DNA damage response
Authors: Ciccia Alberto , Huang Jen-Wei , Izhar Lior , Sowa Mathew E. , Harper J. Wade , Elledge Stephen J.
Published: December 2014

Significance

The DNA damage response (DDR) maintains genomic integrity following DNA damage to prevent cancer and developmental disorders. The DDR operates in part through controlling localization of factors to chromatin. Here, we detail an interaction between the DDR protein NBS1 and TCOF1, a nucleolar protein mutated in Treacher Collins syndrome that regulates ribosomal DNA transcription. We show that NBS1 relocalizes to nucleoli after DNA damage in a manner dependent on TCOF1 and independent on the NBS1-associated protein MRE11. This process is regulated by casein kinase II and ATM, two protein kinases that phosphorylate TCOF1 and promote NBS1 nucleolar localization. Our work identifies TCOF1 as a DDR factor that cooperates with NBS1 to preserve genomic stability after DNA damage.
Positive Correlation Between Inhibition of Branchial and Renal Carbonic Anhydrase and Ammonia Produced by Cultured Silver Catfish Rhamdia quelen
Authors: Souza-Bastos Luciana R , Bastos Leonardo P , Freire Carolina A
Published: December 2014

Silver Catfish Rhamdia quelen, a native South American catfish relevant in intensive culture systems in Brazil, were exposed to three ammonia concentrations added to the water (0.5, 1.0, and 2.0 mg/L as ammonium chloride). After 5 and 24 h, measured water ammonia levels increased to maximum levels of 15.8–41.1 mg/L, reflecting the addition of ammonia excreted by the fish. Aquaria were aerated but kept closed, and pH and temperature were kept constant. Hematocrit, plasma ammonia, osmolality, Na+, Cl−, K+, glucose, and cortisol were assayed. Branchial and muscle hydration levels and branchial and renal specific activities of the carbonic anhydrase (CA) were determined. Silver Catfish did not show stress responses or signs of osmoregulatory disturbance upon the increased water ammonia levels. However, there was inhibition of the CA in gills and kidneys, especially after 24 h, in a dose-dependent manner to the total ammonia accumulated in the water. Although Silver Catfish are tolerant of increase in ammonia, care should be taken to limit increases in ammonia levels and time of exposure because the severity of the deleterious effects will certainly increase. In addition, results have shown that the fish carbonic anhydrase (branchial and renal) is a sensitive biomarker of effect of ammonia.
Variability in Size Traits of Sunshine Bass Larvae from Different Male Striped Bass
Authors: Lochmann S E , Goodwin K J
Published: December 2014

We examined the amount of variability in size at hatch and size at yolk absorption among sunshine bass (female White Bass Morone chrysops × male Striped Bass M. saxatilis) due to sire effects. Eggs from a female White Bass were separated into four aliquots. Each aliquot was fertilized by sperm from a different male Striped Bass. Single fertilized eggs were place in 6-mL vials and incubated at 18°C. Eggs were examined every 6 h until the first eggs hatched and every 3 h thereafter. Approximately 50–100 yolk sac larvae were removed from the vials at hatching, photographed, and returned live to the vials when possible. At 5 d posthatch (dph), the remaining larvae were photographed and enumerated. Standard lengths of larvae at hatch and at 5 dph were estimated from photographs. Growth (i.e., increase in length) during the endogenous larval stage was calculated for a subset of individuals photographed at both times. This process was repeated in two subsequent trials. There were significant sire effects for size at hatch (P = 0.003), size at 5 dph (P < 0.001), and growth (P < 0.001). The sire effect explained 3.0–39.0% of the variability in these size traits. Genetic selection for favorable size traits at early life stages among both parent species could lead to larger sunshine bass larvae at yolk absorption and eliminate the need for rotifers at first feeding. Rapid growth at early life stages may be an indicator of rapid growth at later life stages. Efforts to select for rapid growth at several life stages could enhance multiple aspects of the hybrid Striped Bass industry.
Efficacy of Iodine for Disinfection of Lake Sturgeon Eggs from the St. Lawrence River, New York
Authors: Chalupnicki Marc , Dittman Dawn , Starliper Clifford E , Iwanowicz Deborah D
Published: December 2014

Optimal fish husbandry to reduce the risk of disease is particularly important when using wild fish as the source for gametes. The propagation and reestablishment of Lake Sturgeon Acipenser fulvescens in New York waters to become a viable self-sustaining population is considered a high priority by managers. While standard hatchery egg disinfection practices have been used to prevent the transmission of diseases, data on the bacterial loads present on egg surfaces following iodine disinfection is lacking. Our study investigated the bacteria present on the outer surface of Lake Sturgeon eggs and the effectiveness of an iodine disinfection treatment in eliminating bacteria that could pose a threat to egg survival and cause hatchery disease outbreaks. During the springs of 2011–2013, 12 to 41 different species of bacteria were recovered from the outer egg surfaces prior to an iodine treatment; Aeromonas, Pseudomonas, Shewanella, and Chryseobacterium were the most common genera identified. Cohort eggs treated using the standard protocol of a single treatment of 50 mg/L iodine for 30 min resulted in an average of 57.8% reduction in bacterial CFU/g. While this is a significant reduction, bacteria were not completely eliminated and hatchery managers should be aware that pathogens could remain on Lake Sturgeon eggs following the standard iodine disinfection treatment.
Japan's Approach to Peacebuilding in Afghanistan: Money, Diplomacy and the Challenges of Effective Assistance
Authors: Ashizawa Kuniko
Published: December 2014

Japan has been a principal player in international assistance to Afghanistan, ranked second only to the United States in its overall financial assistance disbursed since 2002. This article places a spotlight on the largely underappreciated subject of Japan's primarily non-military and economic infrastructure-oriented assistance by articulating three major characteristics of Japan's policies and practices in Afghanistan — relatively large disbursements for reconstruction programmes, designating disarmament, demobilisation, and reintegration as Japan's niche area, and substantial reliance on international organisations for fund disbursement. Despite its comparatively advantageous position vis-à-vis other donors, Japan has faced a set of institutional and structural impediments to carrying out effective stabilisation and reconstruction assistance, not just in Afghanistan, but also in other conflict-prone and fragile societies. These include, among other things, the shortage of expertise, bureaucratic pressure for ‘cash burning’, inter-agency coordination problems, and waning political interest. As a result, this article argues that Japan has been underequipped to provide peacebuilding assistance on the large scale it committed in Afghanistan. If Tokyo hopes to safeguard its major investments in Afghanistan, it needs to revive the substantive political leadership it exercised in the early years of Afghan peacebuilding.
The Challenging Dynamics of Global North-South Peacebuilding Partnerships: Practitioner Stories from the Field
Authors: Cohen Seth B.
Published: December 2014

Critical dynamics arise when Northern-based outsiders partner with local insiders in the Global South. This article investigates how power asymmetry, funding challenges, and other crucial dynamics impact on North–South partnerships through the lived experiences of both Northern- and Southern-based ‘peacebuilding’ practitioners. Practitioner narratives from Nepal, Sri Lanka, East Timor, Nigeria and Kenya provide insights into the complexities of what it means to be in partnership. Despite the skills of seasoned conflict resolution and peacebuilding professionals to help transform conflict settings, pervasive asymmetry in access to resources and donor relationships leads to problematic dependency. It creates numerous challenges for successful collaboration and vertical coordination between local, national and international actors. The article concludes with several considerations of how peacebuilding practitioners, and their organisations, might improve partnerships, including ways to ‘decolonise’ peacebuilding efforts by further utilising local knowledge, methods and skills, and shifting control over resources and project implementation to local insider-partners.
Iranian bilinguals’ reverse code-switching: an implicit quest for power?
Authors: Ghahari Shima
Published: December 2014

Positioned within the discipline of sociocultural linguistics, this study redefines the concept of code-switching (CS) by focusing on switches to L2 within one’s mainstream speech in L1-a phenomenon called reverse code-switching (RCS). It further studies the role that age, educational background, second language proficiency (SLP), and familiarity with second language culture (FSLC) factors play on these perceptions. Applying a mixed-method approach, a researcher-made instrument was validated through Rasch modeling and exploratory factorial analyses, and the results were computed through a multivariate regression. The older and less educated the audiences, the more they labeled RCS as a symbolic resource. The younger generation and the more educated considered it more as a metaphorical switch. Socially negative attitudes were negatively correlated with SLP, but statistically unaffected by FSLC. The study concludes with a discussion of the results and a body of implications for future research.
Remodeling of secretory compartments creates CUPS during nutrient starvation
Authors: Cruz-Garcia David , Curwin Amy J. , Popoff Jean-François , Bruns Caroline , Duran Juan M. , Malhotra Vivek
Published: December 2014

Upon starvation, Grh1, a peripheral membrane protein located at endoplasmic reticulum (ER) exit sites and early Golgi in Saccharomyces cerevisiae under growth conditions, relocates to a compartment called compartment for unconventional protein secretion (CUPS). Here we report that CUPS lack Golgi enzymes, but contain the coat protein complex II (COPII) vesicle tethering protein Uso1 and the Golgi t-SNARE Sed5. Interestingly, CUPS biogenesis is independent of COPII- and COPI-mediated membrane transport. Pik1- and Sec7-mediated membrane export from the late Golgi is required for complete assembly of CUPS, and Vps34 is needed for their maintenance. CUPS formation is triggered by glucose, but not nitrogen starvation. Moreover, upon return to growth conditions, CUPS are absorbed into the ER, and not the vacuole. Altogether our findings indicate that CUPS are not specialized autophagosomes as suggested previously. We suggest that starvation triggers relocation of secretory and endosomal membranes, but not their enzymes, to generate CUPS to sort and secrete proteins that do not enter, or are not processed by enzymes of the ER–Golgi pathway of secretion.
Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element
Authors: Majumder Kinjal , Koues Olivia I. , Chan Elizabeth A.W. , Kyle Katherine E. , Horowitz Julie E. , Yang-Iott Katherine , Bassing Craig H. , Taniuchi Ichiro , Krangel Michael S. , Oltz Eugene M.
Published: December 2014

Gene regulation relies on dynamic changes in three-dimensional chromatin conformation, which are shaped by composite regulatory and architectural elements. However, mechanisms that govern such conformational switches within chromosomal domains remain unknown. We identify a novel mechanism by which cis-elements promote long-range interactions, inducing conformational changes critical for diversification of the TCRβ antigen receptor locus (Tcrb). Association between distal Vβ gene segments and the highly expressed DβJβ clusters, termed the recombination center (RC), is independent of enhancer function and recruitment of V(D)J recombinase. Instead, we find that tissue-specific folding of Tcrb relies on two distinct architectural elements located upstream of the RC. The first, a CTCF-containing element, directly tethers distal portions of the Vβ array to the RC. The second element is a chromatin barrier that protects the tether from hyperactive RC chromatin. When the second element is removed, active RC chromatin spreads upstream, forcing the tether to serve as a new barrier. Acquisition of barrier function by the CTCF element disrupts contacts between distal Vβ gene segments and significantly alters Tcrb repertoires. Our findings reveal a separation of function for RC-flanking regions, in which anchors for long-range recombination must be cordoned off from hyperactive RC landscapes by chromatin barriers.
Structural model of the open–closed–inactivated cycle of prokaryotic voltage-gated sodium channels
Authors: Bagnéris Claire , Naylor Claire E. , McCusker Emily C. , Wallace B.A.
Published: December 2014

In excitable cells, the initiation of the action potential results from the opening of voltage-gated sodium channels. These channels undergo a series of conformational changes between open, closed, and inactivated states. Many models have been proposed for the structural transitions that result in these different functional states. Here, we compare the crystal structures of prokaryotic sodium channels captured in the different conformational forms and use them as the basis for examining molecular models for the activation, slow inactivation, and recovery processes. We compare structural similarities and differences in the pore domains, specifically in the transmembrane helices, the constrictions within the pore cavity, the activation gate at the cytoplasmic end of the last transmembrane helix, the C-terminal domain, and the selectivity filter. We discuss the observed differences in the context of previous models for opening, closing, and inactivation, and present a new structure-based model for the functional transitions. Our proposed prokaryotic channel activation mechanism is then compared with the activation transition in eukaryotic sodium channels.
Stability of subsea pipelines during large storms
Authors: Draper Scott , An Hongwei , Cheng Liang , White David J. , Griffiths Terry
Published: December 2014

On-bottom stability design of subsea pipelines transporting hydrocarbons is important to ensure safety and reliability but is challenging to achieve in the onerous metocean (meteorological and oceanographic) conditions typical of large storms (such as tropical cyclones, hurricanes or typhoons). This challenge is increased by the fact that industry design guidelines presently give no guidance on how to incorporate the potential benefits of seabed mobility, which can lead to lowering and self-burial of the pipeline on a sandy seabed. In this paper, we demonstrate recent advances in experimental modelling of pipeline scour and present results investigating how pipeline stability can change in a large storm. An emphasis is placed on the initial development of the storm, where scour is inevitable on an erodible bed as the storm velocities build up to peak conditions. During this initial development, we compare the rate at which peak near-bed velocities increase in a large storm (typically less than 10
−3
 m s
−2
) to the rate at which a pipeline scours and subsequently lowers (which is dependent not only on the storm velocities, but also on the mechanism of lowering and the pipeline properties). We show that the relative magnitude of these rates influences pipeline embedment during a storm and the stability of the pipeline.