bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elimination of the antimicrobial action of the organoarsenical cancer therapeutic, 4-(N-(S-glutathionylacetyl)amino) phenylarsonous acid, before finished product sterility testing
Authors: Dick Lindsay J , Gray Andrew , Ram Asha , Hume Aileen , Parris Caroline , Hogg Philip J , Elliott Moira A , Ford Steven J , Halbert Gavin W 
Published: October 2013

Abstract

Objectives
Arsenical compounds have been used therapeutically for over 2000 years finding particular relevance as antimicrobials. After being replaced by more selective and consequently less toxic antibiotics in the last century, arsenicals have recently made a resurgence as anticancer drugs (specifically arsenic trioxide and its derivatives). Arsenical parenteral formulations require post-manufacture sterility testing; however, their intrinsic antimicrobial activity must be neutralised before testing to eliminate the possibility of false (no-growth) test results.

Methods
A range of thiol-containing compounds was screened to establish a suitable deactivation agent for the novel organoarsenical compound, 4-(N-(S-glutathionylacetyl)amino) phenylarsonous acid (GSAO). Dimercatopropanol (DMP) was found to successful deactivate GSAO and was validated according to pharmacopoeial sterility test guidelines (specifically the method suitability test/sterility validation test).

Key findings
DMP is an effective way of deactivating GSAO before sterility testing and can be used for pharmacopoeial sterility tests. Our results affirm previous research highlighting the sensitivity of Staphylococcus aureus to arsenical compounds

Conclusions
A method of deactivating the arsenical drug GSAO before the post-manufacture sterility test was established and validated. DMP is a commonly used chelator/deactivation agent so this work may have implications for other inorganic therapeutic agents.
The RNA‐seq approach to discriminate gene expression profiles in response to melatonin on cucumber lateral root formation
Authors: Zhang Na , Zhang Hai‐Jun , Zhao Bing , Sun Qian‐Qian , Cao Yun‐Yun , Li Ren , Wu Xin‐Xin , Weeda Sarah , Li Li , Ren Shuxin , Reiter Russel J. , Guo Yang‐Dong 
Published: October 2013

AbstractCucumber is a model cucurbitaceous plant with a known genome sequence which is important for studying molecular mechanisms of root development. In this study, RNA sequencing was employed to explore the mechanism of melatonin‐induced lateral root formation in cucumber under salt stress. Three groups of seeds were examined, that is, seeds primed without melatonin (CK), seeds primed in a solution containing 10 or 500 μmol/L melatonin (M10 and M500, respectively). These seeds were then germinated in NaCl solution. The RNA‐seq analysis generated 16,866,670 sequence reads aligned with 17,920 genes, which provided abundant data for the analysis of lateral root formation. A total of 17,552, 17,450, and 17,393 genes were identified from roots of the three treatments (CK, M10 and M500, respectively). The expression of 121 genes was significantly up‐regulated, and 196 genes were significantly down‐regulated in M500 which showed an obvious increase on the number of lateral roots. These genes were significantly enriched in 57 KEGG pathways and 16 GO terms (M500 versus CK). Based on their expression pattern, peroxidase‐related genes were selected as the candidates to be involved in the melatonin response. Several transcription factor families might play important roles in lateral root formation processes. A number of genes related to cell wall formation, carbohydrate metabolic processes, oxidation/reduction processes, and catalytic activity also showed different expression patterns as a result of melatonin treatments. This RNA‐sequencing study will enable the scientific community to better define the molecular processes that affect lateral root formation in response to melatonin treatment.
Extinction and recolonization of maritime Antarctica in the limpet Nacella concinna (Strebel, 1908) during the last glacial cycle: toward a model of Quaternary biogeography in shallow Antarctic invertebrates
Authors: González‐Wevar C. A. , Saucède T. , Morley S. A. , Chown S. L. , Poulin E. 
Published: October 2013

AbstractQuaternary glaciations in Antarctica drastically modified geographical ranges and population sizes of marine benthic invertebrates and thus affected the amount and distribution of intraspecific genetic variation. Here, we present new genetic information in the Antarctic limpet Nacella concinna, a dominant Antarctic benthic species along shallow ice‐free rocky ecosystems. We examined the patterns of genetic diversity and structure in this broadcast spawner along maritime Antarctica and from the peri‐Antarctic island of South Georgia. Genetic analyses showed that N. concinna represents a single panmictic unit in maritime Antarctic. Low levels of genetic diversity characterized this population; its median‐joining haplotype network revealed a typical star‐like topology with a short genealogy and a dominant haplotype broadly distributed. As previously reported with nuclear markers, we detected significant genetic differentiation between South Georgia Island and maritime Antarctica populations. Higher levels of genetic diversity, a more expanded genealogy and the presence of more private haplotypes support the hypothesis of glacial persistence in this peri‐Antarctic island. Bayesian Skyline plot and mismatch distribution analyses recognized an older demographic history in South Georgia. Approximate Bayesian computations did not support the persistence of N. concinna along maritime Antarctica during the last glacial period, but indicated the resilience of the species in peri‐Antarctic refugia (South Georgia Island). We proposed a model of Quaternary Biogeography for Antarctic marine benthic invertebrates with shallow and narrow bathymetric ranges including (i) extinction of maritime Antarctic populations during glacial periods; (ii) persistence of populations in peri‐Antarctic refugia; and (iii) recolonization of maritime Antarctica following the deglaciation process.
Whole‐genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection
Authors: Campo D. , Lehmann K. , Fjeldsted C. , Souaiaia T. , Kao J. , Nuzhdin S. V. 
Published: October 2013

AbstractThe prevailing demographic model for Drosophila melanogaster suggests that the colonization of North America occurred very recently from a subset of European flies that rapidly expanded across the continent. This model implies a sudden population growth and range expansion consistent with very low or no population subdivision. As flies adapt to new environments, local adaptation events may be expected. To describe demographic and selective events during North American colonization, we have generated a data set of 35 individual whole‐genome sequences from inbred lines of D. melanogaster from a west coast US population (Winters, California, USA) and compared them with a public genome data set from Raleigh (Raleigh, North Carolina, USA). We analysed nuclear and mitochondrial genomes and described levels of variation and divergence within and between these two North American D. melanogaster populations. Both populations exhibit negative values of Tajima's D across the genome, a common signature of demographic expansion. We also detected a low but significant level of genome‐wide differentiation between the two populations, as well as multiple allele surfing events, which can be the result of gene drift in local subpopulations on the edge of an expansion wave. In contrast to this genome‐wide pattern, we uncovered a 50‐kilobase segment in chromosome arm 3L that showed all the hallmarks of a soft selective sweep in both populations. A comparison of allele frequencies within this divergent region among six populations from three continents allowed us to cluster these populations in two differentiated groups, providing evidence for the action of natural selection on a global scale.
Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias
Authors: Thomas Austen C. , Jarman Simon N. , Haman Katherine H. , Trites Andrew W. , Deagle Bruce E. 
Published: October 2013

AbstractEcologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high‐throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer's diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical biases introduced during amplicon sequencing and biological biases such as variable gene copy number. Using the Ion Torrent PGM©, we sequenced prey DNA amplified from scats of captive harbour seals (Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals’ diet to generate tissue correction factors (TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate error from 28 ± 15% (uncorrected) to 14 ± 9% (TCF‐corrected). The experimental design also allowed us to infer the magnitude of prey‐specific digestion biases and calculate digestion correction factors (DCFs). The DCFs were compared with possible proxies for differential digestion (e.g. fish protein%, fish lipid%) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey‐specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis.
Simulation‐Optimization Models for the Dynamic Berth Allocation Problem
Authors: Arango Carlos , Cortés Pablo , Onieva Luis , Escudero Alejandro 
Published: October 2013

AbstractContainer terminals (CTs) are designed to provide support for the continuous changes in container ships. The most common schemes used for dock management are based on discrete and continuous locations. In view of the steadily growing trend in increasing container ship size, more flexible berth allocation planning is mandatory. The consideration of continuous location in the CT is a good option. This article addresses the berth allocation problem with continuous dock, which is called dynamic berth allocation problem. We propose a mathematical model and develop a heuristic procedure, based on a genetic algorithm, to solve the corresponding mixed integer problem. Allocation planning aims to minimize distances traveled by the forklifts and the quay crane, for container loading and unloading operations for each ship, according to the quay crane scheduling. Simulations are undertaken using Arena software, and experimental analysis is carried out for the most important CT in Spain.
Oligomerization and higher‐order assembly contribute to sub‐cellular localization of a bacterial scaffold
Authors: Bowman Grant R. , Perez Adam M. , Ptacin Jerod L. , Ighodaro Eseosa , Folta‐Stogniew Ewa , Comolli Luis R. , Shapiro Lucy 
Published: October 2013

SummaryIn Caulobacter crescentus, the PopZ polar scaffold protein supports asymmetric cell division by recruiting distinct sets of binding partners to opposite cell poles. To understand how polar organizing centres are established by PopZ, we investigated a set of mutated PopZ proteins for defects in sub‐cellular localization and recruitment activity. We identified a domain within the C‐terminal 76 amino acids that is necessary and sufficient for accumulation as a single subcellular focus, a domain within the N‐terminal 23 amino acids that is necessary for bipolar targeting, and a linker domain between these localization determinants that tolerates large variation. Mutations that inhibited dynamic PopZ localization inhibited the recruitment of other factors to cell poles. Mutations in the C‐terminal domain also blocked discrete steps in the assembly of higher‐order structures. Biophysical analysis of purified wild type and assembly defective mutant proteins indicates that PopZ self‐associates into an elongated trimer, which readily forms a dimer of trimers through lateral contact. The final six amino acids of PopZ are necessary for connecting the hexamers into filaments, and these structures are important for sub‐cellular localization. Thus, PopZ undergoes multiple orders of self‐assembly, and the formation of an interconnected superstructure is a key feature of polar organization in Caulobacter.
Comamonas testosteroni uses a chemoreceptor for tricarboxylic acid cycle intermediates to trigger chemotactic responses towards aromatic compounds
Authors: Ni Bin , Huang Zhou , Fan Zheng , Jiang Cheng‐Ying , Liu Shuang‐Jiang 
Published: October 2013

SummaryBacterial chemotaxis towards aromatic compounds has been frequently observed; however, knowledge of how bacteria sense aromatic compounds is limited. Comamonas testosteroni CNB‐1 is able to grow on a range of aromatic compounds. This study investigated the chemotactic responses of CNB‐1 to 10 aromatic compounds. We constructed a chemoreceptor‐free, non‐chemotactic mutant, CNB‐1Δ20, by disruption of all 19 putative methyl‐accepting chemotaxis proteins (MCPs) and the atypical chemoreceptor in strain CNB‐1. Individual complementation revealed that a putative MCP (tagged MCP2201) was involved in triggering chemotaxis towards all 10 aromatic compounds. The recombinant sensory domain of MCP2201 did not bind to 3‐ or 4‐hydroxybenzoate, protocatechuate, catechol, benzoate, vanillate and gentisate, but bound oxaloacetate, citrate, cis‐aconitate, isocitrate, α‐ketoglutarate, succinate, fumarate and malate. The mutant CNB‐1ΔpmdF that lost the ability to metabolize 4‐hydroxybenzoate and protocatechuate also lost its chemotactic response to these compounds, suggesting that taxis towards aromatic compounds is metabolism‐dependent. Based on the ligand profile, we proposed that MCP2201 triggers taxis towards aromatic compounds by sensing TCA cycle intermediates. Our hypothesis was further supported by the finding that introduction of the previously characterized pseudomonad chemoreceptor (McpS) for TCA cycle intermediates into CNB‐1Δ20 likewise triggered chemotaxis towards aromatic compounds.
The putative Poc complex controls two distinct Pseudomonas aeruginosa polar motility mechanisms
Authors: Cowles Kimberly N. , Moser Theresa S. , Siryaporn Albert , Nyakudarika Natsai , Dixon William , Turner Jonathan J. , Gitai Zemer 
Published: October 2013

SummaryEach Pseudomonas aeruginosa cell localizes two types of motility structures, a single flagellum and one or two clusters of type IV pili, to the cell poles. Previous studies suggested that these motility structures arrive at the pole through distinct mechanisms. Here we performed a swimming motility screen to identify polar flagellum localization factors and discovered three genes homologous to the TonB/ExbB/ExbD complex that have defects in both flagella‐mediated swimming and pilus‐mediated twitching motility. We found that deletion of tonB3, PA2983 or PA2982 led to non‐polar localization of the flagellum and FlhF, which was thought to sit at the top of the flagellar localization hierarchy. Surprisingly, these mutants also exhibited pronounced changes in pilus formation or localization, indicating that these proteins may co‐ordinate both the pilus and flagellum motility systems. Thus, we have renamed PA2983 and PA2982, pocA and pocB, respectively, for polar organelle co‐ordinator to reflect this function. Our results suggest that TonB3, PocA and PocB may form a membrane‐associated complex, which we term the Poc complex. These proteins do not exhibit polar localization themselves, but are required for increased expression of pilus genes upon surface association, indicating that they regulate motility structures through either localization or transcriptional mechanisms.
Organizational support in the recruitment and transition of overseas‐qualified nurses: Lessons learnt from a study tour
Authors: Ohr Se Ok , Jeong Sarah , Parker Vicki , McMillan Margaret 
Published: October 2013

AbstractThe migration of nurses has been a global phenomenon, and the integration of overseas‐qualified nurses within host countries has led to debate worldwide. Evidence suggests that support provided by organizations can vary and that there is minimal information on the nature and extent of organizational support required to enhance a smooth transition of overseas‐qualified nurses into nursing practice. This explorative study tour examined the organizational support provided to enhance overseas‐qualified nurses' transition into the nursing workforce in two countries. The various support mechanisms provided to overseas‐qualified nurses in different organizations include transition, acculturation, mentoring programs, and initial settlement assistance. The successful transition of overseas‐qualified nurses into a host country is a complex issue. A robust support system for these nurses should be based on ethical considerations and a team approach that is linked to strong leadership. In addition, education and support for existing staff is essential for a successful transition of overseas‐qualified nurses into practice. Lessons learnt from this study tour might also be relevant to the transition of other overseas‐qualified health professionals, such as doctors and allied health professionals, in host countries.
Isoprene emission protects photosynthesis but reduces plant productivity during drought in transgenic tobacco (Nicotiana tabacum) plants
Authors: Ryan Annette C. , Hewitt C. Nicholas , Possell Malcolm , Vickers Claudia E. , Purnell Anna , Mullineaux Philip M. , Davies William J. , Dodd Ian C. 
Published: October 2013

Summary

Isoprene protects the photosynthetic apparatus of isoprene‐emitting plants from oxidative stress. The role of isoprene in the response of plants to drought is less clear.

Water was withheld from transgenic isoprene‐emitting and non‐emitting tobacco (Nicotiana tabacum) plants, to examine: the response of isoprene emission to plant water deficit; a possible relationship between concentrations of the drought‐induced phytohormone abscisic acid (ABA) and isoprene; and whether isoprene affected foliar reactive oxygen species (ROS) and lipid peroxidation levels.

Isoprene emission did not affect whole‐plant water use, foliar ABA concentration or leaf water potential under water deficit. Compared with well‐watered controls, droughted non‐emitting plants significantly increased ROS content (31–46%) and lipid peroxidation (30–47%), concomitant with decreased operating and maximum efficiencies of photosystem II photochemistry and lower leaf and whole‐plant water use efficiency (WUE). Droughted isoprene‐emitting plants showed no increase in ROS content or lipid peroxidation relative to well‐watered controls, despite isoprene emission decreasing before leaf wilting.

Although isoprene emission protected the photosynthetic apparatus and enhanced leaf and whole‐plant WUE, non‐emitting plants had 8–24% more biomass under drought, implying that isoprene emission incurred a yield penalty.
Indirect effects drive evolutionary responses to global change
Authors: Lau Jennifer A. , Shaw Ruth G. , Reich Peter B. , Tiffin Peter 
Published: October 2013

SummaryAnthropogenic environmental changes pose significant threats to plant and animal populations. These changes also may affect the evolution of natural populations either directly or indirectly by altering the outcome of species interactions that are important drivers of evolution. This latter indirect pathway may be especially important for evolutionary responses to elevated atmosphericCO2concentrations (eCO2), which appear to have minimal direct effects on plant evolution but have large effects on interspecific interactions, such as competition.We manipulated competitive andCO2environments of experimentalArabidopsis thalianapopulations to test whethereCO2alters evolutionary trajectories indirectly by altering selection imposed by competitors.We found that interspecific competition increased selection on growth traits, reduced heritabilities, and altered genetic covariances between traits and that the magnitude of these effects depended upon theCO2environment. Although eCO2had minimal direct effects on evolutionary processes, eCO2typically reduced the strength of selection imposed by competitors and, therefore, relaxed selection on plant traits when competitors were present.Our results indicate that global changes may affect plant evolution indirectly by altering competitive interactions and underscore the importance of conducting research in natural communities when attempting to predict population responses to global change.
Combinatorial functions of diverse histone methylations in Arabidopsis thaliana flowering time regulation
Authors: Shafiq Sarfraz , Berr Alexandre , Shen Wen‐Hui 
Published: October 2013

Summary

Previous studies in Arabidopsis thaliana have identified several histone methylation enzymes, including ARABIDOPSIS TRITHORAX1 (ATX1)/SET DOMAIN GROUP 27 (SDG27), ATX2/SDG30, LSD1‐LIKE1 (LDL1), LDL2, SDG8, SDG25, and CURLY LEAF (CLF)/SDG1, as regulators of the key flowering repressor FLOWERING LOCUS C (FLC) and the florigen FLOWERING LOCUS T (FT). However, the combinatorial functions of these enzymes remain largely uninvestigated.

Here, we investigated functional interplays of different histone methylation enzymes by studying higher order combinations of their corresponding gene mutants.

We showed that H3K4me2/me3 and H3K36me3 depositions occur largely independently and that SDG8‐mediated H3K36me3 overrides ATX1/ATX2‐mediated H3K4me2/me3 or LDL1/LDL2‐mediated H3K4 demethylation in regulating FLC expression and flowering time. By contrast, a reciprocal inhibition was observed between deposition of the active mark H3K4me2/me3 and/or H3K36me3 and deposition of the repressive mark H3K27me3 at both FLC and FT chromatin; and the double mutants sdg8 clf and sdg25 clf displayed enhanced early‐flowering phenotypes of the respective single mutants.

Collectively, our results provide important insights into the interactions of different types of histone methylation and enzymes in the regulation of FLC and FT expression in flowering time control.
N‐acyl‐homoserine lactone uptake and systemic transport in barley rest upon active parts of the plant
Authors: Sieper Tina , Forczek Sandor , Matucha Miroslav , Krämer Petra , Hartmann Anton , Schröder Peter 
Published: October 2013

Summary

Bacteria communicate with each other in a population density‐dependent process known as quorum sensing. N‐acyl‐homoserine lactones (HSLs) are the autoinducers of Gram‐negative bacteria and the best‐studied quorum sensing signals so far. HSLs induce various responses in plants, including systemic resistance and root development.

Here, we used different methods, including tritium labelling, sensor strain assays and monoclonal antibodies (mAbs), to analyse the uptake and translocation of C8‐ and C10‐ homoserine lactones into barley (Hordeum vulgare cv Barke).

Both HSLs were already systemically transported into the shoot at 2 h after application. HSL uptake could be inhibited by orthovanadate, demonstrating that ABC transporters are involved in the uptake. Root transport occurs predominantly via the central cylinder, which was shown by transport inhibition via KCl application and autoradiography of root cross‐sections. Furthermore, a newly established detection method with mAbs allowed the first detection of a systemic transport of long‐chain HSLs in plants.

The coupled use of different HSL detection methods demonstrated that the uptake and transport of HSLs into barley does not occur passively, but relies, at least partially, on active processes in the plant.