bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Protective Efficacy between Formalin‐killed and aroA Gene‐knockout Vibrio anguillarum Vaccines in Olive Flounder, Paralichthys olivaceus
Authors: Choi Seung Hyuk , Kim Dong Soo , Kim Ki Hong 
Published: March 2017

AbstractThe aro genes in bacteria encode enzymes needed for the biosynthesis of aromatic amino acids, and mutant bacteria that are defective in the enzymes can replicate only a limited number in vertebrates owing to the lack or scarceness of chorismate, through which the mutant bacteria of the aro genes become attenuated. In the present study, the 5‐enolpyruvylshikimate‐3‐phosphate synthase (aroA) gene‐knockout Vibrio anguillarum (ΔaroA V. anguillarum) were generated by the allelic exchange method, and its vaccine potential was evaluated in the olive flounder, Paralichthys olivaceus, by comparing the protective efficacy of a formalin‐inactivated V. anguillarum. The LD50 (50% lethal dose) value of ΔaroA V. anguillarum was 1000 times higher than that of wild‐type V. anguillarum in olive flounder fingerlings, and the growth of ΔaroA V. anguillarum was significantly suppressed by coincubation with nonimmune olive flounder serum compared with that of wild‐type V. anguillarum. The survival rates and serum agglutination titers of fish immunized with ΔaroA V. anguillarum were significantly higher than those of fish immunized with the same amount of formalin‐inactivated V. anguillarum, suggesting that although the inactivated V. anguillarum vaccine can provide a high protection in olive flounder, the protective efficacy can be enhanced by immunization with an auxotrophic mutant ΔaroA V. anguillarum.
Methionine Requirement for Juvenile White Seabass, Atractoscion nobilis, Using Nonlinear Models
Authors: Salze Guillaume P. , Davis Donald A. , Jirsa Dave O. , Drawbridge Mark A. 
Published: March 2017

AbstractTwo trials were conducted to estimate the methionine (Met) requirement of juvenile white seabass, Atractoscion nobilis. Diets were formulated to contain 40% crude protein, 10% lipids, and 0.51% cysteine. Graded levels of dl‐Met were added to create seven diets with dietary Met levels ranging from 0.72 to 0.98%, and nine diets ranging from 0.64 to 1.28% Met in Trials A and B, respectively. Thermal‐unit growth coefficient was fitted to dietary Met levels to estimate the Met requirement using the saturation kinetic model (SKM), the quadratic model (QM), or the broken quadratic model (BQM). The 95% confidence interval (CI) was estimated through the iterative fitting process for the BQM and using a bootstrapping approach for the QM and SKM. In Trial A, the three models estimated the requirement between 0.88 and 1.08%, with wide CI. In Trial B, precisions of the requirement estimates by the SKM and BQM were significantly improved compared with Trial A, though BQM evidently overestimated the requirement. SKM provided the best fit; hence, we conclude that the Met requirement for juvenile white seabass is 0.88% (95% CI: 0.80–1.08%) in the presence of 0.51% cysteine. This estimate provides valuable basis for the formulation of practical diets for juvenile white seabass.
The Vakkejokk Breccia: An Early Cambrian proximal impact ejecta layer in the North‐Swedish Caledonides
Authors: Ormö J. , Nielsen A. T. , Alwmark C. 
Published: March 2017

AbstractThe ≤27 m thick Vakkejokk Breccia is intercalated in autochthon Lower Cambrian along the Caledonian front north of Lake Torneträsk, Lapland, Sweden. The spectacular breccia is here interpreted as a proximal ejecta layer associated with an impact crater, probably ~2–3 km in size, located below Caledonian overthrusts immediately north of the main breccia section. The impact would have taken place in a shallow‐marine environment ~520 Ma ago. The breccia comprises i) a strongly disturbed lower polymict subunit with occasional, in themselves brecciated, crystalline mega‐clasts locally exceeding 50 m surrounded by contorted sediments; ii) a middle, commonly normally graded, crystalline‐rich, polymict subunit, in turn locally overlain by iii) a thin fine‐grained quartz sandstone, <30 cm thick. The upper sandstone is sporadically either overlain, or replaced, by a conglomerate. In progressively more distal parts of the ejecta layer, the lower subunit is better described as only slightly disturbed strata. The lower subunit is suggested to have formed by ejecta bombardment of the strata surrounding the impact crater, even causing some net outwards mobilization of the sediments. The middle subunit and the uppermost quartz sandstone are considered resurge deposits. The top conglomerate may be caused by subsequent wave reworking and slumping of material from the elevated rim. Quartz grains showing planar deformation features are present in the graded polymict subunit and the upper sandstone, that is, the inferred resurge deposits.
Signatures of local adaptation in lowland and highland teosintes from whole‐genome sequencing of pooled samples
Authors: Fustier M.‐A. , Brandenburg J.‐T. , Boitard S. , Lapeyronnie J. , Eguiarte L. E. , Vigouroux Y. , Manicacci D. , Tenaillon M. I. 
Published: March 2017

AbstractSpatially varying selection triggers differential adaptation of local populations. Here, we mined the determinants of local adaptation at the genomewide scale in the two closest maize wild relatives, the teosintes Zea mays ssp parviglumis and ssp. mexicana. We sequenced 120 individuals from six populations: two lowland, two intermediate and two highland populations sampled along two altitudinal gradients. We detected 8 479 581 single nucleotide polymorphisms (SNPs) covered in the six populations with an average sequencing depth per site per population ranging from 17.0× to 32.2×. Population diversity varied from 0.10 to 0.15, and linkage disequilibrium decayed very rapidly. We combined two differentiation‐based methods, and correlation of allele frequencies with environmental variables to detect outlier SNPs. Outlier SNPs displayed significant clustering. From clusters, we identified 47 candidate regions. We further modified a haplotype‐based method to incorporate genotype uncertainties in haplotype calling, and applied it to candidate regions. We retrieved evidence for selection at the haplotype level in 53% of our candidate regions, and in 70% of the cases the same haplotype was selected in the two lowland or the two highland populations. We recovered a candidate region located within a previously characterized inversion on chromosome 1. We found evidence of a soft sweep at a locus involved in leaf macrohair variation. Finally, our results revealed frequent colocalization between our candidate regions and loci involved in the variation of traits associated with plant–soil interactions such as root morphology, aluminium and low phosphorus tolerance. Soil therefore appears to be a major driver of local adaptation in teosintes.
Characterization of lysine acetylation of a phosphoenolpyruvate carboxylase involved in glutamate overproduction in Corynebacterium glutamicum
Authors: Nagano‐Shoji Megumi , Hamamoto Yuma , Mizuno Yuta , Yamada Ayuka , Kikuchi Masaki , Shirouzu Mikako , Umehara Takashi , Yoshida Minoru , Nishiyama Makoto , Kosono Saori 
Published: March 2017

SummaryProtein Nε‐acylation is emerging as a ubiquitous post‐translational modification. In Corynebacterium glutamicum, which is utilized for industrial production of l‐glutamate, the levels of protein acetylation and succinylation change drastically under the conditions that induce glutamate overproduction. Here, the acylation of phosphoenolpyruvate carboxylase (PEPC), an anaplerotic enzyme that supplies oxaloacetate for glutamate overproduction was characterized. It was shown that acetylation of PEPC at lysine 653 decreased enzymatic activity, leading to reduced glutamate production. An acetylation‐mimic (KQ) mutant of K653 showed severely reduced glutamate production, while the corresponding KR mutant showed normal production levels. Using an acetyllysine‐incorporated PEPC protein, we verified that K653‐acetylation negatively regulates PEPC activity. In addition, NCgl0616, a sirtuin‐type deacetylase, deacetylated K653‐acetylated PEPC in vitro. Interestingly, the specific activity of PEPC was increased during glutamate overproduction, which was blocked by the K653R mutation or deletion of sirtuin‐type deacetylase homologues. These findings suggested that deacetylation of K653 by NCgl0616 likely plays a role in the activation of PEPC, which maintains carbon flux under glutamate‐producing conditions. PEPC deletion increased protein acetylation levels in cells under glutamate‐producing conditions, supporting the hypothesis that PEPC is responsible for a large carbon flux change under glutamate‐producing conditions.
Involvement of a conserved GFG motif region in substrate binding by RseP, an Escherichia coliS2P protease
Authors: Akiyama Koichiro , Hizukuri Yohei , Akiyama Yoshinori 
Published: March 2017

SummaryRseP, an Escherichia coli S2P family intramembrane cleaving protease, is involved in regulation of the extracytoplasmic stress response and membrane quality control through specific cleavage of substrates. Recent research suggested that the PDZ domains and the MRE β‐loop (membrane‐reentrant β‐loop) are involved in substrate discrimination; the former would serve to prevent cleavage of substrates with a large periplasmic domain, whereas the latter would directly interact with the substrate's transmembrane segment and induce its conformational change. However, the mechanisms underlying specific substrate recognition and cleavage by RseP are not fully understood. Here, the roles of the N‐terminal part of the first cytoplasmic loop region (C1N) of RseP that contains a highly conserved GFG motif were investigated. A Cys modifiability assay suggested that C1N is partly membrane‐inserted like the MRE β‐loop. Pro, but not Cys, substitutions in the GFG motif region compromised the proteolytic function of RseP, suggesting the importance of a higher order structure of this motif region. Several lines of evidence indicated that the GFG motif region directly interacts with the substrate and also aids the function of the MRE β‐loop that participates in substrate recognition by RseP. These findings provide insights into the substrate recognition mechanisms of S2P proteases.
The processive kinetics of gene conversion in bacteria
Authors: Paulsson Johan , El Karoui Meriem , Lindell Monica , Hughes Diarmaid 
Published: March 2017

SummaryGene conversion, non‐reciprocal transfer from one homologous sequence to another, is a major force in evolutionary dynamics, promoting co‐evolution in gene families and maintaining similarities between repeated genes. However, the properties of the transfer – where it initiates, how far it proceeds and how the resulting conversion tracts are affected by mismatch repair – are not well understood. Here, we use the duplicate tuf genes in Salmonella as a quantitatively tractable model system for gene conversion. We selected for conversion in multiple different positions of tuf, and examined the resulting distributions of conversion tracts in mismatch repair‐deficient and mismatch repair‐proficient strains. A simple stochastic model accounting for the essential steps of conversion showed excellent agreement with the data for all selection points using the same value of the conversion processivity, which is the only kinetic parameter of the model. The analysis suggests that gene conversion effectively initiates uniformly at any position within a tuf gene, and proceeds with an effectively uniform conversion processivity in either direction limited by the bounds of the gene.
Molting phenology of the Pacific harbor seal (Phoca vitulina richardii) on two islands off the Baja California Peninsula, Mexico
Authors: Tapia‐Harris Claudia , Heckel Gisela , Schramm Yolanda , Fernández‐Martín Eva María 
Published: March 2017

AbstractWe document and compare the annual molt of the Pacific harbor seal (Phoca vitulina richardii) on two islands off the west coast of the Baja California Peninsula that are the northern and southern extremes of its distribution in Mexico. During 2014, observations were made from March to July on Todos Santos Island (northern extreme) and from January to June on San Roque Island (southern extreme). On Todos Santos, the premolt lasted 15 wk (March–June) and the molt 12 wk (April–July). On San Roque, the premolt lasted 22 wk (January–June) and the molt 17 wk (February–June). The proportion of seals undergoing molt peaked on 26 May on Todos Santos and on 7 June on San Roque. Shedding of old hair most commonly initiated on the torso and progressed to the head and flippers (reverse molting pattern). The period when the highest number of harbor seals haul out in Mexico is in late April on the more southerly islands and in early May on the more northerly islands, when a large proportion of seals are in premolt.
Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification
Authors: Pawar Prashant Mohan‐Anupama , Ratke Christine , Balasubramanian Vimal K. , Chong Sun‐Li , Gandla Madhavi Latha , Adriasola Mathilda , Sparrman Tobias , Hedenström Mattias , Szwaj Klaudia , Derba‐Maceluch Marta , Gaertner Cyril , Mouille Gregory , Ezcurra Ines , Tenkanen Maija , Jönsson Leif J. , Mellerowicz Ewa J. 
Published: March 2017

Summary

High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production.

We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification.

The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA‐A and ‐B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21. Histochemical analysis of promoter::GUS lines in hybrid aspen (Populus tremula × tremuloides) showed activation of RWA‐A and ‐B promoters in the secondary wall formation zone, while RWA‐C and ‐D promoter activity was diffuse. Ectopic downregulation of either clade reduced wood xylan and xyloglucan acetylation. Suppressing both clades simultaneously using the wood‐specific promoter reduced wood acetylation by 25% and decreased acetylation at position 2 of Xylp in the dimethyl sulfoxide‐extracted xylan. This did not affect plant growth but decreased xylose and increased glucose contents in the noncellulosic monosaccharide fraction, and increased glucose and xylose yields of wood enzymatic hydrolysis without pretreatment.

Both RWA clades regulate wood xylan acetylation in aspen and are promising targets to improve wood saccharification.
Adjusting phenotypes via within‐ and across‐generational plasticity
Authors: Auge Gabriela A. , Leverett Lindsay D. , Edwards Brianne R. , Donohue Kathleen 
Published: March 2017

SummaryThere is renewed interest in how transgenerational environmental effects, including epigenetic inheritance, contribute to adaptive evolution. The contribution of across‐generation plasticity to adaptation, however, needs to be evaluated within the context of within‐generation plasticity, which is often proposed to contribute more efficiently to adaptation because of the potentially greater accuracy of progeny than parental cues to predict progeny selective environments. We highlight recent empirical studies of transgenerational plasticity, and find that they do not consistently support predictions based on the higher predictive ability of progeny environmental cues. We discuss these findings within the context of the relative predictive ability of maternal and progeny cues, costs and constraints of plasticity in parental and progeny generations, and the dynamic nature of the adaptive value of within‐ and across‐generation plasticity that varies with the process of adaptation itself. Such contingent and dynamically variable selection could account for the diversity of patterns of within‐ and across‐generation plasticity observed in nature, and can influence the adaptive value of the persistence of environmental effects across generations.

Contents

Summary
343

I.
Introduction
343

II.
When are responses to parental vs progeny environmental cues adaptive?
343

III.
Constraints, costs and conflicts
347

IV.
Conclusions
348

Acknowledgements
348

References
348
Disentangling above‐ and below‐ground facilitation drivers in arid environments: the role of soil microorganisms, soil properties and microhabitat
Authors: Lozano Yudi M. , Armas Cristina , Hortal Sara , Casanoves Fernando , Pugnaire Francisco I. 
Published: March 2017

Summary

Nurse plants promote establishment of other plant species by buffering climate extremes and improving soil properties. Soil biota plays an important role, but an analysis to disentangle the effects of soil microorganisms, soil properties and microclimate on facilitation is lacking.

In three microhabitats (gaps, small and large Retama shrubs), we placed six microcosms with sterilized soil, two per soil origin (i.e. from each microhabitat). One in every pair received an alive, and the other a sterile, inoculum from its own soil. Seeds of annual plants were sown into the microcosms. Germination, survival and biomass were monitored. Soil bacterial communities were characterized by pyrosequencing.

Germination in living Retama inoculum was nearly double that of germination in sterile inoculum. Germination was greater under Retama canopies than in gaps. Biomass was up to three times higher in nurse than in gap soils. Soil microorganisms, soil properties and microclimate showed a range of positive to negative effects on understory plants depending on species identity and life stage.

Nurse soil microorganisms promoted germination, but the effect was smaller than the positive effects of soil properties and microclimate under nurses. Nurse below‐ground environment (soil properties and microorganisms) promoted plant growth and survival more than nurse microhabitat.
Covariation and phenotypic integration in chemical communication displays: biosynthetic constraints and eco‐evolutionary implications
Authors: Junker Robert R. , Kuppler Jonas , Amo Luisa , Blande James D. , Borges Renee M. , van Dam Nicole M. , Dicke Marcel , Dötterl Stefan , Ehlers Bodil K. , Etl Florian , Gershenzon Jonathan , Glinwood Robert , Gols Rieta , Groot Astrid T. , Heil Martin , Hoffmeister Mathias , Holopainen Jarmo K. , Jarau Stefan , John Lena , Kessler Andre , Knudsen Jette T. , Kost Christian , Larue‐Kontic Anne‐Amélie C. , Leonhardt Sara Diana , Lucas‐Barbosa Dani , Majetic Cassie J. , Menzel Florian , Parachnowitsch Amy L. , Pasquet Rémy S. , Poelman Erik H. , Raguso Robert A. , Ruther Joachim , Schiestl Florian P. , Schmitt Thomas , Tholl Dorothea , Unsicker Sybille B. , Verhulst Niels , Visser Marcel E. , Weldegergis Berhane T. , Köllner Tobias G. 
Published: March 2017

SummaryChemical communication is ubiquitous. The identification of conserved structural elements in visual and acoustic communication is well established, but comparable information on chemical communication displays (CCDs) is lacking.We assessed the phenotypic integration of CCDs in a meta‐analysis to characterize patterns of covariation in CCDs and identified functional or biosynthetically constrained modules.Poorly integrated plant CCDs (i.e. low covariation between scent compounds) support the notion that plants often utilize one or few key compounds to repel antagonists or to attract pollinators and enemies of herbivores. Animal CCDs (mostly insect pheromones) were usually more integrated than those of plants (i.e. stronger covariation), suggesting that animals communicateviafixed proportions among compounds. Both plant and animal CCDs were composed of modules, which are groups of strongly covarying compounds. Biosynthetic similarity of compounds revealed biosynthetic constraints in the covariation patterns of plant CCDs.We provide a novel perspective on chemical communication and a basis for future investigations on structural properties of CCDs. This will facilitate identifying modules and biosynthetic constraints that may affect the outcome of selection and thus provide a predictive framework for evolutionary trajectories of CCDs in plants and animals.
Business Experts on Public Sector Boards: What Do They Contribute?
Authors: Kirkpatrick Ian , Vallascas Francesco , Veronesi Gianluca 
Published: March 2017

AbstractAlthough public management reforms around the world have given business experts an enhanced role in the governance of public sector organizations, the impact of this change is poorly understood. Drawing from the literature on board human capital as a theoretical framework and focusing on the case of hospital boards in the English National Health Service, this concern is addressed by investigating whether increasing the presence of individuals with business expertise has any significant relationship with organizational performance. The findings show that while business expertise appears to have no influence on service quality, it does have a positive effect on financial performance. However, this only applies to governing boards that are less experienced in terms of their collective tenure. The findings lend partial support to board capital theory but also show that in certain conditions generic business expertise can be a valuable asset for public sector organizations.
The beginnings of comparative anatomy and Renaissance reflections on the human–animal divide
Authors: Arbel Benjamin 
Published: March 2017

AbstractThis essay is part of a larger research project on Renaissance attitudes to animals. It considers the extent to which early developments in the new field of comparative anatomy were influenced by Renaissance discussions concerning the nature and capacities of animals, compared to those of humans. It mainly focuses on the writings of Leonardo da Vinci (1452–1519), Andreas Vesalius (1514–64), Pierre Belon du Mans (1517–64) and Girolamo Fabrici di Acquapendente (c. 1533–1619), all of whom can be considered as pioneers in the field of comparative anatomy. The insights that they derived from their experience in dissections of animal bodies are examined against the background of changing sensitivities with regard to animals, which have already been observed in other writings of the same period, particularly literary ones. Rather than going into a detailed comparison of anatomical findings, this essay focuses on perceptions that transcended strictly anatomical knowledge, particularly on reflections concerning the animal soul, animal intelligence and animal speech that were expressed in the writings of the above‐mentioned protagonists.