bluuebunny/crossref_metadata_2025_split huggingface dataset:
A highly efficient sulfadiazine selection system for the generation of transgenic plants and algae
Authors: Tabatabaei Iman , Dal Bosco Cristina , Bednarska Marta , Ruf Stephanie , Meurer Jörg , Bock Ralph 
Published: August 2018

SummaryThe genetic transformation of plant cells is critically dependent on the availability of efficient selectable marker gene. Sulfonamides are herbicides that, by inhibiting the folic acid biosynthetic pathway, suppress the growth of untransformed cells. Sulfonamide resistance genes that were previously developed as selectable markers for plant transformation were based on the assumption that, in plants, the folic acid biosynthetic pathway resides in the chloroplast compartment. Consequently, the Sul resistance protein, a herbicide‐insensitive dihydropteroate synthase, was targeted to the chloroplast. Although these vectors produce transgenic plants, the transformation efficiencies are low compared to other markers. Here, we show that this inefficiency is due to the erroneous assumption that the folic acid pathway is located in chloroplasts. When the RbcS transit peptide was replaced by a transit peptide for protein import into mitochondria, the compartment where folic acid biosynthesis takes place in yeast, much higher resistance to sulfonamide and much higher transformation efficiencies are obtained, suggesting that current sul vectors are likely to function due to low‐level mistargeting of the resistance protein to mitochondria. We constructed a series of optimized transformation vectors and demonstrate that they produce transgenic events at very high frequency in both the seed plant tobacco and the green alga Chlamydomonas reinhardtii. Co‐transformation experiments in tobacco revealed that sul is even superior to nptII, the currently most efficient selectable marker gene, and thus provides an attractive marker for the high‐throughput genetic transformation of plants and algae.
Worker Absenteeism: Peer Influences, Monitoring and Job Flexibility
Authors: Johansson Per , Karimi Arizo , Peter Nilsson J. 
Published: August 2018

SummaryWe study the presence of other-regarding preferences in the workplace by exploiting a randomized experiment that changed the monitoring of workers’ health during sick leave. We show that workers’ response to an increase in co-worker shirking, induced by the experiment, is much stronger than the response to a decrease in co-worker shirking. The asymmetric spillover effects are consistent with evidence of fairness concerns documented in laboratory experiments. Moreover, we find that the spillover effect is driven by workers with highly flexible and autonomous jobs, suggesting that co-worker monitoring may be at least as important as formal monitoring in alleviating shirking.
Full Likelihood Inference for Abundance from Continuous Time Capture–Recapture Data
Authors: Liu Yang , Liu Yukun , Li Pengfei , Qin Jing 
Published: August 2018

SummaryCapture–recapture experiments are widely used cost-effective sampling techniques for estimating population sizes or abundances in biology, ecology, demography, epidemiology and reliability studies. For continuous time capture–recapture data, existing estimation methods are based on conditional likelihoods and an inverse weighting estimating equation. The corresponding Wald-type confidence intervals for the abundance may have severe undercoverage, and their lower limits can be below the number of individuals captured. We propose a full likelihood inference approach by combining a parametric or partial likelihood with the empirical likelihood. Under both parametric and semiparametric intensity models, we demonstrate that the maximum likelihood estimator attains the semiparametric efficiency lower bound and that the full likelihood ratio statistic for the abundance is asymptotically χ2 with 1 degree of freedom. Simulations indicate that compared with conditional-likelihood-based methods, the maximum full likelihood estimator has a smaller mean-square error, and the likelihood ratio confidence intervals often have remarkable gains in coverage probability. We illustrate the advantages of the proposed approach by analysing illegal immigrant data for the Netherlands and Prinia flaviventris data from Hong Kong.
Formation of magnesium‐smectite during lacustrine carbonates early diagenesis: Study case of the volcanic crater lake Dziani Dzaha (Mayotte – Indian Ocean)
Authors: Milesi Vincent P. , Jézéquel Didier , Debure Mathieu , Cadeau Pierre , Guyot François , Sarazin Gérard , Claret Francis , Vennin Emmanuelle , Chaduteau Carine , Virgone Aurélien , Gaucher Eric C. , Ader Magali 
Published: August 2018

AbstractThe volcanic crater lake of Dziani Dzaha in Mayotte is studied to constrain the geochemical settings and the diagenetic processes at the origin of Mg‐phyllosilicates associated with carbonate rocks. The Dziani Dzaha is characterized by intense primary productivity, volcanic gases bubbling in three locations and a volcanic catchment of phonolitic/alkaline composition. The lake water has an alkalinity of ca 0·2 mol l−1 and pH values of ca 9·3. Cores of the lake sediments reaching up to one metre in length were collected and studied by means of carbon–hydrogen–nitrogen elemental analyzer, X‐ray fluorescence spectrometry and X‐ray powder diffraction. In surface sediments, the content of total organic carbon reaches up to 20 weight %. The mineral content consists of aragonite and hydromagnesite with minor amounts of alkaline feldspar and clinopyroxene from the volcanic catchment. Below 30 cm depth, X‐ray diffraction analyses of the <2 μm clay fraction indicate the presence of a saponite‐like mineral, a Mg‐rich smectite. The saponite‐like mineral accumulates at depth to reach up to ca 30 weight %, concurrent with a decrease of the contents of hydromagnesite and organic matter. Thermodynamic considerations and mineral assemblages suggest that the evolution of the sediment composition resulted from early diagenetic reactions. The formation of the saponite‐like mineral instead of Al‐free Mg‐silicates resulted from high aluminum availability, which is favoured in restricted lacustrine environments hosted in alkaline volcanic terrains commonly emplaced during early stages of continental rifting. Supersaturation of the lake water relative to saponite is especially due to high pH values, themselves derived from high primary productivity. This suggests that a genetic link may exist between saponite and the development of organic‐rich carbonate rocks, which may be fuelled by the input of CO2‐rich volcanic gases. This provides novel insights into the composition and formation of saponite‐rich deposits under a specific geodynamic context such as the Cretaceous South Atlantic carbonate reservoirs.
Sediment dispersal and organic carbon preservation in a dynamic mudstone‐dominated system, Juana Lopez Member, Mancos Shale
Authors: DeReuil Aubry A. , Birgenheier Lauren P. 
Published: August 2018

AbstractA balance between primary production, rates of sediment accumulation or dilution, and biological or diagenetic destruction has long been considered a key control on organic carbon preservation in modern offshore marine environments. Additionally, current understanding of sediment transport processes in offshore environments has advanced in the last decade to include variable energy and dynamic mechanisms, requiring a re‐evaluation of ancient deposits in these systems. The Juana Lopez Member of the Mancos Shale preserves organic carbon‐rich mudstone interbedded and interlaminated with sandstone that records high energy traction flow conditions. Core, outcrop and geochemical data from the Juana Lopez Member were used to elucidate sediment provenance and processes controlling organic carbon preservation and distribution in this mudstone‐dominated system. Five dominant lithofacies with varying grain size, sedimentary fabrics, composition and grain origins were differentiated and were deposited in three main environments: the prodelta, fringe zone and low angle offshore ramp. Basal deposits of the Juana Lopez Member consist of siliceous sandstone‐dominated, heterolithic deposits with characteristic sedimentary structures (for example, current ripples and normal grading) that indicate offshore‐directed underflows, or hyperpycnites, delivered from the updip Ferron/Frontier deltaic system. In the upper portion of the Juana Lopez Member, a compositional change to biogenic carbonate‐rich sandstone and mudstone is interpreted to be as a result of increased accommodation in central Utah (USA), associated base‐level rise and shoreline‐parallel sediment transport. Non‐parallel laminated, organic carbon‐rich mudstone is preserved throughout the Juana Lopez Member. Depositional fabrics and trace element signatures suggest that these deposits are the result of dynamic conditions at the sea floor and in the oxic to suboxic water column, further challenging the notion that organic‐bearing mudstone is deposited solely through suspension settling in anoxic waters. Punctuated delivery of organic carbon laden sediment from mixed terrestrial and marine sources resulted in an event‐bed style of organic carbon deposition and preservation.
Holocene and Pleistocene fringing reef growth and the role of accommodation space and exposure to waves and currents (Bora Bora, Society Islands, French Polynesia)
Authors: Gischler Eberhard , Hudson J. Harold , Humblet Marc , Braga Juan Carlos , Schmitt Dominik , Isaack Anja , Eisenhauer Anton , Camoin Gilbert F. 
Published: August 2018

AbstractHolocene fringing reef development around Bora Bora is controlled by variations in accommodation space (as a function of sea‐level and antecedent topography) and exposure to waves and currents. Subsidence ranged from 0 to 0·11 m kyr−1, and did not create significant accommodation space. A windward fringing reef started to grow 8·7 kyr bp, retrograded towards the coast over a Pleistocene fringing reef until ca 6·0 kyr bp, and then prograded towards the lagoon after sea‐level had reached its present level. The retrograding portion of the reef is dominated by corals, calcareous algae and microbialite frameworks; the prograding portion is largely detrital. The reef is up to 13·5 m thick and accreted vertically with an average rate of 3·12 m kyr−1. Lateral growth amounts to 13·3 m kyr−1. Reef corals are dominated by an inner Pocillopora assemblage and an outer Acropora assemblage. Both assemblages comprise thick crusts of coralline algae. Palaeobathymetry suggests deposition in 0 to 10 m depth. An underlying Pleistocene fringing reef formed during the sea‐level highstand of Marine Isotope Stage 5e, and is also characterized by the occurrence of corals, coralline algal crusts and microbialites. A previously investigated, leeward fringing reef started to form contemporaneously (8·78 kyr bp), but is thicker (up to 20 m) and solely prograded throughout the Holocene. A shallow Pocillopora assemblage and a deeper water Montipora assemblage were identified, but detrital facies dominate. At the Holocene reef base, only basalt was recovered. The Holocene windward–leeward differences are a consequence of less accommodation space on the eastern island side that eventually led to a more complex reef architecture. As a result of higher rates of exposure and flushing, the reef framework on the windward island side is more abundant and experienced stronger cementation. In the Pleistocene, the environmental conditions on the leeward island side were presumably unfavourable for fringing reef growth.
Phylogenetic analysis of cuckoo wasps (Hymenoptera: Chrysididae) reveals a partially artificial classification at the genus level and a species‐rich clade of bee parasitoids
Authors: Pauli Thomas , Castillo‐Cajas Ruth F. , Rosa Paolo , Kukowka Sandra , Berg Alexander , van den Berghe Eric , Fornoff Felix , Hopfenmüller Sebastian , Niehuis Manfred , Peters Ralph S. , Staab Michael , Strumia Franco , Tischendorf Stefan , Schmitt Thomas , Niehuis Oliver 
Published: August 2018

AbstractCuckoo wasps (Hymenoptera: Chrysididae) are a species‐rich family of obligate brood parasites (i.e. parasitoids and kleptoparasites) whose hosts range from sawflies, wasps and bees, to walking sticks and moths. Their brood parasitic lifestyle has led to the evolution of fascinating adaptations, including chemical mimicry of host odours by some species. Long‐term nomenclatural stability of the higher taxonomic units (e.g. genera, tribes, and subfamilies) in this family and a thorough understanding of the family's evolutionary history critically depend on a robust phylogeny of cuckoo wasps. Here we present the results from phylogenetically analysing ten nuclear‐encoded genes and one mitochondrial gene, all protein‐coding, in a total of 186 different species of cuckoo wasps representing most major cuckoo wasp lineages. The compiled data matrix comprised 4946 coding nucleotide sites and was phylogenetically analysed using classical maximum‐likelihood and Bayesian inference methods. The results of our phylogenetic analyses are mostly consistent with earlier ideas on the phylogenetic relationships of the cuckoo wasps' subfamilies and tribes, but cast doubts on the hitherto hypothesized phylogenetic position of the subfamily Amiseginae. However, the molecular data are not fully conclusive in this respect due to low branch support values at deep nodes. In contrast, our phylogenetic estimates clearly indicate that the current systematics of cuckoo wasps at the genus level is artificial. Several of the currently recognized genera are para‐ or polyphyletic (e.g.Cephaloparnops,Chrysis,Chrysura,Euchroeus,Hedychridium,Praestochrysis,Pseudochrysis,Spintharina, andSpinolia). At the same time, our data support the validity of the genusColpopyga, previously synonymized withHedychridium. We discuss possible solutions for how to resolve the current shortcomings in the systematics of cuckoo wasp genera and decided to grantProspinoliathe status of a valid genus (Prospinoliastat.n.) and transferringSpinolia theresae[du Buysson 1900] fromSpinoliatoProspinolia(Prospinolia theresaestat.restit.). We discuss the implications of our phylogenetic inferences for understanding the evolution of host associations in this group. The results of our study not only shed new light on the evolutionary history of cuckoo wasps, but also set the basis for future phylogenomic investigations on this captivating group of wasps by guiding taxonomic sampling efforts and the design of probes for target DNA enrichment approaches.
Ornithine δ‐aminotransferase is critical for floret development and seed setting through mediating nitrogen reutilization in rice
Authors: Liu Changzhen , Xue Zhihui , Tang Ding , Shen Yi , Shi Wenqing , Ren Lijun , Du Guijie , Li Yafei , Cheng Zhukuan 
Published: August 2018

SummaryNitrogen is one of the most important nutrient element that is essential for plant growth and development. Many genes have been reported to contribute to nitrogen absorption and transportation. However, genes involved in nitrogen reutilization are seldom reported. Ornithine δ‐aminotransferase (δOAT) is the enzyme connecting arginine cycling and proline cycling. Here, we found that OsOAT, the homologue of δOAT in rice, is essential for nitrogen reutilization through mediating arginase activity. In the Osoat mutant, metabolic abnormality induced by nitrogen deficiency in floret causes malformed glumes, incapable glume opening and anther indehiscence. These defects in the mutant affect the pollination process and lead to a low seed setting rate as well as abnormal seed shape. Intriguingly, urea can rescue the phenotypes of the Osoat mutant. Therefore, OsOAT is crucial for nitrogen reutilization and plays a critical role in floret development and seed setting in rice.
Tuning of SlARF10A dosage by sly‐miR160a is critical for auxin‐mediated compound leaf and flower development
Authors: Damodharan Subha , Corem Shira , Gupta Suresh Kumar , Arazi Tzahi 
Published: August 2018

SummarymiR160 adjusts auxin‐mediated development by post‐transcriptional regulation of the auxin response factors ARF10/16/17. In tomato, knockdown of miR160 (sly‐miR160) suggested that it is required for auxin‐driven leaf blade outgrowth, but whether additional developmental events are adjusted by sly‐miR160 is not clear. Here, the SlMIR160 genes and the genes of its SlARFs targets were edited by CRISPR/Cas9 resulting in the isolation of loss‐of‐function mutants. In addition, hypomorphic mutants that accumulate variable reduced levels of sly‐miR160a were isolated. We found that the loss‐of‐function mutants in SlMIR160a (CR‐slmir160a‐6/7) produced only four wiry leaves, whereas the hypomorphic mutants developed leaves and flowers with graded developmental abnormalities. Phenotypic severity correlated with the upregulation of SlARF10A. Consistent with that, double mutants in SlMIR160a and SlARF10A restored leaf and flower development indicating that over‐accumulation of SlARF10A underlay the developmental abnormalities exhibited in the CR‐slmir160a mutants. Phenotype severity also correlated with the upregulation of the SHOOT MERISTEMLESS homolog Tomato Knotted 2, which in turn activated the transcription of the cytokinin biosynthesis genes SlIPT2 and SlIPT4. However, no change in Tomato Knotted 2 was detected in the absence of SlARF10A, suggesting that it is upregulated due to auxin signaling suppression by SlARF10A. Knockout of sly‐miR160a‐targeted SlARFs showed that whereas SlARF10A is indispensable for leaf blade outgrowth and floral organ patterning, the functions of SlARF16A and SlARF17 are redundant. Taken together our results suggest that sly‐miR160a promotes blade outgrowth as well as leaf and leaflet initiation and floral organ development through the quantitative regulation of its major target SlARF10A.
The Patagonian Steppe biogeographic province: Andean region or South American transition zone?
Authors: Roig‐Juñent Sergio A. , Griotti Mariana , Cecilia Domínguez Martha , Agrain Federico A. , Campos‐Soldini Paula , Carrara Rodolfo , Cheli Germán , Fernández‐Campón Florencia , Flores Gustavo E. , Katinas Liliana , Muzón Javier R. , Neita‐Moreno Jhon C. , Pessacq Pablo , San Blas German , Scheibler Erica E. , Crisci Jorge V. 
Published: August 2018

AbstractAmerica comprises three biogeographic regions: Nearctic, Neotropical and Andean. In between them, two transition zones (TZ) have been proposed: Mexican and South American. The biogeographic provinces belonging to a TZ have no predominance of biotic elements pertaining to each of its bordering regions. Regarding the Andean region, one of its provinces, the Patagonian Steppe, presents a mixture of different biogeographic elements, which are typical of transition zones. Because of this, we assessed whether the Patagonian Steppe belongs to the Andean region or whether it forms the southernmost part of the South American TZ. We gathered phylogenetic information from 177 taxa that inhabit the Patagonian Steppe and established to which biogeographic element they belong. We followed the criterion that an area can be considered as part of a region when at least 70% of its biota has the same origin, that is belongs to the same biogeographic element. In contrast, when the biota of an area presents a similar percentage of its different biogeographic elements, it could be considered as belonging to a transition zone. We found that the Patagonian Steppe presents a similar proportion of genera of Andean as well as neotropical origin. Therefore, we propose that this province should be included in the South American transition zone. Moreover, inclusion of the Patagonian Steppe as part of this TZ will make it the largest TZ of America, encompassing most of the arid lands of South America.
Novel insights into the genetic diversity of Parafavella based on mitochondrial CO1 sequences
Authors: Jung Jae‐Ho , Moon Ji Hye , Park Kyung‐Min , Kim Sanghee , Dolan John R. , Yang Eun Jin 
Published: August 2018

AbstractWe used both nuclear ribosomal genes (28S rDNA, 18S rDNA, 5.8S rDNA, internal transcribed spacer regions: ITS1, ITS2) and mitochondrial CO1 sequences to group or distinguish morphotypes of Parafavella, a problematic genus of tintinnid ciliates of the marine microzooplankton. We sequenced 30 single cells of Parafavella from the Bering Sea, the Greenland Sea, and the East/Japan Sea. Sequences were obtained from 4 morphotypes, typically ascribed to P. gigantea, P. greenlandica, P. jorgenseni, and P. subrotundata and from GenBank, the nuclear ribosomal genes of P. parumdentata were retrieved. Cells of the five morphotypes had identical 18S and 5.8S gene sequences. ITS1, ITS2 and 28S sequences produced two clusters: one grouping P. greenlandica and P. parumdentata and the other grouping P. jorgenseni, P. gigantea, and P. subrotundata. In contrast, CO1 nucleotide data yielded eight haplotypes clustered into five groups: one composed of P. greenlandica morphotypes, two distinct haplotypes of P. jorgenseni, and two distinct haplotypes of P. gigantea with one including P. subrotundata morphotypes. We investigated the co‐occurrence of different morphotypes in samples from sites across a large gradient of latitude and concentrations of Parafavella cells. Natural communities contained 2–6 different morphotypes. We conclude that both crypticity and polymorphism characterize Parafavella, as known for other tintinnid genera.
Ageing changes in biventricular cardiac function in male and female baboons (Papio spp.)
Authors: Kuo Anderson H. , Li Cun , Huber Hillary F. , Nathanielsz Peter W. , Clarke Geoffrey D. 
Published: August 2018

Key points
Life course changes in cardiovascular function in a non‐human primate have been comprehensively characterized.
Age‐related declines in normalized left ventricular stroke volume and cardiac output were found with corresponding decreases in biventricular ejection fractions and filling rates.
There were age‐related decreases in male and female baboon normalized left ventricular myocardial mass index, which declined at similar rates.
Systolic functional declines in right ventricular function were observed with age, similar to the left ventricle.
Sex differences were found in the rates and directions of right ventricular volume changes along with decreased end‐systolic right ventricular sphericity.
The results validate the baboon as an appropriate model for translational studies of cardiovascular functional decline with ageing.
AbstractPrevious studies reported cardiac function declines with ageing. This study determined changes in biventricular cardiac function in a well‐characterized baboon model. Cardiac magnetic resonance imaging measured key biventricular parameters in 47 baboons (22 female, age 4–23 years). ANCOVA assessed sex and age changes with P < 0.05 deemed significant. Stroke volume, cardiac output and other cardiac functional parameters were normalized to body surface area. There were similar, age‐related rates of decrease in male (M) and female (F) normalized left ventricular (LV) myocardial mass index (M: −1.2 g m−2 year−1, F: −0.9 g m−2 year−1). LV ejection fraction declined at −0.96% year−1 (r = −0.43, P = 0.002) and right ventricular (RV) ejection fraction decreased at −1.2% year−1 (r = −0.58, P < 0.001). Normalized LV stroke volume fell at −1.1 ml m−2 year−1 (r = −0.47, P = 0.001), normalized LV ejection rate at −3.8 ml s−1 m−2 year−1 (r = −0.43, P < 0.005) and normalized LV filling rate at −4.1 ml s−1 m−2 year−1 (r = −0.44, P < 0.005). Also, RV wall thickening fraction decreased with age (slope = −1% year−1, P = 0.008). RV ejection rate decreased at −3.6 ml s−1 m−2 year−1 (P = 0.002) and the normalized average RV filling rate dropped at −3.7 ml s−1 m−2 year−1 (P < 0.0001). End‐systolic RV sphericity index also dropped with age (r = −0.33, P = 0.02). Many observed changes parallel previously reported data in human and animal studies. These measured biventricular functional declines in hearts with ageing from the closest experimental primate species to man underscore the utility of the baboon model for investigating mechanisms related to heart ageing.