bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leptothoe, a new genus of marine cyanobacteria (Synechococcales) and three new species associated with sponges from the Aegean Sea
Authors: Konstantinou Despoina , Voultsiadou Eleni , Panteris Emmanuel , Zervou Sevasti‐Kiriaki , Hiskia Anastasia , Gkelis Spyros 
Published: April 2019

Cyanobacterial diversity associated with sponges remains underestimated, though it is of great scientific interest in order to understand the ecology and evolutionary history of the symbiotic relationships between the two groups. Of the filamentous cyanobacteria, the genus Leptolyngbya is the most frequently found in association with sponges as well as the largest and obviously polyphyletic group. In this study, five Leptolyngbya‐like sponge‐associated isolates were investigated using a combination of molecular, chemical, and morphological approach and revealed a novel marine genus herein designated Leptothoe gen. nov. In addition, three new species of Leptothoe, Le. sithoniana, Le. kymatousa, and Le. spongobia, are described based on a suite of distinct characters compared to other marine Leptolyngbyaceae species/strains. The three new species, hosted by four sponge species, showed different degrees of host specificity. Leptothoe sithoniana and Le. kymatousa hosted by the sponges Petrosia ficiformis and Chondrilla nucula, respectively, seem to be more specialized than Le. spongobia, which was hosted by the sponges Dysidea avara and Acanthella acuta. All three species contained nitrogen‐fixing genes and may contribute to the nitrogen budget of sponges. Leptothoe spongobia TAU‐MAC 1115 isolated from Acanthella acuta was shown to produce microcystin‐RR indicating that microcystin production among marine cyanobacteria could be more widespread than previously determined.
Oceanographic barriers, divergence, and admixture: Phylogeography and taxonomy of two putative subspecies of short‐finned pilot whale
Authors: Van Cise Amy M. , Baird Robin W. , Baker Charles Scott , Cerchio Salvatore , Claridge Diane , Fielding Russell , Hancock‐Hanser Brittany , Marrero Jacobo , Martien Karen K. , Mignucci‐Giannoni Antonio A. , Oleson Erin M. , Oremus Marc , Poole M. Michael , Rosel Patricia E. , Taylor Barbara L. , Morin Phillip A. 
Published: April 2019

AbstractGenomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short‐finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the “Naisa” and “Shiho” forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short‐finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short‐finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally‐distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.
Specific amino acid substitutions in β strand S2 of FtsZ cause spiraling septation and impair assembly cooperativity in Streptomyces spp.
Authors: Sen Beer Chakra , Wasserstrom Sebastian , Findlay Kim , Söderholm Niklas , Sandblad Linda , von Wachenfeldt Claes , Flärdh Klas 
Published: April 2019

SummaryBacterial cell division is orchestrated by the Z ring, which is formed by single‐stranded treadmilling protofilaments of FtsZ. In Streptomyces, during sporulation, multiple Z rings are assembled and lead to formation of septa that divide a filamentous hyphal cell into tens of prespore compartments. We describe here mutant alleles of ftsZ in Streptomyces coelicolor and Streptomyces venezuelae that perturb cell division in such a way that constriction is initiated along irregular spiral‐shaped paths rather than as regular septa perpendicular to the cell length axis. This conspicuous phenotype is caused by amino acid substitutions F37I and F37R in β strand S2 of FtsZ. The F37I mutation leads, instead of regular Z rings, to formation of relatively stable spiral‐shaped FtsZ structures that are capable of initiating cell constriction. Further, we show that the F37 mutations affect the polymerization properties and impair the cooperativity of FtsZ assembly in vitro. The results suggest that specific residues in β strand S2 of FtsZ affect the conformational switch in FtsZ that underlies assembly cooperativity and enable treadmilling of protofilaments, and that these features are required for formation of regular Z rings. However, the data also indicate FtsZ‐directed cell constriction is not dependent on assembly cooperativity.
Knockout of apolipoprotein A‐I decreases parenchymal and vascular β‐amyloid pathology in the Tg2576 mouse model of Alzheimer's disease
Authors: Contu L. , Carare R. O. , Hawkes C. A. 
Published: April 2019

AimsApolipoprotein A‐I (apoA‐I), the principal apolipoprotein associated with high‐density lipoproteins in the periphery, is also found at high concentrations in the cerebrospinal fluid. Previous studies have reported either no impact or vascular‐specific effects of apoA‐I knockout (KO) on β‐amyloid (Aβ) pathology. However, the putative mechanism(s) by which apoA‐I may influence Aβ deposition is unknown.MethodsWe evaluated the effect of apoA‐I deletion on Aβ pathology, Aβ production and clearance from the brain in the Tg2576 mouse model of Alzheimer's disease (AD).ResultsContrary to previous reports, deletion of the APOA1 gene significantly reduced concentrations of insoluble Aβ40 and Aβ42 and reduced plaque load in both the parenchyma and blood vessels of apoA‐I KO × Tg2576 mice compared to Tg2576 animals. This was not due to decreased Aβ production or alterations in Aβ species. Levels of soluble clusterin/apoJ were significantly higher in neurons of apoA‐I KO mice compared to both wildtype (WT) and apoA‐I KO × Tg2576 mice. In addition, clearance of Aβ along intramural periarterial drainage pathways was significantly higher in apoA‐I KO mice compared to WT animals.ConclusionThese data suggest that deletion of apoA‐I is associated with increased clearance of Aβ and reduced parenchymal and vascular Aβ pathology in the Tg2576 model. These results suggest that peripheral dyslipidaemia can modulate the expression of apolipoproteins in the brain and may influence Aβ clearance and aggregation in AD.
Using a reaction‐diffusion model to estimate day respiration and reassimilation of (photo)respired CO2 in leaves
Authors: Berghuijs Herman N. C. , Yin Xinyou , Ho Q. Tri , Retta Moges A. , Nicolaï Bart M. , Struik Paul C. 
Published: April 2019

Summary

Methods using gas exchange measurements to estimate respiration in the light (day respiration ) make implicit assumptions about reassimilation of (photo)respired CO2; however, this reassimilation depends on the positions of mitochondria.

We used a reaction‐diffusion model without making these assumptions to analyse datasets on gas exchange, chlorophyll fluorescence and anatomy for tomato leaves. We investigated how values obtained by the Kok and the Yin methods are affected by these assumptions and how those by the Laisk method are affected by the positions of mitochondria.

The Kok method always underestimated . Estimates of by the Yin method and by the reaction‐diffusion model agreed only for nonphotorespiratory conditions. Both the Yin and Kok methods ignore reassimilation of (photo)respired CO2, and thus underestimated for photorespiratory conditions, but this was less so in the Yin than in the Kok method. Estimates by the Laisk method were affected by assumed positions of mitochondria. It did not work if mitochondria were in the cytosol between the plasmamembrane and the chloroplast envelope. However, mitochondria were found to be most likely between the tonoplast and chloroplasts.

Our reaction‐diffusion model effectively estimates , enlightens the dependence of estimates on reassimilation and clarifies (dis)advantages of existing methods.
Meta‐analysis of the role of entomopathogenic and unspecialized fungal endophytes as plant bodyguards
Authors: Gange Alan C. , Koricheva Julia , Currie Amanda F. , Jaber Lara R. , Vidal Stefan 
Published: April 2019

Summary

Herbaceous plants harbour species‐rich communities of asymptomatic endophytic fungi. Although some of these endophytes are entomopathogenic, many are not, and remarkably little is known about how the presence of these fungi in plant tissues affects phytophagous insects.

Here we show through a meta‐analysis that both entomopathogenic and nonentomopathogenic endophytes have a negative effect on insect herbivores. Growth and performance of polyphagous and sucking insects are reduced by nonentomopathogenic endophytes, but monophages are unaffected, likely because the latter are better adapted to secondary metabolites produced or induced by the fungi.

Furthermore, studies using excised leaves report weaker effects than those with intact plants, likely caused by chemical changes being masked by leaf excision. Most surprisingly, endophyte infection of seeds produces the greatest effect on insect herbivores in subsequent mature plants, even though the usual mode of fungal transmission is infection of leaves by airborne spores.

We conclude that these ubiquitous hidden fungi may be important bodyguards of plants. However, in order to fully understand their roles in plant protection, we must be aware that minor differences in experimental design can lead to contradictory results.
The effect of pediatric patient temperament on postoperative outcomes
Authors: Uhl Kristen , Litvinova Anna , Sriswasdi Patcharee , Zurakowski David , Logan Deirdre , Cravero Joseph P. 
Published: April 2019

SummaryBackgroundResearch has improved practitioner awareness of the impact of individual characteristics on responses to painful procedures. However, there is little data relating preexisting temperament profiles and postsurgical/anesthesia outcomes in pediatric patients. In particular, it is not clear how best to identify which patients are at risk of poor postsurgical outcomes.AimIn this prospective study, we examined relationships between preoperative measures of child temperament and postoperative pain/behavioral outcomes of children undergoing tonsillectomy/adenoidectomy surgeries. We sought to determine which temperament profiles were predictive of poor outcomes.MethodsAfter IRB approval and informed consent, validated temperament surveys were administered to the parents of a cohort of children undergoing tonsillectomy/adenoidectomy surgery. These data were combined with preoperative, intraoperative, and postoperative outcome measures collected from the electronic medical record utilizing a large integrated anesthesia outcome database. The dataset was further augmented with surveys addressing remote postoperative behaviors. Analysis of the temperament data yielded four groups (positive, negative, excitable, and inhibitory). The probability of high perioperative pain, agitation, emesis, and postoperative behavior changes based on cluster membership was then assessed.ResultsA total of 260 patients undergoing tonsillectomy and/or adenoidectomy surgeries were enrolled in the study. ANOVA and chi‐squared analyses indicated no statistically significant age, gender, or anesthesia technique differences across the four temperament clusters. Temperament cluster membership was not related to emesis, agitation, or behavioral changes. However, it was found to be predictive of high postoperative pain. Members of the excitable cluster (high positive and negative emotionality) were more likely to report high pain than those in positive cluster (high positive, low negative emotionality) (OR 7.97, 95% CI: 1.62‐39.26; P < 0.05). Comparisons among other clusters were not significant.ConclusionOur data indicate that preoperative temperament characteristics may differentially influence pediatric postoperative pain experience in children. Specifically, children with high levels of positive and negative emotionality may exhibit more postsurgical pain behaviors.
CRISPR/Cas9‐mediated functional recovery of the recessive rc allele to develop red rice
Authors: Zhu Yiwang , Lin Yarong , Chen Songbiao , Liu Huaqing , Chen Zaijie , Fan Meiying , Hu Taijiao , Mei Fating , Chen Jianmin , Chen Liang , Wang Feng 
Published: April 2019

SummaryRed rice contains high levels of proanthocyanidins and anthocyanins, which have been recognized as health‐promoting nutrients. The red coloration of rice grains is controlled by two complementary genes, Rc and Rd. The RcRd genotype produces red pericarp in wild species Oryza rufipogon, whereas most cultivated rice varieties produce white grains resulted from a 14‐bp frame‐shift deletion in the seventh exon of the Rc gene. In the present study, we developed a CRISPR/Cas9‐mediated method to functionally restore the recessive rc allele through reverting the 14‐bp frame‐shift deletion to in‐frame mutations in which the deletions were in multiples of three bases, and successfully converted three elite white pericarp rice varieties into red ones. Rice seeds from T1 in‐frame Rc lines were measured for proanthocyanidins and anthocyanidins, and high accumulation levels of proanthocyanidins and anthocyanidins were observed in red grains from the mutants. Moreover, there was no significant difference between wild‐type and in‐frame Rc mutants in major agronomic traits, indicating that restoration of Rc function had no negative effect on important agronomic traits in rice. Given that most white pericarp rice varieties are resulted from the 14‐bp deletion in Rc, it is conceivable that our method could be applied to most white pericarp rice varieties and would greatly accelerate the breeding of new red rice varieties with elite agronomic traits. In addition, our study demonstrates an effective approach to restore recessive frame‐shift alleles for crop improvement.
A gamma‐thionin protein from apple, MdD1, is required for defence against S‐RNase‐induced inhibition of pollen tube prior to self/non‐self recognition
Authors: Gu Zhaoyu , Li Wei , Doughty James , Meng Dong , Yang Qing , Yuan Hui , Li Yang , Chen Qiuju , Yu Jie , Liu Chun sheng , Li Tianzhong 
Published: April 2019

SummaryApple exhibits S‐RNase‐mediated self‐incompatibility. Although the cytotoxic effect of S‐RNase inside the self‐pollen tube has been studied extensively, the underlying defence mechanism in pollen tube in Rosaceae remains unclear. On exposure to stylar S‐RNase, plant defence responses are activated in the pollen tube; however, how these are regulated is currently poorly understood. Here, we show that entry of both self and non‐self S‐RNase into pollen tubes of apple (Malus domestica) stimulates jasmonic acid (JA) production, in turn inducing the accumulation of MdMYC2 transcripts, a transcription factor in the JA signalling pathway widely considered to be involved in plant defence processes. MdMYC2 acts as a positive regulator in the pollen tube activating expression of MdD1, a gene encoding a defence protein. Importantly, MdD1 was shown to bind to the RNase activity sites of S‐RNase leading to inhibition of enzymatic activity. This work provides intriguing insights into an ancient defence mechanism present in apple pollen tubes where MdD1 likely acts as a primary line of defence to inhibit S‐RNase cytotoxicity prior to self/non‐self recognition.
Nitrogen utilisation and metabolism in maize (Zea mays L.) plants under different rates of biochar addition and nitrogen input conditions
Authors: Sun C.X. , Hao L. , Wang D. , Li C. , Zhang C. , Chen X. , Fu J. , Zhang Y.L. 
Published: April 2019

Abstract

Biochar (BC) application could improve plant nitrogen (N) utilisation and potentially reduce N fertiliser requirements. However, the fate of N in crop–soil systems and the metabolic responses of crops under conditions of BC co‐applied with reduced N are not well understood.

The urea‐15N isotope and pot experiments with three BC rates (0%, 5% and 15%; w/w) combined with three N fertiliser levels (100% N, 85% N and 55% N) were conducted for maize. The metabolome, 15N abundance and gene expression in plants were analysed using nuclear magnetic resonance, gas isotope mass spectrometry and quantitative real‐time reverse transcription PCR, respectively.

The results showed that recovery of N by maize ranged from 27.4% to 23.6% and decreased as the N application rate decreased (from 100% to 55%) without BC addition, but ranged from 24.6% to 29.4% when BC was added at a rate of 5% and increased as the N application rate decreased. BC addition had major effects on global metabolic profiles and metabolic networks at the metabolomics level as well as on the expression of related genes (zmGS1and zmAS1) and the content of mineral N (NO3−, NO2− and NH4+) in maize seedlings; moreover, the interaction effects of the BC application rates and N fertiliser levels were evident (P ≤ 0.001).

BC addition induced a decrease in the flux toward sugar hydrolysis and maintained homeostasis in the amino acid pool, which was perturbed by reduced N levels; after which the maize plants adapted to the reduced N condition, and the N recovery efficiency ultimately improved with reduced N loss.
The comparison of reproductive hormone receptor expressions of the sheep ovary and hormone concentrations in two Chinese breeds
Authors: Li Liangyuan , Lu Shouliang , Ma Qiman , Wan Pengcheng , Liu Changbin , Yang Hanyulu , Yang Hua , Yang Yonglin , Dai Rong , Shi Guoqing 
Published: April 2019

AbstractThe aim of this research was to investigate the changes in reproductive hormone receptor expressions of the ovary and hormone concentrations between oestrous cycle pattern of two different sheep breeds in China. Ovarian tissues were collected from Chinese Merino (Junken type) and Hu sheep with different reproductive states in spring and autumn. Serum samples were assayed for oestrogen (E2), progesterone (P), luteinizing hormone (LH) and follicle‐stimulating hormone (FSH) concentrations by radioimmunoassay during spring. The ovarian expression of hormone receptors (ERα, ERβ, PR, LHR and FSHR) was analysed using real‐time reverse transcription polymerase chain reaction (RT‐PCR). In Chinese Merino, there was no corpora lutea and ovulation point on the surfaces of ovaries in spring and low basal levels of both LH and P in serum. ERα, ERβ and FSHR were expressed significantly higher in Merino ovaries during anoestrus compared with oestrous or luteal phases of Hu sheep (p < 0.05 or p < 0.01). However, both varieties of sheep exhibited a similar tendency to secrete E2 and FSH. Compared with Hu sheep, FSH levels were slightly higher in Merino serum. In Hu sheep, ERα, ERβ, FSHR, LHR and PR expressed in luteal phase ovaries during spring were significantly lower (p < 0.05, p < 0.01 or p < 0.001) than autumn. Interestingly, LHR and PR expressed in anoestrous ovaries were similar to that in oestrous phase of both sheep breeds. The above results suggest that seasonal reproductive sheep increased the expression of E2 and FSH receptors in ovary during spring may enhance the effects of E2 and FSH on follicular development. It is likely that this enhancement prevents the ovary from progressing to the luteal phase.
Confidence in Risk Assessments
Authors: Rougier Jonathan 
Published: April 2019

SummaryRisk is assessed with varying degrees of confidence, and the degree of confidence is relevant to the risk manager. The paper proposes an operational framework for representing confidence, based on an expert's current beliefs about how her beliefs might be different in the future. Two modelling simplifications, ‘no unknown unknowns’ and a homogeneous Poisson process, make this framework trivial to apply. This is illustrated for assessing an exceedance probability for a large event, with volcanic risk as a specific example. The paper ends with a discussion about risk and confidence assessments for national scale risk assessment, including several further illustrations.
Heterogeneous macrophages: Supersensors of exogenous inducing factors
Authors: Qian Caiyun , Yun Zehui , Yao Yudi , Cao Minghua , Liu Qiang , Hu Song , Zhang Shuhua , Luo Daya 
Published: April 2019

AbstractAs heterogeneous immune cells, macrophages mount effective responses to various internal and external changes during disease progression. Macrophage polarization, rather than macrophage heterogenization, is often used to describe the functional differences between macrophages. While macrophage polarization partially contributes to heterogeneity, it does not completely explain the concept of macrophage heterogeneity. At the same time, there are abundant and sophisticated endogenous and exogenous substances that can affect macrophage heterogeneity. While the research on endogenous factors has been systematically reviewed, the findings on exogenous factors have not been well summarized. Hence, we reviewed the characteristics and inducing factors of heterogeneous macrophages to reveal their functional plasticity as well as their targeting manoeuvreability. In the process of constructing and analysing a network organized by disease‐related cells and molecules, paying more attention to heterogeneous macrophages as mediators of this network may help to explore a novel entry point for early prevention of and intervention in disease.
Questions of Order in the U.S. Senate: Procedural Uncertainty and the Role of the Parliamentarian*
Authors: Madonna Anthony J. , Lynch Michael S. , Williamson Ryan D. 
Published: April 2019

ObjectivesScholarship on the U.S. Senate has demonstrated the pivotal role the presiding officer can play when asked to interpret the chamber's rules and precedents. Therefore, our objective is to broadly evaluate how questions of order are arbitrated in the U.S. Senate.MethodsUsing a multinomial logistic regression, we estimate the effect of partisanship on adjudicating questions of order in the Senate before and after the institutionalization of the parliamentarian.ResultsOur results indicate that while short‐term partisan interests play an important role in determining how presiding officers interpret rules and precedents, the emergence of the Senate parliamentarian in the 1920s served to reduce uncertainty regarding procedural matters in the chamber.ConclusionsThis change has led to fewer instances of partisan rulings on questions of order and raised the costs of executing a drastic change in Senate procedure via unorthodox procedures. However, the introduction of the parliamentarian has not reduced the likelihood a ruling is overturned. As such, more narrow procedural changes have been used to support majorities over time.