bluuebunny/crossref_metadata_2025 huggingface dataset:
Acute and Chronic Toxicity of Indole Alkaloids from Leaves of Alstonia scholaris (L.) R. Br. in Mice and Rats
Authors: Zhao Yun-Li , Su Min , Shang Jian-Hua , Wang Xia , Njateng Guy Sedar Singor , Bao Guang-Lei , Ma Jia , Sun Qing-Di , Yuan Fang , Wang Jing-Kun , Luo Xiao-Dong
Published: March 2020

Alstonia scholaris (L.) R. Br. (Apocynaceae) is an evergreen tree that has been used to treat lung diseases. In this study, the toxicity profile of indole alkaloids from leaves of A. scholaris was investigated. In acute toxicity tests, mice were administered total alkaloids (TA) and five indole alkaloids. In a chronic toxicity test, rats were continuously administered TA (50, 100, and 300 mg/kg bw) for 13 weeks, followed by a 4-week recovery. A single administration of TA affected the behavior of mice, and at 12.8 g/kg bw, prone position, shortness of breath, wheezing, and convulsion were observed. The half-lethal dose (LD50) in mice was 5.48 g/kg bw, almost 2740 times the clinical dose in humans. Among the five indole alkaloids, the maximum tolerance dose in mice ranged from 0.75 to 4 g/kg bw. The TA-treated rats did not die and showed no adverse effects or dose-dependent changes in weight or food and water consumption, despite fluctuations in hematological and biochemical parameters compared with historical data. Furthermore, both gross and histopathological observations revealed no abnormalities in any organ. With daily oral administration to rats, the non-observed-adverse-effect-level of TA was 100 mg/kg bw. The results indicate that TA is safe for clinical use.

Graphic Abstract
An ethico-legal framework for social data science
Authors: Forgó Nikolaus , Hänold Stefanie , van den Hoven Jeroen , Krügel Tina , Lishchuk Iryna , Mahieu René , Monreale Anna , Pedreschi Dino , Pratesi Francesca , van Putten David
Published: March 2020

This paper presents a framework for research infrastructures enabling ethically sensitive and legally compliant data science in Europe. Our goal is to describe how to design and implement an open platform for big data social science, including, in particular, personal data. To this end, we discuss a number of infrastructural, organizational and methodological principles to be developed for a concrete implementation. These include not only systematically tools and methodologies that effectively enable both the empirical evaluation of the privacy risk and data transformations by using privacy-preserving approaches, but also the development of training materials (a massive open online course) and organizational instruments based on legal and ethical principles. This paper provides, by way of example, the implementation that was adopted within the context of the SoBigData Research Infrastructure.
Effects of climate change on cherry production in Naoussa, Greece and Bonn, Germany: adaptation strategies
Authors: Drogoudi P. , Kazantzis K. , Kunz Achim , Blanke Michael M.
Published: March 2020

The aim of the present study was to identify sweet cherry varieties and growing regions that are resilient to climate change as well as strategies for mitigating the effects of climate change on sweet cherry production in a Northern European location (Meckenheim, Germany) and a Southern European location (Naoussa, Imathia, Greece). Sweet cherry was chosen for this study as it is sensitive to reduced chill accumulation (i.e., fewer chilling hours in winter) and to late frost damage caused by flower opening time advancement. Whereas initial predictions suggested that fruit growing in Southern Europe is particularly sensitive to climate change, our comparison of long-term records of both phenological (flowering) data and weather (frost, temperature) at both locations indicated the opposite. The annual mean temperature in Naoussa increased during 1984–2018 by 1.6 °C to 15.8 °C, whereas it increased during 1958–2018 by 1.5 °C to 9.8 °C in Meckenheim. In Naoussa, flowering was found to have advanced by 6.7 days in the late-flowering cherry cultivar ‘Tragana Edessis,’ but by as much as 8.3 days in the early flowering ‘B. Burlat,’ 1.5 days in ‘Vogue,’ and 3.2 days ‘Larian’ over the last 35 years (1984–2019). In the temperate climate of the Meckenheim cherry-growing area, flowering advanced by 14.1 days during the period 1978–2019 in the early flowering and early maturing cultivar ‘B. Burlat,’ such that it now coincides with the late spring frost. This flowering advancement in Meckenheim was almost twice that observed for ‘B. Burlat’ cherries in Naoussa. Thus, in contrast to what was previously thought, cherries grown in Naoussa may be more resilient to climate change due to the essentially frost-free climate during and after cherry flowering and the occurrence of sufficient chilling hours during winter. This strength may enable Imathia to export sweet cherries to Northern Europe in May, a time of the year when the fruit of this region is not yet available. By contrast, sweet cherry production in the colder climate at Meckenhein shows greater lowering advancement is more susceptible to frost (and therefore requires frost protection technology), making it less resilient to climate change.
Diagnostik – Indikationen für CT und MRT bei Tibiaplateaufrakturen
Authors: Dust Tobias , Korthaus Alexander , Frosch Karl-Heinz , Krause Matthias
Published: March 2020

Tibiaplateaufrakturen stellen im klinischen Alltag eine vergleichsweise seltene Verletzung dar. Aufgrund des heterogenen Patientenkollektivs, des divergierenden Traumamechanismus und der Vielzahl an möglichen weichteiligen Begleitverletzungen ist die adäquate Diagnostik und bedarfsgerechte Behandlung weiterhin eine große Herausforderung im klinischen Alltag. Neben der konventionellen Röntgenaufnahme in zwei Ebenen hat sich die Computertomographie (CT) mit zusätzlicher 3‑D-Rekonstruktion als probates und reliables diagnostisches Werkzeug im Alltag vieler Kliniken etabliert. Die so angefertigten Befunde zeigen dem Chirurgen mit hoher Genauigkeit die Frakturmorphologie und lassen Rückschlüsse auf Begleitverletzungen zu. Die Diagnostik der weichteiligen Begleitverletzungen erfolgt aktuell u. a. im Rahmen der klinischen Untersuchung, dem chirurgischen Befund sowie der intraoperativen Arthroskopie. Mit der Magnetresonanztomographie (MRT) steht eine Technik zur Verfügung, welche die diagnostische Lücke zwischen der CT-Bildgebung und dem intraoperativen Befund schließen kann. Mit hoher Sensitivität kann eine adäquate präoperative Diagnostik der weichteiligen Begleitverletzungen erfolgen und so entscheidenden Einfluss nicht nur auf die Frakturklassifikation, sondern vor allem auf das operative Vorgehen nehmen. Neben der klinischen Verfügbarkeit und (noch) hohen Kosten im Vergleich zur CT stellt vor allem die fehlende Erfahrung mit präoperativ angefertigten MRT-Befunden eine große Herausforderung in der umfassenden Anwendung dieses diagnostischen Tools bei der Behandlung von Tibiaplateaufrakturen dar.
A systematic review of the effectiveness of cohorting to reduce transmission of healthcare-associatedC. difficileand multidrug-resistant organisms
Authors: Abad Cybele L. , Barker Anna K. , Safdar Nasia
Published: March 2020

Background:

Cohorting of patients and staff is a control strategy often used to prevent the spread of infection in healthcare institutions. However, a comprehensive evaluation of cohorting as a prevention approach is lacking.

Methods:

We performed a systematic review of studies that used cohorting as part of an infection control strategy to reduce hospital-acquired infections. We included studies published between 1966 and November 30, 2019, on adult populations hospitalized in acute-care hospitals.

Results:

In total, 87 studies met inclusion criteria. Study types were quasi-experimental “before and after” (n = 35), retrospective (n = 49), and prospective (n = 3). Case-control analysis was performed in 7 studies. Cohorting was performed with other infection control strategies in the setting of methicillin-resistantStaphylococcus aureus(MRSA, n = 22),Clostridioides difficileinfection (CDI, n = 6), vancomycin-resistantEnterococcus(VRE, n = 17), carbapenem-resistant Enterobacteriaceae infections (CRE, n = 22),A. baumannii(n = 15), and other gram-negative infections (n = 5). Cohorting was performed either simultaneously (56 of 87, 64.4%) or in phases (31 of 87, 35.6%) to help contain transmission. In 60 studies, both patients and staff were cohorted. Most studies (77 of 87, 88.5%) showed a decline in infection or colonization rates after a multifaceted approach that included cohorting as part of the intervention bundle. Hand hygiene compliance improved in approximately half of the studies (8 of 15) during the respective intervention.

Conclusion:

Cohorting of staff, patients, or both is a frequently used and reasonable component of an enhanced infection control strategy. However, determining the effectiveness of cohorting as a strategy to reduce transmission of MDRO andC. difficileinfections is difficult, particularly in endemic situations.
Fragmented evidence for the contribution of ex situ management to species conservation indicates the need for better reporting
Authors: Gant Jennifer R. , Mair Louise , McGowan Philip J. K.
Published: March 2020

Conserving species and achieving the Convention on Biological Diversity's international conservation targets necessitates stopping extinctions, recovering depleted populations and maintaining viable populations. The contribution of ex situ management to species conservation has long been debated, and there is limited information on ex situ management activities available in a format that allows success to be assessed. We therefore gathered information from three sources to explore cases in which ex situ management was considered to have had a positive conservation impact for terrestrial vertebrate species. We (1) reviewed the published literature, (2) examined for which taxa ex situ management had contributed to the downlisting of species on the IUCN Red List and (3) surveyed a global network of ex situ management practitioners. We found that ex situ management has contributed to improvements in conservation status for a range of vertebrate species. Ex situ management was reported as contributing to the downlisting of 18 species on the IUCN Red List over a 10-year period. Across sources, the most common role of ex situ management was the provision of individuals to increase population numbers in situ. The strength of evidence for the impact of ex situ management varied within and among sources. Therefore, for the role of ex situ activities in conservation to be understood fully, and for such interventions to reach their potential, documentation of intended and actual benefits needs to be improved. Better reporting of ex situ activities would enable improved learning, facilitating better targeting of ex situ activities to global species conservation goals.
History, Archaeology and Cultural Comparison
Authors: Bagge Sverre Håkon
Published: March 2020

Ian Morris’s Why the West Rules – for Now (2010) is a brilliant book, dealing with Eurasian history from the first civilisations to the present. It takes an intermediate position in the famous debate about Europe and the rest of the world and European dominance during the last few centuries. Morris uses all kinds of sources. However, his general approach is staunchly materialistic: the motors of history are fear, sloth and greed. Cultural differences do exist, but can be explained by the former factors. This is an attitude not confined to archaeologists, nor necessarily shared by all of them, but may nevertheless have something to do with Morris’s background in this field. One objection is that Morris may have underestimated the importance of institutional factors; he does not discuss the division of Europe into separate states, which has often been regarded as a central factor in ‘the Rise of the West’. This in turn raises the question of the ‘two hand-maidens’ and their relationship to the EU. If political division is an essential feature of Europe, what will happen if this division disappears?
Closing the gap: unmet needs of individuals with impulsive aggressive behavior observed in children and adolescents
Authors: Robb Adelaide S. , Connor Daniel F. , Amann Birgit H. , Vitiello Benedetto , Nasser Azmi , O’Neal Welton , Schwabe Stefan , Ceresoli-Borroni Gianpiera , Newcorn Jeffrey H. , Candler Shawn A. , Buitelaar Jan K. , Findling Robert L.
Published: March 2020

Impulsive aggressive (IA, or impulsive aggression) behavior describes an aggregate set of maladaptive, aggressive behaviors occurring across multiple neuropsychiatric disorders. IA is reactive, eruptive, sudden, and unplanned; it provides information about the severity, but not the nature, of its associated primary disorder. IA in children and adolescents is of serious clinical concern for patients, families, and physicians, given the detrimental impact pediatric IA can have on development. Currently, the ability to properly identify, monitor, and treat IA behavior across clinical populations is hindered by two major roadblocks: (1) the lack of an assessment tool designed for and sensitive to the set of behaviors comprising IA, and (2) the absence of a treatment indicated for IA symptomatology. In this review, we discuss the clinical gaps in the approach to monitoring and treating IA behavior, and highlight emerging solutions that may improve clinical outcomes in patients with IA.
Retirement plan wealth inequality: measurement and trends
Authors: Ghilarducci Teresa , Radpour Siavash , Webb Anthony
Published: March 2020

Using Health and Retirement Study data linked to summary plan descriptions and W-2s, this study reports trends in retirement wealth inequality of older employees 1992–2010. The study identifies and corrects methodological flaws in past research. Retirement wealth is highly unequally distributed; the top lifetime earnings quintile holds half of all retirement wealth, the bottom quintile, only 1%. The top earnings quintile fared better in 2010 than in 1992, whereas bottom-quintile earners fared worse. But retirement wealth inequality mainly reflects inequality within earnings quintiles, resulting from inadequate savings, not outsize accumulations. Systemic flaws reduce median retirement wealth by 84%
Compact UWB BPF with a notched band using a single perturbed HMSIW cavity
Authors: Qu Lili , Zhang Yonghong , Li Qun , Fan Yong
Published: March 2020

This paper presents a notched band ultra-wideband bandpass filter using a single perturbed quint-mode half-mode substrate-integrated waveguide cavity. The cavity is perturbed by loading four stubs at two corners of the magnetic walls of the single cavity. The variable parameters of stubs are selected to move down the first five resonant modes to the predetermined passband during the design process. Meanwhile, microstrip lines with a transition structure located on two loaded stubs are employed to feed the resonator. Moreover, the filter also firstly designs a notched band by introducing a complementary split-ring resonator inside the cavity to mitigate potential interference signals at 8 GHz (satellite communication). Finally, a prototype filter was implemented and measured to verify.
Are Suicidal Thoughts and Behaviors a Temporary Phenomenon in Early Adolescence?
Authors: van Vuuren Cornelia Leontine , van der Wal Marcel Franciscus , Cuijpers Pim , Chinapaw Mai Jeanette Maidy
Published: March 2020

Abstract. Background: The incidence of first suicidal thoughts and behaviors (STBs) peaks during early adolescence. After experiencing their first STBs, adolescents differ greatly in the extent to which they continue to have STBs. Aim: We determined the course of STBs in Dutch students at two ages: 13–14 years ( t1) and 15–16 years ( t2). Methods: Longitudinal data on STBs and sociodemographic factors were collected by self-report ( n = 8,499). Associations between having STBs at t1 and t2 were determined with multinomial logistic regression analysis. Results: Students who reported suicidal thoughts at baseline ( n = 1,077; 13%) reported suicidal thoughts ( OR = 6.60; 95% CI [5.52, 7.88]) and suicidal attempts ( OR = 6.97; 95% CI [4.20, 11.54]) at t2 more often than students with no STBs at t1. Students who reported a suicidal attempt at baseline ( n = 144; 2%) also reported suicidal thoughts and suicidal attempts more often at t2 ( OR = 5.98; 95% CI [3.89, 9.21]; OR = 30.00; 95% CI [15.84, 56.82], respectively). Limitations: The use of confidential self-reported data and the loss of cases after merging could have biased the results. Conclusion: For a subgroup of adolescents, STBs persisted and worsened over the 2 years. This demonstrates the importance of accurate identification of those at increased risk of suicide, in combination with personalized care.
Systematic Review and Network Meta-Analysis of Anodal tDCS Effects on Verbal Episodic Memory
Authors: Bartl Gergely Janos , Blackshaw Emily , Crossman Margot , Allen Paul , Sandrini Marco
Published: March 2020

Abstract. There is growing interest in the study of transcranial direct current stimulation (tDCS), a non-invasive brain stimulation technique, as an effective intervention to improve memory. In order to evaluate the relative efficacy of tDCS based on the location of anodal electrode sites, we conducted a systematic review examining the effect of stimulation applied during encoding on subsequent verbal episodic memory in healthy adults. We performed a network meta-analysis of 20 studies (23 experiments) with N = 978 participants. Left ventrolateral prefrontal and temporo-parietal sites appeared most likely to enhance episodic memory, although any significant effects were based on findings from single studies only. We did not find evidence for verbal retrieval enhancement of tDCS versus sham stimulation where the effect was based on more than one experimental paper. More frequent replication efforts and stricter reporting standards may improve the quality of evidence and allow more precise estimation of population-level effects of tDCS.
Effect of Subsurface Microseisms on the Motion of Dispersed Droplets in Pores
Authors: Zeng Chao , Deng Wen
Published: March 2020

Human‐induced seismicity has drawn substantial attention in recent years. The effect of seismicity on subsurface structures has been studied extensively. However, the effect of seismicity, especially microseismicity, on surrounding immiscible fluids is rarely investigated. In porous media with two or more immiscible fluids, different amplitudes of vibration induced by seismicity have distinct effects on the dynamic behavior of the fluids. Three types of pore‐scale models are prevalent for analyzing the motion of immiscible droplets. The underlying assumptions and accuracy of these models are compared in this study in both the frequency and time domains. The frequency domain analysis shows that resonance can be addressed in all three of the models; the frequency response curves, however, present significant differences, which are attributed to the missing physics considered in some models. Time domain analysis is performed in both small‐amplitude and large‐amplitude oscillation. The nonlinearity in large‐amplitude oscillation is attributed to the constricted geometry of the capillary tube. Although the term “large‐amplitude” is used in this study, the corresponding amplitude is still within the amplitude range of microseisms. The momentum balance model is identified as the most accurate oscillatory model so far in comparison with computational fluid dynamics simulations. In addition, the potential approach to incorporate this pore‐scale model in seismic wave attenuation analysis is found to be possible. The frequency correction function and structural factor are calculated to embed the momentum balance model into Biot's poroelastic model. The resonance of the dispersed phase can also be addressed theoretically in porous media of random packed spheres.
Saturable plasmonic metasurfaces for laser mode locking
Authors: Wang Jiyong , Coillet Aurelien , Demichel Olivier , Wang Zhiqiang , Rego Davi , Bouhelier Alexandre , Grelu Philippe , Cluzel Benoit
Published: March 2020

Metamaterials are artificial materials made of subwavelength elementary cells that give rise to unexpected wave properties that do not exist naturally. However, these properties are generally achieved due to 3D patterning, which is hardly feasible at short wavelengths in the visible and near-infrared regions targeted by most photonic applications. To overcome this limitation, metasurfaces, which are the 2D counterparts of metamaterials, have emerged as promising platforms that are compatible with planar nanotechnologies and thus mass production, which platforms the properties of a metamaterial into a 2D sheet. In the linear regime, wavefront manipulation for lensing, holography, and polarization control has been achieved recently. Interest in metasurfaces operating in the nonlinear regime has also increased due to the ability of metasurfaces to efficiently convert incident light into harmonic frequencies with unusual polarization properties. However, to date, the nonlinear absorption of metasurfaces has been mostly ignored. Here, we demonstrate that plasmonic metasurfaces behave as saturable absorbers with modulation performances superior to the modulation performance of other 2D materials and exhibit unusual polarimetric nonlinear transfer functions. We quantify the link between saturable absorption, the plasmonic resonances of the unit cell and their distribution in a 2D metasurface, and finally provide a practical implementation by integrating the metasurfaces into a fiber laser cavity operating in pulsed regimes driven by the metasurface properties. As such, this work provides new perspectives on ultrathin nonlinear saturable absorbers for applications where tunable nonlinear transfer functions are needed, such as in ultrafast lasers or neuromorphic circuits.
A 14 nucleotide deletion mutation in the coding region of the PpBBX24 gene is associated with the red skin of “Zaosu Red” pear (Pyrus pyrifolia White Pear Group): a deletion in the PpBBX24 gene is associated with the red skin of pear
Authors: Ou Chunqing , Zhang Xiaoli , Wang Fei , Zhang Liyi , Zhang Yanjie , Fang Ming , Wang Jiahong , Wang Jixun , Jiang Shuling , Zhang Zhihong
Published: March 2020

Red skin is an important quality trait for pear fruits and is determined by the concentration and composition of anthocyanins. The regulatory mechanism underlying anthocyanin accumulation is a popular topic in fruit research. Red mutants are ideal materials for studying the molecular mechanism of color diversity in pear. Although several red pear mutants have been cultivated and are in production, no exact locus containing the responsible genetic mutation has been identified. In this study, by combining the bulked segregant analysis with whole-genome sequencing, we identified a 14 nucleotide deletion mutation in the coding region of thePpBBX24gene from the red pear mutant “Zaosu Red”. We further verified that the deletion was present only in the red mutant of “Zaosu” and in its red offspring, which was different from that which occurred in other red pear fruits. This deletion results in a coding frame shift such that there is an early termination of thePpBBX24gene and loss of key NLS and VP domains from PpBBX24. The lost domains may reduce or alter the normal function of PpBBX24. In addition, we found that the transcript levels of thePpMYB10andPpHY5genes in red samples were significantly higher than those in green samples, whereas the results for the normal-typePpBBX24gene were the opposite. We ultimately revealed that the 14 nucleotide deletion mutation in the coding region of thePpBBX24gene is associated with the red skin of the “Zaosu Red” pear. This finding of somatic mutational events will be helpful for breeding new red pear cultivars and for understanding the regulatory mechanisms involved in pear skin pigmentation.
Chromosome doubling mediates superior drought tolerance in Lycium ruthenicum via abscisic acid signaling
Authors: Rao Shupei , Tian Yuru , Xia Xinli , Li Yue , Chen Jinhuan
Published: March 2020

Plants are continuously affected by unfavorable external stimuli, which influences their productivity and growth. Differences in gene composition and expression patterns lead homologous polyploid plants to exhibit different physiological phenomena, among which enhanced environmental adaptability is a powerful phenotype conferred by polyploidization. The mechanisms underlying the differences in stress tolerance between diploids and autotetraploids at the molecular level remain unclear. In this research, a full-length transcription profile obtained via the single-molecule real-time (SMRT) sequencing of high-quality single RNA molecules for use as background was combined with next-generation transcriptome and proteome technologies to probe the variation in the molecular mechanisms of autotetraploids. Tetraploids exhibited an increase in ABA content of 78.4% under natural conditions and a superior stress-resistance phenotype under severe drought stress compared with diploids. The substantial differences in the transcriptome profiles observed between diploids and autotetraploids under normal growth conditions were mainly related to ABA biosynthesis and signal transduction pathways, and 9-cis-epoxycarotenoid dioxygenase 1 (NCED1) and NCED2, which encode key synthetic enzymes, were significantly upregulated. The increased expression of the ABRE-binding factor 5-like (ABF5-like) gene was a pivotal factor in promoting the activation of the ABA signaling pathway and downstream target genes. In addition, ABA strongly induced the expression of osmotic proteins to increase the stress tolerance of the plants at the translational level. We consider the intrinsic mechanisms by which ABA affects drought resistance in tetraploids and diploids to understand the physiological and molecular mechanisms that enhance abiotic stress tolerance in polyploid plants.
Lipidomic and transcriptomic analysis reveals reallocation of carbon flux from cuticular wax into plastid membrane lipids in a glossy “Newhall” navel orange mutant
Authors: Wan Haoliang , Liu Hongbo , Zhang Jingyu , Lyu Yi , Li Zhuoran , He Yizhong , Zhang Xiaoliang , Deng Xiuxin , Brotman Yariv , Fernie Alisdair R. , Cheng Yunjiang , Wen Weiwei
Published: March 2020

Both cuticle and membrane lipids play essential roles in quality maintenance and disease resistance in fresh fruits. Many reports have indicated the modification of alternative branch pathways in epicuticular wax mutants; however, the specific alterations concerning lipids have not been clarified thus far. Here, we conducted a comprehensive, time-resolved lipidomic, and transcriptomic analysis on the “Newhall” navel orange (WT) and its glossy mutant (MT) “Gannan No. 1”. The results revealed severely suppressed wax formation accompanied by significantly elevated production of 36-carbon plastid lipids with increasing fruit maturation in MT. Transcriptomics analysis further identified a series of key functional enzymes and transcription factors putatively involved in the biosynthesis pathways of wax and membrane lipids. Moreover, the high accumulation of jasmonic acid (JA) in MT was possibly due to the need to maintain plastid lipid homeostasis, as the expression levels of two significantly upregulated lipases (CsDAD1 and CsDALL2) were positively correlated with plastid lipids and characterized to hydrolyze plastid lipids to increase the JA content. Our results will provide new insights into the molecular mechanisms underlying the natural variation of plant lipids to lay a foundation for the quality improvement of citrus fruit.
CsWAKL08, a pathogen-induced wall-associated receptor-like kinase in sweet orange, confers resistance to citrus bacterial canker via ROS control and JA signaling
Authors: Li Qiang , Hu Anhua , Qi Jingjing , Dou Wanfu , Qin Xiujuan , Zou Xiuping , Xu Lanzhen , Chen Shanchun , He Yongrui
Published: March 2020

Citrus bacterial canker (CBC) is a disease resulting from Xanthomonas citri subsp. citri (Xcc) infection and poses a grave threat to citrus production worldwide. Wall-associated receptor-like kinases (WAKLs) are proteins with a central role in resisting a range of fungal and bacterial diseases. The roles of WAKLs in the context of CBC resistance, however, remain unclear. Here, we explored the role of CsWAKL08, which confers resistance to CBC, and we additionally analyzed the molecular mechanisms of CsWAKL08-mediated CBC resistance. Based on systematic annotation and induced expression analysis of the CsWAKL family in Citrus sinensis, CsWAKL08 was identified as a candidate that can be upregulated by Xcc infection in the CBC-resistant variety. CsWAKL08 can also be induced by the phytohormones salicylic acid (SA) and methyl jasmonic acid (MeJA) and spans the plasma membrane. Overexpression of CsWAKL08 resulted in strong CBC resistance in transgenic sweet oranges, whereas silencing of CsWAKL08 resulted in susceptibility to CBC. The peroxidase (POD) and superoxide dismutase (SOD) activities were significantly enhanced in the CsWAKL08-overexpressing plants compared to the control plants, thereby mediating reactive oxygen species (ROS) homeostasis in the transgenic plants. Moreover, the JA levels and the expression of JA biosynthesis and JA responsive genes were substantially elevated in the CsWAKL08 overexpression plants relative to the controls upon Xcc infection. Based on these findings, we conclude that the wall-associated receptor-like kinase CsWAKL08 positively regulates CBC resistance through a mechanism involving ROS control and JA signaling. These results further highlight the importance of this kinase family in plant pathogen resistance.
Al-induced proteomics changes in tomato plants over-expressing a glyoxalase I gene
Authors: Sun Xudong , Li Hui , Thapa Santosh , Reddy Sangireddy Sasikiran , Pei Xiaobo , Liu Wei , Jiang Yuping , Yang Shaolan , Hui Dafeng , Bhatti Sarabjit , Zhou Suping , Yang Yong , Fish Tara , Thannhauser Theodore W.
Published: March 2020

Glyoxalase I (Gly I) is the first enzyme in the glutathionine-dependent glyoxalase pathway for detoxification of methylglyoxal (MG) under stress conditions. Transgenic tomato ‘Money Maker’ plants overexpressing tomato SlGlyI gene (tomato unigene accession SGN-U582631/Solyc09g082120.3.1) were generated and homozygous lines were obtained after four generations of self-pollination. In this study, SlGlyI-overepxressing line (GlyI), wild type (WT, negative control) and plants transformed with empty vector (ECtr, positive control), were subjected to Al-treatment by growing in Magnavaca’s nutrient solution (pH 4.5) supplemented with 20 µM Al3+ ion activity. After 30 days of treatments, the fresh and dry weight of shoots and roots of plants from Al-treated conditions decreased significantly compared to the non-treated conditions for all the three lines. When compared across the three lines, root fresh and dry weight of GlyI was significant higher than WT and ECtr, whereas there was no difference in shoot tissues. The basal 5 mm root-tips of GlyI plants expressed a significantly higher level of glyoxalase activity under both non-Al-treated and Al-treated conditions compared to the two control lines. Under Al-treated condition, there was a significant increase in MG content in ECtr and WT lines, but not in GlyI line. Quantitative proteomics analysis using tandem mass tags mass spectrometry identified 4080 quantifiable proteins and 201 Al-induced differentially expressed proteins (DEPs) in root-tip tissues from GlyI, and 4273 proteins and 230 DEPs from ECtr. The Al-down-regulated DEPs were classified into molecular pathways of gene transcription, RNA splicing and protein biosynthesis in both GlyI and ECtr lines. The Al-induced DEPs in GlyI associated with tolerance to Al3+ and MG toxicity are involved in callose degradation, cell wall components (xylan acetylation and pectin degradation), oxidative stress (antioxidants) and turnover of Al-damaged epidermal cells, repair of damaged DNA, epigenetics, gene transcription, and protein translation. A protein–protein association network was constructed to aid the selection of proteins in the same pathway but differentially regulated in GlyI or ECtr lines. Proteomics data are available via ProteomeXchange with identifiers PXD009456 under project title ‘25Dec2017_Suping_XSexp2_ITAG3.2’ for SlGlyI-overexpressing tomato plants and PXD009848 under project title ‘25Dec2017_Suping_XSexp3_ITAG3.2’ for positive control ECtr line transformed with empty vector.
A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)
Authors: Xue Ting , Zheng Xuehai , Chen Duo , Liang Limin , Chen Nan , Huang Zhen , Fan Wenfang , Chen Jiannan , Cen Wan , Chen Shuai , Zhu Jinmao , Chen Binghua , Zhang Xingtan , Chen Youqiang
Published: March 2020

The Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of extinction. The taxonomic status of Podostemaceae has always been controversial. Here, we report the first high-quality genome assembly forCladopus chinensisof Podostemaceae, obtained by incorporating Hi-C, Illumina and PacBio sequencing. We generated an 827.92 Mb genome with a contig N50 of 1.42 Mb and 27,370 annotated protein-coding genes. The assembled genome size was close to the estimated size, and 659.42 Mb of the assembly was assigned to 29 superscaffolds (scaffold N50 21.22 Mb). A total of 59.20% repetitive sequences were identified, among which long terminal repeats (LTRs) were the most abundant class (28.97% of the genome). Genome evolution analysis suggested that the divergence time ofCladopus chinensis(106 Mya) was earlier than that of Malpighiales (82 Mya) and that this taxon diverged into an independent branch of Podestemales. A recent whole-genome duplication (WGD) event occurred 4.43 million years ago. Comparative genomic analysis revealed that the expansion and contraction of oxidative phosphorylation, photosynthesis and isoflavonoid metabolism genes inCladopus chinensisare probably related to the genomic characteristics of this growing submerged species. Transcriptome analysis revealed that upregulated genes in the shoot group compared to the root group were enriched in the NAC gene family and transcription factors associated with shoot development and defense responses, including WUSCHEL (WUS), ASYMMETRIC LEAVES (ASL), SHOOT MERISTEMLESS (STM), NAC2, NAC8, NAC29, NAC47, NAC73, NAC83 and NAC102. These findings provide new insights into the genomic diversity of unusual aquatic angiosperms and serve as a valuable reference for the taxonomic status and unusual shoot apical meristem of Podostemaceae.
Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus
Authors: Li Shu-Fen , Wang Jin , Dong Ran , Zhu Hong-Wei , Lan Li-Na , Zhang Yu-Lan , Li Ning , Deng Chuan-Liang , Gao Wu-Jun
Published: March 2020

Asparagus setaceusis a popular ornamental plant cultivated in tropical and subtropical regions globally. Here, we constructed a chromosome-scale reference genome ofA. setaceusto facilitate the investigation of its genome characteristics and evolution. Using a combination of Nanopore long reads, Illumina short reads, 10× Genomics linked reads, and Hi-C data, we generated a high-quality genome assembly ofA. setaceuscovering 710.15 Mb, accounting for 98.63% of the estimated genome size. A total of 96.85% of the sequences were anchored to ten superscaffolds corresponding to the ten chromosomes. The genome ofA. setaceuswas predicted to contain 28,410 genes, 25,649 (90.28%) of which were functionally annotated. A total of 65.59% of the genome was occupied by repetitive sequences, among which long terminal repeats were predominant (42.51% of the whole genome). Evolutionary analysis revealed an estimated divergence time ofA. setaceusfrom its close relativeA. officinalisof ~9.66 million years ago, andA. setaceusunderwent two rounds of whole-genome duplication. In addition, 762 specific gene families, 96 positively selected genes, and 76 resistance (R) genes were detected and functionally predicted inA. setaceus. These findings provide new knowledge about the characteristics and evolution of theA. setaceusgenome, and will facilitate comparative genetic and genomic research on the genusAsparagus.
Investigation of the transcriptomic and metabolic changes associated with superficial scald physiology impaired by lovastatin and 1-methylcyclopropene in pear fruit (cv. “Blanquilla”)
Authors: Giné-Bordonaba Jordi , Busatto Nicola , Larrigaudière Christian , Lindo-García Violeta , Echeverria Gemma , Vrhovsek Urska , Farneti Brian , Biasioli Franco , De Quattro Concetta , Rossato Marzia , Delledonne Massimo , Costa Fabrizio
Published: March 2020

To elucidate the physiology underlying the development of superficial scald in pears, susceptible “Blanquilla” fruit was treated with different compounds that either promoted (ethylene) or repressed (1-methylcyclopropene and lovastatin) the incidence of this disorder after 4 months of cold storage. Our data show that scald was negligible for the fruit treated with 1-methylcyclopropene or lovastatin, but highly manifested in untreated (78% incidence) or ethylene-treated fruit (97% incidence). The comparison between the fruit metabolomic profile and transcriptome evidenced a distinct reprogramming associated with each treatment. In all treated samples, cold storage led to an activation of a cold-acclimation-resistance mechanism, including the biosynthesis of very-long-chain fatty acids, which was especially evident in 1-methylcyclopropane-treated fruit. Among the treatments applied, only 1-methylcyclopropene inhibited ethylene production, hence supporting the involvement of this hormone in the development of scald. However, a common repression effect on thePPOgene combined with higher sorbitol content was found for both lovastatin and 1-methylcyclopropene-treated samples, suggesting also a non-ethylene-mediated process preventing the development of this disorder. The results presented in this work represent a step forward to better understand the physiological mechanisms governing the etiology of superficial scald in pears.
(E)-Nerolidol is a volatile signal that induces defenses against insects and pathogens in tea plants
Authors: Chen Shenglong , Zhang Liping , Cai Xiaoming , Li Xin , Bian Lei , Luo Zongxiu , Li Zhaoqun , Chen Zongmao , Xin Zhaojun
Published: March 2020

Plants release large amounts of volatile organic compounds (VOCs) in response to attackers. Several VOCs can serve as volatile signals to elicit defense responses in undamaged tissues and neighboring plants, but many questions about the ecological functions of VOCs remain unanswered. Tea plants are impacted by two harmful invaders, the piercing herbivore Empoasca (Matsumurasca) onukii Matsuda and the pathogen Colletotrichum fructicola. To determine the VOC signals in tea, we confirmed CsOPR3 as a marker gene and set up a rapid screening method based on a 1.51 kb CsOPR3 promoter fused with a β-glucuronidase (GUS) reporter construct (OPR3p::GUS) in Arabidopsis. Using this screening system, a terpenoid volatile (E)-nerolidol was identified as a potent signal that elicits plant defenses. The early responses triggered by (E)-nerolidol included the activation of a mitogen-activated protein kinase and WRKY, an H2O2 burst, and the induction of jasmonic acid and abscisic acid signaling. The induced plants accumulated high levels of defense-related chemicals, which possessed broad-spectrum anti-herbivore or anti-pathogen properties, and ultimately triggered resistance against Empoasca onukii and Colletotrichum fructicola in tea. We propose that these findings can supply an environmentally friendly management strategy for controlling an insect pest and a disease of tea plants.
Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6
Authors: Garcia-Doval Carmela , Schwede Frank , Berk Christian , Rostøl Jakob T. , Niewoehner Ole , Tejero Oliver , Hall Jonathan , Marraffini Luciano A. , Jinek Martin
Published: March 2020

Bacterial and archaeal CRISPR-Cas systems provide RNA-guided immunity against genetic invaders such as bacteriophages and plasmids. Upon target RNA recognition, type III CRISPR-Cas systems produce cyclic-oligoadenylate second messengers that activate downstream effectors, including Csm6 ribonucleases, via their CARF domains. Here, we show that Enteroccocus italicus Csm6 (EiCsm6) degrades its cognate cyclic hexa-AMP (cA6) activator, and report the crystal structure of EiCsm6 bound to a cA6 mimic. Our structural, biochemical, and in vivo functional assays reveal how cA6 recognition by the CARF domain activates the Csm6 HEPN domains for collateral RNA degradation, and how CARF domain-mediated cA6 cleavage provides an intrinsic off-switch to limit Csm6 activity in the absence of ring nucleases. These mechanisms facilitate rapid invader clearance and ensure termination of CRISPR interference to limit self-toxicity.
Synthetic antibodies against BRIL as universal fiducial marks for single−particle cryoEM structure determination of membrane proteins
Authors: Mukherjee Somnath , Erramilli Satchal K. , Ammirati Mark , Alvarez Frances J. D. , Fennell Kimberly F. , Purdy Michael D. , Skrobek Blazej M. , Radziwon Katarzyna , Coukos John , Kang Yanyong , Dutka Przemysław , Gao Xiang , Qiu Xiayang , Yeager Mark , Eric Xu H. , Han Seungil , Kossiakoff Anthony A.
Published: March 2020

We propose the concept of universal fiducials based on a set of pre-made semi-synthetic antibodies (sABs) generated by customized phage display selections against the fusion protein BRIL, an engineered variant of apocytochrome b562a. These sABs can bind to BRIL fused either into the loops or termini of different GPCRs, ion channels, receptors and transporters without disrupting their structure. A crystal structure of BRIL in complex with an affinity-matured sAB (BAG2) that bound to all systems tested delineates the footprint of interaction. Negative stain and cryoEM data of several examples of BRIL-membrane protein chimera highlight the effectiveness of the sABs as universal fiducial marks. Taken together with a cryoEM structure of sAB bound human nicotinic acetylcholine receptor, this work demonstrates that these anti-BRIL sABs can greatly enhance the particle properties leading to improved cryoEM outcomes, especially for challenging membrane proteins.
Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric mouse brain
Authors: Xu Ranjie , Li Xiaoxi , Boreland Andrew J. , Posyton Anthony , Kwan Kelvin , Hart Ronald P. , Jiang Peng
Published: March 2020

Microglia, the brain-resident macrophages, exhibit highly dynamic functions in neurodevelopment and neurodegeneration. Human microglia possess unique features as compared to mouse microglia, but our understanding of human microglial functions is largely limited by an inability to obtain human microglia under homeostatic states. Here, we develop a human pluripotent stem cell (hPSC)-based microglial chimeric mouse brain model by transplanting hPSC-derived primitive macrophage progenitors into neonatal mouse brains. Single-cell RNA-sequencing of the microglial chimeric mouse brains reveals that xenografted hPSC-derived microglia largely retain human microglial identity, as they exhibit signature gene expression patterns consistent with physiological human microglia and recapitulate heterogeneity of adult human microglia. Importantly, the engrafted hPSC-derived microglia exhibit dynamic response to cuprizone-induced demyelination and species-specific transcriptomic differences in the expression of neurological disease-risk genes in microglia. This model will serve as a tool to study the role of human microglia in brain development and degeneration.
Integrated omics profiling of dextran sodium sulfate-induced colitic mice supplemented with Wolfberry (Lycium barbarum)
Authors: Aw Wanping , Jia Huijuan , Lyu Weida , Fukuda Shinji , Tomita Masaru , Otani Lila , Kato Hisanori
Published: March 2020

We used a multi-omics profiling approach to investigate the suppressive effects of 2% Wolfberry (WOL)-enriched diets on dextran sodium sulfate (DSS)-induced colitis in mice. It was observed that in mice fed the WOL diet, the disease activity index, colon shortening, plasma concentrations of matrix metalloproteinase-3 and relative mesenteric fat weight were significantly improved as compared to the DSS group. Results from colon transcriptome and proteome profiles showed that WOL supplementation significantly ameliorated the expression of genes and proteins associated with the integrity of the colonic mucosal wall and colonic inflammation. Based on the hepatic transcriptome, proteome and metabolome data, genes involved in fatty acid metabolism, proteins involved in inflammation and metabolites related to glycolysis were downregulated in WOL mice, leading to lowered inflammation and changes in these molecules may have led to improvement in body weight loss. The integrated nutrigenomic approach thus revealed the molecular mechanisms underlying the ameliorative effect of whole WOL fruit consumption on inflammatory bowel disease.
A systematic study of hexavalent chromium adsorption and removal from aqueous environments using chemically functionalized amorphous and mesoporous silica nanoparticles
Authors: Jang Eun-Hye , Pack Seung Pil , Kim Il , Chung Sungwook
Published: March 2020

We report on the synthesis and characterization of highly monodisperse amorphous silica nanoparticles (ASNs) and mesoporous silica nanoparticles (MSNs) with particle sizes of 15–60 nm. We demonstrate adsorption of Cr(VI) ions on amino-functionalized ASNs (NH2–ASNs) and MSNs (NH2–MSNs) and their removal from aqueous environments and show the specific surface area (SSA) of NH2–MSNs is four times as larger as that of NH2–ASNs and that more than 70% of the total SSA of NH2–MSNs is due to the presence of nanopores. Analyses of Cr(VI) adsorption kinetics on NH2–ASNs and NH2–MSNs exhibited relatively rapid adsorption behavior following pseudo-second order kinetics as determined by nonlinear fitting. NH2–ASNs and NH2–MSNs exhibited significantly higher Cr(VI) adsorption capacities of 34.0 and 42.2 mg·g−1 and removal efficiencies of 61.9 and 76.8% than those of unfunctionalized ASNs and MSNs, respectively. The Langmuir model resulted in best fits to the adsorption isotherms of NH2–ASNs and NH2–MSNs. The adsorption of Cr(VI) on NH2–ASNs and NH2–MSNs was an endothermic and spontaneous process according to the thermodynamic analyses of temperature-dependent adsorption isotherms. The removal efficiencies of NH2–ASNs and NH2–MSNs exhibited a moderate reduction of less than 25% of the maximum values after five regeneration cycles. Furthermore, NH2–MSNs were also found to reduce adsorbed Cr(VI) into less harmful Cr(III).