Shotgun proteomic analysis of mulberry dwarf phytoplasma

<p>Abstract</p> <p>Background</p> <p>Mulberry dwarf (MD), which is caused by phytoplasma, is one of the most serious infectious diseases of mulberry. Phytoplasmas have been associated with diseases in several hundred plant species. The inability to culture phytoplasmas <it>in vitro </it>has hindered their characterization at the molecular level. Though the complete genomes of two phytoplasmas have been published, little information has been obtained about the proteome of phytoplasma. Therefore, the proteomic information of phytoplasmas would be useful to elucidate the functional mechanisms of phytoplasma in many biological processes.</p> <p>Results</p> <p>MD phytoplasmas, which belong to the 16SrI-B subgroup based on the 16S DNA analysis, were purified from infected tissues using a combination of differential centrifugation and density gradient centrifugation. The expressed proteome of phytoplasma was surveyed by one-dimensional SDS-PAGE and nanocapillary liquid chromatography-tandem mass spectrometry. A total of 209 phytoplasma proteins were unambiguously assigned, including the proteins with the functions of amino acid biosynthesis, cell envelope, cellular processes, energy metabolism, nucleosides and nucleotide metabolism, replication, transcription, translation, transport and binding as well as the proteins with other functions. In addition to these known function proteins, 63 proteins were annotated as hypothetical or conserved hypothetical proteins.</p> <p>Conclusions</p> <p>Taken together, a total of 209 phytoplasma proteins have been experimentally verified, representing the most extensive survey of any phytoplasma proteome to date. This study provided a valuable dataset of phytoplasma proteins, and a better understanding of the energy metabolism and virulence mechanisms of MD phytoplasma.</p

Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice

<p>Abstract</p> <p>Background</p> <p>Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. They have been known to play important roles in RNA processing as RNA-binding proteins in animals. To date, few plant CCCH proteins have been studied functionally.</p> <p>Results</p> <p>In this study, a comprehensive computational analysis identified 68 and 67 CCCH family genes in Arabidopsis and rice, respectively. A complete overview of this gene family in Arabidopsis was presented, including the gene structures, phylogeny, protein motifs, and chromosome locations. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. These results revealed that the CCCH families in Arabidopsis and rice were divided into 11 and 8 subfamilies, respectively. The gene duplication contributed to the expansion of the CCCH gene family in Arabidopsis genome. Expression studies indicated that CCCH proteins exhibit a variety of expression patterns, suggesting diverse functions. Finally, evolutionary analysis showed that one subfamily is higher plant specific. The expression profile indicated that most members of this subfamily are regulated by abiotic or biotic stresses, suggesting that they could have an effective role in stress tolerance.</p> <p>Conclusion</p> <p>Our comparative genomics analysis of CCCH genes and encoded proteins in two model plant species provides the first step towards the functional dissection of this emerging family of potential RNA-binding proteins.</p

Outcome Predictors in Patients Presenting With Acute Aortic Dissection

ObjectiveTo investigate the role of thyroid hormones and other factors in acute aortic dissection and an association with in-hospital adverse events.DesignA retrospective analysis.SettingA university-affiliated cardiac center.ParticipantsA total of 151 patients with aortic dissection admitted to the authors’ hospital between January 2011 and May 2015.InterventionNone.Measurements and ResultsThe total in-hospital mortality rate was 12.6%. Triiodothyronine (T3) level was lower in nonsurviving than surviving patients (0.8±0.3 v 1.0±0.4 nmol/L, p<0.05). T3 independently predicted in-hospital mortality (hazard ratio [HR] 0.07, 95% CI 0.01-0.43, p<0.01) and in-hospital acute renal failure (HR 0.22, 0.05-0.89, p<0.05) for all patients. Other independent predictors of in-hospital mortality were pericardial effusion (HR 8.18, 2.11-31.67, p<0.01), conservative treatment (HR 82.12, 12.49-540.09, p<0.01) and Stanford type-A aortic dissection (HR 3.86, 1.06-14.09, p<0.05). Inpatient conservative treatment, T3 (HR 0.01, 0.00-0.18, p<0.01) as well as pericardial effusion (HR 11.80, 2.46-56.59, p<0.01), Stanford type-A dissection (HR 22.35, 3.15-158.40, p<0.01), and in-hospital acute renal failure (HR 16.95, 2.04-140.86, p<0.01) were predictors for in-hospital mortality. In nonconservatively treated patients, T3 (HR 0.02, 0.00-0.88, p<0.05) as well as cardiac care unit stay (HR 0.74, 0.59-0.94, p<0.01) and postoperative acute renal failure (HR 21.32, 3.07-147.88, p<0.01) were predictors for in-hospital mortality.ConclusionT3 was downregulated in acute aortic dissection. Low T3 level was a risk factor for in-hospital death and acute renal failure in patients with acute aortic dissection

Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis

<p>Abstract</p> <p>Background</p> <p>The protein phosphatase 2Cs (PP2Cs) from various organisms have been implicated to act as negative modulators of protein kinase pathways involved in diverse environmental stress responses and developmental processes. A genome-wide overview of the PP2C gene family in plants is not yet available.</p> <p>Results</p> <p>A comprehensive computational analysis identified 80 and 78 PP2C genes in <it>Arabidopsis thaliana </it>(AtPP2Cs) and <it>Oryza sativa </it>(OsPP2Cs), respectively, which denotes the PP2C gene family as one of the largest families identified in plants. Phylogenic analysis divided PP2Cs in Arabidopsis and rice into 13 and 11 subfamilies, respectively, which are supported by the analyses of gene structures and protein motifs. Comparative analysis between the PP2C genes in Arabidopsis and rice identified common and lineage-specific subfamilies and potential 'gene birth-and-death' events. Gene duplication analysis reveals that whole genome and chromosomal segment duplications mainly contributed to the expansion of both OsPP2Cs and AtPP2Cs, but tandem or local duplication occurred less frequently in Arabidopsis than rice. Some protein motifs are widespread among the PP2C proteins, whereas some other motifs are specific to only one or two subfamilies. Expression pattern analysis suggests that 1) most PP2C genes play functional roles in multiple tissues in both species, 2) the induced expression of most genes in subfamily A by diverse stimuli indicates their primary role in stress tolerance, especially ABA response, and 3) the expression pattern of subfamily D members suggests that they may constitute positive regulators in ABA-mediated signaling pathways. The analyses of putative upstream regulatory elements by two approaches further support the functions of subfamily A in ABA signaling, and provide insights into the shared and different transcriptional regulation machineries in dicots and monocots.</p> <p>Conclusion</p> <p>This comparative genome-wide overview of the PP2C family in Arabidopsis and rice provides insights into the functions and regulatory mechanisms, as well as the evolution and divergence of the PP2C genes in dicots and monocots. Bioinformatics analyses suggest that plant PP2C proteins from different subfamilies participate in distinct signaling pathways. Our results have established a solid foundation for future studies on the functional divergence in different PP2C subfamilies.</p

Genetically engineered magnetic nanocages for cancer magneto-catalytic theranostics

磁热疗法是一种利用磁热敏剂在磁场中把磁能转换为热能以杀死肿瘤的新型癌症治疗方法，并已成功应用于临床。但是，目前临床所用磁热敏剂的磁-热转换效率低而使得治疗剂量过大，从而给病人带来潜在的副作用，因此大大限制了磁热疗法的广泛应用。该研究利用基因工程和仿生矿化技术制备出具有优异磁-热转化能力及纳米酶催化性能的磁性蛋白纳米笼（eMIONs），成功克服了临床磁热疗法中磁热敏剂低效的瓶颈，为新一代磁热敏剂的研发提供新的思路。该研究工作在刘刚教授指导下完成，博士生张阳为文章第一作者。【Abstract】The clinical applications of magnetic hyperthermia therapy (MHT) have been largely hindered by the poor magnetic-to-thermal conversion efficiency of MHT agents. Herein, we develop a facile and efficient strategy for engineering encapsulin-produced magnetic iron oxide nanocomposites (eMIONs) via a green biomineralization procedure. We demonstrate that eMIONs have excellent magnetic saturation and remnant magnetization properties, featuring superior magnetic-to-thermal conversion efficiency with an ultrahigh specific absorption rate of 2390 W/g to overcome the critical issues of MHT. We also show that eMIONs act as a nanozyme and have enhanced catalase-like activity in the presence of an alternative magnetic field, leading to tumor angiogenesis inhibition with a corresponding sharp decrease in the expression of HIF-1α. The inherent excellent magnetic-heat capability, coupled with catalysis-triggered tumor suppression, allows eMIONs to provide an MRI-guided magneto-catalytic combination therapy, which may open up a new avenue for bench-to-bed translational research of MHT.This work was supported by the Major State Basic Research Development Program of China (2017YFA0205201), the National Natural Science Foundation of China (81925019, 81422023, 81603015, 81871404, and U1705281), the Fundamental Research Funds for the Central Universities (20720190088 and 20720200019), and the Program for New Century Excellent Talents in University, China (NCET-13-0502). We acknowledge Jingru Huang and Baoying Xie from Central Laboratory in School of Medicine, Xiamen University, for assistance with inductively coupled plasma experiments and data analysis. 研究工作得到了科技部重大专项课题、973课题、国家自然科学基金委杰出青年基金等项目的支持

PwHAP5, a CCAAT-binding transcription factor, interacts with PwFKBP12 and plays a role in pollen tube growth orientation in Picea wilsonii

The HAP complex occurs in many eukaryotic organisms and is involved in multiple physiological processes. Here it was found that in Picea wilsonii, HAP5 (PwHAP5), a putative CCAAT-binding transcription factor gene, is involved in pollen tube development and control of tube orientation. Quantitative real-time reverse transcription-PCR showed that PwHAP5 transcripts were expressed strongly in germinating pollen and could be induced by Ca2+. Overexpression of PwHAP5 in pollen altered pollen tube orientation, whereas the tube with PwHAP5RNAi showed normal growth without diminishing pollen tube growth. Furthermore, PwFKBP12, which encodes an FK506-binding protein (FKBP) was screened and a bimolecular fluorescence complementation assay performed to confirm the interaction of PwHAP5 and PwFKBP12 in vivo. Transient expression of PwFKBP12 in pollen showed normal pollen tube growth, whereas the tube with PwFKBP12RNAi bent. The phenotype of overexpression of HAP5 on pollen tube was restored by FKBP12. Altogether, our study supported the role of HAP5 in pollen tube development and orientation regulation and identified FKBP12 as a novel partner to interact with HAP5 involved in the process

Molecular Detection of Fungal Communities in the Hawaiian Marine Sponges Suberites zeteki and Mycale armata▿

Symbiotic microbes play a variety of fundamental roles in the health and habitat ranges of their hosts. While prokaryotes in marine sponges have been broadly characterized, the diversity of sponge-inhabiting fungi has barely been explored using molecular approaches. Fungi are an important component of many marine and terrestrial ecosystems, and they may be an ecologically significant group in sponge-microbe interactions. This study tested the feasibility of using existing fungal primers for molecular analysis of sponge-associated fungal communities. None of the eight selected primer pairs yielded satisfactory results in fungal rRNA gene or internal transcribed spacer (ITS) clone library constructions. However, 3 of 10 denaturing gradient gel electrophoresis (DGGE) primer sets, which were designed to preferentially amplify fungal rRNA gene or ITS regions from terrestrial environmental samples, were successfully amplified from fungal targets in marine sponges. DGGE analysis indicated that fungal communities differ among different sponge species (Suberites zeteki and Mycale armata) and also vary between sponges and seawater. Sequence analysis of DGGE bands identified 23 and 21 fungal species from each of the two sponge species S. zeteki and M. armata, respectively. These species were representatives of 11 taxonomic orders and belonged to the phyla of Ascomycota (seven orders) and Basidiomycota (four orders). Five of these taxonomic orders (Malasseziales, Corticiales, Polyporales, Agaricales, and Dothideomycetes et Chaetothyriomcetes incertae sedis) have now been identified for the first time in marine sponges. Seven and six fungal species from S. zeteki and M. armata, respectively, are potentially new species because of their low sequence identity (≤98%) with their references in GenBank. Phylogenetic analysis indicated sponge-derived sequences were clustered into “marine fungus clades” with those from other marine habitats. This is the first report of molecular analysis of fungal communities in marine sponges, adding depth and dimension to our understanding of sponge-associated microbial communities

Reinforcement Learning-Based Collision Avoidance Guidance Algorithm for Fixed-Wing UAVs

A deep reinforcement learning-based computational guidance method is presented, which is used to identify and resolve the problem of collision avoidance for a variable number of fixed-wing UAVs in limited airspace. The cooperative guidance process is first analyzed for multiple aircraft by formulating flight scenarios using multiagent Markov game theory and solving it by machine learning algorithm. Furthermore, a self-learning framework is established by using the actor-critic model, which is proposed to train collision avoidance decision-making neural networks. To achieve higher scalability, the neural network is customized to incorporate long short-term memory networks, and a coordination strategy is given. Additionally, a simulator suitable for multiagent high-density route scene is designed for validation, in which all UAVs run the proposed algorithm onboard. Simulated experiment results from several case studies show that the real-time guidance algorithm can reduce the collision probability of multiple UAVs in flight effectively even with a large number of aircraft

Correction: Genome-Wide Comparative In Silico Analysis of the RNA Helicase Gene Family in Zea mays and Glycine max: A Comparison with Arabidopsis and Oryza sativa.

[This corrects the article DOI: 10.1371/journal.pone.0078982.]