bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chlamydia Serine Protease Inhibitor, targeting HtrA, as a New Treatment for Koala Chlamydia infection
Authors: Lawrence Amba , Fraser Tamieka , Gillett Amber , Tyndall Joel D. A. , Timms Peter , Polkinghorne Adam , Huston Wilhelmina M. 
Published: August 2016

AbstractThe koala, an iconic marsupial native to Australia, is a threatened species in many parts of the country. One major factor in the decline is disease caused by infection with Chlamydia. Current therapeutic strategies to treat chlamydiosis in the koala are limited. This study examines the effectiveness of an inhibitor, JO146, which targets the HtrA serine protease for treatment of C. pecorum and C. pneumoniae in vitro and ex vivo with the aim of developing a novel therapeutic for koala Chlamydia infections. Clinical isolates from koalas were examined for their susceptibility to JO146. In vitro studies demonstrated that treatment with JO146 during the mid-replicative phase of C. pecorum or C. pneumoniae infections resulted in a significant loss of infectious progeny. Ex vivo primary koala tissue cultures were used to demonstrate the efficacy of JO146 and the non-toxic nature of this compound on peripheral blood mononuclear cells and primary cell lines established from koala tissues collected at necropsy. Our results suggest that inhibition of the serine protease HtrA could be a novel treatment strategy for chlamydiosis in koalas.
Efficient Genome Editing in Apple Using a CRISPR/Cas9 system
Authors: Nishitani Chikako , Hirai Narumi , Komori Sadao , Wada Masato , Okada Kazuma , Osakabe Keishi , Yamamoto Toshiya , Osakabe Yuriko 
Published: August 2016

AbstractGenome editing is a powerful technique for genome modification in molecular research and crop breeding and has the great advantage of imparting novel desired traits to genetic resources. However, the genome editing of fruit tree plantlets remains to be established. In this study, we describe induction of a targeted gene mutation in the endogenous apple phytoene desaturase (PDS) gene using the CRISPR/Cas9 system. Four guide RNAs (gRNAs) were designed and stably transformed with Cas9 separately in apple. Clear and partial albino phenotypes were observed in 31.8% of regenerated plantlets for one gRNA and bi-allelic mutations in apple PDS were confirmed by DNA sequencing. In addition, an 18-bp gRNA also induced a targeted mutation. These CRIPSR/Cas9 induced-mutations in the apple genome suggest activation of the NHEJ pathway, but with some involvement also of the HR pathway. Our results demonstrate that genome editing can be practically applied to modify the apple genome.
Feedback control of ErbB2 via ERK-mediated phosphorylation of a conserved threonine in the juxtamembrane domain
Authors: Kawasaki Yuki , Sakimura Ayaka , Park Chul Min , Tomaru Rika , Tanaka Tomohiro , Ozawa Tatsuhiko , Zhou Yue , Narita Kaori , Kishi Hiroyuki , Muraguchi Atsushi , Sakurai Hiroaki 
Published: August 2016

AbstractTyrosine kinase activity of the asymmetric EGFR homodimer is negatively regulated via ERK-mediated phosphorylation of Thr-669 in the juxtamembrane domain. In the present study, we investigated in human breast cancer cells whether a similar mechanism plays a role in the feedback regulation of the ErbB2/ErbB3 heterodimer, the most potent ErbB receptor dimer. Constitutive tyrosine phosphorylation of ErbB2 and ErbB3 was significantly decreased in phorbol ester- and growth factor-treated BT-474 and MDA-MB-453 cells. In contrast to the decreased tyrosine phosphorylation, Phos-tag Western blot analysis revealed that TPA induced phosphorylation of ErbB2 in an ERK-dependent manner. The target threonine residue corresponding to EGFR Thr-669 and the surrounding residues are highly conserved in ErbB2, but not in ErbB3. Therefore, we demonstrated ERK-mediated phosphorylation of ErbB2 at Thr-677 by generating phospho-specific monoclonal antibodies. Moreover, treatment with trametinib and SCH772984, inhibitors of the MEK-ERK pathway and substitution of Thr-677 to alanine impaired the feedback inhibition of ErbB2 and ErbB3. These results demonstrated that ERK-mediated phosphorylation of the conserved threonine is a common mechanism for the negative feedback control of active ErbB receptor dimers.
Resonant vortex-core reversal in magnetic nano-spheres as robust mechanism of efficient energy absorption and emission
Authors: Kim Sang-Koog , Yoo Myoung-Woo , Lee Jehyun , Lee Jae-Hyeok , Kim Min-Kwan 
Published: August 2016

AbstractWe report on novel vortex-core reversal dynamics in nano-spheres of single-vortex spin configuration as revealed by micromagnetic simulations combined with analytical derivations. When the frequency of an AC magnetic field is tuned to the frequency of the vortex-core precession around the direction of a given static field, oscillatory vortex-core reversals occur, and additionally, the frequency is found to change with both the strength of the applied AC field and the particle size. Such resonant vortex-core reversals in nano-spheres may provide a new and efficient means of energy absorption by, and emission from, magnetic nanoparticles, which system can be effectively implemented in bio-applications such as magnetic hyperthermia.
Systematic evaluation of sericin protein as a substitute for fetal bovine serum in cell culture
Authors: Liu Liyuan , Wang Jinhuan , Duan Shengchang , Chen Lei , Xiang Hui , Dong Yang , Wang Wen 
Published: August 2016

AbstractFetal bovine serum (FBS) shows obvious deficiencies in cell culture, such as low batch to batch consistency, adventitious biological contaminant risk and high cost, which severely limit the development of the cell culture industry. Sericin protein derived from the silkworm cocoon has become increasingly popular due to its diverse and beneficial cell culture characteristics. However, systematic evaluation of sericin as a substitute for FBS in cell culture medium remains limited. In this study, we conducted cellular morphological, physiological and transcriptomic evaluation on three widely used mammalian cells. Compared with cells cultured in the control, those cultured in sericin-substitute medium showed similar cellular morphology, similar or higher cellular overall survival, lower population doubling time (PDT) and a higher percentage of S-phase with similar G2/G1 ratio, indicating comparable or better cell growth and proliferation. At the transcriptomic level, differentially expressed genes between cells in the two media were mainly enriched in function and biological processes related to cell growth and proliferation, reflecting that genes were activated to facilitate cell growth and proliferation. The results of this study suggest that cells cultured in sericin-substituted medium perform as well as, or even better than, those cultured in FBS-containing medium.
Tolerance and responsive gene expression of Sogatella furcifera under extreme temperature stresses are altered by its vectored plant virus
Authors: Xu Donglin , Zhong Ting , Feng Wendi , Zhou Guohui 
Published: August 2016

AbstractSouthern rice black-streaked dwarf virus (SRBSDV), a newly emerged fijivirus causing great loss to rice production in eastern and southeastern Asian countries in recent years, is efficiently transmitted by a rice pest, white-backed planthopper (WBPH, Sogatella furcifera) in a persistent, circulative propagative manner and can be considered as an insect virus. In this study, SRBSDV infection in WBPH was found to increase the vector’s death rate under extreme cold stress but improve its survival rate under extreme heat stress. Digital gene expression profiling based on RNA-Seq revealed different gene regulation patterns in WBPH under viral and/or temperature stress. Under cold stress, the virus infection upregulated 1540 genes and downregulated 131 genes in the insect, most of which were related to membrane properties and biological processes of actin and cytoskeleton; whereas under heat stress, it upregulated 363 genes and downregulated 548 genes, most of which were associated to metabolism and intracellular organelles. Several types of stress-responsive genes involving intestinal mucin, cuticle protein, ubiquitin protease, immune response, RNA interference and heat shock response, were largely upregulated under cold stress, but largely downregulated under heat stress, by SRBSDV infection. Our results suggest two distinct mechanisms of virus-altered vector insect tolerance to temperature stress.
Measurement of Histone Methylation Dynamics by One-Carbon Metabolic Isotope Labeling and High-energy Collisional Dissociation Methylation Signature Ion Detection
Authors: Tang Hui , Tian Bing , Brasier Allan R. , Sowers Lawrence C. , Zhang Kangling 
Published: August 2016

AbstractAccumulating evidence suggests that cellular metabolites and nutrition levels control epigenetic modifications, including histone methylation. However, it is not currently possible to measure the metabolic control of histone methylation. Here we report a novel detection method to monitor methyl transfer from serine to histones through the one-carbon metabolic pathway, using stable-isotope labeling and detection of lysine methylation signature ions generated in high-energy-dissociation (HCD) tandem mass spectrometry. This method is a long-needed tool to study the metabolic control of histone methylation.
Use of slow-release plant infochemicals to control aphids: a first investigation in a Belgian wheat field
Authors: Zhou Haibo , Chen Longsheng , Liu Yong , Chen Julian , Francis Frédéric 
Published: August 2016

AbstractUsing infochemicals to develop a push–pull strategy in pest control is a potential way to promote sustainable crop production. Infochemicals from plant essential oils were mixed with paraffin oil for slow release in field experiments on wheat to control the population density of cereal aphids and to enhance their natural enemies. (Z)-3-Hexenol (Z3H) attracted Metopolophum dirhodum and Sitobion avenae, the predominant species on wheat in Belgium, and may be a useful infochemical for aphid control by attracting aphids away from field plots. Release of (E)-β-farnesene (EBF) or a garlic extract (GE) led to a significant decrease in the abundance of wheat aphids. The main natural enemies of cereal aphids found were lacewings (47.8%), hoverflies (39.4%), and ladybirds (12.8%). Ladybird abundance varied little before the end of the wheat-growing season. Our results suggest that these chemicals can form the basis of a “push–pull” strategy for aphid biological control, with GE and EBF acting as a pest- and beneficial-pulling stimulus and Z3H for aphid pulling.
ELBW survivors in early adulthood have higher hepatic, pancreatic and subcutaneous fat
Authors: Crane Justin D. , Yellin Samuel A. , Ong Frank J. , Singh Nina P. , Konyer Norman , Noseworthy Michael D. , Schmidt Louis A. , Saigal Saroj , Morrison Katherine M. 
Published: August 2016

AbstractPremature birth in conjunction with extremely low birth weight (<1 kg, ELBW) is associated with insulin resistance and increased cardiometabolic health risk compared to birth at full term with normal birth weight (NBW). However, little is known regarding the biologic mediators of these effects. Abdominal and ectopic lipid accumulation is linked to insulin resistance and metabolic dysfunction, yet whether ELBW survivors are predisposed to aberrant lipid deposition in adulthood is unknown. We used magnetic resonance imaging in a cohort of 16 NBW and 29 ELBW participants to determine if ELBW survivors have differences in pancreatic, hepatic, subcutaneous and visceral fat distribution compared to NBW participants. ELBW individuals had a higher proportion of liver and pancreatic fat compared to NBW subjects (P < 0.05). Abdominal subcutaneous fat, but not visceral fat, area was higher in ELBW survivors compared to NBW individuals. In multivariate analyses, tissue fat measures were most highly related to BMI and sex, but not preterm birth. This work highlights that fat deposition is enhanced in adults born preterm and suggests that ectopic fat accretion driven by their relatively greater adiposity may contribute to the higher rates of metabolic dysfunction seen in ELBW survivors.
Sorting protein decoys by machine-learning-to-rank
Authors: Jing Xiaoyang , Wang Kai , Lu Ruqian , Dong Qiwen 
Published: August 2016

AbstractMuch progress has been made in Protein structure prediction during the last few decades. As the predicted models can span a broad range of accuracy spectrum, the accuracy of quality estimation becomes one of the key elements of successful protein structure prediction. Over the past years, a number of methods have been developed to address this issue, and these methods could be roughly divided into three categories: the single-model methods, clustering-based methods and quasi single-model methods. In this study, we develop a single-model method MQAPRank based on the learning-to-rank algorithm firstly, and then implement a quasi single-model method Quasi-MQAPRank. The proposed methods are benchmarked on the 3DRobot and CASP11 dataset. The five-fold cross-validation on the 3DRobot dataset shows the proposed single model method outperforms other methods whose outputs are taken as features of the proposed method, and the quasi single-model method can further enhance the performance. On the CASP11 dataset, the proposed methods also perform well compared with other leading methods in corresponding categories. In particular, the Quasi-MQAPRank method achieves a considerable performance on the CASP11 Best150 dataset.
Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus
Authors: Wu Wei , Yang Yu-Lan , He Wei-Ming , Rouard Mathieu , Li Wei-Ming , Xu Meng , Roux Nicolas , Ge Xue-Jun 
Published: August 2016

AbstractCrop wild relatives are valuable resources for future genetic improvement. Here, we report the de novo genome assembly of Musa itinerans, a disease-resistant wild banana relative in subtropical China. The assembled genome size was 462.1 Mb, covering 75.2% of the genome (615.2Mb) and containing 32, 456 predicted protein-coding genes. Since the approximate divergence around 5.8 million years ago, the genomes of Musa itinerans and Musa acuminata have shown conserved collinearity. Gene family expansions and contractions enrichment analysis revealed that some pathways were associated with phenotypic or physiological innovations. These include a transition from wood to herbaceous in the ancestral Musaceae, intensification of cold and drought tolerances and reduced diseases resistance genes for subtropical marginally distributed Musa species. Prevalent purifying selection and transposed duplications were found to facilitate the diversification of NBS-encoding gene families for two Musa species. The population genome history analysis of M. itinerans revealed that the fluctuated population sizes were caused by the Pleistocene climate oscillations and that the formation of Qiongzhou Strait might facilitate the population downsizing on the isolated Hainan Island about 10.3 Kya. The qualified assembly of the M. itinerans genome provides deep insights into the lineage-specific diversification and also valuable resources for future banana breeding.
Controlled release of liraglutide using thermogelling polymers in treatment of diabetes
Authors: Chen Yipei , Li Yuzhuo , Shen Wenjia , Li Kun , Yu Lin , Chen Qinghua , Ding Jiandong 
Published: August 2016

AbstractIn treatment of diabetes, it is much desired in clinics and challenging in pharmaceutics and material science to set up a long-acting drug delivery system. This study was aimed at constructing a new delivery system using thermogelling PEG/polyester copolymers. Liraglutide, a fatty acid-modified antidiabetic polypeptide, was selected as the model drug. The thermogelling polymers were presented by poly(ε-caprolactone-co-glycolic acid)-poly(ethylene glycol)-poly(ε-caprolactone-co-glycolic acid) (PCGA-PEG-PCGA) and poly(lactic acid-co-glycolic acid)-poly(ethylene glycol)-poly(lactic acid-co-glycolic acid) (PLGA-PEG-PLGA). Both the copolymers were soluble in water and their concentrated solutions underwent temperature-induced sol-gel transitions. The drug-loaded polymer solutions were injectable at room temperature and gelled in situ at body temperature. Particularly, the liraglutide-loaded PCGA-PEG-PCGA thermogel formulation exhibited a sustained drug release manner over one week in both in vitro and in vivo tests. This feature was attributed to the combined effects of an appropriate drug/polymer interaction and a high chain mobility of the carrier polymer, which facilitated the sustained diffusion of drug out of the thermogel. Finally, a single subcutaneous injection of this formulation showed a remarkably improved glucose tolerance of mice for one week. Hence, the present study not only developed a promising long-acting antidiabetic formulation, but also put forward a combined strategy for controlled delivery of polypeptide.
Structural and functional characterization of endothelial microparticles released by cigarette smoke
Authors: Serban Karina A. , Rezania Samin , Petrusca Daniela N. , Poirier Christophe , Cao Danting , Justice Matthew J. , Patel Milan , Tsvetkova Irina , Kamocki Krzysztof , Mikosz Andrew , Schweitzer Kelly S. , Jacobson Sean , Cardoso Angelo , Carlesso Nadia , Hubbard Walter C. , Kechris Katerina , Dragnea Bogdan , Berdyshev Evgeny V. , McClintock Jeanette , Petrache Irina 
Published: August 2016

AbstractCirculating endothelial microparticles (EMPs) are emerging as biomarkers of chronic obstructive pulmonary disease (COPD) in individuals exposed to cigarette smoke (CS), but their mechanism of release and function remain unknown. We assessed biochemical and functional characteristics of EMPs and circulating microparticles (cMPs) released by CS. CS exposure was sufficient to increase microparticle levels in plasma of humans and mice and in supernatants of primary human lung microvascular endothelial cells. CS-released EMPs contained predominantly exosomes that were significantly enriched in let-7d, miR-191; miR-126; and miR125a, microRNAs that reciprocally decreased intracellular in CS-exposed endothelium. CS-released EMPs and cMPs were ceramide-rich and required the ceramide-synthesis enzyme acid sphingomyelinase (aSMase) for their release, an enzyme which was found to exhibit significantly higher activity in plasma of COPD patients or of CS-exposed mice. The ex vivo or in vivo engulfment of EMPs or cMPs by peripheral blood monocytes-derived macrophages was associated with significant inhibition of efferocytosis. Our results indicate that CS, via aSMase, releases circulating EMPs with distinct microRNA cargo and that EMPs affect the clearance of apoptotic cells by specialized macrophages. These targetable effects may be important in the pathogenesis of diseases linked to endothelial injury and inflammation in smokers.
The association of medication-related osteonecrosis of the jaw with Actinomyces spp. infection
Authors: Russmueller Guenter , Seemann Rudolf , Weiss Kathrin , Stadler Victoria , Speiss Manuel , Perisanidis Christos , Fuereder Thorsten , Willinger Birgit , Sulzbacher Irene , Steininger Christoph 
Published: August 2016

AbstractMedication-related osteonecrosis of the jaw (MRONJ) represents a complication of bisphosphonate treatment that responds poorly to standard treatment. In a retrospective cohort study we investigated a possible role of Actinomyces spp. in the pathogenesis of MRONJ. Deep biopsies of necrotic bone were collected during surgical treatment of MRONJ and evaluated by histology and microbiology for the presence of Actinomyces spp. Microbiological, demographic and clinicpathological data were analyzed for risk of Actinomyces-associated MRONJ. Between 2005 and 2014, 111 patients suffering from histologically-confirmed MRONJ were identified. Actinomyces spp. were detected in 99 cases (89%) by histology and in six further patients by microbiological culture. A diverse microbial flora was found in all specimens without association with Actinomyces spp. Demographic and clinicopathological characteristics did not separate significantly Actinomyces-positive from Actinomyces-negative cases. Our observations confirm previous reports of a high prevalence of Actinomyces spp. in MRONJ in the single largest cohort available up to now. The high prevalence of Actinomyces spp. and the lack of clinicopathological risk factors underline the prominent role of Actinomyces spp. in MRONJ and may change the current understanding of MRONJ. Established prolonged antimicrobial treatment regimens against Actinomyces spp. infection could therefore be a mainstay of future MRONJ management.
Biochar amendment immobilizes lead in rice paddy soils and reduces its phytoavailability
Authors: Li Honghong , Liu Yuting , Chen Yanhui , Wang Shanli , Wang Mingkuang , Xie Tuanhui , Wang Guo 
Published: August 2016

AbstractThis study aimed to determine effects of rice straw biochar on Pb sequestration in a soil-rice system. Pot experiments were conducted with rice plants in Pb-contaminated paddy soils that had been amended with 0, 2.5, and 5% (w/w) biochar. Compared to the control treatment, amendment with 5% biochar resulted in 54 and 94% decreases in the acid soluble and CaCl2-extractable Pb, respectively, in soils containing rice plants at the maturity stage. The amount of Fe-plaque on root surfaces and the Pb concentrations of the Fe-plaque were also reduced in biochar amended soils. Furthermore, lead species in rice roots were determined using Pb L3-edge X-ray absorption near edge structure (XANES), and although Pb-ferrihydrite complexes dominated Pb inventories, increasing amounts of organic complexes like Pb-pectins and Pb-cysteine were found in roots from the 5% biochar treatments. Such organic complexes might impede Pb translocation from root to shoot and subsequently reduce Pb accumulation in rice with biochar amendment.
Imipenem represses CRISPR-Cas interference of DNA acquisition through H-NS stimulation in Klebsiella pneumoniae
Authors: Lin Tzu-Lung , Pan Yi-Jiun , Hsieh Pei-Fang , Hsu Chun-Ru , Wu Meng-Chuan , Wang Jin-Town 
Published: August 2016

AbstractAnalysis of the genome of Klebsiella pneumoniae NTUH-K2044 strain revealed the presence of two clustered regularly interspaced short palindromic repeats (CRISPR) arrays separated with CRISPR-associated (cas) genes. Carbapenem-resistant K. pneumoniae isolates were observed to be less likely to have CRISPR-Cas than sensitive strains (5/85 vs. 22/132). Removal of the transcriptional repressor, H-NS, was shown to prevent the transformation of plasmids carrying a spacer and putative proto-spacer adjacent motif (PAM). The CRISPR-Cas system also decreased pUC-4K plasmid stability, resulting in plasmid loss from the bacteria with acquisition of new spacers. Analysis of the acquired proto-spacers in pUC-4K indicated that 5′-TTN-3′ was the preferred PAM in K. pneumoniae. Treatment of cells by imipenem induced hns expression, thereby decreasing cas3 expression and consequently repressed CRISPR-Cas activity resulted in increase of plasmid stability. In conclusion, NTUH-K2044 CRISPR-Cas contributes to decrease of plasmid transformation and stability. Through repression of CRISPR-Cas activity by induced H-NS, bacteria might be more able to acquire DNA to confront the challenge of imipenem.