bluuebunny/crossref_metadata_2025 huggingface dataset:
Circulating Tumour Cells as an Independent Prognostic Factor in Patients with Advanced Oesophageal Squamous Cell Carcinoma Undergoing Chemoradiotherapy
Authors: Su Po-Jung , Wu Min-Hsien , Wang Hung-Ming , Lee Chia-Lin , Huang Wen-Kuan , Wu Chiao-En , Chang Hsien-Kun , Chao Yin-Kai , Tseng Chen-Kan , Chiu Tzu-Keng , Lin Nina Ming-Jung , Ye Siou-Ru , Lee Jane Ying-Chieh , Hsieh Chia-Hsun
Published: August 2016

The role of circulating tumour cells (CTCs) in advanced oesophageal cancer (EC) patients undergoing concurrent chemoradiotherapy (CCRT) remains uncertain. A negative selection protocol plus flow cytometry was validated to efficiently identify CTCs. The CTC number was calculated and analysed for survival impact. The protocol’s efficacy in CTC identification was validated with a recovery rate of 44.6 ± 9.1% and a coefficient of variation of 20.4%. Fifty-seven patients and 20 healthy donors were enrolled. Initial staging, first response to CRT, and surgery after CRT were prognostic for overall survival, with P values of <0.0001, <0.0001, and <0.0001, respectively. The CTC number of EC patients is significantly higher (P = 0.04) than that of healthy donors. Multivariate analysis for disease-specific progression-free survival showed that surgery after response to CCRT, initial stage, and CTC number (≥21.0 cells/mL) played independent prognostic roles. For overall survival, surgery after CCRT, performance status, initial stage, and CTC number were significant independent prognostic factors. In conclusion, a negative selection plus flow cytometry protocol efficiently detected CTCs. The CTC number before CCRT was an independent prognostic factor in patients with unresectable oesophageal squamous cell carcinoma. Further large-scale prospective studies for validation are warranted.
Comparative Analysis of piggyBac, CRISPR/Cas9 and TALEN Mediated BAC Transgenesis in the Zygote for the Generation of Humanized SIRPA Rats
Authors: Jung Chris J. , Ménoret Séverine , Brusselle Lucas , Tesson Laurent , Usal Claire , Chenouard Vanessa , Remy Séverine , Ouisse Laure-Hélène , Poirier Nicolas , Vanhove Bernard , de Jong Pieter J. , Anegon Ignacio
Published: August 2016

BAC transgenic mammalian systems offer an important platform for recapitulating human gene expression and disease modeling. While the larger body mass, and greater genetic and physiologic similarity to humans render rats well suited for reproducing human immune diseases and evaluating therapeutic strategies, difficulties of generating BAC transgenic rats have hindered progress. Thus, an efficient method for BAC transgenesis in rats would be valuable. Immunodeficient mice carrying a human SIRPA transgene have previously been shown to support improved human cell hematopoiesis. Here, we have generated for the first time, human SIRPA BAC transgenic rats, for which the gene is faithfully expressed, functionally active, and germline transmissible. To do this, human SIRPA BAC was modified with elements to work in coordination with genome engineering technologies-piggyBac, CRISPR/Cas9 or TALEN. Our findings show that piggyBac transposition is a more efficient approach than the classical BAC transgenesis, resulting in complete BAC integration with predictable end sequences, thereby permitting precise assessment of the integration site. Neither CRISPR/Cas9 nor TALEN increased BAC transgenesis. Therefore, an efficient generation of human SIRPA transgenic rats using piggyBac opens opportunities for expansion of humanized transgenic rat models in the future to advance biomedical research and therapeutic applications.
Functional characterization of a monoclonal antibody epitope using a lambda phage display-deep sequencing platform
Authors: Domina Maria , Lanza Cariccio Veronica , Benfatto Salvatore , Venza Mario , Venza Isabella , Borgogni Erica , Castellino Flora , Midiri Angelina , Galbo Roberta , Romeo Letizia , Biondo Carmelo , Masignani Vega , Teti Giuseppe , Felici Franco , Beninati Concetta
Published: August 2016

We have recently described a method, named PROFILER, for the identification of antigenic regions preferentially targeted by polyclonal antibody responses after vaccination. To test the ability of the technique to provide insights into the functional properties of monoclonal antibody (mAb) epitopes, we used here a well-characterized epitope of meningococcal factor H binding protein (fHbp), which is recognized by mAb 12C1. An fHbp library, engineered on a lambda phage vector enabling surface expression of polypeptides of widely different length, was subjected to massive parallel sequencing of the phage inserts after affinity selection with the 12C1 mAb. We detected dozens of unique antibody-selected sequences, the most enriched of which (designated as FrC) could largely recapitulate the ability of fHbp to bind mAb 12C1. Computational analysis of the cumulative enrichment of single amino acids in the antibody-selected fragments identified two overrepresented stretches of residues (H248-K254 and S140-G154), whose presence was subsequently found to be required for binding of FrC to mAb 12C1. Collectively, these results suggest that the PROFILER technology can rapidly and reliably identify, in the context of complex conformational epitopes, discrete “hot spots” with a crucial role in antigen-antibody interactions, thereby providing useful clues for the functional characterization of the epitope.
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

The 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

Genome 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

Tyrosine 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

We 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

Fetal 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

Southern 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

Accumulating 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

Using 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

Premature 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

Much 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

Crop 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

In 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

Circulating 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

Medication-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

This 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

Analysis 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.
Detailed Experimental Study of Ion Acceleration by Interaction of an Ultra-Short Intense Laser with an Underdense Plasma
Authors: Kahaly S. , Sylla F. , Lifschitz A. , Flacco A. , Veltcheva M. , Malka V.
Published: August 2016

Ion acceleration from intense (Iλ2 > 1018 Wcm−2 μm2) laser-plasma interaction is experimentally studied within a wide range of He gas densities. Focusing an ultrashort pulse (duration "Equation missing" ion plasma period) on a newly designed submillimetric gas jet system, enabled us to inhibit total evacuation of electrons from the central propagation channel reducing the radial ion acceleration associated with ponderomotive Coulomb explosion, a mechanism predominant in the long pulse scenario. New ion acceleration mechanism have been unveiled in this regime leading to non-Maxwellian quasi monoenergetic features in the ion energy spectra. The emitted nonthermal ion bunches show a new scaling of the ion peak energy with plasma density. The scaling identified in this new regime differs from previously reported studies.
Cell fusion as the formation mechanism of unreduced gametes in the gynogenetic diploid hybrid fish
Authors: Wang Jing , Liu Qingfeng , Luo Kaikun , Chen Xuan , Xiao Jun , Zhang Chun , Tao Min , Zhao Rurong , Liu Shaojun
Published: August 2016

The gynogenetic diploid hybrid clone line (GDH) derived from red crucian carp (♀ RCC) × common carp (♂ CC) possesses the unusual reproductive trait of producing unreduced diploid eggs. To identify the mechanism underlying this phenomenon, we examined the structure, in vivo developmental process and in vitro dynamic development of the GDH gonad. In summary, compared with RCC and CC, GDH showed certain special straits. First, a high frequency (84.7%) of germ cell fusion occurred in gonadal tissue culture in vitro as observed by time-lapse microscopy. Second, microstructural and ultrastructural observation showed numerous binucleated and multinucleated germ cells in the gonad, providing evidence of germ cell fusion in vivo. By contrast, in the diploid RCC and CC ovaries, neither cell fusion nor multinucleated cells were observed during the development of gonads. Third, the ovary of GDH remained at stage I for 10 months, whereas those of RCC and CC remained at that stage for 2 months, indicating that the GDH germ cells underwent abnormal development before meiosis. This report is the first to demonstrate that cell fusion facilitates the formation of unreduced gametes in vertebrates, which is a valuable finding for both evolutionary biology and reproductive biology.
CRISPR/Cas9 mediated genome editing in ES cells and its application for chimeric analysis in mice
Authors: Oji Asami , Noda Taichi , Fujihara Yoshitaka , Miyata Haruhiko , Kim Yeon Joo , Muto Masanaga , Nozawa Kaori , Matsumura Takafumi , Isotani Ayako , Ikawa Masahito
Published: August 2016

Targeted gene disrupted mice can be efficiently generated by expressing a single guide RNA (sgRNA)/CAS9 complex in the zygote. However, the limited success of complicated genome editing, such as large deletions, point mutations, and knockins, remains to be improved. Further, the mosaicism in founder generations complicates the genotypic and phenotypic analyses in these animals. Here we show that large deletions with two sgRNAs as well as dsDNA-mediated point mutations are efficient in mouse embryonic stem cells (ESCs). The dsDNA-mediated gene knockins are also feasible in ESCs. Finally, we generated chimeric mice with biallelic mutant ESCs for a lethal gene, Dnajb13, and analyzed their phenotypes. Not only was the lethal phenotype of hydrocephalus suppressed, but we also found that Dnajb13 is required for sperm cilia formation. The combination of biallelic genome editing in ESCs and subsequent chimeric analysis provides a useful tool for rapid gene function analysis in the whole organism.
Vitality of Neural Networks under Reoccurring Catastrophic Failures
Authors: Sardi Shira , Goldental Amir , Amir Hamutal , Vardi Roni , Kanter Ido
Published: August 2016

Catastrophic failures are complete and sudden collapses in the activity of large networks such as economics, electrical power grids and computer networks, which typically require a manual recovery process. Here we experimentally show that excitatory neural networks are governed by a non-Poissonian reoccurrence of catastrophic failures, where their repetition time follows a multimodal distribution characterized by a few tenths of a second and tens of seconds timescales. The mechanism underlying the termination and reappearance of network activity is quantitatively shown here to be associated with nodal time-dependent features, neuronal plasticity, where hyperactive nodes damage the response capability of their neighbors. It presents a complementary mechanism for the emergence of Poissonian catastrophic failures from damage conductivity. The effect that hyperactive nodes degenerate their neighbors represents a type of local competition which is a common feature in the dynamics of real-world complex networks, whereas their spontaneous recoveries represent a vitality which enhances reliable functionality.
New evidence for grain specific C4 photosynthesis in wheat
Authors: Rangan Parimalan , Furtado Agnelo , Henry Robert J
Published: August 2016

The C4 photosynthetic pathway evolved to allow efficient CO2 capture by plants where effective carbon supply may be limiting as in hot or dry environments, explaining the high growth rates of C4 plants such as maize. Important crops such as wheat and rice are C3 plants resulting in efforts to engineer them to use the C4 pathway. Here we show the presence of a C4 photosynthetic pathway in the developing wheat grain that is absent in the leaves. Genes specific for C4 photosynthesis were identified in the wheat genome and found to be preferentially expressed in the photosynthetic pericarp tissue (cross- and tube-cell layers) of the wheat caryopsis. The chloroplasts exhibit dimorphism that corresponds to chloroplasts of mesophyll- and bundle sheath-cells in leaves of classical C4 plants. Breeding to optimize the relative contributions of C3 and C4 photosynthesis may adapt wheat to climate change, contributing to wheat food security.
Serum pharmacodynamic biomarkers for chronic corticosteroid treatment of children
Authors: Hathout Yetrib , Conklin Laurie S. , Seol Haeri , Gordish-Dressman Heather , Brown Kristy J. , Morgenroth Lauren P. , Nagaraju Kanneboyina , Heier Christopher R. , Damsker Jesse M. , van den Anker John N. , Henricson Erik , Clemens Paula R. , Mah Jean K. , McDonald Craig , Hoffman Eric P.
Published: August 2016

Corticosteroids are extensively used in pediatrics, yet the burden of side effects is significant. Availability of a simple, fast and reliable biochemical read out of steroidal drug pharmacodynamics could enable a rapid and objective assessment of safety and efficacy of corticosteroids and aid development of corticosteroid replacement drugs. To identify potential corticosteroid responsive biomarkers we performed proteome profiling of serum samples from DMD and IBD patients with and without corticosteroid treatment using SOMAscan aptamer panel testing 1,129 proteins in <0.1 cc of sera. Ten pro-inflammatory proteins were elevated in untreated patients and suppressed by corticosteroids (MMP12, IL22RA2, CCL22, IGFBP2, FCER2, LY9, ITGa1/b1, LTa1/b2, ANGPT2 and FGG). These are candidate biomarkers for anti-inflammatory efficacy of corticosteroids. Known safety concerns were validated, including elevated non-fasting insulin (insulin resistance) and elevated angiotensinogen (salt retention). These were extended by new candidates for metabolism disturbances (leptin, afamin), stunting of growth (growth hormone binding protein) and connective tissue remodeling (MMP3). Significant suppression of multiple adrenal steroid hormones was also seen in treated children (reductions of 17-hydroxyprogesterone, corticosterone, 11-deoxycortisol and testosterone). A panel of new pharmacodynamic biomarkers for corticosteroids in children was defined. Future studies will need to bridge specific biomarkers to mechanism of drug action and specific clinical outcomes.
Isozygous and selectable marker-free MSTN knockout cloned pigs generated by the combined use of CRISPR/Cas9 and Cre/LoxP
Authors: Bi Yanzhen , Hua Zaidong , Liu Ximei , Hua Wenjun , Ren Hongyan , Xiao Hongwei , Zhang Liping , Li Li , Wang Zhirui , Laible Götz , Wang Yan , Dong Faming , Zheng Xinmin
Published: August 2016

Predictable, clean genetic modification (GM) in livestock is important for reliable phenotyping and biosafety. Here we reported the generation of isozygous, functional myostatin (MSTN) knockout cloned pigs free of selectable marker gene (SMG) by CRISPR/Cas9 and Cre/LoxP. CRISPR/Cas9-mediated homologous recombination (HR) was exploited to knock out (KO) one allele of MSTN in pig primary cells. Cre recombinase was then used to excise the SMG with an efficiency of 82.7%. The SMG-free non-EGFP cells were isolated by flow cytometery and immediately used as donor nuclei for nuclear transfer. A total of 685 reconstructed embryos were transferred into three surrogates with one delivering two male live piglets. Molecular testing verified the mono-allelic MSTN KO and SMG deletion in these cloned pigs. Western blots showed approximately 50% decrease in MSTN and concurrent increased expression of myogenic genes in muscle. Histological examination revealed the enhanced myofiber quantity but myofiber size remained unaltered. Ultrasonic detection showed the increased longissimus muscle size and decreased backfat thickness. Precision editing of pig MSTN gene has generated isozygous, SMG-free MSTN KO cloned founders, which guaranteed a reliable route for elite livestock production and a strategy to minimize potential biological risks.
Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon
Authors: Pinho Marcos D. , Erol Erdal , Ribeiro-Gonçalves Bruno , Mendes Catarina I. , Carriço João A. , Matos Sandra C. , Preziuso Silvia , Luebke-Becker Antina , Wieler Lothar H. , Melo-Cristino Jose , Ramirez Mario
Published: August 2016

The pathogenic role of beta-hemolytic Streptococcus dysgalactiae in the equine host is increasingly recognized. A collection of 108 Lancefield group C (n = 96) or L (n = 12) horse isolates recovered in the United States and in three European countries presented multilocus sequence typing (MLST) alleles, sequence types and emm types (only 56% of the isolates could be emm typed) that were, with few exceptions, distinct from those previously found in human Streptococcus dysgalactiae subsp. equisimilis. Characterization of a subset of horse isolates by multilocus sequence analysis (MLSA) and 16S rRNA gene sequence showed that most equine isolates could also be differentiated from S. dysgalactiae strains from other animal species, supporting the existence of a horse specific genomovar. Draft genome information confirms the distinctiveness of the horse genomovar and indicates the presence of potentially horse-specific virulence factors. While this genomovar represents most of the isolates recovered from horses, a smaller MLST and MLSA defined sub-population seems to be able to cause infections in horses, other animals and humans, indicating that transmission between hosts of strains belonging to this group may occur.
Limited phosphorus availability is the Achilles heel of tropical reef corals in a warming ocean
Authors: Ezzat Leïla , Maguer Jean-François , Grover Renaud , Ferrier-Pagès Christine
Published: August 2016

During the 20th century, seawater temperatures have significantly increased, leading to profound alterations in biogeochemical cycles and ecosystem processes. Elevated temperatures have also caused massive bleaching (symbiont/pigment loss) of autotrophic symbioses, such as in coral-dinoflagellate association. As symbionts provide most nutrients to the host, their expulsion during bleaching induces host starvation. However, with the exception of carbon, the nutritional impact of bleaching on corals is still unknown, due to the poorly understood requirements in inorganic nutrients during stress. We therefore assessed the uptake rates of nitrogen and phosphate by five coral species maintained under normal and thermal stress conditions. Our results showed that nitrogen acquisition rates were significantly reduced during thermal stress, while phosphorus uptake rates were significantly increased in most species, suggesting a key role of this nutrient. Additional experiments showed that during thermal stress, phosphorus was required to maintain symbiont density and photosynthetic rates, as well as to enhance the translocation and retention of carbon within the host tissue. These findings shed new light on the interactions existing between corals and inorganic nutrients during thermal stress and highlight the importance of phosphorus for symbiont health.
In-depth phylogenetic analysis of hepatitis C virus subtype 1a and occurrence of 80K and associated polymorphisms in the NS3 protease
Authors: Santos André F. , Bello Gonzalo , Vidal Luãnna L. , Souza Suiane L. , Mir Daiana , Soares Marcelo A.
Published: August 2016

HCV genetic diversity is high and impacts disease progression, treatment and drug resistance. HCV subtype 1a is divided in two clades (I and II), and the 80 K natural polymorphism in the viral NS3 protease is prevalent in clade I. Paradoxically, countries dominated by this clade have contrasting frequencies of 80 K. Over 2,000 HCV 1a NS3 sequences were retrieved from public databases representing Europe, Oceania and the Americas. Sequences were aligned with HCV reference sequences and subjected to phylogenetic analysis to investigate the relative presence of different subtype 1a clades and NS3 protease mutations. HCV-1a sequences split into clades I and II. Clade I was further structured into three subclades, IA to C. Sub-clade IA prevailed in the U.S., while subclade IC was major in Brazil. The NS3 80 K polymorphism was associated with subclade IA, but nearly absent in subclades IB and IC, a pattern similarly seen for the 91S/T compensatory mutation. Three HCV-1a-I sub-clades have been identified, with different frequencies in distinct regions. The 80 K and 91A/S mutations were associated with subclade IA, which provide an explanation for the disparities seen in simeprevir resistance profiles of countries dominated by HCV 1a-I, like the U.S. and Brazil.
Spatiotemporal Divergence of the Warming Hiatus over Land Based on Different Definitions of Mean Temperature
Authors: Zhou Chunlüe , Wang Kaicun
Published: August 2016

Existing studies of the recent warming hiatus over land are primarily based on the average of daily minimum and maximum temperatures (T2). This study compared regional warming rates of mean temperature based on T2 and T24 calculated from hourly observations available from 1998 to 2013. Both T2 and T24 show that the warming hiatus over land is apparent in the mid-latitudes of North America and Eurasia, especially in cold seasons, which is closely associated with the negative North Atlantic Oscillation (NAO) and Arctic Oscillation (AO) and cold air propagation by the Arctic-original northerly wind anomaly into mid-latitudes. However, the warming rates of T2 and T24 are significantly different at regional and seasonal scales because T2 only samples air temperature twice daily and cannot accurately reflect land-atmosphere and incoming radiation variations in the temperature diurnal cycle. The trend has a standard deviation of 0.43 °C/decade for T2 and 0.41 °C/decade for T24 and 0.38 °C/decade for their trend difference in 5° × 5° grids. The use of T2 amplifies the regional contrasts of the warming rate, i.e., the trend underestimation in the US and overestimation at high latitudes by T2.
Portable instrumentation & point of care technologies
Authors: Masson Jean-François , Ouyang Zheng
Published: August 2016

Welcome to this Analytical Methods themed collection on portable instrumentation & point of care technologies, guest edited by Jean-François Masson and Zheng Ouyang.
Nanoscale chirality in metal and semiconductor nanoparticles
Authors: Kumar Jatish , Thomas K. George , Liz-Marzán Luis M.
Published: August 2016

We discuss optical activity in metal nanoclusters and semiconductor quantum dots, broadly focusing on recent advances in nanoscale chirality in plasmonic nanoparticles and their assemblies.
Selective shrinkage and separation of isomeric naphthoic acids via supramolecular gelation
Authors: Chen Jie , Wang Tianyu , Liu Minghua
Published: August 2016

The isomeric non-gelator molecules 1- or 2-naphthoic acid (NA1, or NA2) were found to form two-component supramolecular gels with an amphiphilic gelator LHC18, and the NA2/LHC18 gel underwent shrinking at room temperature.
Elastic coupling between spin-crossover particles and cellulose fibers
Authors: Rat S. , Nagy V. , Suleimanov I. , Molnár G. , Salmon L. , Demont P. , Csóka L. , Bousseksou A.
Published: August 2016

Composite materials made of cellulose fibers and spin crossover micro-particles investigated by dynamic mechanical analysis revealed an abrupt and reversible stiffening upon spin transition from the low spin to the high spin state.
Is the manifestation of the local dynamics in the spin–lattice NMR relaxation in dendrimers sensitive to excluded volume interactions?
Authors: Shavykin Oleg V. , Neelov Igor M. , Darinskii Anatolii A.
Published: August 2016

The maximum of the spin–lattice NMR relaxation function is shifted (not shifted) towards lower frequencies with increasing distance from terminal groups to the center for semiflexible (flexible) phantom and excluded volume models of dendrimers.
Photodissociation dynamics of dinitrite at 355 nm: initiation of a reactive pathway
Authors: Wang Lingxuan , Zu Lily
Published: August 2016

Vinoxy and 1-methylvinoxy radicals were detected along with formaldehyde as the products in the photodissociation of 1,3-butyl dinitrite.
Tuning the structure and mechanical property of polymer nanocomposites by employing anisotropic nanoparticles as netpoints
Authors: Zheng Zijian , Li Fanzhu , Liu Hongji , Shen Jianxiang , Liu Jun , Wu Youping , Zhang Liqun , Wang Wenchuan
Published: August 2016

We report a new kind of polymer nanocomposite by means of employing anisotropic nanoparticles as netpoints, to chemically connect the dual end-groups of each polymer chain to form a network.
Biphasic aggregation of a perylene bisimide dye identified by exciton-vibrational spectra
Authors: Plötz P.-A. , Polyutov S. P. , Ivanov S. D. , Fennel F. , Wolter S. , Niehaus T. , Xie Z. , Lochbrunner S. , Würthner F. , Kühn O.
Published: August 2016

The quantum efficiency of light emission supramolecular aggregates strongly depends on the intermolecular coupling. We present a molecule which demonstrates two different aggregated structures with high and low quantum efficiency. The spectral signatures can be understood by simulating the aggregated structures and the corresponding exciton-vibrational spectra.
The effect of halide and iodate anions on the hydrogen-bonding network of water in aqueous nanodrops
Authors: Chakrabarty Satrajit , Williams Evan R.
Published: August 2016

The hydration of halide and iodate anions was investigated using electrospray ionization (ESI) mass spectrometry and infrared photodissociation (IRPD) spectroscopy.
Nanoparticle electrochemistry
Authors: Robbs Peter H. , Rees Neil V.
Published: August 2016

This perspective article provides a survey of recent advances in nanoscale electrochemistry, with a brief theoretical background and a detailed discussion of experimental results of nanoparticle based electrodes, including the rapidly expanding field of “impact electrochemistry”.