bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of genetic and phenotypic parameters of some important economic traits in Khazak native hen in Iran
Authors: Ebrahimzadeh-Allahabad Ahmad , Mahmodian Zhila , Pezeshkian Zahra , Mollaei A. 
Published: December 2015

SummaryThe purpose of this study was the estimation of genetic and phenotypic parameters of important economic traits in Khazak native hens in Iran. The registered records of 7 434 Khazak native chickens containing 5 238 hens and 2 196 cocks in the research centre of Zabol University from 2007 to 2011 were used. The results of this study were compared with the results of studies on other native chickens breeding in Iran (Yazd: 4198, Mazandaran: 49 536, Esfahan: 23 108, West Azarbaijan: 24 890 and Fars: 30 279). Genotypic and phenotypic correlations between traits and heritability of traits were evaluated by univariate and bivariate animal models using ASREML software. The quantity of some traits such as the average egg production, weight of eggs produced, fertility, hatchability, age of sexual maturity and broodiness were a month 120, 45.15 g, 65.25 percent, 74.83 percent, 5.54 and 1.90, respectively. The heritability of sexual maturity age, the number of eggs produced and egg weight were 0.22 ± 0.41, 0.16 ± 0.13 and 0.50, respectively. The genetic correlation between the age of sexual maturity and the number of eggs produced were 0.95 ± 0.02 and 0.29 ± 0.07, respectively. The results of the study showed that decreasing the sexual age of maturity will lead to an increase in the number of eggs produced. The results of variance analysis showed that some factors such as hen age, broodiness (P&lt; 0.01) and the weight of hens have a significant effect on hatchability.
A generic strategy for CRISPR-Cas9-mediated gene tagging
Authors: Lackner Daniel H. , Carré Alexia , Guzzardo Paloma M. , Banning Carina , Mangena Ramu , Henley Tom , Oberndorfer Sarah , Gapp Bianca V. , Nijman Sebastian M.B. , Brummelkamp Thijn R. , Bürckstümmer Tilmann 
Published: December 2015

AbstractGenome engineering has been greatly enhanced by the availability of Cas9 endonuclease that can be targeted to almost any genomic locus using so called guide RNAs (gRNAs). However, the introduction of foreign DNA sequences to tag an endogenous gene is still cumbersome as it requires the synthesis or cloning of homology templates. Here we present a strategy that enables the tagging of endogenous loci using one generic donor plasmid. It contains the tag of interest flanked by two gRNA recognition sites that allow excision of the tag from the plasmid. Co-transfection of cells with Cas9, a gRNA specifying the genomic locus of interest, the donor plasmid and a cassette-specific gRNA triggers the insertion of the tag by a homology-independent mechanism. The strategy is efficient and delivers clones that display a predictable integration pattern. As showcases we generated NanoLuc luciferase- and TurboGFP-tagged reporter cell lines.
Exploring the variation in implementation of a COPD disease management programme and its impact on health outcomes: a post hoc analysis of the RECODE cluster randomised trial
Authors: Boland Melinde R S , Kruis Annemarije L , Huygens Simone A , Tsiachristas Apostolos , Assendelft Willem J J , Gussekloo Jacobijn , Blom Coert M G , Chavannes Niels H , Rutten-van Mölken Maureen P M H 
Published: December 2015

AbstractThis study aims to (1) examine the variation in implementation of a 2-year chronic obstructive pulmonary disease (COPD) management programme called RECODE, (2) analyse the facilitators and barriers to implementation and (3) investigate the influence of this variation on health outcomes. Implementation variation among the 20 primary-care teams was measured directly using a self-developed scale and indirectly through the level of care integration as measured with the Patient Assessment of Chronic Illness Care (PACIC) and the Assessment of Chronic Illness Care (ACIC). Interviews were held to obtain detailed information regarding the facilitators and barriers to implementation. Multilevel models were used to investigate the association between variation in implementation and change in outcomes. The teams implemented, on average, eight of the 19 interventions, and the specific package of interventions varied widely. Important barriers and facilitators of implementation were (in)sufficient motivation of healthcare provider and patient, the high starting level of COPD care, the small size of the COPD population per team, the mild COPD population, practicalities of the information and communication technology (ICT) system, and hurdles in reimbursement. Level of implementation as measured with our own scale and the ACIC was not associated with health outcomes. A higher level of implementation measured with the PACIC was positively associated with improved self-management capabilities, but this association was not found for other outcomes. There was a wide variety in the implementation of RECODE, associated with barriers at individual, social, organisational and societal level. There was little association between extent of implementation and health outcomes.
HIV-1 CCR5 gene therapy will fail unless it is combined with a suicide gene
Authors: Pandit Aridaman , de Boer Rob J. 
Published: December 2015

AbstractHighly active antiretroviral therapy (ART) has successfully turned Human immunodeficiency virus type 1 (HIV-1) from a deadly pathogen into a manageable chronic infection. ART is a lifelong therapy which is both expensive and toxic and HIV can become resistant to it. An alternative to lifelong ART is gene therapy that targets the CCR5 co-receptor and creates a population of genetically modified host cells that are less susceptible to viral infection. With generic mathematical models we show that gene therapy that only targets the CCR5 co-receptor fails to suppress HIV-1 (which is in agreement with current data). We predict that the same gene therapy can be markedly improved if it is combined with a suicide gene that is only expressed upon HIV-1 infection.
GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1
Authors: Miglietta Giulia , Cogoi Susanna , Pedersen Erik B. , Xodo Luigi E. 
Published: December 2015

AbstractHRAS is regulated by two neighbouring quadruplex-forming GC-elements (hras-1 and hras-2), located upstream of the major transcription start sites (doi: 10.1093/nar/gku 5784). In this study we demonstrate that the C-rich strands of hras-1 and hras-2 fold into i-motif conformations (iMs) characterized under crowding conditions (PEG-300, 40% w/v) by semi-transitions at pH 6.3 and 6.7, respectively. Nondenaturing PAGE shows that the HRAS C-rich sequences migrate at both pH 5 and 7 as folded intramolecular structures. Chromatin immunoprecipitation shows that hnRNP A1 is associated under in vivo conditions to the GC-elements, while EMSA proves that hnRNP A1 binds tightly to the iMs. FRET and CD show that hnRNP A1 unfolds the iM structures upon binding. Furthermore, when hnRNP A1 is knocked out in T24 bladder cancer cells by a specific shRNA, the HRAS transcript level drops to 44 ± 5% of the control, suggesting that hnRNP A1 is necessary for gene activation. The sequestration by decoy oligonucleotides of the proteins (hnRNP A1 and others) binding to the HRAS iMs causes a significant inhibition of HRAS transcription. All these outcomes suggest that HRAS is regulated by a G-quadruplex/i-motif switch interacting with proteins that recognize non B-DNA conformations.
Effect of edge pruning on structural controllability and observability of complex networks
Authors: Mengiste Simachew Abebe , Aertsen Ad , Kumar Arvind 
Published: December 2015

AbstractControllability and observability of complex systems are vital concepts in many fields of science. The network structure of the system plays a crucial role in determining its controllability and observability. Because most naturally occurring complex systems show dynamic changes in their network connectivity, it is important to understand how perturbations in the connectivity affect the controllability of the system. To this end, we studied the control structure of different types of artificial, social and biological neuronal networks (BNN) as their connections were progressively pruned using four different pruning strategies. We show that the BNNs are more similar to scale-free networks than to small-world networks, when comparing the robustness of their control structure to structural perturbations. We introduce a new graph descriptor, ‘the cardinality curve’, to quantify the robustness of the control structure of a network to progressive edge pruning. Knowing the susceptibility of control structures to different pruning methods could help design strategies to destroy the control structures of dangerous networks such as epidemic networks. On the other hand, it could help make useful networks more resistant to edge attacks.
The N-terminal domain of the thermo-regulated surface protein PrpA of Enterococcus faecium binds to fibrinogen, fibronectin and platelets
Authors: Guzmán Prieto Ana M. , Urbanus Rolf T. , Zhang Xinglin , Bierschenk Damien , Koekman C. Arnold , van Luit-Asbroek Miranda , Ouwerkerk Janneke P. , Pape Marieke , Paganelli Fernanda L. , Wobser Dominique , Huebner Johannes , Hendrickx Antoni P. A. , Bonten Marc J. M. , Willems Rob J. L. , van Schaik Willem 
Published: December 2015

AbstractEnterococcus faecium is a commensal of the mammalian gastrointestinal tract, but is also found in non-enteric environments where it can grow between 10 °C and 45 °C. E. faecium has recently emerged as a multi-drug resistant nosocomial pathogen. We hypothesized that genes involved in the colonization and infection of mammals exhibit temperature-regulated expression control and we therefore performed a transcriptome analysis of the clinical isolate E. faecium E1162, during mid-exponential growth at 25 °C and 37 °C. One of the genes that exhibited differential expression between 25 °C and 37 °C, was predicted to encode a peptidoglycan-anchored surface protein. The N-terminal domain of this protein is unique to E. faecium and closely related enterococci, while the C-terminal domain is homologous to the Streptococcus agalactiae surface protein BibA. This region of the protein contains proline-rich repeats, leading us to name the protein PrpA for proline-rich protein A. We found that PrpA is a surface-exposed protein which is most abundant during exponential growth at 37 °C in E. faecium E1162. The heterologously expressed and purified N-terminal domain of PrpA was able to bind to the extracellular matrix proteins fibrinogen and fibronectin. In addition, the N-terminal domain of PrpA interacted with both non-activated and activated platelets.
Diiron centre mutations in Ciona intestinalis alternative oxidase abolish enzymatic activity and prevent rescue of cytochrome oxidase deficiency in flies
Authors: Andjelković Ana , Oliveira Marcos T. , Cannino Giuseppe , Yalgin Cagri , Dhandapani Praveen K. , Dufour Eric , Rustin Pierre , Szibor Marten , Jacobs Howard T. 
Published: December 2015

AbstractThe mitochondrial alternative oxidase, AOX, carries out the non proton-motive re-oxidation of ubiquinol by oxygen in lower eukaryotes, plants and some animals. Here we created a modified version of AOX from Ciona instestinalis, carrying mutations at conserved residues predicted to be required for chelation of the diiron prosthetic group. The modified protein was stably expressed in mammalian cells or flies, but lacked enzymatic activity and was unable to rescue the phenotypes of flies knocked down for a subunit of cytochrome oxidase. The mutated AOX transgene is thus a potentially useful tool in studies of the physiological effects of AOX expression.
Metabolomic analysis with GC-MS to reveal potential metabolites and biological pathways involved in Pb & Cd stress response of radish roots
Authors: Wang Yan , Xu Liang , Shen Hong , Wang Juanjuan , Liu Wei , Zhu Xianwen , Wang Ronghua , Sun Xiaochuan , Liu Liwang 
Published: December 2015

AbstractThe radish (Raphanus sativus L.) is an important root vegetable crop. In this study, the metabolite profiling analysis of radish roots exposed to lead (Pb) and cadmium (Cd) stresses has been performed using gas chromatography-mass spectrometry (GC-MS). The score plots of principal component analysis (PCA) and partial least squares-discriminate analysis (PLS-DA) showed clear discrimination between control and Pb- or Cd-treated samples. The metabolic profiling indicated Pb or Cd stress could cause large metabolite alteration mainly on sugars, amino acids and organic acids. Furthermore, an integrated analysis of the effects of Pb or Cd stress was performed on the levels of metabolites and gene transcripts from our previous transcriptome work in radish roots. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of integration data demonstrated that exposure of radish to Pb stress resulted in profound biochemical changes including carbohydrate metabolism, energy metabolism and glutathione metabolism, while the treatment of Cd stress caused significant variations in energy production, amino acid metabolism and oxidative phosphorylation-related pathways. These results would facilitate further dissection of the mechanisms of heavy metal (HM) accumulation/tolerance in plants and the effective management of HM contamination in vegetable crops by genetic manipulation.
Development of a real-time flexible multiphoton microendoscope for label-free imaging in a live animal
Authors: Ducourthial Guillaume , Leclerc Pierre , Mansuryan Tigran , Fabert Marc , Brevier Julien , Habert Rémi , Braud Flavie , Batrin Renaud , Vever-Bizet Christine , Bourg-Heckly Geneviève , Thiberville Luc , Druilhe Anne , Kudlinski Alexandre , Louradour Frédéric 
Published: December 2015

AbstractWe present a two-photon microendoscope capable of in vivo label-free deep-tissue high-resolution fast imaging through a very long optical fiber. First, an advanced light-pulse spectro-temporal shaping device optimally precompensates for linear and nonlinear distortions occurring during propagation within the endoscopic fiber. This enables the delivery of sub-40-fs duration infrared excitation pulses at the output of 5 meters of fiber. Second, the endoscopic fiber is a custom-made double-clad polarization-maintaining photonic crystal fiber specifically designed to optimize the imaging resolution and the intrinsic luminescence backward collection. Third, a miniaturized fiber-scanner of 2.2 mm outer diameter allows simultaneous second harmonic generation (SHG) and two-photon excited autofluorescence (TPEF) imaging at 8 frames per second. This microendoscope’s transverse and axial resolutions amount respectively to 0.8 μm and 12 μm, with a field-of-view as large as 450 μm. This microendoscope’s unprecedented capabilities are validated during label-free imaging, ex vivo on various fixed human tissue samples and in vivo on an anesthetized mouse kidney demonstrating an imaging penetration depth greater than 300 μm below the surface of the organ. The results reported in this manuscript confirm that nonlinear microendoscopy can become a valuable clinical tool for real-time in situ assessment of pathological states.
TALEN-mediated homologous recombination in Daphnia magna
Authors: Nakanishi Takashi , Kato Yasuhiko , Matsuura Tomoaki , Watanabe Hajime 
Published: December 2015

AbstractTranscription Activator-Like Effector Nucleases (TALENs) offer versatile tools to engineer endogenous genomic loci in various organisms. We established a homologous recombination (HR)-based knock-in using TALEN in the crustacean Daphnia magna, a model for ecological and toxicological genomics. We constructed TALENs and designed the 67 bp donor insert targeting a point deletion in the eyeless mutant that shows eye deformities. Co-injection of the TALEN mRNA with donor DNA into eggs led to the precise integration of the donor insert in the germ line, which recovered eye deformities in offspring. The frequency of HR events in the germ line was 2% by using both plasmid and single strand oligo DNA with 1.5 kb and 80 nt homology to the target. Deficiency of ligase 4 involved in non-homologous end joining repair did not increase the HR efficiency. Our data represent efficient HR-based knock-in by TALENs in D. magna, which is a promising tool to understand Daphnia gene functions.
The effect of androgens on ovarian follicle maturation: Dihydrotestosterone suppress FSH-stimulated granulosa cell proliferation by upregulating PPARγ-dependent PTEN expression.
Authors: Chen Mei-Jou , Chou Chia-Hung , Chen Shee-Uan , Yang Wei-Shiung , Yang Yu-Shih , Ho Hong-Nerng 
Published: December 2015

AbstractIntraovarian hyperandrogenism is one of the determining factors of follicular arrest in women with polycystic ovary syndrome (PCOS). Using androgenized rat models, we investigated the effects of androgens on metabolism, as well as on factors involved in follicular arrest and the reduced number of estrus cycles. The dihydrotestosterone (DHT)-treated rats had fewer estrus cycles, higher numbers of large arrested follicles and an increased in body weight gain compared with the dehydroepiandrostenedione (DHEA)- and placebo-treated rats. In cultured rat granulosa cells, DHT suppressed follicle stimulating hormone (FSH)-induced granulosa cell proliferation and increased the accumulation of cells in the G2/M phase. DHT decreased phosphorylated Akt (p-Akt) and cyclin D1 levels through increasing PTEN. DHT-promoted PTEN expression was regulated by peroxisome proliferator-activated receptor gamma (PPARγ) in granulosa cells. Meanwhile, in the large follicles of the DHT-treated rats, the expressions of PPARγ and PTEN were higher, but the expression of p-Akt and proliferating cell nuclear antigen (PCNA) were lower. Conclusively, DHT and DHEA produced differential effects on metabolism in prepubertal female rats like clinical manifestations of women with PCOS. DHT treatment may affect ovarian follicular maturation by altering granulosa cell proliferation through the regulation of enhancing PPARγ dependent PTEN/p-Akt expression in the granulosa cells.
Heterogeneous distribution of dye-labelled biomineralizaiton proteins in calcite crystals
Authors: Liu Chuang , Xie Liping , Zhang Rongqing 
Published: December 2015

AbstractBiominerals are highly ordered crystals mediated by organic matters especially proteins in organisms. However, how specific proteins are distributed inside biominerals are not well understood. In the present study, we use fluorescein isothiocyanate (FITC) to label extracted proteins from the shells of bivalve Pinctada fucata. By confocal laser scanning microscopy (CLSM), we observe a heterogeneous distribution of dye-labelled proteins inside synthetic calcite at the microscale. Proteins from the prismatic calcite layers accumulate at the edge of crystals while proteins from the nacreous aragonite layers accumulate at the center of crystals. Raman and X-ray powder diffraction show that both the proteins cannot alter the crystal phase. Scanning electron microscope demonstrates both proteins are able to affect the crystal morphology. This study may provide a direct approach for the visualization of protein distributions in crystals by small-molecule dye-labelled proteins as the additives in the crystallization process and improve our understanding of intracrystalline proteins distribution in biogenic calcites.
Synthesis of heavy hydrocarbons at the core-mantle boundary
Authors: Belonoshko Anatoly B. , Lukinov Timofiy , Rosengren Anders , Bryk Taras , Litasov Konstantin D. 
Published: December 2015

AbstractThe synthesis of complex organic molecules with C-C bonds is possible under conditions of reduced activity of oxygen. We have found performing ab initio molecular dynamics simulations of the C-O-H-Fe system that such conditions exist at the core-mantle boundary (CMB). H2O and CO2 delivered to the CMB by subducting slabs provide a source for hydrogen and carbon. The mixture of H2O and CO2 subjected to high pressure (130 GPa) and temperature (4000 to 4500 K) does not lead to synthesis of complex hydrocarbons. However, when Fe is added to the system, C-C bonds emerge. It means that oil might be a more abundant mineral than previously thought.
Fully epitaxial C1b-type NiMnSb half-Heusler alloy films for current-perpendicular-to-plane giant magnetoresistance devices with a Ag spacer
Authors: Wen Zhenchao , Kubota Takahide , Yamamoto Tatsuya , Takanashi Koki 
Published: December 2015

AbstractRemarkable magnetic and spin-dependent transport properties arise from well-designed spintronic materials and heterostructures. Half-metallic Heusler alloys with high spin polarization exhibit properties that are particularly advantageous for the development of high-performance spintronic devices. Here, we report fully (001)-epitaxial growth of a high-quality half-metallic NiMnSb half-Heusler alloy films and their application to current-perpendicular-to-plane giant magnetoresistance (CPP-GMR) devices with Ag spacer layers. Fully (001)-oriented NiMnSb epitaxial films with very flat surface and high magnetization were prepared on Cr/Ag-buffered MgO(001) single crystalline substrates by changing the substrate temperature. Epitaxial CPP-GMR devices using the NiMnSb films and a Ag spacer were fabricated and room-temperature (RT) CPP-GMR ratios for the C1b-type half-Heusler alloy were determined for the first time. A CPP-GMR ratio of 8% (21%) at RT (4.2 K) was achieved in the fully epitaxial NiMnSb/Ag/NiMnSb structures. Furthermore, negative anisotropic magnetoresistance (AMR) ratio and small discrepancy of the AMR amplitudes between RT and 10 K were observed in a single epitaxial NiMnSb film, indicating robust bulk half metallicity against thermal fluctuation in the half-Heusler compound. The modest CPP-GMR ratios could be attributed to interface effects between NiMnSb and Ag. This work provides a pathway for engineering a new class of ordered alloy materials with particular emphasis on spintronics.
IL-8 as mediator in the microenvironment-leukaemia network in acute myeloid leukaemia
Authors: Kuett Alexander , Rieger Christina , Perathoner Deborah , Herold Tobias , Wagner Michaela , Sironi Silvia , Sotlar Karl , Horny Hans-Peter , Deniffel Christian , Drolle Heidrun , Fiegl Michael 
Published: December 2015

AbstractThe bone marrow microenvironment is physiologically hypoxic with areas being as low as 1% O2, e.g. the stem cell niche. Acute myeloid leukaemia (AML) blasts misuse these bone marrow niches for protection by the local microenvironment, but also might create their own microenvironment. Here we identify IL-8 as a hypoxia-regulated cytokine in both AML cell lines and primary AML samples that is induced within 48 hours of severe hypoxia (1% O2). IL-8 lacked effects on AML cells but induced migration in mesenchymal stromal cells (MSC), an integral part of the bone marrow. Accordingly, MSC were significantly increased in AML bone marrow as compared to healthy bone marrow. Interestingly, mononuclear cells obtained from healthy bone marrow displayed both significantly lower endogenous and hypoxia-induced production of IL-8. IL-8 mRNA expression in AML blasts from 533 patients differed between genetic subgroups with significantly lower expression of IL-8 in acute promyelocytic leukaemia (APL), while in non APL-AML patients with FLT ITD had the highest IL-8 expression. In this subgroup, high IL-8 expression was also prognostically unfavourable. In conclusion, hypoxia as encountered in the bone marrow specifically increases IL-8 expression of AML, which in turn impacts niche formation. High IL-8 expression might be correlated with poor prognosis in certain AML subsets.