bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes
Authors: Suh Alexander , Witt Christopher C. , Menger Juliana , Sadanandan Keren R. , Podsiadlowski Lars , Gerth Michael , Weigert Anne , McGuire Jimmy A. , Mudge Joann , Edwards Scott V. , Rheindt Frank E. 
Published: April 2016

AbstractParasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodesBrugia,WuchereriaandLoa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving theBrugia/Wuchererialineage and >20–17 Myr ago involving theLoalineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity.
Nonadditivity of critical Casimir forces
Authors: Paladugu Sathyanarayana , Callegari Agnese , Tuna Yazgan , Barth Lukas , Dietrich Siegfried , Gambassi Andrea , Volpe Giovanni 
Published: April 2016

AbstractIn soft condensed matter physics, effective interactions often emerge due to the spatial confinement of fluctuating fields. For instance, microscopic particles dissolved in a binary liquid mixture are subject to critical Casimir forces whenever their surfaces confine the thermal fluctuations of the order parameter of the solvent close to its critical demixing point. These forces are theoretically predicted to be nonadditive on the scale set by the bulk correlation length of the fluctuations. Here we provide direct experimental evidence of this fact by reporting the measurement of the associated many-body forces. We consider three colloidal particles in optical traps and observe that the critical Casimir force exerted on one of them by the other two differs from the sum of the forces they exert separately. This three-body effect depends sensitively on the distance from the critical point and on the chemical functionalisation of the colloid surfaces.
Differences in vulnerability of neurons and astrocytes to heme oxygenase-1 modulation: Implications for mitochondrial ferritin
Authors: Yu Xiaojun , Song Ning , Guo Xinli , Jiang Hong , Zhang Haoyun , Xie Junxia 
Published: April 2016

AbstractInduction of the antioxidant enzyme heme oxygenase-1 (HO-1) was observed in both astrocytes and neurons in the substantia nigra of patients with Parkinson’s disease (PD). In the current study, we investigated whether HO-1 behaves differently between neurons and astrocytes under the condition of neurotoxicity related to PD. The results showed a time-dependent HO-1 upregulation in primary cultured ventral mesencephalon neurons and astrocytes treated with the mitochondria complex I inhibitor 1-methyl-4-phenylpyridinium (MPP+) or recombinant α-synuclein. However, HO-1 upregulation appeared much later in neurons than in astrocytes. The HO-1 inhibitor zinc protoporphyrin (ZnPP) aggravated MPP+- or α-synuclein-induced oxidative damage in both astrocytes and neurons, indicating that this HO-1 response was cytoprotective. For neurons, the HO-1 activator cobalt protoporphyrin IX (CoPPIX) exerted protective effects against MPP+ or α-synuclein during moderate HO-1 upregulation, but it aggravated damage at the peak of the HO-1 response. For astrocytes, CoPPIXalways showed protective effects. Higher basal and CoPPIX-induced mitochondrial ferritin (MtFt) levels were detected in astrocytes. Lentivirus-mediated MtFt overexpression rescued the neuronal damage induced by CoPPIX, indicating that large MtFt buffering capacity contributes to pronounced HO-1 tolerance in astrocytes. Such findings suggest that astrocyte-targeted HO-1 interventions and MtFt modulations have potential as novel pharmacological strategies in PD.
Fine-scale behavioural differences distinguish resource use by ecomorphs in a closed ecosystem
Authors: Hawley Kate L. , Rosten Carolyn M. , Christensen Guttorm , Lucas Martyn C. 
Published: April 2016

AbstractTemporal differences in habitat use and foraging specialisms between ecomorphs represent aspects of behavioural phenotype that are poorly understood with regard to the origin and maintenance of ecological diversity. We tested the role of behaviour in resource use divergence of two Arctic charr (Salvelinus alpinus) phenotypes, a slim, putatively pelagic-dwelling morph and a robust, putatively littoral-dwelling generalist morph, over an annual cycle, using biotelemetry and stable isotopes. Pelagic morph charr exhibited significantly greater δC13 depletion, concordant with increased zooplanktivory, than for the Littoral morph. Although three-dimensional space-use of the morphs strongly overlapped, on average, the Littoral morph used that habitat 19.3% more than the Pelagic morph. Pelagic morph fish were significantly more active, further from the lake bed and at greater depth than Littoral fish (annual means respectively, Pelagic, 0.069BLs−1, 8.21 m and 14.11 m; Littoral, 0.047BLs−1, 5.87 m and 10.47 m). Patterns of habitat use differed between ecomorphs at key times, such as during autumn and at ice break, likely related to spawning and resumption of intensive foraging respectively. Extensive space-use overlap, but fine-scale differences in habitat use between charr ecomorphs, suggests the importance of competition for generating and maintaining polymorphism, and its potential for promoting reproductive isolation and evolution in sympatry.
Circulating microRNA profiles of Ebola virus infection
Authors: Duy Janice , Koehler Jeffrey W. , Honko Anna N. , Schoepp Randal J. , Wauquier Nadia , Gonzalez Jean-Paul , Pitt M. Louise , Mucker Eric M. , Johnson Joshua C. , O’Hearn Aileen , Bangura James , Coomber Moinya , Minogue Timothy D. 
Published: April 2016

AbstractEarly detection of Ebola virus (EBOV) infection is essential to halting transmission and adjudicating appropriate treatment. However, current methods rely on viral identification, and this approach can misdiagnose presymptomatic and asymptomatic individuals. In contrast, disease-driven alterations in the host transcriptome can be exploited for pathogen-specific diagnostic biomarkers. Here, we present for the first time EBOV-induced changes in circulating miRNA populations of nonhuman primates (NHPs) and humans. We retrospectively profiled longitudinally-collected plasma samples from rhesus macaques challenged via intramuscular and aerosol routes and found 36 miRNAs differentially present in both groups. Comparison of miRNA abundances to viral loads uncovered 15 highly correlated miRNAs common to EBOV-infected NHPs and humans. As proof of principle, we developed an eight-miRNA classifier that correctly categorized infection status in 64/74 (86%) human and NHP samples. The classifier identified acute infections in 27/29 (93.1%) samples and in 6/12 (50%) presymptomatic NHPs. These findings showed applicability of NHP-derived miRNAs to a human cohort, and with additional research the resulting classifiers could impact the current capability to diagnose presymptomatic and asymptomatic EBOV infections.
The germline-enriched Ppp1r36 promotes autophagy
Authors: Zhang Qinghua , Gao Maomao , Zhang Ying , Song Ying , Cheng Hanhua , Zhou Rongjia 
Published: April 2016

AbstractSpermatogenesis is a highly regulated process during which haploid sperm cells are generated. Although autophagy is involved in the spermatogenesis process, the molecular pathways and regulations of autophagy in germ cell development remain elusive. Here, we showed that Ppp1r36, a regulatory subunit of protein phosphatase 1, is expressed during gonadal development, mainly in testes during spermatogenesis. Autophagy protein LC3 (microtubule associated protein 1 light chain 3), especially its active form LC3-II, had a similar expression pattern to Ppp1r36. Moreover, LC3-II level and puncta analysis showed that autophagy is up-regulated around 21 dpp (day postpartum) in postnatal testis, indicating a potential role of autophagy during the first wave of spermatogenesis. We demonstrated that Ppp1r36 promotes autophagosome formation upon starvation induction. Further autophagy flux analysis using a tandem fluorescent indicator, mCherry-GFP-LC3, confirmed that Ppp1r36 participated in autophagy. We further determined that Ppp1r36 is associated with Atg16L1 (autophagy related 16-like 1) in autophagy of starvation induction. Thus, our results uncover a potential role of the regulatory subunit Ppp1r36 of protein phosphatase 1 in enhancing autophagy during spermatogenesis.
CD14 in the TLRs signaling pathway is associated with the resistance to E. coli F18 in Chinese domestic weaned piglets
Authors: Wu Zhengchang , Liu Ying , Dong Wenhua , Zhu Guo-qiang , Wu Shenglong , Bao Wenbin 
Published: April 2016

AbstractEscherichia coli F18 (E. coli F18) is mainly responsible for post-weaning diarrhea (PWD) in piglets. The genetic basis and regulatory mechanism of E. coli F18 resistance in Chinese domestic weaned piglets remain unclear. Meishan piglets were used as model animals to test their susceptibility to E. coli F18. By performing a comparative transcriptome study on duodenum tissues of sensitive and resistant pigs, we identified 198 differentially expressed genes (DEGs; 125 upregulated and 73 downregulated) in the resistant pigs. DEGs were predominately involved in immune system pathways, including the Toll-like receptor (TLR) signaling pathway. qPCR and western blot showed CD14, IFN-α, TLR4 and IL-1β, etc. in the TLR signaling pathway had significantly higher expression levels in lipopolysaccharide (LPS)-induced small intestinal epithelial cell lines (IPEC-J2) than those in normal IPEC-J2 cells. Immunohistochemical analysis showed the increased expression of CD14 gene in the E. coli F18-resistant individuals. After CD14 knockdown, the levels of cytokines IL-6 and IL-12 were significantly reduced in IPEC-J2 cell supernatants. The adhesion ability of F18ab strain with IPEC-J2 cells was significantly increased (p < 0.01). This study revealed the TLR signaling pathway, and especially CD14, probably plays an important role in resistance to E. coli F18 infection in Chinese domestic piglets.
Revealing the acute asthma ignorome: characterization and validation of uninvestigated gene networks
Authors: Riba Michela , Garcia Manteiga Jose Manuel , Bošnjak Berislav , Cittaro Davide , Mikolka Pavol , Le Connie , Epstein Michelle M. , Stupka Elia 
Published: April 2016

AbstractSystems biology provides opportunities to fully understand the genes and pathways in disease pathogenesis. We used literature knowledge and unbiased multiple data meta-analysis paradigms to analyze microarray datasets across different mouse strains and acute allergic asthma models. Our combined gene-driven and pathway-driven strategies generated a stringent signature list totaling 933 genes with 41% (440) asthma-annotated genes and 59% (493) ignorome genes, not previously associated with asthma. Within the list, we identified inflammation, circadian rhythm, lung-specific insult response, stem cell proliferation domains, hubs, peripheral genes, and super-connectors that link the biological domains (Il6, Il1ß, Cd4, Cd44, Stat1, Traf6, Rela, Cadm1, Nr3c1, Prkcd, Vwf, Erbb2). In conclusion, this novel bioinformatics approach will be a powerful strategy for clinical and across species data analysis that allows for the validation of experimental models and might lead to the discovery of novel mechanistic insights in asthma.
Field trial of medicinal plant, Bidens pilosa, against eimeriosis in broilers
Authors: Chang Cicero Lee-Tian , Yang Cheng-Ying , Muthamilselvan Thangarasu , Yang Wen-Chin 
Published: April 2016

AbstractEimeriosis is a severe protozoan disease in poultry. Because of increasing concern about drug residue and drug resistance with the use of anticoccidial drugs, natural products are emerging as an alternative and complementary approach to control avian eimeriosis. Our previous publication showed that feed supplemented with B. pilosa (BP) was effective at combating chicken eimeriosis in experimental settings. However, its efficacy against chicken eimeriosis under field conditions is not known. Here, we investigated the efficacy of BP against eimeriosis on an organic chicken farm. We found that feed supplemented with BP, at the dose of 0.025% of feed or more, significantly reduced Eimeria infection. This treatment increased body weight gain and reduced feed conversion ratio, leading to superior growth performance. It lowered morbidity/mortality rate, decreased oocysts per gram of feces and gut pathology and augmented the anticoccidial index. Collectively, these data demonstrated the potential of BP to control chicken eimeriosis on chicken farms. BP can, therefore, be used as an effective means to control eimeriosis.
Posttranslational hypusination of the eukaryotic translation initiation factor-5A regulates Fusarium graminearum virulence
Authors: Martinez-Rocha Ana Lilia , Woriedh Mayada , Chemnitz Jan , Willingmann Peter , Kröger Cathrin , Hadeler Birgit , Hauber Joachim , Schäfer Wilhelm 
Published: April 2016

AbstractActivation of eukaryotic translation initiation factor eIF5A requires a posttranslational modification, forming the unique amino acid hypusine. This activation is mediated by two enzymes, deoxyhypusine synthase, DHS, and deoxyhypusine hydroxylase, DOHH. The impact of this enzymatic complex on the life cycle of a fungal pathogen is unknown. Plant pathogenic ascomycetes possess a single copy of the eIF5A activated by hypusination. We evaluated the importance of imbalances in eIF5A hypusination in Fusarium graminearum, a devastating fungal pathogen of cereals. Overexpression of DHS leads to increased virulence in wheat, elevated production of the mycotoxin deoxynivalenol, more infection structures, faster wheat tissue invasion in plants and increases vegetatively produced conidia. In contrast, overexpression of DOHH completely prevents infection structure formation, pathogenicity in wheat and maize, leads to overproduction of ROS, reduced DON production and increased sexual reproduction. Simultaneous overexpression of both genes restores wild type-like phenotypes. Analysis of eIF5A posttranslational modification displayed strongly increased hypusinated eIF5A in DOHH overexpression mutant in comparison to wild type, and the DHS overexpression mutants. These are the first results pointing to different functions of differently modified eIF5A.
Resveratrol enhances HBV replication through activating Sirt1-PGC-1α-PPARα pathway
Authors: Shi Yixian , Li Yongjun , Huang Chenjie , Ying Lixiong , Xue Jihua , Wu Haicong , Chen Zhi , Yang Zhenggang 
Published: April 2016

AbstractThe population of hepatitis B combined with a number of metabolic disorders is increasing significantly. Resveratrol (RSV) has been used as a preclinical drug for the treatment of the metabolic disorders. However, the impact of RSV on HBV replication remains unknown. In this study, the HBV-expressing hepatocelluar carcinoma cell line and mouse model created by hydrodynamic injection of viral DNA were used. We found that RSV activates Sirt1, which in turn deacetylates PGC-1α and subsequently increases the transcriptional activity of PPARα, leading to the enhanced HBV transcription and replication in vitro and in vivo. In addition, we found that this pathway is also required for fasting-induced HBV transcription. Taken together, this study identifies that RSV enhances HBV transcription and replication especially acting on the core promoter, which depends on Sirt1-PGC-1α-PPARα pathway. We conclude that RSV may exacerbate the progression of hepatitis B and that patients with hepatitis B infection should be cautious taking RSV as a dietary supplement.
Autophagy inhibition of hsa-miR-19a-3p/19b-3p by targeting TGF-β R II during TGF-β1-induced fibrogenesis in human cardiac fibroblasts
Authors: Zou Meijuan , Wang Fang , Gao Rui , Wu Jingjing , Ou Yingwei , Chen Xuguan , Wang Tongshan , Zhou Xin , Zhu Wei , Li Ping , Qi Lian-Wen , Jiang Ting , Wang Weiwei , Li Chunyu , Chen Jun , He Qifang , Chen Yan 
Published: April 2016

AbstractTransforming growth factor-β1 (TGF-β1) plays an important role on fibrogenesis in heart disease. MicroRNAs have exhibited as crucial regulators of cardiac homeostasis and remodeling in various heart diseases. MiR-19a-3p/19b-3p expresses with low levels in the plasma of heart failure patients. The purpose of our study is to determine the role of MiR-19a-3p/19b-3p in regulating autophagy-mediated fibrosis of human cardiac fibroblasts. We elucidate our hypothesis in clinical samples and human cardiac fibroblasts (HCF) to provide valuable basic information. TGF-β1 promotes collagen I α2 and fibronectin synthesis in HCF and that is paralleled by autophagic activation in these cells. Pharmacological inhibition of autophagy by 3-methyladenine decreases the fibrotic response, while autophagy induction of rapamycin increases the response. BECN1 knockdown and Atg5 over-expression either inhibits or enhances the fibrotic effect of TGF-β1 in experimental HCF. Furthermore, miR-19a-3p/19b-3p mimics inhibit epithelial mesenchymal transition (EMT) and extracellular matrix (ECM) prodution and invasion of HCF. Functional studies suggest that miR-19a-3p/19b-3p inhibits autophagy of HCF through targeting TGF-β R II mRNA. Moreover, enhancement of autophagy rescues inhibition effect of miR-19a-3p/19b-3p on Smad 2 and Akt phosphorylation through TGF-β R II signaling. Our study uncovers a novel mechanism that miR-19a-3p/19b-3p inhibits autophagy-mediated fibrogenesis by targeting TGF-β R II.
LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots
Authors: Zhu Zhenglin , Tan Shengjun , Zhang Yaqiong , Zhang Yong E. 
Published: April 2016

AbstractRNA-based duplicated genes or functional retrocopies (retrogenes) are known to drive phenotypic evolution. Retrogenes emerge via retroposition, which is mainly mediated by long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in mammals. By contrast, long terminal repeat (LTR) retrotransposons appear to be the major player in plants, although an L1-like mechanism has also been hypothesized to be involved in retroposition. We tested this hypothesis by searching for young retrocopies, as these still retain the sequence features associated with the underlying retroposition mechanism. Specifically, we identified polymorphic retrocopies (retroCNVs) by analyzing public Arabidopsis (Arabidopsis thaliana) resequencing data. Furthermore, we searched for recently originated retrocopies encoded by the reference genome of Arabidopsis and Manihot esculenta. Across these two datasets, we found cases with L1-like hallmarks, namely, the expected target site sequence, a polyA tail and target site duplications. Such data suggest that an L1-like mechanism could operate in plants, especially dicots.
Centennial-scale solar forcing of the South American Monsoon System recorded in stalagmites
Authors: Novello Valdir F. , Vuille Mathias , Cruz Francisco W. , Stríkis Nicolás M. , de Paula Marcos Saito , Edwards R. Lawrence , Cheng Hai , Karmann Ivo , Jaqueto Plínio F. , Trindade Ricardo I. F. , Hartmann Gelvam A. , Moquet Jean S. 
Published: April 2016

AbstractThe South American Monsoon System (SAMS) is generally considered to be highly sensitive to Northern Hemisphere (NH) temperature variations on multi-centennial timescales. The direct influence of solar forcing on moisture convergence in global monsoon systems on the other hand, while well explored in modeling studies, has hitherto not been documented in proxy data from the SAMS region. Hence little is known about the sensitivity of the SAMS to solar forcing over the past millennium and how it might compete or constructively interfere with NH temperature variations that occurred primarily in response to volcanic forcing. Here we present a new annually-resolved oxygen isotope record from a 1500-year long stalagmite recording past changes in precipitation in the hitherto unsampled core region of the SAMS. This record details how solar variability consistently modulated the strength of the SAMS on centennial time scales during the past 1500 years. Solar forcing, besides the previously recognized influence from NH temperature changes and associated Intertropical Convergence Zone (ITCZ) shifts, appears as a major driver affecting SAMS intensity at centennial time scales.
In situ 3D topographic and shape analysis by synchrotron radiation X-ray microtomography for crystal form identification in polymorphic mixtures
Authors: Yin Xian-Zhen , Xiao Ti-Qiao , Nangia Ashwini , Yang Shuo , Lu Xiao-Long , Li Hai-Yan , Shao Qun , He You , York Peter , Zhang Ji-Wen 
Published: April 2016

AbstractPolymorphism denotes the existence of more than one crystal structure of a substance and great practical and theoretical interest for the chemical and pharmaceutical industries. In many cases, it is challenging to produce a pure crystal form and establish a sensitive detection method for the identification of crystal form in a mixture of polymorphs. In this study, an accurate and sensitive method based on synchrotron radiation X-ray computed microtomography (SR-μCT) was devised to identify the polymorphs of clopidogrel bisulphate (CLP). After 3D reconstruction, crystal particles were extracted and dozens of structural parameters were calculated. Whilst, the particle shapes of the two crystal forms were all irregular, the surface of CLP II was found to be rougher than CLP I. In order to classify the crystal form based on the quantitative morphological property of particles, Volume Bias Percentage based on Surface Smoothing (VBP) was defined and a new method based on VBP was successfully developed, with a total matching rate of 99.91% for 4544 particles and a lowest detectable limit of 1%. More important for the mixtures in solid pharmaceutical formulations, the interference of excipients can be avoided, a feature cannot achieved by other available analytical methods.
Radiation Resistant Vanadium-Graphene Nanolayered Composite
Authors: Kim Youbin , Baek Jinwook , Kim Sunghwan , Kim Sangmin , Ryu Seunghwa , Jeon Seokwoo , Han Seung Min 
Published: April 2016

AbstractUltra high strength V-graphene nanolayers were developed for the first time that was demonstrated to have an excellent radiation tolerance as revealed by the He+ irradiation study. Radiation induced hardening, evaluated via nanopillar compressions before and after He+ irradiation, is significantly reduced with the inclusion of graphene layers; the flow stresses of V-graphene nanolayers with 110 nm repeat layer spacing showed an increase of 25% while pure V showed an increase of 88% after He+ dosage of 13.5 dpa. The molecular dynamics simulations confirmed that the graphene interface can spontaneously absorb the nearby crystalline defects that are produced from a collision cascade, thereby enhancing the lifetime of the V-graphene nanolayers via this self-healing effect. In addition, the impermeability of He gas through the graphene resulted in suppression of He bubble agglomerations that in turn reduced embrittlement. In-situ SEM compression also showed the ability of graphene to hinder crack propagation that suppressed the failure.