bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metazoan Ribosome Inactivating Protein encoding genes acquired by Horizontal Gene Transfer
Authors: Lapadula Walter J. , Marcet Paula L. , Mascotti María L. , Sanchez-Puerta M. Virginia , Juri Ayub Maximiliano 
Published: May 2017

AbstractRibosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first time in silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history. A detailed study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and microsynteny analyses, indicating that mosquito RIP genes derived from a single Horizontal Gene Transfer (HGT) event, probably from a cyanobacterial donor species. Moreover, evolutionary analyses show that, after the HGT event, these genes evolved under purifying selection, strongly suggesting they play functional roles in these organisms.
Impact of Hepatitis C Treatment as Prevention for People Who Inject Drugs is sensitive to contact network structure
Authors: Metzig Cornelia , Surey Julian , Francis Marie , Conneely Jim , Abubakar Ibrahim , White Peter J. 
Published: May 2017

AbstractTreatment as Prevention (TasP) using directly-acting antivirals has been advocated for Hepatitis C Virus (HCV) in people who inject drugs (PWID), but treatment is expensive and TasP’s effectiveness is uncertain. Previous modelling has assumed a homogeneously-mixed population or a static network lacking turnover in the population and injecting partnerships. We developed a transmission-dynamic model on a dynamic network of injecting partnerships using data from survey of injecting behaviour carried out in London, UK. We studied transmission on a novel exponential-clustered network, as well as on two simpler networks for comparison, an exponential unclustered and a random network, and found that TasP’s effectiveness differs markedly. With respect to an exponential-clustered network, the random network (and homogeneously-mixed population) overestimate TasP’s effectiveness, whereas the exponential-unclustered network underestimates it. For all network types TasP’s effectiveness depends on whether treated patients change risk behaviour, and on treatment coverage: higher coverage requires fewer total treatments for the same health gain. Whilst TasP can greatly reduce HCV prevalence, incidence of infection, and incidence of reinfection in PWID, assessment of TasP’s effectiveness needs to take account of the injecting-partnership network structure and post-treatment behaviour change, and further empirical study is required.
Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus
Authors: McKown Athena D. , Klápště Jaroslav , Guy Robert D. , Soolanayakanahally Raju Y. , La Mantia Jonathan , Porth Ilga , Skyba Oleksandr , Unda Faride , Douglas Carl J. , El-Kassaby Yousry A. , Hamelin Richard C. , Mansfield Shawn D. , Cronk Quentin C. B. 
Published: May 2017

AbstractThe evolution of sexual dimorphism and expansion of sex chromosomes are both driven through sexual conflict, arising from differing fitness optima between males and females. Here, we pair work in poplar (Populus) describing one of the smallest sex-determining regions known thus far in complex eukaryotes (~100 kbp) with comprehensive tests for sexual dimorphism using >1300 individuals from two Populus species and assessing 96 non-reproductive functional traits. Against expectation, we found sexual homomorphism (no non-reproductive trait differences between the sexes), suggesting that gender is functionally neutral with respect to non-reproductive features that affect plant survival and fitness. Combined with a small sex-determining region, we infer that sexual conflict may be effectively stymied or non-existent within these taxa. Both sexual homomorphism and the small sex-determining region occur against a background of strong environmental selection and local adaptation in Populus. This presents a powerful hypothesis for the evolution of dioecious species. Here, we suggest that environmental selection may be sufficient to suppress and stymy sexual conflict if it acts orthogonal to sexual selection, thereby placing limitations on the evolution of sexual dimorphism and genomic expansion of sex chromosomes.
Spatial topologies affect local food web structure and diversity in evolutionary metacommunities
Authors: Bolchoun Lev , Drossel Barbara , Allhoff Korinna Theresa 
Published: May 2017

AbstractAn important challenge in theoretical ecology is to better predict ecological responses to environmental change, and in particular to spatial changes such as habitat fragmentation. Classical food-web models have focused on purely ecological predictions, without taking adaptation or evolution of species traits into account. We address this issue using an eco-evolutionary model, which is based on body masses and diets as the key traits that determine metabolic rates and trophic interactions. The model implements evolution by the introduction of new morphs that are related to the existing ones, so that the network structure itself evolves in a self-organized manner. We consider the coupling and decoupling of habitats in multi-trophic metacommunities consisting of 2 or 4 habitats. Our model thus integrates metacommunity models, which describe ecosystems as networks of networks, with large community evolution models. We find that rescue effects and source-sink effects occur within coupled habitats, which have the potential to change local selection pressures so that the local food web structure shows a fingerprint of its spatial conditions. Within our model system, we observe that habitat coupling increases the lifetimes of top predators and promotes local biodiversity.
Stapled BIG3 helical peptide ERAP potentiates anti-tumour activity for breast cancer therapeutics
Authors: Yoshimaru Tetsuro , Aihara Keisuke , Komatsu Masato , Matsushita Yosuke , Okazaki Yasumasa , Toyokuni Shinya , Honda Junko , Sasa Mitsunori , Miyoshi Yasuo , Otaka Akira , Katagiri Toyomasa 
Published: May 2017

AbstractEstradiol (E2) and the oestrogen receptor-alpha (ERα) signalling pathway play pivotal roles in the proliferative activity of breast cancer cells. Recent findings show that the brefeldin A-inhibited guanine nucleotide-exchange protein 3-prohibitin 2 (BIG3-PHB2) complex plays a crucial role in E2/ERα signalling modulation in breast cancer cells. Moreover, specific inhibition of the BIG3-PHB2 interaction using the ERα activity-regulator synthetic peptide (ERAP: 165–177 amino acids), derived from α-helical BIG3 sequence, resulted in a significant anti-tumour effect. However, the duration of this effect was very short for viable clinical application. We developed the chemically modified ERAP using stapling methods (stapledERAP) to improve the duration of its antitumour effects. The stapledERAP specifically inhibited the BIG3-PHB2 interaction and exhibited long-lasting suppressive activity. Its intracellular localization without the membrane-permeable polyarginine sequence was possible via the formation of a stable α-helix structure by stapling. Tumour bearing-mice treated daily or weekly with stapledERAP effectively prevented the BIG3-PHB2 interaction, leading to complete regression of E2-dependent tumours in vivo. Most importantly, combination of stapledERAP with tamoxifen, fulvestrant, and everolimus caused synergistic inhibitory effects on growth of breast cancer cells. Our findings suggested that the stapled ERAP may be a promising anti-tumour drug to suppress luminal-type breast cancer growth.
Fine-tune regulation of carboxypeptidase N1 controls vascular patterning during zebrafish development
Authors: Wu Ting-Yun , Wang Yi-Shan , Song Yi-Chun , Chen Zih-Ying , Chen Yi-Ting , Chiu Chien-Chih , Wu Chang-Yi 
Published: May 2017

AbstractVascular development is regulated by complicated signals and molecules in vertebrates. In this study, we characterized a novel function of carboxypeptidase N1 (Cpn1) in the vasculature. We show that cpn1 mRNA is expressed in developing vessels. The knockdown of cpn1 by morpholino injection impairs the growth of intersegmental vessels (ISV) and caudal vein plexus (CVP), suggesting the role of cpn1 in vascular development. We showed that vascular defects are not caused by cell death but are due to the impairment of migration and proliferation. Consistent with vascular growth defects, loss of cpn1 affects the expression of the vascular markers flt4, mrc1, flk, stabilin, and ephrinb2. Furthermore, the overexpression of cpn1 impaired the growth of ISV and CVP, but the remodeling expression of vascular markers was different from the knockdown of cpn1, indicating the differential regulation mechanisms in cpn1-overexpressing embryos. We examine the interaction between cpn1 and multiple signals and observed that cpn1 is regulated by Notch/VEGF signals for ISV growth and likely regulates BMP signals for CVP patterning. In conclusion, we demonstrate that cpn1 has a critical role in the vascular development of zebrafish. We also reveal a fine-tune regulation of cpn1 that controls vascular patterning mediated by multiple signals.
Optical properties of monolayer tinene in electric fields
Authors: Chen Rong-Bin , Chen Szu-Chao , Chiu Chih-Wei , Lin Ming-Fa 
Published: May 2017

AbstractThe absorption spectra of monolayer tinene in perpendicular electric fields are studied by the tight-binding model. There are three kinds of special structures, namely shoulders, logarithmical symmetric peaks and asymmetric peaks in the square-root form, corresponding to the optical excitations of the extreme points, saddle points and constant-energy loops. With the increasing field strength, two splitting shoulder structures, which are dominated by the parabolic bands of 5p
z
orbitals, come to exist because of the spin-split energy bands. The frequency of threshold shoulder declines to zero and then linearly grows. The third shoulder at 0.75~0.85 eV mainly comes from (5p
x
, 5p
y
) orbitals. The former and the latter orbitals, respectively, create the saddle-point symmetric peaks near the M point, while they hybridize with one another to generate the loop-related asymmetric peaks. Tinene quite differs from graphene, silicene, and germanene. The special relationship among the multi-orbital chemical bondings, spin-orbital couplings and Coulomb potentials accounts for the feature-rich optical properties.
Network and role analysis of autophagy in Phytophthora sojae
Authors: Chen Linlin , Zhang Xiong , Wang Wen , Geng Xuejing , Shi Yan , Na Risong , Dou Daolong , Li Honglian 
Published: May 2017

AbstractAutophagy is an evolutionarily conserved mechanism in eukaryotes with roles in development and the virulence of plant fungal pathogens. However, few reports on autophagy in oomycete species have been published. Here, we identified 26 autophagy-related genes (ATGs) belonging to 20 different groups in Phytophthora sojae using a genome-wide survey, and core ATGs in oomycetes were used to construct a preliminary autophagy pathway model. Expression profile analysis revealed that these ATGs are broadly expressed and that the majority of them significantly increase during infection stages, suggesting a central role for autophagy in virulence. Autophagy in P. sojae was detected using a GFP-PsAtg8 fusion protein and the fluorescent dye MDC during rapamycin and starvation treatment. In addition, autophagy was significantly induced during sporangium formation and cyst germination. Silencing PsAtg6a in P. sojae significantly reduced sporulation and pathogenicity. Furthermore, a PsAtg6a-silenced strain showed haustorial formation defects. These results suggested that autophagy might play essential roles in both the development and infection mechanism of P. sojae.
Structural studies of the periplasmic portion of the diguanylate cyclase CdgH from Vibrio cholerae
Authors: Xu Min , Wang Yi-Zhi , Yang Xiu-An , Jiang Tao , Xie Wei 
Published: May 2017

AbstractCyclic diguanylate monophosphate (c-di-GMP) is a second messenger involved in bacterial signal transduction and produced by diguanylate cyclases (DGCs) generally containing highly variable periplasmic signal-recognition domains. CdgH is a DGC enzyme that regulates rugosity associated phenotypes in Vibrio cholerae. CdgH has two N-terminal tandem periplasmic substrate-binding (PBPb) domains for its signal recognition; however, the role of the tandem PBPb domains remains unclear. Here, we reported the crystal structure of the periplasmic portion of CdgH, which indicated that both tandem PBPb domains consist of typical interlobe ligand-binding architecture. Unexpectedly, the PBPb-I domain binds an L-arginine which apparently has been co-purified from the E. coli expression system, whereas the PBPb-II domain is in an unliganded open state. Structural comparison with other amino acid-binding proteins indicated that despite similar ligand-binding pockets, the PBPb-I domain possesses two ligand-binding residues (E122 and Y148) not conserved in homologs and involved in hydrophilic and hydrophobic interactions with L-arginine. Isothermal titration calorimetry indicated that the PBPb-I is primarily an L-arginine/L-lysine/L-ornithine-binding domain, whereas the PBPb-II domain exhibits a preference for L-glutamine and L-histidine. Remarkably, we found that the periplasmic portion of CdgH forms a stable dimer in solution and L-arginine binding would cause conformational changes of the dimer.
Characterization of prophages of Lactococcus garvieae
Authors: Eraclio Giovanni , Fortina Maria G. , Labrie Simon J. , Tremblay Denise M. , Moineau Sylvain 
Published: May 2017

AbstractThis report describes the morphological characterization and genome analysis of an induced prophage (PLg-TB25) from a dairy strain of Lactococcus garvieae. The phage belongs to the Siphoviridae family and its morphology is typical of other lactococcal phages. A general analysis of its genome did not reveal similarities with other lactococcal phage genomes, confirming its novelty. However, similarities were found between genes of its morphogenesis cluster and genes of Gram-positive bacteria, suggesting that this phage genome resulted from recombination events that took place in a heterogeneous microbial environment. An in silico search for other prophages in 16 L. garvieae genomes available in public databases, uncovered eight seemingly complete prophages in strains isolated from dairy and fish niches. Genome analyses of these prophages revealed three novel L. garvieae phages. The remaining prophages had homology to phages of Lactococcus lactis (P335 group) suggesting a close relationship between these lactococcal species. The similarity in GC content of L. garvieae prophages to the genomes of L. lactis phages further supports the hypothesis that these phages likely originated from the same ancestor.
A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content
Authors: Martin Pauline , Palhière Isabelle , Maroteau Cyrielle , Bardou Philippe , Canale-Tabet Kamila , Sarry Julien , Woloszyn Florent , Bertrand-Michel Justine , Racke Ines , Besir Hüseyin , Rupp Rachel , Tosser-Klopp Gwenola 
Published: May 2017

AbstractThe quantity of milk and milk fat and proteins are particularly important traits in dairy livestock. However, little is known about the regions of the genome that influence these traits in goats. We conducted a genome wide association study in French goats and identified 109 regions associated with dairy traits. For a major region on chromosome 14 closely associated with fat content, the Diacylglycerol O-Acyltransferase 1 (DGAT1) gene turned out to be a functional and positional candidate gene. The caprine reference sequence of this gene was completed and 29 polymorphisms were found in the gene sequence, including two novel exonic mutations: R251L and R396W, leading to substitutions in the protein sequence. The R251L mutation was found in the Saanen breed at a frequency of 3.5% and the R396W mutation both in the Saanen and Alpine breeds at a frequencies of 13% and 7% respectively. The R396W mutation explained 46% of the genetic variance of the trait, and the R251L mutation 6%. Both mutations were associated with a notable decrease in milk fat content. Their causality was then demonstrated by a functional test. These results provide new knowledge on the genetic basis of milk synthesis and will help improve the management of the French dairy goat breeding program.
The complete chloroplast genome sequence of tung tree (Vernicia fordii): Organization and phylogenetic relationships with other angiosperms
Authors: Li Ze , Long Hongxu , Zhang Lin , Liu Zhiming , Cao Heping , Shi Mingwang , Tan Xiaofeng 
Published: May 2017

AbstractTung tree (Vernicia fordii) is an economically important tree widely cultivated for industrial oil production in China. To better understand the molecular basis of tung tree chloroplasts, we sequenced and characterized its genome using PacBio RS II sequencing platforms. The chloroplast genome was sequenced with 161,528 bp in length, composed with one pair of inverted repeats (IRs) of 26,819 bp, which were separated by one small single copy (SSC; 18,758 bp) and one large single copy (LSC; 89,132 bp). The genome contains 114 genes, coding for 81 protein, four ribosomal RNAs and 29 transfer RNAs. An expansion with integration of an additional rps19 gene in the IR regions was identified. Compared to the chloroplast genome of Jatropha curcas, a species from the same family, the tung tree chloroplast genome is distinct with 85 single nucleotide polymorphisms (SNPs) and 82 indels. Phylogenetic analysis suggests that V. fordii is a sister species with J. curcas within the Eurosids I. The nucleotide sequence provides vital molecular information for understanding the biology of this important oil tree.
Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma
Authors: Al-hebshi Nezar Noor , Nasher Akram Thabet , Maryoud Mohamed Yousef , Homeida Husham E. , Chen Tsute , Idris Ali Mohamed , Johnson Newell W. 
Published: May 2017

AbstractStudies on the possible association between bacteria and oral squamous cell carcinoma (OSCC) remain inconclusive, largely due to methodological variations/limitations. The objective of this study was to characterize the species composition as well as functional potential of the bacteriome associated with OSCC. DNA obtained from 20 fresh OSCC biopsies (cases) and 20 deep-epithelium swabs (matched control subjects) was sequenced for the V1-V3 region using Illumina’s 2 × 300 bp chemistry. High quality, non-chimeric merged reads were classified to species level using a prioritized BLASTN-algorithm. Downstream analyses were performed using QIIME, PICRUSt, and LEfSe. Fusobacterium nucleatum subsp. polymorphum was the most significantly overrepresented species in the tumors followed by Pseudomonas aeruginosa and Campylobacter sp. Oral taxon 44, while Streptococcus mitis, Rothia mucilaginosa and Haemophilus parainfluenzae were the most significantly abundant in the controls. Functional prediction showed that genes involved in bacterial mobility, flagellar assembly, bacterial chemotaxis and LPS synthesis were enriched in the tumors while those responsible for DNA repair and combination, purine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, ribosome biogenesis and glycolysis/gluconeogenesis were significantly associated with the controls. This is the first epidemiological evidence for association of F. nucleatum and P. aeruginosa with OSCC. Functionally, an “inflammatory bacteriome” is enriched in OSSC.
Different Polyubiquitinated Bodies in Human Dendritic Cells: IL-4 Causes PaCS During Differentiation while LPS or IFNα Induces DALIS During Maturation
Authors: Montagna Daniela , Sommi Patrizia , Necchi Vittorio , Vitali Agostina , Montini Enrica , Turin Ilaria , Ferraro Daniela , Ricci Vittorio , Solcia Enrico 
Published: May 2017

AbstractTwo types of polyubiquitin-reactive cytoplasmic bodies, particulate cytoplasmic structures (PaCS) and dendritic cell (DC) aggresome-like induced structures (DALIS), were analyzed by electron microscopy, immunocytochemistry, immunoblotting, and flow cytometry in DC obtained from human blood monocytes incubated with GM-CSF plus IL-4 (IL4-DC), GM-CSF plus IFNα (IFN-DC), or GM-CSF alone (GM-DC), with or without LPS maturation. PaCS developed as monomorphic aggregates of proteasome-reactive barrel-like particles only in ribosomes-rich cytoplasmic areas of differentiating IL4-DC. In contrast, DALIS formed as vesicular bodies storing K63-linked ubiquitinated proteins by coalescence of increased endosomal structures, in IFN-DC or after LPS maturation of GM-DC. DALIS-forming cells showed incomplete morphological and functional DC-type differentiation when compared to PaCS-forming IL4-DC. PaCS and DALIS may have different function as well as different origin and cytochemistry. DALIS may be a transient accumulation site of potentially antigenic polyubiquitinated proteins during their processing and presentation. PaCS are found under physiologic or pathologic conditions associated with increased/deranged protein synthesis and increased ubiquitin–proteasome activity. Given its high heat-shock protein content PaCS may work as a quality control structure for newly synthesized, cytosolic proteins. This comparative analysis suggests that PaCS and DALIS have distinctive roles in DC.
Alterations of cerebral perfusion in asymptomatic internal carotid artery steno-occlusive disease
Authors: Chen Ya-Fang , Tang Sung-Chun , Wu Wen-Chau , Kao Hsien-Li , Kuo Yen-Shu , Yang Shun-Chung 
Published: May 2017

AbstractPatients with asymptomatic occlusion in the internal carotid arteries (ICA) have been shown to have a better preserved hemodynamic status of the brain as compared to patients with symptoms. This study was aimed to explore the cerebral perfusion alterations in asymptomatic patients using multi-parametric arterial spin-labeling (ASL) magnetic resonance (MR) imaging. Forty-two patients diagnosed with asymptomatic ICA stenosis/occlusion were prospectively included and divided into high-grade (ultrasonographic stenosis ≥70%, N = 20) and low-grade groups (N = 22). On a 3-Tesla clinical MR scanner, pseudo-continuous ASL was performed to measure cerebral blood flow CBF, arterial transit time ATT, and flow territory. Fisher’s exact test indicates that the high-grade group has higher frequency in asymmetric ATT (p < 10−3) and asymmetric flow territory (p < 10−3) as compared to the low-grade group. The between-group difference in CBF asymmetry is marginal (p = 0.062). Logistic regression further reveals that hemispherical asymmetry in ATT and flow territory is associated with the existence of high-grade ICA stenosis (odds ratio = 12 and 21, respectively), whereas hemispherical asymmetry in CBF is not. Our data suggest that ATT and flow territory may be better predictors of asymptomatic high-grade ICA stenosis diagnosed by carotid ultrasonography than CBF.