bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges
Authors: Gouin Anaïs , Bretaudeau Anthony , Nam Kiwoong , Gimenez Sylvie , Aury Jean-Marc , Duvic Bernard , Hilliou Frédérique , Durand Nicolas , Montagné Nicolas , Darboux Isabelle , Kuwar Suyog , Chertemps Thomas , Siaussat David , Bretschneider Anne , Moné Yves , Ahn Seung-Joon , Hänniger Sabine , Grenet Anne-Sophie Gosselin , Neunemann David , Maumus Florian , Luyten Isabelle , Labadie Karine , Xu Wei , Koutroumpa Fotini , Escoubas Jean-Michel , Llopis Angel , Maïbèche-Coisne Martine , Salasc Fanny , Tomar Archana , Anderson Alisha R. , Khan Sher Afzal , Dumas Pascaline , Orsucci Marion , Guy Julie , Belser Caroline , Alberti Adriana , Noel Benjamin , Couloux Arnaud , Mercier Jonathan , Nidelet Sabine , Dubois Emeric , Liu Nai-Yong , Boulogne Isabelle , Mirabeau Olivier , Le Goff Gaelle , Gordon Karl , Oakeshott John , Consoli Fernando L. , Volkoff Anne-Nathalie , Fescemyer Howard W. , Marden James H. , Luthe Dawn S. , Herrero Salvador , Heckel David G. , Wincker Patrick , Kergoat Gael J. , Amselem Joelle , Quesneville Hadi , Groot Astrid T. , Jacquin-Joly Emmanuelle , Nègre Nicolas , Lemaitre Claire , Legeai Fabrice , d’Alençon Emmanuelle , Fournier Philippe 
Published: September 2017

AbstractEmergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world’s worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains (“C” and “R”) that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.
Mesoscopic model for DNA G-quadruplex unfolding
Authors: Bergues-Pupo A. E. , Gutiérrez I. , Arias-Gonzalez J. R. , Falo F. , Fiasconaro A. 
Published: September 2017

AbstractGenomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been reported to date by all-atom simulations, which cannot dissect the major physical interactions responsible for their cohesion. Here, we propose a mesoscopic model to describe both the mechanical and thermal stability of DNA G-quadruplexes, where each nucleotide of the structure, as well as each central cation located at the inner channel, is mapped onto a single bead. In this framework we are able to simulate loading rates similar to the experimental ones, which are not reachable in simulations with atomistic resolution. In this regard, we present single-molecule force-induced unfolding experiments by a high-resolution optical tweezers on a DNA telomeric sequence capable of adopting a G-quadruplex conformation. Fitting the parameters of the model to the experiments we find a correct prediction of the rupture-force kinetics and a good agreement with previous near equilibrium measurements. Since G-quadruplex unfolding dynamics is halfway in complexity between secondary nucleic acids and tertiary protein structures, our model entails a nanoscale paradigm for non-equilibrium processes in the cell.
Determination of unique power conversion efficiency of solar cell showing hysteresis in the I-V curve under various light intensities
Authors: Cojocaru Ludmila , Uchida Satoshi , Tamaki Koichi , Jayaweera Piyankarage V. V. , Kaneko Shoji , Nakazaki Jotaro , Kubo Takaya , Segawa Hiroshi 
Published: September 2017

AbstractEnergy harvesting at low light intensities has recently attracted a great deal of attention of perovskite solar cells (PSCs) which are regarded as promising candidate for indoor application. Anomalous hysteresis of the PSCs a complex issue for reliable evaluation of the cell performance. In order to address these challenges, we constructed two new evaluation methods to determinate the power conversion efficiencies (PCEs) of PSCs. The first setup is a solar simulator based on light emitting diodes (LEDs) allowing evaluation of the solar cells at wider range of light intensities, ranging from 102 to 10−3 mW·cm−2. As the overestimate error, we found that the PCEs of dye sensitized solar cell (DSC) and PSCs increase dramatically at low light intensities conditions. Due to the internal capacitance at the interfaces on hybrid solar cells, the measurement of current below 10−2 mW·cm−2 shows constant value given high PCE, which is related to the capacitive current and origin of the hysteresis. The second setup is a photovoltaic power analyzing system, designed for tracking the maximum power (﻿Pmax) with time. The paper suggests the combination of the LED solar simulator and Pmax tracking technique as a standard to evaluate the PCE of capacitive solar cells.
Logical gates in actin monomer
Authors: Adamatzky Andrew 
Published: September 2017

AbstractWe evaluate information processing capacity of a single actin molecule by calculating distributions of logical gates implemented by the molecule via propagating patterns of excitation. We represent a filamentous actin molecule as an excitable automaton network (F-actin automaton). where every atom updates its state depending on states of atoms its connected to with chemical bonds (hard neighbours) and atoms being in physical proximity to the atom (soft neighbours). A resting atom excites if a sum of its excited hard neighbours and a weighted sum of its soft neighbours belong to some specified interval. We demonstrate that F-actin automata implement OR, AND, XOR and AND-NOT gates via interacting patterns of excitation. Gate AND is the most common gate and gate XOR is the rarest. Using the architectures of gates discovered we implement one bit half-adder and controlled-not circuits in the F-actin automata. Speed and space values of the F-actin molecular computers are discussed.
HMGA1 regulates the Plasminogen activation system in the secretome of breast cancer cells
Authors: Resmini Giulia , Rizzo Serena , Franchin Cinzia , Zanin Rossella , Penzo Carlotta , Pegoraro Silvia , Ciani Yari , Piazza Silvano , Arrigoni Giorgio , Sgarra Riccardo , Manfioletti Guidalberto 
Published: September 2017

AbstractCancer cells secrete proteins that modify the extracellular environment acting as autocrine and paracrine stimulatory factors and have a relevant role in cancer progression. The HMGA1 oncofetal protein has a prominent role in controlling the expression of an articulated set of genes involved in various aspect of cancer cell transformation. However, little is known about its role in influencing the secretome of cancer cells. Performing an iTRAQ LC–MS/MS screening for the identification of secreted proteins, in an inducible model of HMGA1 silencing in breast cancer cells, we found that HMGA1 has a profound impact on cancer cell secretome. We demonstrated that the pool of HMGA1–linked secreted proteins has pro–migratory and pro-invasive stimulatory roles. From an inspection of the HMGA1–dependent secreted factors it turned out that HMGA1 influences the presence in the extra cellular milieu of key components of the Plasminogen activation system (PLAU, SERPINE1, and PLAUR) that has a prominent role in promoting metastasis, and that HMGA1 has a direct role in regulating the transcription of two of them, i.e. PLAU and SERPINE1. The ability of HMGA1 to regulate the plasminogen activator system may constitute an important mechanism by which HMGA1 promotes cancer progression.
Proxies of energy expenditure for marine mammals: an experimental test of “the time trap”
Authors: Ladds Monique A. , Rosen David A. S. , Slip David J. , Harcourt Robert G. 
Published: September 2017

AbstractDirect measures of energy expenditure are difficult to obtain in marine mammals, and accelerometry may be a useful proxy. Recently its utility has been questioned as some analyses derived their measure of activity level by calculating the sum of accelerometry-based values and then comparing this summation to summed (total) energy expenditure (the so-called “time trap”). To test this hypothesis, we measured oxygen consumption of captive fur seals and sea lions wearing accelerometers during submerged swimming and calculated total and rate of energy expenditure. We compared these values with two potential proxies of energy expenditure derived from accelerometry data: flipper strokes and dynamic body acceleration (DBA). Total number of strokes, total DBA, and submergence time all predicted total oxygen consumption $$({\boldsymbol{sV}}{{\boldsymbol{O}}}_{{\boldsymbol{2}}}$$
(
sV

O

2

ml kg−1). However, both total DBA and total number of strokes were correlated with submergence time. Neither stroke rate nor mean DBA could predict the rate of oxygen consumption ($$s\mathop{{\boldsymbol{V}}}\limits^{{\boldsymbol{.}}}{{\boldsymbol{O}}}_{{\boldsymbol{2}}}$$
s

V
.

O

2

ml min−1 kg−1). The relationship of total DBA and total strokes with total oxygen consumption is apparently a result of introducing a constant (time) into both sides of the relationship. This experimental evidence supports the conclusion that proxies derived from accelerometers cannot estimate the energy expenditure of marine mammals.
Variations in oral microbiota associated with oral cancer
Authors: Zhao Hongsen , Chu Min , Huang Zhengwei , Yang Xi , Ran Shujun , Hu Bin , Zhang Chenping , Liang Jingping 
Published: September 2017

AbstractIndividual bacteria and shifts in microbiome composition are associated with human disease, including cancer. To unravel the connections underlying oral bacterial dysbiosis and oral squamous cell carcinoma (OSCC), cancer lesion samples and anatomically matched normal samples were obtained from the same patients. We then profiled the bacteria within OSCC lesion surface samples at the species level using next-generation sequencing to comprehensively investigate bacterial community composition and functional genes in these samples. Significantly greater bacterial diversity was observed in the cancer samples than in the normal samples. Compared with previous studies, we identified many more taxa demonstrating remarkably different distributions between the groups. In particular, a group of periodontitis-correlated taxa, includingFusobacterium, Dialister, Peptostreptococcus, Filifactor, Peptococcus, CatonellaandParvimonas, was significantly enriched in OSCC samples. Additionally, several operational taxonomic units (OTUs) associated withFusobacteriumwere highly involved in OSCC and demonstrated good diagnostic power. Our study revealed drastic changes in surface bacterial communities of OSCC. The findings enrich knowledge of the association between oral bacterial communities and oral cancer.
Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions
Authors: Cornejo-Granados Fernanda , Lopez-Zavala Alonso A. , Gallardo-Becerra Luigui , Mendoza-Vargas Alfredo , Sánchez Filiberto , Vichido Rodrigo , Brieba Luis G. , Viana Maria Teresa , Sotelo-Mundo Rogerio R. , Ochoa-Leyva Adrián 
Published: September 2017

AbstractCrustaceans form the second largest subphylum on Earth, which includes Litopeneaus vannamei (Pacific whiteleg shrimp), one of the most cultured shrimp worldwide. Despite efforts to study the shrimp microbiota, little is known about it from shrimp obtained from the open sea and the role that aquaculture plays in microbiota remodeling. Here, the microbiota from the hepatopancreas and intestine of wild type (wt) and aquacultured whiteleg shrimp and pond sediment from hatcheries were characterized using sequencing of seven hypervariable regions of the 16S rRNA gene. Cultured shrimp with AHPND/EMS disease symptoms were also included. We found that (i) microbiota and their predicted metagenomic functions were different between wt and cultured shrimp; (ii) independent of the shrimp source, the microbiota of the hepatopancreas and intestine was different; (iii) the microbial diversity between the sediment and intestines of cultured shrimp was similar; and (iv) associated to an early development of AHPND/EMS disease, we found changes in the microbiome and the appearance of disease-specific bacteria. Notably, under cultured conditions, we identified bacterial taxa enriched in healthy shrimp, such as Faecalibacterium prausnitzii and Pantoea agglomerans, and communities enriched in diseased shrimp, such as Aeromonas taiwanensis, Simiduia agarivorans and Photobacterium angustum.
Tumor suppression via inhibition of SWI/SNF complex-dependent NF-κB activation
Authors: Kobayashi Kazuyoshi , Hiramatsu Hiroaki , Nakamura Shinya , Kobayashi Kyousuke , Haraguchi Takeshi , Iba Hideo 
Published: September 2017

AbstractThe transcription factor NF-κB is constitutively activated in many epithelial tumors but few NF-κB inhibitors are suitable for cancer therapy because of its broad biological effects. We previously reported that the d4-family proteins (DPF1, DPF2, DPF3a/b) function as adaptor proteins linking NF-κB with the SWI/SNF complex. Here, using epithelial tumor cell lines, A549 and HeLaS3, we demonstrate that exogenous expression of the highly-conserved N-terminal 84-amino acid region (designated “CT1”) of either DPF2 or DPF3a/b has stronger inhibitory effects on anchorage-independent growth than the single knockdown of any d4-family protein. This indicates that CT1 can function as an efficient dominant-negative mutant of the entire d4-family proteins. By in situ proximity ligation assay, CT1 was found to retain full adaptor function, indicating that the C-terminal region of d4-family proteins lacking in CT1 would include essential domains for SWI/SNF-dependent NF-κB activation. Microarray analysis revealed that CT1 suppresses only a portion of the NF-κB target genes, including representative SWI/SNF-dependent genes. Among these genes, IL6 was shown to strongly contribute to anchorage-independent growth. Finally, exogenous CT1 expression efficiently suppressed tumor formation in a mouse xenograft model, suggesting that the d4-family proteins are promising cancer therapy targets.
Cyclipostins and Cyclophostin analogs as promising compounds in the fight against tuberculosis
Authors: Nguyen Phuong Chi , Delorme Vincent , Bénarouche Anaïs , Martin Benjamin P. , Paudel Rishi , Gnawali Giri R. , Madani Abdeldjalil , Puppo Rémy , Landry Valérie , Kremer Laurent , Brodin Priscille , Spilling Christopher D. , Cavalier Jean-François , Canaan Stéphane 
Published: September 2017

AbstractA new class of Cyclophostin and Cyclipostins (CyC) analogs have been investigated against Mycobacterium tuberculosis H37Rv (M. tb) grown either in broth medium or inside macrophages. Our compounds displayed a diversity of action by acting either on extracellular M. tb bacterial growth only, or both intracellularly on infected macrophages as well as extracellularly on bacterial growth with very low toxicity towards host macrophages. Among the eight potential CyCs identified, CyC
17
exhibited the best extracellular antitubercular activity (MIC50 = 500 nM). This compound was selected and further used in a competitive labelling/enrichment assay against the activity-based probe Desthiobiotin-FP in order to identify its putative target(s). This approach, combined with mass spectrometry, identified 23 potential candidates, most of them being serine or cysteine enzymes involved in M. tb lipid metabolism and/or in cell wall biosynthesis. Among them, Ag85A, CaeA and HsaD, have previously been reported as essential for in vitro growth of M. tb and/or survival and persistence in macrophages. Overall, our findings support the assumption that CyC
17
may thus represent a novel class of multi-target inhibitor leading to the arrest of M. tb growth through a cumulative inhibition of a large number of Ser- and Cys-containing enzymes participating in important physiological processes.
The epistemic and aleatory uncertainties of the ETAS-type models: an application to the Central Italy seismicity
Authors: Lombardi A. M. 
Published: September 2017

AbstractStochastic models provide quantitative evaluations about the occurrence of earthquakes. A basic component of this type of models are the uncertainties in defining main features of an intrinsically random process. Even if, at a very basic level, any attempting to distinguish between types of uncertainty is questionable, an usual way to deal with this topic is to separate epistemic uncertainty, due to lack of knowledge, from aleatory variability, due to randomness. In the present study this problem is addressed in the narrow context of short-term modeling of earthquakes and, specifically, of ETAS modeling. By mean of an application of a specific version of the ETAS model to seismicity of Central Italy, recently struck by a sequence with a main event of Mw6.5, the aleatory and epistemic (parametric) uncertainty are separated and quantified. The main result of the paper is that the parametric uncertainty of the ETAS-type model, adopted here, is much lower than the aleatory variability in the process. This result points out two main aspects: an analyst has good chances to set the ETAS-type models, but he may retrospectively describe and forecast the earthquake occurrences with still limited precision and accuracy.
The multifunctional polydnavirus TnBVANK1 protein: impact on host apoptotic pathway
Authors: Salvia Rosanna , Grossi Gerarda , Amoresano Angela , Scieuzo Carmen , Nardiello Marisa , Giangrande Chiara , Laurenzana Ilaria , Ruggieri Vitalba , Bufo Sabino A. , Vinson S. Bradleigh , Carmosino Monica , Neunemann David , Vogel Heiko , Pucci Pietro , Falabella Patrizia 
Published: September 2017

AbstractToxoneuron nigriceps (Hymenoptera, Braconidae) is an endophagous parasitoid of the larval stages of the tobacco budworm, Heliothis virescens (Lepidoptera, Noctuidae). The bracovirus associated with this wasp (TnBV) is currently being studied. Several genes expressed in parasitised host larvae have been isolated and their possible roles partly elucidated. TnBVank1 encodes an ankyrin motif protein similar to insect and mammalian IκB, an inhibitor of the transcription nuclear factor κB (NF-κB). Here we show that, when TnBVank1 was stably expressed in polyclonal Drosophila S2 cells, apoptosis is induced. Furthermore, we observed the same effects in haemocytes of H. virescens larvae, after TnBVank1 in vivo transient transfection, and in haemocytes of parasitised larvae. Coimmunoprecipitation experiments showed that TnBVANK1 binds to ALG-2 interacting protein X (Alix/AIP1), an interactor of apoptosis-linked gene protein 2 (ALG-2). Using double-immunofluorescence labeling, we observed the potential colocalization of TnBVANK1 and Alix proteins in the cytoplasm of polyclonal S2 cells. When Alix was silenced by RNA interference, TnBVANK1 was no longer able to cause apoptosis in both S2 cells and H. virescens haemocytes. Collectively, these results indicate that TnBVANK1 induces apoptosis by interacting with Alix, suggesting a role of TnBVANK1 in the suppression of host immune response observed after parasitisation by T. nigriceps.
Conjugation of wildtype and hypoallergenic mugwort allergen Art v 1 to flagellin induces IL-10-DC and suppresses allergen-specific TH2-responses in vivo
Authors: Schülke Stefan , Kuttich Kirsten , Wolfheimer Sonja , Duschek Nadine , Wangorsch Andrea , Reuter Andreas , Briza Peter , Pablos Isabel , Gadermaier Gabriele , Ferreira Fatima , Vieths Stefan , Toda Masako , Scheurer Stephan 
Published: September 2017

AbstractAllergies to weed pollen including members of the Compositae family, such as mugwort, ragweed, and feverfew are spreading worldwide. To efficiently treat these newly arising allergies, allergen specific immunotherapy needs to be improved. Therefore, we generated novel vaccine candidates consisting of the TLR5-ligand Flagellin A from Listeria and the major mugwort allergen Art v 1 including either the wild type Art v 1 sequence (rFlaA:Artv1) or a hypoallergenic variant (rFlaA:Artv1hyp) with reduced IgE-binding capacity. Immune modulating capacity of these constructs and respective controls was evaluated in vitro and in vivo. Incorporation of hypoallergenic Art v 1 derivative did not interfere with the resulting fusion proteins’ immune stimulatory capacity. Both rFlaA:Artv1 and rFlaA:Artv1hyp induced a prominent, mTOR-dependent, IL-10 secretion from murine dendritic cells, and suppressed allergen-specific TH2-cytokine secretion in vitro and in vivo. Both conjugates retained the capacity to induce rFlaA-specific antibody responses while efficiently inducing production of Art v 1-specific IgG1 and IgG2a antibodies in mice. Interestingly, only the suppression of TH2-cytokine secretion by rFlaA:Artv1 (but not rFlaA:Artv1hyp) was paralleled by a strong secretion of IFN-γ. In summary, we provided evidence that incorporating hypoallergens into flagellin:allergen fusion proteins is a suitable strategy to further improve these promising vaccine candidates.
Detrimental effect of Hypoxia-inducible factor-1α-induced autophagy on multiterritory perforator flap survival in rats
Authors: Wang Long , Jin Zhicheng , Wang Jieke , Chen Shao , Dai Li , Lin Dingsheng , Wu Lingfeng , Gao Weiyang 
Published: September 2017

AbstractHypoxia-inducible factor-1α (HIF-1α) plays a key role in angiogenesis, improves flap survival, and activates autophagy. The effect of HIF-1α-induced autophagy is still debatable. Thus, we investigated the effect of HIF-1α-induced autophagy on multiterritory perforator flap survival. In this study, 99 male Sprague-Dawley rats received multiterritory perforator flap procedure and were divided into three groups with 33 each. The dimethyloxalylglycine (DMOG) plus 3-methyladenine (3-MA) group received intraperitoneal injection of DMOG (40 mg/kg) and 3-MA (10 mg/kg). The DMOG group and control group received comparative DMOG and saline respectively. On postoperative day (POD) 7, HIF-1α’s activities of flap survival and perfusion improvement were confirmed in DMOG group, however, its positive effects were further enhanced by co-administration of autophagy inhibitor, 3-MA. On POD 1, vascular endothelial growth factor, mean microvascular density and blood perfusion were not affected by HIF-1α up-regulation or autophagy inactivation. However, HIF-1α-induced autophagy augments apoptosis and oxidative stress. The increased level of apoptosis and oxidative stress was reversed by 3-MA and resulted in further flap survival improvement. In conclusion, HIF-1α-induced autophagy has a detrimental effect on multiterritory perforator flap survival and the flap survival was determined by the combined effects of ischemia and reperfusion injury.