bluuebunny/crossref_metadata_2025_split huggingface dataset:
Innovation and constraint leading to complex multicellularity in the Ascomycota
Authors: Nguyen Tu Anh , Cissé Ousmane H. , Yun Wong Jie , Zheng Peng , Hewitt David , Nowrousian Minou , Stajich Jason E. , Jedd Gregory 
Published: February 2017

AbstractThe advent of complex multicellularity (CM) was a pivotal event in the evolution of animals, plants and fungi. In the fungal Ascomycota, CM is based on hyphal filaments and arose in the Pezizomycotina. The genus Neolecta defines an enigma: phylogenetically placed in a related group containing mostly yeasts, Neolecta nevertheless possesses Pezizomycotina-like CM. Here we sequence the Neolecta irregularis genome and identify CM-associated functions by searching for genes conserved in Neolecta and the Pezizomycotina, which are absent or divergent in budding or fission yeasts. This group of 1,050 genes is enriched for functions related to diverse endomembrane systems and their organization. Remarkably, most show evidence for divergence in both yeasts. Using functional genomics, we identify new genes involved in fungal complexification. Together, these data show that rudimentary multicellularity is deeply rooted in the Ascomycota. Extensive parallel gene divergence during simplification and constraint leading to CM suggest a deterministic process where shared modes of cellular organization select for similarly configured organelle- and transport-related machineries.
Redox preconditioning deep cratonic lithosphere for kimberlite genesis – evidence from the central Slave Craton
Authors: Yaxley G. M. , Berry A. J. , Rosenthal A. , Woodland A. B. , Paterson D. 
Published: February 2017

AbstractWe present the first oxygen fugacity (fO2) profile through the cratonic lithospheric mantle under the Panda kimberlite (Ekati Diamond Mine) in the Lac de Gras kimberlite field, central Slave Craton, northern Canada. Combining this data with new and existing data from garnet peridotite xenoliths from an almost coeval kimberlite (A154-N) at the nearby Diavik Diamond Mine demonstrates that the oxygen fugacity of the Slave cratonic mantle varies by several orders of magnitude as a function of depth and over short lateral distances. The lower part of the diamond-bearing Slave lithosphere (>120–130 km deep) has been oxidized by up to 4 log units in fO2, and this is clearly linked to metasomatic enrichment. Such coupled enrichment and oxidation was likely caused by infiltrating carbonate-bearing, hydrous, silicate melts in the presence of diamond, a process proposed to be critical for “pre-conditioning” deep lithospheric mantle and rendering it suitable for later generation of kimberlites and other SiO2-undersaturated magmas.
Microbial shifts in the porcine distal gut in response to diets supplemented with Enterococcus Faecalis as alternatives to antibiotics
Authors: Li Pinghua , Niu Qing , Wei Qingtian , Zhang Yeqiu , Ma Xiang , Kim Sung Woo , Lin Mingxin , Huang Ruihua 
Published: February 2017

AbstractGut microbiota plays an important role in host health and nutrient digestion of animals. Probiotics have become one of effective alternatives to antibiotics enhancing animal health and performance through modulating gut microbiota. Previously, our research demonstrated that dietary Enterococcus Faecalis UC-100 substituting antibiotics enhanced growth and health of weaned pigs. To investigate the alterations of microbiota in the distal gut of pigs fed E. faecalis UC-100 substituting antibiotics, this study assessed fecal microbiota in pigs from different dietary treatments: the basal diet group, the E. faecalis group, and the antibiotic group on d 0, 14, and 28 of feeding through 16 S rRNA sequencing. Twenty-one phyla and 137 genera were shared by all pigs, whereas 12 genera were uniquely identified in the E. faecalis group on d 14 and 28. Bacterial abundance and diversity in the E. faecalis group, bacterial diversity in the antibiotic group, especially abundances of Fibrobacteres phylum and 12 genera in the E. faecalis group and antibiotics group were lower than that in the basal diet group on d 28. These results showed that microbial shifts in the porcine gut in response to diets containing E. faecalis were similar to the response to which containing antibiotics.
Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)
Authors: Moodley Yoshan , Russo Isa-Rita M. , Dalton Desiré L. , Kotzé Antoinette , Muya Shadrack , Haubensak Patricia , Bálint Boglárka , Munimanda Gopi K. , Deimel Caroline , Setzer Andrea , Dicks Kara , Herzig-Straschil Barbara , Kalthoff Daniela C. , Siegismund Hans R. , Robovský Jan , O’Donoghue Paul , Bruford Michael W. 
Published: February 2017

AbstractThe black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species’ once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide genetic structure of historic and modern populations using the largest and most geographically representative sample of black rhinoceroses ever assembled. Using both mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species’ mitochondrial genetic variation, including the most ancestral lineages that are now absent from modern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad, Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historic range of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southern Kenya, where a handful of individuals survive in the Masai Mara. We also identify conservation units that will help maintain evolutionary potential. Our results suggest a complete re-evaluation of current conservation management paradigms for the black rhinoceros.
AMPK regulates lipid accumulation in skeletal muscle cells through FTO-dependent demethylation of N6-methyladenosine
Authors: Wu Weiche , Feng Jie , Jiang Denghu , Zhou Xihong , Jiang Qin , Cai Min , Wang Xinxia , Shan Tizhong , Wang Yizhen 
Published: February 2017

AbstractSkeletal muscle plays important roles in whole-body energy homeostasis. Excessive skeletal muscle lipid accumulation is associated with some metabolic diseases such as obesity and Type 2 Diabetes. The energy sensor AMPK (AMP-activated protein kinase) is a key regulator of skeletal muscle lipid metabolism, but the precise regulatory mechanism remains to be elucidated. Here, we provide a novel mechanism by which AMPK regulates skeletal muscle lipid accumulation through fat mass and obesity-associated protein (FTO)-dependent demethylation ofN6-methyladenosine (m6A). We confirmed an inverse correlation between AMPK and skeletal muscle lipid content. Moreover, inhibition of AMPK enhanced lipid accumulation, while activation of AMPK reduced lipid accumulation in skeletal muscle cells. Notably, we found that mRNA m6A methylation levels were inversely correlated with lipid content in skeletal muscle. Furthermore, AMPK positively regulated the m6A methylation levels of mRNA, which could negatively regulate lipid accumulation in C2C12. At the molecular level, we demonstrated that AMPK regulated lipid accumulation in skeletal muscle cells by regulating FTO expression and FTO-dependent demethylation of m6A. Together, these results provide a novel regulatory mechanism of AMPK on lipid metabolism in skeletal muscle cells and suggest the possibility of controlling skeletal muscle lipid deposition by targeting AMPK or using m6A related drugs.
Schottky barrier at graphene/metal oxide interfaces: insight from first-principles calculations
Authors: Cheng Kai , Han Nannan , Su Yan , Zhang Junfeng , Zhao Jijun 
Published: February 2017

AbstractAnode materials play an important role in determining the performance of lithium ion batteries. In experiment, graphene (GR)/metal oxide (MO) composites possess excellent electrochemical properties and are promising anode materials. Here we perform density functional theory calculations to explore the interfacial interaction between GR and MO. Our result reveals generally weak physical interactions between GR and several MOs (including Cu2O, NiO). The Schottky barrier height (SBH) in these metal/semiconductor heterostructures are computed using the macroscopically averaged electrostatic potential method, and the role of interfacial dipole is discussed. The calculated SBHs below 1 eV suggest low contact resistance; thus these GR/MO composites are favorable anode materials for better lithium ion batteries.
New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex
Authors: Ishchenko A. , Round E. , Borshchevskiy V. , Grudinin S. , Gushchin I. , Klare J. P. , Remeeva A. , Polovinkin V. , Utrobin P. , Balandin T. , Engelhard M. , Büldt G. , Gordeliy V. 
Published: February 2017

AbstractThe complex of two membrane proteins, sensory rhodopsin II (NpSRII) with its cognate transducer (NpHtrII), mediates negative phototaxis in halobacteria N. pharaonis. Upon light activation NpSRII triggers a signal transduction chain homologous to the two-component system in eubacterial chemotaxis. Here we report on crystal structures of the ground and active M-state of the complex in the space group I212121. We demonstrate that the relative orientation of symmetrical parts of the dimer is parallel (“U”-shaped) contrary to the gusset-like (“V”-shaped) form of the previously reported structures of the NpSRII/NpHtrII complex in the space group P21212, although the structures of the monomers taken individually are nearly the same. Computer modeling of the HAMP domain in the obtained “V”- and “U”-shaped structures revealed that only the “U”-shaped conformation allows for tight interactions of the receptor with the HAMP domain. This is in line with existing data and supports biological relevance of the “U” shape in the ground state. We suggest that the “V”-shaped structure may correspond to the active state of the complex and transition from the “U” to the “V”-shape of the receptor-transducer complex can be involved in signal transduction from the receptor to the signaling domain of NpHtrII.
Paeoniflorin Ameliorates Experimental Autoimmune Encephalomyelitis via Inhibition of Dendritic Cell Function and Th17 Cell Differentiation
Authors: Zhang Han , Qi Yuanyuan , Yuan Yuanyang , Cai Li , Xu Haiyan , Zhang Lili , Su Bing , Nie Hong 
Published: February 2017

AbstractPaeoniflorin (PF) is a monoterpene glycoside and exhibits multiple effects, including anti-inflammation and immunoregulation. To date, the effect of PF on multiple sclerosis (MS) has not been investigated. In this study, we investigated the effect of PF in experimental autoimmune encephalomyelitis (EAE), an animal model for MS. After administered with PF, the onset and clinical symptoms of EAE mice were significantly ameliorated, and the number of Th17 cells infiltrated in central nervous system (CNS) and spleen was also dramatically decreased. Instead of inhibiting the differentiation of Th17 cells directly, PF influenced Th17 cells via suppressing the expression of costimulatory molecules and the production of interlukin-6 (IL-6) of dendritic cells (DCs)in vivoandin vitro, which may be attributable to the inhibition of IKK/NF-κB and JNK signaling pathway. When naïve CD4+T cells were co-cultured with PF-treated dendritic cells under Th17-polarizing condition, the percentage of Th17 cells and the phosphorylation of STAT3 were decreased, as well as the mRNA levels of IL-17, RORα, and RORγt. Our study provided insights into the role of PF as a unique therapeutic agent for the treatment of multiple sclerosis and illustrated the underlying mechanism of PF from a new perspective.
Anhedonia to music and mu-opioids: Evidence from the administration of naltrexone
Authors: Mallik Adiel , Chanda Mona Lisa , Levitin Daniel J. 
Published: February 2017

AbstractMusic’s universality and its ability to deeply affect emotions suggest an evolutionary origin. Previous investigators have found that naltrexone (NTX), a μ-opioid antagonist, may induce reversible anhedonia, attenuating both positive and negative emotions. The neurochemical basis of musical experience is not well-understood, and the NTX-induced anhedonia hypothesis has not been tested with music. Accordingly, we administered NTX or placebo on two different days in a double-blind crossover study, and assessed participants’ responses to music using both psychophysiological (objective) and behavioral (subjective) measures. We found that both positive and negative emotions were attenuated. We conclude that endogenous opioids are critical to experiencing both positive and negative emotions in music, and that music uses the same reward pathways as food, drug and sexual pleasure. Our findings add to the growing body of evidence for the evolutionary biological substrates of music.
A combinational CRISPR/Cas9 gene-editing approach can halt HIV replication and prevent viral escape
Authors: Lebbink Robert Jan , de Jong Dorien C. M. , Wolters Femke , Kruse Elisabeth M. , van Ham Petra M. , Wiertz Emmanuel J. H. J. , Nijhuis Monique 
Published: February 2017

AbstractHIV presents one of the highest evolutionary rates ever detected and combination antiretroviral therapy is needed to overcome the plasticity of the virus population and control viral replication. Conventional treatments lack the ability to clear the latent reservoir, which remains the major obstacle towards a cure. Novel strategies, such as CRISPR/Cas9 gRNA-based genome-editing, can permanently disrupt the HIV genome. However, HIV genome-editing may accelerate viral escape, questioning the feasibility of the approach. Here, we demonstrate that CRISPR/Cas9 targeting of single HIV loci, only partially inhibits HIV replication and facilitates rapid viral escape at the target site. A combinatorial approach of two strong gRNAs targeting different regions of the HIV genome can completely abrogate viral replication and prevent viral escape. Our data shows that the accelerating effect of gene-editing on viral escape can be overcome and as such gene-editing may provide a future alternative for control of HIV-infection.
Spatial variation and inconsistency between estimates of onset of muscle activation from EMG and ultrasound
Authors: Dieterich Angela V. , Botter Alberto , Vieira Taian Martins , Peolsson Anneli , Petzke Frank , Davey Paul , Falla Deborah 
Published: February 2017

AbstractDelayed onset of muscle activation can be a descriptor of impaired motor control. Activation onset can be estimated from electromyography (EMG)-registered muscle excitation and from ultrasound-registered muscle motion, which enables non-invasive measurements in deep muscles. However, in voluntary activation, EMG- and ultrasound-detected activation onsets may not correspond. To evaluate this, ten healthy men performed isometric elbow flexion at 20% to 70% of their maximal force. Utilising a multi-channel electrode transparent to ultrasound, EMG and M(otion)-mode ultrasound were recorded simultaneously over the biceps brachii muscle. The time intervals between automated and visually estimated activation onsets were correlated with the regional variation of EMG and muscle motion onset, contraction level and speed. Automated and visual onsets indicated variable time intervals between EMG- and motion onset, median (interquartile range) 96 (121) ms and 48 (72) ms, respectively. In 17% (computed analysis) or 23% (visual analysis) of trials, motion onset was detected before local EMG onset. Multi-channel EMG and M-mode ultrasound revealed regional differences in activation onset, which decreased with higher contraction speed (Spearman ρ ≥ 0.45, P < 0.001). In voluntary activation the heterogeneous motor unit recruitment together with immediate motion transmission may explain the high variation of the time intervals between local EMG- and ultrasound-detected activation onset.
The interaction of perceptual biases in bistable perception
Authors: Zhang Xue , Xu Qian , Jiang Yi , Wang Ying 
Published: February 2017

AbstractWhen viewing ambiguous stimuli, people tend to perceive some interpretations more frequently than others. Such perceptual biases impose various types of constraints on visual perception, and accordingly, have been assumed to serve distinct adaptive functions. Here we demonstrated the interaction of two functionally distinct biases in bistable biological motion perception, one regulating perception based on the statistics of the environment – the viewing-from-above (VFA) bias, and the other with the potential to reduce costly errors resulting from perceptual inference – the facing-the-viewer (FTV) bias. When compatible, the two biases reinforced each other to enhance the bias strength and induced less perceptual reversals relative to when they were in conflict. Whereas in the conflicting condition, the biases competed with each other, with the dominant percept varying with visual cues that modulate the two biases separately in opposite directions. Crucially, the way the two biases interact does not depend on the dominant bias at the individual level, and cannot be accounted for by a single bias alone. These findings provide compelling evidence that humans robustly integrate biases with different adaptive functions in visual perception. It may be evolutionarily advantageous to dynamically reweight diverse biases in the sensory context to resolve perceptual ambiguity.
Enhancing the biocatalytic manufacture of the key intermediate of atorvastatin by focused directed evolution of halohydrin dehalogenase
Authors: Luo Yu , Chen Yangzi , Ma Hongmin , Tian ZhenHua , Zhang Yeqi , Zhang Jian 
Published: February 2017

AbstractHalohydrin dehalogenases (HHDHs) are biocatalytically interesting enzymes due to their ability to form C-C, C-N, C-O, and C-S bonds. One of most important application of HHDH was the protein engineering of HheC (halohydrin dehalogenase from Agrobacterium radiobacter AD1) for the industrial manufacturing of ethyl (R)-4-cyano-3-hydroxybutanoate (HN), a key chiral synthon of a cholesterol-lowering drug of atorvastatin. During our development of an alternative, more efficient and economic route for chemo-enzymatic preparation of the intermediate of atorvastatin, we found that the HheC2360 previously reported for HN manufacture, had insufficient activity for the cyanolysis production of tert-butyl (3 R,5 S)-6-cyano-3,5-dihydroxyhexanoate (A7). Herein, we present the focused directed evolution of HheC2360 with higher activity and enhanced biocatalytic performance using active site mutagenesis. Through docking of the product, A7, into the crystal structure of HheC2360, 6 residues was selected for combined active sites testing (CASTing). After library screening, the variant V84G/W86F was identified to have a 15- fold increase in activity. Time course analysis of the cyanolysis reaction catalyzed by this variant, showed 2- fold increase in space time productivity compared with HheC2360. These results demonstrate the applicability of the variant V84G/W86F as a biocatalyst for the efficient and practical production of atorvastatin intermediate.
Interplay between the static ordering and dynamical heterogeneities determining the dynamics of rotation and ordinary liquid phases in 1,6-anhydro-β-D-glucose
Authors: Madejczyk O. , Kaminski K. , Kaminska E. , Jurkiewicz K. , Tarnacka M. , Burian A. , Paluch M. 
Published: February 2017

AbstractIn this letter, we reported thorough the structural and molecular dynamics studies on 1,6-anhydro-β-D-glucose, the second compound reported so far that is capable to form rotator and supercooled liquid phases. In contrast to the data presented for ethanol, temperature dependences of structural dynamics in both phases are very comparable. On the other hand, X ray measurements revealed unusually long range ordering/correlations between molecules in the ODIC (d ≈ 95 Å) and supercooled phases (d ≈ 30–40 Å) of this carbohydrate. Our consideration clearly demonstrated that the interplay between length scales of static range ordering and dynamical heterogeneities as well as internal molecular arrangement seem to be the key to understanding the molecular dynamics of different materials characterized by varying degree of disorder in the vicinity of the glass transition temperature.
Characterization of Adipogenic Chemicals in Three Different Cell Culture Systems: Implications for Reproducibility Based on Cell Source and Handling
Authors: Kassotis Christopher D. , Masse Lauren , Kim Stephanie , Schlezinger Jennifer J. , Webster Thomas F. , Stapleton Heather M. 
Published: February 2017

AbstractThe potential for chemical exposures to exacerbate the development and/or prevalence of metabolic disorders, such as obesity, is currently of great societal concern. Various in vitro assays are available to assess adipocyte differentiation, though little work has been done to standardize protocols and compare models effectively. This study compares several adipogenic cell culture systems under a variety of conditions to assess variability in responses. Two sources of 3T3-L1 preadipocytes as well as OP9 preadipocytes were assessed for cell proliferation and triglyceride accumulation following different induction periods and using various tissue culture plates. Both cell line and cell source had a significant impact on potencies and efficacies of adipogenic chemicals. Gene expression analyses suggested that differential expression of nuclear receptors involved in adipogenesis underlie the differences between OP9 and 3T3-L1 cells; however, there were also differences based on 3T3-L1 cell source. Induction period modulated potency and efficacy of response depending on cell line and test chemical, and large variations were observed in triglyceride accumulation and cell proliferation between brands of tissue culture plates. Our results suggest that the selection of a cell system and differentiation protocol significantly impacts the detection of adipogenic chemicals, and therefore, influences reproducibility of these studies.
A versatile assay to determine bacterial and host factors contributing to opsonophagocytotic killing in hirudin-anticoagulated whole blood
Authors: van der Maten Erika , de Jonge Marien I. , de Groot Ronald , van der Flier Michiel , Langereis Jeroen D. 
Published: February 2017

AbstractMost bacteria entering the bloodstream will be eliminated through complement activation on the bacterial surface and opsonophagocytosis. However, when these protective innate immune systems do not work optimally, or when bacteria are equipped with immune evasion mechanisms that prevent killing, this can lead to serious infections such as bacteremia and meningitis, which is associated with high morbidity and mortality. In order to study the complement evasion mechanisms of bacteria and the capacity of human blood to opsonize and kill bacteria, we developed a versatile whole blood killing assay wherein both phagocyte function and complement activity can easily be monitored and modulated. In this assay we use a selective thrombin inhibitor hirudin to fully preserve complement activity of whole blood. This assay allows controlled analysis of the requirements for active complement by replacing or heat-inactivating plasma, phagocyte function and bacterial immune evasion mechanisms that contribute to survival in human blood.