bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered mitochondrial quality control in Atg7-deficient VSMCs promotes enhanced apoptosis and is linked to unstable atherosclerotic plaque phenotype
Authors: Nahapetyan Hripsimé , Moulis Manon , Grousset Elisa , Faccini Julien , Grazide Marie-Hélène , Mucher Elodie , Elbaz Meyer , Martinet Wim , Vindis Cécile 
Published: February 2019

AbstractVascular smooth muscle cells (VSMCs) are one of the main cellular determinants in arterial pathology. A large body of evidence indicates that death of VSMCs is associated with features of high-risk/vulnerable atherosclerotic plaques. Mitochondrial turnover is an essential aspect of the mitochondrial quality control in which dysfunctional mitochondria are selectively eliminated through autophagy and replaced through expansion of preexisting mitochondria. Even though successful autophagy promotes VSMC survival, it is unclear whether reduced autophagic flux affects mitochondrial quality control of VSMCs in atherosclerotic plaques. By using apolipoprotein E-deficient (ApoE−/−) mice carrying a VSMC-specific deletion of the essential autophagy gene Atg7, we show in the present study that impaired VSMC autophagy promotes an unstable plaque phenotype, as well as the accumulation of fragmented mitochondria with reduced bioenergetic efficiency and more oxidative stress. Furthermore, we demonstrate that disrupted autophagic flux is linked to defective mitophagy and biogenesis of mitochondria, which exacerbate VSMC apoptosis and in turn plaque vulnerability. Overall, our data indicate that mitochondrial quality control is a promising therapeutic target to stabilize atherosclerotic plaques.
Tomonaga–Luttinger liquid behavior and spinon confinement in YbAlO3
Authors: Wu L. S. , Nikitin S. E. , Wang Z. , Zhu W. , Batista C. D. , Tsvelik A. M. , Samarakoon A. M. , Tennant D. A. , Brando M. , Vasylechko L. , Frontzek M. , Savici A. T. , Sala G. , Ehlers G. , Christianson A. D. , Lumsden M. D. , Podlesnyak A. 
Published: February 2019

AbstractLow dimensional quantum magnets are interesting because of the emerging collective behavior arising from strong quantum fluctuations. The one-dimensional (1D) S = 1/2 Heisenberg antiferromagnet is a paradigmatic example, whose low-energy excitations, known as spinons, carry fractional spin S = 1/2. These fractional modes can be reconfined by the application of a staggered magnetic field. Even though considerable progress has been made in the theoretical understanding of such magnets, experimental realizations of this low-dimensional physics are relatively rare. This is particularly true for rare-earth-based magnets because of the large effective spin anisotropy induced by the combination of strong spin–orbit coupling and crystal field splitting. Here, we demonstrate that the rare-earth perovskite YbAlO3 provides a realization of a quantum spin S = 1/2 chain material exhibiting both quantum critical Tomonaga–Luttinger liquid behavior and spinon confinement–deconfinement transitions in different regions of magnetic field–temperature phase diagram.
A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation
Authors: Hadzhiev Yavor , Qureshi Haseeb K. , Wheatley Lucy , Cooper Ledean , Jasiulewicz Aleksandra , Van Nguyen Huy , Wragg Joseph W. , Poovathumkadavil Divyasree , Conic Sascha , Bajan Sarah , Sik Attila , Hutvàgner György , Tora Làszlò , Gambus Agnieszka , Fossey John S. , Müller Ferenc 
Published: February 2019

AbstractMost metazoan embryos commence development with rapid, transcriptionally silent cell divisions, with genome activation delayed until the mid-blastula transition (MBT). However, a set of genes escapes global repression and gets activated before MBT. Here we describe the formation and the spatio-temporal dynamics of a pair of distinct transcription compartments, which encompasses the earliest gene expression in zebrafish. 4D imaging of pri-miR430and zinc-finger-gene activities by a novel, native transcription imaging approach reveals transcriptional sharing of nuclear compartments, which are regulated by homologous chromosome organisation. These compartments carry the majority of nascent-RNAs and active Polymerase II, are chromatin-depleted and represent the main sites of detectable transcription before MBT. Transcription occurs during the S-phase of increasingly permissive cleavage cycles. It is proposed, that the transcription compartment is part of the regulatory architecture of embryonic nuclei and offers a transcriptionally competent environment to facilitate early escape from repression before global genome activation.
NADP+ is an endogenous PARP inhibitor in DNA damage response and tumor suppression
Authors: Bian Chunjing , Zhang Chao , Luo Tao , Vyas Aditi , Chen Shih-Hsun , Liu Chao , Kassab Muzaffer Ahmad , Yang Ying , Kong Mei , Yu Xiaochun 
Published: February 2019

AbstractADP-ribosylation is a unique posttranslational modification catalyzed by poly(ADP-ribose) polymerases (PARPs) using NAD+ as ADP-ribose donor. PARPs play an indispensable role in DNA damage repair and small molecule PARP inhibitors have emerged as potent anticancer drugs. However, to date, PARP inhibitor treatment has been restricted to patients with BRCA1/2 mutation-associated breast and ovarian cancer. One of the major challenges to extend the therapeutic potential of PARP inhibitors to other cancer types is the absence of predictive biomarkers. Here, we show that ovarian cancer cells with higher level of NADP+, an NAD+ derivative, are more sensitive to PARP inhibitors. We demonstrate that NADP+ acts as a negative regulator and suppresses ADP-ribosylation both in vitro and in vivo. NADP+ impairs ADP-ribosylation-dependent DNA damage repair and sensitizes tumor cell to chemically synthesized PARP inhibitors. Taken together, our study identifies NADP+ as an endogenous PARP inhibitor that may have implications in cancer treatment.
eg occupancy as an effective descriptor for the catalytic activity of perovskite oxide-based peroxidase mimics
Authors: Wang Xiaoyu , Gao Xuejiao J. , Qin Li , Wang Changda , Song Li , Zhou Yong-Ning , Zhu Guoyin , Cao Wen , Lin Shichao , Zhou Liqi , Wang Kang , Zhang Huigang , Jin Zhong , Wang Peng , Gao Xingfa , Wei Hui 
Published: February 2019

AbstractA peroxidase catalyzes the oxidation of a substrate with a peroxide. The search for peroxidase-like and other enzyme-like nanomaterials (called nanozymes) mainly relies on trial-and-error strategies, due to the lack of predictive descriptors. To fill this gap, here we investigate the occupancy of eg orbitals as a possible descriptor for the peroxidase-like activity of transition metal oxide (including perovskite oxide) nanozymes. Both experimental measurements and density functional theory calculations reveal a volcano relationship between the eg occupancy and nanozymes’ activity, with the highest peroxidase-like activities corresponding to eg occupancies of ~1.2. LaNiO3-δ, optimized based on the eg occupancy, exhibits an activity one to two orders of magnitude higher than that of other representative peroxidase-like nanozymes. This study shows that the eg occupancy is a predictive descriptor to guide the design of peroxidase-like nanozymes; in addition, it provides detailed insight into the catalytic mechanism of peroxidase-like nanozymes.
Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities
Authors: Santillan Ezequiel , Seshan Hari , Constancias Florentin , Drautz-Moses Daniela I. , Wuertz Stefan 
Published: February 2019

AbstractDisturbance is known to affect the ecosystem structure, but predicting its outcomes remains elusive. Similarly, community diversity is believed to relate to ecosystem functions, yet the underlying mechanisms are poorly understood. Here, we tested the effect of disturbance on the structure, assembly, and ecosystem function of complex microbial communities within an engineered system. We carried out a microcosm experiment where activated sludge bioreactors operated in daily cycles were subjected to eight different frequency levels of augmentation with a toxic pollutant, from never (undisturbed) to every day (press-disturbed), for 35 days. Microbial communities were assessed by combining distance-based methods, general linear multivariate models, α-diversity indices, and null model analyses on metagenomics and 16S rRNA gene amplicon data. A stronger temporal decrease in α-diversity at the extreme, undisturbed and press-disturbed, ends of the disturbance range led to a hump-backed pattern, with the highest diversity found at intermediate levels of disturbance. Undisturbed and press-disturbed levels displayed the highest community and functional similarity across replicates, suggesting deterministic processes were dominating. The opposite was observed amongst intermediately disturbed levels, indicating stronger stochastic assembly mechanisms. Trade-offs were observed in the ecosystem function between organic carbon removal and both nitrification and biomass productivity, as well as between diversity and these functions. Hence, not every ecosystem function was favoured by higher community diversity. Our results show that the assessment of changes in diversity, along with the underlying stochastic–deterministic assembly processes, is essential to understanding the impact of disturbance in complex microbial communities.
Bioactive glycoalkaloides isolated from Solanum melongena fruit peels with potential anticancer properties against hepatocellular carcinoma cells
Authors: Fekry Mostafa I. , Ezzat Shahira M. , Salama Maha M. , Alshehri Ohoud Y. , Al-Abd Ahmed M. 
Published: February 2019

AbstractHepatocellular carcinoma (HCC) is progressively increasing tumor with lack of accurate prognosis and inadequate systemic treatment approaches. Solanum sp. (such as Solanum melongena) is a folk herb which is reported to possess anticancer properties. In a continuity for our interest in pursuing the anticancer activity of compounds isolated from the fruit peels of Solanum melongena, the HPLC profiling and ESI-MS assessment for the methanolic extract evidenced the presence of bioactive glycoalkaloids (solasonine, solasodine and solamargine). These glycoalkaloids were isolated, purified and proved to possess in vitro cytotoxicity against human liver cancer cell lines (Huh7 and HepG2). Herein, we investigated the potential mechanism of action of these compounds using DNA content flow-cytometry and apoptosis/necrosis differential anaylsis using annexin-V/FITC staining. Solasonine, solasodine and solamargine inducd significant antiproliferative effect against liver cancer cells (Huh7 and HepG2) which was attributed to cell cycle arrest at S-phase. Solamargine, solasodine and solasonine induced significant apoptosis in Huh7 cells. Only solamargine-induced cell cycle arrest, was reflected as apoptotic cell killing effect against HepG2 cells. In conclusion, glycoalkaloids derived from Solanum melongena and particularly, solamargine are promising antiproliferative agents with potential anticancer effects.
Early stages of aggregation of engineered α-synuclein monomers and oligomers in solution
Authors: Li Xi , Dong Chunhua , Hoffmann Marion , Garen Craig R. , Cortez Leonardo M. , Petersen Nils O. , Woodside Michael T. 
Published: February 2019

Abstractα-Synuclein is a protein that aggregates as amyloid fibrils in the brains of patients with Parkinson’s disease and dementia with Lewy bodies. Small oligomers of α-synuclein are neurotoxic and are thought to be closely associated with disease. Whereas α-synuclein fibrillization and fibril morphologies have been studied extensively with various methods, the earliest stages of aggregation and the properties of oligomeric intermediates are less well understood because few methods are able to detect and characterize early-stage aggregates. We used fluorescence spectroscopy to investigate the early stages of aggregation by studying pairwise interactions between α-synuclein monomers, as well as between engineered tandem oligomers of various sizes (dimers, tetramers, and octamers). The hydrodynamic radii of these engineered α-synuclein species were first determined by fluorescence correlation spectroscopy and dynamic light scattering. The rate of pairwise aggregation between different species was then monitored using dual-color fluorescence cross-correlation spectroscopy, measuring the extent of association between species labelled with different dyes at various time points during the early aggregation process. The aggregation rate and extent increased with tandem oligomer size. Self-association of the tandem oligomers was found to be the preferred pathway to form larger aggregates: interactions between oligomers occurred faster and to a greater extent than interactions between oligomers and monomers, indicating that the oligomers were not as efficient in seeding further aggregation by addition of monomers. These results suggest that oligomer-oligomer interactions may play an important role in driving aggregation during its early stages.
Genome-wide Identification, Expression Profiling and Evolutionary Analysis of Auxin Response Factor Gene Family in Potato (Solanum tuberosum Group Phureja)
Authors: Song Shuangwei , Hao Liaoyang , Zhao Pan , Xu Ya , Zhong Naiqin , Zhang Hongji , Liu Ning 
Published: February 2019

AbstractAuxin response factors (ARFs) play central roles in conferring auxin-mediated responses through selection of target genes in plants. Despite their physiological importance, systematic analysis of ARF genes in potato have not been investigated yet. Our genome-wide analysis identified 20 StARF (Solanum tuberosum ARF) genes from potato and found that they are unevenly distributed in all the potato chromosomes except chromosome X. Sequence alignment and conserved motif analysis suggested the presence of all typical domains in all but StARF18c that lacks B3 DNA-binding domain. Phylogenetic analysis indicated that potato ARF could be clustered into 3 distinct subgroups, a result supported by exon-intron structure, consensus motifs, and domain architecture. In silico expression analysis and quantitative real-time PCR experiments revealed that several StARFs were expressed in tissue-specific, biotic/abiotic stress-responsive or hormone-inducible manners, which reflected their potential roles in plant growth, development or under various stress adaptions. Strikingly, most StARFs were identified as highly abiotic stress responsive, indicating that auxin signaling might be implicated in mediating environmental stress-adaptation responses. Taken together, this analysis provides molecular insights into StARF gene family, which paves the way to functional analysis of StARF members and will facilitate potato breeding programs.
Particle Diffusometry: An Optical Detection Method for Vibrio cholerae Presence in Environmental Water Samples
Authors: Clayton Katherine N. , Moehling Taylor J. , Lee Dong Hoon , Wereley Steven T. , Linnes Jacqueline C. , Kinzer-Ursem Tamara L. 
Published: February 2019

AbstractThere is a need for a rapid, robust, and sensitive biosensor to identify low concentrations of pathogens in their native sample matrix without enrichment or purification. Nucleic acid-based detection methods are widely accepted as the gold standard in diagnostics, but robust detection of low concentrations of pathogens remains challenging. Amplified nucleic acids produce more viscous solutions, which can be measured by combining these products with fluorescent particles and measuring the change in the particle diffusion coefficient using a technique known as particle diffusometry. Here, we utilize Vibrio cholerae (V. cholerae) as a proof-of-concept for our detection system due to its inherently low concentration in environmental water samples. We demonstrate that particle diffusometry can be used to detect down to 1 V. cholerae cell in molecular-grade water in 20 minutes and 10 V. cholerae cells in pond water in just 35 minutes in 25 µL reaction volumes. The detection limit in pond water is environmentally relevant and does not require any enrichment or sample preparation steps. Particle diffusometry is 10-fold more sensitive than current gold standard fluorescence detection of nucleic acid amplification. Therefore, this novel measurement technique is a promising approach to detect low levels of pathogens in their native environments.
Dense genotyping-by-sequencing linkage maps of two Synthetic W7984×Opata reference populations provide insights into wheat structural diversity
Authors: Gutierrez-Gonzalez Juan J. , Mascher Martin , Poland Jesse , Muehlbauer Gary J. 
Published: February 2019

AbstractWheat (Triticum aestivum) genetic maps are a key enabling tool for genetic studies. We used genotyping-by-sequencing-(GBS) derived markers to map recombinant inbred line (RIL) and doubled haploid (DH) populations from crosses of W7984 by Opata, and used the maps to explore features of recombination control. The RIL and DH populations, SynOpRIL and SynOpDH, were composed of 906 and 92 individuals, respectively. Two high-density genetic linkage framework maps were constructed of 2,842 and 2,961 cM, harboring 3,634 and 6,580 markers, respectively. Using imputation, we added 43,013 and 86,042 markers to the SynOpRIL and SynOpDH maps. We observed preferential recombination in telomeric regions and reduced recombination in pericentromeric regions. Recombination rates varied between subgenomes, with the D genomes of the two populations exhibiting the highest recombination rates of 0.26–0.27 cM/Mb. QTL mapping identified two additive and three epistatic loci associated with crossover number. Additionally, we used published POPSEQ data from SynOpDH to explore the structural variation in W7984 and Opata. We found that chromosome 5AS is missing from W7984. We also found 2,332 variations larger than 100 kb. Structural variants were more abundant in distal regions, and overlapped 9,196 genes. The two maps provide a resource for trait mapping and genomic-assisted breeding.
Changes in species richness and composition of boreal waterbird communities: a comparison between two time periods 25 years apart
Authors: Pöysä Hannu , Holopainen Sari , Elmberg Johan , Gunnarsson Gunnar , Nummi Petri , Sjöberg Kjell 
Published: February 2019

AbstractGlobal measures of biodiversity indicate consistent decline, but trends reported for local communities are more varied. Therefore, we need better understanding of mechanisms that drive changes in diversity of local communities and of differences in temporal trends between components of local diversity, such as species richness and species turnover rate. Freshwater ecosystems are vulnerable to multiple stressors, and severe impacts on their biodiversity have been documented. We studied species richness and composition of local boreal waterbird communities in 1990/1991 and 2016 at 58 lakes distributed over six regions in Finland and Sweden. The study lakes represented not only local trophic gradients but also a latitudinal gradient in the boreal biome. While species richness tended to be lower in 2016 than in 1990/1991, species turnover was relatively high. Within foraging guilds, local species richness of diving ducks and surface feeding waterbirds decreased, whereas that of large herbivores increased. The number of species gained in local communities was higher in lakes with rich vegetation than in lakes with sparse vegetation. Conservation of boreal freshwater ecosystems would benefit from recognizing that large-scale environmental changes can affect local diversity via processes operating at finer scales.
Early Stage Alpha-Synuclein Amyloid Fibrils are Reservoirs of Membrane-Binding Species
Authors: Skamris Thomas , Marasini Carlotta , Madsen Kenneth L. , Foderà Vito , Vestergaard Bente 
Published: February 2019

AbstractThe presence of αSN fibrils indisputably associates with the development of synucleinopathies. However, while certain fibril morphologies have been linked to downstream pathological phenotypes, others appear less harmful, leading to the concept of fibril strains, originally described in relation to prion disease. Indeed, the presence of fibrils does not associate directly with neurotoxicity. Rather, it has been suggested that the toxic compounds are soluble amyloidogenic oligomers, potentially co-existing with fibrils. Here, combining synchrotron radiation circular dichroism, transmission electron microscopy and binding assays on native plasma membrane sheets, we reveal distinct biological and biophysical differences between initial and matured fibrils, transformed within the timespan of few days. Immature fibrils are reservoirs of membrane-binding species, which in response to even gentle experimental changes release into solution in a reversible manner. In contrast, mature fibrils, albeit macroscopically indistinguishable from their less mature counterparts, are structurally robust, shielding the solution from the membrane active soluble species. We thus show that particular biological activity resides transiently with the fibrillating sample, distinct for one, but not the other, spontaneously formed fibril polymorph. These results shed new light on the principles of fibril polymorphism with consequent impact on future design of assays and therapeutic development.
A comparison of different GRACE solutions in terrestrial water storage trend estimation over Tibetan Plateau
Authors: Jing Wenlong , Zhang Pengyan , Zhao Xiaodan 
Published: February 2019

AbstractThe Gravity Recovery and Climate Experiment (GRACE) terrestrial water storage anomalies (TWSA) estimations provide valuable information for the monitoring of land water resources changes. Multiple parameters and strategies for inversion of the water storage changes have been explored. The explorations on differences between GRACE solutions in local regions and basins are fundamental and important. This study focuses on comparisons of TWSA trends between different GRACE solutions over Tibetan Plateau (TP), both storage and flux among solutions were compared. Results show that great discrepancies exist in TWSA between GRACE solutions derived from the standard spherical harmonic approach (SSH) and the mascon approach. Three SSH-based GRACE solutions (JPL, CSR, and GFZ) detect no significant TWSA changes for the whole area of Tibetan Plateau, whereas JPL mascon solution (JPL-M) and CSR mascon solution (CSR-M) gave decreasing trends of 3.10 km3/yr and 3.77 km3/yr, respectively. This difference also exists in the Yangtze River-Yellow River basin (YYR basin) in the TP. Although five solutions derived consistent TWSA trends in northwest river basin (NWR basin) and southwest river basin (SWR basin) in the TP, the variations between different solutions are 2.88 km3/yr and 4.75 km3/yr for NWR and SWR basin respectively, which could not be neglected. The JPL-M solution, as a result, would overestimate both TWSA decreasing and increasing trends comparing with other GRACE solutions. The results of this study are expected to provide references for the studies of water resource dynamics over Tibetan Plateau and the surrounding areas based on GRACE TWSA products.