bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal variations in group leaf characteristics in species with red young leaves
Authors: Zhang Tai-Jie , Tian Xing-Shan , Liu Xiao-Tao , Huang Xuan-Dong , Peng Chang-Lian 
Published: November 2019

AbstractThe leaves of many plants are red during particular stages of their lives, but the adaptive significance of leaf colouration is not yet clearly understood. In order to reveal whether anthocyanins play a similar role (i.e. antioxidants) in different seasonal contexts, this study investigated species with red young leaves in the subtropical forest of Dinghushan biosphere reserve (South China) during summer and winter and compared group leaf characteristics between the two seasons. Of 62 total species, 33 exhibited red young leaves in summer only, 6 in winter only, and 23 in both seasons. The anthocyanins extracted from most of these species had an absorption peak at ~530 nm. Frequency distribution analysis showed that the species containing anthocyanins at levels ranging from 0.02 to 0.04 μmol cm−2 occurred most frequently in summer or winter. Based on conditional grouping of the species, no significant variation was observed in the average anthocyanin contents and antioxidant abilities between summer and winter; the flavonoid content in summer was 2-fold that in winter, whereas the anthocyanin:flavonoid ratio in summer was only half that in winter. Moreover, a positive correlation between anthocyanins and flavonoids was found in summer. Therefore, it is less likely for anthocyanins to serve as antioxidants in summer than winter, because such a function in summer leaves is readily replaced by other flavonoids.
Stability of cytoplasmic nanoviscosity during cell cycle of HeLa cells synchronized with Aphidicolin
Authors: Szczepański Krzysztof , Kwapiszewska Karina , Hołyst Robert 
Published: November 2019

AbstractNanoviscosity of the cytoplasm is a key factor affecting diffusion of biomolecules and – as a consequence – rates of biochemical reactions in a cell. Nanoviscosity is an outcome of variable chemical and structural factors, which can temporarily change with cell-cycle associated changes of intracellular architecture. Thus, the question arises, whether rates of biochemical reactions depend on the point of cell cycle. In this paper we address this topic by constant observation of nanoviscosity of HeLa cells cytoplasm during S, G2 and G1 phases after Aphidicolin synchronization. For this purpose we measured diffusion rates of EGFP molecules using fluorescence correlation spectroscopy (FCS). To our surprise, a counter-intuitive stability of cytoplasmic viscosity was observed during the cell cycle. Our results hint at possible existence of robust mechanism maintaining stable physiological viscosity of the cytoplasm, despite huge structural changes during cell cycle.
Parrots do not show inequity aversion
Authors: Krasheninnikova Anastasia , Brucks Désirée , Buffenoir Nina , Rivas Blanco Dániel , Soulet Delphine , von Bayern Auguste 
Published: November 2019

AbstractInequity aversion, the negative reaction to unequal treatment, is considered a mechanism for stabilizing cooperative interactions between non-kin group members. However, this might only be adaptive for species that switch cooperative partners. Utilizing a comparative approach, inequity aversion has been assessed in many mammalian species and recently also in corvids and one parrot species, kea, revealing mixed results. To broaden our knowledge about the phylogenetic distribution of inequity aversion, we tested four parrot species in the token exchange paradigm. We varied the quality of rewards delivered to dyads of birds, as well as the effort required to obtain a reward. Blue-headed macaws and African grey parrots showed no reaction to being rewarded unequally. The bigger macaws were less willing to exchange tokens in the “unequal” condition compared to the “equal high” condition in which both birds obtained high quality rewards, but a closer examination of the results and the findings from the control conditions reveal that inequity aversion does not account for it. None of the species responded to inequity in terms of effort. Parrots may not exhibit inequity aversion due to interdependence on their life-long partner and the high costs associated with finding a new partner.
Binding and structural analyses of potent inhibitors of the human Ca2+/calmodulin dependent protein kinase kinase 2 (CAMKK2) identified from a collection of commercially-available kinase inhibitors
Authors: Profeta Gerson S. , dos Reis Caio V. , Santiago André da S. , Godoi Paulo H. C. , Fala Angela M. , Wells Carrow I. , Sartori Roger , Salmazo Anita P. T. , Ramos Priscila Z. , Massirer Katlin B. , Elkins Jonathan M. , Drewry David H. , Gileadi Opher , Couñago Rafael M. 
Published: November 2019

AbstractCalcium/Calmodulin-dependent Protein Kinase Kinase 2 (CAMKK2) acts as a signaling hub, receiving signals from various regulatory pathways and decoding them via phosphorylation of downstream protein kinases - such as AMPK (AMP-activated protein kinase) and CAMK types I and IV. CAMKK2 relevance is highlighted by its constitutive activity being implicated in several human pathologies. However, at present, there are no selective small-molecule inhibitors available for this protein kinase. Moreover, CAMKK2 and its closest human homolog, CAMKK1, are thought to have overlapping biological roles. Here we present six new co-structures of potent ligands bound to CAMKK2 identified from a library of commercially-available kinase inhibitors. Enzyme assays confirmed that most of these compounds are equipotent inhibitors of both human CAMKKs and isothermal titration calorimetry (ITC) revealed that binding to some of these molecules to CAMKK2 is enthalpy driven. We expect our results to advance current efforts to discover small molecule kinase inhibitors selective to each human CAMKK.
Unified Monogamy Relations of Multipartite Entanglement
Authors: Khan Awais , ur Rehman Junaid , Wang Kehao , Shin Hyundong 
Published: November 2019

AbstractUnified-(q, s) entanglement $$({{\mathscr{U}}}_{q,s})$$
(

U

q
,
s

)
is a generalized bipartite entanglement measure, which encompasses Tsallis-q entanglement, Rényi-q entanglement, and entanglement of formation as its special cases. We first provide the extended (q; s) region of the generalized analytic formula of $${{\mathscr{U}}}_{q,s}$$

U

q
,
s

. Then, the monogamy relation based on the squared $${{\mathscr{U}}}_{q,s}$$

U

q
,
s

for arbitrary multiqubit mixed states is proved. The monogamy relation proved in this paper enables us to construct an entanglement indicator that can be utilized to identify all genuine multiqubit entangled states even the cases where three tangle of concurrence loses its efficiency. It is shown that this monogamy relation also holds true for the generalized W-class state. The αth power $${{\mathscr{U}}}_{q,s}$$

U

q
,
s

based general monogamy and polygamy inequalities are established for tripartite qubit states.
Global distribution of modern shallow-water marine carbonate factories: a spatial model based on environmental parameters
Authors: Laugié Marie , Michel Julien , Pohl Alexandre , Poli Emmanuelle , Borgomano Jean 
Published: November 2019

AbstractPrediction of carbonate distributions at a global scale through geological time represents a challenging scientific issue, which is critical for carbonate reservoir studies and the understanding of past and future climate changes. Such prediction is even more challenging because no numerical spatial model allows for the prediction of shallow-water marine carbonates in the Modern. This study proposes to fill this gap by providing for the first time a global quantitative model based on the identification of carbonate factories and associated environmental affinities. The relationships among the four carbonate factories, i.e., “biochemical”, “photozoan-T”, “photo-C” and “heterozoan-C” factories, and sea-surface oceanographic parameters (i.e., temperature, salinity and marine primary productivity) is first studied using spatial analysis. The sea-surface temperature seasonality is shown to be the dominant steering parameter discriminating the carbonate factories. Then, spatial analysis is used to calibrate different carbonate factory functions that predict oceanic zones favorable to specific carbonate factories. Our model allows the mapping of the global distribution of modern carbonate factories with an 82% accuracy. This modeling framework represents a powerful tool that can be adapted and coupled to general circulation models to predict the spatial distribution of past and future shallow-water marine carbonates.
New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies
Authors: Qi Weihong , Colarusso Andrea , Olombrada Miriam , Parrilli Ermenegilda , Patrignani Andrea , Tutino Maria Luisa , Toll-Riera Macarena 
Published: November 2019

AbstractPseudoalteromonas haloplanktisTAC125 is among the most commonly studied bacteria adapted to cold environments. Aside from its ecological relevance,P. haloplanktishas a potential use for biotechnological applications. Due to its importance, we decided to take advantage of next generation sequencing (Illumina) and third generation sequencing (PacBio and Oxford Nanopore) technologies to resequence its genome. The availability of a reference genome, obtained using whole genome shotgun sequencing, allowed us to study and compare the results obtained by the different technologies and draw useful conclusions for futurede novogenome assembly projects. We found that assembly polishing using Illumina reads is needed to achieve a consensus accuracy over 99.9% when using Oxford Nanopore sequencing, but not in PacBio sequencing. However, the dependency of consensus accuracy on coverage is lower in Oxford Nanopore than in PacBio, suggesting that a cost-effective solution might be the use of low coverage Oxford Nanopore sequencing together with Illumina reads. Despite the differences in consensus accuracy, all sequencing technologies revealed the presence of a large plasmid, pMEGA, which was undiscovered until now. Among the most interesting features of pMEGA is the presence of a putative error-prone polymerase regulated through the SOS response. Aside from the characterization of the newly discovered plasmid, we confirmed the sequence of the small plasmid pMtBL and uncovered the presence of a potential partitioning system. Crucially, this study shows that the combination of next and third generation sequencing technologies give us an unprecedented opportunity to characterize our bacterial model organisms at a very detailed level.
Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently
Authors: Makashov A. A. , Malov S. V. , Kozlov A. P. 
Published: November 2019

AbstractEarlier we showed that human genome contains many evolutionarily young or novel genes with tumor-specific or tumor-predominant expression. We suggest calling such genes Tumor Specifically Expressed, Evolutionarily New (TSEEN) genes. In this paper we performed a study of the evolutionary ages of different classes of human genes, using homology searches in genomes of different taxa in human lineage. We discovered that different classes of human genes have different evolutionary ages and confirmed the existence of TSEEN gene classes. On the other hand, we found that oncogenes, tumor-suppressor genes and differentiation genes are among the oldest gene classes in humans and their evolution occurs concurrently. These findings confirm non-trivial predictions made by our hypothesis of the possible evolutionary role of hereditary tumors. The results may be important for better understanding of tumor biology. TSEEN genes may become the best tumor markers.
Pioglitazone Modulates the Vascular Contractility in Hypertension by Interference with ET-1 Pathway
Authors: Palacios-Ramírez Roberto , Hernanz Raquel , Martín Angela , Pérez-Girón José V. , Barrús María T. , González-Carnicero Zoe , Aguado Andrea , Jaisser Frederic , Briones Ana M. , Salaices Mercedes , Alonso María J. 
Published: November 2019

AbstractEndothelin-1 (ET-1) is an important modulator of the vascular tone and a proinflammatory molecule that contributes to the vascular damage observed in hypertension. Peroxisome-proliferator activated receptors-γ (PPARγ) agonists show cardioprotective properties by decreasing inflammatory molecules such as COX-2 and reactive oxygen species (ROS), among others. We investigated the possible modulatory effect of PPARγ activation on the vascular effects of ET-1 in hypertension. In spontaneously hypertensive rats (SHR), but not in normotensive rats, ET-1 enhanced phenylephrine-induced contraction through ETA by a mechanism dependent on activation of TP receptors by COX-2-derived prostacyclin and reduction in NO bioavailability due to enhanced ROS production. In SHR, the PPARγ agonist pioglitazone (2.5 mg/Kg·day, 28 days) reduced the increased ETA levels and increased those of ETB. After pioglitazone treatment of SHR, ET-1 through ETB decreased ROS levels that resulted in increased NO bioavailability and diminished phenylephrine contraction. In vascular smooth muscle cells from SHR, ET-1 increased ROS production through AP-1 and NFκB activation, leading to enhanced COX-2 expression. These effects were blocked by pioglitazone. In summary, in hypertension, pioglitazone shifts the vascular ETA/ETB ratio, reduces ROS/COX-2 activation and increases NO availability; these changes explain the effect of ET-1 decreasing phenylephrine-induced contraction.
Mild chronic perturbation of inhibition severely alters hippocampal function
Authors: Sun Min-Yu , Ziolkowski Luke , Lambert Peter , Shu Hong-Jin , Keiser Micah , Rensing Nicholas , Warikoo Natasha , Martinek Monika , Platnick Carson , Benz Ann , Bracamontes John , Akk Gustav , Steinbach Joe Henry , Zorumski Charles F. , Wong Michael , Mennerick Steven 
Published: November 2019

AbstractPentameric GABAA receptors mediate a large share of CNS inhibition. The γ2 subunit is a typical constituent. At least 11 mutations in the γ2 subunit cause human epilepsies, making the role of γ2-containing receptors in brain function of keen basic and translational interest. How small changes to inhibition may cause brain abnormalities, including seizure disorders, is unclear. In mice, we perturbed fast inhibition with a point mutation T272Y (T6′Y in the second membrane-spanning domain) to the γ2 subunit. The mutation imparts resistance to the GABAA receptor antagonist picrotoxin, allowing verification of mutant subunit incorporation. We confirmed picrotoxin resistance and biophysical properties in recombinant receptors. T6′Y γ2-containing receptors also exhibited faster deactivation but unaltered steady-state properties. Adult T6′Y knockin mice exhibited myoclonic seizures and abnormal cortical EEG, including abnormal hippocampal-associated theta oscillations. In hippocampal slices, picrotoxin-insensitive inhibitory synaptic currents exhibited fast decay. Excitatory/inhibitory balance was elevated by an amount expected from the IPSC alteration. Partial pharmacological correction of γ2-mediated IPSCs with diazepam restored total EEG power toward baseline, but had little effect on the abnormal low-frequency peak in the EEG. The results suggest that at least part of the abnormality in brain function arises from the acute effects of truncated inhibition.
FOXH1 Is Regulated by NANOG and LIN28 for Early-stage Reprogramming
Authors: Wang Ling , Su Yue , Huang Chang , Yin Yexuan , Zhu Jiaqi , Knupp Alec , Chu Alexander , Tang Young 
Published: November 2019

AbstractFOXH1 is a primitive-streak specifier and ACTIVIN co-effector that plays an important role in development, and positively regulates the generation of human induced pluripotent stem cells (iPSCs) from somatic cells by OCT4, SOX2, KLF4, and MYC (OSKM) transduction. However, the mechanism and upstream regulation for FOXH1 expression in reprogramming are unclear. We found FOXH1 expression plays a significant role to enhance epithelial marker and suppress mesenchymal gene expression in OSKM-mediated human cell reprogramming. Furthermore, NANOG and LIN28 (NL) co-stimulate FOXH1 expression, which correlates with the enhanced reprogramming efficiency by NL-factors. FOXH1 expression is also stimulated by a specific inhibitor for H3K79 methyltransferase DOT1L (iDOT1L) but not by inhibition of the canonical WNT signaling. We further show that blocking endogenous FOXH1 expression eliminates the enhanced reprogramming effect by NL and iDOT1L. However, overexpressing FOXH1 in NL plus iDOT1L condition results in significantly reduced TRA-1-60 positively expressed cells and decreases pluripotent marker expression in reprogramming. Our study elucidated an essential role for properly stimulated FOXH1 expression by NANOG, LIN28, and H3K79 demethylation for dramatic enhancement of reprograming.
Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers
Authors: Verma H. , Borah J. L. , Sarma R. N. 
Published: November 2019

AbstractThe studies on genetic variation, diversity and population structure of rice germplasm of North East India could be an important step for improvements of abiotic and biotic stress tolerance in rice. Genetic diversity and genetic relatedness among 114 rice genotypes of North East India were assessed using genotypic data of 65 SSR markers and phenotypic data. The phenotypic diversity analysis showed the considerable variation across genotypes for root, shoot and drought tolerance traits. The principal component analysis (PCA) revealed the fresh shoot weight, root volume, dry shoot weight, fresh root weight and drought score as a major contributor to diversity. Genotyping of 114 rice genotypes using 65 SSR markers detected 147 alleles with the average polymorphic information content (PIC) value of 0.51. Population structure analysis using the Bayesian clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the accession into three sub-populations. Population structure analysis revealed that rice accession was moderately structured based on FST value estimates. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. AMOVA revealed that most of the variation in rice accession mainly occurred among individuals. The present study suggests that diverse germplasm of NE India could be used for the improvement of root and drought tolerance in rice breeding programmes.
DNA sequence differences are determinants of meiotic recombination outcome
Authors: Brown Simon D. , Mpaulo Samantha J. , Asogwa Mimi N. , Jézéquel Marie , Whitby Matthew C. , Lorenz Alexander 
Published: November 2019

AbstractMeiotic recombination is essential for producing healthy gametes, and also generates genetic diversity. DNA double-strand break (DSB) formation is the initiating step of meiotic recombination, producing, among other outcomes, crossovers between homologous chromosomes (homologs), which provide physical links to guide accurate chromosome segregation. The parameters influencing DSB position and repair are thus crucial determinants of reproductive success and genetic diversity. Using Schizosaccharomyces pombe, we show that the distance between sequence polymorphisms across homologs has a strong impact on meiotic recombination rate. The closer the sequence polymorphisms are to each other across the homologs the fewer recombination events were observed. In the immediate vicinity of DSBs, sequence polymorphisms affect the frequency of intragenic recombination events (gene conversions). Additionally, and unexpectedly, the crossover rate of flanking markers tens of kilobases away from the sequence polymorphisms was affected by their relative position to each other amongst the progeny having undergone intragenic recombination. A major regulator of this distance-dependent effect is the MutSα-MutLα complex consisting of Msh2, Msh6, Mlh1, and Pms1. Additionally, the DNA helicases Rqh1 and Fml1 shape recombination frequency, although the effects seen here are largely independent of the relative position of the sequence polymorphisms.
Surrogates for myocardial power and power efficiency in patients with aortic valve disease
Authors: Lee Chong-Bin , Goubergrits Leonid , Fernandes Joao Filipe , Nordmeyer Sarah , Knosalla Christoph , Berger Felix , Falk Volkmar , Kuehne Titus , Kelm Marcus 
Published: November 2019

AbstractWe aimed to assess surrogate markers for left ventricular (LV) myocardial power and efficiency in patients with isolated aortic stenosis (AS) and combined stenosis/regurgitation (AS/AR). In AS (n = 59), AS/AR (n = 21) and controls (n = 14), surrogates for LV myocardial power and circulatory/external myocardial efficiency were obtained from cardiac MRI. Median surrogate LV myocardial power was increased in AS, 7.7 W/m2 (interquartile range 6.0–10.2; p = 0.010) and AS/AR, 10.8 W/m2 (8.9–13.4; p < 0.001) when compared to controls, 5.4 W/m2 (4.2–6.5), and was lower in AS than AS/AR (p < 0.001). Surrogate circulatory efficiency was decreased in AS, 8.6% (6.8–11.1; p < 0.001) and AS/AR, 5.4% (4.1–6.2; p < 0.001) when compared to controls, 11.8% (9.8–16.9). Surrogate external myocardial efficiency was higher in AS, 15.2% (11.9–18.6) than in AS/AR, 12.2% (10.1–14.2; p = 0.031) and was significantly lower compared to controls, 12.2% (10.7–18.1) in patients with reduced ejection fraction (EF), 9.8% (8.1–11.7; p = 0.025). In 16% of all cases, left ventricular mass/volume indices and EF were within normal ranges, wheras surrogate LV myocardial power was elevated and patients were symptomatic. Although influenced by pressure/volume load, the myocardium is additionally affected by remodelling processes. Surrogates for circulatory efficiency and LV myocardial power gradually reflect alterations in patients with AS and AS/AR, even when surrogate external myocardial efficiency, EF, mass and volume indices still remain compensated.
Identification and characterization of circular RNAs in Ganoderma lucidum
Authors: Shao Junjie , Wang Liqiang , Liu Xinyue , Yang Meng , Chen Haimei , Wu Bin , Liu Chang 
Published: November 2019

AbstractCircular RNAs (circRNAs) play important roles in animals, plants, and fungi. However, no circRNAs have been reported in Ganoderma lucidum. Here, we carried out a genome-wide identification of the circRNAs in G.lucidum using RNA-Seq data, and analyzed their features. In total, 250 and 2193 circRNAs were identified from strand-specific RNA-seq data generated from the polyA(−) and polyA(−)/RNase R-treated libraries, respectively. Six of 131 (4.58%) predicted circRNAs were experimentally confirmed. Across three developmental stages, 731 exonic circRNAs (back spliced read counts ≥ 5) and their parent genes were further analyzed. CircRNAs were preferred originating from exons with flanking introns, and the lengths of the flanking intron were longer than those of the control introns. A total of 200 circRNAs were differentially expressed across the three developmental stages of G. lucidum. The expression profiles of 119 (16.3%) exonic circRNAs and their parent genes showed significant positive correlations (r ≥ 0.9, q < 0.01), whereas 226 (30.9%) exonic circRNAs and their parent genes exhibited significant negative correlations (r ≤ −0.9, q < 0.01), in which 53 parent genes are potentially involved in the transcriptional regulation, polysaccharide biosynthesis etc. Our results indicated that circRNAs are present in G. lucidum, with potentially important regulatory roles.