bluuebunny/crossref_metadata_2025_split huggingface dataset:
Embryonic transcription is controlled by maternally defined chromatin state
Authors: Hontelez Saartje , van Kruijsbergen Ila , Georgiou Georgios , van Heeringen Simon J. , Bogdanovic Ozren , Lister Ryan , Veenstra Gert Jan C. 
Published: December 2015

AbstractHistone-modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origins of the epigenome during embryonic development. Here we generate a comprehensive set of epigenome reference maps, which we use to determine the extent to which maternal factors shape chromatin state in Xenopus embryos. Using α-amanitin to inhibit zygotic transcription, we find that the majority of H3K4me3- and H3K27me3-enriched regions form a maternally defined epigenetic regulatory space with an underlying logic of hypomethylated islands. This maternal regulatory space extends to a substantial proportion of neurula stage-activated promoters. In contrast, p300 recruitment to distal regulatory regions requires embryonic transcription at most loci. The results show that H3K4me3 and H3K27me3 are part of a regulatory space that exerts an extended maternal control well into post-gastrulation development, and highlight the combinatorial action of maternal and zygotic factors through proximal and distal regulatory sequences.
Degradation in carbon stocks near tropical forest edges
Authors: Chaplin-Kramer Rebecca , Ramler Ivan , Sharp Richard , Haddad Nick M. , Gerber James S. , West Paul C. , Mandle Lisa , Engstrom Peder , Baccini Alessandro , Sim Sarah , Mueller Carina , King Henry 
Published: December 2015

AbstractCarbon stock estimates based on land cover type are critical for informing climate change assessment and landscape management, but field and theoretical evidence indicates that forest fragmentation reduces the amount of carbon stored at forest edges. Here, using remotely sensed pantropical biomass and land cover data sets, we estimate that biomass within the first 500 m of the forest edge is on average 25% lower than in forest interiors and that reductions of 10% extend to 1.5 km from the forest edge. These findings suggest that IPCC Tier 1 methods overestimate carbon stocks in tropical forests by nearly 10%. Proper accounting for degradation at forest edges will inform better landscape and forest management and policies, as well as the assessment of carbon stocks at landscape and national levels.
Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution
Authors: Senavirathne Gayan , Bertram Jeffrey G. , Jaszczur Malgorzata , Chaurasiya Kathy R. , Pham Phuong , Mak Chi H. , Goodman Myron F. , Rueda David 
Published: December 2015

AbstractActivation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of stalled bubbles. AID scans randomly when constrained in an 8 nt model bubble. When unconstrained on single-stranded (ss) DNA, AID moves in random bidirectional short slides/hops over the entire molecule while remaining bound for ∼5 min. Our analysis distinguishes dynamic scanning from static ssDNA creasing. That AID alone can track along with RNAP during transcription and scan within stalled transcription bubbles suggests a mechanism by which AID can initiate SHM and CSR when properly regulated, yet when unregulated can access non-Ig genes and cause cancer.
Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection
Authors: Wang Jinyan , Yu Wengui , Yang Yuwen , Li Xiao , Chen Tianzi , Liu Tingli , Ma Na , Yang Xu , Liu Renyi , Zhang Baolong 
Published: December 2015

AbstractRecently, a large number of long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes in animals and plants. However, how lncRNAs function during plant DNA virus infection is largely unknown. We performed strand-specific paired-end RNA sequencing of tomato samples infected with Tomato yellow leaf curl virus (TYLCV) with three biological replicates. Overall, we predicted 1565 lncRNAs including long intergenic ncRNAs (lincRNAs) and natural antisense transcripts (lncNATs) and definitively identified lnRNAs that are involved in TYLCV infection by virus-induced gene silencing (VIGS). We also verified the functions of a set of lncRNAs that were differentially expressed between 0 and 7 days post inoculation (dpi). More importantly, we found that several lncRNAs acted as competing endogenous target mimics (eTMs) for tomato microRNAs involved in the TYLCV infection. These results provide new insight into lncRNAs involved in the response to TYLCV infection that are important components of the TYLCV network in tomatoes.
Comparison of owner-reported behavioral characteristics among genetically clustered breeds of dog (Canis familiaris).
Authors: Tonoike Akiko , Nagasawa Miho , Mogi Kazutaka , Serpell James A. , Ohtsuki Hisashi , Kikusui Takefumi 
Published: December 2015

AbstractDuring the domestication process, dogs were selected for their suitability for multiple purposes, resulting in a variety of behavioral characteristics. In particular, the ancient group of breeds that is genetically closer to wolves may show different behavioral characteristics when compared to other breed groups. Here, we used questionnaire evaluations of dog behavior to investigate whether behavioral characteristics of dogs were different among genetically clustered breed groups. A standardized questionnaire, the Canine Behavioral Assessment and Research Questionnaire (C-BARQ), was used and breed group differences of privately-owned dogs from Japan (n = 2,951) and the United States (n = 10,389) were analyzed. Results indicated that dogs in the ancient and spitz breed group showed low attachment and attention-seeking behavior. This characteristic distinguished the ancient group from any other breed groups with presumed modern European origins and may therefore, be an ancestral trait.
Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks
Authors: Zhu Shijia , Wang Yadong 
Published: December 2015

AbstractDynamic Bayesian Networks (DBN) have been widely used to recover gene regulatory relationships from time-series data in computational systems biology. Its standard assumption is ‘stationarity’ and therefore, several research efforts have been recently proposed to relax this restriction. However, those methods suffer from three challenges: long running time, low accuracy and reliance on parameter settings. To address these problems, we propose a novel non-stationary DBN model by extending each hidden node of Hidden Markov Model into a DBN (called HMDBN), which properly handles the underlying time-evolving networks. Correspondingly, an improved structural EM algorithm is proposed to learn the HMDBN. It dramatically reduces searching space, thereby substantially improving computational efficiency. Additionally, we derived a novel generalized Bayesian Information Criterion under the non-stationary assumption (called BWBIC), which can help significantly improve the reconstruction accuracy and largely reduce over-fitting. Moreover, the re-estimation formulas for all parameters of our model are derived, enabling us to avoid reliance on parameter settings. Compared to the state-of-the-art methods, the experimental evaluation of our proposed method on both synthetic and real biological data demonstrates more stably high prediction accuracy and significantly improved computation efficiency, even with no prior knowledge and parameter settings.
High-temperature superconductivity from fine-tuning of Fermi-surface singularities in iron oxypnictides
Authors: Charnukha A. , Evtushinsky D. V. , Matt C. E. , Xu N. , Shi M. , Büchner B. , Zhigadlo N. D. , Batlogg B. , Borisenko S. V. 
Published: December 2015

AbstractIn the family of the iron-based superconductors, the REFeAsO-type compounds (with RE being a rare-earth metal) exhibit the highest bulk superconducting transition temperatures (Tc) up to 55 K and thus hold the key to the elusive pairing mechanism. Recently, it has been demonstrated that the intrinsic electronic structure of SmFe0.92Co0.08AsO (Tc = 18 K) is highly nontrivial and consists of multiple band-edge singularities in close proximity to the Fermi level. However, it remains unclear whether these singularities are generic to the REFeAsO-type materials and if so, whether their exact topology is responsible for the aforementioned record Tc. In this work, we use angle-resolved photoemission spectroscopy (ARPES) to investigate the inherent electronic structure of the NdFeAsO0.6F0.4 compound with a twice higher Tc = 38 K. We find a similarly singular Fermi surface and further demonstrate that the dramatic enhancement of superconductivity in this compound correlates closely with the fine-tuning of one of the band-edge singularities to within a fraction of the superconducting energy gap Δ below the Fermi level. Our results provide compelling evidence that the band-structure singularities near the Fermi level in the iron-based superconductors must be explicitly accounted for in any attempt to understand the mechanism of superconducting pairing in these materials.
Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence
Authors: Rumyantsev Konstantin A. , Shcherbakova Daria M. , Zakharova Natalia I. , Emelyanov Alexander V. , Turoverov Konstantin K. , Verkhusha Vladislav V. 
Published: December 2015

AbstractFluorescent proteins (FP) are used to study various biological processes. Recently, a series of near-infrared (NIR) FPs based on bacterial phytochromes was developed. Finding ways to improve NIR FPs is becoming progressively important. By applying rational design and molecular evolution we have engineered R. palustris bacterial phytochrome into a single-domain NIR FP of 19.6 kDa, termed GAF-FP, which is 2-fold and 1.4-fold smaller than bacterial phytochrome-based NIR FPs and GFP-like proteins, respectively. Engineering of GAF-FP involved a substitution of 15% of its amino acids and a deletion of the knot structure. GAF-FP covalently binds two tetrapyrrole chromophores, biliverdin (BV) and phycocyanobilin (PCB). With the BV chromophore GAF-FP absorbs at 635 nm and fluoresces at 670 nm. With the PCB chromophore GAF-FP becomes blue-shifted and absorbs at 625 nm and fluoresces at 657 nm. The GAF-FP structure has a high tolerance to small peptide insertions. The small size of GAF-FP and its additional absorbance band in the violet range has allowed for designing a chimeric protein with Renilla luciferase. The chimera exhibits efficient non-radiative energy transfer from luciferase to GAF-FP, resulting in NIR bioluminescence. This study opens the way for engineering of small NIR FPs and NIR luciferases from bacterial phytochromes.
Genetic dissection of heterosis using epistatic association mapping in a partial NCII mating design
Authors: Wen Jia , Zhao Xinwang , Wu Guorong , Xiang Dan , Liu Qing , Bu Su-Hong , Yi Can , Song Qijian , Dunwell Jim M. , Tu Jinxing , Zhang Tianzhen , Zhang Yuan-Ming 
Published: December 2015

AbstractHeterosis refers to the phenomenon in which an F1hybrid exhibits enhanced growth or agronomic performance. However, previous theoretical studies on heterosis have been based on bi-parental segregating populations instead of F1hybrids. To understand the genetic basis of heterosis, here we used a subset of F1hybrids, named a partial North Carolina II design, to perform association mapping for dependent variables: original trait value, general combining ability (GCA), specific combining ability (SCA) and mid-parental heterosis (MPH). Our models jointly fitted all the additive, dominance and epistatic effects. The analyses resulted in several important findings: 1) Main components are additive and additive-by-additive effects for GCA and dominance-related effects for SCA and MPH and additive-by-dominant effect for MPH was partly identified as additive effect; 2) the ranking of factors affecting heterosis was dominance > dominance-by-dominance > over-dominance > complete dominance; and 3) increasing the proportion of F1hybrids in the population could significantly increase the power to detect dominance-related effects and slightly reduce the power to detect additive and additive-by-additive effects. Analyses of cotton and rapeseed datasets showed that more additive-by-additive QTL were detected from GCA than from trait phenotype and fewer QTL were from MPH than from other dependent variables.
Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing
Authors: Suárez-Vega Aroa , Gutiérrez-Gil Beatriz , Klopp Christophe , Robert-Granie Christèle , Tosser-Klopp Gwenola , Arranz Juan José 
Published: December 2015

AbstractThis study presents a dynamic characterization of the sheep milk transcriptome aiming at achieving a better understanding of the sheep lactating mammary gland. Transcriptome sequencing (RNA-seq) was performed on total RNA extracted from milk somatic cells from ewes on days 10, 50, 120 and 150 after lambing. The experiment was performed in Spanish Churra and Assaf breeds, which differ in their milk production traits. Nearly 67% of the annotated genes in the reference genome (Oar_v3.1) were expressed in ovine milk somatic cells. For the two breeds and across the four lactation stages studied, the most highly expressed genes encoded caseins and whey proteins. We detected 573 differentially expressed genes (DEGs) across lactation points, with the largest differences being found, between day 10 and day 150. Upregulated GO terms at late lactation stages were linked mainly to developmental processes linked to extracellular matrix remodeling. A total of 256 annotated DEGs were detected in the Assaf and Churra comparison. Some genes selectively upregulated in the Churra breed grouped under the endopeptidase and channel activity GO terms. These genes could be related to the higher cheese yield of this breed. Overall, this study provides the first integrated overview on sheep milk gene expression.
Mechanism for attenuated outward conductance induced by mutations in the cytoplasmic pore of Kir2.1 channels
Authors: Chang Hsueh-Kai , Iwamoto Masayuki , Oiki Shigetoshi , Shieh Ru-Chi 
Published: December 2015

AbstractOutward currents through Kir2.1 channels regulate the electrical properties of excitable cells. These currents are subject to voltage-dependent attenuation by the binding of polyamines to high- and low-affinity sites, which leads to inward rectification, thereby controlling cell excitability. To examine the effects of positive charges at the low-affinity site in the cytoplasmic pore on inward rectification, we studied a mutant Kir channel (E224K/H226E) and measured single-channel currents and streaming potentials (Vstream), the latter provide the ratio of water to ions queued in a single-file permeation process in the selectivity filter. The water-ion coupling ratio was near one at a high K+ concentration ([K+]) for the wild-type channel and increased substantially as [K+] decreased. On the other hand, fewer ions occupied the selectivity filter in the mutant at all [K+]. A model for the Kir channel involving a K+ binding site in the wide pore was introduced. Model analyses revealed that the rate constants associated with the binding and release to and from the wide-pore K+ binding site was modified in the mutant. These effects lead to the reduced contribution of a conventional two-ion permeation mode to total conductance, especially at positive potentials, thereby inward rectification.
Effects of storage on mixed-culture biological electrodes
Authors: Saheb Alam Soroush , Persson Frank , Wilén Britt-Marie , Hermansson Malte , Modin Oskar 
Published: December 2015

AbstractStorage methods are important to preserve the viability and biochemical characteristics of microbial cultures between experiments or during periods when bioreactors are inactive. Most of the research on storage has focused on isolates; however, there is an increasing interest in methods for mixed cultures, which are of relevance in environmental biotechnology. The purpose of this study was to investigate the effect of different storage methods on electrochemically active enrichment cultures. Acetate-oxidizing bioanodes generating a current density of about 5 A m−2 were enriched in a microbial electrolysis cell. The effect of five weeks of storage was evaluated using electrochemical techniques and microbial community analysis. Storage by refrigeration resulted in quicker re-activation than freezing in 10% glycerol, while the bioelectrochemical activity was entirely lost after storage using dehydration. The results showed that the bioelectrochemical activity of bioanodes stored at low temperature could be retained. However, during the re-activation period the bioanodes only recovered 75% of the current density generated before storage and the bacterial communities were different in composition and more diverse after storage than before.
Speckle lithography for fabricating Gaussian, quasi-random 2D structures and black silicon structures
Authors: Bingi Jayachandra , Murukeshan Vadakke Matham 
Published: December 2015

AbstractLaser speckle pattern is a granular structure formed due to random coherent wavelet interference and generally considered as noise in optical systems including photolithography. Contrary to this, in this paper, we use the speckle pattern to generate predictable and controlled Gaussian random structures and quasi-random structures photo-lithographically. The random structures made using this proposed speckle lithography technique are quantified based on speckle statistics, radial distribution function (RDF) and fast Fourier transform (FFT). The control over the speckle size, density and speckle clustering facilitates the successful fabrication of black silicon with different surface structures. The controllability and tunability of randomness makes this technique a robust method for fabricating predictable 2D Gaussian random structures and black silicon structures. These structures can enhance the light trapping significantly in solar cells and hence enable improved energy harvesting. Further, this technique can enable efficient fabrication of disordered photonic structures and random media based devices.
Full controlling of Fano resonances in metal-slit superlattice
Authors: Deng Zi-Lan , Yogesh Natesan , Chen Xiao-Dong , Chen Wen-Jie , Dong Jian-Wen , Ouyang Zhengbiao , Wang Guo Ping 
Published: December 2015

AbstractControlling of the lineshape of Fano resonance attracts much attention recently due to its wide capabilities for lasing, biosensing, slow-light applications and so on. However, the controllable Fano resonance always requires stringent alignment of complex symmetry-breaking structures and thus the manipulation could only be performed with limited degrees of freedom and narrow tuning range. Furthermore, there is no report so far on independent controlling of both the bright and dark modes in a single structure. Here, we semi-analytically show that the spectral position and linewidth of both the bright and dark modes can be tuned independently and/or simultaneously in a simple and symmetric metal-slit superlattice and thus allowing for a free and continuous controlling of the lineshape of both the single and multiple Fano resonances. The independent controlling scheme is applicable for an extremely large electromagnetic spectrum range from optical to microwave frequencies, which is demonstrated by the numerical simulations with real metal and a microwave experiment. Our findings may provide convenient and flexible strategies for future tunable electromagnetic devices.
Cancer associated missense mutations in BAP1 catalytic domain induce amyloidogenic aggregation: A new insight in enzymatic inactivation
Authors: Bhattacharya Sushmita , Hanpude Pranita , Maiti Tushar Kanti 
Published: December 2015

AbstractBRCA1 associated protein 1 (BAP1) is a nuclear deubiquitinase that regulates tumor suppressor activity and widely involves many cellular processes ranging from cell cycle regulation to gluconeogenesis. Impairment of enzymatic activity and nuclear localization induce abnormal cell proliferation. It is considered to be an important driver gene, which undergoes frequent mutations in several cancers. However the role of mutation and oncogenic gain of function of BAP1 are poorly understood. Here, we investigated cellular localization, enzymatic activity and structural changes for four missense mutants of the catalytic domain of BAP1, which are prevalent in different types of cancer. These mutations triggered cytoplasmic/perinuclear accumulation in BAP1 deficient cells, which has been observed in proteins that undergo aggregation in cellular condition. Amyloidogenic activity of mutant BAP1 was revealed from its reactivity towards anti oligomeric antibody in HEK293T cells. We have also noted structural destabilization in the catalytic domain mutants, which eventually produced beta amyloid structure as indicated in atomic force microscopy study. The cancer associated mutants up-regulate heat shock response and activates transcription of genes normally co-repressed by BAP1. Overall, our results unambiguously demonstrate that structural destabilization and subsequent aggregation abrogate its cellular mechanism leading to adverse outcome.
The northern limit of corals of the genus Acropora in temperate zones is determined by their resilience to cold bleaching
Authors: Higuchi Tomihiko , Agostini Sylvain , Casareto Beatriz Estela , Suzuki Yoshimi , Yuyama Ikuko 
Published: December 2015

AbstractThe distribution of corals in Japan covers a wide range of latitudes, encompassing tropical to temperate zones. However, coral communities in temperate zones contain only a small subset of species. Among the parameters that determine the distribution of corals, temperature plays an important role. We tested the resilience to cold stress of three coral species belonging to the genus Acropora in incubation experiments. Acropora pruinosa, which is the northernmost of the three species, bleached at 13 °C, but recovered once temperatures were increased. The two other species, A. hyacinthus and A. solitaryensis, which has a more southerly range than A. pruinosa, died rapidly after bleaching at 13 °C. The physiological effects of cold bleaching on the corals included decreased rates of photosynthesis, respiration and calcification, similar to the physiological effects observed with bleaching due to high temperature stress. Contrasting hot bleaching, no increases in antioxidant enzyme activities were observed, suggesting that reactive oxygen species play a less important role in bleaching under cold stress. These results confirmed the importance of resilience to cold stress in determining the distribution and northern limits of coral species, as cold events causing coral bleaching and high mortality occur regularly in temperate zones.