bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of metabolic divergence in Pseudomonas aeruginosa during long-term infection facilitates a proto-cooperative interspecies interaction
Authors: Frydenlund Michelsen Charlotte , Hossein Khademi Seyed Mohammad , Krogh Johansen Helle , Ingmer Hanne , Dorrestein Pieter C , Jelsbak Lars
Published: December 2015

The effect of polymicrobial interactions on pathogen physiology and how it can act either to limit pathogen colonization or to potentiate pathogen expansion and virulence are not well understood. Pseudomonas aeruginosa and Staphylococcus aureus are opportunistic pathogens commonly found together in polymicrobial human infections. However, we have previously shown that the interactions between these two bacterial species are strain dependent. Whereas P. aeruginosa PAO1, a commonly used laboratory strain, effectively suppressed S. aureus growth, we observed a commensal-like interaction between the human host-adapted strain, DK2-P2M24-2003, and S. aureus. In this study, characterization by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) imaging mass spectrometry (IMS) and mass spectral (MS) molecular networking revealed a significant metabolic divergence between P. aeruginosa PAO1 and DK2-P2M24-2003, which comprised several virulence factors and signaling 4-hydroxy-2-alkylquinoline (HAQ) molecules. Strikingly, a further modulation of the HAQ profile was observed in DK2-P2M24-2003 during interaction with S. aureus, resulting in an area with thickened colony morphology at the P. aeruginosa–S. aureus interface. In addition, we found an HAQ-mediated protection of S. aureus by DK2-P2M24-2003 from the killing effect of tobramycin. Our findings suggest a model where the metabolic divergence manifested in human host-adapted P. aeruginosa is further modulated during interaction with S. aureus and facilitate a proto-cooperative P. aeruginosa–S. aureus relationship.
An evidence-based framework for predicting the impact of differing autotroph-heterotroph thermal sensitivities on consumer–prey dynamics
Authors: Yang Zhou , Zhang Lu , Zhu Xuexia , Wang Jun , Montagnes David J S
Published: December 2015

Increased temperature accelerates vital rates, influencing microbial population and wider ecosystem dynamics, for example, the predicted increases in cyanobacterial blooms associated with global warming. However, heterotrophic and mixotrophic protists, which are dominant grazers of microalgae, may be more thermally sensitive than autotrophs, and thus prey could be suppressed as temperature rises. Theoretical and meta-analyses have begun to address this issue, but an appropriate framework linking experimental data with theory is lacking. Using ecophysiological data to develop a novel model structure, we provide the first validation of this thermal sensitivity hypothesis: increased temperature improves the consumer’s ability to control the autotrophic prey. Specifically, the model accounts for temperature effects on auto- and mixotrophs and ingestion, growth and mortality rates, using an ecologically and economically important system (cyanobacteria grazed by a mixotrophic flagellate). Once established, we show the model to be a good predictor of temperature impacts on consumer–prey dynamics by comparing simulations with microcosm observations. Then, through simulations, we indicate our conclusions remain valid, even with large changes in bottom-up factors (prey growth and carrying capacity). In conclusion, we show that rising temperature could, counterintuitively, reduce the propensity for microalgal blooms to occur and, critically, provide a novel model framework for needed, continued assessment.
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

Histone-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

Carbon 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

Activation-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.
Erratum: Non-perturbative effects in spin glasses
Authors: Castellana Michele , Parisi Giorgio
Published: December 2015

We present a numerical study of an Ising spin glass with hierarchical interactions—the hierarchical Edwards-Anderson model with an external magnetic field (HEA). We study the model with Monte Carlo (MC) simulations in the mean-field (MF) and non-mean-field (NMF) regions corresponding to d ≥ 4 and d < 4 for the d-dimensional ferromagnetic Ising model respectively.
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

Recently, 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.
Erratum: A Novel, Stable, Estradiol-Stimulating, Osteogenic Yam Protein with Potential for the Treatment of Menopausal Syndrome
Authors: Wong Kam Lok , Lai Yau Ming , Li Ka Wan , Lee Kai Fai , Ng Tzi Bun , Cheung Ho Pan , Zhang Yan Bo , Lao Lixing , Wong Ricky Ngok-Shun , Shaw Pang Chui , Wong Jack Ho , Zhang Zhang-Jin , Lam Jenny Ka Wing , Ye Wen-cai , Sze Stephen Cho Wing
Published: December 2015

A novel protein, designated as DOI, isolated from the Chinese yam (Dioscorea opposita Thunb.) could be the first protein drug for the treatment of menopausal syndrome and an alternative to hormone replacement therapy (HRT), which is known to have undesirable side effects. DOI is an acid- and thermo-stable protein with a distinctive N-terminal sequence Gly-Ile-Gly-Lys-Ile-Thr-Thr-Tyr-Trp-Gly-Gln-Tyr-Ser-Asp-Glu-Pro-Ser-Leu-Thr-Glu. DOI was found to stimulate estradiol biosynthesis in rat ovarian granulosa cells; induce estradiol and progesterone secretion in 16- to 18-month-old female Sprague Dawley rats by upregulating expressions of follicle-stimulating hormone receptor and ovarian aromatase; counteract the progression of osteoporosis and augment bone mineral density; and improve cognitive functioning by upregulating protein expressions of brain-derived neurotrophic factor and TrkB receptors in the prefrontal cortex. Furthermore, DOI did not stimulate the proliferation of breast cancer and ovarian cancer cells, which suggest it could be a more efficacious and safer alternative to HRT.
Erratum: Tristetraprolin regulation of interleukin-22 production
Authors: Härdle Lorena , Bachmann Malte , Bollmann Franziska , Pautz Andrea , Schmid Tobias , Eberhardt Wolfgang , Kleinert Hartmut , Pfeilschifter Josef , Mühl Heiko
Published: December 2015

Interleukin (IL)-22 is a STAT3-activating cytokine displaying characteristic AU-rich elements (ARE) in the 3′-untranslated region (3′-UTR) of its mRNA. This architecture suggests gene regulation by modulation of mRNA stability. Since related cytokines undergo post-transcriptional regulation by ARE-binding tristetraprolin (TTP), the role of this destabilizing protein in IL-22 production was investigated. Herein, we demonstrate that TTP-deficient mice display augmented serum IL-22. Likewise, IL-22 mRNA was enhanced in TTP-deficient splenocytes and isolated primary T cells. A pivotal role for TTP is underscored by an extended IL-22 mRNA half-life detectable in TTP-deficient T cells. Luciferase-reporter assays performed in human Jurkat T cells proved the destabilizing potential of the human IL-22-3′-UTR. Furthermore, overexpression of TTP in HEK293 cells substantially decreased luciferase activity directed by the IL-22-3′-UTR. Transcript destabilization by TTP was nullified upon cellular activation by TPA/A23187, an effect dependent on MEK1/2 activity. Accordingly, IL-22 mRNA half-life as determined in TPA/A23187-stimulated Jurkat T cells decreased under the influence of the MEK1/2 inhibitor U0126. Altogether, data indicate that TTP directly controls IL-22 production, a process counteracted by MEK1/2. The TTP-dependent regulatory pathway described herein likely contributes to the role of IL-22 in inflammation and cancer and may evolve as novel target for pharmacological IL-22 modulation.
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

During 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

Dynamic 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

In 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

Fluorescent 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

Heterosis 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

This 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

Outward 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

Storage 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

Laser 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

Controlling 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

BRCA1 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

The 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.
“Cation-Stitching Cascade”: exquisite control of terpene cyclization in cyclooctatin biosynthesis
Authors: Sato Hajime , Teramoto Kazuya , Masumoto Yui , Tezuka Noriyuki , Sakai Kenta , Ueda Shota , Totsuka Yusuke , Shinada Tetsuro , Nishiyama Makoto , Wang Chao , Kuzuyama Tomohisa , Uchiyama Masanobu
Published: December 2015

Terpene cyclization is orchestrated by terpene cyclases, which are involved in the biosynthesis of various cyclic natural products, but understanding the origin and mechanism of the selectivity of terpene cyclization is challenging. In this work, we describe an in-depth mechanistic study on cyclooctatin biosynthesis by means of theoretical calculations combined with experimental methods. We show that the main framework of cyclooctatin is formed through domino-type carbocation transportation along the terpene chain, which we call a “cation-stitching cascade”, including multiple hydrogen-shifts and a ring rearrangement that elegantly determine the stereoselectivity.
Microbial properties explain temporal variation in soil respiration in a grassland subjected to nitrogen addition
Authors: Li Yue , Liu Yinghui , Wu Shanmei , Niu Lei , Tian Yuqiang
Published: December 2015

The role of soil microbial variables in shaping the temporal variability of soil respiration has been well acknowledged but is poorly understood, particularly under elevated nitrogen (N) deposition conditions. We measured soil respiration along with soil microbial properties during the early, middle and late growing seasons in temperate grassland plots that had been treated with N additions of 0, 2, 4, 8, 16, or 32 g N m−2 yr−1 for 10 years. Representing the averages over three observation periods, total (Rs) and heterotrophic (Rh) respiration were highest with 4 g N m−2 yr−1, but autotrophic respiration (Ra) was highest with 8 to 16 g N m−2 yr−1. Also, the responses of Rh and Ra were unsynchronized considering the periods separately. N addition had no significant impact on the temperature sensitivity (Q10) for Rs but inhibited the Q10 for Rh. Significant interactions between observation period and N level occurred in soil respiration components and the temporal variations in soil respiration components were mostly associated with changes in microbial biomass carbon (MBC) and phospholipid fatty acids (PLFAs). Further observation on soil organic carbon and root biomass is needed to reveal the long-term effect of N deposition on soil C sequestration.
A Fluorescent Tile DNA Diagnocode System for In Situ Rapid and Selective Diagnosis of Cytosolic RNA Cancer Markers
Authors: Park Kyung Soo , Shin Seung Won , Jang Min Su , Shin Woojung , Yang Kisuk , Min Junhong , Cho Seung-Woo , Oh Byung-Keun , Bae Jong Wook , Jung Sunghwan , Choi Jeong-Woo , Um Soong Ho
Published: December 2015

Accurate cancer diagnosis often requires extraction and purification of genetic materials from cells and sophisticated instrumentations that follow. Otherwise in order to directly treat the diagnostic materials to cells, multiple steps to optimize dose concentration and treatment time are necessary due to diversity in cellular behaviors. These processes may offer high precision but hinder fast analysis of cancer, especially in clinical situations that need rapid detection and characterization of cancer. Here we present a novel fluorescent tile DNA nanostructure delivered to cancer cytosol by employing nanoparticle technology. Its structural anisotropicity offers easy manipulation for multifunctionalities, enabling the novel DNA nanostructure to detect intracellular cancer RNA markers with high specificity within 30 minutes post treatment, while the nanoparticle property bypasses the requirement of treatment optimization, effectively reducing the complexity of applying the system for cancer diagnosis. Altogether, the system offers a precise and rapid detection of cancer, suggesting the future use in the clinical fields.
Zirconia based superhydrophobic coatings on cotton fabrics exhibiting excellent durability for versatile use
Authors: Das Indranee , De Goutam
Published: December 2015

A fluorinated silyl functionalized zirconia was synthesized by the sol-gel method to fabricate an extremely durable superhydrophobic coating on cotton fabrics by simple immersion technique. The fabric surfaces firmly attached with the coating material through covalent bonding, possessed superhydrophobicity with high water contact angle ≈163 ± 1°, low hysteresis ≈3.5° and superoleophilicity. The coated fabrics were effective to separate oil/water mixture with a considerably high separation efficiency of 98.8 wt% through ordinary filtering. Presence of highly stable (chemically and mechanically) superhydrophobic zirconia bonded with cellulose makes such excellent water repelling ability of the fabrics durable under harsh environment conditions like high temperature, strong acidic or alkaline solutions, different organic solvents and mechanical forces including extensive washings. Moreover, these coated fabrics retained self-cleanable superhydrophobic property as well as high water separation efficiency even after several cycles, launderings and abrasions. Therefore, such robust superhydrophobic ZrO2coated fabrics have strong potential for various industrial productions and uses.
The colour of an avifauna: A quantitative analysis of the colour of Australian birds
Authors: Delhey Kaspar
Published: December 2015

Animal coloration is a poorly-understood aspect of phenotypic variability. Here I expand initial studies of the colour gamut of birds by providing the first quantitative description of the colour variation of an entire avifauna: Australian landbirds (555 species). The colour of Australian birds occupies a small fraction (19%) of the entire possible colour space and colour variation is extremely uneven. Most colours are unsaturated, concentrated in the centre of colour space and based on the deposition of melanins. Other mechanisms of colour production are less common but account for larger portions of colour space and for most saturated colours. Male colours occupy 45–25% more colour space than female colours, indicating that sexual dichromatism translates into a broader range of male colours. Male-exclusive colours are often saturated, at the edge of chromatic space and have most likely evolved for signalling. While most clades of birds occupy expected or lower-than-expected colour volumes, parrots and cockatoos (Order Psittaciformes) occupy a much larger volume than expected. This uneven distribution of colour variation across mechanisms of colour production, sexes and clades is probably shared by avifaunas in other parts of the world, but this remains to be tested with comparable data.
Testing the fecundity advantage hypothesis with Sitobion avenae, Rhopalosiphum padi and Schizaphis graminum (Hemiptera: Aphididae) feeding on ten wheat accessions
Authors: Hu Xiang-Shun , Liu Xiao-Feng , Thieme Thomas , Zhang Gai-Sheng , Liu Tong-Xian , Zhao Hui-Yan
Published: December 2015

The fecundity advantage hypothesis suggests that females with a large body size produce more offspring than smaller females. We tested this hypothesis by exploring the correlations between life-history traits of three aphid species feeding on ten wheat accessions at three levels of analysis with respect to the host plant: overall, inter-accession and intra-accession. We found that fecundity was significantly correlated with mean relative growth rate (MRGR), weight gain and development time and that the faster aphid develops the greater body and fecundity, depending on aphid species, wheat accession and analyses level. Larger aphids of all three species produced more offspring overall; this held true for Sitobion avenae and Schizaphis graminum at the inter-accession level and for S. avenae, Rhopalosiphum padi, and S. graminum for three, five and eight accessions respectively at the intra-accession level. Only one correlation, between intrinsic rates of natural increase (rm) and MRGR, was significant for all aphid species at all three analysis levels. A more accurate statement of the fecundity advantage hypothesis is that cereal aphids with greater MRGR generally maintain higher rm on wheat. Our results also provide a method for exploring relationships between individual life-history traits and population dynamics for insects on host plants.
Association of telomere length and mitochondrial DNA copy number with risperidone treatment response in first-episode antipsychotic-naïve schizophrenia
Authors: Li Zongchang , Hu Maolin , Zong Xiaofen , He Ying , Wang Dong , Dai Lulin , Dong Min , Zhou Jun , Cao Hongbao , Lv Luxian , Chen Xiaogang , Tang Jinsong
Published: December 2015

Accumulating evidence indicates a putative association of telomere length and mitochondrial function with antipsychotics response in schizophrenia (SCZ). However, pharmacological findings were limited and no previous work has assessed this in a prospective longitudinal study. This study assessed telomere length and mitochondrial DNA copy number in first-episode antipsychotic-naïve SCZ patients with 8-week risperidone treatment to evaluate the association between these biomarkers and clinical treatment response. We recruited 137 first-episode antipsychotic-naive SCZ patients (and 144 controls) at baseline and 89 patients completed the 8-week follow-up. Patients, completed follow-up, were divided into Responders (N = 46) and Non-Responders (N = 43) according to the percentage of symptoms improvement. Linear regression analyses show that SCZ patients had significantly lower mtDNA copy number (β = −0.108, p = 0.002) and no alteration of telomere length when compared with healthy controls. In addition, compared with Non-Responders, Responders had significantly lower mtDNA copy number (β = −0.178, p = 0.001) and longer telomere length (β = 0.111, p = 0.071) before the 8-week treatment. After treatment, Responders persisted lower mtDNA copy number comparing with No-Responders (partial η2 = 0.125, p = 0.001). These findings suggest that telomere length and mtDNA copy number may hold the potential to serve as predictors of antipsychotic response of SCZ patients.
From an imbalance to a new imbalance: Italian-style gluten-free diet alters the salivary microbiota and metabolome of African celiac children
Authors: Ercolini Danilo , Francavilla Ruggiero , Vannini Lucia , De Filippis Francesca , Capriati Teresa , Di Cagno Raffaella , Iacono Giuseppe , De Angelis Maria , Gobbetti Marco
Published: December 2015

Fourteen Saharawi celiac children following an African-style gluten-free diet for at least two years were subjected to a change of diet to an Italian-style gluten-free diet for 60 days. Significant differences were identified in the salivary microbiota and metabolome when Saharawi celiac children switched from African- to Italian-style dietary habits. An Italian-style gluten-free diet caused increases in the abundance of Granulicatella, Porphyromonas and Neisseria and decreases in Clostridium, Prevotella and Veillonella, altering the ‘salivary type’ of the individuals. Furthermore, operational taxonomic unit co-occurrence/exclusion patterns indicated that the initial equilibrium of co-occurring microbial species was perturbed by a change in diet: the microbial diversity was reduced, with a few species out-competing the previously established microbiota and becoming dominant. Analysis of predicted metagenomes revealed a remarkable change in the metabolic potential of the microbiota following the diet change, with increased potential for amino acid, vitamin and co-factor metabolism. High concentrations of acetone and 2-butanone during treatment with the Italian-style gluten-free diet suggested metabolic dysfunction in the Saharawi celiac children. The findings of this study support the need for a translational medicine pipeline to examine interactions between food and microbiota when evaluating human development, nutritional needs and the impact and consequences of westernisation.
Wireless fluorescence capsule for endoscopy using single photon-based detection
Authors: Al-Rawhani Mohammed A. , Beeley James , Cumming David R. S.
Published: December 2015

Fluorescence Imaging (FI) is a powerful technique in biological science and clinical medicine. Current FI devices that are used either for in-vivo or in-vitro studies are expensive, bulky and consume substantial power, confining the technique to laboratories and hospital examination rooms. Here we present a miniaturised wireless fluorescence endoscope capsule with low power consumption that will pave the way for future FI systems and applications. With enhanced sensitivity compared to existing technology we have demonstrated that the capsule can be successfully used to image tissue autofluorescence and targeted fluorescence via fluorophore labelling of tissues. The capsule incorporates a state-of-the-art complementary metal oxide semiconductor single photon avalanche detector imaging array, miniaturised optical isolation, wireless technology and low power design. When in use the capsule consumes only 30.9 mW and deploys very low-level 468 nm illumination. The device has the potential to replace highly power-hungry intrusive optical fibre based endoscopes and to extend the range of clinical examination below the duodenum. To demonstrate the performance of our capsule, we imaged fluorescence phantoms incorporating principal tissue fluorophores (flavins) and absorbers (haemoglobin). We also demonstrated the utility of marker identification by imaging a 20 μM fluorescein isothiocyanate (FITC) labelling solution on mammalian tissue.
De novo assembly and characterization of root transcriptome in two distinct morphotypes of vetiver, Chrysopogon zizaniodes (L.) Roberty
Authors: Chakrabarty Debasis , Chauhan Puneet Singh , Chauhan Abhishek Singh , Indoliya Yuvraj , Lavania Umesh Chandra , Nautiyal Chandra Shekhar
Published: December 2015

Vetiver, a perennial C4 grass, has long been known for its multifarious uses in perfumery, medicine and environmental protection. Two distinct vetiver morphotypes have been identified in India, i.e., A. North Indian type characterized by thick and smooth fast growing roots that produce superior quality of laevorotatory oil; and B. South Indian type with more number of thin and hairy roots that produce inferior quality of dextrorotatory oil. The two morphotypes were targeted for transcriptome analysis to understand the contribution of genetic background on oil quality and root morphology. Sample A showed enhanced activity of flavonoid and terpenoid biosynthesis related genes, i.e. ERF, MYB, bHLH, bZIP and WRKY. Interestingly, expression analysis revealed that the genes involved in sesquiterpene biosynthesis pathway were up regulated in Sample A. Moreover, some of the genes involved in mevalonate pathway of sesquiterpene biosynthesis were unique to Sample A. Our results also demonstrated several transcripts involved in root development and hormonal regulation being up regulated in Sample A. To validate gene expression results of RNA-seq data, 20 transcripts were validated by qRT-PCR experiment. The present study provided an important start point for further discovery of genes related to root oil quality in different ecotypes of vetiver.
Supramolecular recognition control of polyethylene glycol modified N-doped graphene quantum dots: tunable selectivity for alkali and alkaline-earth metal ions
Authors: Yang Siwei , Sun Jing , Zhu Chong , He Peng , Peng Zheng , Ding Guqiao
Published: December 2015

The graphene quantum dot based fluorescent probe community needs unambiguous evidence about the control on the ion selectivity.
A highly proton-conducting, methanol-blocking Nafion composite membrane enabled by surface-coating crosslinked sulfonated graphene oxide
Authors: He Guangwei , He Xueyi , Wang Xinglin , Chang Chaoyi , Zhao Jing , Li Zongyu , Wu Hong , Jiang Zhongyi
Published: December 2015

Coating an ultrathin graphene oxide film onto a Nafion membrane confers a distinct anti-tradeoff behavior: 93% decrease of methanol permeability while retaining the high proton conductivity.
Excitation wavelength-induced color-tunable and white-light emissions in lanthanide(iii) coordination polymers constructed using an environment-dependent luminescent tetrazolate–dicarboxylate ligand
Authors: Xiao Yu , Wang Shuai-Hua , Zheng Fa-Kun , Wu Mei-Feng , Xu Ju , Liu Zhi-Fa , Chen Jun , Li Rong , Guo Guo-Cong
Published: December 2015

Color-tunable and white-light emitting lanthanide(iii) polymers with a selective light-emitting ligand have been constructed.
Synthesis, structure and adsorption properties of lanthanide–organic frameworks with pyridine-3,5-bis(phenyl-4-carboxylate)
Authors: Cui Pei-Pei , Zhang Xiu-Du , Zhao Yue , Fu Ai-Yun , Sun Wei-Yin
Published: December 2015

Three new lanthanide–organic frameworks with two-fold interpenetrating structures and lcy topology show selective and hysteretic sorption of CO2 over N2.
The synthesis, structure and properties of a new lithium-rich manganese(ii) phosphate Li5CsMn(P2O7)2: a congruently melting compound with a ‘lithium hamburger’ structure
Authors: Gao Jianhua , Sha Xunshan , Song Limei , Zhao Pan , Liu Xi
Published: December 2015

A new layered lithium manganese diphosphate, possessing a high Li ion conductivity, has been proposed.
Substituent directed selectivity in anion recognition by a new class of simple osmium-pyrazole derived receptors
Authors: Das Ankita , Mondal Prasenjit , Dasgupta Moumita , Kishore Nand , Lahiri Goutam Kumar
Published: December 2015

The remarkable impact of the 3,5-dimethylpyrazole derived osmium framework with hydrogen bonded NH for the selective recognition of F−has been ascertained.