bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development
Authors: Nair Sreejith J. , Zhang Xiaowen , Chiang Huai-Chin , Jahid Md Jamiul , Wang Yao , Garza Paula , April Craig , Salathia Neeraj , Banerjee Tapahsama , Alenazi Fahad S. , Ruan Jianhua , Fan Jian-Bing , Parvin Jeffrey D. , Jin Victor X. , Hu Yanfen , Li Rong
Published: March 2016

The breast cancer susceptibility gene BRCA1 is well known for its function in double-strand break (DSB) DNA repair. While BRCA1 is also implicated in transcriptional regulation, the physiological significance remains unclear. COBRA1 (also known as NELF-B) is a BRCA1-binding protein that regulates RNA polymerase II (RNAPII) pausing and transcription elongation. Here we interrogate functional interaction between BRCA1 and COBRA1 during mouse mammary gland development. Tissue-specific deletion of Cobra1 reduces mammary epithelial compartments and blocks ductal morphogenesis, alveologenesis and lactogenesis, demonstrating a pivotal role of COBRA1 in adult tissue development. Remarkably, these developmental deficiencies due to Cobra1 knockout are largely rescued by additional loss of full-length Brca1. Furthermore, Brca1/Cobra1 double knockout restores developmental transcription at puberty, alters luminal epithelial homoeostasis, yet remains deficient in homologous recombination-based DSB repair. Thus our genetic suppression analysis uncovers a previously unappreciated, DNA repair-independent function of BRCA1 in antagonizing COBRA1-dependent transcription programme during mammary gland development.
Evolutionary diversification of the BetaM interactome acquired through co-option of the ATP1B4 gene in placental mammals
Authors: Korneenko Tatyana V. , Pestov Nikolay B. , Ahmad Nisar , Okkelman Irina A. , Dmitriev Ruslan I. , Shakhparonov Mikhail I. , Modyanov Nikolai N.
Published: March 2016

ATP1B4 genes represent a rare instance of orthologous vertebrate gene co-option that radically changed properties of the encoded BetaM proteins, which function as Na,K-ATPase subunits in lower vertebrates and birds. Eutherian BetaM has lost its ancestral function and became a muscle-specific resident of the inner nuclear membrane. Our earlier work implicated BetaM in regulation of gene expression through direct interaction with the transcriptional co-regulator SKIP. To gain insight into evolution of BetaM interactome we performed expanded screening of eutherian and avian cDNA libraries using yeast-two-hybrid and split-ubiquitin systems. The inventory of identified BetaM interactors includes lamina-associated protein LAP-1, myocyte nuclear envelope protein Syne1, BetaM itself, heme oxidases HMOX1 and HMOX2; transcription factor LZIP/CREB3, ERGIC3, PHF3, reticulocalbin-3 and β-sarcoglycan. No new interactions were found for chicken BetaM and human Na,K-ATPase β1, β2 and β3 isoforms, indicating the uniqueness of eutherian BetaM interactome. Analysis of truncated forms of BetaM indicates that residues 72-98 adjacent to the membrane in nucleoplasmic domain are important for the interaction with SKIP. These findings demonstrate that evolutionary alterations in structural and functional properties of eutherian BetaM proteins are associated with the increase in its interactome complexity.
Atlantic SSTs control regime shifts in forest fire activity of Northern Scandinavia
Authors: Drobyshev Igor , Bergeron Yves , Vernal Anne de , Moberg Anders , Ali Adam A. , Niklasson Mats
Published: March 2016

Understanding the drivers of the boreal forest fire activity is challenging due to the complexity of the interactions driving fire regimes. We analyzed drivers of forest fire activity in Northern Scandinavia (above 60 N) by combining modern and proxy data over the Holocene. The results suggest that the cold climate in northern Scandinavia was generally characterized by dry conditions favourable to periods of regionally increased fire activity. We propose that the cold conditions over the northern North Atlantic, associated with low SSTs, expansion of sea ice cover and the southward shift in the position of the subpolar gyre, redirect southward the precipitation over Scandinavia, associated with the westerlies. This dynamics strengthens high pressure systems over Scandinavia and results in increased regional fire activity. Our study reveals a previously undocumented teleconnection between large scale climate and ocean dynamics over the North Atlantic and regional boreal forest fire activity in Northern Scandinavia. Consistency of the pattern observed annually through millennium scales suggests that a strong link between Atlantic SST and fire activity on multiple temporal scales over the entire Holocene is relevant for understanding future fire activity across the European boreal zone.
Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution
Authors: Janssen Toon , Karssen Gerrit , Verhaeven Myrtle , Coyne Danny , Bert Wim
Published: March 2016

The polyphagous parthenogenetic root-knot nematodes of the genus Meloidogyne are considered to be the most significant nematode pest in sub-tropical and tropical agriculture. Despite the crucial need for correct diagnosis, identification of these pathogens remains problematic. The traditionally used diagnostic strategies, including morphometrics, host-range tests, biochemical and molecular techniques, now appear to be unreliable due to the recently-suggested hybrid origin of root-knot nematodes. In order to determine a suitable barcode region for these pathogens nine quickly-evolving mitochondrial coding genes were screened. Resulting haplotype networks revealed closely related lineages indicating a recent speciation, an anthropogenic-aided distribution through agricultural practices, and evidence for reticulate evolution within M. arenaria. Nonetheless, nucleotide polymorphisms harbor enough variation to distinguish these closely-related lineages. Furthermore, completeness of lineage sorting was verified by screening 80 populations from widespread geographical origins and variable hosts. Importantly, our results indicate that mitochondrial haplotypes are strongly linked and consistent with traditional esterase isozyme patterns, suggesting that different parthenogenetic lineages can be reliably identified using mitochondrial haplotypes. The study indicates that the barcode region Nad5 can reliably identify the major lineages of tropical root-knot nematodes.
Class III-specific HDAC inhibitor Tenovin-6 induces apoptosis, suppresses migration and eliminates cancer stem cells in uveal melanoma
Authors: Dai Wei , Zhou Jingfeng , Jin Bei , Pan Jingxuan
Published: March 2016

Uveal melanoma (UM) is the most common intraocular malignancy in adults. Despite improvements in surgical, radiation and chemotherapy treatments, the overall survival of UM and prognosis remain poor. In the present study, we hypothesized that Sirtuin 1 and 2 (SIRT1/2), class III histone deacetylases (HDACs), were critical in controlling the destiny of bulk tumor cells and cancer stem cells (CSCs) of UM. We testified this hypothesis in four lines of UM cells (92.1, Mel 270, Omm 1 and Omm 2.3). Our results showed that inhibition of SIRT1/2 by Tenovin-6 induced apoptosis in UM cells by activating the expression of tumor suppressor genes such as p53 and elevating reactive oxygen species (ROS). Tenovin-6 inhibited the growth of UM cells. Tenovin-6 and vinblastine was synergistic in inducing apoptosis of UM cell line 92.1 and Mel 270. Furthermore, Tenovin-6 eliminated cancer stem cells in 92.1 and Mel 270 cells. In conclusion, our findings suggest that Tenovin-6 may be a promising agent to kill UM bulk tumor cells and CSCs.
H/C atomic ratio as a smart linkage between pyrolytic temperatures, aromatic clusters and sorption properties of biochars derived from diverse precursory materials
Authors: Xiao Xin , Chen Zaiming , Chen Baoliang
Published: March 2016

Biochar is increasingly gaining attention due to multifunctional roles in soil amelioration, pollution mitigation and carbon sequestration. It is a significant challenge to compare the reported results from world-wide labs regarding the structure and sorption of biochars derived from various precursors under different pyrolytic conditions due to a lack of a simple linkage. By combining the published works on various biochars, we established a quantitative relationship between H/C atomic ratio and pyrolytic temperature (T), aromatic structure and sorption properties for naphthalene and phenanthrene. A reverse sigmoid shape between T and the H/C ratio was observed, which was independent of the precursors of biochars, including the ash contents. Linear correlations of Freundlich parameters (N, log Kf) and sorption amount (log Qe, log QA) with H/C ratios were found. A rectangle-like model was proposed to predict the aromatic cluster sizes of biochars from their H/C ratios and then a good structure-sorption relationship was derived. These quantitative relationships indicate that the H/C atomic ratio is a universal linkage to predict pyrolytic temperatures, aromatic cluster sizes and sorption characteristics. This study would guide the global study of biochars toward being comparable and then the development of the structure-sorption relationships will benefit the structural design and environmental application of biochars.
The γH2AX DNA damage assay from a drop of blood
Authors: Heylmann Daniel , Kaina Bernd
Published: March 2016

DNA double-strand breaks (DSB) and blocked replication forks activate the DNA damage response (DDR), a signaling pathway marked by phosphorylation of histone 2AX (H2AX). The phosphorylated form, γH2AX, accumulates at the site of damage and can be detected as foci by immunocytochemistry. Therefore, γH2AX is a sensitive and robust biomarker of DNA damage, notably DSB. Cells from peripheral blood are often used for studies on genotoxic exposure of humans. They are limited, however, by the amount of blood required and the costly blood purification method. Here, we present a method that enables the detection of DNA damage by the analysis of γH2AX foci in a drop of blood. The blood drop method (BDM) is simple, fast, inexpensive and allows large series of blood sampling and storage over time. It can be combined with genotoxic treatment of cells in the collected blood sample for experimental purposes on DNA damage induction and repair. The BDM is suitable for rapid and large-scale screenings of genetic damage in human and animal populations.
Acetylation mimic of lysine 280 exacerbates human Tau neurotoxicity in vivo
Authors: Gorsky Marianna Karina , Burnouf Sylvie , Dols Jacqueline , Mandelkow Eckhard , Partridge Linda
Published: March 2016

Dysfunction and accumulation of the microtubule-associated human Tau (hTau) protein into intraneuronal aggregates is observed in many neurodegenerative disorders including Alzheimer’s disease (AD). Reversible lysine acetylation has recently emerged as a post-translational modification that may play an important role in the modulation of hTau pathology. Acetylated hTau species have been observed within hTau aggregates in human AD brains and multi-acetylation of hTau in vitro regulates its propensity to aggregate. However, whether lysine acetylation at position 280 (K280) modulates hTau-induced toxicity in vivo is unknown. We generated new Drosophila transgenic models of hTau pathology to evaluate the contribution of K280 acetylation to hTau toxicity, by analysing the respective toxicity of pseudo-acetylated (K280Q) and pseudo-de-acetylated (K280R) mutant forms of hTau. We observed that mis-expression of pseudo-acetylated K280Q-hTau in the adult fly nervous system potently exacerbated fly locomotion defects and photoreceptor neurodegeneration. In addition, modulation of K280 influenced total hTau levels and phosphorylation without changing hTau solubility. Altogether, our results indicate that pseudo-acetylation of the single K280 residue is sufficient to exacerbate hTau neurotoxicity in vivo, suggesting that acetylated K280-hTau species contribute to the pathological events leading to neurodegeneration in AD.
Changes in the morphology and protein expression of germ cells and Sertoli cells in plateau pikas testes during non-breeding season
Authors: Liu Ming , Cao Guangming , Zhang Yanming , Qu Jiapeng , Li Wei , Wan Xinrong , Li Yu-xia , Zhang Zhibin , Wang Yan-ling , Gao Fei
Published: March 2016

Plateau pikas are seasonally breeding small herbivores that inhabit the meadow ecosystem of the Qinghai-Tibetan Plateau. Testis regression in plateau pikas begins in early June, and the male pikas are completely infertile, with a dramatically reduced testis size, in late July. In this study, a decreased germ cell number in the testes was first noted in early June. By late June, only Sertoli cells and a small number of spermatogonia remained. Interestingly, large gonocyte-like germ cells were observed in early July. In late July, the number of gonocyte-like cells per tubule increased significantly, and most of the Sertoli cell nuclei moved to and clustered in the center of the seminiferous tubules. The gonocyte-like germ cells and Sertoli cells began to express AP-2γ and anti-Mullerian hormone (AMH) proteins, which were detected in the germ cells and Sertoli cells of juvenile pikas but not in adult testes. Simultaneously, LC3 puncta dramatically increased in the seminiferous tubules of the pikas’ testes during the non-breeding season. Our study found that spermatogonia and Sertoli cells in non-breeding adult pikas morphologically resembled those in juvenile pikas and expressed specific markers, indicating that de-differentiation-like transitions may occur during this process.
Genetic diversity and population structure of Lactobacillus delbrueckii subspecies bulgaricus isolated from naturally fermented dairy foods
Authors: Song Yuqin , Sun Zhihong , Guo Chenyi , Wu Yarong , Liu Wenjun , Yu Jie , Menghe Bilige , Yang Ruifu , Zhang Heping
Published: March 2016

Lactobacillus delbrueckii subsp. bulgaricus is one of the most widely used starter culture strains in industrial fermented dairy manufacture. It is also common in naturally fermented dairy foods made using traditional methods. The subsp. bulgaricus strains found in naturally fermented foods may be useful for improving current industrial starter cultures; however, little is known regarding its genetic diversity and population structure. Here, a collection of 298 L. delbrueckii strains from naturally fermented products in Mongolia, Russia and West China was analyzed by multi-locus sequence typing based on eight conserved genes. The 251 confirmed subsp. bulgaricus strains produced 106 unique sequence types, the majority of which were assigned to five clonal complexes (CCs). The geographical distribution of CCs was uneven, with CC1 dominated by Mongolian and Russian isolates and CC2–CC5 isolates exclusively from Xinjiang, China. Population structure analysis suggested six lineages, L1–L6, with various homologous recombination rates. Although L2–L5 were mainly restricted within specific regions, strains belonging to L1 and L6 were observed in diverse regions, suggesting historical transmission events. These results greatly enhance our knowledge of the population diversity of subsp. bulgaricus strains and suggest that strains from CC1 and L4 may be useful as starter strains in industrial fermentation.
Continuous nucleus extraction by optically-induced cell lysis on a batch-type microfluidic platform
Authors: Huang Shih-Hsuan , Hung Lien-Yu , Lee Gwo-Bin
Published: March 2016

An innovative, microfluidics-based approach featuring optically-induced cell lysis (OICL) for nucleus extraction and collection in an automatic format was demonstrated. The efficiency of cell membrane lysis and the ODEP nucleus separation was measured to be 78.04 ± 5.70% and 80.90 ± 5.98%, respectively, leading to an overall nucleus extraction efficiency of 58.21 ± 2.21%.
Influence of the component interaction over Cu/ZrO2 catalysts induced with fractionated precipitation method on the catalytic performance for methanol steam reforming
Authors: Zhou Jiajia , Zhang Ye , Wu Guisheng , Mao Dongsen , Lu Guanzhong
Published: March 2016

A series of binary Cu/ZrO2 catalysts by choosing different composition ratios and different precipitation sequences have been prepared for the production of hydrogen by steam reforming of methanol (SRM).
Isoreticular zirconium-based metal–organic frameworks: discovering mechanical trends and elastic anomalies controlling chemical structure stability
Authors: Ryder Matthew R. , Civalleri Bartolomeo , Tan Jin-Chong
Published: March 2016

Understanding the mechanical properties of MOFs is crucial not only to yield robust practical applications, but also to advance fundamental research underpinning flexibility of a myriad of open-framework compounds.
In vitro extraction and fermentation of polyphenols from grape seeds (Vitis vinifera) by human intestinal microbiota
Authors: Zhou Li , Wang Wei , Huang Jun , Ding Yu , Pan Zhouqiang , Zhao Ya , Zhang Renkang , Hu Bing , Zeng Xiaoxiong
Published: March 2016

The effects of several parameters on the extraction yield of total polyphenols from grape seeds by pressurized liquid extraction were investigated.
Copper(ii) supported on magnetic chitosan: a green nanocatalyst for the synthesis of 2,4,6-triaryl pyridines by C–N bond cleavage of benzylamines
Authors: Shaabani Ahmad , Borjian Boroujeni Mahmoud , Laeini Mohmmad Sadegh
Published: March 2016

In this paper, Cu/magnetic chitosan has been synthesized and used as a new green nanocatalyst for highly efficient synthesis of 2,4,6-triaryl pyridines via C–N bond cleavage of benzylamines under aerobic oxidation at 90 °C.
A high-voltage poly(methylethyl α-cyanoacrylate) composite polymer electrolyte for 5 V lithium batteries
Authors: Chai Jingchao , Zhang Jianjun , Hu Pu , Ma Jun , Du Huiping , Yue Liping , Zhao Jianghui , Wen Huijie , Liu Zhihong , Cui Guanglei , Chen Liquan
Published: March 2016

A polytetrafluoroethylene supported poly(methylethyl α-cyanoacrylate) with high ionic conductivity and excellent electrochemical stability is developed for high-voltage LiNi0.5Mn1.5O4/Li battery.
Cross‐connection abatement in dense loosely coupled wireless charging pad environments
Authors: Kim Nam Yoon , Yoon Sang‐Woong , Kim Chang‐Woo
Published: March 2016

In a dense environment of loosely‐coupled wireless charging pads to which out‐of‐band signalling is applied, cross‐connection errors occur according to the wireless communication distance of out‐of‐band signalling. A cross‐connect abatement technique using received‐signal‐strength‐indicator measurement is proposed to prevent this problem and to provide stable wireless charging. To evaluate the performance of the proposed technique, two compact wireless charger environments are created in an RF shield room. The experimental results indicate that the wireless charging system using the proposed technology provides wireless charging services without cross‐connection errors.
Interdigitated transducer ammonia sensors based on nanodiamond/polyaniline thin film
Authors: Wu Zuquan , Chen Xiangdong , Tian Xin , Chen Xinpeng , Li Ning , Ding Xing
Published: March 2016

The interdigitated transducers sensor based on nanodiamond (ND)/polyaniline (PANI) thin film for ammonia (NH3) sensing is investigated, which is synthesised by in situ chemical oxidative polymerisation. The experimental result reveals that the response of 30ND/PANI thin film sensor is much higher than that of PANI for NH3 gas detection. The ND is homogeneously combined into PANI to form ND/PANI nanocomposite, which may increase the specific surface area and improve the response of ND/PANI sensor. Moreover, the response mechanism of ND/PANI for NH3 gas detection is discussed. The synthesised thin films are characterised by Fourier transform infrared spectroscopy and SEM.
Buffer‐aided relaying for the multi‐user uplink: outage analysis and power allocation
Authors: Zhang Bo , Dong Chen , Lei Jing , El‐Hajjar Mohammed , Yang Lie‐Liang , Hanzo Lajos
Published: March 2016

In this study, the authors consider a two‐hop network, where multiple source nodes (SNs) transmit to a destination node (DN) with the aid of a relay node (RN). The RN is equipped with a buffer, which is capable of storing multiple frames received from the SNs. During each time slot, the proposed protocol activates either the SN–RN hop or the RN–DN hop, depending on the channel quality of each hop and the buffer state at the RN. To optimise the hop activation for the network, they design a hop quality metric and propose a multi‐user buffer‐aided‐relaying uplink (MU‐BR‐UL) protocol, with the aid of the minimum signal‐to‐noise power ratio approximation. The benefits of the proposed protocol are analysed in terms of the end‐to‐end (e2e) outage probability and the e2e transmission delay. Then, the optimal power allocation is proposed for minimising the e2e outage probability under the total power constraint. The results indicate that the outage performance is significantly improved when the proposed power allocation is utilised in the MU‐BR‐UL protocol.
The effect of Argon ion irradiation on the thickness and structure of ultrathin amorphous carbon films
Authors: Xie J. , Komvopoulos K.
Published: March 2016

Carbon films synthesized by plasma-enhanced chemical vapor deposition (PECVD) and filtered cathodic vacuum arc (FCVA) exhibit a layered structure consisting of a bottom (interface) and a top (surface) layer rich in sp2 atomic carbon bonding and a middle (bulk) layer of much higher sp3 content. Because of significant differences in the composition, structure, and thickness of these layers, decreasing the film thickness may negatively affect its properties. In this study, transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS) were used to examine the effect of Ar+ ion irradiation on the structure and thickness of ultrathin films of hydrogenated amorphous carbon (a-C:H) and hydrogen-free amorphous carbon (a-C) deposited by PECVD and FCVA, respectively. The TEM and EELS results show that 2-min ion irradiation decreases the film thickness without markedly changing the film structure and composition, whereas 4-min ion irradiation results in significant film thinning and a moderate decrease of the sp3 content of the bulk layer. This study demonstrates that Ar+ ion irradiation is an effective post-deposition process for reducing the thickness and tuning the structure of ultrathin carbon films. This capability has direct implications in the synthesis of ultrathin protective carbon overcoats for extremely high-density magnetic recording applications.
Onset of normal and inverse homoclinic bifurcation in a double plasma system near a plasma fireball
Authors: Mitra Vramori , Sarma Bornali , Sarma Arun , Janaki M. S. , Sekar Iyengar A. N.
Published: March 2016

Plasma fireballs are generated due to a localized discharge and appear as a luminous glow with a sharp boundary, which suggests the presence of a localized electric field such as electrical sheath or double layer structure. The present work reports the observation of normal and inverse homoclinic bifurcation phenomena in plasma oscillations that are excited in the presence of fireball in a double plasma device. The controlling parameters for these observations are the ratio of target to source chamber (nT/nS) densities and applied electrode voltage. Homoclinic bifurcation is noticed in the plasma potential fluctuations as the system evolves from narrow to long time period oscillations and vice versa with the change of control parameter. The dynamical transition in plasma fireball is demonstrated by spectral analysis, recurrence quantification analysis (RQA), and statistical measures, viz., skewness and kurtosis. The increasing trend of normalized variance reflects that enhancing nT/nS induces irregularity in plasma dynamics. The exponential growth of the time period is strongly indicative of homoclinic bifurcation in the system. The gradual decrease of skewness and increase of kurtosis with the increase of nT/nS also reflect growing complexity in the system. The visual change of recurrence plot and gradual enhancement of RQA variables DET, Lmax, and ENT reflects the bifurcation behavior in the dynamics. The combination of RQA and spectral analysis is a clear evidence that homoclinic bifurcation occurs due to the presence of plasma fireball with different density ratios. However, inverse bifurcation takes place due to the change of fireball voltage. Some of the features observed in the experiment are consistent with a model that describes the dynamics of ionization instabilities.
Effects of ionization and ion loss on dust ion-acoustic solitary waves in a collisional dusty plasma with suprathermal electrons
Authors: Mayout Saliha , Gougam Leila Ait , Tribeche Mouloud
Published: March 2016

The combined effects of ionization, ion loss, and electron suprathermality on dust ion-acoustic solitary waves in a collisional dusty plasma are examined. Carrying out a small but finite amplitude analysis, a damped Korteweg-de Vries (dK–dV) equation is derived. The damping term decreases with the increase of the spectral index and saturates for Maxwellian electrons. Choosing typical plasma parameters, the analytical approximate solution of the dK-dV equation is numerically analyzed. We first neglect the ionization and ion loss effects and account only for collisions to estimate the relative importance between these damping terms which can act concurrently. Interestingly, we found that as the suprathermal character of the electrons becomes important, the strength of the collisions related dissipation becomes more important and causes the dust ion-acoustic solitary wave amplitude to decay more rapidly. Moreover, the collisional damping may largely prevail over the ionization and ion loss related damping. The latter becomes more effective as the electrons evolve far away from their thermal equilibrium. Our results complement and provide new insights into previously published work on this problem.
Walleye Foraging Ecology in an Interconnected Chain of Lakes Influenced by Nonnative Species
Authors: Herbst Seth J. , Roth Brian M. , Hayes Daniel B. , Stockwell Jason D.
Published: March 2016

The Laurentian Great Lakes are a source of nonnative species for smaller inland lakes throughout the region; however, the foraging ecology of predators in smaller systems invaded by nonnative species has not been well studied. We used diet and stable isotope analyses to describe the contributions of native and nonnative forage species to the diets of Walleyes Sander vitreus within an inland lake chain invaded by multiple nonnative species. Our hypothesis was that the Walleyes' diet would be associated with the relative amount of prey available in littoral or offshore–pelagic habitats and would ultimately be linked to the dominant habitat type. We found that Walleyes in the study lakes exhibited flexibility in their dietary inclusion of nonnative prey species. Similar to predators in the Laurentian Great Lakes, Walleyes in smaller inland lakes integrated littoral nonnative species into their diets. However, Walleyes unexpectedly showed limited usage of accessible nonnative pelagic forage. We suggest that predator responses to species introductions are likely context dependent and warrant further investigation in multiple systems and with multiple predators to determine the full extent of nonnative species' integration into the food web and their influence on native populations.

Received June 27, 2015; accepted November 2, 2015
Secondary metabolites in plants: transport and self-tolerance mechanisms
Authors: Shitan Nobukazu
Published: March 2016

Plants produce a host of secondary metabolites with a wide range of biological activities, including potential toxicity to eukaryotic cells. Plants generally manage these compounds by transport to the apoplast or specific organelles such as the vacuole, or other self-tolerance mechanisms. For efficient production of such bioactive compounds in plants or microbes, transport and self-tolerance mechanisms should function cooperatively with the corresponding biosynthetic enzymes. Intensive studies have identified and characterized the proteins responsible for transport and self-tolerance. In particular, many transporters have been isolated and their physiological functions have been proposed. This review describes recent progress in studies of transport and self-tolerance and provides an updated inventory of transporters according to their substrates. Application of such knowledge to synthetic biology might enable efficient production of valuable secondary metabolites in the future.
Powerful decomposition of complex traits in a diploid model using Phased Outbred Lines
Authors: Hallin Johan , Märtens Kaspar , Young Alexander I. , Zackrisson Martin , Salinas Francisco , Parts Leopold , Warringer Jonas , Liti Gianni
Published: March 2016

Explaining trait differences between individuals is a core but challenging aim of life sciences. Here, we introduce a powerful framework for complete decomposition of trait variation into its underlying genetic causes in diploid model organisms. We intercross two natural genomes over many sexual generations, sequence and systematically pair the recombinant gametes into a large array of diploid hybrids with fully assembled and phased genomes, termed Phased Outbred Lines (POLs). We demonstrate the capacity of the framework by partitioning fitness traits of 7310 yeast POLs across many environments, achieving near complete trait heritability (meanH2= 91%) and precisely estimating additive (74%), dominance (8%), second (9%) and third (1.8%) order epistasis components. We found nonadditive quantitative trait loci (QTLs) to outnumber (3:1) but to be weaker than additive loci; dominant contributions to heterosis to outnumber overdominant (3:1); and pleiotropy to be the rule rather than the exception. The POL approach presented here offers the most complete decomposition of diploid traits to date and can be adapted to most model organisms.
Environmental gene regulatory influence networks in rice (Oryza sativa):response to water deficit, high temperature and agricultural environments
Authors: Wilkins Olivia , Hafemeister Christoph , Plessis Anne , Holloway-Phillips Meisha-Marika , Pham Gina M. , Nicotra Adrienne B. , Gregorio Glenn B. , Jagadish S.V. Krishna , Septiningsih Endang M. , Bonneau Richard , Purugganan Michael
Published: March 2016

Environmental Gene Regulatory Influence Networks (EGRINs) coordinate the timing and rate of gene expression in response to environmental and developmental signals. EGRINs encompass many layers of regulation, which culminate in changes in the level of accumulated transcripts. Here we infer EGRINs for the response of five tropical Asian rice cultivars to high temperatures, water deficit, and agricultural field conditions, by systematically integrating time series transcriptome data (720 RNA-seq libraries), patterns of nucleosome-free chromatin (18 ATAC-seq libraries), and the occurrence of known cis-regulatory elements. First, we identify 5,447 putative target genes for 445 transcription factors (TFs) by connecting TFs with genes with known cis-regulatory motifs in nucleosome-free chromatin regions proximal to transcriptional start sites (TSS) of genes. We then use network component analysis to estimate the regulatory activity for these TFs from the expression of these putative target genes. Finally, we inferred an EGRIN using the estimated TFA as the regulator. The EGRIN included regulatory interactions between 4,052 target genes regulated by 113 TFs. We resolved distinct regulatory roles for members of a large TF family, including a putative regulatory connection between abiotic stress and the circadian clock, as well as specific regulatory functions for TFs in the drought response. TFA estimation using network component analysis is an effective way of incorporating multiple genome-scale measurements into network inference and that supplementing data from controlled experimental conditions with data from outdoor field conditions increases the resolution for EGRIN inference.
SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export
Authors: Müller-McNicoll Michaela , Botti Valentina , de Jesus Domingues Antonio M. , Brandl Holger , Schwich Oliver D. , Steiner Michaela C. , Curk Tomaz , Poser Ina , Zarnack Kathi , Neugebauer Karla M.
Published: March 2016

Nuclear export factor 1 (NXF1) exports mRNA to the cytoplasm after recruitment to mRNA by specific adaptor proteins. How and why cells use numerous different export adaptors is poorly understood. Here we critically evaluate members of the SR protein family (SRSF1–7) for their potential to act as NXF1 adaptors that couple pre-mRNA processing to mRNA export. Consistent with this proposal, >1000 endogenous mRNAs required individual SR proteins for nuclear export in vivo. To address the mechanism, transcriptome-wide RNA-binding profiles of NXF1 and SRSF1–7 were determined in parallel by individual-nucleotide-resolution UV cross-linking and immunoprecipitation (iCLIP). Quantitative comparisons of RNA-binding sites showed that NXF1 and SR proteins bind mRNA targets at adjacent sites, indicative of cobinding. SRSF3 emerged as the most potent NXF1 adaptor, conferring sequence specificity to RNA binding by NXF1 in last exons. Interestingly, SRSF3 and SRSF7 were shown to bind different sites in last exons and regulate 3′ untranslated region length in an opposing manner. Both SRSF3 and SRSF7 promoted NXF1 recruitment to mRNA. Thus, SRSF3 and SRSF7 couple alternative splicing and polyadenylation to NXF1-mediated mRNA export, thereby controlling the cytoplasmic abundance of transcripts with alternative 3′ ends.
Mechanisms of metabolic dysfunction in cancer-associated cachexia
Authors: Petruzzelli Michele , Wagner Erwin F.
Published: March 2016

Metabolic dysfunction contributes to the clinical deterioration observed in advanced cancer patients and is characterized by weight loss, skeletal muscle wasting, and atrophy of the adipose tissue. This systemic syndrome, termed cancer-associated cachexia (CAC), is a major cause of morbidity and mortality. While once attributed solely to decreased food intake, the present description of cancer cachexia is a disorder of multiorgan energy imbalance. Here we review the molecules and pathways responsible for metabolic dysfunction in CAC and the ideas that led to the current understanding.
Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs
Authors: Wilk Ronit , Hu Jack , Blotsky Dmitry , Krause Henry M.
Published: March 2016

In a previous analysis of 2300 mRNAs via whole-mount fluorescent in situ hybridization in cellularizing Drosophila embryos, we found that 70% of the transcripts exhibited some form of subcellular localization. To see whether this prevalence is unique to early Drosophila embryos, we examined ∼8000 transcripts over the full course of embryogenesis and ∼800 transcripts in late third instar larval tissues. The numbers and varieties of new subcellular localization patterns are both striking and revealing. In the much larger cells of the third instar larva, virtually all transcripts observed showed subcellular localization in at least one tissue. We also examined the prevalence and variety of localization mechanisms for >100 long noncoding RNAs. All of these were also found to be expressed and subcellularly localized. Thus, subcellular RNA localization appears to be the norm rather than the exception for both coding and noncoding RNAs. These results, which have been annotated and made available on a recompiled database, provide a rich and unique resource for functional gene analyses, some examples of which are provided.
Crystal structure of bis[(acetato-κO)(imidazolidine-2-thione-κS)bis(triphenylphosphane-κP)silver(I)] di-μ-imidazolidine-2-thione-κ4S:S-bis[(imidazolidine-2-thione-κS)bis(triphenylphosphane-κP)silver(I)] diacetate acetonitrile disolvate tetrahydrate
Authors: Nimthong-Roldán Arunpatcha , Ratthiwan Janejira , Lakmas Sawanya , Wattanakanjana Yupa
Published: March 2016

In the title compound, [Ag2(C3H6N2S)4(C18H15P)2](C2H3O2)2·[Ag(C2H3O2)(C3H6N2S)(C18H15P)2]2·2C2H3N·4H2O, the AgIion in the mononuclear neutral complex exhibits a distorted tetrahedral environment with coordination by two P atoms from triphenylphosphane (PPh3) ligands, one S atom of an imidazolidine-2-thione (etu) ligand and one O atom of an acetate anion. The binuclear cationic complex comprises two inversion-related [Ag(C3H6N2S)2(C18H15P)] units with AgIions bridged by two S atoms from etu ligands forming a four-membered Ag–S–Ag–S ring. Each AgIion is coordinated by a P atom of a PPh3ligand, two S atoms of bridging etu ligands and the terminal S atom of an etu ligand in a distorted tetrahedral environment. In the crystal, the mononuclear complex is linked to lattice water molecules through O—H...O and N—H...O hydrogen bonds, forming a chain along [100]. In addition, the binuclear complex molecules are connected to acetate anions and lattice water moleculesviaO—H...O, N—H...O and O—H...S hydrogen bonds, also along [100].
Crystal structure of poly[(4-aminopyridine-κN)(N,N-dimethylformamide-κO)(μ3-pyridine-3,5-dicarboxylato-κ3N:O3:O5)copper(II)]
Authors: Shen Cheng-Chen , Hua Xiu-Ni , Han Lei
Published: March 2016

The title compound, [Cu(C7H3NO4)(C5H6N2)(C3H7NO]n, is an amino-functionalized chiral metal–organic framework with (10,3)-atopology. It has been constructedviathe assembly of the achiral triconnected pyridine-3,5-dicarboxylate (3,5-PDC) building block and a triconnected CuIIatom. Each CuIIion is coordinated by two O atoms and one N atom, respectively, of three crystallographically independent 3,5-PDC ligands. The square-pyramidal (CuN2O3) coordination geometry of the CuIIion is completed by an N atom of a terminal 4-aminopyridine (4-APY) ligand and the O atom of a terminalN,N-dimethylformamide (DMF) ligand to give a triconnected `T'-shaped secondary building unit, which becomes trigonal in the resulting (10,3)-atopology. In the three-dimensional structure, weak N—H...O hydrogen bonds are observed in which the donor N—H groups are provided by the 4-APY ligands and the acceptor O atoms are provided by the non-coordinating carboxylate O atoms of the 3,5-PDC ligands.
Crystal structure of octakis(N,N-dimethylformamide-κO)europium(III) tetracosa-μ2-oxido-dodecaoxido-μ12-phosphato-dodecamolybdate(VI)
Authors: Ghandour Yassine , Hammami Imen , Najmudin Shabir , Bonifácio Cecilia , Belkhiria Mohamed Salah
Published: March 2016

In the title salt, [Eu(C3H7NO)8][PMo12O40], the asymmetric unit comprises one α-Keggin-type [PMo12O40]3−polyoxidometalate anion and one distorted dodecahedral [Eu(C3H7NO)8]3+complex cation. In the crystal, the isolated polyoxidometalate anions are packed into hexagonally arranged rows extending parallel to [001]. The complex cations are situated between the rows and are linked to the neighbouring anions through weak C—H...O hydrogen-bonding interactions, leading to the formation of a three-dimensional network structure.
Crystal structure oftrans-diammine(1,4,8,11-tetraazacyclotetradecane-κ4N)chromium(III) tetrachloridozincate chloride monohydrate from synchrotron data
Authors: Moon Dohyun , Choi Jong-Ha
Published: March 2016

The asymmetric unit of the title complex salt, [Cr(C10H24N4)(NH3)2][ZnCl4]Cl·H2O, is comprised of four halves of the CrIIIcomplex cations (the counterparts being generated by application of inversion symmetry), two tetrachloridozincate anions, two chloride anions and two water molecules. Each CrIIIion is coordinated by the four N atoms of the cyclam (1,4,8,11-tetraazacyclotetradecane) ligand in the equatorial plane and by two N atoms of ammine ligands in axial positions, displaying an overall distorted octahedral coordination environment. The Cr—N(cyclam) bond lengths range from 2.0501 (15) to 2.0615 (15) Å, while the Cr—(NH3) bond lengths range from 2.0976 (13) to 2.1062 (13) Å. The macrocyclic cyclam moieties adopt thetrans-III conformation with six- and five-membered chelate rings in chair andgaucheconformations. The [ZnCl4]2−anions have a slightly distorted tetrahedral shape. In the crystal, the Cl−anions link the complex cations, as well as the solvent water molecules, through N—H...Cl and O—H...Cl hydrogen-bonding interactions. The supramolecular set-up also includes N—H...Cl, C—H...Cl, N—H...O and O—H...Cl hydrogen bonding between N—H or C—H groups of cyclam, ammine N—H and water O—H donor groups, and O atoms of the water molecules, Cl−anions or Cl atoms of the [ZnCl4]2−anions as acceptors, leading to a three-dimensional network structure.
A Mannich base 1-phenyl-3-(1-pyrrolidinyl)-1-propanone: synthesis and performance study on corrosion inhibition for N80 steel in 15% hydrochloric acid
Authors: Pan Yuan , Zhan Fengtao , Lu Zhifeng , Lin Yan , Yang Zhen , Wang Zheng
Published: March 2016

Purpose

– The purpose of this paper is to set out a study of a Mannich base, which was synthesized and used as an acidizing corrosion inhibitor first, and to the corrosion inhibitor mechanism.

Design/methodology/approach

– A Mannich base, 1-phenyl-3-(1-pyrrolidinyl)-propanone (PHPP), was synthesized with acetophenone, pyrrolidine and formaldehyde at pH = approximately 2-3. The structure of PHPP was characterized by elemental analysis and Fourier transform infrared spectroscopy (FTIR). The corrosion inhibition of PHPP on N80 steel in 15 per cent hydrochloric acid (HCl) was studied by weight loss method, scanning electron microscope (SEM) and energy dispersive X-ray analysis (EDAX), and the adsorption behavior of PHPP on the surface of N80 steel was discussed.

Findings

– The results showed that the inhibition efficiency reached to 99.8 per cent and corrosion rate was 2.65 gÂ·m-2Â·h-1 at 0.6 per cent of PHPP concentration in 15 per cent HCl, which indicated that PHPP presented excellent corrosion inhibition performance. The results of SEM and EDAX analysis showed that PHPP could be absorbed on the surface of N80 steel. The adsorption process of PHPP on the surface of N80 steel was chemisorption. This process was spontaneous and obeyed Langmuir adsorption isotherm.

Originality/value

– It was found that PHPP presented excellent corrosion inhibition performance, and it is practicable to enhance oil production in oilfield development as a oil-well acidizing inhibitor. The study results can provide theoretical guidelines for the development of the inhibitor.
Perceived discrimination against immigrants in the workplace
Authors: Enoksen Elisabeth
Published: March 2016

Purpose

– The purpose of this paper is to examine how perceptions of organizational justice and social-focussed personal values influence perceived discrimination against immigrants in the workplace.

Design/methodology/approach

– A sample of 224 employees of a mental health clinic in Norway completed Schwartz’s Portrait Values Questionnaire that measures personal values, Colquitt’s Organizational Justice Scale, and scale measuring perceived discrimination against immigrant in the workplace.

Findings

– Perceived organizational justice and the social-focussed value universalism contributed significantly in explaining variance in perceived discrimination against immigrants in the workplace. Employees who scored low on perceived organizational justice scored high on perceived discrimination against immigrants, and employees who scored high on the value universalism scored high on perceived discrimination against immigrants in the workplace.

Research limitations/implications

– The cross-sectional design cannot determine causality. The direction of the relationship between the variables is founded on prevailing empirical and theoretical contributions in the field.

Practical implications

– Cultural diversity training programs should make employees aware of how their personal values and personal justice experiences influence their perceptions of discrimination against immigrants. Culturally diverse workplaces could benefit from recruiting employees who emphasize universalism.

Originality/value

– Co-workers’ perception of exclusion and discriminating behavior against immigrants in the workplace is critical in order to reduce such unjust treatment. There is limited research on factors that influence perceptions of discrimination against others.
A voyage of discovery: setting up a recovery college in a secure setting
Authors: Frayn Elizabeth , Duke Joanna , Smith Helen , Wayne Philip , Roberts Glenn
Published: March 2016

Purpose

– The potential transformative role of recovery colleges is well-documented in community mental health settings. The purpose of this paper is to reproduce the principles of the recovery college approach in a forensic setting in Devon.

Design/methodology/approach

– This paper describes the inaugural two-year development process, from ideas to a functioning service, accessible to patients in both medium secure, low and open settings on the Langdon hospital site, drawing on qualitative accounts from staff and service users involved.

Findings

– Creating and maintaining an educational space within the forensic environment where people have real choices to learn and work on their recovery is possible and valued by service users and clinicians alike.

Originality/value

– Langdon was one of the first forensic hospitals in the UK to introduce a recovery college, and the report of the positive impact and challenges involved may be useful to others setting out on this journey.
Functionally graded carbon nanotube and nafion/silica nanofibre for electrical actuation of carbon fibre reinforced shape memory polymer
Authors: Lu Haibao , Yao Yongtao , Yin Jinying  , Lin Long
Published: March 2016

Purpose

– This paper aims to study the synergistic effect of self-assembled carboxylic acid-functionalised carbon nanotube (CNT) and nafion/silica nanofibre nanopaper on the electro-activated shape memory effect (SME) and shape recovery behaviour of shape memory polymer (SMP) nanocomposite.

Design/methodology/approach

– Carboxylic acid-functionalised CNT and nafion/silica nanofibre are first self-assembled onto carbon fibre by means of deposition and electrospinning approaches, respectively, to form functionally graded nanopaper. The combination of carbon fibre and CNT is introduced to enable the actuation of the SME in SMP by means of Joule heating at a low electric voltage of 3.0-5.0 V.

Findings

– Nafion/silica nanofibre is used to improve the shape recovery behaviour and performance of the SMP for enhanced heat transfer and electrical actuation effectiveness. Low electrical voltage actuation and high electrical actuation effectiveness of 32.5 per cent in SMP has been achieved.

Research limitations/implications

– A simple way for fabricating electro-activated SMP nanocomposites has been developed by using functionally graded CNT and nafion/silica nanofibre nanopaper.

Originality/value

– The outcome of this study will help to fabricate the SMP composite with high electrical actuation effectiveness under low electrical voltage actuation.