bluuebunny/crossref_metadata_2025 huggingface dataset:
An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.)
Authors: Parween Sabiha , Nawaz Kashif , Roy Riti , Pole Anil K. , Venkata Suresh B. , Misra Gopal , Jain Mukesh , Yadav Gitanjali , Parida Swarup K. , Tyagi Akhilesh K. , Bhatia Sabhyata , Chattopadhyay Debasis
Published: August 2015

Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.
UV-responsive nano-sponge for oil absorption and desorption
Authors: Kim Do Hyun , Jung Min Chan , Cho So-Hye , Kim Sang Hoon , Kim Ho-Young , Lee Heon Ju , Oh Kyu Hwan , Moon Myoung-Woon
Published: August 2015

Controlled surface wettability for oil has been intensively studied to remove industrial oil waste or oil spill pollution from seas or rivers. In particular, external stimuli-induced special wetting materials, such as photo-responsive TiO2, have attracted considerable attention for oil-water separation. In this study, a novel method is reported to fabricate a nano-sponge which is composed of hydrophobic hydrocarbon and hydrophilic TiO2 nanoparticles for oil absorption or desorption that are responsive to UV irradiation. The hydrocarbon in the nano-sponge could selectively absorb oil from water, whereas the absorbed oil is released into the water by TiO2 in response to UV irradiation. The nano-sponge functionalized porous polydimethylsiloxane released more than 98% of the absorbed crude oil with UV irradiation and air-bubbling. It could be continuously reused while maintaining a high absorption capacity and desorption efficiency without incurring secondary air or water pollution. This smart oil absorption/desorption methodology with excellent selectivity and recyclability with almost perfect removal of absorbed oil can be applied for oil-water separation, oil spill cleanup and reuse of spilled oil.
Effect of Support on the Activity of Ag-based Catalysts for Formaldehyde Oxidation
Authors: Zhang Jianghao , Li Yaobin , Zhang Yan , Chen Min , Wang Lian , Zhang Changbin , He Hong
Published: August 2015

Ag-based catalysts with different supports (TiO2, Al2O3 and CeO2) were prepared by impregnation method and subsequently tested for the catalytic oxidation of formaldehyde (HCHO) at low temperature. The Ag/TiO2 catalyst showed the distinctive catalytic performance, achieving the complete HCHO conversion at around 95 °C. In contrast, the Ag/Al2O3 and Ag/CeO2 catalysts displayed much lower activity and the 100% conversion was reached at 110 °C and higher than 125 °C, respectively. The Ag-based catalysts were next characterized by several methods. The characterization results revealed that supports have the dramatic influence on the Ag particle sizes and dispersion. Kinetic tests showed that the Ag based catalyst on the TiO2, Al2O3 or CeO2 supports have the similar apparent activation energy of 65 kJ mol−1, indicating that the catalytic mechanism keep immutability over these three catalysts. Therefore, Ag particle size and dispersion was confirmed to be the main factor affecting the catalytic performance for HCHO oxidation. The Ag/TiO2 catalyst has the highest Ag dispersion and the smallest Ag particle size, accordingly presenting the best catalytic performance for HCHO oxidation.
Automated biphasic morphological assessment of hepatitis B-related liver fibrosis using second harmonic generation microscopy
Authors: Wang Tong-Hong , Chen Tse-Ching , Teng Xiao , Liang Kung-Hao , Yeh Chau-Ting
Published: August 2015

Liver fibrosis assessment by biopsy and conventional staining scores is based on histopathological criteria. Variations in sample preparation and the use of semi-quantitative histopathological methods commonly result in discrepancies between medical centers. Thus, minor changes in liver fibrosis might be overlooked in multi-center clinical trials, leading to statistically non-significant data. Here, we developed a computer-assisted, fully automated, staining-free method for hepatitis B-related liver fibrosis assessment. In total, 175 liver biopsies were divided into training (n = 105) and verification (n = 70) cohorts. Collagen was observed using second harmonic generation (SHG) microscopy without prior staining and hepatocyte morphology was recorded using two-photon excitation fluorescence (TPEF) microscopy. The training cohort was utilized to establish a quantification algorithm. Eleven of 19 computer-recognizable SHG/TPEF microscopic morphological features were significantly correlated with the ISHAK fibrosis stages (P < 0.001). A biphasic scoring method was applied, combining support vector machine and multivariate generalized linear models to assess the early and late stages of fibrosis, respectively, based on these parameters. The verification cohort was used to verify the scoring method and the area under the receiver operating characteristic curve was >0.82 for liver cirrhosis detection. Since no subjective gradings are needed, interobserver discrepancies could be avoided using this fully automated method.
Scale-dependency of the global mean surface temperature trend and its implication for the recent hiatus of global warming
Authors: Lin Yong , Franzke Christian L. E.
Published: August 2015

Studies of the global mean surface temperature trend are typically conducted at a single (usually annual or decadal) time scale. The used scale does not necessarily correspond to the intrinsic scales of the natural temperature variability. This scale mismatch complicates the separation of externally forced temperature trends from natural temperature fluctuations. The hiatus of global warming since 1999 has been claimed to show that human activities play only a minor role in global warming. Most likely this claim is wrong due to the inadequate consideration of the scale-dependency in the global surface temperature (GST) evolution. Here we show that the variability and trend of the global mean surface temperature anomalies (GSTA) from January 1850 to December 2013, which incorporate both land and sea surface data, is scale-dependent and that the recent hiatus of global warming is mainly related to natural long-term oscillations. These results provide a possible explanation of the recent hiatus of global warming and suggest that the hiatus is only temporary.
Glutathione Decrement Drives Thermogenic Program In Adipose Cells
Authors: Lettieri Barbato Daniele , Tatulli Giuseppe , Maria Cannata Stefano , Bernardini Sergio , Aquilano Katia , Ciriolo Maria R.
Published: August 2015

Adipose tissue metabolically adapts to external stimuli. We demonstrate that the induction of the thermogenic program in white adipocytes, through cold exposure in mice or in vitro adrenergic stimulation, is accompanied by a decrease in the intracellular content of glutathione (GSH). Moreover, the treatment with a GSH depleting agent, buthionine sulfoximine (BSO), recapitulates the effect of cold exposure resulting in the induction of thermogenic program. In particular, BSO treatment leads to enhanced uncoupling respiration as demonstrated by increased expression of thermogenic genes (e.g. Ucp1, Ppargc1a), augmented oxygen consumption and decreased mitochondrial transmembrane potential. Buffering GSH decrement by pre-treatment with GSH ester prevents the up-regulation of typical markers of uncoupling respiration. We demonstrate that FoxO1 activation is responsible for the conversion of white adipocytes into a brown phenotype as the “browning” effects of BSO are completely abrogated in cells down-regulating FoxO1. In mice, the BSO-mediated up-regulation of uncoupling genes results in weight loss that is at least in part ascribed to adipose tissue mass reduction. The induction of thermogenic program has been largely proposed to counteract obesity-related diseases. Based on these findings, we propose GSH as a novel therapeutic target to increase energy expenditure in adipocytes.
Bioanalytical and chemical sensors using living taste, olfactory, and neural cells and tissues: a short review
Authors: Wu Chunsheng , Lillehoj Peter B. , Wang Ping
Published: August 2015

This review summarizes the state of the art in taste, olfactory, and neural tissue- and cell-based biosensors.
Development and validation of a modified QuEChERS method based on magnetic zirconium dioxide microspheres for the determination of 52 pesticides in oil crops by gas chromatography tandem mass spectrometry
Authors: Lu Wei , Peng Xitian , Shen Jing , Hu Xizhou , Peng Lijun , Feng Yuqi
Published: August 2015

A modified QuEChERS method based on magnetic zirconium dioxide microspheres for the determination of 52 pesticides in oil crops is demonstrated.
Polymorphic cross-seeding amyloid assemblies of amyloid-β and human islet amyloid polypeptide
Authors: Zhang Mingzhen , Hu Rundong , Chen Hong , Chang Yung , Ma Jie , Liang Guizhao , Mi Jingyan , Wang Yaru , Zheng Jie
Published: August 2015

Epidemiological studies have shown that the development of Alzheimer's disease (AD) is associated with type 2 diabetes (T2D), but it still remains unclear how AD and T2D are connected.
Specific effects in microwave chemistry explored through reactor vessel design, theory, and spectroscopy
Authors: Ashley Bridgett , Lovingood Derek D. , Chiu Yu-Che , Gao Hanwei , Owens Jeffery , Strouse Geoffrey F.
Published: August 2015

The interaction of microwave photons is directly measured using dielectric spectroscopy and heating rates for improved understanding of MW chemistry.
Miniaturized optogenetic neural implants: a review
Authors: Fan B. , Li W.
Published: August 2015

This article reviews recent developments in miniaturized neural implants for optogenetics, highlights major improvements enabled by microtechnologies, and discusses challenges faced by developers and adopters of these new technologies.
Structural design for anodes of lithium-ion batteries: emerging horizons from materials to electrodes
Authors: Zhong Yiren , Yang Mei , Zhou Xianlong , Zhou Zhen
Published: August 2015

We highlight burgeoning design horizons from materials to electrodes to push energy storage in Li ion batteries to next-generation levels.
Application of the energetic span model to the electrochemical catalysis of proton reduction by a diiron azadithiolate complex
Authors: Bourrez Marc , Gloaguen Frederic
Published: August 2015

A method for the computation of TOF of catalysis of electrochemical reaction as a function of the potential was developed.
Self-assembled material of palladium nanoparticles and a thiacalix[4]arene Cd(ii) complex as an efficient catalyst for nitro-phenol reduction
Authors: Rambabu Darsi , Pradeep Chullikkattil P. , Pooja Pooja , Dhir Abhimanew
Published: August 2015

A cadmium complex based on the thiacalix[4]arene scaffold is utilized to synthesize a material with palladium nanoparticles, which behaves as an efficient catalyst for the conversion of 4-nitrophenol to 4-aminophenol.
A facile photoluminescence modulated nanosensor based on nitrogen-doped graphene quantum dots for sulfite detection
Authors: Chen Shufan , Song Yu , Li Yang , Liu Yunling , Su Xingguang , Ma Qiang
Published: August 2015

Sulfite is detected based on the N-GQDs for the first time and the proposed nanosensor is simple and highly selective.
Investigation of a deep eutectic solvent formed by levulinic acid with quaternary ammonium salt as an efficient SO2 absorbent
Authors: Deng Dongshun , Han Guoqiang , Jiang Yaotai
Published: August 2015

Six new deep eutectic solvents with good absorption and separation performance for SO2 were developed.
Pyrenyl-functionalized ferrocenes for multisignaling recognition of anions
Authors: Zhou Li , Fan Xiang-Tian , Xu Yu-Di , Cao Qian-Yong
Published: August 2015

New pyrenyl-functionalized ferrocenes for fluorescence and electrochemical dual sensing of anions in organic solution are introduced.
Nanoscale-alumina induces oxidative stress and accelerates amyloid beta (Aβ) production in ICR female mice
Authors: Shah Shahid Ali , Yoon Gwang Ho , Ahmad Ashfaq , Ullah Faheem , Amin Faiz Ul , Kim Myeong Ok
Published: August 2015

The adverse effects of nanoscale-alumina (Al2O3-NPs) have been previously demonstrated in bothin vitroandin vivostudies, whereas little is known about their mechanism of neurotoxicity.
PRED treatment mediated stable and efficient water oxidation performance of the Fe2O3 nano-coral structure
Authors: Shinde Pravin S. , Lee Hyun Hwi , Lee Su Yong , Lee Young Mi , Jang Jum Suk
Published: August 2015

Herein, we show that an electrochemical surface treatment of Fe foil with pulse reverse electrodeposition (PRED) prior to thermal oxidation can substantially enhance photoelectrochemical stability and water oxidation performance of Fe2O3/Fe photoanodes.
Hybrids of acylated homoserine lactone and nitric oxide donors as inhibitors of quorum sensing and virulence factors in Pseudomonas aeruginosa
Authors: Kutty Samuel K. , Barraud Nicolas , Ho Kitty K. K. , Iskander George M. , Griffith Renate , Rice Scott A. , Bhadbhade Mohan , Willcox Mark D. P. , Black David StC , Kumar Naresh
Published: August 2015

This paper discusses conversion of agonist acylated homoserine lactones (AHL) to antagonist AHLs with dual properties of quorum sensing inhibition and nitric oxide release.
A palladium-catalyzed enantioselective hydroesterification of alkenylphenols with phenyl formate. A facile approach to optically active dihydrocoumarins
Authors: Li Jingfu , Chang Wenju , Ren Wenlong , Liu Wei , Wang Haining , Shi Yian
Published: August 2015

An effective palladium-catalyzed enantioselective hydroesterification of alkenylphenols with phenyl formate as a CO source is described.
The effect of N-methylation of amino acids (Ac-X-OMe) on solubility and conformation: a DFT study
Authors: Md. Abdur Rauf Shah , Arvidsson Per I. , Albericio Fernando , Govender Thavendran , Maguire Glenn E. M. , Kruger Hendrik G. , Honarparvar Bahareh
Published: August 2015

N-Methylation of amino acid derivatives (Ac-X-OMe, X = Gly, Val, Leu, Ile, Phe, Met, Cys, Ser, Asp and His) leads to an increase in aqueous solubility, lipophilicity and lowering of thecis/transamide conformational energy barrier (EA).
Supramolecular polymer networks based on cucurbit[8]uril host–guest interactions as aqueous photo-rheological fluids
Authors: Tan Cindy S. Y. , del Barrio Jesús , Liu Ji , Scherman Oren A.
Published: August 2015

A low-mass fraction (≤0.75 wt%) supramolecular polymer network is fabricated as an aqueous photo-rheological fluid (PRF) via cucurbit[8]uril mediated host–guest interactions. UV irradiation can induce the transition from a highly viscous and rigid gel into a Newtonian-like fluid.
Automated evaluation of the inhibition of glutathione reductase activity: application to the prediction of ionic liquids' toxicity
Authors: Cunha Edite , L. C. Passos Marieta , Pinto Paula C. A. G. , Saraiva M. Lúcia M. F. S.
Published: August 2015

An automated bioassay based on glutathione reductase was developed and applied to the evaluation of the toxicity of ionic liquids.
Synthesis, structure, characterization and theoretical studies of NLO active furan-2-carbohydrazide monohydrate derivative single crystals
Authors: Meenatchi V. , Agilandeshwari R. , Meenakshisundaram SP.
Published: August 2015

Single crystals of (E)-N′-(4-isopropylbenzylidene)furan-2-carbohydrazide monohydrate were grown by the slow evaporation solution growth technique from ethanol at room temperature.
Electrochemical properties of Li2MnO3 nanocrystals synthesized using a hydrothermal method
Authors: Cheng Meng , Tang Weiping , Sun Yi , Zhu Kongjun
Published: August 2015

Li2MnO3 nanocrystals are synthesized with controlled size and morphology via a hydrothermal method with the oxidant KMnO4, controlling the amount of KMnO4 leads to a decrease of grain size from 28.7 nm to 9.8 nm and increased discharge capacities in a linear relationship.
Reactivity of iron-based nanoparticles by green synthesis under various atmospheres and their removal mechanism of methylene blue
Authors: Lin Jiewen , Weng Xiulan , Jin Xiaoying , Megharaj Mallavarapu , Naidu Ravi , Chen Zuliang
Published: August 2015

The reduction degradation pathway of MB molecules.
Green integrated process for mitigation of municipal and industrial liquid and solid waste mixes for enhanced microalgal biomass and lipid synthesis for biodiesel
Authors: Karemore Ankush , Sen Ramkrishna
Published: August 2015

We herein report: a sustainable green integrated process for effective waste mitigation and microalgal biomass production for biodiesel feedstock generation in a biorefinery model.
Enhancing the dielectric properties of highly compatible new polyimide/γ-ray irradiated MWCNT nanocomposites
Authors: Akhter Toheed , Mun Sung Cik , Saeed Shaukat , Park O. Ok , Siddiqi Humaira Masood
Published: August 2015

Novel polyimide/γ-ray irradiated MWCNT (PI/γ-MWCNT) nanocomposites with improved dielectric properties were fabricated by casting and curing processes.
Enhanced electrochemical performance of barium hexaferrite nanoplates by Zn2+ doping serving as anode materials
Authors: Hu Chenxi , Qiu Song , Lu Guixia , Cao Huili , Lv Hailong , Guo Shimei , Liu Jiurong
Published: August 2015

The Zn2+-doped BaFe12O19 nanoplates synthesized by a facile approach exhibit superior cycling performances as anode material, attributing to the Zn2+ doping.
A cell-penetrating protein designed for bimodal fluorescence and magnetic resonance imaging
Authors: Wu Qin , Cheng Qinqin , Yuan Siming , Qian Junchao , Zhong Kai , Qian Yinfeng , Liu Yangzhong
Published: August 2015

A protein-based fluorescence and magnetic resonance bimodal imaging probe was explored in vitro, in cells and in mice.
Towards accurate prediction of catalytic activity in IrO2 nanoclusters via first principles-based variable charge force field
Authors: Sen F. G. , Kinaci A. , Narayanan B. , Gray S. K. , Davis M. J. , Sankaranarayanan S. K. R. S. , Chan M. K. Y.
Published: August 2015

DFT-based variable-charge force field (MS-Q) developed to accurately predicted bulk and nanoscale properties of IrO2. Catalytic properties pertaining to oxygen reduction reaction found to depend on the coordination and charge transfer at the IrO2 nanocluster surface.
Draining the photoinduced electrons away from an anode: the preparation of Ag/Ag3PO4 composite nanoplate photoanodes for highly efficient water splitting
Authors: Wu Qingyong , Diao Peng , Sun Jie , Xu Di , Jin Tao , Xiang Min
Published: August 2015

Ag/Ag3PO4 composite photoanodes based on vertically aligned Ag nanoplates exhibited high activity and stability toward photoelectrochemical oxygen evolution reaction.
Elucidating the origins of phase transformation hysteresis during electrochemical cycling of Li–Sb electrodes
Authors: Chang Donghee , Huo Hua , Johnston Karen E. , Ménétrier Michel , Monconduit Laure , Grey Clare P. , Van der Ven Anton
Published: August 2015

In this combined computational and experimental study, we identify the origins of phase transformation hysteresis during cycling of Sb electrodes, which undergoes alloying reactions upon lithiation.
Tunable controlled release of bioactive SDF-1α via specific protein interactions within fibrin/nanoparticle composites
Authors: Dutta D. , Fauer C. , Mulleneux H. L. , Stabenfeldt S. E.
Published: August 2015

Control over burst release from SDF-1α-loaded PLGA nanoparticles when embedded in varying densities of fibrin matrices using specific protein/protein interactions.
4-Diphenylamino-phenyl substituted pyrazine: nonlinear optical switching by protonation
Authors: Xu Liang , Zhu Hai , Long Guankui , Zhao Jun , Li Dongsheng , Ganguly Rakesh , Li Yongxin , Xu Qing-Hua , Zhang Qichun
Published: August 2015

A series of novel pyrazine–triphenylamine fused structures have been synthesized and the nonlinear optical absorptions of these compounds can be overturned by the protonation.
Key mechanisms involved in ionizing radiation-induced systemic effects. A current review
Authors: Mavragani Ifigeneia V. , Laskaratou Danae A. , Frey Benjamin , Candéias Serge M. , Gaipl Udo S. , Lumniczky Katalin , Georgakilas Alexandros G.
Published: August 2015

Organisms respond to physical, chemical and biological threats by a potent inflammatory response, aimed at preserving tissue integrity and restoring tissue homeostasis and function. Systemic effects in an organism refer to an effect or phenomenon which originates at a specific point and can spread throughout the body affecting a group of organs or tissues. Ionizing radiation (IR)-induced systemic effects arise usually from a local exposure of an organ or part of the body. This stress induces a variety of responses in the irradiated cells/tissues, initiated by the DNA damage response and DNA repair (DDR/R), apoptosis or immune response, including inflammation. Activation of this IR-response (IRR) system, especially at the organism level, consists of several subsystems and exerts a variety of targeted and non-targeted effects. Based on the above, we believe that in order to understand this complex response system better one should follow a ‘holistic’ approach including all possible mechanisms and at all organization levels. In this review, we describe the current status of knowledge on the topic, as well as the key molecules and main mechanisms involved in the ‘spreading’ of the message throughout the body or cells. Last but not least, we discuss the danger-signal mediated systemic immune effects of radiotherapy for the clinical setup.
Circadian timekeeping in Neurospora crassa and Synechococcus elongatus
Authors: Crosthwaite Susan K
Published: August 2015

At first, the saprophytic eukaryote Neurospora crassa and the photosynthetic prokaryote Synechococcus elongatus may seem to have little in common. However, in both organisms a circadian clock organizes cellular biochemistry, and each organism lends itself to classical and molecular genetic investigations that have revealed a detailed picture of the molecular basis of circadian rhythmicity. In the present chapter, an overview of the molecular clockwork in each organism will be described, highlighting similarities, differences and some as yet unexplained phenomena.
The ways of a killer: how does Entamoeba histolytica elicit host cell death?
Authors: Ralston Katherine S. , Petri William A.
Published: August 2015

Entamoeba histolytica is the causative agent of amoebiasis in humans and is responsible for an estimated 100 000 deaths annually, making it the second leading cause of death due to a protozoan parasite after Plasmodium. Pathogenesis appears to result from the potent cytotoxic activity of the parasite, which kills host cells within minutes. The mechanism is unknown, but progress has been made in determining that cytotoxicity requires parasite Gal (galactose)/GalNAc (N-acetylgalactosamine) lectin-mediated adherence, target cell calcium influx, dephosphorylation and activation of caspase 3. Putative cytotoxic effector proteins such as amoebapores, proteases and various parasite membrane proteins have also been identified. Nonetheless the bona fide cytotoxic effector molecules remain unknown and it is unclear how the lethal hit is delivered. To better understand the basic mechanism of pathogenesis and to enable the development of new therapeutics, more work will be needed in order to determine how the parasite elicits host cell death.
Intracellular low molecular weight iron
Authors: DEIGHTON N. , HIDER R. C.
Published: August 2015

Summary

A low molecular weight complex of an iron oligomer (Mr ~ 1000) has been isolated from rat liver and characterized physically and chemically. The h.p.l.c.-purified material contains the free amino acids glutamate and aspartate. Chemical techniques suggest the iron present in the factor is as iron(III) and is readily donated to high-affinity chelators such as the hydroxypyridinones and desferoxamine.
The antioxidant hypothesis of cardiovascular disease: epidemiology and mechanisms
Authors: GEY K. FRED
Published: August 2015

Summary

Plasma levels of major essential antioxidants were determined in representative random samples of middleaged men from 16 European study populations which differed up to 6-fold in age-specific mortality from ischaemic heart disease (IHD). In 12 study populations having total plasma cholesterol in the medium range (5.7–6.2 mmol/1) and usual blood pressure, both these classical risk factors lacked a significant correlation to IHD mortality, whereas the absolute level of vitamin E (α-tocopherol) showed a strong inverse correlation (r2 = 0.63, P = 0.002). On evaluation of all study populations, cholesterol and diastolic blood pressure had a moderate direct association with IHD, but their importance still remained inferior to that of vitamin E as an inversely associated, presumably protective factor. In stepwise regression and multiple regression analysis, the IHD mortality of the study populations was predictable to 62% by lipid-standardized vitamin E, to 79% by vitamin E and total cholesterol, to 83% after inclusion of lipid-standardized vitamin A (retinol) and to 87% by all the above parameters plus diastolic blood pressure. In conclusion, in the present study the plasma status of vitamin E is the most important factor to explain cross-cultural differences of IHD mortality. This finding is consistent with the hypothesis of the prevention of arteriosclerosis by antioxidant protection against peroxidative lipoprotein modification, but does not exclude additional effects of antioxidant vitamins, e.g. on the cellular or immunological level.
Carotenoids, tocopherols and thiols as biological singlet molecular oxygen quenchers
Authors: MASCIO PAOLO Di , DEVASAGAYAM THOMAS P. A. , KAISER STEPHAN , SIES HELMUT
Published: August 2015

Singlet molecular oxygen (1O2) has been shown to be generated in biological systems and is capable of damaging proteins, lipids and DNA. The ability of some biological antioxidants to quench 1O2 was studied by using singlet oxygen generated by the thermodissociation of the endoperoxide of 3,3′-(1,4-naphthylidene) dipropionate (NDPO2). The carotenoid lycopene was the most efficient 1O2 quencher (kq + kr = 31 × 109m-1s-1). Tocopherols and thiols were less effective. The singlet oxygen quenching ability decreased in the following order: lycopene, γ-carotene, astaxanthin, canthaxanthin, α-carotene, β-carotene, bixin, zeaxanthin, lutein, bilirubin, biliverdin, tocopherols and thiols. However, the compounds with low quenching rate constants occur at higher levels in biological tissues. Thus, carotenoids and tocopherols may contribute almost equally to the protection of tissues against the deleterious effects of 1O2. The quenching abilities of carotenoids and tocopherols were mainly due to physical quenching. In case of some thiols chemical quenching also plays a significant role. Carotenoids and tocopherols have been reported to exert a protective action against some types of cancer.
Dielectric-based biosensors
Authors: Pethig Ronald
Published: August 2015

A basic background is given of the concepts and measurements of dielectric phenomena, and two examples of dielectric-based biosensors are described. The way in which the dielectric properties of immobilized urease can be used to monitor the hydrolysis of urea is first outlined, while the second example describes how the phenomenon of dielectrophoresis can be used to monitor the concentration and viability of suspensions of cells or micro-organisms.
The Nrf2 transcription factor contributes both to the basal expression of glutathione S-transferases in mouse liver and to their induction by the chemopreventive synthetic antioxidants, butylated hydroxyanisole and ethoxyquin
Authors: Hayes J. D. , Chanas S. A. , Henderson C.J. , McMahon M. , Sun C. , Moffat G.J. , Wolf C. R. , Yamamoto M.
Published: August 2015

An overview is provided of the cancer chemo-prevention actions of phenolic antioxidants and 6-ethoxy-1,2-dihydro-2,2,4-trimethylquinoline (ethoxyquin). These agents principally appear to exert their beneficial effects through induction of phase II drug-metabolizing enzymes such as glutathione S-transferase (GST). The requirement for oxidative metabolism of the synthetic antioxidants to carbonyl-containing compounds, including quinones, in order that they can induce gene expression is discussed. Previous work has shown that the basic leucine zipper transcription factor Nrf2 is involved in induction of GST by the phenolic antioxidant butylated hydroxyanisole (BHA). Evidence is provided from a mouse possessing a targeted disruption of the Nrf2 gene that, in murine liver, the transcription factor regulates basal expression of several class Alpha and class Mu GST subunits, but not class Pi GST. In the Nrf2 knock-out mouse, hepatic induction of class Alpha and class Mu GST by BHA and the synthetic antioxidant ethoxyquin is similarly impaired, suggesting that these agents affect gene activation by a related mechanism. Significantly, residual induction of GST by antioxidants is apparent in the Nrf2 mutant mouse, indicating the existence of an alternative mechanism of gene activation.
The use of in situ haemoglobin-free perfused liver in metabolic-control analysis
Authors: Soboll S. , Brown G. C.
Published: August 2015

In this study the network of ATP-consuming and -producing reactions, interacting via the cytosolic ATP/ADP + P1 system, was studied for the first time in an intact organ, the isolated perfused rat liver, using top-down metabolic-control analysis. Flux control in the metabolically resting state (only oxidative phosphorylation and ion pumps active) was only in the ATP-consumers, whereas in the metabolically active state (biosyntheses and ion-pumping ATPases active) most control over oxidative phosphorylation was in itself and some control was in ion-pumping ATPases. All ATP-consumers had high control over themselves, and ion-pumping ATPases had high negative control over the other ATP-consuming branches. Oxidative phosphorylation had high positive control over ATP-consuming reactions exept for ion-pumping ATPases. It is concluded that in the active state ATP-consumers compete for cytosolic ATP, but as the ion-pumping ATPases and oxidative phosphorylation are less sensitive towards the cytosolic ATP, other ATP-consumers have low control over these pathways.
The carnitine acyltransferases: modulators of acyl-CoA-dependent reactions
Authors: Ramsay R. R.
Published: August 2015

Carnitine and carnitine acyltransferases were thought to be merely a mechanism for the rapid transfer of activated long-chain fatty acids into the mitochondrion for β-oxidation [1], until enzymologists came along. By kinetic, physical and localization studies, eight different mammalian carnitine acyltransferases have been characterized (reviewed in [2,3]). Of these, five have been cloned and sequenced. The carnitine: acylcarnitine exchange carrier, first characterized in mitochondria [4,5], has now been demonstrated immunologically in peroxisomal membranes too [6]. This cell-wide carnitine system consisting of at least six proteins linking at least four intracellular pools of acyl-CoA that supply a multitude of lipid metabolic pathways is clearly more complex than was first thought. In this article, I describe the location and properties of the components to show how they can modulate acyl-CoA-dependent reactions in the cell.
Recombinant expression systems for the production of collagen
Authors: Bulleid N. J. , John D. C. A. , Kadler K. E.
Published: August 2015

The ability of triple-helical collagen molecules to assemble into supramolecular structures forms the basis of commercial uses of collagen in the food industry and in medical applications such as cosmetic surgery and tissue repair. We have used cDNA techniques to engineer novel collagens with potentially enhanced biological properties; however, expression of fully functional novel molecules is difficult due to the complex nature of procollagen biosynthesis. This article outlines the application of various expression systems to procollagen production and details the use of the mammary gland as a suitable bioreactor for the synthesis of significant amounts of novel procollagens from cDNA constructs.
Helical repeat of DNA in the nucleosome core particle
Authors: Negri R. , Buttinelli M. , Panetta G. , De Arcangelis V. , Di Mauro E. , Travers A.
Published: August 2015

Although the crystal structure of nucleosome core particle is essentially symmetrical in the vicinity of the dyad, the linker histone binds asymmetrically in this region to select a single high-affinity site from potentially two equivalent sites. To try to resolve this apparent paradox we mapped to base-pair resolution the dyads and rotational settings of nucleosome core particles reassembled on synthetic tandemly repeating 20 bp DNA sequences. In agreement with previous observations, we observed (1) that the helical repeat on each side of the dyad cluster is 10 bp maintaining register with the sequence repeat and (2) that this register changes by 2 bp in the vicinity of the dyad. The additional 2 bp required to effect the change in the rotational settings is accommodated by an adjustment immediately adjacent to the dyad. At the dyad the hydroxyl radical cleavage is asymmetric and we suggest that the inferred structural asymmetry could direct the binding of the linker histone to a single preferred site.
Dynamics of gene targeting and chromatin remodelling by nuclear receptors
Authors: Hager G. L. , Fletcher T. M. , Xiao N. , Baumann C. T. , Müller W. G. , McNally J. G.
Published: August 2015

Activation of the murine-mammary-tumour virus (MMTV) promoter by the glucocorticoid receptor (GR) is associated with a chromatin structural transition in the B nucleosome region of the viral long terminal repeat (LTR). We have reconstituted this nucleoprotein transition with chromatin assembled on MMTV LTR DNA with Drosophila embryo extracts, purified GR, and HeLa nuclear extract. Chromatin remodelling in vitro is ATP-dependent and maps to a region identical with that found in vivo. We demonstrate specific, glucocorticoid response element dependent, binding of purified GR to a large, multi-nucleosome MMTV chromatin array and show that GR-dependent chromatin remodelling is a multistep process. In the absence of ATP, GR binds to multiple sites on the chromatin array and inhibits nuclease access to GR recognition sites. On the addition of ATP, GR induces remodelling resulting in a large increase in access of enzymes to their sites within the transition region. These findings are complemented by studies in living cells; using a tandem array of MMTV-Ras reporter elements and a form of GR labelled with the green fluorescent protein, we have observed direct targeting of the receptor to response elements in live mouse cells. Whereas the ligand-activated receptor is associated with the MMTV promoter for observable periods, photobleaching experiments provide direct evidence that the hormone-occupied receptor undergoes rapid exchange between chromatin and the nucleoplasmic compartment. The results both in vitro and in vivo are consistent with a dynamic model ('hit and run') in which GR first binds to chromatin after ligand activation, recruits a remodelling activity and is then lost from the template.
Cyclic-nucleotide- and Ca2+/calmodulin-regulated channels in plants: targets for manipulating heavy-metal tolerance, and possible physiological roles
Authors: Arazi T. , Kaplan B. , Sunkar R. , Fromm H.
Published: August 2015

Recently we discovered a tobacco protein (designated NtCBP4) that modulates heavy-metal tolerance in transgenic plants. Structurally, NtCBP4 is similar to mammalian cyclic-nucleotide-gated non-selective cation channels containing six putative transmembrane domains, a predicted pore region, a conserved cyclic-nucleotide-binding domain, and a high-affinity calmodulin-binding site that coincides with its cyclic-nucleotide-binding domain. Transgenic tobacco expressing the plasma-membrane-localized NtCBP4 exhibit improved tolerance to Ni2+ and hypersensitivity to Pb2+, which are associated with a decreased accumulation of Ni2+ and an enhanced accumulation of Pb2+ respectively. Transgenic plants expressing a truncated version of NtCBP4, from which regulatory domains had been removed, have a different phenotype. Here we describe our approach to studying the involvement of NtCBP4 in heavy-metal tolerance and to elucidate its physiological role.
Auxin transport: providing a sense of direction during plant development
Authors: Swarup R. , Marchant A. , Bennett M. J.
Published: August 2015

Auxins are key regulators of plant development. Plants employ a specialized delivery system termed polar auxin transport to convey indole-3-acetic acid from source to target tissues. Auxin transport is mediated by the combined activities of specialized influx and efflux carriers. Mutational approaches in the model plant, Arabidopsis thaliana, have led to the molecular genetic characterization of putative auxin influx and efflux carrier components, AUX1 and AtPIN1. Both genes belong to distinct gene families that are being functionally characterized by using a reverse genetic approach in Arabidopsis. AtPIN proteins are asymmetrically localized within plant plasma membranes, providing a molecular mechanism for the characteristic polarity of auxin transport. We outline the epitope tagging strategy being used in our laboratory to immunolocalize AUX1 and discuss the implications of its subcellular localization for auxin redistribution within root apical tissues. Lastly, we describe a novel carrier-based mechanism that plant cells might use to determine their relative position(s) within an auxin gradient, drawing parallels with the mechanism of glucose perception in yeast.
Mechanism of protein import across the chloroplast envelope
Authors: Chen K. , Chen X. , Schnell D. J.
Published: August 2015

The development and maintenance of chloroplasts relies on the contribution of protein subunits from both plastid and nuclear genomes. Most chloroplast proteins are encoded by nuclear genes and are post-translationally imported into the organelle across the double membrane of the chloroplast envelope. Protein import into the chloroplast consists of two essential elements: the specific recognition of the targeting signals (transit sequences) of cytoplasmic preproteins by receptors at the outer envelope membrane and the subsequent translocation of preproteins simultaneously across the double membrane of the envelope. These processes are mediated via the co-ordinate action of protein translocon complexes in the outer (Toe apparatus) and inner (Tic apparatus) envelope membranes.
The polymorphic telomeres of the African trypanosome Trypanosoma brucei
Authors: Rudenko G.
Published: August 2015

African trypanosomes have plastic genomes with extensive variability at the chromosome ends. The genes encoding the expressed major surface protein of the infective bloodstream form stages of Trypanosoma brucei and are located at telomeres. These telomeric expression-site transcription units are turning out to be surprisingly polymorphic in structure and sequence.
Genomics and post-genomics in parasitology: genome babble or a real opportunity?
Authors: Gull K.
Published: August 2015

The genome projects represent one of the most important developments in our knowledge of parasites. However, translation of this knowledge into an understanding of parasite biology and then on to drugs, vaccines and other healthcare developments for the diseases will need some élan and clarity of thought by scientists and funding organizations. Only then will the activity associated with post-genomics be turned from what I have termed ‘genome babble’ to real opportunities in understanding these parasites.
Hairpin and hammerhead ribozymes: how different are they?
Authors: Burke J. M.
Published: August 2015

Recent experimental work on the hairpin and hammerhead ribozymes suggests that they have more similarities than previously suspected. Notably, each is now known to function as a true RNA catalyst, not requiring metal ions for folding or catalytic function. The active conformation of the hairpin ribozyme has been established by crystallography, and is well supported by biochemical and biophysical evidence that has identified conformational changes and key nucleotides required for catalysis. Analogous work is under way to establish the active structure of the hammerhead ribozyme.
Specific protein–lipid interactions in membrane proteins
Authors: Hunte C.
Published: August 2015

Many membrane proteins selectively bind defined lipid species. This specificity has an impact on correct insertion, folding, structural integrity and full functionality of the protein. How are these different tasks achieved? Recent advances in structural research of membrane proteins provide new information about specific protein–lipid interactions. Tightly bound lipids in membrane protein structures are described and general principles of the binding interactions are deduced. Lipid binding is stabilized by multiple non-covalent interactions from protein residues to lipid head groups and hydrophobic tails. Distinct lipid-binding motifs have been identified for lipids with defined head groups in membrane protein structures. The stabilizing interactions differ between the electropositive and electronegative membrane sides. The importance of lipid binding for vertical positioning and tight integration of proteins in the membrane, for assembly and stabilization of oligomeric and multisubunit complexes, for supercomplexes, as well as for functional roles are pointed out.
Synchronizing the Neurospora crassa circadian clock with the rhythmic environment
Authors: Price-Lloyd N. , Elvin M. , Heintzen C.
Published: August 2015

The metronomic predictability of the environment has elicited strong selection pressures for the evolution of endogenous circadian clocks. Circadian clocks drive molecular and behavioural rhythms that approximate the 24 h periodicity of our environment. Found almost ubiquitously among phyla, circadian clocks allow preadaptation to rhythms concomitant with the natural cycles of the Earth. Cycles in light intensity and temperature for example act as important cues that couple circadian clocks to the environment via a process called entrainment. This review summarizes our current understanding of the general and molecular principles of entrainment in the model organism Neurospora crassa, a simple eukaryote that has one of the best-studied circadian systems and light-signalling pathways.
Degradation of the Neurospora circadian clock protein FREQUENCY through the ubiquitin–proteasome pathway
Authors: He Q. , Liu Y.
Published: August 2015

Phosphorylation of the Neurospora circadian clock protein FREQUENCY (FRQ) promotes its degradation through the ubiquitin–proteasome pathway. Ubiquitination of FRQ requires FWD-1 (F-box/WD-40 repeat-containing protein-1), which is the substrate-recruiting subunit of an SCF (SKP/Cullin/F-box)-type ubiquitin ligase. In the fwd-1 mutant strains, FRQ degradation is defective, resulting in the accumulation of hyperphosphorylated FRQ and the loss of the circadian rhythmicities. The CSN (COP9 signalosome) promotes the function of SCF complexes in vivo. But in vitro, deneddylation of cullins by CSN inhibits SCF activity. In Neurospora, the disruption of the csn-2 subunit impairs FRQ degradation and compromises the normal circadian functions. These defects are due to the dramatically reduced levels of FWD-1 in the csn-2 mutant, a result of its rapid degradation. Other components of the SCFFWD−1 complex, SKP-1 and CUL-1 are also unstable in the mutant. These results establish important roles for SCFFWD−1 and CSN in the circadian clock of Neurospora and suggest that they are conserved components of the eukaryotic circadian clocks. In addition, these findings resolve the CSN paradox and suggest that the major function of CSN is to maintain the stability of SCF ubiquitin ligases in vivo.
What the genome sequence is revealing about trypanosome antigenic variation
Authors: Barry J.D. , Marcello L. , Morrison L.J. , Read A.F. , Lythgoe K. , Jones N. , Carrington M. , Blandin G. , Böhme U. , Caler E. , Hertz-Fowler C. , Renauld H. , El-Sayed N. , Berriman M.
Published: August 2015

African trypanosomes evade humoral immunity through antigenic variation, whereby they switch expression of the gene encoding their VSG (variant surface glycoprotein) coat. Switching proceeds by duplication of silent VSG genes into a transcriptionally active locus. The genome project has revealed that most of the silent archive consists of hundreds of subtelomeric VSG tandem arrays, and that most of these are not functional genes. Precedent suggests that they can contribute combinatorially to the formation of expressed, functional genes through segmental gene conversion. These findings from the genome project have major implications for evolution of the VSG archive and for transmission of the parasite in the field.
ABC proteins and antibiotic drug resistance: is it all about transport?
Authors: Kerr I.D. , Reynolds E.D. , Cove J.H.
Published: August 2015

The precise mechanism of antibiotic-resistance-conferring ABC (ATP-binding-cassette) proteins (termed NBD2) remains open to debate. Currently, two hypotheses are recognized. In one, the NBD2 proteins are envisaged to act at the ribosome to impair antibiotic access to the target site on the 23 S rRNA. In the other, NBD2 proteins are believed to act as the components of ATP driven efflux pumps by associating with membrane spanning proteins capable of binding and transporting antibiotics. Pertinent data in support of these two hypotheses are discussed in this paper.
Diseases of adipose tissue: genetic and acquired lipodystrophies
Authors: Capeau J. , Magré J. , Lascols O. , Caron M. , Béréziat V. , Vigouroux C. , Bastard J.P.
Published: August 2015

Human lipodystrophies represent a group of diseases characterized by altered body fat amount and/or repartition and major metabolic alterations with insulin resistance leading to diabetic complications and increased cardiovascular and hepatic risk. Genetic forms of lipodystrophies are rare. Congenital generalized lipodystrophy or Berardinelli–Seip syndrome, autosomal recessive, is characterized by a complete early lipoatrophy and severe insulin resistance and results, in most cases, from mutations either in the seipin gene of unknown function or AGPAT2 encoding an enzyme involved in triacylglycerol synthesis. The Dunnigan syndrome [FPLD2 (familial partial lipodystrophy of the Dunnigan type)] is due to mutations in LMNA encoding the lamin A/C, belonging to the complex group of laminopathies that could comprise muscular and cardiac dystrophies, neuropathies and syndromes of premature aging. Some FPLDs are linked to loss-of-function mutations in the PPAR-γ gene (peroxisome-proliferator-activated receptor γ; FPLD3) with severe metabolic alterations but a less severe lipodystrophy compared with FPLD2. The metabolic syndrome, acquired, represents the most common form of lipodystrophy. HIV-infected patients often present lipodystrophies, mainly related to side effects of antiretroviral drugs together with insulin resistance and metabolic alterations. Such syndromes help to understand the mechanisms involved in insulin resistance resulting from altered fat repartition and could benefit from insulin-sensitizing effects of lifestyle modifications or of specific medications.