bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti-obesity activity of the water extract of Lactobacillus paracasei subsp. paracasei NTU 101 fermented soy milk products
Authors: Cheng Meng-Chun , Tsai Tsung-Yu , Pan Tzu-Ming
Published: August 2015

The anti-obesity activity of the water extract of soy milk fermented withLactobacillus paracaseisubsp.paracaseiNTU 101 (W101) was investigated.
Complexity in structure-directed prebiotic chemistry. Effect of a defective competing reactant in tetrapyrrole formation
Authors: Deans Richard M. , Chandrashaker Vanampally , Taniguchi Masahiko , Lindsey Jonathan S.
Published: August 2015

A reactive but defective pyrrole, derived from the simple β-diketone acetylacetone, terminates chain-growth in a quantitative combinatorial manner in tetrapyrrole formation.
POSS-derived mesoporous ionic copolymer–polyoxometalate catalysts with a surfactant function for epoxidation reactions
Authors: Zhao Jiwei , Leng Yan , Jiang Pingping , Wang Jun , Zhang Chenjun
Published: August 2015

Novel mesoporous POSS-derived POM-paired polymeric hybrids were demonstrated to be highly efficient interfacial solid catalysts for the epoxidation of alkenes with H2O2.
Solvent-controlled structural diversity observed in three Cu(ii) MOFs with a 2,2′-dinitro-biphenyl-4,4′-dicarboxylate ligand: synthesis, structures and magnetism
Authors: Zhang Na , Zhang Jian-Yong , Jia Qin-Xiang , Deng Wei , Gao En-Qing
Published: August 2015

Three solvent-dependent 3D CuII-based MOFs with diverse topology net have been successfully separated under controllable solvothermal conditions and magnetic studies suggest homo-spin topological ferrimagnetic and antiferromagnetic interactions.
Hierarchical CuCo2O4nanowire@NiCo2O4nanosheet core/shell arrays for high-performance supercapacitors
Authors: Zhang Kang , Zeng Wei , Zhang Guanhua , Hou Sucheng , Wang Fei , Wang Taihong , Duan Huigao
Published: August 2015

In this work, CuCo2O4nanowire@NiCo2O4nanosheet core/shell arrays were designed and synthesized on Ni foam. Taking the advantage of the synergistic effect and 3D core/shell nanostructure, the hybrid electrode exhibited a notable increased electrochemical performance.
The prediction of the morphology and PCE of small molecular organic solar cells
Authors: Xu Xiaojuan , Ji Yujin , Du Chunmiao , Hou Tingjun , Li Youyong
Published: August 2015

The predicted morphology, domain size, PCE (power conversion efficiency) of Small Molecular Organic Solar Cells.
Facile synthesis of (Ni,Co)@(Ni,Co)xFe3−xO4 core@shell chain structures and (Ni,Co)@(Ni,Co)xFe3−xO4/graphene composites with enhanced microwave absorption
Authors: Lin Yuan , Xu Lu , Jiang Zhiyuan , Li Hongli , Xie Zhaoxiong , Zheng Lansun
Published: August 2015

A facile strategy was developed to fabricate (Ni,Co)@(Ni,Co)xFe3−xO4 chain structures and (Ni,Co)@(Ni,Co)xFe3−xO4/graphene composites, which show excellent microwave absorption performances.
Self-healing elastomer assembly towards three-dimensional shape memory devices
Authors: Feng Xianqi , Zhang Gongzheng , Xu Bo , Jiang Haoyang , Bai Quanming , Li Huanjun
Published: August 2015

The superior self-healing elastomers were readily prepared by free-radical copolymerization of methoxyethyl acrylate (MEA) and N,N-dimethylacrylamide (DMAA).
Cytotoxic metabolites from the endophytic fungus Penicillium chermesinum: discovery of a cysteine-targeted Michael acceptor as a pharmacophore for fragment-based drug discovery, bioconjugation and click reactions
Authors: Darsih Cici , Prachyawarakorn Vilailak , Wiyakrutta Suthep , Mahidol Chulabhorn , Ruchirawat Somsak , Kittakoop Prasat
Published: August 2015

A novel tetracyclic polyketide uniquely spiro-attached with a γ-lactone ring and a potent cytotoxic agent possessing a thiol-reactive pharmacophore were isolated from the mangrove endophytic fungusPenicillium chermesinum.
Facile synthesis of size and wavelength tunable hollow gold nanostructures for the development of a LSPR based label-free fiber-optic biosensor
Authors: Satija Jitendra , Tharion Joseph , Mukherji Soumyo
Published: August 2015

Hollow bimetallic nanostructures have recently emerged as attractive plasmonic materials due to the ease of optical tunability by changing their size/composition.
Arginine–glycine–aspartic acid functional branched semi-interpenetrating hydrogels
Authors: Plenderleith Richard A. , Pateman Christopher J. , Rodenburg Cornelia , Haycock John W. , Claeyssens Frederik , Sammon Chris , Rimmer Stephen
Published: August 2015

Semi-interpenetrating hydrogel networks containing a branched but soluble component are described and use as supports for cell culture.
Clustering and phase behaviour of attractive active particles with hydrodynamics
Authors: Navarro Ricard Matas , Fielding Suzanne M.
Published: August 2015

The level of activity relative to the strength of attraction plays the role of an effective non-equilibrium temperature, counterpart to the thermodynamic temperature in the passive system. Even in the presence of an attractive potential, hydrodynamic interactions strongly suppress motility induced phase separation.
Insect circadian clock outputs
Authors: Helfrich-Förster Charlotte , N. Nitabach Michael , Holmes Todd C
Published: August 2015

Insects display an impressive variety of daily rhythms, which are most evident in their behaviour. Circadian timekeeping systems that generate these daily rhythms of physiology and behaviour all involve three interacting elements: the timekeeper itself (i.e. the clock), inputs to the clock through which it entrains and otherwise responds to environmental cues such as light and temperature, and outputs from the clock through which it imposes daily rhythms on various physiological and behavioural parameters. In insects, as in other animals, cellular clocks are embodied in clock neurons capable of sustained autonomous circadian rhythmicity, and those clock neurons are organized into clock circuits. Drosophila flies spend their entire lives in small areas near the ground, and use their circadian brain clock to regulate daily rhythms of rest and activity, so as to organize their behaviour appropriately to the daily rhythms of their local environment. Migratory locusts and butterflies, on the other hand, spend substantial portions of their lives high up in the air migrating long distances (sometimes thousands of miles) and use their circadian brain clocks to provide time-compensation to their sun-compass navigational systems. Interestingly, however, there appear to be substantial similarities in the cellular and network mechanisms that underlie circadian outputs in all insects.
Cytotoxicity, genotoxicity and oxidative reactions in cell-culture models: modulatory effects of phytochemicals
Authors: O'Brien N. M. , Woods J. A. , Aherne S. A. , O'Callaghan Y. C.
Published: August 2015

Much research effort has focused on the identification of phytochemicals in fruit and vegetables which exert beneficial effects. Our research examines modulatory effects of phytochemicals on cytotoxicity, genotoxicity and oxidative reactions in cell systems. Two examples of our studies are discussed. First, the potential beneficial effects of flavonoids are demonstrated. Flavonoids are reported to exhibit a wide variety of biological effects, including antioxidant and free-radical-scavenging activities. The aim of the study was to determine if flavonoids could protect against H2O2-induced DNA damage, as measured by the comet assay, in Caco-2 and HepG2 cells. Both cell lines were supplemented with increasing concentrations of myricetin, quercetin and rutin for 24 h followed by exposure to H2O2 (50 μM) for 30 min. Exposure to H2O2 for 30 min at 37 °C resulted in significant DNA damage and pre-incubation with the flavonoids before H2O2 exposure significantly (P <0.05) protected Caco-2 and HepG2 cells against H2O2-induced DNA damage. Secondly, we illustrate the use of cellular models to study oxysterol-induced toxicity. Oxy-sterols are generated during the cooking and processing of foods and may be produced endogenously by the oxidation of membrane lipids. Recent findings suggest that oxysterols may modulate cytotoxicity by exerting effects on the induction of apoptosis. 7β-Hydroxycholesterol (7β-OHC) and 25-hydroxycholesterol, both of which are commonly found in foods, were investigated for their abilities to induce apoptosis in a human monocytic blood cell line, U937, and in the human hepatoma cell line, HepG2 cells. U937 and HepG2 cells were incubated for up to 48 h with 30 μM oxysterol. 7β-OHC induced apoptosis in U937 cells as measured by non-random DNA fragmentation, condensed and fragmented nuclei, and the generation of hypodiploid cells. In contrast, oxysterols may induce cell death by a different mechanism in the hepatoma cells, possibly by necrosis.
Use of in vivo and in vitro techniques for the study of the effects of insulin on hepatic triacylglycerol secretion in different insulinaemic states
Authors: Zammit V. A.
Published: August 2015

This review illustrates how the use of several in vitro and in vivo techniques was necessary to show that the effect of insulin on hepatic triacylglycerol (TAG) secretion in the rat depends on the prior physiological state of the animal. The effect of insulin was always inhibitory when cultured cells were used, irrespective of the physiological state of the donor rats. By contrast, when perfused livers were used, insulin stimulated TAG secretion by livers isolated from fed, normoinsulinaemic rats, but inhibited it in livers from fasted or streptozotocin diabetic animals. This switch in insulin action was also shown to occur in vivo in experiments that involved the liver-specific targeting of both insulin (delivered within liposomes) and labelled fatty acids (delivered as cholesteryl esters within very-low-density lipoprotein remnants) in awake, unrestrained rats during a euglycaemic clamp. It is concluded that observations obtained with perfused liver preparations are more representative of the actual changes that occur in vivo with respect to the effects of insulin on hepatic TAG secretion.
The isolated hepatocyte preparation: 30 years on
Authors: Berry M. N. , Phillips J. W.
Published: August 2015

A method for the preparation of intact rat hepatocytes in high yield was first described in 1969. The procedure involved digestion of hepatic tissue by perfusion of the liver with crude collagenase; later, purified collagenase without other enzymic additions was shown to be ineffective. Recently it has been discovered that the combination of purified collagenase plus elastase is superior to crude collagenase in that it consistently provides high yields of undamaged hepatocytes. The isolated hepatocyte preparation has proved particularly useful for the study of mechanisms responsible for long-range interactions within the cell. These can be studied over prolonged time courses and in the presence of graded concentrations of specific inhibitors. Studies of this kind have demonstrated a close relationship between cytoplasmic metabolic flows and mitochondrial forces and have also revealed that the cytoplasmic and mitochondrial free NAD-linked redox potentials are maintained by energy-dependent reactions.
Leucocyte populations and cytokine regulation in human uteroplacental tissues
Authors: Vince G. S. , Johnson P. M.
Published: August 2015

Human endometrial tissue and the decidualized endometrium in pregnancy contain relatively large numbers of leucocytes, the proportions of which vary during both the menstrual cycle and early pregnancy. CD3+ T-cells, CD14+ macrophages and a population of phenotypically unusual CD3−CD16−CD56++ large granular lymphocytes (LGL) are present, whereas B-cells are virtually absent. Relative T-cell numbers decrease in first-trimester decidua; T-cells are therefore unlikely to have an important role in the immunological maintenance of pregnancy but could be more important in implantation, when their relative numbers are greater. Extensive numbers of class II MHC-positive tissue macrophages in both the endometrium and placenta will provide an immediate antigen non-specific host defence to infection at this important site. Nevertheless, most attention has focused on a role for the predominant LGL endometrial cell population in the implantation and maintenance of pregnancy because, at the time of implantation, these LGLs comprise 70–80% of all leucocytes in the endometrium. It is now well recognized that there is substantial and complex cytokine activity within human uteroplacental tissues; both leucocytic and non-leucocytic cells have been shown to be capable of producing a significant array of cytokines. However, to avoid excessive pathological sequelae, such cytokine activity must be locally regulated. This has been highlighted by recent reports indicating that abnormal Th1-type cytokine responses could be a reason for immunological reproductive failure in women. Key cytokines controlling differentiation into a Th1 (interleukin 12) or Th2 (interleukin 4) type pattern both exist in unusual molecular forms at the human maternal-fetal tissue interface and hence might be fundamental regulatory elements controlling cytokine action locally by an antagonistic action.
Cell senescence and human aging: where's the link?
Authors: Faragher R. G. A.
Published: August 2015

Normal human cells will not divide forever in culture. After a defined number of passages, every culture enters a viable non-dividing state termed senescence. This led to the proposal that the progressive accumulation of senescent cells contributes to (but does not exclusively cause) the aging process. Data now suggest that cell senescence, like apoptosis, occurs as an anti-cancer mechanism. In vivo, extremely low rates of division occur over very long periods of time. Thus, by the end of its lifespan, an organism has performed a surprisingly large amount of cell turnover. In a normal culture the fraction of senescent cells increases smoothly with proliferation in vitro. This process can be accurately modelled by the progressive loss of telomeric sequence (proposed as a counting mechanism for senescence). Telomere length is usually maintained by the enzyme telomerase (repressed in many human tissues). Re-introduction of telomerase prevents the onset of senescence. However, data suggest that a separate telomere-independent pathway exists. Evidence that this pathway is present in humans is now emerging.
Mechanisms for ATP-dependent chromatin remodelling
Authors: Whitehouse I. , Flaus A. , Havas K. , Owen-Hughes T.
Published: August 2015

Gene regulation involves the generation of a local chromatin topology that is conducive to transcription. Several classes of chromatin remodelling activity have been shown to play a role in this process. ATP-dependent chromatin-remodelling activities use energy derived from the hydrolysis of ATP to alter the structure of chromatin, making it more accessible for transcription factor binding. The yeast SWI-SWF complex is the founding member of this family of ATP-dependent chromatin-remodelling activities. We have developed a model system to study the ability of the SWI-SWF complex to alter chromatin structure. Using this system, we find that SWI-SWF is able to alter the position of nucleosomes along the DNA. This is consistent with recent reports that other ATP-dependent chromatin-remodelling activities can alter the positions of nucleosomes along DNA. This suggests that nucleosome mobilization may be a general feature of the activity of ATP-dependent chromatin-remodelling activities. Some of the mechanisms by which nucleosomes may be moved along DNA are discussed.
Co-repressor complexes and remodelling chromatin for repression
Authors: Wolffe A. P. , Urnov F. D. , Guschin D.
Published: August 2015

Recent progress identifies targeted chromatin remodelling by co-repressor complexes as being an integral component of transcriptional silencing. Here we discuss how chromatin structure and the basal transcriptional machinery are manipulated by the co-repressor complex containing the Mi-2 nucleosomal ATPase, the histone-binding protein RbAp48 and histone deacetylase and by the co-repressor complex containing SIN3, RbAp48 and histone deacetylase. Remarkably, both of these complexes also contain methyl-CpG-binding proteins. This observation provides a molecular mechanism to integrate DNA methylation fully into gene control in vertebrates.
Transcriptional repression by nuclear receptors: mechanisms and role in disease
Authors: Love J. D. , Gooch J. T. , Nagy L. , Chatterjee V. K. K. , Schwabe J. W. R.
Published: August 2015

Co-repressor proteins mediate transcriptional repression by nuclear receptors in the absence of ligand. The identification of a co-repressor-receptor interaction motif, and the finding that compressors and co-activators compete for the same site on the receptor, suggests a simple mechanism for the switch from repression to activation upon ligand binding. Defects in this mechanism result in dominant-negative receptors that repress transcription. Such receptors have been implicated in several clinically important diseases, including thyroid hormone resistance and diabetes mellitus.
Recruitment of chromatin remodelling factors during gene activation via the glucocorticoid receptor N-terminal domain
Authors: Wallberg A. E. , Flinn E. M. , Gustafsson J.-Å. , Wright A. P. H.
Published: August 2015

We have shown that yeast mutants with defects in the Ada adaptor proteins are defective in hormone-dependent gene activation by ectopically expressed human glucocorticoid receptor (GR). Others have shown that the Ada2 protein is required for physical interactions between some activation domains and TBP (TATA-binding protein), whereas the Gcn5 (Ada4) protein has a histone acetyltransferase (HAT) activity. Although all HAT enzymes are able to acetylate histone substrates, some also acetylate non-histone proteins. Taken together, these observations suggest that the Ada proteins have the ability to effect different steps in the process of gene activation. It has recently been shown that the Ada proteins are present in two distinct protein complexes, the Ada complex and a larger SAGA complex. Our recent work has focused on determining (1) which of the Ada-containing complexes mediates gene activation by GR, (2) whether the HAT activity encoded by GCN5 is required for GR-dependent gene activation, (3) whether the Ada proteins contribute to GR-mediated activation at the level of chromatin remodelling and (4) how the role of these HAT complexes is integrated with other chromatin remodelling activities during GR-mediated gene activation. Our results suggest a model in which GR recruits the SAGA complex and that this contributes to chromatin remodelling via a mechanism involving the acetylation of histones. Furthermore, recruitment of the SWI/SNF remodelling complex also has a role in GR-mediated activation that is independent of the role of SAGA. These complexes are similar to analogous mammalian complexes and therefore these results are likely to be relevant to the human system.
Co-operation between protein-acetylating and protein-methylating co-activators in transcriptional activation
Authors: Stallcup M. R. , Chen D. , Koh S. S. , Ma H. , Lee Y.-H. , Li H. , Schurter B. T. , Aswad D. W.
Published: August 2015

Nuclear hormone receptors (NRs) activate transcription by binding to specific enhancer elements associated with target genes. Transcriptional activation is accomplished with the help of complexes of co-activator proteins that bind to NRs. p160 co-activators, a family of three related 160 kDa proteins, serve as primary co-activators by binding directly to NRs and recruiting additional secondary co-activators. Some of these (CBP/p300 and p/CAF) can acetylate histones and other proteins in the transcription complex, thus helping to modify chromatin structure and form an active transcription initiation complex. We recently discovered co-activator-associated arginine methyltransferase 1 (CARM1), which binds to p160 co-activators and thereby enhances transcriptional activation by NRs on transiently transfected reporter genes. CARM1 also methylates specific arginine residues in the N-terminal tail of histone H3 in vitro. A related arginine-specific protein methyltransferase, PRMT1, also binds p160 co-activators and enhances NR function. PRMT1 methylates histone H4 in vitro. The enhancement of NR function by CARM1, PRMT1 and p300 depends on their interactions with p160 co-activators. In the presence of p160 co-activators, some pairs of these three secondary co-activators provide a highly synergistic enhancement of NR function on transiently transfected reporter genes. We have also observed an enhancement of NR function on stably integrated reporter genes by these co-activators. We propose that the synergy of co-activator function between p300, CARM1 and PRMT1 is due to their different but complementary protein modification activities.
Phosphinic peptide inhibitors as tools in the study of the function of zinc metallopeptidases
Authors: Dive V. , Lucet-Levannier K. , Georgiadis D. , Cotton J. , Vassiliou S. , Cuniasse P. , Yiotakis A.
Published: August 2015

The development of the combinatorial chemistry of phosphinic peptides has led to the discovery of both highly potent and selective inhibitors of various zinc metalloproteinases. Several properties of these compounds are reviewed, supporting the view that this class of inhibitors should represent useful tools for probing several aspects of the function of this broad family of proteases in vivo.
Conserved roles for peptidases in the processing of invertebrate neuropeptides
Authors: Isaac R. E. , Siviter R. J. , Stancombe P. , Coates D. , Shirras A. D.
Published: August 2015

Invertebrates use a wide range of peptides as transmitters and hormones to regulate complex behaviour, physiology and development. These animals, especially those that are amenable to genetic study and are the subject of genome-sequencing projects, provide powerful model systems for understanding the functions of peptidases in controlling the bioactivity of peptides. Neprilysin, a zinc metallopeptidase and a key enzyme in the metabolism of mammalian peptides, is also implicated in the inactivation of peptides at synapses and of circulating peptide hormones in insects and nematodes. A family of neprilysin-like genes are present in the genomes of both Drosophila melanogaster and Caenorhabditis elegans; in C. elegans it seems that individual family members have evolved to take on different physiological functions, because they are expressed in a tissue-specific manner. Angiotensin I-converting enzymes (peptidyl dipeptidase A, angiotensin-converting enzyme) are another group of zinc metallopeptidases found in some invertebrates that lack angiotensin peptides. In D. melanogaster there are two functional angiotensin-converting enzymes that are essential for normal development. One of these (Acer) is expressed in the embryonic heart, whereas the second enzyme (Ance) is expressed in several tissues at different stages of the life cycle. The accumulation of Ance within secretory vesicles of some peptide-synthesizing cells suggests a role for the enzyme in the intracellular processing of insect peptides. Ance is very efficient at cleaving pairs of basic residues from the C-terminus of partly processed peptides, suggesting a novel role for the enzyme in prohormone processing. Invertebrates will continue to provide insights into the evolutionarily conserved functions of known peptidases and of those additional family members that are expected to be identified in the future from genome-sequencing projects.
Membrane protein import in yeast mitochondria
Authors: Tokatlidis K. , Vial S. , Luciano P. , Vergnolle M. , Clémence S.
Published: August 2015

The protein import pathway that targets proteins to the mitochondrial matrix has been extensively characterized in the past 15 years. Variations of this import pathway account for the sorting of proteins to other compartments as well, but the insertion of integral inner membrane proteins lacking a presequence is mediated by distinct translocation machinery. This consists of a complex of Tim9 and Tim10, two homologous, Zn2+-binding proteins that chaperone the passage of the hydrophobic precursor across the aqueous inter-membrane space. The precursor is then targeted to another, inner-membrane-bound, complex of at least five subunits that facilitates insertion. Biochemical and genetic experiments have identified the key components of this process; we are now starting to understand the molecular mechanism. This review highlights recent advances in this new membrane protein insertion pathway.
Expression, purification and properties of multidrug efflux proteins
Authors: Henderson P.J. F. , Hoyle C. K. , Ward A.
Published: August 2015

A general strategy is described for the amplified expression, purification and characterization in Escherichia coli of multidrug efflux proteins from Staphylococcus aureus, Bacillus subtilis, Methanococcus janaschii and E. coli. They all catalyse drug/H+ antiport of substrates such as quinolones and ethidium and exemplify a family of putatively 12-helix membrane proteins. The gene for each protein was cloned downstream of the tac promoter in plasmid pTTQ18; an oligonucleotide encoding six histidine residues was added, in frame, to the C-terminus to facilitate purification. Growth conditions were optimized in 1–25-litre cultures of E. coli host strains to amplify the expression of each protein; the retention of activity was confirmed by assays of antibiotic resistance in vivo and/or assays of energized transport activity in vitro with synthetic substrates. Proteins were solubilized in dodecylmaltoside and purified to more than 90% homogeneity with Ni2+-nitrilo-triacetate-affinity column chromography, yielding 5–25 mg per 25 litres of original culture. All the transport proteins migrated anomalously in SDS/PAGE at apparent molecular masses below those predicted from the gene sequence; identity and integrity were therefore confirmed by N-terminal amino acid sequencing and Western blotting for the C-terminal hexahistidine tag. Examination of the secondary structure of detergent-solubilized proteins by CD or Fourier-transform infrared spectroscopy following purification indicated a high content of α-helix (more than 75%). Matrix-assisted laser desorption ionization MS confirmed the high degree of purity and the true molecular mass. The formation of three-dimensional crystals is being attempted but crystals have yet to be grown that diffract X-rays. The growth of two-dimensional protein arrays has been more successful, with diffraction of electrons at low resolution. Proteins have been fused to green fluorescent protein or maltose-binding protein to facilitate these structural analyses. In addition, ligands for efflux proteins labelled with 13C or 15N have been synthesized to implement solid-state NMR studies of the ligand-binding site.
The efficiency and plasticity of mitochondrial energy transduction
Authors: Brand M.D.
Published: August 2015

Since it was first realized that biological energy transduction involves oxygen and ATP, opinions about the amount of ATP made per oxygen consumed have continually evolved. The coupling efficiency is crucial because it constrains mechanistic models of the electron-transport chain and ATP synthase, and underpins the physiology and ecology of how organisms prosper in a thermodynamically hostile environment. Mechanistically, we have a good model of proton pumping by complex III of the electron-transport chain and a reasonable understanding of complex IV and the ATP synthase, but remain ignorant about complex I. Energy transduction is plastic: coupling efficiency can vary. Whether this occurs physiologically by molecular slipping in the proton pumps remains controversial. However, the membrane clearly leaks protons, decreasing the energy funnelled into ATP synthesis. Up to 20% of the basal metabolic rate may be used to drive this basal leak. In addition, UCP1 (uncoupling protein 1) is used in specialized tissues to uncouple oxidative phosphorylation, causing adaptive thermogenesis. Other UCPs can also uncouple, but are tightly regulated; they may function to decrease coupling efficiency and so attenuate mitochondrial radical production. UCPs may also integrate inputs from different fuels in pancreatic β-cells and modulate insulin secretion. They are exciting potential targets for treatment of obesity, cachexia, aging and diabetes.
Molecular simulations and lipid–protein interactions: potassium channels and other membrane proteins
Authors: Sansom M.S.P. , Bond P.J. , Deol S.S. , Grottesi A. , Haider S. , Sands Z.A.
Published: August 2015

Molecular dynamics simulations may be used to probe the interactions of membrane proteins with lipids and with detergents at atomic resolution. Examples of such simulations for ion channels and for bacterial outer membrane proteins are described. Comparison of simulations of KcsA (an α-helical bundle) and OmpA (a β-barrel) reveals the importance of two classes of side chains in stabilizing interactions with the head groups of lipid molecules: (i) tryptophan and tyrosine; and (ii) arginine and lysine. Arginine residues interacting with lipid phosphate groups play an important role in stabilizing the voltage-sensor domain of the KvAP channel within a bilayer. Simulations of the bacterial potassium channel KcsA reveal specific interactions of phosphatidylglycerol with an acidic lipid-binding site at the interface between adjacent protein monomers. A combination of molecular modelling and simulation reveals a potential phosphatidylinositol 4,5-bisphosphate-binding site on the surface of Kir6.2.
Lipids in and around photosynthetic reaction centres
Authors: Fyfe P.K. , Jones M.R.
Published: August 2015

Reaction centres are membrane-embedded pigment–protein complexes that transduce the energy of sunlight into a biologically useful form. The most heavily studied reaction centres are the PS-I (Photosystem I) and PS-II complexes from oxygenic phototrophs, and the reaction centre from purple photosynthetic bacteria. A great deal is known about the compositions and structures of these reaction centres, and the mechanism of light-activated transmembrane electron transfer, but less is known about how they interact with other components of the photosynthetic membrane, including the membrane lipids. X-ray crystallography has provided high-resolution structures for PS-I and the purple bacterial reaction centre, and revealed binding sites for a number of lipids, either embedded in the protein interior or attached to the protein surface. These lipids play a variety of roles, including the binding of cofactors and the provision of structural support. The challenges of modelling surface-associated electron density features such as lipids, detergents, small amphiphiles and ions are discussed.
Organization of endogenous clocks in insects
Authors: Helfrich-Förster C.
Published: August 2015

Insect and mammalian circadian clocks show striking similarities. They utilize homologous clock genes, generating self-sustained circadian oscillations in distinct master clocks of the brain, which then control rhythmic behaviour. The molecular mechanisms of rhythm generation were first uncovered in the fruit fly Drosophila melanogaster, whereas cockroaches were among the first animals where the brain master clock was localized. Despite many similarities, there exist obvious differences in the organization and functioning of insect master clocks. These similarities and differences are reviewed on a molecular and anatomical level.
The extraordinary mitochondrion and unusual citric acid cycle inTrypanosoma brucei
Authors: van Hellemond J.J. , Opperdoes F.R. , Tielens A.G.M.
Published: August 2015

African trypanosomes are parasitic protozoa that cause sleeping sickness and nagana. Trypanosomes are not only of scientific interest because of their clinical importance, but also because these protozoa contain several very unusual biological features, such as their specially adapted mitochondrion and the compartmentalization of glycolytic enzymes in glycosomes. The energy metabolism of Trypanosoma brucei differs significantly from that of their hosts and changes drastically during the life cycle. Despite the presence of all citric acid cycle enzymes in procyclic insect-stage T. brucei, citric acid cycle activity is not used for energy generation. Recent investigations on the influence of substrate availability on the type of energy metabolism showed that absence of glycolytic substrates did not induce a shift from a fermentative metabolism to complete oxidation of substrates. Apparently, insect-stage T. brucei use parts of the citric acid cycle for other purposes than for complete degradation of mitochondrial substrates. Parts of the cycle are suggested to be used for (i) transport of acetyl-CoA units from the mitochondrion to the cytosol for the biosynthesis of fatty acids, (ii) degradation of proline and glutamate to succinate, (iii) generation of malate, which can then be used for gluconeogenesis. Therefore the citric acid cycle in trypanosomes does not function as a cycle.
Pathways for protein transport to seed storage vacuoles
Authors: Jolliffe N.A. , Craddock C.P. , Frigerio L.
Published: August 2015

Plant vacuoles have multiple functions: they can act both as digestive organelles and as receptacles for storage proteins. Different types of vacuoles can coexist in the same cell, which adds complexity to the process of targeting to these compartments. A fuller understanding of this process is of evident value when endeavouring to exploit the plant secretory pathway for heterologous protein production. Positive sorting signals are required in order to sort proteins to vacuoles, and these have been split into three groups: ctVSS [C-terminal VSS (vacuolar sorting signals)], ssVSS (sequence-specific VSS) and physical structure VSS. The current working model posits that soluble proteins are delivered from the Golgi apparatus to the lytic vacuoles in clathrin-coated vesicles by virtue of their ssVSS, or to the storage vacuole [PSV (protein-storage vacuole)] in dense vesicles in a manner dependent on ctVSS or physical structure VSS. Although targeting to LV appears to be receptor-mediated, no such receptor has been identified for the recruitment of proteins to the PSV. We have studied the vacuolar targeting of two castor bean (Ricinus communis L.) storage proteins, proricin and pro 2 S albumin, in their native endosperm and in the heterologous system of tobacco protoplasts. We have found that both these proteins contain bona fide ssVSS and bind to sorting receptors in vitro in a similarly sequence-specific manner. The apparent similarities to lytic VSS and possible implications with respect to the working model for transport to storage vacuoles are discussed.
Regulation of lipid metabolism via angiopoietin-like proteins
Authors: Kersten S.
Published: August 2015

Regulation of mammalian energy metabolism is an intricate process involving numerous hormones, transcription factors and signal transduction cascades. Much of the regulation occurs via secreted factors that relay information from one organ to another. One group of secreted factors that recently emerged as having a major impact on lipid and possibly glucose metabolism are the ANGPTLs (angiopoietin-like proteins). This includes ANGPTL3, ANGPTL4/FIAF (fasting-induced adipose factor), and ANGPTL6/AGF (angiopoietin-related growth factor). Although the receptors for these proteins have yet to be identified, it is nevertheless increasingly clear that these proteins have important effects on plasma triacylglycerol clearance, adipose tissue lipolysis, and adiposity. This review summarizes contemporary data on ANGPTLs with emphasis on the connection with energy metabolism.
Signalling role of adipose tissue: adipokines and inflammation in obesity
Authors: Trayhurn P. , Wood I.S.
Published: August 2015

White adipose tissue (WAT) is a major endocrine and secretory organ, which releases a wide range of protein signals and factors termed adipokines. A number of adipokines, including leptin, adiponectin, tumour necrosis factor α, IL-1β (interleukin 1β), IL-6, monocyte chemotactic protein-1, macrophage migration inhibitory factor, nerve growth factor, vascular endothelial growth factor, plasminogen activator inhibitor 1 and haptoglobin, are linked to inflammation and the inflammatory response. Obesity is characterized by a state of chronic mild inflammation, with raised circulating levels of inflammatory markers and the expression and release of inflammation-related adipokines generally rises as adipose tissue expands (adiponectin, which has anti-inflammatory action is an exception). The elevated production of inflammation-related adipokines is increasingly considered to be important in the development of diseases linked to obesity, particularly Type II diabetes and the metabolic syndrome. WAT is involved in extensive cross-talk with other organs and multiple metabolic systems through the various adipokines.
Novel heparan sulphate analogues: inhibition of β-secretase cleavage of amyloid precursor protein
Authors: Patey S.J. , Yates E.A. , Turnbull J.E.
Published: August 2015

The role of HS (heparan sulphate) in the pathology of AD (Alzheimer's disease) is multifaceted. HS and other glycosaminoglycans have been widely reported to be associated with neuritic plaques. HS has also been shown to promote the aggregation of Aβ (amyloid β-peptide), the proteinaceous component of neuritic plaques. Recently, we described a novel and contrasting role for HS in the pathology of AD: HS can inhibit the formation of Aβ, by directly interacting with the protease BACE1 (β-site amyloid precursor protein cleaving enzyme 1; β-secretase 1), that cleaves the amyloid precursor protein and is the rate limiting step in the generation of Aβ. Here, we review the current roles of HS and the potential for HS-derivatives in the treatment of AD.
Atypical L-type channels are down-regulated in hypoxia
Authors: Callinan L. , McCarthy T.V. , Maulet Y. , Mackrill J.J.
Published: August 2015

One type of cellular response to hypoxia is an increase in cytosolic Ca2+. VDCCs (voltage-dependent calcium channels) open upon membrane depolarization allowing inward current of Ca2+ ions. Two of the so-called L-type VDCC α1 subunits, Cav1.2 and Cav1.3, are found in the brain. We sought to investigate the effect of chronic hypoxia or treatment with a hypoxia-mimicking agent DFX (desferrioxamine mesylate) on expression of L-type VDCC in the SH-SY5Y neuroblastoma cell line. Western blotting identified two atypical forms of the L-type channel with apparent molecular masses of approx. 100 and 150 kDa, compared with typical forms of approx. 200 kDa. Immunofluorescence microscopy shows the approx. 100 kDa protein located within the cell and on the cell surface, while the approx. 150 kDa protein is intracellular with punctate staining. Further analysis revealed that this approx. 150 kDa protein co-localizes with nuclear proteins but not with markers for other intracellular compartments. In addition, these proteins are both down-regulated in DFX-treated and hypoxic cells, suggesting that the mechanism of down-regulation is along the HIF (hypoxia-inducible factor) pathway. This atypical localization of the 150 kDa protein suggests that it might play a role in nuclear calcium signalling in health and disease.
Regulation of phospholipid synthesis in yeast by zinc
Authors: Carman G.M.
Published: August 2015

The yeast Saccharomyces cerevisiae has the ability to cope with a variety of stress conditions (e.g. zinc deficiency) by regulating the expression of enzyme activities including those involved with phospholipid synthesis. Zinc is an essential mineral required for the growth and metabolism of S. cerevisiae. Depletion of zinc from the growth medium of wild-type cells results in alterations in phospholipid composition including an increase in PI (phosphatidylinositol) and a decrease in phosphatidylethanolamine. These changes can be attributed to an increase in PIS1-encoded PI synthase activity and a decrease in the activities of several CDP-diacylglycerol pathway enzymes including the CHO1-encoded PS (phosphatidylserine) synthase. The reduction in PS synthase in response to zinc depletion is due to a repression mechanism that involves the UASINO (inositol upstream activating sequence) element in the CHO1 promoter and the negative transcription factor Opi1p. These factors are also responsible for the inositol-mediated repression of CHO1. This regulation may play an important role in allowing cells to adapt to zinc deficiency given the essential roles that phospholipids play in the structure and function of cellular membranes.
Saccharomyces cerevisiae, a model to study sterol uptake and transport in eukaryotes
Authors: Reiner S. , Micolod D. , Schneiter R.
Published: August 2015

The molecular mechanisms that govern intracellular transport of sterols in eukaryotic cells are only poorly understood. Saccharomyces cerevisiae is a facultative anaerobic organism that requires supplementation with unsaturated fatty acids and sterols to grow in the absence of oxygen, as the synthesis of these lipids requires molecular oxygen. The fact that yeast grows well under anaerobic conditions indicates that lipid uptake is rapid and efficient. To identify components in this lipid uptake and transport pathway, we screened the yeast mutant collection for genes that are essential under anaerobic conditions. Out of the approx. 4800 non-essential genes represented in the mutant collection, 37 were required for growth under anaerobic conditions. Uptake assays using radiolabelled cholesterol revealed that 16 of these genes are required for cholesterol uptake/transport and esterification. Further characterization of the precise role of these genes is likely to advance our understanding of this elusive pathway in yeast and may prove to be relevant to understand sterol homoeostasis in higher eukaryotic cells.
Dystroglycan: a multifunctional adaptor protein
Authors: Higginson J.R. , Winder S.J.
Published: August 2015

Dystroglycan, a ubiquitous membrane-spanning cell adhesion molecule, is a crucial link between the actin cytoskeleton and the extracellular matrix. With a wide expression pattern and multiple interacting proteins, not only is dystroglycan now thought to be important as a structural molecule but also new research has suggested that it has a role in cell signalling, cytoskeleton reorganization and as a potential tumour suppressor.
Centaurin-α1 and KIF13B kinesin motor protein interaction in ARF6 signalling
Authors: Kanamarlapudi V.
Published: August 2015

The ARF (ADP-ribosylation factor) family of small GTPases regulate intracellular membrane trafficking by cycling between an inactive GDP- and an active GTP-bound form. Among the six known mammalian ARFs (ARF1–ARF6), ARF6 is the least conserved and plays critical roles in membrane trafficking and cytoskeletal dynamics near the cell surface. Since ARFs have undetectable levels of intrinsic GTP binding and hydrolysis, they are totally dependent on extrinsic GEFs (guanine nucleotide-exchange factors) for GTP binding and GAPs (GTPase-activating proteins) for GTP hydrolysis. We have recently isolated a novel KIF (kinesin) motor protein (KIF13B) that binds to centaurin-α1, an ARF6GAP that binds to the second messenger PIP3 [PtdIns(3,4,5)P3]. KIFs transport intracellular vesicles and recognize their cargo by binding to proteins (receptors) localized on the surface of the cargo vesicles. Identification of centaurin-α1 as a KIF13B interactor suggests that KIF13B may transport ARF6 and/or PIP3 using centaurin-α1 as its receptor. This paper reviews the studies carried out to assess the interaction and regulation of centaurin-α1 by KIF13B.
Retrograde signalling at the synapse: a role for Wnt proteins
Authors: Salinas P.C.
Published: August 2015

The formation of functional synapses requires a proper dialogue between incoming axons and their future synaptic targets. As axons approach their target, they are instructed to slow down and remodel to form proper presynaptic terminals. Although significant progress has been made in the identification of the mechanisms that control axon guidance, little is known about the mechanisms that regulate the conversion of actively growing axon into a presynaptic terminal. We found that Wnt secreted proteins are retrograde signals that regulate the terminal arborization of axons and synaptic differentiation. Wnts released from postsynaptic neurons induce extensive remodelling on incoming axons. This remodelling is manifested by a decrease in axon extension with a concomitant increase in growth-cone size. This morphological change is correlated with changes in the dynamics and organization of microtubules. Studies of a vertebrate synapse and the Drosophila neuromuscular junction suggest that a conserved Wnt signalling pathway modulates presynaptic microtubules as axons remodel during synapse formation. In this paper I discuss the role of the Wnt–Dvl (Dishevelled protein)–GSK-3β (glycogen synthase kinase-3β) signalling pathway in axon remodelling during synapse formation in the central nervous system.
Imaging the cAMP-dependent signal transduction pathway
Authors: Zaccolo M. , Cesetti T. , Di Benedetto G. , Mongillo M. , Lissandron V. , Terrin A. , Zamparo I.
Published: August 2015

In recent years, the development of new technologies based on the green fluorescent protein and FRET (fluorescence resonance energy transfer) has introduced a new perspective in the study of cAMP signalling. Real-time imaging of fluorescent biosensors is making it possible to visualize cAMP dynamics directly as they happen in intact, living cells, providing important and original insights for our understanding of the spatiotemporal organization of the cAMP/PKA (protein kinase A) signalling pathway.
Multifaceted role of the Saccharomyces cerevisiae Srs2 helicase in homologous recombination regulation
Authors: Macris M.A. , Sung P.
Published: August 2015

Homologous recombination (HR) is a major pathway for the elimination of DNA DSBs (double-strand breaks) induced by high-energy radiation and chemicals, or that arise due to endogenous damage and stalled DNA replication forks. If not processed properly, DSBs can lead to cell death, chromosome aberrations and tumorigenesis. Even though HR is important for genome maintenance, it can also interfere with other DNA repair mechanisms and cause gross chromosome rearrangements. In addition, HR can generate DNA or nucleoprotein intermediates that elicit prolonged cell-cycle arrest and sometimes cell death. Genetic analyses in the yeast Saccharomyces cerevisiae have revealed a central role of the Srs2 helicase in preventing untimely HR events and in inhibiting the formation of potentially deleterious DNA structures or nucleoprotein complexes upon DNA replication stress. Paradoxically, efficient repair of DNA DSBs by HR is dependent on Srs2. In this paper, we review recent molecular studies aimed at deciphering the multifaceted role of Srs2 in HR and other cellular processes. These studies have provided critical insights into how HR is regulated in order to preserve genomic integrity and promote cell survival.