bluuebunny/crossref_metadata_2025 huggingface dataset:
Human metabolic pathways of dietary flavonoids and cinnamates
Authors: Williamson G. , Day A. J. , Plumb G. W. , Couteau D.
Published: August 2015

Flavonoids and cinnamates are widespread phenolic secondary metabolites synthesized by plants for defensive purposes. Many foods and beverages contain high levels of phenolic compounds. Certain phenolics in the diet are particularly bio-active and have pronounced effects on mammalian cells. These effects, together with epidemiological studies and animal models, have led to the hypothesis that dietary phenolics contribute to the health benefits of a diet rich in fruit and vegetables. This paper examines the biochemistry of the uptake and metabolic route of two groups of plant phenolics, the flavonols and hydroxycinnamates.
Regulation of survival signals from the insulin-like growth factor-I receptor
Authors: O'Connor R. , Fennelly C. , Krause D.
Published: August 2015

Suppression of apoptosis by survival factors is important for the maintenance of normal tissue homoeostasis and the response to infection or injury. Survival factors such as insulin-like growth factor-I (IGF-I) initiate a signalling cascade that starts by tyrosine phosphorylation of substrates leading to the activation of serine kinases that modulate the activity of members of the Bcl-2 family, which regulates the apoptotic machinery in most cells. Tumour cells often have enhanced survival mechanisms due either to up-regulation of the IGF-I receptor and its ligands or to loss of function of a phosphatase (PTEN) that regulates part of this survival pathway. The C-terminus of the IGF-I receptor appears to be a regulatory domain for the anti-apoptotic activity of this receptor, and certain residues within the C-terminus are essential for this regulatory activity. Knowledge of the proteins and pathways, which interact with these C-terminal domains, should lead us to ways of modulating IGF-I-mediated survival in tumours.
Electrochemical investigation of cellobiose oxidation by cellobiose dehydrogenase in the presence of cytochrome c as mediator
Authors: Fridman V. , Wollenberger U. , Bogdanovskaya V. , Lisdat F. , Ruzgas T. , Lindgren A. , Gorton L. , Scheller F. W.
Published: August 2015

An important aspect of the cytochrome c electrochemistry is the possibility of coupling the ‘heterogeneous reactions’ with other redox enzymes. Cellobiose dehydrogenase, a 89170 Da glycoprotein that contains both FAD and a b-type haem as prosthetic groups, donates electrons to a number of acceptors, including cytochrome c. While haem b is surrounded mainly by acidic amino acids, cytochrome c displays positive charged lysine groups around the haem site. Thus a fast reaction between both proteins is explicable. In the presence of cellobiose, a catalytic current was observed, owing to the interaction of cellobiose dehydrogenase with electrostatically adsorbed cytochrome c. Adsorption of cytochrome c provides a technological model surface for vectorial electron transfer.
Double-stranded DNA liquid-crystalline dispersions as biosensing units
Authors: Yevdokimov Y. M.
Published: August 2015

Three different approaches to constructing bio-sensing units based on double-stranded (ds) DNA molecules, capable of detecting various biologically active compounds, are considered. The first approach is based on the abnormal optical activity of the liquid-crystalline dispersion formed from ds DNA molecules, modified by relevant physical factors or treated with biologically active compounds. The second one is based on the abnormal optical activity of the liquid-crystalline dispersions formed first from the ds DNA and then treated with coloured biologically active compounds. The third one is based on the abnormal optical activity, specific to particles of the liquid-crystalline dispersions, where the neighbouring DNA molecules are crosslinked by artifical polymeric bridges. These approaches permit the detection of biologically relevant compounds of various origins.
The multifunctional protein At MFP2 is co-ordinately expressed with other genes of fatty acid β-oxidation during seed germination in Arabidopsis thaliana (L.) Heynh
Authors: Eastmond P.J. , Graham I. A.
Published: August 2015

In germinating oilseeds peroxisomal fatty acid β-oxidation is responsible for the mobilization of storage lipids. This pathway also occurs in other tissues where it has a variety of additional physiological functions. The central enzymatic steps of peroxisomal β-oxidation are performed by acyl-CoA oxidase (ACOX), the multifunctional protein (MFP) and 3-ketoacyl-CoA thiolase (thiolase). In order to investigate the function and regulation of β-oxidation in plants it is first necessary to identify and characterize genes encoding the relevant enzymes in a single model species. Recently we and others have reported on the cloning and characterization of genes encoding four ACOXs and a thiolase from the oilseed Arabidopsis thaliana. Here we identify a gene encoding an Arabidopsis MFP (AtMFP2) that is induced transiently during germination. The pattern of AtMFP2 expression closely reflects changes in the activities of 2-trans-enoyl-CoA hydratase and l-3-hydroxyacyl-CoA dehydrogenase. Similar patterns of expression have previously been reported for ACOX and thiolase genes. We conclude that genes encoding the three main proteins responsible for β-oxidation are co-ordinately expressed during oilseed germination and may share a common mechanism of regulation.
Does the mitochondrial transcription-termination complex play an essential role in controlling differential transcription of mitochondrial DNA?
Authors: Selwood S. P. , Chrzanowska-Lightowlers Z. M. A. , Lightowlers R. N.
Published: August 2015

The mechanism of mitochondrial transcription is well documented although the method of regulation remains obscure. The mitochondrial transcription-termination complex, mTERF, holds a key position in determining the fate of heavy-strand promotor-initiated transcripts and has been suggested as a candidate in the regulation of mitochondrial DNA (mtDNA) transcription. We report here the first example of a modulation of mTERF-complex binding activity concomitant with a differential mtDNA transcription rate. We suggest that these observations are indicative of a method of intra-organellar transcriptional fine tuning.
The mitochondrial trifunctional protein: centre of a β-oxidation metabolon?
Authors: Eaton S. , Bursby T. , Middleton B. , Pourfarzam M. , Mills K. , Johnson A. W. , Bartlecc K.
Published: August 2015

The trifunctional enzyme comprises three consecutive steps in the mitochondrial β-oxidation of long-chain acyl-CoA esters: 2-enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and 3-ketoacyl-CoA thiolase. Deficiencies in either 3-hydroxyacyl-CoA dehydrogenase activity, or all three activities, are important causes of human disease. The dehydrogenase and thiolase have a requirement for NAD+ and CoA respectively, whose levels are conserved within the mitochondrion and thus provide possible means for control and regulation of β-oxidation. Using analysis of the intact CoA ester intermediates produced by the complex, we have examined the sensitivity of the complex to NAD+/NADH and acetyl-CoA. We consider the evidence for channelling within the trifunctional protein and propose a model for a β-oxidation ‘metabolon’.
Leishmania pyruvate kinase: the crystal structure reveals the structural basis of its unique regulatory properties
Authors: Fothergill-Gilmore L. A. , Rigden D. J. , Michels P. A. M. , Phillips S. E. V.
Published: August 2015

Glycolysis occupies a central role in cellular metabolism, and is of particular importance for the catabolic production of ATP in protozoan parasites such as Leishmania and Trypanosoma. In these organisms pyruvate kinase plays a key regulatory role, and is unique in responding to fructose 2,6-bisphosphate as allosteric activator. The determination of the crystal structure of the first eukaryotic pyruvate kinase in the T-state (the inactive or ‘tense’ conformation of allosteric enzymes) is described. A comparison of the effector sites of the Leishmania and yeast enzymes reveals the structural basis for the different effector specificity. Two loops, comprising residues 443–453 and 480–489, adopt very different conformations in the two enzymes, and Lys-453 and His-480 that are a feature of trypanosomatid enzymes provide probable ligands for the 2-phospho group of the effector molecule. These and other differences offer an opportunity for the design of drugs that would exploit regulatory differences between parasite and host.
Organization of transport from endoplasmic reticulum to Golgi in higher plants
Authors: Andreeva A. V. , Zheng H. , Saint-Jore C. M. , Kutuzov M. A. , Evans D. E. , Hawes C. R.
Published: August 2015

In plant cells, the organization of the Golgi apparatus and its interrelationships with the endoplasmic reticulum differ from those in mammalian and yeast cells. Endoplasmic reticulum and Golgi apparatus can now be visualized in plant cells in vivo with green fluorescent protein (GFP) specifically directed to these compartments. This makes it possible to study the dynamics of the membrane transport between these two organelles in the living cells. The GFP approach, in conjunction with a considerable volume of data about proteins participating in the transport between endoplasmic reticulum and Golgi in yeast and mammalian cells and the identification of their putative plant homologues, should allow the establishment of an experimental model in which to test the involvement of the candidate proteins in plants. As a first step towards the development of such a system, we are using Sar1, a small G-protein necessary for vesicle budding from the endoplasmic reticulum. This work has demonstrated that the introduction of Sar1 mutants blocks the transport from endoplasmic reticulum to Golgi in vivo in tobacco leaf epidermal cells and has therefore confirmed the feasibility of this approach to test the function of other proteins that are presumably involved in this step of endo-membrane trafficking in plant cells.
Maintaining the protective variant surface glycoprotein coat of African trypanosomes
Authors: Rudenko G.
Published: August 2015

The African trypanosome Trypanosoma brucei has a precarious existence as an extracellular parasite of the mammalian bloodstream, where it is faced with continuous immune attack. Key to survival is a dense VSG (variant surface glycoprotein) coat, which is repeatedly switched during the course of a chronic infection. New data demonstrate a link between VSG synthesis and cell cycle progression, indicating that VSG is monitored during the trypanosome cell cycle.
Glycosylation and misfolding of PrP
Authors: Wiseman F. , Cancellotti E. , Manson J.
Published: August 2015

The TSEs (transmissible spongiform encephalopathies) are not only devastating neurological diseases but also provide a biochemical conundrum; how can a disease agent replicate in the apparent absence of genetic material? The prion hypothesis proposes that the TSE agent is a misfolded form of the host glycoprotein PrP (prion protein). However, a number of questions regarding the hypothesis remain to be addressed. We are using gene-targeted PrP transgenics models to investigate these issues. Here we discuss our recent results that examine the importance of PrP's N-glycans to the misfolding of the protein.
Studies of the aggregation of an amyloidogenic α-synuclein peptide fragment
Authors: Madine J. , Doig A.J. , Kitmitto A. , Middleton D.A.
Published: August 2015

The deposition of α-syn (α-synuclein) fibrils in Lewy bodies is a characteristic feature of individuals with neurodegenerative disorders. A peptide comprising the central residues 71–82 of α-syn [α-syn(71–82)] is capable of forming β-sheet-rich, amyloid-like fibrils with similar morphologies to fibrils of the full-length protein, providing a useful model of pathogenic α-syn fibrils that is suitable for detailed structural analysis. We have studied the morphology and gross structural features of α-syn(71–82) fibrils formed under different conditions in order to obtain reliable conditions for producing fibrils for further structural investigations. The results indicate that the rate of aggregation and the morphology of the fibrils formed are sensitive to pH and temperature.
Reactive oxygen species (ROS)-mediated β-cleavage of the prion protein in the mechanism of the cellular response to oxidative stress
Authors: Watt N.T. , Hooper N.M.
Published: August 2015

The PrPC [cellular isoform of PrP (prion protein)] can undergo a conformational conversion to produce a proteinase-resistant form PrPSc (scrapie isoform of PrP), a step critical for the development of prion disease. Although essential for disease progression, the normal cellular function of PrPC remains unknown. Suggestions to date have centred on a protective role against oxidative stress. We have demonstrated that ROS (reactive oxygen species)-mediated β-cleavage of PrPC occurs at the cell surface, can be inhibited following hydroxyl radical quenching and has a prerequisite for the octarepeat region in the N-terminus of the protein. Significantly, two disease-associated mutants of PrP, namely PG14 and A116V (Ala116→Val), were unable to undergo β-cleavage and this lack of proteolysis was accompanied by functional consequences in cells expressing these mutant proteins. The cells were found to be less viable following exposure to copper and H2O2, had reduced levels of glutathione peroxidase and increased amounts of intracellular oxygen radicals. These results suggest that β-cleavage of PrPC is an initial consequence following exposure to ROS in the extracellular environment contributing to a pathway involved in antioxidant protection of neuronal cells.
In Saccharomyces cerevisiae, impaired PRPP synthesis is accompanied by valproate and Li+ sensitivity
Authors: Vavassori S. , Wang K. , Schweizer L.M. , Schweizer M.
Published: August 2015

The biosynthetic intermediate PRPP (phosphoribosylpyrophosphate) has a central role in cellular biochemistry since it links carbon and nitrogen metabolism. Its importance may be reflected in the fact that, in the Saccharomyces cerevisiae (yeast) genome, there are five unlinked genes, PRS1–PRS5, each of which is theoretically capable of encoding the enzyme synthesizing PRPP. Interference with the complement of PRS genes in S. cerevisiae has far-reaching consequences for yeast physiology and has uncovered unexpected metabolic links including cell wall integrity and phospholipid metabolism.
Deficiency in mitochondrial anionic phospholipid synthesis impairs cell wall biogenesis
Authors: Zhong Q. , Greenberg M.L.
Published: August 2015

Cardiolipin (CL) is the signature lipid of the mitochondrial membrane and plays a key role in mitochondrial physiology and cell viability. The importance of CL is underscored by the finding that the severe genetic disorder Barth syndrome results from defective CL composition and acylation. Disruption of PGS1, which encodes the enzyme that catalyses the committed step of CL synthesis, results in loss of the mitochondrial anionic phospholipids phosphatidylglycerol and CL. The pgs1Δ mutant exhibits severe growth defects at 37°C. To understand the essential functions of mitochondrial anionic lipids at elevated temperatures, we isolated suppressors of pgs1Δ that grew at 37°C. The present review summarizes our analysis of suppression of pgs1Δ growth defects by a mutant that has a loss-of-function mutation in KRE5, a gene involved in cell wall biogenesis.
Enzyme redesign and interactions of substrate analogues with sterol methyltransferase to understand phytosterol diversity, reaction mechanism and the nature of the active site
Authors: Nes W.D.
Published: August 2015

Several STM (sterol methyltransferase) genes have been cloned, sequenced and expressed in bacteria recently, making it possible to address questions of the relationship between sterol structure and function. The active site and mechanism of action of a set of phylogenetically diverse SMTs have been probed by site-directed mutagenesis as well as by using substrate and related analogues of the SMT-catalysed reaction. An active-site model has been developed that is in accord with the results presented, which is consistent with the hypothesis that SMTs are bifunctional enzymes kinetically responsible to bind Δ24-acceptor sterols of specific steric and electronic character and rigid orientation imposed by multiple hydrophobic active site contacts exacted from a common waxy core. Functional divergence influenced by the architectural role of sterols in membranes is considered to govern the evolution of product distribution and specificity of individual SMTs as discussed.
Membrane raft lipid constituents affect drug susceptibilities of Candida albicans
Authors: Pasrija R. , Prasad T. , Prasad R.
Published: August 2015

By exploiting the biosynthetic pathways of raft lipid constituents, in this study we demonstrate that fluctuations in either sphingolipid or ergosterol levels result in increased drug sensitivity and morphological defects in Candida albicans cells. We show that any change in either ergosterol composition by conditionally disrupting ERG1 or in sphingolipid composition by homozygously disrupting its biosynthetic gene IPT1 leads to improper surface localization of a major ABC (ATP-binding cassette) drug efflux protein, Cdr1p. Results suggest that sterol/sphingolipid-rich membrane microdomains play an important role in positioning and functional maintenance of the integral efflux protein. The impaired ability of erg1/ipt1 mutant cells to efflux drugs mediated through Cdr1p appears to be the main cause of increased drug sensitivity of Candida cells.
The structure of the bacterial protein translocation complex SecYEG
Authors: Collinson I.
Published: August 2015

Proteins destined for secretion, membrane insertion or organellar import contain signal sequences that direct them to the membrane. Once there, transport machines receive and translocate them appropriately across or into the membrane. The related SecY and Sec61 protein translocation complexes are ubiquitous components of machines that are essential for protein transport. They co-operate with various partners such that the substrate polypeptide is pulled or pushed through the membrane by post- or co-translational mechanisms. In bacteria and archaea, the SecY complex (SecYEG/SecYEβ) is a heterotrimer, which associates with ribosomes so that the polypeptide is threaded through the channel during its synthesis. Bacteria possess an additional pathway, whereby the newly synthesized substrate protein is maintained in an unfolded conformation and is engaged by the ATPase SecA and delivered to the translocon. Recent medium- (cryo-electron microscopy) and high-resolution (X-ray) structures of the Sec complex have dramatically increased our understanding about how proteins pass through membranes, but have posed a number of new questions. The Sec complex is active as an oligomer, but the structure indicates that the protein-conducting channel is formed by a monomer of SecYEG. Structures of the membrane-bound dimer of Escherichia coli SecYEG and the detergent-solubilized monomer of Methanococcus jannaschii SecYEβ will be described and discussed in the context of the mechanism that underlies protein secretion and membrane insertion.
Coupling the dynamics of two actin networks – new views on the mechanics of cell protrusion
Authors: Danuser G.
Published: August 2015

We study how mechanical forces integrate spatially and temporally with regulatory signals at the leading edge of migrating cells. To probe the dynamics of this system, we developed quantitative fluorescent speckle microscopy, which maps out actin cytoskeleton transport, assembly and disassembly with high spatial resolution. Statistical processing of single speckle properties revealed two kinetically, kinematically and molecularly distinct, yet spatially overlapping, actin arrays at the leading edge of migrating epithelial cells. The first network, referred to as the lamellipodium, polymerizes and depolymerizes 1–2 μm from the edge in an Arp2/3 (actin-related protein 2/3)- and cofilin-dependent fashion. The second network, referred to as the lamella, exhibits Arp2/3-independent polymerization. To elucidate the dynamic relationship between the two networks, we have begun to examine how assembly and flow are temporally modulated with respect to a protrusion event. In control cells we found bursts of protrusion preceding bursts of F-actin assembly. The time lag disappears in cells where Arp2/3-function is impaired. This and other results allowed us to propose a model in which tropomyosin protects lamella filaments from branching and severing, and to conjecture that Arp2/3-mediated lamellipodium assembly is a natural consequence of lamella expansion, but not the initiator of cell protrusion.
Arf family GTPases: roles in membrane traffic and microtubule dynamics
Authors: Kahn R.A. , Volpicelli-Daley L. , Bowzard B. , Shrivastava-Ranjan P. , Li Y. , Zhou C. , Cunningham L.
Published: August 2015

Database mining and phylogenetic analysis of the Arf (ADP-ribosylation factor) superfamily revealed the presence in mammals of at least 22 members, including the six Arfs, two Sars and 14 Arl (Arf-like) proteins. At least six Arf family members were found in very early eukaryotes, including orthologues of Arf, Sar, Arl2, Arl3, Arl6 and Arl8. While roles for Arfs in membrane traffic are well known, those for most of the Arls remain unknown. Depletion in cells of the most closely related human Arf proteins, Arf1–Arf5, reveals specificities among their cellular roles and suggests that they may function in pairs at different steps in endocytic and secretory membrane traffic. In addition, recent results from a number of laboratories suggest that several of the Arl proteins may be involved in different aspects of microtubule-dependent functions. Thus, a second major role for Arf family GTPases, that of regulating microtubules, is emerging. Because membrane traffic is often dependent upon movement of vesicles along microtubules this raises the possibility that these two fundamental functions of Arf family members, regulation of vesicle traffic and microtubule dynamics, diverged from one function of Arfs in the earliest cells that has continued to branch and allow additional levels of regulation.
Physiological roles of spine motility: development, plasticity and disorders
Authors: McKinney R.A.
Published: August 2015

The vast majority of excitatory connections in the hippocampus are made on dendritic spines. Both dendritic spines and molecules within the membrane are able to move, but the physiological role of these movements is unclear. In the developing brain, spines show highly dynamic behaviour thought to facilitate new synaptic connections. Dynamic movements also occur in adults but the role of this movement is unclear. We have studied the effects of the most important excitatory neurotransmitter, glutamat, and found receptor activation to enhance movement of molecules within the spine membrane. This action of glutamate may be important in regulating the trafficking of neurotransmitter receptors that mediate change in synaptic function. In addition, we have studied the dynamic interactions between pre- and postsynaptic structures labelled with FM 4-64 and a membrane-targeted GFP (green fluorescent protein), respectively, in hippocampal slice cultures under conditions of increased activity, such as epilepsy. Our findings suggest a novel form of activity-dependent synaptic plasticity where spontaneous glutamate release is sufficient to trigger changes in the hippocampal microcircuitry by attracting neighbouring spines responsive to an enhanced level of extracellular glutamate.
Genetic, biochemical and structural approaches to talin function
Authors: Critchley D.R.
Published: August 2015

The cytoskeletal protein talin plays a key role in coupling the integrin family of cell adhesion molecules to the actin cytoskeleton. In this paper I present a brief review on talin and summarize our recent studies, in which we have taken both genetic and structural approaches to further elucidate the function of the protein.
Two functionally distinct pools of Src kinases for PDGF receptor signalling
Authors: Veracini L. , Franco M. , Boureux A. , Simon V. , Roche S. , Benistant C.
Published: August 2015

The cytoplasmic tyrosine kinases of the Src family (SFK) play important roles in cell responses induced by growth factors, including cell growth, survival and migration. Here, we review how SFK participate in PDGF (platelet-derived growth factor) receptor signalling leading to DNA synthesis and actin assembly. Furthermore, evidence for a spatial compartmentalization of SFK signalling is also discussed.
β-Arrestin-recruited phosphodiesterase-4 desensitizes the AKAP79/PKA-mediated switching of β2-adrenoceptor signalling to activation of ERK
Authors: Houslay M.D. , Baillie G.S.
Published: August 2015

Using combined dominant-negative and siRNA (small interfering RNA)-mediated knockdown strategies, the functional importance of specific PDE4 (phosphodiesterase-4) isoforms in modifying signalling through the β2-AR (β2-adrenoceptor) has been uncovered. The PDE4D5 isoform preferentially interacts with the signalling scaffold protein β-arrestin and is thereby recruited to the β2-AR upon agonist challenge. Delivery of an active PDE to the site of cAMP synthesis at the plasma membrane specifically attenuates the activity of a pool of PKA (protein kinase A) that is tethered to the β2-AR via AKAP79 (A-kinase anchoring protein 79). The specific functional role of this anchored PKA is to phosphorylate the β2-AR and allow it to switch its coupling with Gi and thereby activation of ERK (extracellular-signal-regulated kinase). Our studies uncover a novel facet of the regulation of β2-AR signalling by showing that β-arrestin-recruited PDE4 provides the means of desensitizing the agonist-dependent coupling of β2-AR with Gi and its consequential activation of ERK.
Oxidoreduction of protein thiols in redox regulation
Authors: Ghezzi P.
Published: August 2015

Protein cysteines can undergo various forms of oxidation, some of them reversible (disulphide formation, glutathionylation and S-nitrosylation). While in the past these were viewed as protein damage in the context of oxidative stress, there is growing interest in oxidoreduction of protein thiols/disulphides as a regulatory mechanism. This review discusses the evolution of the concept of redox regulation from that of oxidative stress and the redox state of protein cysteines in different cellular compartments.
What else has to happen for nitric oxide to induce cell death?
Authors: Borutaite V. , Brown G.
Published: August 2015

Nitric oxide (NO) can induce cell death; however, NO-induced cell death may be dependent/conditional on factors other than NO itself. Whether NO kills a particular cell depends on the amount of NO, source of NO, time of exposure to NO, cell type and the levels of other factors including, particularly oxygen, superoxide, H2O2, antioxidants, thiols and glycolysis.
Mitochondria and regulated tyrosine nitration
Authors: Koeck T. , Stuehr D.J. , Aulak K.S.
Published: August 2015

The conditions of the cellular microenvironment in complex multicellular organisms fluctuate, enforcing permanent adaptation of cells at multiple regulatory levels. Covalent post-translational modifications of proteins provide the short-term response tools for cellular adjustment and growing evidence supports the possibility that protein tyrosine nitration is part of this cellular toolkit and not just a marker for oxidative damage. We have demonstrated that protein tyrosine nitration fulfils the major criteria for signalling and suggest that the normally highly regulated process may lead to disease upon excessive or inappropriate nitration.
RNAi libraries and kinetoplast DNA
Authors: Englund P.T. , Agbo E.E.C. , Lindsay M.E. , Liu B. , Liu Y. , Motyka S.A. , Yildirir G. , Zhao Z.
Published: August 2015

African trypanosomes have a remarkable mitochondrial DNA termed kDNA (kinetoplast DNA) that contains several thousands of topologically interlocked DNA rings. Because of its highly unusual structure, kDNA has a complex replication mechanism. Our approach to understanding this mechanism is to identify the proteins involved and to characterize their function. So far approx. 30 candidate proteins have been discovered and we predict that there are over 100. To identify genes for more kDNA replication proteins, we are using an RNA interference library, which is the first forward genetic approach used for these parasites.
Modelling and simulation for metabolomics data analysis
Authors: Mendes P. , Camacho D. , de la Fuente A.
Published: August 2015

The advent of large data sets, such as those produced in metabolomics, presents a considerable challenge in terms of their interpretation. Several mathematical and statistical methods have been proposed to analyse these data, and new ones continue to appear. However, these methods often disagree in their analyses, and their results are hard to interpret. A major contributing factor for the difficulties in interpreting these data lies in the data analysis methods themselves, which have not been thoroughly studied under controlled conditions. We have been producing synthetic data sets by simulation of realistic biochemical network models with the purpose of comparing data analysis methods. Because we have full knowledge of the underlying ‘biochemistry’ of these models, we are better able to judge how well the analyses reflect true knowledge about the system. Another advantage is that the level of noise in these data is under our control and this allows for studying how the inferences are degraded by noise. Using such a framework, we have studied the extent to which correlation analysis of metabolomics data sets is capable of recovering features of the biochemical system. We were able to identify four major metabolic regulatory configurations that result in strong metabolite correlations. This example demonstrates the utility of biochemical simulation in the analysis of metabolomics data.
Shoot development – genetic interactions in the meristem
Authors: Byrne M.E.
Published: August 2015

Development of the plant shoot is dependent on the shoot apical meristem. Interactions between KNOX homeodomain transcription factors and the myb domain transcription factor AS1 (ASYMMETRIC LEAVES1) regulate both meristem function as well as leaf patterning. This review summarizes these interactions.
Role of MBD2 in gene regulation and tumorigenesis
Authors: Berger J. , Bird A.
Published: August 2015

DNA methylation is an epigenetic mechanism involved in transcriptional silencing of imprinted genes, genes located on the inactive X chromosome, and a number of tumour suppressor genes in cancer. MBD (methyl-CpG-binding domain) proteins selectively bind to methylated DNA and recruit chromatin remodelling and transcriptional repressor complexes, thereby establishing a repressive chromatin state. MBD2, a member of the MBD protein family, binds to methylated promoter CpG islands (clusters of high-density CpG dinucleotides) and acts as a methylation-dependent transcriptional repressor. Previous work has demonstrated that decreased CpG island methylation in mice lacking the DNA methyltransferase DNMT1 is associated with impaired tumorigenesis when crossed on the tumour-susceptible ApcMin/+ background. Mbd2 deficiency also dramatically reduces adenoma burden and extends life span in a gene dosage-dependent manner in this mouse model. Mbd2 is therefore essential for tumorigenesis in the murine intestine, although it is dispensable for the viability of the host animals. These findings validate MBD2 as a potential target for therapeutic intervention in colorectal cancer.
Inhibition of antimicrobial peptides by group A streptococci: SIC and DRS
Authors: Fernie-King B.A. , Seilly D.J. , Lachmann P.J.
Published: August 2015

SIC (streptococcal inhibitor of complement) is a 31 kDa protein secreted by a few highly virulent strains of GAS (group A streptococci), predominantly by the M1 strain. Initially described as an inhibitor of the membrane attack complex of complement, it has turned out to be a polyfunctional inhibitor of the innate mucosal immune response. The SIC protein sequence contains three domains: an N-terminal SRR (short repeat region), followed by three longer tandem repeats [LRR (long repeat region)] and a C-terminal PRR (proline-rich region). SIC inhibits the antibacterial activity of a wide range of antimicrobial peptides and proteins: i.e. lysozyme, SLPI (secretory leucocyte proteinase inhibitor), LL-37, hNP-1 (human neutrophil peptide-1) and the human β-defensins 1, 2 and 3. Analysis of the functional properties of recombinant domains of SIC shows that binding and inhibition of lysozyme and human β-defensin-3 require the SRR+LRR, as does binding to SLPI. Complement inhibition is confined to the SRR. M12 GAS secrete a protein ‘distantly related to SIC’ (DRS). DRS contains a C-terminal PRR which is significantly similar to that of SIC, but it has no central LRR and the N-terminal SRR is very different. DRS inhibits human β-defensin-3, but has no effect on lysozyme, SLPI or complement.
Choice of biocatalyst form for scalable processes
Authors: Woodley J.M.
Published: August 2015

The design of biocatalytic processes for industrial synthetic chemistry is determined in large part by the choice of isolated enzyme or whole-cell catalyst form. In the present paper, the considerations for choice are identified and some important classes of bioconversion are discussed in relation to the choice to be made. Recent developments in cell and protein engineering as well as reactor and process engineering are discussed in addition.
Membrane proteins: from bench to bits
Authors: von Heijne Gunnar
Published: August 2015

Membrane proteins currently receive a lot of attention, in large part thanks to a steady stream of high-resolution X-ray structures. Although the first few structures showed proteins composed of tightly packed bundles of very hydrophobic more or less straight transmembrane α-helices, we now know that helix-bundle membrane proteins can be both highly flexible and contain transmembrane segments that are neither very hydrophobic nor necessarily helical throughout their lengths. This raises questions regarding how membrane proteins are inserted into the membrane and fold in vivo, and also complicates life for bioinformaticians trying to predict membrane protein topology and structure.
Lipid–protein interactions as determinants of membrane protein structure and function
Authors: Dowhan William , Bogdanov Mikhail
Published: August 2015

To determine how the lipid environment affects membrane protein structure and function, strains of Escherichia coli were developed in which normal phospholipid composition can be altered or foreign lipids can be introduced. The properties of LacY (lactose permease) were investigated as a function of lipid environment. Assembly of LacY in membranes lacking PE (phosphatidylethanolamine) results in misorientation of the N-terminal six-TM (transmembrane domain) helical bundle with loss of energy-dependent uphill transport and retention of energy-independent downhill transport. Post-assembly introduction of PE results in nearly native orientation of TMs and restoration of uphill transport. Foreign lipids with no net charge can substitute for PE in supporting native LacY topology, but restoration of uphill transport is dependent on native topology and the proper folding of a solvent-exposed domain. Increasing the positive charge density of the cytoplasmically exposed surface of LacY counters TM misorientation in the absence of neutral lipids, demonstrating that charge interactions between these domains and the surface of the membrane bilayer are determinants of TM orientation. Therefore membrane protein organization or reorganization is determined either during initial assembly or post-insertionally through direct interactions between the protein and the lipid environment, which affects the topogenic potency of opposing charged residues as topological signals independent of the translocon.
Membrane microenvironment regulation of carnitine palmitoyltranferases I and II
Authors: Kashfi Khosrow , Mynatt Randall L. , Park Edwards A. , Cook George A.
Published: August 2015

CPT (carnitine palmitoyltransferase) 1 and CPT2 regulate fatty acid oxidation. Recombinant rat CPT2 was isolated from the soluble fractions of bacterial extracts and expressed in Escherichia coli. The acyl-CoA chain-length-specificity of the recombinant CPT2 was identical with that of the purified enzyme from rat liver mitochondrial inner membranes. The Km for carnitine for both the mitochondrial preparation and the recombinant enzyme was identical. In isolated mitochondrial outer membranes, cardiolipin (diphosphatidylglycerol) increased CPT1 activity 4-fold and the Km for carnitine 6-fold. It decreased the Ki for malonyl-CoA inhibition 60-fold, but had no effect on the apparent Km for myristoyl-CoA. Cardiolipin also activated recombinant CPT2 almost 4-fold, whereas phosphatidylglycerol, phosphatidylserine and phosphatidylcholine activated the enzyme 3-, 2- and 2-fold respectively. Most of the recombinant CPT2 was found to have substantial interaction with cardiolipin. A model is proposed whereby cardiolipin may hold the fatty-acid-oxidizing enzymes in the active functional conformation between the mitochondrial inner and outer membranes in conjunction with the translocase and the acyl-CoA synthetase, thus combining all four enzymes into a functional unit.
α-Synuclein as a ferrireductase
Authors: Brown David R.
Published: August 2015

Many proteins associated with neurodegenerative diseases have poorly defined or unknown functions. α-Synuclein is one such protein which is associated with a range of diseases including Parkinson's disease. Now accepted as a metal-binding protein, α-synuclein's function could possibly be defined in relation to the binding of cofactors. It has been suggested recently that α-synuclein is able to reduce iron using copper as its catalytic centre. The consequence of this is that possibly the function of α-synuclein can now be defined. The evidence for this and the consequences for Parkinson's disease are discussed in the present review.
Programmable DNA cleavage in vitro by Cas9
Authors: Karvelis Tautvydas , Gasiunas Giedrius , Siksnys Virginijus
Published: August 2015

The ternary Cas9–crRNA–tracrRNA complex (Cas9t) of the Type II CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) system functions as an Mg2+-dependent RNA-directed DNA endonuclease that locates its DNA target guided by the crRNA (CRISPR RNA) in the tracrRNA–crRNA structure and introduces a double-strand break at a specific site in DNA. The simple modular organization of Cas9t, where specificity for the DNA target is encoded by a small crRNA and the cleavage reaction is executed by the Cas9 endonuclease, provides a versatile platform for the engineering of universal RNA-directed DNA endonucleases. By altering the crRNA sequence within the Cas9t complex, programmable endonucleases can be designed for both in vitro and in vivo applications. Cas9t has been recently employed as a gene-editing tool in various eukaryotic cell types. Using Streptococcus thermophilus Cas9t as a model system, we demonstrate the feasibility of Cas9t as a programmable molecular tool for in vitro DNA manipulations.
Neuroimmmune interactions of cannabinoids in neurogenesis: focus on interleukin-1β (IL-1β) signalling
Authors: García-Ovejero Daniel , Arévalo-Martín Ángel , Navarro-Galve Beatriz , Pinteaux Emmanuel , Molina-Holgado Eduardo , Molina-Holgado Francisco
Published: August 2015

Neuroimmune networks and the brain endocannabinoid system contribute to the maintenance of neurogenesis. Activation of cannabinoid receptors suppresses chronic inflammatory responses through the attenuation of pro-inflammatory mediators. Moreover, the endocannabinoid system directs cell fate specification of NSCs (neural stem cells) in the CNS (central nervous sytem). The aim of our work is to understand better the relationship between the endocannabinoid and the IL-1β (interleukin-1β) associated signalling pathways and NSC biology, in order to develop therapeutical strategies on CNS diseases that may facilitate brain repair. NSCs express functional CB1 and CB2 cannabinoid receptors, DAGLα (diacylglycerol lipase α) and the NSC markers SOX-2 and nestin. We have investigated the role of CB1 and CB2 cannabinoid receptors in the control of NSC proliferation and in the release of immunomodulators [IL-1β and IL-1Ra (IL-1 receptor antagonist)] that control NSC fate decisions. Pharmacological blockade of CB1 and/or CB2 cannabinoid receptors abolish or decrease NSC proliferation, indicating a critical role for both CB1 and CB2 receptors in the proliferation of NSC via IL-1 signalling pathways. Thus the endocannabinoid system, which has neuroprotective and immunomodulatory actions mediated by IL-1 signalling cascades in the brain, could assist the process of proliferation and differentiation of embryonic or adult NSCs, and this may be of therapeutic interest in the emerging field of brain repair.
Influence of long terminal repeat retrotransposons in the genomes of fission yeasts
Authors: Zaratiegui Mikel
Published: August 2015

LTR (long terminal repeat) RTs (retrotransposons) are almost ubiquitous in eukaryotic genomes. Their abundance and selfish properties make them a major influence in the regulation and evolution of their host genome. Recently, several striking properties of the LTR RTs of fission yeast have been uncovered, affecting important cellular processes such as gene regulation, nuclear architecture and genome integrity. The present review summarizes the current information and puts it in the context of the wider search for understanding the influence of transposable elements on the host genome.
The Cmr complex: an RNA-guided endoribonuclease
Authors: Bailey Scott
Published: August 2015

The CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) system protects prokaryotes from infection by viruses and other potential genome invaders. This system represents an inheritable and adaptable immune system that is mediated by large ribonucleoprotein complexes, the CRISPR–Cas effector complexes. The Cmr complex is unique among CRISPR–Cas effector complexes in that it destroys invading RNA and not DNA. To date, the Cmr complexes from two species have been characterized in vitro and, strikingly, they degrade RNA via distinct mechanisms. The possible in vivo targets, as well as our current knowledge of the Cmr complex, is reviewed in the present paper.
Microtubules: greater than the sum of the parts
Authors: Lawson Jonathan L.D. , Salas Rafael E. Carazo
Published: August 2015

The post-genomic era has produced a variety of new investigation technologies, techniques and approaches that may offer exciting insights into many long-standing questions of scientific research. The microtubule cytoskeleton is a highly conserved system that shows a high degree of internal complexity, is known to be integral to many cell systems and functions on a fundamental level. After decades of study, much is still unknown about microtubules in vivo from the control of dynamics in living cells to their responses to environmental changes and responses to other cellular processes. In the present article, we examine some outstanding questions in the microtubule field and propose a combination of emerging interdisciplinary approaches, i.e. high-throughput functional genomics techniques, quantitative and super-resolution microscopy, and in silico modelling, that could shed light on the systemic regulation of microtubules in cells by networks of regulatory factors. We propose that such an integrative approach is key to elucidate the function of the microtubule cytoskeleton as a complete responsive integral biological system.
Cholesterylation: a tail of hedgehog
Authors: Ciepla Paulina , Magee Anthony I. , Tate Edward W.
Published: August 2015

Cholesterylation is a post-translational attachment of sterol to proteins. This modification has been a characteristic of a single family of hedgehog proteins (Hh). Hh is a well-established morphogenic molecule important in embryonic development. It was also found to be involved in the progression of many cancer types. Herein, we describe the mechanism of biosynthesis of cholesterylated Hh, the role of this unusual modification on protein functions and novel chemical probes, which could be used to specifically target this modification, both in vitro and in vivo.
Frequency modulated translocational oscillations of Nrf2, a transcription factor functioning like a wireless sensor
Authors: Xue Mingzhan , Momiji Hiroshi , Rabbani Naila , Bretschneider Till , Rand David A. , Thornalley Paul J.
Published: August 2015

The discovery that nuclear factor erythroid 2-related factor 2 (Nrf2) undergoes translocational oscillations from cytoplasm to nucleus in human cells with frequency modulation linked to activation of a stress-stimulated cytoprotective response raises the prospect that the Nrf2 works mechanistically analogous to a wireless sensor. Herein, we consider how this new model of Nrf2 oscillation resolves previous inexplicable experimental findings on Nrf2 regulation and why it is fit-for-purpose. Further investigation is required to assess how generally applicable the oscillatory mechanism is and if characteristics of this regulatory control can be found in vivo. It suggests there are multiple, potentially re-enforcing receptors for Nrf2 activation, indicating that potent Nrf2 activation for improved health and treatment of disease may be achieved through combination of Nrf2 system stimulants.
CD8+ T-cell senescence: no role for mTOR
Authors: Henson Sian M
Published: August 2015

Aging is accompanied by immune decline leading to increased incidence of infections and malignancies, given the demographic shift of humans towards an older age the identification of strategies for the manipulation of immunity is an important goal. Evidence implicates mammalian target of rapamycin (mTOR) to be a key modulator of aging and the use of mTOR inhibitors has been shown to ameliorate much age-related pathology; however, recent data suggest that senescent CD8+ T-cells function independently of mTOR. This review article will challenge the perceived dogma that mTOR universally controls CD8+ T-cell function.
Control of Auditory Attention in Children With Specific Language Impairment
Authors: Victorino Kristen R. , Schwartz Richard G.
Published: August 2015

Purpose

Children with specific language impairment (SLI) appear to demonstrate deficits in attention and its control. Selective attention involves the cognitive control of attention directed toward a relevant stimulus and simultaneous inhibition of attention toward irrelevant stimuli. The current study examined attention control during a cross-modal word recognition task.

Method

Twenty participants with SLI (ages 9–12 years) and 20 age-matched peers with typical language development (TLD) listened to words through headphones and were instructed to attend to the words in 1 ear while ignoring the words in the other ear. They were simultaneously presented with pictures and asked to make a lexical decision about whether the pictures and auditory words were the same or different. Accuracy and reaction time were measured in 5 conditions, in which the stimulus in the unattended channel was manipulated.

Results

The groups performed with similar accuracy. Compared with their peers with TLD, children with SLI had slower reaction times overall and different within-group patterns of performance by condition.

Conclusions

Children with TLD showed efficient inhibitory control in conditions that required active suppression of competing stimuli. Participants with SLI had difficulty exerting control over their auditory attention in all conditions, with particular difficulty inhibiting distractors of all types.