bluuebunny/crossref_metadata_2025 huggingface dataset:
eIF2B, a mediator of general and gene-specific translational control
Authors: Pavitt G.D.
Published: August 2015

eIF2B (eukaryotic initiation factor 2B) is a multisubunit protein that is required for protein synthesis initiation and its regulation in all eukaryotic cells. Mutations in eIF2B have also recently been found to cause a fatal human disease called CACH (childhood ataxia with central nervous system hypomyelination) or VWM (vanishing white matter disease). This review provides a general background to translation initiation and mechanisms known to control eIF2B function, before describing molecular genetic and biochemical analysis of eIF2B structure and function, integrating work from studies of the yeast and mammalian eIF2B proteins.
Contrasting mechanisms of regulating translation of specific Drosophila germline mRNAs at the level of 5′-cap structure binding
Authors: Lasko P. , Cho P. , Poulin F. , Sonenberg N.
Published: August 2015

Translational control is a key genetic regulatory mechanism underlying the initial establishment of the major spatial axes of the Drosophila embryo. Many translational control mechanisms target eIF4E (eukaryotic initiation factor 4E), an initiation factor that recognizes the 5′-cap structure of the mRNA. Cap recognition by eIF4E, in complex with eIF4G, is essential for recruitment of the mRNA to the small ribosomal subunit. One established mechanism for repressing translation involves eIF4E-binding proteins, which competitively inhibit the eIF4E–eIF4G interaction. Our group has uncovered a novel mechanism for repression in which an eIF4E cognate protein called d4EHP, which cannot bind eIF4G, binds to the 5′-cap structure of cad mRNA thus rendering it translationally inactive. These two related, but distinct, mechanisms are discussed and contrasted in this review.
Insulin secretion in health and disease: genomics, proteomics and single vesicle dynamics
Authors: Rutter G.A. , Varadi A. , Tsuboi T. , Parton L. , Ravier M.
Published: August 2015

Defective insulin secretion from pancreatic islet β-cells is a sine qua non of Type II (non-insulin-dependent) diabetes. Digital imaging analysis of the nanomechanics of individual exocytotic events, achieved using total internal reflection fluorescence microscopy, has allowed us to demonstrate that insulin is released via transient or ‘cavicapture’ events whereby the vesicle and plasma membranes fuse transiently and reversibly. Such studies reveal that an increase in the number of abortive fusion events contributes to defective insulin secretion in in vitro models of Type II diabetes. Complementary analyses of genome-wide changes in β-cell gene expression, at both the mRNA and protein levels, are now facilitating the identification of key molecular players whose altered expression may contribute to the secretory defects in the diabetic β-cell.
β-Defensin evolution: selection complexity and clues for residues of functional importance
Authors: Semple C.A.M. , Taylor K. , Eastwood H. , Barran P.E. , Dorin J.R.
Published: August 2015

We have examined the evolution of the genes at the major human β-defensin locus and the orthologous loci in a range of other primates and mammals. For the first time, these data allow us to examine selective episodes in the more recent evolutionary history of this locus as well as in the ancient past. We have used a combination of maximum-likelihood-based tests and a maximum-parsimony-based sliding window approach to give a detailed view of the varying modes of selection operating at this locus. We provide evidence for strong positive selection soon after the duplication of these genes within an ancestral mammalian genome. During the divergence of primates, however, variable selective pressures have acted on β-defensin genes in different evolutionary lineages, with episodes of both negative and, more rarely, positive selection. Positive selection appears to have been more common in the rodent lineage, accompanying the birth of novel rodent-specific β-defensin gene clades. Sites in the second exon have been subject to positive selection and, by implication, are important in functional diversity. A small number of sites in the mature human peptides were found to have undergone repeated episodes of selection in different primate lineages. Particular sites were consistently implicated by multiple methods at positions throughout the mature peptides. These sites are clustered at positions that are predicted to be important for the function of β-defensins.
Human neutrophil elastase inhibitors in innate and adaptive immunity
Authors: Fitch P.M. , Roghanian A. , Howie S.E.M. , Sallenave J.-M.
Published: August 2015

Recent evidence shows that human neutrophil elastase inhibitors can be synthesized locally at mucosal sites. In addition to efficiently targeting bacterial and host enzymes, they can be released in the interstitium and in the lumen of mucosa, where they have been shown to have antimicrobial activities, and to activate innate immune responses. This review will address more particularly the pleiotropic functions of low-molecular-mass neutrophil elastase inhibitors [SLPI (secretory leucocyte proteinase inhibitor) and elafin] and, more specifically, their role in the development of the adaptive immune response.
Manipulation of dendritic cells for host defence against intracellular infections
Authors: McCormick S. , Santosuosso M. , Zhang X.Z. , Xing Z.
Published: August 2015

Dendritic cells (DCs) are an important innate immune cell type which is the bridge between innate and adaptive immunity. Mounting experimental evidence suggests that manipulating DCs represents a powerful means to enhance host defence against intracellular infectious diseases. We have developed several strategies to manipulate DCs either in vivo or in vitro for the purpose of enhancing the effect of vaccination or immunotherapeutics. In vivo delivery of transgene encoding GM-CSF (granulocyte/macrophage colony-stimulating factor), a DC-activating cytokine, increases the number and activation status of DCs at various tissue sites and enhances antimicrobial immune responses in murine models. Co-expression or co-delivery of GM-CSF gene transfer vector with an antimicrobial vaccine enhances microbial antigen-specific T-cell responses and immune protection. Murine bone marrow-derived DCs are being manipulated in vitro and exploited as a vaccine delivery system. Transduction of DCs with a virus-vectored tuberculosis vaccine is a powerful way to activate T-cells in vivo. Such genetically modified DC vaccines can be administered either parenterally or mucosally via the respiratory tract.
Sensing bilayer tension: bacterial mechanosensitive channels and their gating mechanisms
Authors: Booth Ian R. , Rasmussen Tim , Edwards Michelle D. , Black Susan , Rasmussen Akiko , Bartlett Wendy , Miller Samantha
Published: August 2015

Mechanosensitive channels sense and respond to changes in bilayer tension. In many respects, this is a unique property: the changes in membrane tension gate the channel, leading to the transient formation of open non-selective pores. Pore diameter is also high for the bacterial channels studied, MscS and MscL. Consequently, in cells, gating has severe consequences for energetics and homoeostasis, since membrane depolarization and modification of cytoplasmic ionic composition is an immediate consequence. Protection against disruption of cellular integrity, which is the function of the major channels, provides a strong evolutionary rationale for possession of such disruptive channels. The elegant crystal structures for these channels has opened the way to detailed investigations that combine molecular genetics with electrophysiology and studies of cellular behaviour. In the present article, the focus is primarily on the structure of MscS, the small mechanosensitive channel. The description of the structure is accompanied by discussion of the major sites of channel–lipid interaction and reasoned, but limited, speculation on the potential mechanisms of tension sensing leading to gating.
Improving cardiac Ca2+ transport into the sarcoplasmic reticulum in heart failure: lessons from the ubiquitous SERCA2b Ca2+ pump
Authors: Vangheluwe Peter , Wuytack Frank
Published: August 2015

As a major Ca2+ pump in the sarcoplasmic reticulum of the cardiomyocyte, SERCA2a (sarcoplasmic/endoplasmic reticulum Ca2+-ATPase 2a) controls the relaxation and contraction of the cardiomyocyte. It is meticulously regulated by adapting its expression levels and affinity for Ca2+ ions to the physiological demand of the heart. Dysregulation of the SERCA2a activity entails poor cardiomyocyte contractility, resulting in heart failure. Conversely, improving cardiac SERCA2a activity, e.g. by boosting its expression level or by increasing its affinity for Ca2+, is a promising strategy to rescue contractile dysfunction of the failing heart. The structures of the related SERCA1a Ca2+ pump and the Na+/K+-ATPase of the plasma membrane exposed the pumping mechanism and conserved domain architecture of these ion pumps. However, how the Ca2+ affinity of SERCA2a is regulated at the molecular level remained unclear. A structural and functional analysis of the closely related SERCA2b Ca2+ pump, i.e. the housekeeping Ca2+ pump found in the endoplasmic reticulum and the only SERCA isoform characterized by a high Ca2+ affinity, aimed to fill this gap. We demonstrated the existence of a novel and highly conserved site on the SERCA2 pump mediating Ca2+ affinity regulation by the unique C-terminus of SERCA2b (2b-tail). It differs from the earlier-described target site of the affinity regulator phospholamban. Targeting this novel site may provide a new approach to improve SERCA2a function in the failing heart. Strikingly, the intramembrane interaction site of the 2b-tail in SERCA2b shares sequence and structural homology with the binding site of the β-subunit on the α Na+/K+-ATPase. Thus P-type ATPases seem to have developed related mechanisms of regulation, and it is a future challenge for us to discover these general principles of P-type regulation.
The choreography of multidrug export
Authors: Doshi Rupak , Gutmann Daniel A.P. , Khoo Yvonne S.K. , Fagg Lisa A. , van Veen Hendrik W.
Published: August 2015

Multidrug transporters have a crucial role in causing the drug resistance that can arise in infectious micro-organisms and tumours. These integral membrane proteins mediate the export of a broad range of unrelated compounds from cells, including antibiotics and anticancer agents, thus reducing the concentration of these compounds to subtoxic levels in target cells. In spite of intensive research, it is not clear exactly how multidrug transporters work. The present review focuses on recent advancements in the biochemistry and structural biology of bacterial and human multidrug ABC (ATP-binding cassette) transporters. These advancements point to a common mechanism in which polyspecific drug-binding surfaces in the membrane domains are alternately exposed to the inside and outside surface of the membrane in response to the ATP-driven dimerization of nucleotide-binding domains and their dissociation following ATP hydrolysis.
The RNA- and DNA-targeting CRISPR–Cas immune systems of Pyrococcus furiosus
Authors: Terns Rebecca M. , Terns Michael P.
Published: August 2015

Using the hyperthermophile Pyrococcus furiosus, we have delineated several key steps in CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) invader defence pathways. P. furiosus has seven transcriptionally active CRISPR loci that together encode a total of 200 crRNAs (CRISPR RNAs). The 27 Cas proteins in this organism represent three distinct pathways and are primarily encoded in two large gene clusters. The Cas6 protein dices CRISPR locus transcripts to generate individual invader-targeting crRNAs. The mature crRNAs include a signature sequence element (the 5′ tag) derived from the CRISPR locus repeat sequence that is important for function. crRNAs are tailored into distinct species and integrated into three distinct crRNA–Cas protein complexes that are all candidate effector complexes. The complex formed by the Cmr [Cas module RAMP (repeat-associated mysterious proteins)] (subtype III-B) proteins cleaves complementary target RNAs and can be programmed to cleave novel target RNAs in a prokaryotic RNAi-like manner. Evidence suggests that the other two CRISPR–Cas systems in P. furiosus, Csa (Cas subtype Apern) (subtype I-A) and Cst (Cas subtype Tneap) (subtype I-B), target invaders at the DNA level. Studies of the CRISPR–Cas systems from P. furiosus are yielding fundamental knowledge of mechanisms of crRNA biogenesis and silencing for three of the diverse CRISPR–Cas pathways, and reveal that organisms such as P. furiosus possess an arsenal of multiple RNA-guided mechanisms to resist diverse invaders. Our knowledge of the fascinating CRISPR–Cas pathways is leading in turn to our ability to co-opt these systems for exciting new biomedical and biotechnological applications.
Uptake and metabolism of iron and iron oxide nanoparticles in brain astrocytes
Authors: Hohnholt Michaela C. , Dringen Ralf
Published: August 2015

Astrocytes are considered key regulators of the iron metabolism of the brain. These cells are able to rapidly accumulate iron ions and various iron-containing compounds, store iron efficiently in ferritin and also export iron. The present short review summarizes our current knowledge of the molecular mechanisms involved in the handling of iron by astrocytes. Cultured astrocytes efficiently take up iron as ferrous or ferric iron ions or as haem by specific iron transport proteins in their cell membrane. In addition, astrocytes accumulate large amounts of iron oxide nanoparticles by endocytotic mechanisms. Despite the rapid accumulation of high amounts of iron from various iron-containing sources, the viability of astrocytes is hardly affected. A rather slow liberation of iron from accumulated haem or iron oxide nanoparticles as well as the strong up-regulation of the synthesis of the iron storage protein ferritin are likely to contribute to the high resistance of astrocytes to iron toxicity. The efficient uptake of extracellular iron by cultured astrocytes as well as their strong up-regulation of ferritin after iron exposure also suggests that brain astrocytes deal well with an excess of iron and protect the brain against iron-mediated toxicity.
Are bacteriophage defence and virulence two sides of the same coin in Campylobacter jejuni?
Authors: Louwen Rogier , van Baarlen Peter
Published: August 2015

The continuous battle for survival in the environment has led to the development or acquisition of sophisticated defence systems in bacteria. These defence systems have contributed to the survival of the bacterial species in the environment for millions of years. Some systems appear to have evolved in a number of pathogenic bacteria towards a role in virulence and host immune evasion. Recently, different bacterial cell envelope components from diverse bacterial species have been linked not only to bacteriophage defence, but also to virulence features. In the present review we focus specifically on the bacterial cell envelope-expressed sialic-acid-containing LOS (lipo-oligosaccharide) structures and Type II CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) genes that both occur in specific Gram-negative pathogens. In Campylobacter jejuni circumstantial evidence points at a potential intertwined dual function between sialylated LOS structures and subtype II-C CRISPR–Cas, i.e. in phage defence and virulence. In the present review we discuss whether a dual functionality of sialylated LOS and subtype II-C CRISPR–Cas is exclusive to C. jejuni only or could be more widespread within the group of Type II CRISPR–Cas-harbouring bacteria. We conclude from the literature that, at least in C. jejuni, circumstantial evidence exists for a complex intertwined dual functionality between sialylated LOS and Type II CRISPR–Cas, and that other bacteria show similar genomic signatures.
RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns
Authors: Zoephel Judith , Randau Lennart
Published: August 2015

In bacteria and archaea, RNA-Seq deep sequencing methodology allows for the detection of abundance and processing sites of the small RNAs that comprise a CRISPR (clustered regularly interspaced short palindromic repeats) RNome. Comparative analyses of these CRISPR RNome sets highlight conserved patterns that include the gradual decline of CRISPR RNA abundance from the leader-proximal to the leader-distal end. In the present review, we discuss exceptions to these patterns that indicate the extensive impact of individual spacer sequences on CRISPR array transcription and RNA maturation. Spacer sequences can contain promoter and terminator elements and can promote the formation of CRISPR RNA–anti-CRISPR RNA duplexes. In addition, potential RNA duplex formation with host tRNA was observed. These factors can influence the functionality of CRISPR–Cas (CRISPR-associated) systems and need to be considered in the design of synthetic CRISPR arrays.
The intriguing case of motor neuron disease: ALS and SMA come closer
Authors: Achsel Tilmann , Barabino Silvia , Cozzolino Mauro , Carrì Maria Teresa
Published: August 2015

MNDs (motor neuron diseases) form a heterogeneous group of pathologies characterized by the progressive degeneration of motor neurons. More and more genetic factors associated with MND encode proteins that have a function in RNA metabolism, suggesting that disturbed RNA metabolism could be a common underlying problem in several, perhaps all, forms of MND. In the present paper we review recent developments showing a functional link between SMN (survival of motor neuron), the causative factor of SMA (spinal muscular atrophy), and FUS (fused in sarcoma), a genetic factor in ALS (amyotrophic lateral sclerosis). SMN is long known to have a crucial role in the biogenesis and localization of the spliceosomal snRNPs (small nuclear ribonucleoproteins), which are essential assembly modules of the splicing machinery. Now we know that FUS interacts with SMN and pathogenic FUS mutations have a significant effect on snRNP localization. Together with other recently published evidence, this finding potentially links ALS pathogenesis to disturbances in the splicing machinery, and implies that pre-mRNA splicing may be the common weak point in MND, although other steps in mRNA metabolism could also play a role. Certainly, further comparison of the RNA metabolism in different MND will greatly help our understanding of the molecular causes of these devastating diseases.
Electron microscopy studies of Type III CRISPR machines in Sulfolobus solfataricus
Authors: Cannone Giuseppe , Webber-Birungi Mariam , Spagnolo Laura
Published: August 2015

The CRISPR (clustered regularly interspaced short palindromic repeats) system is an adaptive immune system that targets viruses and other mobile genetic elements in bacteria and archaea. Cells store information of past infections in their genome in repeat–spacer arrays. After transcription, these arrays are processed into unit-length crRNA (CRISPR RNA) that is loaded into effector complexes encoded by Cas (CRISPR-associated) genes. CRISPR–Cas complexes target invading nucleic acid for degradation. CRISPR effector complexes have been classified into three main types (I–III). Type III effector complexes share the Cas10 subunit. In the present paper, we discuss the structures of the two Type III effector complexes from Sulfolobus solfataricus, SsoCSM (subtype III-A) and SsoCMR (subtype III-B), obtained by electron microscopy and single particle analysis. We also compare these structures with Cascade (CRISPR-associated complex for antiviral defence) and with the RecA nucleoprotein.
Emerging roles for centromere-associated proteins in DNA repair and genetic recombination
Authors: Osman Fekret , Whitby Matthew C.
Published: August 2015

Centromere proteins CENP-S and CENP-X are members of the constitutive centromere-associated network, which is a conserved group of proteins that are needed for the assembly and function of kinetochores at centromeres. Intriguingly CENP-S and CENP-X have alter egos going by the names of MHF1 (FANCM-associated histone-fold protein 1) and MHF2 respectively. In this guise they function with a DNA translocase called FANCM (Fanconi’s anemia complementation group M) to promote DNA repair and homologous recombination. In the present review we discuss current knowledge of the biological roles of CENP-S and CENP-X and how their dual existence may be a common feature of CCAN (constitutive centromere-associated network) proteins.
mRNA quality control goes transcriptional
Authors: Kilchert Cornelia , Vasiljeva Lidia
Published: August 2015

Eukaryotic mRNAs are extensively processed to generate functional transcripts, which are 5′ capped, spliced and 3′ polyadenylated. Accumulation of unprocessed (aberrant) mRNAs can be deleterious for the cell, hence processing fidelity is closely monitored by QC (quality control) mechanisms that identify erroneous transcripts and initiate their selective removal. Nucleases including Xrn2/Rat1 and the nuclear exosome have been shown to play an important role in the turnover of aberrant mRNAs. Recently, with the growing appreciation that mRNA processing occurs concomitantly with polII (RNA polymerase II) transcription, it has become evident that QC acts at the transcriptional level in addition to degrading aberrant RNAs. In the present review, we discuss mechanisms that allow cells to co-transcriptionally initiate the removal of RNAs as well as down-regulate transcription of transcripts where processing repeatedly fails.
Formin-based control of the actin cytoskeleton during cytokinesis
Authors: Bohnert K. Adam , Willet Alaina H. , Kovar David R. , Gould Kathleen L.
Published: August 2015

Cytokinesis, the terminal event in the canonical cell cycle, physically separates daughter cells following mitosis. For cleavage to occur in many eukaryotes, a cytokinetic ring must assemble and constrict between divided genomes. Although dozens of different molecules localize to and participate within the cytokinetic ring, the core machinery comprises linear actin filaments. Accordingly, formins, which nucleate and elongate F-actin (filamentous actin) for the cytokinetic ring, are required for cytokinesis in diverse species. In the present article, we discuss specific modes of formin-based actin regulation during cell division and highlight emerging mechanisms and questions on this topic.
Regulation of entry into gametogenesis by Ste11: the endless game
Authors: Anandhakumar Jayamani , Fauquenoy Sylvain , Materne Philippe , Migeot Valérie , Hermand Damien
Published: August 2015

Sexual reproduction is a fundamental aspect of eukaryotic cells, and a conserved feature of gametogenesis is its dependency on a master regulator. The ste11 gene was isolated more than 20 years ago by the Yamamoto laboratory as a suppressor of the uncontrolled meiosis driven by a pat1 mutant. Numerous studies from this laboratory and others have established the role of the Ste11 transcription factor as the master regulator of the switch between proliferation and differentiation in fission yeast. The transcriptional and post-transcriptional controls of ste11 expression are intricate, but most are not redundant. Whereas the transcriptional controls ensure that the gene is transcribed at a high level only when nutrients are rare, the post-transcriptional controls restrict the ability of Ste11 to function as a transcription factor to the G1-phase of the cell cycle from where the differentiation programme is initiated. Several feedback loops ensure that the cell fate decision is irreversible. The complete panel of molecular mechanisms operating to warrant the timely expression of the ste11 gene and its encoded protein basically mirrors the advances in the understanding of the numerous ways by which gene expression can be modulated.
Seeing the invisible by paramagnetic and diamagnetic NMR
Authors: Clore G. Marius
Published: August 2015

Sparsely populated transient states of proteins and their complexes play an important role in many biological processes including protein–protein and protein–DNA recognition, allostery, conformational selection, induced fit and self-assembly. These states are difficult to study as their low population and transient nature makes them effectively invisible to conventional structural and biophysical techniques. In the present article, I summarize recent NMR developments in our laboratory, including the use of paramagnetic relaxation enhancement, lifetime line broadening and dark-state exchange saturation transfer spectroscopy, that have permitted such sparsely populated states to be detected, characterized and, in some instances, visualized. I illustrate the application of these methods to the elucidation of mechanisms whereby transcription factors locate their specific target sites within an overwhelming sea of non-specific DNA, to the characterization of encounter complexes in protein–protein recognition, to large-scale interdomain motions involved in ligand binding, and to the interaction of monomeric amyloid β-peptide with the surface of amyloid protofibrils and the internal cavity surface of the chaperonin GroEL.
Modelling the CDK-dependent transcription cycle in fission yeast
Authors: Sansó Miriam , Fisher Robert P.
Published: August 2015

CDKs (cyclin-dependent kinases) ensure directionality and fidelity of the eukaryotic cell division cycle. In a similar fashion, the transcription cycle is governed by a conserved subfamily of CDKs that phosphorylate Pol II (RNA polymerase II) and other substrates. A genetic model organism, the fission yeast Schizosaccharomyces pombe, has yielded robust models of cell-cycle control, applicable to higher eukaryotes. From a similar approach combining classical and chemical genetics, fundamental principles of transcriptional regulation by CDKs are now emerging. In the present paper, we review the current knowledge of each transcriptional CDK with respect to its substrate specificity, function in transcription and effects on chromatin modifications, highlighting the important roles of CDKs in ensuring quantity and quality control over gene expression in eukaryotes.
Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations
Authors: Comitani Federico , Melis Claudio , Molteni Carla
Published: August 2015

Pentameric ligand-gated ion channels (pLGICs) are important biomolecules that mediate fast synaptic transmission. Their malfunctions are linked to serious neuronal disorders and they are major pharmaceutical targets; in invertebrates, they are involved in insecticide resistance. The complexity of pLGICs and the limited crystallographic information available prevent a detailed understanding of how they function. State-of-the-art computational techniques are therefore crucial to build an accurate picture at the atomic level of the mechanisms which drive the activation of pLGICs, complementing the available experimental data. We have used a series of simulation methods, including homology modelling, ligand–protein docking, density functional theory, molecular dynamics and metadynamics, a powerful scheme for accelerating rare events, with the guidance of mutagenesis electrophysiology experiments, to explore ligand-binding mechanisms, the effects of mutations and the potential role of a proline molecular switch for the gating of the ion channels. Results for the insect RDL receptor, the GABAC receptor, the 5-HT3 receptor and the nicotinic acetylcholine receptor will be reviewed.
Stimulation of electron transport as potential novel therapy in Parkinson's disease with mitochondrial dysfunction
Authors: Vos Melissa , Verstreken Patrik , Klein Christine
Published: August 2015

Parkinson's disease (PD) is a neurodegenerative motor disorder characterized by the loss of dopaminergic neurons. This loss of dopaminergic neurons is the pathological hallmark of the disease that results in the characteristic motor syndrome. Restoration of dopamine levels is the basis of current therapy; however, this does not tackle the cause of the disease. While the aetiology of PD remains mostly elusive, mitochondrial dysfunction has been linked to (at least) part of the PD cases. In this review we discuss recent findings in Drosophila melanogaster showing that stimulation of the electron transport chain is beneficial for PD fly models showing Complex I defects and discuss the possible clinical applications of these findings.
TSPO is a REDOX regulator of cell mitophagy
Authors: Gatliff Jemma , Campanella Michelangelo
Published: August 2015

The mitochondrial 18-kDa translocator protein (TSPO) was originally discovered as a peripheral binding site of benzodiazepines to be later described as a core element of cholesterol trafficking between cytosol and mitochondria from which the current nomenclature originated. The high affinity it exhibits with chemicals (i.e. PK11195) has generated interest in the development of mitochondrial based TSPO-binding drugs for in vitro and in vivo analysis. Increased TSPO expression is observed in numerous pathologies such as cancer and inflammatory conditions of the central nervous system (CNS) that have been successfully exploited via protocols of positron emission tomography (PET) imaging. We endeavoured to dissect the molecular role of TSPO in mitochondrial cell biology and discovered a functional link with quality control mechanisms operated by selective autophagy. This review focuses on the current understanding of this pathway and focuses on the interplay with reactive oxygen species (ROS) and the voltage-dependent anion channel (VDAC), to which TSPO binds, in the regulation of cell mitophagy and hence homoeostasis of the mitochondrial network as a whole.
The 18-kDa mitochondrial translocator protein in gliomas: from the bench to bedside
Authors: Janczar Karolina , Su Zhangjie , Raccagni Isabella , Anfosso Andrea , Kelly Charlotte , Durrenberger Pascal F. , Gerhard Alexander , Roncaroli Federico
Published: August 2015

The 18-kDa mitochondrial translocator protein (TSPO) is known to be highly expressed in several types of cancer, including gliomas, whereas expression in normal brain is low. TSPO functions in glioma are still incompletely understood. The TSPO can be quantified pre-operatively with molecular imaging making it an ideal candidate for personalized treatment of patient with glioma. Studies have proposed to exploit the TSPO as a transporter of chemotherapics to selectively target tumour cells in the brain. Our studies proved that positron emission tomography (PET)-imaging can contribute to predict progression of patients with glioma and that molecular imaging with TSPO-specific ligands is suitable to stratify patients in view of TSPO-targeted treatment. Finally, we proved that TSPO in gliomas is predominantly expressed by tumour cells.
Role of chemokine receptors CXCR4 and CXCR7 for platelet function
Authors: Chatterjee Madhumita , Rath Dominik , Gawaz Meinrad
Published: August 2015

Platelet-derived SDF-1α (stromal cell derived factor-α) mediates inflammation, immune defence and repair mechanisms at site of tissue injury. This review summarizes the relative expression of CXC chemokine receptor 4 (CXCR4) and CXCR7 in platelets, their dynamic trafficking in presence of ligands like chemokine C-X-C-motif ligand 11 (CXCL11), CXCL12 and MIF (macrophage migration inhibitory factor); how these receptors differentially mediate the functional and survival response to the chemokines CXCL11, CXCL12 and MIF. We further elaborate and emphasize the prognostic significance of platelet surface expression of CXCR4–CXCR7 in the context of coronary artery disease (CAD). SDF-1α/CXCL12, CXCL11, MIF effects mediated through CXCR4 and CXCR7 may play a regulatory role at the site of vascular and tissue inflammation, immune defence and repair where activated platelets reach as forerunners and function as critical players.
Metabolic regulation of natural killer cells
Authors: Finlay David K.
Published: August 2015

Natural killer (NK) cells have key roles in anti-viral and anti-tumour immune responses. Recent research demonstrates that cellular metabolism is an important determinant for the function of pro-inflammatory immune cells, including activated NK cells. The mammalian target of rapamcyin (mTOR) complex 1 (mTORC1) has been identified as a key metabolic regulator that promotes glycolytic metabolism in multiple immune cell subsets. Glycolysis is integrally linked to pro-inflammatory immune responses such that activated NK cells and effector T-cell subsets are reliant on sufficient glucose availability for maximal effector function. This article will discuss the regulation of cellular metabolism in NK cells as compared with that of T lymphocytes and discuss the implications for NK cell responses to viral infection and cancer.
Poincaré-like approach to Landau theory. I. General theory
Authors: Gaeta Giuseppe
Published: August 2015

We discuss a procedure to simplify the Landau potential, based on Michel’s reduction to orbit space and Poincaré normalization procedure, and illustrate it by concrete examples. The method makes use, as in Poincaré theory, of a chain of near-identity coordinate transformations with homogeneous generating functions; using Michel’s insight, one can work in orbit space. It is shown that it is possible to control the choice of generating functions so to obtain a (in many cases, substantial) simplification of the Landau polynomial, including a reduction of the parameters it depends on. Several examples are considered in detail.
Poincaré-like approach to Landau theory. II. Simplifying the Landau-deGennes potential for nematic liquid crystals
Authors: Gaeta Giuseppe
Published: August 2015

In a previous paper, we have discussed how the Landau potential (entering in Landau theory of phase transitions) can be simplified using the Poincaré normalization procedure. Here, we apply this approach to the Landau-deGennes functional for the isotropic-nematic transitions, and transitions between different nematic phases, in liquid crystals. We give special attention to applying our method in the region near the main transition point, showing in full detail how this can be done via a suitable simple modification of our Poincaré-like method. We also consider the question if biaxial phases can branch directly off the fully symmetric state; some partial results in this direction are presented.
Total internal reflection fluorescence microscopy for determination of size of individual immobilized vesicles: Theory and experiment
Authors: Olsson Thomas , Zhdanov Vladimir P. , Höök Fredrik
Published: August 2015

Lipid vesicles immobilized via molecular linkers at a solid support represent a convenient platform for basic and applied studies of biological processes occurring at lipid membranes. Using total internal reflection fluorescence microscopy (TIRFM), one can track such processes at the level of individual vesicles provided that they contain dyes. In such experiments, it is desirable to determine the size of each vesicle, which may be in the range from 50 to 1000 nm. Fortunately, TIRFM in combination with nanoparticle tracking analysis makes it possible to solve this problem as well. Herein, we present the formalism allowing one to interpret the TIRFM measurements of the latter category. The analysis is focused primarily on the case of unpolarized light. The specifics of the use of polarized light are also discussed. In addition, we show the expected difference in size distribution of suspended and immobilized vesicles under the assumption that the latter ones are deposited under diffusion-controlled conditions. In the experimental part of our work, we provide representative results, showing explicit advantages and some shortcomings of the use of TIRFM in the context under consideration, as well as how our refined formalism improves previously suggested approaches.
Puberty onset is delayed following uteroplacental insufficiency and occurs earlier with improved lactation and growth for pups born small
Authors: Romano Tania , Hryciw Deanne H. , Westcott Kerryn T. , Wlodek Mary E.
Published: August 2015

Being born small programs adult diseases later in life, with the early postnatal growth rate in growth-restricted offspring playing a role in the reduction of the risk of disease in adulthood. In addition, early postnatal growth is critical for puberty onset (PO). Using cross-fostering, we determined the effects of growth restriction and prenatal and postnatal environments on PO and sex steroids. Bilateral uterine vessel ligation (Restricted) or sham surgery (Control), performed on Gestational Day 18 in Wistar-Kyoto rats induced fetal growth restriction. Control, Reduced (Control litter size reduced to five pups) and Restricted pups were cross-fostered onto different Control (normal lactation) or Restricted (impaired lactation) mothers on Day 1. The day of vaginal opening (females) and balanopreputial separation (males) characterised PO. Blood was sampled for sex steroid and leptin analysis. Restricted pups were born lighter than Controls (P < 0.05). PO was delayed by 3.4–4 days in Restricted-on-Restricted males and females (P < 0.05). Plasma leptin concentrations at PO were lower in both sexes in all groups compared with Restricted-on-Control and Control-on-Control (P < 0.05). PO occurred earlier in Restricted-on-Control (~2 days) with normal leptin concentrations and accelerated growth compared with Restricted-on-Restricted (P < 0.05). Testosterone concentrations were lower in male Restricted-on-Restricted than Control-on-Control at 6 months (P < 0.05). Restricted-on-Restricted females had lower progesterone at PO compared with Control-on-Control (P < 0.05). Female Restricted-on-Restricted had lower oestradiol, with Restricted-on-Control having higher testosterone concentrations at 6 months than Control-on-Control (P < 0.05). Growth restriction reduced postnatal growth and leptin concentrations, delaying PO in both sexes and programming altered sex steroids. This highlights the importance of the interaction between prenatal and postnatal growth in the programming of adult reproductive status.
Exploring vaginal ring acceptability for contraception and sexually transmissible infection protection in India: a qualitative research study
Authors: Das Udita , Sharma Mamta , Kilbourne-Brook Maggie , Coffey Patricia S.
Published: August 2015

Background
New vaginal rings are being developed as single and multipurpose prevention technologies to protect women from pregnancy and/or sexually transmissible infections, such as HIV. Data on ring acceptability in low-resource settings is critical for new technologies to meet user needs. Methods: Women from slum and lower-income areas around Delhi, India, participated in focus group discussions on vaginal ring product perceptions and preferences. Participants were recruited based on following eligibility categories: age, marital status, contraceptive use, and number of children. The translated transcriptions of the qualitative data were analysed using a coding scheme generated from the areas of inquiry and relevant literature. Results: A total of 103 women from lower-middle-class or slum areas in Delhi participated in 13 focus group discussions between December 2012 and January 2013. Participants shared perceptions of vaginal ring product attributes, including size, colour, intended use (single indication or dual purpose), duration of use, side effects, biodegradability, and various preferences regarding product use, including access, use during sex, wear patterns, cleaning, and disposal. Participants also reflected on willingness to pay and male partner acceptability. Conclusions: The results of this hypothetical acceptability study indicate that these low-income women in Delhi are: willing to try vaginal rings; unconcerned about wearing them during sex; very interested in protection from infections and unintended pregnancy; indifferent about colour of new rings; emphatic about being told that rings may change colour from menstrual blood staining; comfortable with thinner rings; willing to try thicker rings once familiar with thinner rings; in favour of starting with 1-month rings and then transitioning to longer-term rings; and in favour of first accessing rings at a facility and then managing resupply independently.
Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages
Authors: Chamberlain Michael Dean , Wells Laura A. , Lisovsky Alexandra , Guo Hongbo , Isserlin Ruth , Talior-Volodarsky Ilana , Mahou Redouan , Emili Andrew , Sefton Michael V.
Published: August 2015

Significance

Cells interact with materials, such as those used in implants, through an adsorbed protein layer that causes changes in cell behavior and gene expression. We have identified the activation of signaling pathways in the cell by a material by unbiased screening of changes in phosphorylation patterns in the cell after material exposure to the material. These changes were apparent 10 min after exposure, filling the gap between the seconds of protein adsorption and the hours of gene expression and leading to the identification of hitherto unknown effects of materials on cells.
Lexical shifts, substantive changes, and continuity in State of the Union discourse, 1790–2014
Authors: Rule Alix , Cointet Jean-Philippe , Bearman Peter S.
Published: August 2015

Significance

A synoptic picture of the evolution of American politics is presented, based on analysis of the corpus of presidents’ State of the Union addresses, 1790–2014. The paper presents a strategy for automated text analysis that can identify meaningful categories in textual corpora that span longdurées, where terms, concepts and language use changes, and evolution of topical structure is a priori unknown. Discourse streams identified as river networks reveal how change in contents masks continuity in the articulation of the major tasks of governance over US history.
α-Catenin–mediated cadherin clustering couples cadherin and actin dynamics
Authors: Chen Chi-Shuo , Hong Soonjin , Indra Indrajyoti , Sergeeva Alina P. , Troyanovsky Regina B. , Shapiro Lawrence , Honig Barry , Troyanovsky Sergey M.
Published: August 2015

The function of the actin-binding domain of α-catenin, αABD, including its possible role in the direct anchorage of the cadherin–catenin complex to the actin cytoskeleton, has remained uncertain. We identified two point mutations on the αABD surface that interfere with αABD binding to actin and used them to probe the role of α-catenin–actin interactions in adherens junctions. We found that the junctions directly bound to actin via αABD were more dynamic than the junctions bound to actin indirectly through vinculin and that recombinant αABD interacted with cortical actin but not with actin bundles. This interaction resulted in the formation of numerous short-lived cortex-bound αABD clusters. Our data suggest that αABD clustering drives the continuous assembly of transient, actin-associated cadherin–catenin clusters whose disassembly is maintained by actin depolymerization. It appears then that such actin-dependent αABD clustering is a unique molecular mechanism mediating both integrity and reassembly of the cell–cell adhesive interface formed through weak cis- and trans-intercadherin interactions.
Detection of fundamental and first harmonic cyclotron line in X-ray pulsar Cep X-4
Authors: Jaisawal Gaurava K. , Naik Sachindra
Published: August 2015

We report the broad-band spectral properties of the X-ray pulsar Cep X-4 by using a Suzaku observation in 2014 July. The 0.8–70 keV spectrum was found to be well described by three continuum models – Negative and Positive power-law with Exponential cut-off (NPEX), high-energy cut-off power-law and CompTT models. Additional components such as a cyclotron line at ∼28 keV and two Gaussian components for iron lines at 6.4 and 6.9 keV were required in the spectral fitting. Apart from these, an additional absorption feature at ∼45 keV was clearly detected in residuals obtained from the spectral fitting. This additional feature at ∼45 keV was clearly seen in phase-resolved spectra of the pulsar. We identified this feature as the first harmonic of the fundamental cyclotron line at ∼28 keV. The ratio between the first harmonic and fundamental line energies (1.7) was found to be in disagreement with the conventional factor of 2, indicating that the heights of line-forming regions are different or viewed at larger angles. The phase-resolved spectroscopy of the fundamental and first harmonic cyclotron lines shows significant pulse-phase variation of the line parameters. This can be interpreted as the effect of viewing angle or the role of complicated magnetic field of the pulsar.
Dissecting the function of Atg1 complex in
Dictyostelium
autophagy reveals a connection with the pentose phosphate pathway enzyme transketolase
Authors: Mesquita Ana , Tábara Luis C. , Martinez-Costa Oscar , Santos-Rodrigo Natalia , Vincent Olivier , Escalante Ricardo
Published: August 2015

The network of protein–protein interactions of the
Dictyostelium discoideum
autophagy pathway was investigated by yeast two-hybrid screening of the conserved autophagic proteins Atg1 and Atg8. These analyses confirmed expected interactions described in other organisms and also identified novel interactors that highlight the complexity of autophagy regulation. The Atg1 kinase complex, an essential regulator of autophagy, was investigated in detail here. The composition of the Atg1 complex in
D. discoideum
is more similar to mammalian cells than to
Saccharomyces cerevisiae
as, besides Atg13, it contains Atg101, a protein not conserved in this yeast. We found that Atg101 interacts with Atg13 and genetic disruption of these proteins in
Dictyostelium
leads to an early block in autophagy, although the severity of the developmental phenotype and the degree of autophagic block is higher in Atg13-deficient cells. We have also identified a protein containing zinc-finger B-box and FNIP motifs that interacts with Atg101. Disruption of this protein increases autophagic flux, suggesting that it functions as a negative regulator of Atg101. We also describe the interaction of Atg1 kinase with the pentose phosphate pathway enzyme transketolase (TKT). We found changes in the activity of endogenous TKT activity in strains lacking or overexpressing Atg1, suggesting the presence of an unsuspected regulatory pathway between autophagy and the pentose phosphate pathway in
Dictyostelium
that seems to be conserved in mammalian cells.
The building of a biodiversity hotspot across a land-bridge in the Mediterranean
Authors: Molina-Venegas Rafael , Aparicio Abelardo , Lavergne Sébastien , Arroyo Juan
Published: August 2015

Many of the macroevolutionary processes that have shaped present-day phylogenetic patterns were caused by geological events such as plate tectonics and temporary land-bridges. The study of spatial patterns of phylogenetic diversity can provide insights into these past events. Here we focus on a western Mediterranean biodiversity hotspot located in the southern Iberian Peninsula and northwest Africa, two regions that are separated by the Strait of Gibraltar. We explore the spatial structure of the phylogenetic relationships within and across large-scale plant assemblages. Significant turnover in terminal lineages tends to occur between landmasses, whereas turnover in deep lineages tends to occur within landmasses. Plant assemblages in the western ecoregions of this hotspot tend to be phylogenetically overdispersed but are phylogenetically clustered on its eastern margins. We discuss our results in the light of potential scenarios of niche evolution (or conservatism) and lineage diversification. The significant turnover between landmasses suggests a common scenario of allopatric speciation that could have been facilitated by the intermittent joining of the two continents. This may have constituted an important stimulus for diversification and the emergence of this western Mediterranean biodiversity hotspot.