bluuebunny/crossref_metadata_2025 huggingface dataset:
Hyperactivated MyD88 signaling in dendritic cells, through specific deletion of Lyn kinase, causes severe autoimmunity and inflammation
Authors: Lamagna Chrystelle , Scapini Patrizia , van Ziffle Jessica A. , DeFranco Anthony L. , Lowell Clifford A.
Published: August 2013

Significance

The pathogenesis of systemic lupus erythematosus, a complex autoimmune inflammatory disease triggered by genetic and environmental factors, is generally attributed to defects in lymphocyte function. We show that dendritic cells (DCs) also drive autoimmune disease in mice. Our observations that dysregulation of Toll-like receptor signaling (a key pathway that alerts the immune system of encounter with infectious agents) in DCs alone is sufficient to induce autoimmunity sheds new light on the pathogenesis of this disease. This work implies that DC-specific reduction of Toll-like receptor signaling may prove to be a highly specific approach to reduce the symptoms of autoimmune diseases.
Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors
Authors: Malaby Andrew W. , van den Berg Bert , Lambright David G.
Published: August 2013

Membrane recruitment of cytohesin family Arf guanine nucleotide exchange factors depends on interactions with phosphoinositides and active Arf GTPases that, in turn, relieve autoinhibition of the catalytic Sec7 domain through an unknown structural mechanism. Here, we show that Arf6-GTP relieves autoinhibition by binding to an allosteric site that includes the autoinhibitory elements in addition to the PH domain. The crystal structure of a cytohesin-3 construct encompassing the allosteric site in complex with the head group of phosphatidyl inositol 3,4,5-trisphosphate and N-terminally truncated Arf6-GTP reveals a large conformational rearrangement, whereby autoinhibition can be relieved by competitive sequestration of the autoinhibitory elements in grooves at the Arf6/PH domain interface. Disposition of the known membrane targeting determinants on a common surface is compatible with multivalent membrane docking and subsequent activation of Arf substrates, suggesting a plausible model through which membrane recruitment and allosteric activation could be structurally integrated.
let-7 and miR-140 microRNAs coordinately regulate skeletal development
Authors: Papaioannou Garyfallia , Inloes Jennifer B. , Nakamura Yukio , Paltrinieri Elena , Kobayashi Tatsuya
Published: August 2013

Significance

A global reduction of microRNAs (miRNAs) in growth plate chondrocytes results in defects in both proliferation and differentiation; however, specific miRNAs that regulate these processes have not been identified. In this study, we provide evidence that let-7 miRNAs and microRNA-140 (miR-140), among other miRNAs, play major roles in endochondral bone development. We found that suppression of let-7 miRNAs in chondrocytes reduced proliferation, whereas the chondrocyte-specific miR-140 was necessary for differentiation into proliferating chondrocytes. Deficiency of both let-7 and miR-140 caused a dramatic growth defect, synergistically reducing proliferating chondrocyte mass. Thus, these miRNAs coordinately regulate distinct steps of endochondral bone development.
Mutant
PIK3CA
accelerates HER2-driven transgenic mammary tumors and induces resistance to combinations of anti-HER2 therapies
Authors: Hanker Ariella B. , Pfefferle Adam D. , Balko Justin M. , Kuba María Gabriela , Young Christian D. , Sánchez Violeta , Sutton Cammie R. , Cheng Hailing , Perou Charles M. , Zhao Jean J. , Cook Rebecca S. , Arteaga Carlos L.
Published: August 2013

Human epidermal growth factor receptor 2
(
HER2
;
ERBB2
) amplification and
phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha
(
PIK3CA
) mutations often co-occur in breast cancer. Aberrant activation of the phosphatidylinositol 3-kinase (PI3K) pathway has been shown to correlate with a diminished response to HER2-directed therapies. We generated a mouse model of HER2-overexpressing (HER2
+
),
PIK3CA

H1047R

-mutant breast cancer. Mice expressing both human HER2 and mutant
PIK3CA
in the mammary epithelium developed tumors with shorter latencies compared with mice expressing either oncogene alone. HER2 and mutant
PIK3CA
also cooperated to promote lung metastases. By microarray analysis, HER2-driven tumors clustered with luminal breast cancers, whereas mutant
PIK3CA
tumors were associated with claudin-low breast cancers.
PIK3CA
and HER2
+
/
PIK3CA
tumors expressed elevated transcripts encoding markers of epithelial-to-mesenchymal transition and stem cells. Cells from HER2
+
/
PIK3CA
tumors more efficiently formed mammospheres and lung metastases. Finally, HER2
+
/
PIK3CA
tumors were resistant to trastuzumab alone and in combination with lapatinib or pertuzumab. Both drug resistance and enhanced mammosphere formation were reversed by treatment with a PI3K inhibitor. In sum,
PIK3CA

H1047R

accelerates HER2-mediated breast epithelial transformation and metastatic progression, alters the intrinsic phenotype of HER2-overexpressing cancers, and generates resistance to approved combinations of anti-HER2 therapies.
Transcription termination controls prophage maintenance in
Escherichia coli
genomes
Authors: Menouni Rachid , Champ Stéphanie , Espinosa Leon , Boudvillain Marc , Ansaldi Mireille
Published: August 2013

Prophages represent a large fraction of prokaryotic genomes and often provide new functions to their hosts, in particular virulence and fitness. How prokaryotic cells maintain such gene providers is central for understanding bacterial genome evolution by horizontal transfer. Prophage excision occurs through site-specific recombination mediated by a prophage-encoded integrase. In addition, a recombination directionality factor (or excisionase) directs the reaction toward excision and prevents the phage genome from being reintegrated. In this work, we describe the role of the transcription termination factor Rho in prophage maintenance through control of the synthesis of transcripts that mediate recombination directionality factor expression and, thus, excisive recombination. We show that Rho inhibition by bicyclomycin allows for the expression of prophage genes that lead to excisive recombination. Thus, besides its role in the silencing of horizontally acquired genes, Rho also maintains lysogeny of defective and functional prophages.
Soil food web properties explain ecosystem services across European land use systems
Authors: de Vries Franciska T. , Thébault Elisa , Liiri Mira , Birkhofer Klaus , Tsiafouli Maria A. , Bjørnlund Lisa , Bracht Jørgensen Helene , Brady Mark Vincent , Christensen Søren , de Ruiter Peter C. , d’Hertefeldt Tina , Frouz Jan , Hedlund Katarina , Hemerik Lia , Hol W. H. Gera , Hotes Stefan , Mortimer Simon R. , Setälä Heikki , Sgardelis Stefanos P. , Uteseny Karoline , van der Putten Wim H. , Wolters Volkmar , Bardgett Richard D.
Published: August 2013

Intensive land use reduces the diversity and abundance of many soil biota, with consequences for the processes that they govern and the ecosystem services that these processes underpin. Relationships between soil biota and ecosystem processes have mostly been found in laboratory experiments and rarely are found in the field. Here, we quantified, across four countries of contrasting climatic and soil conditions in Europe, how differences in soil food web composition resulting from land use systems (intensive wheat rotation, extensive rotation, and permanent grassland) influence the functioning of soils and the ecosystem services that they deliver. Intensive wheat rotation consistently reduced the biomass of all components of the soil food web across all countries. Soil food web properties strongly and consistently predicted processes of C and N cycling across land use systems and geographic locations, and they were a better predictor of these processes than land use. Processes of carbon loss increased with soil food web properties that correlated with soil C content, such as earthworm biomass and fungal/bacterial energy channel ratio, and were greatest in permanent grassland. In contrast, processes of N cycling were explained by soil food web properties independent of land use, such as arbuscular mycorrhizal fungi and bacterial channel biomass. Our quantification of the contribution of soil organisms to processes of C and N cycling across land use systems and geographic locations shows that soil biota need to be included in C and N cycling models and highlights the need to map and conserve soil biodiversity across the world.
Metalloproteases meprin α and meprin β are C- and N-procollagen proteinases important for collagen assembly and tensile strength
Authors: Broder Claudia , Arnold Philipp , Vadon-Le Goff Sandrine , Konerding Moritz A. , Bahr Kerstin , Müller Stefan , Overall Christopher M. , Bond Judith S. , Koudelka Tomas , Tholey Andreas , Hulmes David J. S. , Moali Catherine , Becker-Pauly Christoph
Published: August 2013

Type I fibrillar collagen is the most abundant protein in the human body, crucial for the formation and strength of bones, skin, and tendon. Proteolytic enzymes are essential for initiation of the assembly of collagen fibrils by cleaving off the propeptides. We report that

Mep1a
−/−

and
Mep1b
−/−
mice revealed lower amounts of mature collagen I compared with WT mice and exhibited significantly reduced collagen deposition in skin, along with markedly decreased tissue tensile strength. While exploring the mechanism of this phenotype, we found that cleavage of full-length human procollagen I heterotrimers by either meprin α or meprin β led to the generation of mature collagen molecules that spontaneously assembled into collagen fibrils. Thus, meprin α and meprin β are unique in their ability to process and release both C- and N-propeptides from type I procollagen in vitro and in vivo and contribute to the integrity of connective tissue in skin, with consequent implications for inherited connective tissue disorders.
Oxidation of ethanol in the rat brain and effects associated with chronic ethanol exposure
Authors: Wang Jie , Du Hongying , Jiang Lihong , Ma Xiaoxian , de Graaf Robin A. , Behar Kevin L. , Mason Graeme F.
Published: August 2013

It has been reported that chronic and acute alcohol exposure decreases cerebral glucose metabolism and increases acetate oxidation. However, it remains unknown how much ethanol the living brain can oxidize directly and whether such a process would be affected by alcohol exposure. The questions have implications for reward, oxidative damage, and long-term adaptation to drinking. One group of adult male Sprague–Dawley rats was treated with ethanol vapor and the other given room air. After 3 wk the rats received i.v. [2-13C]ethanol and [1, 2-13C2]acetate for 2 h, and then the brain was fixed, removed, and divided into neocortex and subcortical tissues for measurement of13C isotopic labeling of glutamate and glutamine by magnetic resonance spectroscopy. Ethanol oxidation was seen to occur both in the cortex and the subcortex. In ethanol-naïve rats, cortical oxidation of ethanol occurred at rates of 0.017 ± 0.002 µmol/min/g in astroglia and 0.014 ± 0.003 µmol/min/g in neurons, and chronic alcohol exposure increased the astroglial ethanol oxidation to 0.028 ± 0.002 µmol/min/g (P= 0.001) with an insignificant effect on neuronal ethanol oxidation. Compared with published rates of overall oxidative metabolism in astroglia and neurons, ethanol provided 12.3 ± 1.4% of cortical astroglial oxidation in ethanol-naïve rats and 20.2 ± 1.5% in ethanol-treated rats. For cortical astroglia and neurons combined, the ethanol oxidation for naïve and treated rats was 3.2 ± 0.3% and 3.8 ± 0.2% of total oxidation, respectively.13C labeling from subcortical oxidation of ethanol was similar to that seen in cortex but was not affected by chronic ethanol exposure.
Human NAIP and mouse NAIP1 recognize bacterial type III secretion needle protein for inflammasome activation
Authors: Yang Jieling , Zhao Yue , Shi Jianjin , Shao Feng
Published: August 2013

Significance

Our analyses uncover general immunogenic activity of bacterial T3SS needle protein and identify human NAIP and mouse NAIP1 as cytosolic innate immune sensors of bacterial T3SS needle protein. These results, together with our previous studies, establish a complete framework for understanding NLRC4-mediated detection of bacterial virulence products by the NAIP family inflammasome receptors. The inflammasome-stimulating activity of bacterial T3SS needle proteins and the difference between mouse and human NAIP inflammasome also may provide guidance in vaccine development.
A closure scheme for chemical master equations
Authors: Smadbeck Patrick , Kaznessis Yiannis N.
Published: August 2013

Probability reigns in biology, with random molecular events dictating the fate of individual organisms, and propelling populations of species through evolution. In principle, the master probability equation provides the most complete model of probabilistic behavior in biomolecular networks. In practice, master equations describing complex reaction networks have remained unsolved for over 70 years. This practical challenge is a reason why master equations, for all their potential, have not inspired biological discovery. Herein, we present a closure scheme that solves the master probability equation of networks of chemical or biochemical reactions. We cast the master equation in terms of ordinary differential equations that describe the time evolution of probability distribution moments. We postulate that a finite number of moments capture all of the necessary information, and compute the probability distribution and higher-order moments by maximizing the information entropy of the system. An accurate order closure is selected, and the dynamic evolution of molecular populations is simulated. Comparison with kinetic Monte Carlo simulations, which merely sample the probability distribution, demonstrates this closure scheme is accurate for several small reaction networks. The importance of this result notwithstanding, a most striking finding is that the steady state of stochastic reaction networks can now be readily computed in a single-step calculation, without the need to simulate the evolution of the probability distribution in time.
Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences
Authors: Gao Zhen-Yu , Zhao Shan-Cen , He Wei-Ming , Guo Long-Biao , Peng You-Lin , Wang Jin-Jin , Guo Xiao-Sen , Zhang Xue-Mei , Rao Yu-Chun , Zhang Chi , Dong Guo-Jun , Zheng Feng-Ya , Lu Chang-Xin , Hu Jiang , Zhou Qing , Liu Hui-Juan , Wu Hai-Yang , Xu Jie , Ni Pei-Xiang , Zeng Da-Li , Liu Deng-Hui , Tian Peng , Gong Li-Hui , Ye Chen , Zhang Guang-Heng , Wang Jian , Tian Fu-Kuan , Xue Da-Wei , Liao Yi , Zhu Li , Chen Ming-Sheng , Li Jia-Yang , Cheng Shi-Hua , Zhang Geng-Yun , Wang Jun , Qian Qian
Published: August 2013

Significance

Hybrid rice developed in China has been contributing greatly to the world’s food production. The pioneer super hybrid rice developed by crossing
93–11
and
Peiai 64s
,
Liang–You–Pei–Jiu
has been widely grown in China and other Asia-Pacific regions for its high yield. Here, the quality genome sequences for both parental lines were presented and updated, and a high-resolution map of genome-wide graphic genotypes was constructed by deep resequencing a core population of 132
Liang–You–Pei–Jiu
recombinant inbred lines. A series of yield-associated loci were fine-mapped, and two of them were delimited to regions each covering one candidate gene with the large recombinant inbred line population. The study provided an ideal platform for molecular breeding by quantitative trait loci cloning in rice.
Rapid structural change in synaptosomal-associated protein 25 (SNAP25) precedes the fusion of single vesicles with the plasma membrane in live chromaffin cells
Authors: Zhao Ying , Fang Qinghua , Herbst Adam Drew , Berberian Khajak N. , Almers Wolfhard , Lindau Manfred
Published: August 2013

The SNARE complex consists of the three proteins synaptobrevin-2, syntaxin, and synaptosomal-associated protein 25 (SNAP25) and is thought to execute a large conformational change as it drives membrane fusion and exocytosis. The relation between changes in the SNARE complex and fusion pore opening is, however, still unknown. We report here a direct measurement relating a change in the SNARE complex to vesicle fusion on the millisecond time scale. In individual chromaffin cells, we tracked conformational changes in SNAP25 by total internal reflection fluorescence resonance energy transfer (FRET) microscopy while exocytotic catecholamine release from single vesicles was simultaneously recorded using a microfabricated electrochemical detector array. A local rapid and transient FRET change occurred precisely where individual vesicles released catecholamine. To overcome the low time resolution of the imaging frames needed to collect sufficient signal intensity, a method named event correlation microscopy was developed, which revealed that the FRET change was abrupt and preceded the opening of an exocytotic fusion pore by ∼90 ms. The FRET change correlated temporally with the opening of the fusion pore and not with its dilation.
Germ-line variant of human NTH1 DNA glycosylase induces genomic instability and cellular transformation
Authors: Galick Heather A. , Kathe Scott , Liu Minmin , Robey-Bond Susan , Kidane Dawit , Wallace Susan S. , Sweasy Joann B.
Published: August 2013

Base excision repair (BER) removes at least 20,000 DNA lesions per human cell per day and is critical for the maintenance of genomic stability. We hypothesize that aberrant BER, resulting from mutations in BER genes, can lead to genomic instability and cancer. The first step in BER is catalyzed by DNA
N
-glycosylases. One of these, n
th
endonuclease III-like (NTH1), removes oxidized pyrimidines from DNA, including thymine glycol. The rs3087468 single nucleotide polymorphism of the
NTH1
gene is a G-to-T base substitution that results in the NTH1 D239Y variant protein that occurs in ∼6.2% of the global population and is found in Europeans, Asians, and sub-Saharan Africans. In this study, we functionally characterize the effect of the D239Y variant expressed in immortal but nontransformed human and mouse mammary epithelial cells. We demonstrate that expression of the D239Y variant in cells also expressing wild-type NTH1 leads to genomic instability and cellular transformation as assessed by anchorage-independent growth, focus formation, invasion, and chromosomal aberrations. We also show that cells expressing the D239Y variant are sensitive to ionizing radiation and hydrogen peroxide and accumulate double strand breaks after treatment with these agents. The DNA damage response is also activated in D239Y-expressing cells. In combination, our data suggest that individuals possessing the D239Y variant are at risk for genomic instability and cancer.
Process of inducing pores in membranes by melittin
Authors: Lee Ming-Tao , Sun Tzu-Lin , Hung Wei-Chin , Huang Huey W.
Published: August 2013

Melittin is a prototype of the ubiquitous antimicrobial peptides that induce pores in membranes. It is commonly used as a molecular device for membrane permeabilization. Even at concentrations in the nanomolar range, melittin can induce transient pores that allow transmembrane conduction of atomic ions but not leakage of glucose or larger molecules. At micromolar concentrations, melittin induces stable pores allowing transmembrane leakage of molecules up to tens of kilodaltons, corresponding to its antimicrobial activities. Despite extensive studies, aspects of the molecular mechanism for pore formation remain unclear. To clarify the mechanism, one must know the states of the melittin-bound membrane before and after the process. By correlating experiments using giant unilamellar vesicles with those of peptide-lipid multilayers, we found that melittin bound on the vesicle translocated and redistributed to both sides of the membrane before the formation of stable pores. Furthermore, stable pores are formed only above a critical peptide-to-lipid ratio. The initial states for transient and stable pores are different, which implies different mechanisms at low and high peptide concentrations. To determine the lipidic structure of the pore, the pores in peptide–lipid multilayers were induced to form a lattice and examined by anomalous X-ray diffraction. The electron density distribution of lipid labels shows that the pore is formed by merging of two interfaces through a hole. The molecular property of melittin is such that it adsorbs strongly to the bilayer interface. Pore formation can be viewed as the bilayer adopting a lipid configuration to accommodate its excessive interfacial area.
Differential mobilization of terrestrial carbon pools in Eurasian Arctic river basins
Authors: Feng Xiaojuan , Vonk Jorien E. , van Dongen Bart E. , Gustafsson Örjan , Semiletov Igor P. , Dudarev Oleg V. , Wang Zhiheng , Montluçon Daniel B. , Wacker Lukas , Eglinton Timothy I.
Published: August 2013

Mobilization of Arctic permafrost carbon is expected to increase with warming-induced thawing. However, this effect is challenging to assess due to the diverse processes controlling the release of various organic carbon (OC) pools from heterogeneous Arctic landscapes. Here, by radiocarbon dating various terrestrial OC components in fluvially and coastally integrated estuarine sediments, we present a unique framework for deconvoluting the contrasting mobilization mechanisms of surface vs. deep (permafrost) carbon pools across the climosequence of the Eurasian Arctic. Vascular plant-derived lignin phenol
14
C contents reveal significant inputs of young carbon from surface sources whose delivery is dominantly controlled by river runoff. In contrast, plant wax lipids predominantly trace ancient (permafrost) OC that is preferentially mobilized from discontinuous permafrost regions, where hydrological conduits penetrate deeper into soils and thermokarst erosion occurs more frequently. Because river runoff has significantly increased across the Eurasian Arctic in recent decades, we estimate from an isotopic mixing model that, in tandem with an increased transfer of young surface carbon, the proportion of mobilized terrestrial OC accounted for by ancient carbon has increased by 3–6% between 1985 and 2004. These findings suggest that although partly masked by surface carbon export, climate change-induced mobilization of old permafrost carbon is well underway in the Arctic.
Distinctive topology of age-associated epigenetic drift in the human interactome
Authors: West James , Widschwendter Martin , Teschendorff Andrew E.
Published: August 2013

Recently, it has been demonstrated that DNA methylation, a covalent modification of DNA that can regulate gene expression, is modified as a function of age. However, the biological and clinical significance of this age-associated epigenetic drift is unclear. To shed light on the potential biological significance, we here adopt a systems approach and study the genes undergoing age-associated changes in DNA methylation in the context of a protein interaction network, focusing on their topological properties. In contrast to what has been observed for other age-related gene classes, including longevity- and disease-associated genes, as well as genes undergoing age-associated changes in gene expression, we here demonstrate that age-associated epigenetic drift occurs preferentially in genes that occupy peripheral network positions of exceptionally low connectivity. In addition, we show that these genes synergize topologically with disease and longevity genes, forming unexpectedly large network communities. Thus, these results point toward a potentially distinct mechanistic and biological role of DNA methylation in dictating the complex aging and disease phenotypes.
Knots and nonorientable surfaces in chiral nematics
Authors: Machon Thomas , Alexander Gareth P.
Published: August 2013

Knots and knotted fields enrich physical phenomena ranging from DNA and molecular chemistry to the vortices of fluid flows and textures of ordered media. Liquid crystals provide an ideal setting for exploring such topological phenomena through control of their characteristic defects. The use of colloids in generating defects and knotted configurations in liquid crystals has been demonstrated for spherical and toroidal particles and shows promise for the development of novel photonic devices. Extending this existing work, we describe the full topological implications of colloids representing nonorientable surfaces and use it to construct torus knots and links of type (
p
,2) around multiply twisted Möbius strips.
Cryoelectron tomography reveals the sequential assembly of bacterial flagella in
Borrelia burgdorferi
Authors: Zhao Xiaowei , Zhang Kai , Boquoi Tristan , Hu Bo , Motaleb M. A. , Miller Kelly A. , James Milinda E. , Charon Nyles W. , Manson Michael D. , Norris Steven J. , Li Chunhao , Liu Jun
Published: August 2013

Periplasmic flagella are essential for the distinctive morphology, motility, and infectious life cycle of the Lyme disease spirochete
Borrelia burgdorferi
. In this study, we genetically trapped intermediates in flagellar assembly and determined the 3D structures of the intermediates to 4-nm resolution by cryoelectron tomography. We provide structural evidence that secretion of rod substrates triggers remodeling of the central channel in the flagellar secretion apparatus from a closed to an open conformation. This open channel then serves as both a gateway and a template for flagellar rod assembly. The individual proteins assemble sequentially to form a modular rod. The hook cap initiates hook assembly on completion of the rod, and the filament cap facilitates filament assembly after formation of the mature hook. Cryoelectron tomography and mutational analysis thus combine synergistically to provide a unique structural blueprint of the assembly process of this intricate molecular machine in intact cells.
Cavity cooling of an optically levitated submicron particle
Authors: Kiesel Nikolai , Blaser Florian , Delić Uroš , Grass David , Kaltenbaek Rainer , Aspelmeyer Markus
Published: August 2013

The coupling of a levitated submicron particle and an optical cavity field promises access to a unique parameter regime both for macroscopic quantum experiments and for high-precision force sensing. We report a demonstration of such controlled interactions by cavity cooling the center-of-mass motion of an optically trapped submicron particle. This paves the way for a light–matter interface that can enable room-temperature quantum experiments with mesoscopic mechanical systems.
Human circulating influenza-CD4
+
ICOS1
+
IL-21
+
T cells expand after vaccination, exert helper function, and predict antibody responses
Authors: Spensieri Fabiana , Borgogni Erica , Zedda Luisanna , Bardelli Monia , Buricchi Francesca , Volpini Gianfranco , Fragapane Elena , Tavarini Simona , Finco Oretta , Rappuoli Rino , Del Giudice Giuseppe , Galli Grazia , Castellino Flora
Published: August 2013

Protection against influenza is mediated by neutralizing antibodies, and their induction at high and sustained titers is key for successful vaccination. Optimal B cells activation requires delivery of help from CD4
+
T lymphocytes. In lymph nodes and tonsils, T-follicular helper cells have been identified as the T cells subset specialized in helping B lymphocytes, with interleukin-21 (IL-21) and inducible costimulatory molecule (ICOS1) playing a central role for this function. We followed the expansion of antigen-specific IL-21
+
CD4
+
T cells upon influenza vaccination in adults. We show that, after an overnight in vitro stimulation, influenza-specific IL-21
+
CD4
+
T cells can be measured in human blood, accumulate in the CXCR5
−
ICOS1
+
population, and increase in frequency after vaccination. The expansion of influenza-specific ICOS1
+
IL-21
+
CD4
+
T cells associates with and predicts the rise of functionally active antibodies to avian H5N1. We also show that blood-derived CXCR5
−
ICOS1
+
CD4
+
T cells exert helper function in vitro and support the differentiation of influenza specific B cells in an ICOS1- and IL-21–dependent manner. We propose that the expansion of antigen-specific ICOS1
+
IL-21
+
CD4
+
T cells in blood is an early marker of vaccine immunogenicity and an important immune parameter for the evaluation of novel vaccination strategies.
The allosteric communication pathways in KIX domain of CBP
Authors: Palazzesi Ferruccio , Barducci Alessandro , Tollinger Martin , Parrinello Michele
Published: August 2013

Allosteric regulation plays an important role in a myriad of biomacromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the discovery of this phenomenon, models built on static images of proteins are being reconsidered with the knowledge that protein dynamics plays an important role in its function. Molecular dynamics simulations are a valuable tool for studying complex biomolecular systems, providing an atomistic description of their structure and dynamics. Unfortunately, their predictive power has been limited by the complexity of the biomolecule free-energy surface and by the length of the allosteric timescale (in the order of milliseconds). In this work, we are able to probe the origins of the allosteric changes that transcription factor mixed lineage leukemia (MLL) causes to the interactions of KIX domain of CREB-binding protein (CBP) with phosphorylated kinase inducible domain (pKID), by combing all-atom molecular dynamics with enhanced sampling methods recently developed in our group. We discuss our results in relation to previous NMR studies. We also develop a general simulations protocol to study allosteric phenomena and many other biological processes that occur in the micro/milliseconds timescale.
Aurora B suppresses microtubule dynamics and limits central spindle size by locally activating KIF4A
Authors: Nunes Bastos Ricardo , Gandhi Sapan R. , Baron Ryan D. , Gruneberg Ulrike , Nigg Erich A. , Barr Francis A.
Published: August 2013

Anaphase central spindle formation is controlled by the microtubule-stabilizing factor PRC1 and the kinesin KIF4A. We show that an MKlp2-dependent pool of Aurora B at the central spindle, rather than global Aurora B activity, regulates KIF4A accumulation at the central spindle. KIF4A phosphorylation by Aurora B stimulates the maximal microtubule-dependent ATPase activity of KIF4A and promotes its interaction with PRC1. In the presence of phosphorylated KIF4A, microtubules grew more slowly and showed long pauses in growth, resulting in the generation of shorter PRC1-stabilized microtubule overlaps in vitro. Cells expressing only mutant forms of KIF4A lacking the Aurora B phosphorylation site overextended the anaphase central spindle, demonstrating that this regulation is crucial for microtubule length control in vivo. Aurora B therefore ensures that suppression of microtubule dynamic instability by KIF4A is restricted to a specific subset of microtubules and thereby contributes to central spindle size control in anaphase.
Epiblast integrity requires CLASP and Dystroglycan-mediated microtubule anchoring to the basal cortex
Authors: Nakaya Yukiko , Sukowati Erike W. , Sheng Guojun
Published: August 2013

Amniote epiblast cells differentiate into mesoderm and endoderm lineages during gastrulation through a process called epithelial-to-mesenchymal transition (EMT). Molecular regulation of gastrulation EMT is poorly understood. Here we show that epiblast epithelial status was maintained by anchoring microtubules to the basal cortex via CLIP-associated protein (CLASP), a microtubule plus-end tracking protein, and Dystroglycan, a transmembrane protein that bridges the cytoskeleton and basement membrane (BM). Mesoderm formation required down-regulation of CLASP and Dystroglycan, and reducing CLASP activity in pregastrulation epiblast cells caused ectopic BM breakdown and disrupted epiblast integrity. These effects were mediated through the CLASP-binding partner LL5. Live-imaging using EB1–enhanced GFP (eGFP) revealed that reducing CLASP and LL5 levels in the epiblast destabilized basal microtubules. We further show that Dystroglycan is localized to basolateral membrane in epiblast cells. Basal but not lateral localization of Dystroglycan was regulated by CLASP. We propose that epiblast–BM interaction requires CLASP- and Dystroglycan-mediated cortical microtubule anchoring, the disruption of which initiates gastrulation EMT.
Coreceptor affinity for MHC defines peptide specificity requirements for TCR interaction with coagonist peptide–MHC
Authors: Hoerter John A.H. , Brzostek Joanna , Artyomov Maxim N. , Abel Steven M. , Casas Javier , Rybakin Vasily , Ampudia Jeanette , Lotz Carina , Connolly Janet M. , Chakraborty Arup K. , Gould Keith G. , Gascoigne Nicholas R.J.
Published: August 2013

Recent work has demonstrated that nonstimulatory endogenous peptides can enhance T cell recognition of antigen, but MHCI- and MHCII-restricted systems have generated very different results. MHCII-restricted TCRs need to interact with the nonstimulatory peptide–MHC (pMHC), showing peptide specificity for activation enhancers or coagonists. In contrast, the MHCI-restricted cells studied to date show no such peptide specificity for coagonists, suggesting that CD8 binding to noncognate MHCI is more important. Here we show how this dichotomy can be resolved by varying CD8 and TCR binding to agonist and coagonists coupled with computer simulations, and we identify two distinct mechanisms by which CD8 influences the peptide specificity of coagonism. Mechanism 1 identifies the requirement of CD8 binding to noncognate ligand and suggests a direct relationship between the magnitude of coagonism and CD8 affinity for coagonist pMHCI. Mechanism 2 describes how the affinity of CD8 for agonist pMHCI changes the requirement for specific coagonist peptides. MHCs that bind CD8 strongly were tolerant of all or most peptides as coagonists, but weaker CD8-binding MHCs required stronger TCR binding to coagonist, limiting the potential coagonist peptides. These findings in MHCI systems also explain peptide-specific coagonism in MHCII-restricted cells, as CD4–MHCII interaction is generally weaker than CD8–MHCI.
Badger—an accessible genome exploration environment
Authors: Elsworth Ben , Jones Martin , Blaxter Mark
Published: August 2013

Summary: High-quality draft genomes are now easy to generate, as sequencing and assembly costs have dropped dramatically. However, building a user-friendly searchable Web site and database for a newly annotated genome is not straightforward. Here we present Badger, a lightweight and easy-to-install genome exploration environment designed for next generation non-model organism genomes.

Availability: Badger is released under the GPL and is available at http://badger.bio.ed.ac.uk/. We show two working examples: (i) a test dataset included with the source code, and (ii) a collection of four filarial nematode genomes.

Contact: mark.blaxter@ed.ac.uk
Do Political Protests Matter? Evidence from the Tea Party Movement*
Authors: Madestam Andreas , Shoag Daniel , Veuger Stan , Yanagizawa-Drott David
Published: August 2013

Can protests cause political change, or are they merely symptoms of underlying shifts in policy preferences? We address this question by studying the Tea Party movement in the United States, which rose to prominence through coordinated rallies across the country on Tax Day, April 15, 2009. We exploit variation in rainfall on the day of these rallies as an exogenous source of variation in attendance. We show that good weather at this initial, coordinating event had significant consequences for the subsequent local strength of the movement, increased public support for Tea Party positions, and led to more Republican votes in the 2010 midterm elections. Policy making was also affected, as incumbents responded to large protests in their district by voting more conservatively in Congress. Our estimates suggest significant multiplier effects: an additional protester increased the number of Republican votes by a factor well above 1. Together our results show that protests can build political movements that ultimately affect policy making and that they do so by influencing political views rather than solely through the revelation of existing political preferences.
Acute Uterine Irritation Provokes Colonic Motility via Transient Receptor Potential A1-dependent Spinal NR2B Phosphorylation in Rats
Authors: Peng Hsien-Yu , Yeh Chou-Ming , Cheng Jen-Kun , Chau Yat-Pang , Ruan Ting , Chen Gin-Den , Hsieh Ming-Chun , Lai Cheng-Yuan , Lin Tzer-Bin
Published: August 2013

Background:

Patients with inflammatory gynecological/obstetrical problems often complain of irritable bowel syndrome. The authors examined whether acute uterus irritation reflexively provokes colonic motility in rat preparations.

Methods:

A modified colon manometry and striated abdominal muscle electromyogram activity in response to mustard oil (MO) instillation into the uterine horn were continuously recorded in anesthetized rats. The lumbosacral (L6-S1) dorsal horn was dissected to assess the level and the cellular location of phosphorylated NR2B subunit using Western blotting and immunofluorescence analysis, respectively. Finally, the uterine transient receptor potential A1 or spinal NR2B subunit was pharmacologically blocked to elucidate its roles.

Results:

MO (0.1%, 0.2 ml) injected into the lower uterine horn dramatically provoked colonic hypermotility characterized by rhythmic colonic contractions (about 3–4 contractions per 10 min, n = 7) accompanied by synchronized electromyogram firing in the abdominal muscle (about 4–5 folds of control, n = 7). In addition to provoking colonic hypermotility, MO administration also up-regulated phosphorylated (about 2–3 folds of control, n = 7), but not total, NR2B expression in the dorsal horn neurons. Both intrathecal Ro 25–6981 (a selective NR2B subunit antagonist; 10 μM, 10 μl) and intrauterine HC-030031 (a selective transient receptor potential A1 receptor antagonist; 30 mg/kg, 0.2 ml) injected before the MO instillation attenuated the MO-induced colonic hypermotility and spinal NR2B phosphorylation.

Conclusion:

The comorbidity of gynecological/obstetrical and gastrointestinal problems is not coincidental but rather causal in nature, and clinicians should investigate for gynecological/urological diseases in the setting of bowel problems with no known pathological etiology.
Peroral Endoscopic Myotomy for the Treatment of Achalasia in Children
Authors: Familiari Pietro , Marchese Michele , Gigante Giovanni , Boskoski Ivo , Tringali Andrea , Perri Vincenzo , Costamagna Guido
Published: August 2013

Peroral endoscopic myotomy (POEM) is a new endoscopic technique for the treatment of esophageal achalasia, with excellent results in adults. Three children with classic‐type achalasia (mean age 9.6 years) underwent POEM in a single center. Mean basal lower esophageal sphincter pressure and Eckard score were 34.6 mmHg and 5.3, respectively. Mean length of myotomy was 10 cm. On average, POEM was completed in 60.6 minutes. No patients experienced postoperative complications or gastroesophageal reflux disease. In the 2 patients who completed a 12‐month follow‐up, complete symptoms relief was documented (Eckard score 0), as well as a significant drop of the basal lower esophageal sphincter pressure.
Comprehensive analysis of endogenous bornavirus-like elements in eukaryote genomes
Authors: Horie Masayuki , Kobayashi Yuki , Suzuki Yoshiyuki , Tomonaga Keizo
Published: August 2013

Bornaviruses are the only animal RNA viruses that establish a persistent infection in their host cell nucleus. Studies of bornaviruses have provided unique information about viral replication strategies and virus–host interactions. Although bornaviruses do not integrate into the host genome during their replication cycle, we and others have recently reported that there are DNA sequences derived from the mRNAs of ancient bornaviruses in the genomes of vertebrates, including humans, and these have been designated endogenous borna-like (EBL) elements. Therefore, bornaviruses have been interacting with their hosts as driving forces in the evolution of host genomes in a previously unexpected way. Studies of EBL elements have provided new models for virology, evolutionary biology and general cell biology. In this review, we summarize the data on EBL elements including what we have newly identified in eukaryotes genomes, and discuss the biological significance of EBL elements, with a focus on EBL nucleoprotein elements in mammalian genomes. Surprisingly, EBL elements were detected in the genomes of invertebrates, suggesting that the host range of bornaviruses may be much wider than previously thought. We also review our new data on non-retroviral integration of Borna disease virus.
Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals
Authors: Lee Adam , Nolan Alison , Watson Jason , Tristem Michael
Published: August 2013

The evolutionary arms race between mammals and retroviruses has long been recognized as one of the oldest host–parasite interactions. Rapid evolution rates in exogenous retroviruses have often made accurate viral age estimations highly problematic. Endogenous retroviruses (ERVs), however, integrate into the germline of their hosts, and are subjected to their evolutionary rates. This study describes, for the first time, a retroviral orthologue predating the divergence of placental mammals, giving it a minimum age of 104–110 Myr. Simultaneously, other orthologous selfish genetic elements (SGEs), inserted into the ERV sequence, provide evidence for the oldest individual mammalian-wide interspersed repeat and medium-reiteration frequency interspersed repeat mammalian repeats, with the same minimum age. The combined use of shared SGEs and reconstruction of viral orthologies defines new limits and increases maximum ‘lookback’ times, with subsequent implications for the field of paleovirology.
Pushing the endogenous envelope
Authors: Henzy Jamie E. , Johnson Welkin E.
Published: August 2013

The majority of retroviral envelope glycoproteins characterized to date are typical of type I viral fusion proteins, having a receptor binding subunit associated with a fusion subunit. The fusion subunits of lentiviruses and alpha-, beta-, delta- and gammaretroviruses have a very conserved domain organization and conserved features of secondary structure, making them suitable for phylogenetic analyses. Such analyses, along with sequence comparisons, reveal evidence of numerous recombination events in which retroviruses have acquired envelope glycoproteins from heterologous sequences. Thus, the envelope gene (
env
) can have a history separate from that of the polymerase gene (
pol
), which is the most commonly used gene in phylogenetic analyses of retroviruses. Focusing on the fusion subunits of the genera listed above, we describe three distinct types of retroviral envelope glycoproteins, which we refer to as gamma-type, avian gamma-type and beta-type. By tracing these types within the ‘fossil record’ provided by endogenous retroviruses, we show that they have surprisingly distinct evolutionary histories and dynamics, with important implications for cross-species transmissions and the generation of novel lineages. These findings validate the utility of
env
sequences in contributing phylogenetic signal that enlarges our understanding of retrovirus evolution.
Paleovirology of ‘
syncytins
’, retroviral
env
genes exapted for a role in placentation
Authors: Lavialle Christian , Cornelis Guillaume , Dupressoir Anne , Esnault Cécile , Heidmann Odile , Vernochet Cécile , Heidmann Thierry
Published: August 2013

The development of the emerging field of ‘paleovirology’ allows biologists to reconstruct the evolutionary history of fossil endogenous retroviral sequences integrated within the genome of living organisms and has led to the retrieval of conserved, ancient retroviral genes ‘exapted’ by ancestral hosts to fulfil essential physiological roles,
syncytin
genes being undoubtedly among the most remarkable examples of such a phenomenon. Indeed, s
yncytins
are ‘new’ genes encoding proteins derived from the envelope protein of endogenous retroviral elements that have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution. Knockout of
syncytin
genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell–cell fusion of syncytial cell layers at the fetal–maternal interface. These genes of exogenous origin, acquired ‘by chance’ and yet still ‘necessary’ to carry out a basic function in placental mammals, may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral
env
gene, subsequently replaced in the diverse mammalian lineages by new
env-
derived
syncytin
genes, each providing its host with a positive selective advantage.
When parasitic wasps hijacked viruses: genomic and functional evolution of polydnaviruses
Authors: Herniou Elisabeth A. , Huguet Elisabeth , Thézé Julien , Bézier Annie , Periquet Georges , Drezen Jean-Michel
Published: August 2013

The
Polydnaviridae
(PDV), including the
Bracovirus
(BV) and
Ichnovirus
genera, originated from the integration of unrelated viruses in the genomes of two parasitoid wasp lineages, in a remarkable example of convergent evolution. Functionally active PDVs represent the most compelling evolutionary success among endogenous viral elements (EVEs). BV evolved from the domestication by braconid wasps of a nudivirus 100 Ma. The nudivirus genome has become an EVE involved in BV particle production but is not encapsidated. Instead, BV genomes have co-opted virulence genes, used by the wasps to control the immunity and development of their hosts. Gene transfers and duplications have shaped BV genomes, now encoding hundreds of genes. Phylogenomic studies suggest that BVs contribute largely to wasp diversification and adaptation to their hosts. A genome evolution model explains how multidirectional wasp adaptation to different host species could have fostered PDV genome extension. Integrative studies linking ecological data on the wasp to genomic analyses should provide new insights into the adaptive role of particular BV genes. Forthcoming genomic advances should also indicate if the associations between endoparasitoid wasps and symbiotic viruses evolved because of their particularly intimate interactions with their hosts, or if similar domesticated EVEs could be uncovered in other parasites.