bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP
Authors: Hauer Christian , Curk Tomaz , Anders Simon , Schwarzl Thomas , Alleaume Anne-Marie , Sieber Jana , Hollerer Ina , Bhuvanagiri Madhuri , Huber Wolfgang , Hentze Matthias W. , Kulozik Andreas E. 
Published: August 2015

AbstractIndividual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) allows the determination of crosslinking sites of RNA-binding proteins (RBPs) on RNAs. iCLIP is based on ultraviolet light crosslinking of RBPs to RNA, reverse transcription and high-throughput sequencing of fragments terminating at the site of crosslinking. As a result, start sites of iCLIP fragments are expected to cluster with a narrow distribution, typically representing the site of direct interaction between the RBP and the RNA. Here we show that for several RBPs (eIF4A3, PTB, SRSF3, SRSF4 and hnRNP L), the start sites of iCLIP fragments show a fragment length-dependent broader distribution that can be shifted to positions upstream of the known RNA-binding site. We developed an analysis tool that identifies these shifts and can improve the positioning of RBP binding sites.
Whole-central nervous system functional imaging in larval Drosophila
Authors: Lemon William C. , Pulver Stefan R. , Höckendorf Burkhard , McDole Katie , Branson Kristin , Freeman Jeremy , Keller Philipp J. 
Published: August 2015

AbstractUnderstanding how the brain works in tight concert with the rest of the central nervous system (CNS) hinges upon knowledge of coordinated activity patterns across the whole CNS. We present a method for measuring activity in an entire, non-transparent CNS with high spatiotemporal resolution. We combine a light-sheet microscope capable of simultaneous multi-view imaging at volumetric speeds 25-fold faster than the state-of-the-art, a whole-CNS imaging assay for the isolated Drosophila larval CNS and a computational framework for analysing multi-view, whole-CNS calcium imaging data. We image both brain and ventral nerve cord, covering the entire CNS at 2 or 5 Hz with two- or one-photon excitation, respectively. By mapping network activity during fictive behaviours and quantitatively comparing high-resolution whole-CNS activity maps across individuals, we predict functional connections between CNS regions and reveal neurons in the brain that identify type and temporal state of motor programs executed in the ventral nerve cord.
Dynamic markers based on blood perfusion fluctuations for selecting skin melanocytic lesions for biopsy
Authors: Lancaster Gemma , Stefanovska Aneta , Pesce Margherita , Marco Vezzoni Gian , Loggini Barbara , Pingitore Raffaele , Ghiara Fabrizio , Barachini Paolo , Cervadoro Gregorio , Romanelli Marco , Rossi Marco 
Published: August 2015

AbstractSkin malignant melanoma is a highly angiogenic cancer, necessitating early diagnosis for positive prognosis. The current diagnostic standard of biopsy and histological examination inevitably leads to many unnecessary invasive excisions. Here, we propose a non-invasive method of identification of melanoma based on blood flow dynamics. We consider a wide frequency range from 0.005–2 Hz associated with both local vascular regulation and effects of cardiac pulsation. Combining uniquely the power of oscillations associated with individual physiological processes we obtain a marker which distinguishes between melanoma and atypical nevi with sensitivity of 100% and specificity of 90.9%. The method reveals valuable functional information about the melanoma microenvironment. It also provides the means for simple, accurate, in vivo distinction between malignant melanoma and atypical nevi and may lead to a substantial reduction in the number of biopsies currently undertaken.
Integrated miRNA-mRNA analysis in the habenula nuclei of mice intravenously self-administering nicotine
Authors: Lee Sangjoon , Woo Jiwan , Kim Yong Sik , Im Heh-In 
Published: August 2015

AbstractA considerable amount of evidence suggests that microRNAs (miRNAs) play crucial roles in the neuroadaptation of drug addiction. Habenula (Hb), one of the critical brain regions involved in reward and addiction, can be divided into two anatomically and transcriptionally distinct regions: medial habenula (MHb) and lateral habenula (LHb) nuclei. However, very few studies have compared the functional roles of these regions. Here, by using mirConnX integrator and KEGG pathway mapping, we simultaneously analysed the differential expression patterns of miRNAs and messenger RNA (mRNA) within MHb and LHb under nicotine addiction. Significantly altered miRNAs and mRNAs were found in the Hb of mice intravenously self-administering nicotine. Interestingly, some miRNAs were oppositely regulated between the MHb and the LHb and their potential targets included various genes of cell signalling pathways related to the degeneration of fasciculus retroflexus (FR). This study provides an improved insight into the differential regulation of habenular transcripts in nicotine addiction, as well as the potential functions of miRNAs in several biological pathways involved in the nicotine addiction.
miR-98 and its host gene Huwe1 target Caspase-3 in Silica nanoparticles-treated male germ cells
Authors: Xu Bo , Mao Zhilei , Ji Xiaoli , Yao Mengmeng , Chen Minjian , Zhang Xuemei , Hang Bo , Liu Yi , Tang Wei , Tang Qiusha , Xia Yankai 
Published: August 2015

AbstractSilica nanoparticles (NP) is one of the most commonly used nanomaterials with potential health hazards. However, the effects of Silica NP on germ cells and the underlying mechanisms are still unclear. In this study, GC-2 and TM-4, which are two different types of male germ cells were exposed to Silica NP for 24h and then general cytotoxicity and multi-parameter cytotoxicity were evaluated. Our results showed that Silica NP could induce apoptosis in GC-2 cells. Transmission electron microscopy (TEM) results showed that Silica NP was localized in the lysosomes of GC-2 cells. High content screening (HCS) showed that Silica NP exposure could increased cell permeabilization and decreased mitochondrial membrane potential in GC-2 cells. The mRNA and protein levels of apoptosis markers (Bax, Caspase-3, Caspase-9) in GC-2 cells were significantly increased, while Bcl-2 was decreased. Accordingly, the expression level of miR-98, which can regulate Caspase-3, was significantly decreased. Huwe1, the host gene of miR-98, was positively associated with miR-98 expression after Silica NP exposure. Dual luciferase reporter assay suggested that miR-98 directly targets Caspase-3. These results suggest that Silica NP induces apoptosis via loss of mitochondrial membrane potential and Caspase-3 activation, while miR-98 plays key role in modulating this effect.
Highly Pathogenic Avian Influenza A(H5N1) Virus Struck Migratory Birds in China in 2015
Authors: Bi Yuhai , Zhang Zhenjie , Liu Wenjun , Yin Yanbo , Hong Jianmin , Li Xiangdong , Wang Haiming , Wong Gary , Chen Jianjun , Li Yunfeng , Ru Wendong , Gao Ruyi , Liu Di , Liu Yingxia , Zhou Boping , Gao George F. , Shi Weifeng , Lei Fumin 
Published: August 2015

AbstractApproximately 100 migratory birds, including whooper swans and pochards, were found dead in the Sanmenxia Reservoir Area of China during January 2015. The causative agent behind this outbreak was identified as H5N1 highly pathogenic avian influenza virus (HPAIV). Genetic and phylogenetic analyses revealed that this Sanmenxia H5N1 virus was a novel reassortant, possessing a Clade 2.3.2.1c HA gene and a H9N2-derived PB2 gene. Sanmenxia Clade 2.3.2.1c-like H5N1 viruses possess the closest genetic identity to A/Alberta/01/2014 (H5N1), which recently caused a fatal respiratory infection in Canada with signs of meningoencephalitis, a highly unusual symptom with influenza infections in humans. Furthermore, this virus was shown to be highly pathogenic to both birds and mammals and demonstrate tropism for the nervous system. Due to the geographical location of Sanmenxia, these novel H5N1 viruses also have the potential to be imported to other regions through the migration of wild birds, similar to the H5N1 outbreak amongst migratory birds in Qinghai Lake during 2005. Therefore, further investigation and monitoring is required to prevent this novel reassortant virus from becoming a new threat to public health.
High ROR2 expression in tumor cells and stroma is correlated with poor prognosis in pancreatic ductal adenocarcinoma
Authors: Huang Jianfei , Fan Xiangjun , Wang Xudong , Lu Yuhua , Zhu Huijun , Wang Wei , Zhang Shu , Wang Zhiwei 
Published: August 2015

AbstractRTK-like orphan receptor 2 (ROR2) is overexpressed in several cancers and has tumorigenic activity. However, the expression of ROR2 and its functional and prognostic significance have yet to be evaluated in pancreatic ductal adenocarcinoma (PDAC). Quantitative real-time polymerase chain reaction was used to characterize the expression of ROR2 mRNA in PDAC, corresponding peritumoral tissues and PDAC cell lines. Immunohistochemical analysis with tissue microarrays was used to evaluate ROR2 expression in PDAC and to investigate the relationship of this expression to clinicopathological factors and prognosis. The expression of ROR2 mRNA and protein was significantly higher in PDAC than in normal pancreatic tissues. High cytoplasmic ROR2 expression in cancer cells was significantly associated with a primary tumor, distant metastasis and TNM stage and high stromal ROR2 expression was significantly associated with regional lymph node metastasis and TNM stage. The Kaplan–Meier method and Cox regression analyses showed that high ROR2 expression in tumor cytoplasm or stromal cells was significantly associated with malignant attributes and reduced survival in PDAC. We present strong evidence that ROR2 could be used as an indicator of poor prognosis and could represent a novel therapeutic target for PDAC.
Studies in copper status and atherosclerosis
Authors: KINSMAN G. D. , HOWARD A. N. , STONE D. L. , MULLINS P. A. 
Published: August 2015

Summary
Findings of this paper indicate that leucocyte copper has a significant link with the level of atherosclerosis found within the groups studied. Therefore copper may be involved in the mechanisms associated with ischaemic heart disease (IHD).
Rhizobium meliloti exopolysaccharides: genetic analyses and symbiotic importance
Authors: Reuber T. Lynne , Reed Jason , Glazebrook Jane , Glucksmann M. Alexandra , Ahmann Dianne , Marra Andrea , Walker Graham C. 
Published: August 2015

Summary
Genetic experiments have indicated that succinoglycan (EPS I), the acidic Calcofluor-binding exopolysaccharide, of the nitrogen-fixing bacterium Rhizobium meliloti strain Rm1021 is required for nodule invasion and possibly for later events in nodule development on alfalfa and other hosts. Fourteen exo loci on the second megaplasmid have been identified that are required for, or affect, the synthesis of EPS I. Mutations in certain of these loci completely abolish the production of EPS I and result in mutants that form empty Fix- nodules. We have identified two loci, exoR and exoS, that are involved in the regulation of EPS I synthesis in the free-living state. Certain exo mutations which completely abolish EPS I production are lethal in an exoR95 or exoS96 background. Histochemical analyses of the expression of exo genes during nodulation using exo :: TnphoA fusions have indicated that the exo genes are expressed most strongly in the invasion zone. In addition, we have discovered that R. meliloti has a latent capacity to synthesize a second exopolysaccharide (EPS II) that can substitute for the role(s) of EPS I in nodulation of alfalfa but not of other hosts. Possible roles for exopolysaccharides in symbiosis are discussed.
Binding sites of lipophilic quinone and quinone analogue inhibitors in the cytochrome b6f complex of oxygenic photosynthesis
Authors: Cramer W.A. , Zhang H. , Yan J. , Kurisu G. 
Published: August 2015

The main structural features of the cytochrome b6f complex, solved to 3.0–3.1 Å (1 Å=10−10 m) in the cyanobacterium Mastigocladus laminosus and the green alga Chlamydomonas reinhardtii are discussed. The discussion is focused on the binding sites of plastoquinone and quinone analogue inhibitors discerned in the structure. These sites mark the pathway(s) of quinone translocation across the complex.
A molecular understanding of the catalytic cycle of the nucleotide-binding domain of the ABC transporter HlyB
Authors: Zaitseva J. , Jenewein S. , Oswald C. , Jumpertz T. , Holland I.B. , Schmitt L. 
Published: August 2015

The ABC transporter (ATP-binding-cassette transporter) HlyB (haemolysin B) is the central element of a type I secretion machinery, dedicated to the secretion of the toxin HlyA in Escherichia coli. In addition to the ABC transporter, two other indispensable elements are necessary for the secretion of the toxin across two membranes in a single step: the transenvelope protein HlyD and the outer membrane protein TolC. Despite the fact that the hydrolysis of ATP by HlyB fuels secretion of HlyA, the essential features of the underlying transport mechanism remain an enigma. Similar to all other ABC transporters, ranging from bacteria to man, HlyB is composed of two NBDs (nucleotide-binding domains) and two transmembrane domains. Here we summarize our detailed biochemical, biophysical and structural studies aimed at an understanding of the molecular principles of how ATP-hydrolysis is coupled to energy transduction, including the conformational changes occurring during the catalytic cycle, leading to substrate transport. We have obtained individual crystal structures for each single ground state of the catalytic cycle. From these and other biochemical and mutational studies, we shall provide a detailed molecular picture of the steps governing intramolecular communication and the utilization of chemical energy, due to ATP hydrolysis, in relation to resulting structural changes within the NBD. These data will be summarized in a general model to explain how these molecular machines achieve translocation of molecules across biological membranes.
Do protein–lipid interactions determine the recognition of transmembrane helices at the ER translocon?
Authors: White S.H. , von Heijne G. 
Published: August 2015

Membrane-protein integration, folding and assembly processes in vivo depend on complex targeting, translocation, chaperoning, and sorting machineries that somehow read the ‘molecular code’ built into the nascent polypeptide, ultimately producing a properly folded protein integrated into the correct target membrane. Although the main molecular constituents and the basic mechanistic principles of many of these machines are known in outline, the codes remain poorly defined and there is little quantitative information on how protein sequence affects the final structure of membrane proteins. By carefully designing model protein constructs, we have derived the first true biological hydrophobicity scale and have been able to get a first impression of how the position of a given type of residue within a transmembrane segment affects its ability to promote membrane insertion.
The regulation of membrane to cytosol partitioning of signalling proteins by phosphoinositides and their soluble headgroups
Authors: Downes C.P. , Gray A. , Fairservice A. , Safrany S.T. , Batty I.H. , Fleming I. 
Published: August 2015

Inositol phospholipids [PIs (phosphoinositides)] represent a group of membrane-tethered signalling molecules which differ with respect to the number and distribution of monoester phosphate groups around the inositol ring. They function by binding to proteins which possess one of several domains that bind a particular PI species, often with high affinity and specificity. PH (pleckstrin homology) domains for example possess ligand-binding pockets that are often lined with positively charged residues and which bind PIs with varying degrees of specificity. Several PH domains bind not only PIs, but also their cognate headgroups, many of which occur naturally in cells as relatively abundant cytosolic inositol phosphates. The subcellular distributions of proteins possessing such PH domains are therefore determined by the relative levels of competing membrane-bound and soluble ligands. A classic example of the latter is the PH domain of phospholipase Cδ1, which binds both phosphatidylinositol 4,5-bisphosphate and inositol 1,4,5-trisphosphate. We have shown that the N-terminal PH domain of the Rho family guanine nucleotide-exchange factor, Tiam 1, binds PI ligands promiscuously allowing multiple modes of regulation. We also recently analysed the ligand-binding specificity of the PH domain of PI-dependent kinase 1 and found that it could bind abundant inositol polyphosphates such as inositol hexakisphosphate. This could explain the dual distribution of this key signalling component, which needs to access substrates at both the plasma membrane and in the cytosol.
Genetic manipulation and functional analysis of cAMP signalling in cardiac muscle: implications for a new target of pharmacotherapy
Authors: Ishikawa Y. , Iwatsubo K. , Tsunematsu T. , Okumura S. 
Published: August 2015

Adenylate cyclase is a membrane-bound enzyme that catalyses the conversion of ATP into cAMP upon activation of cell-surface G-protein-coupled receptors, such as β-adrenergic receptors, and initiates a cascade of phosphorylation reactions within the cell. Type 5 adenylate cyclase is a major isoform in the heart as well as in the striatum of the brain. Mice with a disrupted type 5 adenylate cyclase gene exhibited normal cardiac function under basal conditions, but a decreased response to isoprenaline stimulation. When mice were subjected to pressure overload stress with aortic banding, they developed cardiac hypertrophy, but with a significant reduction in the number of apoptotic cardiac myocytes as well as preserved cardiac function. When type 5 adenylate cyclase activity was inhibited pharmacologically, by the use of a novel P-site inhibitor with enhanced selectivity for this isoform, there were no changes in cardiac myocyte contractility, but the development of cardiac myocyte apoptosis induced by isoprenaline stimulation was effectively prevented. These results indicate that type 5 adenylate cyclase may serve as a better target of pharmacotherapy to prevent the development of cardiac myocyte apoptosis and thus failure in response to various cardiac stresses.
Myocardial phenotyping using isotopomer analysis of metabolic fluxes
Authors: Des Rosiers C. , Chatham J.C. 
Published: August 2015

Over the past 20 years, stable isotopes combined with isotopomer analysis have proven to be a powerful approach to probe the dynamics of metabolism in various biological systems, including the heart. The aim of this paper is to demonstrate how isotopomer analysis of metabolic fluxes can provide novel insights into the myocardial phenotype. Specifically, building on our past experience using NMR spectroscopy and GC–MS as applied to investigations of cardiac energy metabolism, we highlight specific complex metabolic networks that would not be predicted by classical biochemistry or by static measurements of metabolite, protein and mRNA levels.
Induced pluripotent stem cell (iPSC)-derived dopaminergic models of Parkinson's disease
Authors: Beevers Joel E. , Caffrey Tara M. , Wade-Martins Richard 
Published: August 2015

iPSCs (induced pluripotent stem cells) are the newest tool used to model PD (Parkinson's disease). Fibroblasts from patients carrying pathogenic mutations that lead to PD have been reprogrammed into iPSCs, which can subsequently be differentiated into important cell types. Given the characteristic loss of dopaminergic neurons in the substantia nigra pars compacta of PD patients, iPSC-derived midbrain dopaminergic neurons have been generated to investigate pathogenic mechanisms in this important cell type as a means of modelling PD. iPSC-derived cultures studied so far have been made from patients carrying mutations in LRRK2 (leucine-rich repeat kinase 2), PINK1 [PTEN (phosphatase and tensin homologue deleted on chromosome 10)-induced putative kinase 1], PARK2 (encodes parkin) or GBA (β-glucocerebrosidase), in addition to those with SNCA (α-synuclein) multiplication and idiopathic PD. In some cases, isogenic control lines have been created to minimize inherent variability between lines from different individuals. Disruptions in autophagy, mitochondrial function and dopamine biology at the synapse have been described. Future applications for iPSC-derived models of PD beyond modelling include drug testing and the ability to investigate the genetic diversity of PD.
Metabolic signatures linked to macrophage polarization: from glucose metabolism to oxidative phosphorylation
Authors: Boscá Lisardo , González-Ramos Silvia , Prieto Patricia , Fernández-Velasco María , Mojena Marina , Martín-Sanz Paloma , Alemany Susana 
Published: August 2015

Macrophages are present in a large variety of locations, playing distinct functions that are determined by its developmental origin and by the nature of the activators of the microenvironment. Macrophage activation can be classified as pro-inflammatory (M1 polarization) or anti-inflammatory-pro-resolution-deactivation (M2), these profiles coexisting in the course of the immune response and playing a relevant functional role in the onset of inflammation (Figure 1). Several groups have analysed the metabolic aspects associated with macrophage activation to answer the question about what changes in the regulation of energy metabolism and biosynthesis of anabolic precursors accompany the different types of polarization and to what extent they are necessary for the expression of the activation phenotypes. The interest of these studies is to regulate macrophage function by altering their metabolic activity in a ‘therapeutic way’.
Right Ventricular Protein Expression Profile in End‐Stage Heart Failure
Authors: Su Yan Ru , Chiusa Manuel , Brittain Evan , Hemnes Anna R. , Absi Tarek S. , Lim Chee Chew , Di Salvo Thomas G. 
Published: August 2015

Little is known about the right ventricular (RV) proteome in human heart failure (HF), including possible differences compared to the left ventricular (LV) proteome. We used 2‐dimensional differential in‐gel electrophoresis (pH: 4–7, 10–150 kDa), followed by liquid chromatography tandem mass spectrometry, to compare the RV and LV proteomes in 12 explanted human hearts. We used Western blotting and multiple‐reaction monitoring for protein verification and RNA sequencing for messenger RNA and protein expression correlation. In all 12 hearts, the right ventricles (RVs) demonstrated differential expression of 11 proteins relative to the left ventricles (LVs), including lesser expression of CRYM, TPM1, CLU, TXNL1, and COQ9 and greater expression of TNNI3, SAAI, ERP29, ACTN2, HSPB2, and NDUFS3. Principal‐components analysis did not suggest RV‐versus‐LV proteome partitioning. In the nonischemic RVs (n = 6), 7 proteins were differentially expressed relative to the ischemic RVs (n = 6), including increased expression of CRYM, B7Z964, desmin, ANXA5, and MIME and decreased expression of SERPINA1 and ANT3. Principal‐components analysis demonstrated partitioning of the nonischemic and ischemic RV proteomes, and gene ontology analysis identified differences in hemostasis and atherosclerosis‐associated networks. There were no proteomic differences between RVs with echocardiographic dysfunction (n = 8) and those with normal function (n = 4). Messenger RNA and protein expression did not correlate consistently, suggesting a major role for RV posttranscriptional protein expression regulation. Differences in contractile, cytoskeletal, metabolic, signaling, and survival pathways exist between the RV and the LV in HF and may be related to the underlying HF etiology and differential posttranscriptional regulation.