bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient Trafficking of TGN38 from the Endosome to the trans-Golgi Network Requires a Free Hydroxyl Group at Position 331 in the Cytosolic Domain
Authors: Roquemore Elizabeth P. , Banting George
Published: July 2013

TGN38 is one of the few known resident integral membrane proteins of the trans-Golgi network (TGN). Since it cycles constitutively between the TGN and the plasma membrane, TGN38 is ideally suited as a model protein for the identification of post-Golgi trafficking motifs. Several studies, employing chimeric constructs to detect such motifs within the cytosolic domain of TGN38, have identified the sequence333YQRL336as an autonomous signal capable of localizing reporter proteins to the TGN. In addition, one group has found that an upstream serine residue, S331, may also play a role in TGN38 localization. However, the nature and degree of participation of S331 in the localization of TGN38 remain uncertain, and the effect has been studied in chimeric constructs only. Here we investigate the role of S331 in the context of full-length TGN38. Mutations that abolish the hydroxyl moiety at position 331 (A, D, and E) lead to missorting of endocytosed TGN38 to the lysosome. Conversely, mutation of S331 to T has little effect on the endocytic trafficking of TGN38. Together, these findings indicate that the S331 hydroxyl group has a direct or indirect effect on the ability of the cytosolic tail of TGN38 to interact with trafficking and/or sorting machinery at the level of the early endosome. In addition, mutation of S331 to either A or D results in increased levels of TGN38 at the cell surface. The results confirm that S331 plays a critical role in the intracellular trafficking of TGN38 and further reveal that TGN38 undergoes a signal-mediated trafficking step at the level of the endosome.
Interplay of Signal Mediators of Decapentaplegic (Dpp): Molecular Characterization of Mothers against dpp, Medea, and Daughters against dpp
Authors: Inoue Hirofumi , Imamura Takeshi , Ishidou Yasuhiro , Takase Masao , Udagawa Yoshiyuki , Oka Yoshitomo , Tsuneizumi Kazuhide , Tabata Tetsuya , Miyazono Kohei , Kawabata Masahiro
Published: July 2013

Decapentaplegic (Dpp) plays an essential role inDrosophila development, and analyses of the Dpp signaling pathway have contributed greatly to understanding of the actions of the TGF-β superfamily. Intracellular signaling of the TGF-β superfamily is mediated by Smad proteins, which are now grouped into three classes. Two Smads have been identified inDrosophila. Mothers against dpp (Mad) is a pathway-specific Smad, whereas Daughters against dpp (Dad) is an inhibitory Smad genetically shown to antagonize Dpp signaling. Here we report the identification of a common mediator Smad inDrosophila, which is closely related to human Smad4. Mad forms a heteromeric complex with Drosophila Smad4 (Medea) upon phosphorylation by Thick veins (Tkv), a type I receptor for Dpp. Dad stably associates with Tkv and thereby inhibits Tkv-induced Mad phosphorylation. Dad also blocks hetero-oligomerization and nuclear translocation of Mad. We also show that Mad exists as a monomer in the absence of Tkv stimulation. Tkv induces homo-oligomerization of Mad, and Dad inhibits this step. Finally, we propose a model for Dpp signaling by Drosophila Smad proteins.
Mutations inDrosophilaEnabled and Rescue by Human Vasodilator-stimulated Phosphoprotein (VASP) Indicate Important Functional Roles for Ena/VASP Homology Domain 1 (EVH1) and EVH2 Domains
Authors: Ahern-Djamali Shawn M. , Comer Allen R. , Bachmann Christiane , Kastenmeier Andrew S. , Reddy Srinevas K. , Beckerle Mary C. , Walter Ulrich , Hoffmann F. Michael
Published: July 2013

Drosophila Enabled (Ena) was initially identified as a dominant genetic suppressor of mutations in the Abelson tyrosine kinase and, more recently, as a member of the Ena/human vasodilator-stimulated phosphoprotein (VASP) family of proteins. We have used genetic, biochemical, and cell biological approaches to demonstrate the functional relationship between Ena and human VASP. In addition, we have defined the roles of Ena domains identified as essential for its activity in vivo. We have demonstrated that VASP rescues the embryonic lethality associated with loss of Ena function inDrosophila and have shown that Ena, like VASP, is associated with actin filaments and focal adhesions when expressed in cultured cells. To define sequences that are central to Ena function, we have characterized the molecular lesions present in two lethalena mutant alleles that affected the Ena/VASP homology domain 1 (EVH1) and EVH2. A missense mutation that resulted in an amino acid substitution in the EVH1 domain eliminated in vitro binding of Ena to the cytoskeletal protein zyxin, a previously reported binding partner of VASP. A nonsense mutation that resulted in a C-terminally truncated Ena protein lacking the EVH2 domain failed to form multimeric complexes and exhibited reduced binding to zyxin and the Abelson Src homology 3 domain. Our analysis demonstrates that Ena and VASP are functionally homologous and defines the conserved EVH1 and EVH2 domains as central to the physiological activity of Ena.
Cysteine String Protein Functions Directly in Regulated Exocytosis
Authors: Chamberlain Luke H. , Burgoyne Robert D.
Published: July 2013

Cysteine string protein (Csp) is essential for neurotransmitter release in Drosophila. It has been suggested that Csp functions by regulating the activity of presynaptic Ca2+channels, thus controlling exocytosis. We have examined the effect of overexpressing Csp1 in PC12 cells, a neuroendocrine cell line. PC12 cell clones overexpressing Csp1 did not show any changes in morphology, granule number or distribution, or in the levels of other key exocytotic proteins. This overexpression did not affect intracellular Ca2+signals after depolarization, suggesting that Csp1 has no gross effect on Ca2+channel activity in PC12 cells. In contrast, we show that Csp1 overexpression enhances the extent of exocytosis from permeabilized cells in response to Ca2+or GTPγS in the absence of Ca2+. Because secretion from permeabilized cells is not influenced by Ca2+channel activity, this represents the first demonstration that Csp has a direct role in regulated exocytosis.
The Fission Yeast Mitotic Regulatorwin1+Encodes an MAP Kinase Kinase Kinase That Phosphorylates and Activates Wis1 MAP Kinase Kinase in Response to High Osmolarity
Authors: Samejima Itaru , Mackie Shaun , Warbrick Emma , Weisman Ronit , Fantes Peter A.
Published: July 2013

The Schizosaccharomyces pombe win1-1 mutant has a defect in the G2-M transition of the cell cycle. Although the defect is suppressed by wis1+andwis4+, which are components of a stress-activated MAP kinase pathway that links stress response and cell cycle control, the molecular identity of Win1 has not been known. We show here that win1+encodes a polypeptide of 1436 residues with an apparent molecular size of 180 kDa and demonstrate that Win1 is a MAP kinase kinase kinase that phosphorylates and activates Wis1. Despite extensive similarities between Win1 and Wis4, the two MAP kinase kinase kinases have distinct functions. Wis4 is able to compensate for loss of Win1 only under unstressed conditions to maintain basal Wis1 activity, but it fails to suppress the osmosignaling defect conferred by win1mutations. The win1-1 mutation is a spontaneous duplication of 16 nucleotides, which leads to a frameshift and production of a truncated protein lacking the kinase domain. We discuss the cell cycle phenotype of the win1-1 cdc25-22 wee1-50mutant and its suppression by wis genes.
Evidence for the Presence of 5S rRNA in Mammalian Mitochondria
Authors: Magalhães Paolo J. , Andreu Antonio L. , Schon Eric A.
Published: July 2013

Mammalian mitochondrial ribosomes contain two prokaryotic-like rRNAs, 12S and 16S, both encoded by mitochondrial DNA. As opposed to cytosolic ribosomes, however, these ribosomes are not thought to contain 5S rRNA. For this reason, it has been unclear whether 5S rRNA, which can be detected in mitochondrial preparations, is an authentic organellar species imported from the cytosol or is merely a copurifying cytosol-derived contaminant. We now show that 5S rRNA is tightly associated with highly purified mitochondrial fractions of human and rat cells and that 5S rRNA transcripts derived from a synthetic gene transfected transiently into human cells are both expressed in vivo and present in highly purified mitochondria and mitoplasts. We conclude that 5S rRNA is imported into mammalian mitochondria, but its function there still remains to be clarified.
Partially Processed pre-rRNA Is Preserved in Association with Processing Components in Nucleolus-derived Foci during Mitosis
Authors: Dundr Miroslav , Olson Mark O.J.
Published: July 2013

Previous studies showed that components implicated in pre-rRNA processing, including U3 small nucleolar (sno)RNA, fibrillarin, nucleolin, and proteins B23 and p52, accumulate in perichromosomal regions and in numerous mitotic cytoplasmic particles, termed nucleolus-derived foci (NDF) between early anaphase and late telophase. The latter structures were analyzed for the presence of pre-rRNA by fluorescence in situ hybridization using probes for segments of pre-rRNA with known half-lives. The NDF did not contain the short-lived 5′-external transcribed spacer (ETS) leader segment upstream from the primary processing site in 47S pre-rRNA. However, the NDF contained sequences from the 5′-ETS core, 18S, internal transcribed spacer 1 (ITS1), and 28S segments and also had detectable, but significantly reduced, levels of the 3′-ETS sequence. Northern analyses showed that in mitotic cells, the latter sequences were present predominantly in 45S-46S pre-rRNAs, indicating that high-molecular weight processing intermediates are preserved during mitosis. Two additional essential processing components were also found in the NDF: U8 snoRNA and hPop1 (a protein component of RNase MRP and RNase P). Thus, the NDF appear to be large complexes containing partially processed pre-rRNA associated with processing components in which processing has been significantly suppressed. The NDF may facilitate coordinated assembly of postmitotic nucleoli.
A Novel Synaptobrevin/VAMP Homologous Protein (VAMP5) Is Increased during In Vitro Myogenesis and Present in the Plasma Membrane
Authors: Zeng Qi , Subramaniam V. Nathan , Wong Siew Heng , Tang Bor Luen , Parton Robert G. , Rea Shane , James David E. , Hong Wanjin
Published: July 2013

cDNA clones encoding a novel protein (VAMP5) homologous to synaptobrevins/VAMPs are detected during database searches. The predicted 102–amino acid VAMP5 harbors a 23-residue hydrophobic region near the carboxyl terminus and exhibits an overall amino acid identity of 33% with synaptobrevin/VAMP1 and 2 and cellubrevin. Northern blot analysis reveals that the mRNA for VAMP5 is preferentially expressed in the skeletal muscle and heart, whereas significantly lower levels are detected in several other tissues but not in the brain. During in vitro differentiation (myogenesis) of C2C12 myoblasts into myotubes, the mRNA level for VAMP5 is increased ∼8- to 10-fold. Immunoblot analysis using antibodies specific for VAMP5 shows that the protein levels are also elevated ∼6-fold during in vitro myogenesis of C2C12 cells. Indirect immunofluorescence microscopy and immunoelectron microscopy reveal that VAMP5 is associated with the plasma membrane as well as intracellular perinuclear and peripheral vesicular structures of myotubes. Epitope-tagged versions of VAMP5 are similarly targeted to the plasma membrane.
Activation of Androgen Receptor Function by a Novel Nuclear Protein Kinase
Authors: Moilanen Anu-Maarit , Karvonen Ulla , Poukka Hetti , Jänne Olli A. , Palvimo Jorma J.
Published: July 2013

Androgen receptor (AR) belongs to the nuclear receptor superfamily and mediates the biological actions of male sex steroids. In this work, we have characterized a novel 130-kDa Ser/Thr protein kinase ANPK that interacts with the zinc finger region of AR in vivo and in vitro. The catalytic kinase domain of ANPK shares considerable sequence similarity with the minibrain gene product, a protein kinase suggested to contribute to learning defects associated with Down syndrome. However, the rest of ANPK sequence, including the AR-interacting interface, exhibits no apparent homology with other proteins. ANPK is a nuclear protein that is widely expressed in mammalian tissues. Its overexpression enhances AR-dependent transcription in various cell lines. In addition to the zinc finger region, ligand-binding domain and activation function AF1 of AR are needed, as the activity of AR mutants devoid of these domains was not influenced by ANPK. The receptor protein does not appear to be a substrate for ANPK in vitro, and overexpression of ANPK does not increase the extent of AR phosphorylation in vivo. In view of this, it is likely that ANPK-mediated activation of AR function is exerted through modification of AR-associated proteins, such as coregulatory factors, and/or through stabilization of the receptor protein against degradation.
Human and Yeast Cdk-activating Kinases (CAKs) Display Distinct Substrate Specificities
Authors: Kaldis Philipp , Russo Alicia A. , Chou Hubert S. , Pavletich Nikola P. , Solomon Mark J.
Published: July 2013

Cell cycle progression is controlled by the sequential functions of cyclin-dependent kinases (cdks). Cdk activation requires phosphorylation of a key residue (on sites equivalent to Thr-160 in human cdk2) carried out by the cdk-activating kinase (CAK). Human CAK has been identified as a p40MO15/cyclin H/MAT1 complex that also functions as part of transcription factor IIH (TFIIH) where it phosphorylates multiple transcriptional components including the C-terminal domain (CTD) of the large subunit of RNA polymerase II. In contrast, CAK from budding yeast consists of a single polypeptide (Cak1p), is not a component of TFIIH, and lacks CTD kinase activity. Here we report that Cak1p and p40MO15have strikingly different substrate specificities. Cak1p preferentially phosphorylated monomeric cdks, whereas p40MO15preferentially phosphorylated cdk/cyclin complexes. Furthermore, p40MO15only phosphorylated cdk6 bound to cyclin D3, whereas Cak1p recognized monomeric cdk6 and cdk6 bound to cyclin D1, D2, or D3. We also found that cdk inhibitors, including p21CIP1, p27KIP1, p57KIP2, p16INK4a, and p18INK4c, could block phosphorylation by p40MO15but not phosphorylation by Cak1p. Our results demonstrate that although both Cak1p and p40MO15activate cdks by phosphorylating the same residue, the structural mechanisms underlying the enzyme-substrate recognition differ greatly. Structural and physiological implications of these findings will be discussed.
Rho and Rab Small G Proteins Coordinately Reorganize Stress Fibers and Focal Adhesions in MDCK Cells
Authors: Imamura Hiroshi , Takaishi Kenji , Nakano Katsutoshi , Kodama Atsuko , Oishi Hideto , Shiozaki Hitoshi , Monden Morito , Sasaki Takuya , Takai Yoshimi
Published: July 2013

The Rho subfamily of the Rho small G protein family (Rho) regulates formation of stress fibers and focal adhesions in many types of cultured cells. In moving cells, dynamic and coordinate disassembly and reassembly of stress fibers and focal adhesions are observed, but the precise mechanisms in the regulation of these processes are poorly understood. We previously showed that 12-O-tetradecanoylphorbol-13-acetate (TPA) first induced disassembly of stress fibers and focal adhesions followed by their reassembly in MDCK cells. The reassembled stress fibers showed radial-like morphology that was apparently different from the original. We analyzed here the mechanisms of these TPA-induced processes. Rho inactivation and activation were necessary for the TPA-induced disassembly and reassembly, respectively, of stress fibers and focal adhesions. Both inactivation and activation of the Rac subfamily of the Rho family (Rac) inhibited the TPA-induced reassembly of stress fibers and focal adhesions but not their TPA-induced disassembly. Moreover, microinjection or transient expression of Rab GDI, a regulator of all the Rab small G protein family members, inhibited the TPA-induced reassembly of stress fibers and focal adhesions but not their TPA-induced disassembly, indicating that, furthermore, activation of some Rab family members is necessary for their TPA-induced reassembly. Of the Rab family members, at least Rab5 activation was necessary for the TPA-induced reassembly of stress fibers and focal adhesions. The TPA-induced, small G protein-mediated reorganization of stress fibers and focal adhesions was closely related to the TPA-induced cell motility. These results indicate that the Rho and Rab family members coordinately regulate the TPA-induced reorganization of stress fibers and focal adhesions that may cause cell motility.
Tim23p Contains Separate and Distinct Signals for Targeting to Mitochondria and Insertion into the Inner Membrane
Authors: Davis Alison J. , Ryan Kathleen R. , Jensen Robert E.
Published: July 2013

The Tim23 protein is an essential inner membrane (IM) component of the yeast mitochondrial protein import pathway. Tim23p does not carry an amino-terminal presequence; therefore, the targeting information resides within the mature protein. Tim23p is anchored in the IM via four transmembrane segments and has two positively charged loops facing the matrix. To identify the import signal for Tim23p, we have constructed several altered versions of the Tim23 protein and examined their function and import in yeast cells, as well as their import into isolated mitochondria. We replaced the positively charged amino acids in one or both loops with alanine residues and found that the positive charges are not required for import into mitochondria, but at least one positively charged loop is required for insertion into the IM. Furthermore, we find that the signal to target Tim23p to mitochondria is carried in at least two of the hydrophobic transmembrane segments. Our results suggest that Tim23p contains separate import signals: hydrophobic segments for targeting Tim23p to mitochondria, and positively charged loops for insertion into the IM. We therefore propose that Tim23p is imported into mitochondria in at least two distinct steps.
Differential Distribution of Dynamin Isoforms in Mammalian Cells
Authors: Cao Hong , Garcia Fabiana , McNiven Mark A.
Published: July 2013

Dynamins are 100-kDa GTPases that are essential for clathrin-coated vesicle formation during receptor-mediated endocytosis. To date, three different dynamin genes have been identified, with each gene expressing at least four different alternatively spliced forms. Currently, it is unclear whether these different dynamin gene products perform distinct or redundant cellular functions. Therefore, the focus of this study was to identify additional spliced variants of dynamin from rat tissues and to define the distribution of the dynamin family members in a cultured rat epithelial cell model (Clone 9 cells). After long-distance reverse transcription (RT)-PCR of mRNA from different rat tissues, the full-length cDNAs encoding the different dynamin isoforms were sequenced and revealed four additional spliced variants for dynamin I and nine for dynamin III. Thus, in rat tissues there are a total of at least 25 different mRNAs produced from the three dynamin genes. Subsequently, we generated stably transfected Clone 9 cells expressing full-length cDNAs of six different spliced forms tagged with green fluorescent protein. Confocal or fluorescence microscopy of these transfected cells revealed that many of the dynamin proteins associate with distinct membrane compartments, which include clathrin-coated pits at the plasma membrane and the Golgi apparatus, and several undefined vesicle populations. These results indicate that the dynamin family is more extensive than was originally predicted and suggest that the different dynamin proteins are localized to distinct cytoplasmic or membrane compartments.
Sequence Determinants for Regulated Degradation of Yeast 3-Hydroxy-3-Methylglutaryl-CoA Reductase, an Integral Endoplasmic Reticulum Membrane Protein
Authors: Gardner Richard , Cronin Stephen , Leader Benjamin , Rine Jasper , Hampton Randolph
Published: July 2013

The degradation rate of 3-hydroxy-3-methylglutaryl CoA reductase (HMG-R), a key enzyme of the mevalonate pathway, is regulated through a feedback mechanism by the mevalonate pathway. To discover the intrinsic determinants involved in the regulated degradation of the yeast HMG-R isozyme Hmg2p, we replaced small regions of the Hmg2p transmembrane domain with the corresponding regions from the other, stable yeast HMG-R isozyme Hmg1p. When the first 26 amino acids of Hmg2p were replaced with the same region from Hmg1p, Hmg2p was stabilized. The stability of this mutant was not due to mislocalization, but rather to an inability to be recognized for degradation. When amino acid residues 27–54 of Hmg2p were replaced with those from Hmg1p, the mutant was still degraded, but its degradation rate was poorly regulated. The degradation of this mutant was still dependent on the first 26 amino acid residues and on the function of the HRD genes. These mutants showed altered ubiquitination levels that were well correlated with their degradative phenotypes. Neither determinant was sufficient to impart regulated degradation to Hmg1p. These studies provide evidence that there are sequence determinants in Hmg2p necessary for degradation and optimal regulation, and that independent processes may be involved in Hmg2p degradation and its regulation.
Regulation of the Actin Cytoskeleton by Thrombin in Human Endothelial Cells: Role of Rho Proteins in Endothelial Barrier Function
Authors: Vouret-Craviari Valérie , Boquet Patrice , Pouysségur Jacques , Van Obberghen-Schilling Ellen
Published: July 2013

Endothelial barrier function is regulated at the cellular level by cytoskeletal-dependent anchoring and retracting forces. In the present study we have examined the signal transduction pathways underlying agonist-stimulated reorganization of the actin cytoskeleton in human umbilical vein endothelial cells. Receptor activation by thrombin, or the thrombin receptor (proteinase-activated receptor 1) agonist peptide, leads to an early increase in stress fiber formation followed by cortical actin accumulation and cell rounding. Selective inhibition of thrombin-stimulated signaling systems, including Gi/o (pertussis toxin sensitive), p42/p44, and p38 MAP kinase cascades, Src family kinases, PI-3 kinase, or S6 kinase pathways had no effect on the thrombin response. In contrast, staurosporine and KT5926, an inhibitor of myosin light chain kinase, effectively blocked thrombin-induced cell rounding and retraction. The contribution of Rho to these effects was analyzed by using bacterial toxins that either activate or inhibit the GTPase. Escherichia coli cytotoxic necrotizing factor 1, an activator of Rho, induced the appearance of dense actin cables across cells without perturbing monolayer integrity. Accordingly, lysophosphatidic acid, an activator of Rho-dependent stress fiber formation in fibroblasts, led to reorganization of polymerized actin into stress fibers but failed to induce cell rounding. Inhibition of Rho with Clostridium botulinum exoenzyme C3 fused to the B fragment of diphtheria toxin caused loss of stress fibers with only partial attenuation of thrombin-induced cell rounding. The implication of Rac and Cdc42 was analyzed in transient transfection experiments using either constitutively active (V12) or dominant-interfering (N17) mutants. Expression of RacV12 mimicked the effect of thrombin on cell rounding, and RacN17 blocked the response to thrombin, whereas Cdc42 mutants were without effect. These observations suggest that Rho is involved in the maintenance of endothelial barrier function and Rac participates in cytoskeletal remodeling by thrombin in human umbilical vein endothelial cells.
Fiber Separation from Ground Corn Flour Using an Electrostatic Method
Authors: Pandya Tejas S. , Srinivasan Radhakrishnan , Thompson Courtney Paige
Published: July 2013

Corn kernels contain 9% fiber by weight, which is not digested well by nonruminants such as chicken and swine. Also, fiber is nonreactive in the dry‐grind process for ethanol production and is considered as feedstock for the production of second‐generation bioethanol. Fiber separation can enhance starch concentration in animal feed and increase starch loading in ethanol plants. Electrostatic separation is used to separate particles from granular mixtures under the influence of electrical forces. The Elusieve process, a combination of sieving and air classification, separates fiber by taking advantage of differences in size, shape, and density. Differences in dielectric properties could also be exploited for fiber separation. The aim of this study was to evaluate the effectiveness of electrostatic separation of fiber particles from corn. When the electrostatic method was used in conjunction with Elusieve processing, the fiber product had higher neutral detergent fiber (NDF, 52.9%) compared with Elusieve processing alone (NDF of 40.5%). Also, a higher quantity of enhanced flour (95.0% yield) was produced when the electrostatic method was used in conjunction with Elusieve processing compared with Elusieve processing alone (93.0% yield), without any change in quality of the enhanced flour (NDF of 6.6% in both cases). The electrostatic method improved fiber separation when used in conjunction with Elusieve processing.
Proteomics Analysis of the Regulatory Role of Rpf/DSF Cell-to-Cell Signaling System in the Virulence of Xanthomonas campestris
Authors: O'Connell Aileen , An Shi-Qi , McCarthy Yvonne , Schulte Fabian , Niehaus Karsten , He Yong-Qiang , Tang Ji-Liang , Ryan Robert P. , Dow J. Maxwell
Published: July 2013

The black rot pathogen Xanthomonas campestris utilizes molecules of the diffusible signal factor (DSF) family as signals to regulate diverse processes contributing to virulence. DSF signal synthesis and transduction requires proteins encoded by the rpf gene cluster. RpfF catalyzes DSF synthesis, whereas the RpfCG two-component system links the perception of DSF to alteration in the level of the second messenger cyclic di-GMP. As this nucleotide can exert a regulatory influence at the post-transcriptional and post-translational levels, we have used comparative proteomics to identify Rpf-regulated processes in X. campestris that may not be revealed by transcriptomics. The abundance of a number of proteins was altered in rpfF, rpfC, or rpfG mutants compared with the wild type. These proteins belonged to several functional categories, including biosynthesis and intermediary metabolism, regulation, oxidative stress or antibiotic resistance, and DNA replication. For many of these proteins, the alteration in abundance was not associated with alteration in transcript level. A directed mutational analysis allowed us to describe a number of new virulence factors among these proteins, including elongation factor P and a putative outer membrane protein, which are both widely conserved in bacteria.
Hyperparasites Influence Population Structure of the Chestnut Blight Pathogen, Cryphonectria parasitica
Authors: Springer Joshua C. , Baines Anita L. Davelos , Fulbright Dennis W. , Chansler Matthew T. , Jarosz Andrew M.
Published: July 2013

Vegetative compatibility (VC) is commonly used to characterize structure and diversity in fungal populations. In the chestnut blight fungus, Cryphonectria parasitica, high VC diversity is hypothesized to be responsible for the failure of hyperparasitic mycoviruses to spread through pathogen populations in North America. To test this hypothesis, we assessed VC diversity at three recovering sites in Michigan where mycoviruses had invaded and compared them with four epidemic population sites where mycoviruses were absent. VC diversity was assessed for samples collected in 1996 and 2009, which allowed us to determine how C. parasitica populations changed with time. Twelve VC types were found in 1996 while 29 were found in 2009; 75% of types overlapped between the sample dates. Sites where mycoviruses were present had unique VC structures with the exception of the recovering population site at County Line where the main VC group was also detected at two epidemic sites. With one exception, epidemic sites contained more VC groups and displayed higher population level diversity than recovering sites. Mating-type analyses of blight populations revealed that two of three recovering populations were significantly skewed for MAT2 suggesting asexual reproduction, while epidemic sites with a long history of blight infection had ratios near 50:50 suggesting sexual reproduction. We propose that selection in the largely asexual C. parasitica populations at two recovering sites favors the most-fit fungal genotype by mycovirus combination and results in reduced diversity relative to the sexually reproducing pathogen populations at epidemic sites.
Clinical Features and Treatment Responses in Pediatric Lymphocytic and Collagenous Colitis
Authors: Narla Nirmala P. , Smyrk Thomas C. , Pardi Darrell S. , Tung Jeanne
Published: July 2013

Objective:

Microscopic colitis (MC) is prevalent in adults investigated for chronic watery diarrhea, yet characterization of pediatric MC is limited.

Methods:

Our pathology database was searched from 1995 to 2011 for pediatric cases of lymphocytic colitis (LC) or collagenous colitis (CC). Those with diarrhea persisting for >2 weeks and visually normal colonoscopy were accepted as cases. Demographics, laboratory results, medication use within 3 months of presentation, medical and family history of autoimmune disease, and response to treatment were abstracted.

Results:

A total of 27 cases were histologically consistent with MC on biopsy; 5 with concomitant enteric infection or isolated abdominal pain were excluded. Twenty‐two cases of MC (female patients, 59%; median age at diagnosis, 15.3 years) were included (19 LC and 3 CC). Two had type 1 diabetes mellitus, 2 were anti‐nuclear antibody positive, and 2 had common variable immunodeficiency. Of 20 patients who underwent an esophagogastroduodenoscopy, 1 had collagenous sprue and 4 had celiac disease. One presented after the clearance of recurrent Clostridium difficile infection. Previous drug exposures included nonsteroidal anti‐inflammatory drugs (n = 7), proton pump inhibitors (n = 6), and selective serotonin reuptake inhibitors (n = 3). Common symptoms in addition to diarrhea included abdominal pain (77.3%) and weight loss (27.3%). Of 17 patients with follow‐up, all of the 8 treated with steroids had some response: 57.1% (4/7) responded to mesalamine and 42.9% (3/7) responded to bismuth subsalicylate.

Conclusions:

In this cohort of pediatric patients, LC was much more common than CC. As described in adults, we observed associations with celiac disease, type 1 diabetes mellitus, and medications; we additionally saw an association with immunodeficiency. Our patients showed greater response to steroids than mesalamine or bismuth.
Prospects for conversion of solar energy into chemical fuels: the concept of a solar fuels industry
Authors: Harriman Anthony
Published: July 2013

There is, at present, no solar fuels industry anywhere in the world despite the well-publicized needs to replace our depleting stock of fossil fuels with renewable energy sources. Many obstacles have to be overcome in order to store sunlight in the form of chemical potential, and there are severe barriers to surmount in order to produce energy on a massive scale, at a modest price and in a convenient form. It is also essential to allow for the intermittent nature of sunlight, its diffusiveness and variability and to cope with the obvious need to use large surface areas for light collection. Nonetheless, we have no alternative but to devise viable strategies for storage of sunlight as biomass or chemical feedstock. Simple alternatives, such as solar heating, are attractive in terms of quick demonstrations but are not the answer. Photo-electrochemical devices might serve as the necessary machinery by which to generate electronic charge but the main problem is to couple these charges to the multi-electron catalysis needed to drive energy-storing chemical reactions. Several potential fuels (CO, H
2
, HCOOH, NH
3
, O
2
, speciality organics, etc.) are possible, but the photochemical reduction of CO
2
deserves particular mention because of ever-growing concerns about overproduction of greenhouse gases. The prospects for achieving these reactions under ambient conditions are considered herein.
Roles of cocatalysts in semiconductor-based photocatalytic hydrogen production
Authors: Yang Jinhui , Yan Hongjian , Zong Xu , Wen Fuyu , Liu Meiying , Li Can
Published: July 2013

A photocatalyst is defined as a functional composite material with three components: photo-harvester (e.g. semiconductor), reduction cocatalyst (e.g. for hydrogen evolution) and oxidation cocatalyst (e.g. for oxidation evolution from water). Loading cocatalysts on semiconductors is proved to be an effective approach to promote the charge separation and transfer, suppress the charge recombination and enhance the photocatalytic activity. Furthermore, the photocatalytic performance can be significantly improved by loading dual cocatalysts for reduction and oxidation, which could lower the activation energy barriers, respectively, for the two half reactions. A quantum efficiency (QE) as high as 93 per cent at 420 nm for H
2
production has been achieved for Pt–PdS/CdS, where Pt and PdS, respectively, act as reduction and oxidation cocatalysts and CdS as a photo-harvester. The dual cocatalysts work synergistically and enhance the photocatalytic reaction rate, which is determined by the slower one (either reduction or oxidation). This work demonstrates that the cocatalysts, especially the dual cocatalysts for reduction and oxidation, are crucial and even absolutely necessary for achieving high QEs in photocatalytic hydrogen production, as well as in photocatalytic water splitting.
Solar energy in the context of energy use, energy transportation and energy storage
Authors: MacKay David J. C.
Published: July 2013

Taking the UK as a case study, this paper describes current energy use and a range of sustainable energy options for the future, including solar power and other renewables. I focus on the area involved in collecting, converting and delivering sustainable energy, looking in particular detail at the potential role of solar power. Britain consumes energy at a rate of about 5000 watts per person, and its population density is about 250 people per square kilometre. If we multiply the
per capita
energy consumption by the population density, then we obtain the average primary energy consumption per unit area, which for the UK is 1.25 watts per square metre. This areal power density is uncomfortably similar to the average power density that could be supplied by many renewables: the gravitational potential energy of rainfall in the Scottish highlands has a raw power per unit area of roughly 0.24 watts per square metre; energy crops in Europe deliver about 0.5 watts per square metre; wind farms deliver roughly 2.5 watts per square metre; solar photovoltaic farms in Bavaria, Germany, and Vermont, USA, deliver 4 watts per square metre; in sunnier locations, solar photovoltaic farms can deliver 10 watts per square metre; concentrating solar power stations in deserts might deliver 20 watts per square metre. In a decarbonized world that is renewable-powered, the land area required to maintain today's British energy consumption would have to be similar to the area of Britain. Several other high-density, high-consuming countries are in the same boat as Britain, and many other countries are rushing to join us. Decarbonizing such countries will only be possible through some combination of the following options: the embracing of country-sized renewable power-generation facilities; large-scale energy imports from country-sized renewable facilities in other countries; population reduction; radical efficiency improvements and lifestyle changes; and the growth of non-renewable low-carbon sources, namely ‘clean’ coal, ‘clean’ gas and nuclear power. If solar is to play a large role in the future energy system, then we need new methods for energy storage; very-large-scale solar either would need to be combined with electricity stores or it would need to serve a large flexible demand for energy that effectively stores useful energy in the form of chemicals, heat, or cold.
Molecular approaches to solar energy conversion: the energetic cost of charge separation from molecular-excited states
Authors: Durrant James R.
Published: July 2013

This review starts with a brief overview of the technological potential of molecular-based solar cell technologies. It then goes on to focus on the core scientific challenge associated with using molecular light-absorbing materials for solar energy conversion, namely the separation of short-lived, molecular-excited states into sufficiently long-lived, energetic, separated charges capable of generating an external photocurrent. Comparisons are made between different molecular-based solar cell technologies, with particular focus on the function of dye-sensitized photoelectrochemical solar cells as well as parallels with the function of photosynthetic reaction centres. The core theme of this review is that generating charge carriers with sufficient lifetime and a high quantum yield from molecular-excited states comes at a significant energetic cost—such that the energy stored in these charge-separated states is typically substantially less than the energy of the initially generated excited state. The role of this energetic loss in limiting the efficiency of solar energy conversion by such devices is emphasized, and strategies to minimize this energy loss are compared and contrasted.
Realizing solar power's potential in the European Union
Authors: De Santi G. , Waldau A. Jaeger , Taylor N. , Ossenbrink H.
Published: July 2013

The European Union aims at largely decarbonizing its energy system by 2050. In this context, this paper reviews the status of the solar electricity technologies that can exploit our largest renewable energy resource. Although substantial progress is being made, the possibility, for instance, to more than double the efficiency of photovoltaic systems underlines the continued need for coordinated R&D efforts, aimed also at promoting European expertise and industrial competiveness. In parallel, it is important to expand the market by developing integrated building products and by demonstrating the viability of very large scale systems for both technologies.
Synergistic effect of cisplatin and synchrotron irradiation on F98 gliomas growing in nude mice
Authors: Ricard Clement , Fernandez Manuel , Requardt Herwig , Wion Didier , Vial Jean-Claude , Segebarth Christoph , van der Sanden Boudewijn
Published: July 2013

Among brain tumors, glioblastoma multiforme appears as one of the most aggressive forms of cancer with poor prognosis and no curative treatment available. Recently, a new kind of radio-chemotherapy has been developed using synchrotron irradiation for the photoactivation of molecules with high-Zelements such as cisplatin (PAT-Plat). This protocol showed a cure of 33% of rats bearing the F98 glioma but the efficiency of the treatment was only measured in terms of overall survival. Here, characterization of the effects of the PAT-Plat on tumor volume and tumor blood perfusion are proposed. Changes in these parameters may predict the overall survival. Firstly, changes in tumor growth of the F98 glioma implanted in the hindlimb of nude mice after the PAT-Plat treatment and its different modalities have been characterized. Secondly, the effects of the treatment on tumor blood perfusion have been observed by intravital two-photon microscopy. Cisplatin alone had no detectable effect on the tumor volume. A reduction of tumor growth was measured after a 15 Gy synchrotron irradiation, but the whole therapy (15 Gy irradiation + cisplatin) showed the largest decrease in tumor growth, indicating a synergistic effect of both synchrotron irradiation and cisplatin treatment. A high number of unperfused vessels (52%) were observed in the peritumoral area in comparison with untreated controls. In the PAT-Plat protocol the transient tumor growth reduction may be due to synergistic interactions of tumor-cell-killing effects and reduction of the tumor blood perfusion.
Amino acid sequence variations of signaling lymphocyte activation molecule and mortality caused by morbillivirus infection in cetaceans
Authors: Shimizu Yui , Ohishi Kazue , Suzuki Rintaro , Tajima Yuko , Yamada Tadasu , Kakizoe Yuka , Bando Takeharu , Fujise Yoshihiro , Taru Hajime , Murayama Tsukasa , Maruyama Tadashi
Published: July 2013

Morbillivirus infection is a severe threat to marine mammals. Mass die‐offs caused by this infection have repeatedly occurred in bottlenose dolphins (Turiops truncatus) and striped dolphins (Stenella coeruleoalba), both of which belong to the family Delphinidae, but not in other cetaceans. However, it is unknown whether sensitivity to the virus varies among cetacean species. The signaling lymphocyte activation molecule (SLAM) is a receptor on host cells that allows morbillivirus invasion and propagation. Its immunoguloblin variable domain‐like (V) region provides an interface for the virus hemagglutinin (H) protein. In this study, variations in the amino acid residues of the V region of 26 cetacean species, covering almost all cetacean genera, were examined. Three‐dimensional (3D) models of them were generated in a homology model using the crystal structure of the marmoset SLAM and measles virus H protein complex as a template. The 3D models showed 32 amino acid residues on the interface that possibly bind the morbillivirus. Among the cetacean species studied, variations were found at six of the residues. Bottlenose and striped dolphins have substitutions at five positions (E68G, I74V, R90H, V126I, and Q130H) compared with those of baleen whales. Three residues (at positions 68, 90 and 130) were found to alternate electric charges, possibly causing changes in affinity for the virus. This study shows a new approach based on receptor structure for assessing potential vulnerability to viral infection. This method may be useful for assessing the risk of morbillivirus infection in wildlife.
Multiscale, presence‐only habitat suitability models: fine‐resolution maps for eight bat species
Authors: Bellamy Chloe , Scott Christopher , Altringham John
Published: July 2013

To manage anthropogenic environmental change for the benefit of biodiversity, we must improve our understanding of the complex relationships between organisms and their environment. We have developed multiscale habitat suitability models (HSMs) for bats, a mobile group of mammals, for a geographically varied region of the UK. We ask whether the models have sufficient accuracy to contribute to informed decision‐making in habitat management and in minimizing the impact of climate change and human infrastructural development.

We used acoustic surveys supplemented by catching to gather presence data for eight species from 30 sites across the south of the Lake District National Park in NW England. Species were identified by manual and automated extraction and analysis of echolocation calls. Fine‐resolution (50 and 100 m) habitat maps were generated at twelve spatial scales by calculating the variables across squares of increasing size, from 100 to 6000 m, around each focal 50 or 100 m square. Presence‐only HSM software, MaxEnt, was used to determine the predictive power of each habitat variable at each scale. Multiscale models included data for each variable at the scale at which it had the strongest relationship with the presence of each species.

The best multiscale models were selected using fivefold cross‐validation, with backwards, stepwise variable removal, whilst minimizing residual spatial autocorrelation and sampling bias. Further tests with independent field data indicated good model transferability across the entire National Park.

Foraging bats were generally most strongly associated with variables measured at small spatial scales and distance measures. However, each species responded differently across the range of scales, and strong associations were also found at the largest scale of analysis (6000 m).

Synthesis and applications. The best models for determining habitat suitability had few variables, making them easy to interpret and use in practical conservation planning. The approach is applicable to any taxa for which reliable presence records are available, providing insight into the potential impacts of land‐use and environmental change. Maps identify areas of conservation concern, such as hot spots for diversity, rare or vulnerable species and potential or threatened network corridors, making them useful for ecological impact assessment of proposed developments, and to conservation managers planning habitat creation or improvement.
Inferring extinctions from sighting records of variable reliability
Authors: Lee Tamsin E. , McCarthy Michael A. , Wintle Brendan A. , Bode Michael , Roberts David L. , Burgman Mark A.
Published: July 2013

A range of mathematical models has been developed to infer whether a species is extinct based on a sighting record. Although observations have variable reliability, current methods for detecting extinction do not differentiate observation qualities.

A more suitable approach would consider certain and uncertain sightings throughout the sighting period. We consider a small population system, meaning we assume sighting rates are constant and the population is not declining. Based on such an assumption, we develop a Bayesian method that assumes that certain and uncertain sightings occur independently and at uniform rates. These two types of sightings are connected by a common extinction date. Several rates of false sightings can be calculated to differentiate between observation types. Prior rates of false and true sightings, as well as a prior probability that the species is extant, are included. The model is implemented in OpenBugs, which uses Markov chain Monte Carlo (MCMC).

Based on records of variable reliability, we estimate the probability that the following species are extinct: Caribbean seal Monachus tropicalis, grey, black‐footed ferret Mustela nigripes, Audubon & Bachman, greater stick‐nest rat Leporillus conditor, Sturt, and lesser stick‐nest rat Leporillus apicalis, Gould. As further examples, Birdlife International provided the sighting records for the Alaotra grebe Tachybaptus rufolavatus, Delacour, Jamaica petrel Pterodroma caribbaea, Carte, and Pohnpei mountain starling Aplonis pelzelni, Finsch, with prior probabilities for extinction. The results are compared with existing methods, which ignore uncertain sightings. We find that including uncertain sightings can considerably change the probability that the species is extant, in either direction. However, in our examples, including the quality of the uncertain sighting made little difference. When we ignore uncertain sightings, our results agree with existing methods, especially when the last sighting was near the end of the sighting period.

Synthesis and applications. Estimating the probability that a species is extinct based on sighting records is important when determining conservation priorities and allocating available resources into management activities. Having a model that allows for certain and uncertain observations throughout the sighting period better accommodates the realities of sighting quality, providing a more reliable basis for decision‐making.