bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of intracellular and intraviral localization of the human cytomegalovirus UL53 protein
Authors: Dal Monte P. , Pignatelli S. , Zini N. , Maraldi N. M. , Perret E. , Prevost M. C. , Landini M. P.
Published: August 2015

Human cytomegalovirus (HCMV) UL53 belongs to a family of conserved herpesvirus genes. In this work, the expression and localization of the UL53 gene product was analysed. Results obtained showed that pUL53 is a new structural protein. In infected human fibroblasts, pUL53 localizes in cytoplasmic perinuclear granular formations together with other structural viral proteins. In the nucleus, pUL53 forms patches at the nuclear periphery and co-localizes with lamin B at the internal nuclear membrane level. Immunoelectron microscopy studies have disclosed that nuclear pseudo-inclusions are labelled, whereas nucleocapsid formations within the intranuclear skein are negative. Furthermore, the mature virus particle maintains pUL53 at its tegumental level. These data suggest that pUL53 could be involved either in nucleocapsid maturation or in the egress of nucleocapsids from the nucleus to the cytoplasm through the nuclear membrane, a role compatible with the function hypothesized for UL31, its positional homologue in herpes simplex virus type 1.
Proteolytic processing of potyviral proteins and polyprotein processing intermediates in insect and plant cells
Authors: Merits Andres , Rajamäki Minna-Liisa , Lindholm Päivi , Runeberg-Roos Pia , Kekarainen Tuija , Puustinen Pietri , Mäkeläinen Katri , Valkonen Jari P. T. , Saarma Mart
Published: August 2015

Processing of the polyprotein encoded by Potato virus A (PVA; genus Potyvirus) was studied using expression of the complete PVA polyprotein or its mutants from recombinant baculoviruses in insect cells. The time-course of polyprotein processing by the main viral proteinase (NIaPro) was examined with the pulse–chase method. The sites at the P3/6K1, CI-6K2 and VPg/NIaPro junctions were processed slowly, in contrast to other proteolytic cleavage sites which were processed at a high rate. The CI-6K2 polyprotein was observed in the baculovirus system and in infected plant cells. In both cell types the majority of CI-6K2 was found in the membrane fraction, in contrast to fully processed CI. Deletion of the genomic region encoding the 6K1 protein prevented proper proteolytic separation of P3 from CI, but did not affect processing of VPg, NIaPro, NIb or CP from the polyprotein. The 6K2-encoding sequence could be removed without any detectable effect on polyprotein processing. However, deletion of either the 6K1 or 6K2 protein-encoding regions rendered PVA non-infectious. Mutations at the 6K2/VPg cleavage site reduced virus infectivity in plants, but had a less pronounced, albeit detectable, effect on proteolytic processing in the baculovirus system. The results of this study indicate that NIaPro catalyses proteolytic cleavages preferentially in cis, and that the 6K1/CI and NIb/CP sites can also be processed in trans. Both 6K peptides are indispensable for virus replication, and proteolytic separation of the 6K2 protein from the adjacent proteins by NIaPro is important for the rate of virus replication and movement.
Porcine B-cells recognize epitopes that are conserved between the structural proteins of American- and European-type porcine reproductive and respiratory syndrome virus
Authors: Oleksiewicz M. B. , Bøtner A. , Normann P.
Published: August 2015

By selecting phage display libraries with immune sera from experimentally infected pigs, porcine B-cell epitopes in the open reading frame (ORF) 2, 3, 5 and 6 proteins of European-type porcine reproductive and respiratory syndrome virus (PRRSV) were identified. The sequences of all the epitopes were well conserved in European-type PRRSV and even between European- and American-type PRRSV. Accordingly, sera from pigs infected with American-type PRRSV cross-reacted with the European-type epitopes. Thus, this study showed, for the first time, the presence of highly conserved epitopes in the matrix protein and envelope glycoproteins of PRRSV. ORF5 and 6 epitopes localized to protein parts that are predicted to be hidden in PRRSV virions. In contrast, ORF2 and 3 epitopes localized to putative protein ectodomains. Due to the interesting localization, the sequence surrounding the ORF2 and 3 epitopes was subjected to closer scrutiny. A heptad motif, VSRRIYQ, which is present in a single copy in ORF2 and 3 proteins, was identified; this arrangement is completely conserved in all European-type PRRSV sequences available. The VSRRIYQ repeat motif colocalized closely with one of the ORF2 epitopes and secondary structure modelling showed that this segment of the ORF2 protein could form an amphipathic helix. Intriguingly, a mutation associated with virulence/attenuation of an American vaccine strain of PRRSV also localized to this ORF2 protein segment and affected the hydrophobic face of the predicted amphipathic helix. Further work is needed to determine whether these findings delineate a functional domain in the PRRSV ORF2 protein.
Activity and intracellular localization of the human cytomegalovirus protein pp71
Authors: Marshall Ker R. , Rowley Kate V. , Rinaldi Angela , Nicholson Iain P. , Ishov Alexander M. , Maul Gerd G. , Preston Chris M.
Published: August 2015

The human cytomegalovirus (HCMV) tegument phosphoprotein pp71 activates viral immediate early (IE) transcription and thus has a role in initiating lytic infection. Protein pp71 stimulates expression from a range of promoters in a sequence-independent manner, and in this respect behaves similarly to the herpes simplex virus type 1 (HSV-1) IE protein ICP0. The intracellular localization of pp71 was investigated after its expression from transfected plasmids or from HSV-1 mutants constructed to produce pp71 transiently. The protein colocalized with the cell promyelocytic leukaemia (PML) protein at nuclear domain 10 (ND10) structures but, unlike ICP0, pp71 did not induce disruption of ND10. The activity of pp71 in mouse sensory neuronsin vivowas investigated after co-inoculation of animals with pairs of HSV-1 mutants, one expressing pp71 and the second containing theE.coli lacZgene controlled by various promoters. In this system, pp71 stimulated β-galactosidase expression from a range of viral IE promoters when mice were analysed at 4 days postinoculation. At later times, expression of pp71 resulted in a reduction in numbers of neurons containing β-galactosidase, indicating cytotoxicity or promoter shutoff. The HSV-1 latency-active promoter was not responsive to pp71, demonstrating specificity in the activity of the protein. Pp71 was as active in mice lacking both copies of the PML gene (PML−/−) as in control animals, and in PML−/− fibroblasts pp71 stimulated gene expression as effectively as in other cell types. Therefore, neither the PML protein nor the normal ND10 structure is necessary for pp71 to stimulate gene expression.
Hepatitis C virus core protein expression in human B-cell lines does not significantly modify main proliferative and apoptosis pathways
Authors: Giannini Carlo , Caini Patrizio , Giannelli Francesca , Fontana Francesca , Kremsdorf Dina , Bréchot Christian , Zignego Anna Linda
Published: August 2015

Hepatitis C virus (HCV) chronic infection has been associated with many lymphoproliferative disorders. Several studies performed on hepatoma and fibroblast cell lines suggest a role of the HCV core protein in activation of cellular transduction pathways that lead to cell proliferation and inhibition of apoptosis. However, no data are available concerning the effects of HCV core expression on B-lymphocyte proliferation and apoptosis. B-lymphocyte cell lines permanently expressing full-length HCV 1b core sequences isolated from chronically infected patients were established using B-cell lines at different degrees of differentiation. Clones and pools of clones permanently expressing the HCV core were selected and characterized for protein expression by Western blot and FACS. Expression of HCV core proteins did not significantly enhance cell proliferation rates under normal culture conditions or under mitogenic stimulation. Analysis of NF-κB, CRE, TRE and SRE pathways by luciferase reporter genes did not show a significant influence of HCV core expression on these signal transduction cascades in B-lymphocytes. The effects of HCV core on anti-IgM and anti-FAS-induced apoptosis in B-cell lines was also analysed. In this experimental model, HCV core expression did not significantly modify the apoptotic profile of the B-lymphocyte cell lines tested. These data underline a cell type-specific effect of HCV core expression. In fact, it was not possible to show a significant contribution of the HCV core protein in activation of the major B-cell signal transduction pathways involved in the regulation of proliferation and programmed cell death, which is in contrast with the results reported in hepatoma cell lines.
Interaction between potyvirus helper component-proteinase and capsid protein in infected plants
Authors: Roudet-Tavert Geneviève , German-Retana Sylvie , Delaunay Thierry , Delécolle Brigitte , Candresse Thierry , Le Gall Olivier
Published: August 2015

Monoclonal antibodies were raised against helper component-proteinase (HcPro) purified from plants infected with the potyvirus Lettuce mosaic virus (LMV). These antibodies were used in a two-site triple antibody sandwich ELISA assay together with polyclonal antibodies directed against purified virions. An interaction between HcPro and the viral coat protein (CP) was demonstrated in extracts of LMV-infected leaves, as well as for two other potyviruses, Plum pox virus and Potato virus Y. The CP–HcPro interaction was not abolished in LMV derivatives with an HcPro GFP N-terminal fusion, or with a deletion from the CP of the amino acids involved in aphid transmission. Electron microscopy indicated that HcPro probably does not interact with the CP in the form of assembled virions or virus-like particles. Together, these results suggest that the interaction detected between CP and HcPro might be involved in a process of the potyvirus cycle different from aphid transmission.
RNA 2 of Citrus psorosis virus is of negative polarity and has a single open reading frame in its complementary strand
Authors: de la Torre María Eugenia Sánchez , López Carmelo , Grau Oscar , García María Laura
Published: August 2015

Citrus psorosis virus (CPsV) causes a citrus disease occurring worldwide. Isolate CPV 4 has a genome with three single-stranded RNAs. The complete sequence of RNA 2 (1643 nucleotides) is reported here. Northern blot hybridization with strand-specific probes showed that most of the encapsidated RNA 2 is of negative polarity, although a small amount of the complementary strand may also be present in particles. The RNA 2 complementary strand contained a single open reading frame encoding a protein of 476 amino acids, which includes a motif resembling a nuclear localization signal. The sequence of this putative protein shows no significant similarity to any other in the databases. In the 3′-terminal untranslated region there is a putative polyadenylation signal. No subgenomic RNAs derived from RNA 2 were detected.
The vaccinia virus N1L protein is an intracellular homodimer that promotes virulence
Authors: Bartlett Nathan , Symons Julian A. , Tscharke David C. , Smith Geoffrey L.
Published: August 2015

The vaccinia virus (VV) N1L gene encodes a protein of 14 kDa that was identified previously in the concentrated supernatant of virus-infected cells. Here we show that the protein is present predominantly (>90%) within cells rather than in the culture supernatant and it exists as a non-glycosylated, non-covalent homodimer. The N1L protein present in the culture supernatant was uncleaved at the N terminus and was released from cells more slowly than the VV A41L gene product, a secreted glycoprotein that has a conventional signal peptide. Bioinformatic analyses predict that the N1L protein is largely alpha-helical and show that it is conserved in many VV strains, in other orthopoxviruses and in members of other chordopoxvirus genera. However, database searches found no non-poxvirus proteins with significant amino acid similarity to N1L. A deletion mutant lacking the N1L gene replicated normally in cell culture, but was attenuated in intranasal and intradermal murine models compared to wild-type and revertant controls. The conservation of the N1L protein and the attenuated phenotype of the deletion mutant indicate an important role in the virus life-cycle.
Olfactory receptor neurons prevent dissemination of neurovirulent influenza A virus into the brain by undergoing virus-induced apoptosis
Authors: Mori Isamu , Goshima Fumi , Imai Yoshinori , Kohsaka Shinichi , Sugiyama Tsuyoshi , Yoshida Tomoaki , Yokochi Takashi , Nishiyama Yukihiro , Kimura Yoshinobu
Published: August 2015

Olfactory receptor neurons (ORNs) were infected upon intranasal inoculation with the R404BP strain of neurovirulent influenza A virus. Virus-infected neurons and a small fraction of neighbouring uninfected neurons displayed apoptotic neurodegeneration substantiated by the immunohistochemistry for activated caspase-3 molecules and the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labelling method. However, virus infection was restricted within the peripheral neuroepithelium and all mice survived the infection. Virus-infected ORNs revealed upregulated expression of the Fas ligand molecules, activating the c-Jun N-terminal kinase signal transduction pathway. In addition, Iba1-expressing activated microglia/macrophages appeared to partake in phagocytic activities, eventually clearing apoptotic bodies. These results raise the possibility that induction of apoptosis in olfactory receptor neurons at an early stage of infection may provide protective effects against invasion of the neurovirulent virus from the peripheral to the CNS.
High numbers of IL-2-producing CD8+ T cells during viral infection: correlation with stable memory development
Authors: Kristensen Nanna Ny , Christensen Jan Pravsgaard , Thomsen Allan Randrup
Published: August 2015

Using infections with lymphocytic choriomeningitis virus (LCMV) and vesicular stomatitis virus in mice as model systems, we have investigated the ability of antigen-primed CD8+T cells generated in the context of viral infections to produce IL-2. Our results indicate that acute immunizing infection normally leads to generation of high numbers of IL-2-producing antigen-specific CD8+T cells. By costaining for IL-2 and IFN-γ intracellularly, we found that IL-2-producing cells predominantly constitute a subset of cells also producing IFN-γ. Comparison of the kinetics of generation revealed that IL-2-producing cells appear slightly delayed compared with the majority of IFN-γ producing cells, and the relative frequency of the IL-2-producing subset increases with transition into the memory phase. In contrast to acute immunizing infection, few IL-2-producing cells are generated during chronic LCMV infection. Furthermore, in MHC class II-deficient mice, which only transiently control LCMV infection, IL-2-producing CD8+T cells are initially generated, but by 4 weeks after infection this subset has nearly disappeared. Eventually the capacity to produce IFN-γ also becomes impaired, while cell numbers are maintained at a level similar to those in wild-type mice controlling the infection. Taken together, these findings indicate that phenotyping of T cell populations based on capacity to produce cytokines, and especially IL-2, can provide important information as to the functional status of the analysed cell subset. Specifically, combined analysis of the capacity to produce IL-2 and IFN-γ can be used as a predictor for loss of function within the CD8+T cell compartment.
Replication of a hepatitis A virus replicon detected by genetic recombination in vivo
Authors: Gauss-Müller Verena , Kusov Yuri Y.
Published: August 2015

Unlike other picornaviruses, hepatitis A virus (HAV) replicates so inefficiently in cell culture that the study of its RNA biosynthesis presents a major experimental challenge. To assess viral RNA replication independent of particle formation, a subgenomic replicon representing a self-replicating RNA was constructed by replacing the P1 domain encoding the capsid proteins with the firefly luciferase sequence. Although translation of the HAV replicon was as efficient as a similar poliovirus replicon, the luciferase activity derived from replication of the HAV construct was more than 100-fold lower than that of poliovirus. The replication capacity of the HAV replicon was clearly demonstrated by its ability to recombine genetically with a non-viable, full-length HAV genome that served as capsid donor and thus to rescue a fully infectious virus. In contrast to a replication-deficient replicon, co-expression of the genetically marked and replication-competent HAV replicon with several lethally mutated HAV genomes resulted in the successful rescue of infectious HAV with a unique genetic marker. Our data suggest: (i) that autonomous HAV RNA replication does not require sequences for the HAV structural proteins; and (ii) that low-level genome replication can unequivocally be demonstrated by the rescue of infectious virus after co-expression with non-viable genomes.
The putative capsid protein of the newly identified avian hepatitis E virus shares antigenic epitopes with that of swine and human hepatitis E viruses and chicken big liver and spleen disease virus
Authors: Haqshenas G. , Huang F. F. , Fenaux M. , Guenette D. K. , Pierson F. W. , Larsen C. T. , Shivaprasad H. L. , Toth T. E. , Meng X. J.
Published: August 2015

We recently identified a novel virus, designated avian hepatitis E virus (avian HEV), from chickens with hepatitis–splenomegaly (HS) syndrome in the USA. We showed that avian HEV is genetically related to swine and human HEVs. Here we report the antigenic cross-reactivity of the putative open reading frame 2 (ORF2) capsid protein of avian HEV with those of swine and human HEVs and the Australian chicken big liver and spleen disease virus (BLSV). The region encoding the C-terminal 268 amino acid residues of avian HEV ORF2 was cloned into expression vector pRSET-C. The truncated ORF2 protein was expressed in E. coli as a fusion protein and purified by affinity chromatography. Western blot analysis revealed that the avian HEV ORF2 protein reacted with antisera against the Sar-55 strain of human HEV and with convalescent antisera against swine HEV and the US2 strain of human HEV, as well as with antiserum against BLSV. Convalescent sera from specific-pathogen-free chickens experimentally infected with avian HEV also reacted with the recombinant capsid proteins of swine HEV and Sar-55 human HEV. Antisera against the US2 human HEV also reacted with recombinant ORF2 proteins of both swine HEV and Sar-55 human HEV. The antigenic cross-reactivity of the avian HEV putative capsid protein with those of swine and human HEVs was further confirmed, for the most part, by ELISA assays. The data indicate that avian HEV shares certain antigenic epitopes in its putative capsid protein with swine and human HEVs, as well as with BLSV. The results have implications for HEV diagnosis and taxonomy.
Detection and significance of a G1862T variant of hepatitis B virus in Chinese patients with fulminant hepatitis
Authors: Hou Jinlin , Lin Yulong , Waters Jenny , Wang Zhanhui , Min Jia , Liao Huiyu , Jiang Jiaji , Chen Jinjun , Luo Kangxian , Karayiannis Peter
Published: August 2015

The prevalence of a G1862T variant of hepatitis B virus (HBV) has been investigated in patients with fulminant hepatitis and chronic liver disease, using primer mismatch amplification, followed by restriction fragment length polymorphism analysis. This variant was five times more common in patients with fulminant hepatitis (13·7%, 7 of 52) than in chronic carriers (2·5%, 2 of 81). The G→T substitution at position 1862 leads to an amino acid change in codon 17 of the precore protein of the virus, which is part of a signal peptidase recognition motif. Variants with this mutation were only seen in patients infected with genotype B. In vitro translation experiments showed that this variant has greatly reduced capacity to produce hepatitis B e antigen (HBeAg) from its precore protein precursor. Furthermore, 88·5% of patients with fulminant hepatitis had mutations that are known to be associated with abrogated or reduced production of HBeAg. This suggests that, following HBV infection, the absence or reduced amounts of HBeAg may be a contributing factor in fulminant disease.
Fusobacterium nucleatum supports the growth of Porphyromonas gingivalis in oxygenated and carbon-dioxide-depleted environments
Authors: Diaz P. I , Zilm P. S , Rogers A. H
Published: August 2015

The authors compared the differences in tolerance to oxygen of the anaerobic periodontopathic bacteriaFusobacterium nucleatumandPorphyromonas gingivalis, and explored the possibility thatF. nucleatummight be able to support the growth ofP. gingivalisin aerated and CO2-depleted environments. Both micro-organisms were grown as monocultures and in co-culture in the presence and absence of CO2and under different aerated conditions using a continuous culture system. At steady state, viable counts were performed and the activities of the enzymes superoxide dismutase and NADH oxidase/peroxidase were assayed inP. gingivalis. In co-culture,F. nucleatumwas able to support the growth ofP. gingivalisin aerated and CO2-depleted environments in whichP. gingivalis, as a monoculture, was not able to survive.F. nucleatumnot only appeared to have a much higher tolerance to oxygen thanP. gingivalis, but a significant increase in its numbers occurred under moderately oxygenated conditions.F. nucleatummight have an additional indirect role in dental plaque maturation, contributing to the reducing conditions necessary for the survival ofP. gingivalisand possibly other anaerobes less tolerant to oxygen. Additionally,F. nucleatumis able to generate a capnophilic environment essential for the growth ofP. gingivalis.
Role of the C-terminal YG repeats of the primer-dependent streptococcal glucosyltransferase, GtfJ, in binding to dextran and mutan
Authors: Kingston Kim B , Allen Donna M , Jacques Nicholas A
Published: August 2015

The recombinant primer-dependent glucosyltransferase GtfJ of Streptococcus salivarius possesses a C-terminal glucan-binding domain composed of eighteen 21 aa YG repeats. By engineering a series of C-terminal truncated proteins, the position at which truncation prevented further mutan synthesis was defined to a region of 43 aa, confirming that not all of the YG motifs were required for the formation of mutan by GtfJ. The role of the YG repeats in glucan binding was investigated in detail. Three proteins consisting of 3·8, 7·2 or 11·0 C-terminal YG repeats were expressed in Escherichia coli. Each of the three purified proteins bound to both the 1,6-α-linked glucose residues of dextran and the 1,3-α-linked glucose residues of mutan, indicating that a protein consisting of nothing but 3·8 YG repeats could attach to either substrate. Secondary structure predictions of the primary amino acid sequence suggested that 37% of the amino acids were capable of forming a structure such that five regions of β-sheet were separated by regions capable of forming β-turns and random coils. CD spectral analysis showed that the purified 3·8 YG protein possessed an unordered secondary structure with some evidence of possible β-sheet formation and that the protein maintained this relatively unordered structure on binding to dextran.
Control of dimethylsulfoxide reductase expression in Rhodobacter capsulatus: the role of carbon metabolites and the response regulators DorR and RegA
Authors: Kappler Ulrike , Huston Wilhelmina M , McEwan Alastair G
Published: August 2015

Regulation of the expression of dimethylsulfoxide (DMSO) reductase was investigated in the purple phototrophic bacterium Rhodobacter capsulatus. Under phototrophic, anaerobic conditions with malate as carbon source, DMSO caused an approximately 150-fold induction of DMSO reductase activity. The response regulator DorR was required for DMSO-dependent induction and also appeared to slightly repress DMSO reductase expression in the absence of substrate. Likewise, when pyruvate replaced malate as carbon source there was an induction of DMSO reductase activity in cells grown at low light intensity (16 W m−2) and again this induction was dependent on DorR. The level of DMSO reductase activity in aerobically grown cells was elevated when pyruvate replaced malate as carbon source. One possible explanation for this is that acetyl phosphate, produced from pyruvate, may activate expression of DMSO reductase by direct phosphorylation of DorR, leading to low levels of induction of dor gene expression in the absence of DMSO. A mutant lacking the global response regulator of photosynthesis gene expression, RegA, exhibited high levels of DMSO reductase in the absence of DMSO, when grown phototrophically with malate as carbon source. This suggests that phosphorylated RegA acts as a repressor of dor operon expression under these conditions. It has been proposed elsewhere that RegA-dependent expression is negatively regulated by the cytochrome cbb
3 oxidase. A cco mutant lacking cytochrome cbb
3 exhibited significantly higher levels of Φ[dorA::lacZ] activity in the presence of DMSO compared to wild-type cells and this is consistent with the above model. Pyruvate restored DMSO reductase expression in the regA mutant to the same pattern as found in wild-type cells. These data suggest that R. capsulatus contains a regulator of DMSO respiration that is distinct from DorR and RegA, is activated in the presence of pyruvate, and acts as a negative regulator of DMSO reductase expression.
Influence of pH on bile sensitivity amongst various strains of Listeria monocytogenes under aerobic and anaerobic conditions
Authors: White Sally J. , McClung Daniel M. , Wilson Jessica G. , Roberts Brandy N. , Donaldson Janet R.
Published: August 2015

Listeria monocytogenes is a dangerous bacterium that causes the food-borne disease listeriosis and accounts for nearly 20 % of food-borne deaths. This organism can survive the body's natural defences within the digestive tract, including acidic conditions and bile. Although the bile response has been analysed, limited information is available concerning the ability of L. monocytogenes to resist bile under anaerobic conditions, especially at acidic pH, which mimics conditions within the duodenum. Additionally, it is not known how the bile response varies between serotypes. In this study, the survival of strains representing six serotypes was analysed under aerobic and anaerobic conditions following exposure to bile. Exposure to bile salts at acidic pH increased toxicity of bile, resulting in a significant reduction in survival for all strains tested. However, following this initial reduction, no significant reduction was observed for an additional 2 h except for strain 10403S (P = 0.002). Anaerobic cultivation increased bile resistance, but a significant increase was only observed in virulent strains when exposed to bile at pH 5.5. Exposure to pH 3.0 prior to bile decreased viability amongst avirulent strains in bile in acidic conditions; oxygen availability did not influence viability. Together, the data suggested that being able to sense and respond to oxygen availability may influence the expression of stress response mechanisms, and this response may correspond to disease outcome. Further research is needed on additional strains to determine how L. monocytogenes senses and responds to oxygen and how this varies between invasive and non-invasive strains.
Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
Authors: Ivanov Nikolay A. , Tao Ran , Chenoweth Joshua G. , Brandtjen Anna , Mighdoll Michelle I. , Genova John D. , McKay Ronald D. , Jia Yankai , Weinberger Daniel R. , Kleinman Joel E. , Hyde Thomas M. , Jaffe Andrew E.
Published: August 2015

Differentiating pluripotent cells from fibroblast progenitors is a potentially transformative tool in personalized medicine. We previously identified relatively greater success culturing dura-derived fibroblasts than scalp-derived fibroblasts from postmortem tissue. We hypothesized that these differences in culture success were related to epigenetic differences between the cultured fibroblasts by sampling location, and therefore generated genome-wide DNA methylation and transcriptome data on 11 intrinsically matched pairs of dural and scalp fibroblasts from donors across the lifespan (infant to 85 years). While these cultured fibroblasts were several generations removed from the primary tissue and morphologically indistinguishable, we found widespread epigenetic differences by sampling location at the single CpG (N=101,989), region (N=697), “block” (N=243), and global spatial scales suggesting a strong epigenetic memory of original fibroblast location. Furthermore, many of these epigenetic differences manifested in the transcriptome, particularly at the region-level. We further identified 7,265 CpGs and 11 regions showing significant epigenetic memory related to the age of the donor, as well as an overall increased epigenetic variability, preferentially in scalp-derived fibroblasts -83% of loci were more variable in scalp, hypothesized to result from cumulative exposure to environmental stimuli in the primary tissue. By integrating publicly available DNA methylation datasets on individual cell populations in blood and brain, we identified significantly increased inter-individual variability in our scalp- and other skin-derived fibroblasts on a similar scale as epigenetic differences between different lineages of blood cells. Lastly, these epigenetic differences did not appear to be driven by somatic mutation – while we identified 64 probable de-novo variants across the 11 subjects, there was no association between mutation burden and age of the donor (p=0.71). These results depict a strong component of epigenetic memory in cell culture from primary tissue, even after several generations of daughter cells, related to cell state and donor age.
An alternative RNA polymerase I structure reveals a dimer hinge
Authors: Kostrewa Dirk , Kuhn Claus-D. , Engel Christoph , Cramer Patrick
Published: August 2015

RNA polymerase I (Pol I) is the central, 14-subunit enzyme that synthesizes the ribosomal RNA (rRNA) precursor in eukaryotic cells. The recent crystal structure of Pol I at 2.8 Å resolution revealed two novel elements: the `expander' in the active-centre cleft and the `connector' that mediates Pol I dimerization [Engelet al.(2013),Nature (London),502, 650–655]. Here, a Pol I structure in an alternative crystal form that was solved by molecular replacement using the original atomic Pol I structure is reported. The resulting alternative structure lacks the expander but still shows an expanded active-centre cleft. The neighbouring Pol I monomers form a homodimer with a relative orientation distinct from that observed previously, establishing the connector as a hinge between Pol I monomers.
Combining phase information in reciprocal space for molecular replacement with partial models
Authors: Millán Claudia , Sammito Massimo , Garcia-Ferrer Irene , Goulas Theodoros , Sheldrick George M. , Usón Isabel
Published: August 2015

ARCIMBOLDOallowsab initiophasing of macromolecular structures below atomic resolution by exploiting the location of small model fragments combined with density modification in a multisolution frame. The model fragments can be either secondary-structure elements predicted from the sequence or tertiary-structure fragments. The latter can be derived from libraries of typical local folds or from related structures, such as a low-homology model that is unsuccessful in molecular replacement. In allARCIMBOLDOapplications, fragments are searched for sequentially. Correct partial solutions obtained after each fragment-search stage but lacking the necessary phasing power can, if combined, succeed. Here, an analysis is presented of the clustering of partial solutions in reciprocal space and of its application to a set of different cases. In practice, the task of combining model fragments from anARCIMBOLDOrun requires their referral to a common origin and is complicated by the presence of correct and incorrect solutions as well as by their not being independent. TheF-weighted mean phase difference has been used as a figure of merit. Clustering perfect, non-overlapping fragments dismembered from test structures in polar and nonpolar space groups shows that density modification before determining the relative origin shift enhances its discrimination. In the case of nonpolar space groups, clustering ofARCIMBOLDOsolutions from secondary-structure models is feasible. The use of partially overlapping search fragments provides a more favourable circumstance and was assessed on a test case. Applying the devised strategy, a previously unknown structure was solved from clustered correct partial solutions.
A new polymorph of 1-({[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]iminio}methyl)naphthalen-2-olate
Authors: Guo Ailing , Zhang Shurong , Wang Kun , Zhu Ruitao
Published: August 2015

The title compound, C15H17NO4, containing two molecules in the asymmetric unit is a polymorph of the crystal structure published by Martínezet al.[(2011).Eur. J. Org. Chem. pp. 3137-3145] which at 120 K is monoclinic with one molecule in the asymmetric unit. Both molecules in the title compound are in thetransform. In the crystal, N—H...O and O—H...O hydrogen bonds connect molecules, forming a two-dimensional network parallel to (001).
Crystal structure of chlorido(2-{[2-(phenylcarbamothioyl)hydrazin-1-ylidene](pyridin-2-yl)methyl}pyridin-1-ium)gold(I) chloride sesquihydrate
Authors: Gatto Claudia C. , Lima Iariane J.
Published: August 2015

The title complex, [AuCl(C18H16N5S)]Cl·1.5H2O, may be considered as a gold(I) compound with the corresponding metal site coordinated by a thiosemicarbazone ligand through the S atom. The ligand adopts anEconformation and the gold(I) atom displays the expected linear geometry with a Cl atom also bonded to the metal ion [Cl—Au—S = 174.23 (5)°]. One of the pyridyl rings is protonated, giving the gold complex an overall positive charge. Two solvent water molecules, one of which is located on a twofold rotation axis, and a non-coordinating chloride ion complete the structural assembly. The molecular structure is stabilized by intramolecular and intermolecular N—H...Cl, N—H...N, O—H...Cl and O—H...O hydrogen bonding.
Is small still beautiful? A comparative study of rice farm size and productivity in China and India
Authors: Wang Jianying , Chen Kevin Z. , Das Gupta Sunipa , Huang Zuhui
Published: August 2015

Purpose

– The farm size-productivity relationship has long been the subject of debate among development economists. Few studies address this issue for China, and those that do only with outdated data sets poorly representing the current situation after the past decade of rapid change, which includes the rapid development of land rental markets, village labor out-migration and use of farm machines. Meanwhile, many studies have researched this relationship for Indian, which is undergoing similar changes except for the development of active land rental markets. The purpose of this paper is to measure the farm size-productivity relationship under the situations of rapid transformation in China and India.

Design/methodology/approach

– Based on the data of 325 Jiangxi and 400 Allahabad rice farmers in 2011, the survey covered multiple plots of each household in one/multiple growing season(s). The authors use the production function approach and the yield approach, and control for farmland quality, imperfect factor markets, and farm size measurement error, to identify the farm size-productivity relationship.

Findings

– The regressions show that land yields increase with plot size both by season and over the year in China. This may be one of the reasons that farm sizes are growing in some areas. In India, however, the inverse farm size-productivity relationship is observed by the study, despite recent changes. Moreover, land yields increase with farm machine use in both China and India. This result contributes to the debate over whether mechanization improves yields or just expands the land frontier.

Originality/value

– The paper empirically estimates the farm size-productivity relationship under rapid agrarian transformation in both China and India based on a unique data set collected by the authors in a detailed primary survey. The paper considers measurement error in the analysis, which adds values to this type of analysis.
China’s on-going debates over large-scale farming: what are the pros and cons?
Authors: Zuo Yonghong , Ma Ling , Cai Hailong , Wu Tianlong , Xin Xian
Published: August 2015

Purpose

– The Chinese Government relies heavily on increasing farming scale to address the new challenges facing China’s agricultural development. A basket of polices targeted at increasing farming scale has been issued in recent years thereby resulting to debates over large-scale farming in China. The purpose of this paper is to summarize and highlight the debate over China’s on-going large-scale farming.

Design/methodology/approach

– This paper contributes to the policy debates over large-scale farming in China by reviewing the existing literature on the positive and negative impacts of large-scale farming on agricultural development, land productivity, and national food security. This paper overviews the different ideas and findings of studies associated with the topic.

Findings

– The mainstream literature supports the idea that large-scale farming will address the challenges facing China’s agricultural development, while others argue that it crowds out the benefits of small farmers, and raises concerns over inequalities of resources allocation and income distribution, and undermines social stability. While proponents argue that large-scale farming may lead to rise in land productivity, opponents argue that it may result into decrease in land productivity and national grain output.

Originality/value

– This paper is a policy review based on existing works. It organizes the different debates over large-scale farming in China, and highlights the key arguments put forward.
Food versus crude oil: what do prices tell us? Evidence from China
Authors: Wang Yumeng , Zhao Shuoli , Yang Zhihai , Liu Donald J.
Published: August 2015

Purpose

– The purpose of this paper is to investigate the causal relationship between the prices of rice, crude oil, wheat, corn and soybean in China and estimate the long-run and short-run price relationships.

Design/methodology/approach

– Using monthly price date over the period of January 1998-December 2013 in China, this paper employs an autoregressive distributed lag (ARDL) bounds test to explore the cointegration relationship among the price variables and estimate the ARDL long-run price relationship and the short-run error correction process (ARDL-EC).

Findings

– The empirical results indicate that crude oil, as one of the forcing variables along with wheat, corn, and soybean prices, is effecting rice price in China. Both the long-run and short-run price transmission elasticity estimates suggest the importance of crude oil price on the formation of rice prices. Furthermore, the adjustment speed coefficient is found to be statistically significant, supporting the notion that there is an error correction mechanism for maintaining the long-run price relationship facing short-run shocks.

Originality/value

– This paper adopts four types of commodity food prices to explore the relationships with crude oil price. The evidence of market integration, including the degree of price transmission and the speed of adjustment, remains a crucial step to proceed with the government intervention.
The impacts of international efforts to reduce illegal logging on China’s forest products trade flow
Authors: Guan Zhijie , Gong Peichen
Published: August 2015

Purpose

– The purpose of this paper is to examine the effects of international efforts aimed at reducing illegal logging on bilateral trade of forest products between China and its partner countries.

Design/methodology/approach

– The analysis is conducted using an extended gravity model, where the regulations enforced in different countries, as well as bilateral agreements between China and its trade partners on combating illegal logging are included as explanatory variables. The impacts of the efforts against illegal logging on bilateral trade of forest products are examined based on the estimated coefficients of these policy variables.

Findings

– The results show that the regulations have significant and positive effects on the bilateral trade of total forest products between China and its partner countries. The bilateral agreement on combating illegal logging between showed a negative effect on the bilateral trade of forest products. A further study of three types of forest products shows that the regulations have a negative effect for roundwood, but a positive effect for furniture and wood-based panels. The bilateral agreement, on the other hand, affects negatively the trade of all the three forest products.

Practical implications

– Since the export of roundwood from China is negligible, the results from this study imply that international efforts to reduce illegal logging have caused reduction of the import of roundwood into China. China’s wood processing industry is to a high degree dependent on imported roundwood. To secure timber supply is therefore an important strategy for sustainable development of the wood processing industry in China.

Originality/value

– To the knowledge, this is the first comprehensive assessment of the impacts of international efforts to reduce illegal logging on forest products trade flow between China and its partner countries. The results provide important scientific bases for decisions on reducing international trade of illegally sourced wood products and on promoting sustainable development of the wood processing industry in China.
Consumer perceived brand innovativeness
Authors: Shams Rahil , Alpert Frank , Brown Mark
Published: August 2015

Purpose

– This paper aims to examine brand innovativeness. While innovativeness has been studied at the product and firm levels, there is little research at the brand level. This paper argues for why this is needed, develops a conceptualization of consumer perceived brand innovativeness (CPBI) from a theoretical perspective and then develops and validates a measure for CPBI.

Design/methodology/approach

– Three qualitative studies were conducted to generate an enriched and more detailed understanding of what brand innovativeness means to consumers. Data were collected using free association and open-ended elicitation techniques. Next, a CPBI scale was developed and validated in three quantitative studies.

Findings

– The results indicate that innovative brands are related with several interesting core and secondary associations that have not been adequately addressed in previous research. CPBI is conceptualized as a unidimensional construct. Altogether six studies show that the proposed CPBI measure is valid and reliable.

Originality/value

– The present study is the first to identify the limitations of product and firm innovativeness conceptualizations with regards to brand innovativeness. It develops a unique and theoretically supported conceptualization and operationalization of CPBI. The first brand concept map for the concept of innovative brands is presented. The results of the studies indicate the measure’s ability to successfully predict important consumer behavior variables such as purchase intentions, and to demonstrate superior predictive performance compared with a key related scale in the mobile phone category.
Vulnerable work and strategies for inclusion: an introduction
Authors: Burgess John , Connell Julia
Published: August 2015

Purpose

– The purpose of this paper is to introduce this special issue volume on vulnerable work and strategies for inclusion. Definitions, measurement, analysis and policy responses to vulnerable work and strategies for inclusion are addressed before the key aspects of the nine papers included in the special issue are summarised.

Design/methodology/approach

– The topic of vulnerability at work is explored, before the distinguishing features of jobs that generate vulnerable conditions and the characteristics of vulnerable workers are identified.

Findings

– Vulnerable work is insecure and irregular with few protections accorded to the vulnerable workers who are often characterised by their age, ethnic status, gender and skill profiles. The consequences include: poor job quality, low and irregular incomes and personal/family hardship. Vulnerability is widespread across the workforce, with workers subject to work intensification, employment insecurity and poor work-life balance.

Social implications

– Vulnerable work and workers constitute a growing and global phenomenon. Consequently, governments and employers need to work together on programmes, such as the ILO’s decent work agenda, to ensure that basic human rights at work are widely recognised and provision to ongoing employment, safe working conditions and regular hours are offered across a variety of industries/sectors.

Originality/value

– This volume examines the conceptual, empirical and policy aspects of vulnerability in employment. It documents the international dimensions of vulnerability, the different forms it takes, those groups that are at risk of vulnerable employment and the underlying factors that generate and support vulnerability.
A four quadrant strategy for improving government performance in Ras Al Khaimah
Authors: Jabnoun Naceur , Khalifah Mohamed
Published: August 2015

Purpose

– Quality awards played an important role in improving quality in private and public organizations. The purpose of this paper is to present an integrated four quadrant strategy adopted by Sheikh Saqr Program for Government Excellence (SSPGE) for improving government performance in the Emirate of Ras Al Khaima (RAK) in the United Arab Emirates.

Design/methodology/approach

– The methodology of this case is unusual as it mixes the experience of the authors with theory and literature. The first and second authors are, respectively, the senior consultant and the director general of SSPGE. The authors hereby present the integrated strategy developed and implemented by SSPGE in order to improve government performance in RAK. This paper first presents this improvement strategy along with the relevant literature, and then it outlines the results of its implementation.

Findings

– The use of the four quadrant strategy helped government organizations in RAK achieve as successful launching of the government department award based on the EFQM excellence model. The average total score for all government departments was 311.0 in 2008. This indicates a huge improvement from the self-assessment score in 2007. It was also 106 points higher than the initially projected score for self-assessment in 2008. The average score consistently increased and reached 414 in 2012 indicating a 33 percent increase from 2008.

Practical implications

– This paper outlines a four quadrant strategy that was successfully implemented by a government excellence program. This strategy can be used in other government excellence programs. It may also be adapted for use in large public and private organizations.

Originality/value

– Most researchers focus on excellence strategies in organizations while this case addresses the strategy of an excellence program. This case also shows the importance of integration between the various awards categories, projects, and activities organized by the program. It also presents a successful case of linking activities of the program to the theoretical concepts of quality and excellence.