bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections
Authors: Woelk Christopher H. , Pybus Oliver G. , Jin Li , Brown David W. G. , Holmes Edward C. 
Published: August 2015

We compared the extent of positive selection acting on acute and persistent strains of measles virus (MV). Far stronger positive selection was found in the fusion (F) and haemagglutinin (H) genes from subacute sclerosing panencephalitis (SSPE) compared to acute MV cases. Most of the positively selected sites identified in these surface glycoprotein genes from SSPE cases correspond to structural, functional or antigenic areas, and could not be explained by the effects of cell passaging. The correlations between selected sites and functional studies of MV are discussed in detail with reference to the maintenance of persistent infection. No positive selection was found in the matrix (M) gene from acute cases of MV and the effects of including hypermutated SSPE M gene sequences in phylogenetic inference were also explored. Finally, using H gene data, we estimated the rate of molecular evolution for SSPE strains as 3·4×10−4substitutions/site/year, which is similar to previous estimates obtained for acute strains.
Molecular cloning and characterization of Antheraea mylitta cytoplasmic polyhedrosis virus genome segment 9
Authors: Qanungo Kaustubha R. , Kundu Subhas C. , Mullins James I. , Ghosh Ananta K. 
Published: August 2015

Genome segment 9 of the 11-segment RNA genomes of three cytoplasmic polyhedrosis virus (CPV) isolates from Antheraea mylitta (AmCPV), Antheraea assamensis (AaCPV) and Antheraea proylei (ApCPV) were converted to cDNA, cloned and sequenced. In each case, this genome segment consists of 1473 nucleotides with one long ORF of 1035 bp and encodes a protein of 345 amino acids, termed NSP38, with a molecular mass of 38 kDa. Secondary structure prediction showed the presence of nine α-helices in the central and terminal domains with localized similarity to RNA-binding motifs of bluetongue virus and infectious bursal disease virus RNA polymerases. Nucleotide sequences were 99·6% identical between these three strains of CPVs, but no similarity was found to any other nucleotide or protein sequence in public databases. The ORF from AmCPV cDNA was expressed as a His-tagged fusion protein in E. coli and polyclonal antibody was raised against the purified protein. Immunoblot as well as immunofluorescence analysis with anti-NSP38 antibody showed that the protein was not present in polyhedra or uninfected cells but was present in AmCPV-infected host midgut cells. NSP38 was expressed in insect cells as soluble protein via a baculovirus expression vector and shown to possess the ability to bind poly(rI)–(rC) agarose, which was competitively removed by AmCPV viral RNA. These results indicate that NSP38 is expressed in virus-infected cells as a non-structural protein. By binding to viral RNA, it may play a role in the regulation of genomic RNA function and packaging.
Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread
Authors: Ohshima Kazusato , Yamaguchi Yuka , Hirota Ryo , Hamamoto Tamaki , Tomimura Kenta , Tan Zhongyang , Sano Teruo , Azuhata Fumio , Walsh John A. , Fletcher John , Chen Jishuang , Gera Abed , Gibbs Adrian 
Published: August 2015

Turnip mosaic virus (TuMV), a species of the genus Potyvirus, occurs worldwide. Seventy-six isolates of TuMV were collected from around the world, mostly from Brassica and Raphanus crops, but also from several non-brassica species. Host tests grouped the isolates into one or other of two pathotypes; Brassica (B) and Brassica–Raphanus (BR). The nucleotide sequences of the first protein (P1) and coat protein (CP) genes of the isolates were determined. One-tenth of the isolates were found to have anomalous and variable phylogenetic relationships as a result of recombination. The 5′-terminal 300 nt of the P1 gene of many isolates was also variable and phylogenetically anomalous, whereas the 380 nt 3′ terminus of the CP gene was mostly conserved. Trees calculated from the remaining informative parts of the two genes of the non-recombinant sequences by neighbour-joining, maximum-likelihood and maximum-parsimony methods were closely similar, and so these parts of the sequences were concatenated and trees calculated from the resulting 1150 nt. The isolates fell into four consistent groups; only the relationships of these groups with one another and with the outgroup differed. The ‘basal-B’ cluster of eight B-pathotype isolates was most variable, was not monophyletic, and came from both brassicas and non-brassicas from southwest and central Eurasia. Closest to it, and forming a monophyletic subgroup of it in most trees, and similarly variable, was the ‘basal-BR’ group of eight BR pathotype Eurasian isolates. The third and least variable group, the ‘Asian-BR’ group, was of 22 BR-pathotype isolates, all from brassicas, mostly Raphanus, and all from east Asia mostly Japan. The fourth group of 36 isolates, the ‘world-B’ group, was from all continents, most were isolated from brassicas and most were of the B-pathotype. The simplest of several possible interpretations of the trees is that TuMV originated, like its brassica hosts, in Europe and spread to the other parts of the world, and that the BR pathotype has recently evolved in east Asia.
Adenovirus E1-transformed cells grow despite the continuous presence of transcriptionally active p53
Authors: Löber Christian , Lenz-Stöppler Claudia , Dobbelstein Matthias 
Published: August 2015

The E1 region of adenovirus (Ad) type 5 is capable of transforming cells. According to current concepts, the Ad E1B 55 kDa (E1B 55K) protein enables transformed cells to grow by constantly binding and inactivating the p53 tumour suppressor protein. To test this model, the transcriptional activity of p53 was determined in Ad E1-transformed cells. Surprisingly, it was found that a p53-responsive promoter is highly active in Ad E1-transformed cells and further activated only 3- to 4-fold (compared to 200-fold in p53
−/− cells) by exogenously expressed p53 or p53mt24–28, a p53 mutant that is transcriptionally active but unable to bind the E1B 55K. On the other hand, the transient overexpression of E1B 55K led to a strong downregulation of a p53-responsive promoter relative to its baseline activity in Ad E1-transformed cells but not in p53
−/− cells. COS-7 cells, transformed by simian virus 40 (SV40), also showed constitutive p53 activity, whereas HeLa cells, transformed with oncogenic human papillomavirus, did not. Upon stable transfection, Ad E1-transformed cells but not p53
−/− cells gave rise to colonies that expressed exogenous p53 or p53mt24–28 but, nonetheless, grew at near-wild-type rates. It is proposed that E1B 55K or the SV40 tumour antigen are saturated by the p53 protein, which accumulates in virus-transformed cells, leaving a proportion of active p53 molecules. The transformation of cells by the Ad E1 genes confers permissiveness for active p53, conceivably by inactivating the relevant products of p53 target genes that would otherwise prevent cell growth. Thus, Ad-transformed cells contain and tolerate active p53.
The terminal repeats and latency-associated nuclear antigen of herpesvirus saimiri are essential for episomal persistence of the viral genome
Authors: Collins Christopher M. , Medveczky Maria M. , Lund Troy , Medveczky Peter G. 
Published: August 2015

The simian herpesvirus saimiri (HVS) induces malignant T cell lymphomas and is closely related to Kaposi’s sarcoma-associated herpesvirus (KSHV or HHV-8). Both belong to the gamma-2 herpesvirus subgroup. The viral genome of HVS consists of a unique region (L-DNA) that contains all of the viral genes flanked by non-coding terminal repeats (H-DNA). Here we describe the cloning of a 113 kb restriction fragment containing the L-DNA of an oncogenic HVS strain in an F′ replicon-based E. coli vector. Cloned DNA was infectious and the ends of the progeny viral genome consisted of amplified tandem alternating repeats of vector and a single H-DNA unit. T cells infected with these viruses contained the linear DNA typically found a few weeks after infection, but were unable to form episomal circular viral DNA, which is the latent form of the viral genome. Recombinant viruses with reconstructed H-DNA were generated and T cells infected with these rescued viruses contained high copy numbers of episomal DNA. Plasmids expressing the latency-associated nuclear antigen (LANA) and containing various numbers of H-DNA repeats stably replicated as episomes, but constructs containing three repeat units produced the highest copy numbers. These data show that intact and multiple terminal repeats are essential components for episomal replication in latently infected T cells. Moreover, LANA and terminal repeats are sufficient for stable plasmid persistence. Cloned HVS can also be utilized for mutagenesis of HVS and for the expression of foreign genes through efficient manipulation of plasmids in E. coli.
‘Streptomyces nanchangensis’, a producer of the insecticidal polyether antibiotic nanchangmycin and the antiparasitic macrolide meilingmycin, contains multiple polyketide gene clusters
Authors: Sun Yuhui , Zhou Xiufen , Liu Jun , Bao Kai , Zhang Guiming , Tu Guoquan , Kieser Tobias , Deng Zixin 
Published: August 2015

Several independent gene clusters containing varying lengths of type I polyketide synthase genes were isolated from ‘Streptomyces nanchangensis’ NS3226, a producer of nanchangmycin and meilingmycin. The former is a polyether compound similar to dianemycin and the latter is a macrolide compound similar to milbemycin, which shares the same macrolide ring as avermectin but has different side groups. Clusters A–H spanned about 133, 132, 104, 174, 122, 54, 37 and 59 kb, respectively. Two systems were developed for functional analysis of the gene clusters by gene disruption or replacement. (1) Streptomyces phage ϕC31 and its derived vectors can infect and lysogenize this strain. (2) pSET152, an Escherichia coli plasmid with ϕC31 attP site, and pHZ1358, a Streptomyces–Escherichia coli shuttle cosmid vector, both carrying oriT from RP4, can be mobilized from E. coli into NS3226 by conjugation. pHZ1358 was shown to be generally useful for generating mutant strains by gene disruption and replacement in NS3226 as well as in several other Streptomyces strains. A region in cluster A (∼133 kb) seemed to be involved in nanchangmycin production because replacement of several DNA fragments in this region by an apramycin resistance gene [aac3(IV)] gave rise to nanchangmycin non-producing mutants.
Streptomyces spp. contain class Ia and class II ribonucleotide reductases: expression analysis of the genes in vegetative growth The GenBank/EMBL/DDBJ accession numbers for the sequences determined in this paper are AJ224870, AJ276618, AJ277778, AJ295338 and AJ295339.
Authors: Borovok Ilya , Kreisberg-Zakarin Rachel , Yanko Michaela , Schreiber Rachel , Myslovati Margarita , Aslund Fredrik , Holmgren Arne , Cohen Gerald , Aharonowitz Yair 
Published: August 2015

Genes encoding two ribonucleotide reductases (RNRs) were identified in members of the genusStreptomyces. One gene,nrdJ, encoded an oligomeric protein comprising four identical subunits each with a molecular mass of ∼108 kDa. The activity of this protein depended on the presence of 5′-deoxyadenosylcobalamine (coenzyme B12), establishing it as a class II RNR. TheStreptomyces clavuligerus nrdJgene was cloned, using internal peptide sequences from the purified protein, and was found to encode a polypeptide of 961 aa. Molecular phylogenetic analysis showed that theS. clavuligerusclass II RNR shares significant similarity with most other bacterial and archaeal class II RNRs. Two other genes,nrdAandnrdB, were initially identified in theStreptomyces coelicolorgenome database in unannotated ORFs as encoding a class Ia RNR. Southern analysis demonstrated that thenrdABgenes were present in differentStreptomycesspp. TheS. coelicolor nrdABgenes were cloned and expressed inEscherichia coli, and the recombinant proteins were shown to represent a class I RNR. It was shown, using quantitative real-time PCR, that theS. clavuligerusclass Ia and class II RNR genes were differentially transcribed during vegetative growth. The copy number of the class IInrdJtranscripts was approximately constant throughout the exponential phase of vegetative growth (3–5×105copies per 400 ng total RNA after reverse transcription). In contrast, the copy number of the class IanrdABtranscripts was some 10- to 20-fold less than that ofnrdJin the early-exponential growth phase (2·8×104copies), and decreased markedly at the mid-exponential (4×103copies) and late-exponential phases (1·1×103copies) of growth. A possible role for the involvement of two RNRs during vegetative growth is discussed.
OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data
Authors: Leng Ning , Choi Jeea , Chu Li-Fang , Thomson James A. , Kendziorski Christina , Stewart Ron 
Published: August 2015

SummaryA recent paper identified an artifact in multiple single-cell RNA-seq (scRNA-seq) data sets generated by the Fluidigm C1 platform. Specifically, Leng*et al. showed significantly increased gene expression in cells captured from sites with small or large plate output IDs. We refer to this artifact as an ordering effect (OE). Including OE genes in downstream analyses could lead to biased results. To address this problem, we developed a statistical method and software called OEFinder to identify a sorted list of OE genes. OEFinder is available as an R package along with user-friendly graphical interface implementations that allows users to check for potential artifacts in scRNA-seq data generated by the Fluidigm C1 platform.Availability and ImplementationOEFinder is freely available athttps://github.com/lengning/OEFinderContactrstewart@morgridge.org
Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting
Authors: Mavor David , Barlow Kyle A. , Thompson Samuel , Barad Benjamin A. , Bonny Alain R. , Cario Clinton L. , Gaskins Garrett , Liu Zairan , Deming Laura , Axen Seth D. , Caceres Elena , Chen Weilin , Cuesta Adolfo , Gate Rachel , Green Evan M. , Hulce Kaitlin R. , Ji Weiyue , Kenner Lillian R. , Mensa Bruk , Morinishi Leanna S. , Moss Steven M. , Mravic Marco , Muir Ryan K. , Niekamp Stefan , Nnadi Chimno I. , Palovcak Eugene , Poss Erin M. , Ross Tyler D. , Salcedo Eugenia , See Stephanie , Subramaniam Meena , Wong Allison W. , Li Jennifer , Thorn Kurt S. , Conchúir Shane Ó. , Roscoe Benjamin P. , Chow Eric D. , DeRisi Joseph L. , Kortemme Tanja , Bolon Daniel N. , Fraser James S. 
Published: August 2015

ABSTRACTUbiquitination is an essential post-translational regulatory process that can control protein stability, localization, and activity. Ubiquitin is essential for eukaryotic life and is highly conserved, varying in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies inS. cerevisiaeindicate that ubiquitin is highly tolerant to single amino acid mutations. To resolve this paradox, we hypothesized that the set of tolerated substitutions would be reduced when the cultures are not grown in rich media conditions and that chemically induced physiologic perturbations might unmask constraints on the ubiquitin sequence. To test this hypothesis, a class of first year UCSF graduate students employed a deep mutational scanning procedure to determine the fitness landscape of a library of all possible single amino acid mutations of ubiquitin in the presence of one of five small molecule perturbations: MG132, Dithiothreitol (DTT), Hydroxyurea (HU), Caffeine, and DMSO. Our data reveal that the number of tolerated substitutions is greatly reduced by DTT, HU, or Caffeine, and that these perturbations uncover “shared sensitized positions” localized to areas around the hydrophobic patch and to the C-terminus. We also show perturbation specific effects including the sensitization of His68 in HU and tolerance to mutation at Lys63 in DTT. Taken together, our data suggest that chemical stress reduces buffering effects in the ubiquitin proteasome system, revealing previously hidden fitness defects. By expanding the set of chemical perturbations assayed, potentially by other classroom-based experiences, we will be able to further address the apparent dichotomy between the extreme sequence conservation and the experimentally observed mutational tolerance of ubiquitin. Finally, this study demonstrates the realized potential of a project lab-based interdisciplinary graduate curriculum.
Children, old-age support and pension in rural China
Authors: Zhang Chuanchuan 
Published: August 2015

Purpose– The purpose of this paper is to examine the substitute between social old-age insurance and adult children in providing old-age support, and estimate the effects of China’s old rural pension program (ORPP) on sex ratio.Design/methodology/approach– Using data from China’s 2005 inter-census population survey and China Health and Retirement Longitudinal Study, this paper estimates the effects of children on rural parents’ take-up of pension program and the effects of having access to pension on old parents’ choice of resource for future old-age support. The effects of China’s ORPP on sex ratio are estimated using difference-in-differences identification strategy.Findings– Peasants having sons are less likely to participate in pension program and each additional son and daughter significantly decreases their likelihood of participation. Moreover, the effect of sons is much larger than that of daughters. Peasants having access to pension are less likely to rely on their children for old-age support. The implementation of the ORPP moderately decreased sex ratio.Social implications– Implementing pension program in China’s rural area will probably affect rural people’s fertility behavior and thus be helpful in correcting sex ratio bias.Originality/value– This paper first estimates the effects of having access to pension on old parents’ choices of providers of old-age support, and estimates the causal effect of rural pension on sex ratio using standard DID strategy.
Irrigation investment in China: trends, correlates and impacts
Authors: He Fei , Shi Yaojiang , Luo Renfu , Zhang Linxiu , Johnson Natalie , Rozelle Scott 
Published: August 2015

Purpose
– The purpose of this paper is to describe trends in irrigation investment in China’s rural villages in the 2000s, identify the types of villages in which investment occurred and examine whether this investment had an impact on agricultural land.

Design/methodology/approach
– This study makes use of longitudinal survey data from a nearly nationally representative sample of 101 villages spread across five provinces. The outcome variables are cultivated area, sown area and effectively irrigated area, and ordinary least squares regression and fixed effects models are used for the analysis.

Findings
– In spite of sustained investments into irrigation from 1998 to 2011, there has been almost no impact on agricultural land. Cultivated area and sown area have fallen across all five sample provinces while effectively irrigated area remains largely unchanged. The authors also show that there is no relationship between investment into irrigation and agricultural land. Irrigation facilities also have the lowest rate of rural resident satisfaction of any of the major public services provided.

Research limitations/implications
– More research is needed to understand the impact of irrigation investment on crop yields and water savings.

Practical implications
– Policymakers may need to rethink the current pattern of investment into irrigation.

Originality/value
– This is the first study to quantitatively model the impact of investment into irrigation at the village level all over China.
Market practices in countercultural market emergence
Authors: Hietanen Joel , Rokka Joonas 
Published: August 2015

Purpose– The purpose of this paper is to contribute to the growing marketing literature that investigates markets as “configurations”, i.e. networks of market actors engaged in market-shaping practices and performances. As this pioneering work has been largely focused on established mainstream markets and industries driven by large multi-national companies, the present article extends practice-based market theorizing to countercultural market emergence and also to unconventional market practices shaping it.Design/methodology/approach– Insights are drawn from a four-year multi-sited ethnographic study of a rapidly expanding electronic music scene that serves as an illustrative example of emergent countercultural market.Findings– In contrast to mainstream consumer or industrial markets, the authors identify a distinctive dynamic underlying market emergence. Countercultural markets as well as their appeal and longevity largely depend on an inherent authenticity paradox that focal market actors need to sustain and negotiate through ongoing market-shaping and market-restricting practices.Practical implications– From a practitioner perspective, the authors discuss the implications for market actors wishing to build on countercultural authenticity. They highlight the fragility of countercultural markets and point out practices sustaining them, and also possibilities and challenges in tapping into them.Originality/value– The study contributes by theorizing the tensions that energize and drive countercultural market emergence. In particular, the authors address the important role of market-restricting practices in facilitating countercultural appeal that has not received explicit attention in prior marketing literature.
A relational approach to direct mail consumption
Authors: Françoise Simon , Andrews Lynda 
Published: August 2015

Purpose– This paper aims to investigate how direct mail consumption contributes to brand relationship quality. Store flyers and other direct mailings continue to play a significant role in many companies’ communication strategies. Research on this topic predominantly investigates driving store traffic and sales. Less is known regarding the consumer side, such as the value that consumers may derive from the consumption of direct mailings and the effects of such a value on brand relationship quality. To address this limitation, this paper tests a causal model of the contribution of direct mail value to brand commitment, drawing on a value framework that integrates social theory of engagement regimes and literature on experiential customer value.Design/methodology/approach– The empirical work of this paper is based on a rigorous four-study mixed methods design, involving qualitative study, confirmatory factor analysis and partial least squares structural modeling.Findings– The authors develop two second-order formatively designed scales – familiar value and planned value scales – that illustrate the role of engagement regimes in consumer behavior. Although both types of value contribute equally to direct mail attachment, they exert contrasting effects on other mediational consumer responses, such as reading and gratitude. Finally, the proposed theoretical model appears to be robust in predicting customers’ brand commitment.Research limitations/implications– This study provides new insights into the research on consumer value and brand relational communication.Originality/value– This study is the first to consider consumer benefits from the social perspective of engagement regimes.