bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitro and in vivo expression of foreign genes by transmissible gastroenteritis coronavirus-derived minigenomes
Authors: Alonso Sara , Sola Isabel , Teifke Jens P. , Reimann Ilona , Izeta Ander , Balasch Mónica , Plana-Durán Juan , Moormann Rob J. M. , Enjuanes Luis 
Published: August 2015

A helper-dependent expression system based on transmissible gastroenteritis coronavirus (TGEV) has been developed using a minigenome of 3·9 kb (M39). Expression of the reporter gene β-glucuronidase (GUS) (2–8 μg per 106cells) and the porcine respiratory and reproductive syndrome virus (PRRSV) ORF5 (1–2 μg per 106cells) has been shown using a TGEV-derived minigenome. GUS expression levels increased about eightfold with the m.o.i. and were maintained for more than eight passages in cell culture. Nevertheless, instability of the GUS and ORF5 subgenomic mRNAs was observed from passages five and four, respectively. About a quarter of the cells in culture expressing the helper virus also produced the reporter gene as determined by studying GUS mRNA production byin situhybridization or immunodetection to visualize the protein synthesized. Expression of GUS was detected in the lungs, but not in the gut, of swine immunized with the virus vector. Around a quarter of lung cells showing replication of the helper virus were also positive for the reporter gene. Interestingly, strong humoral immune responses to both GUS and PRRSV ORF5 were induced in swine with this virus vector. The large cloning capacity and the tissue specificity of the TGEV-derived minigenomes suggest that these virus vectors are very promising for vaccine development.
Identification of a cell surface 30 kDa protein as a candidate receptor for Hantaan virus
Authors: Kim Tae-Yeon , Choi Yun , Cheong Hong-Seok , Choe Joonho 
Published: August 2015

Cellular receptors play an important role in virus pathogenesis. As a first step in virus infection, viruses attach to specific receptors on the surface of cells; Hantaan virus infects susceptible cells by attaching to a receptor located on the cell surface. To date, the identity of the Hantaan virus host cell receptor remains unknown. To determine the protein on the cell surface to which Hantaan virus binds, a virus overlay protein-binding assay was performed with radiolabelled virus. A 30 kDa (30K) protein was identified as a putative receptor for Hantaan virus. The specificity of virus interactions with this protein was demonstrated with a competition assay using unlabelled Hantaan virus and poliovirus. Unlabelled Hantaan virus inhibited the binding of radiolabelled Hantaan virus to this 30 kDa protein, whereas poliovirus did not. A polyclonal antibody against the 30K protein blocked binding of Hantaan virus to Vero-E6 cells and, consequently, virus infection. Blocking with the anti-30K antibody reduced virus infection of cells by 70%. These data strongly suggest that the 30 kDa surface protein is a putative receptor for Hantaan virus.
Gill-associated nidovirus of Penaeus monodon prawns transcribes 3′-coterminal subgenomic mRNAs that do not possess 5′-leader sequences
Authors: Cowley Jeff A. , Dimmock Christine M. , Walker Peter J. 
Published: August 2015

Sequence analysis of the ∼20 kb 5′-terminal portion of the ssRNA genome of gill-associated virus (GAV) of Penaeus monodon prawns has previously established that it contains an ORF1a–1b replicase gene equivalent to those of the coronavirus and arterivirus members of the order Nidovirales. Sequence analysis of the remaining ∼6·2 kb of the GAV genome downstream of ORF1a–1b to a 3′-poly(A) tail has identified two highly conserved intergenic sequences in which 29/32 nucleotides are conserved. Northern hybridization using probes to the four putative GAV ORFs and either total or poly(A)-selected RNA identified two 3′-coterminal subgenomic (sg) mRNAs of ∼6 kb and ∼5·5 kb. Primer extension and 5′-RACE analyses showed that the sgmRNAs initiate at the same 5′-AC positions in the central region of the two conserved intergenic sequences. Neither method provided any evidence that the GAV sgmRNAs are fused to genomic 5′-leader RNA sequences as is the case with vertebrate coronaviruses and arteriviruses. Intracellular double-stranded (ds)RNAs equivalent in size to the 26·2 kb genomic RNA and two sgRNAs were also identified by RNase/DNase digestion of total RNA from GAV-infected prawn tissue. The identification of only two sgmRNAs that initiate at the same position in conserved intergenic sequences and the absence of 5′-genomic leader sequences fused to these sgmRNAs confirms that GAV has few genes and suggests that it utilizes a transcription mechanism possibly similar to the vertebrate toroviruses but distinct from coronaviruses and arteriviruses.
Genomic characterization of TT viruses (TTVs) in pigs, cats and dogs and their relatedness with species-specific TTVs in primates and tupaias
Authors: Okamoto Hiroaki , Takahashi Masaharu , Nishizawa Tsutomu , Tawara Akio , Fukai Katsuhiko , Muramatsu Umetaro , Naito Yoshihisa , Yoshikawa Akira 
Published: August 2015

Using PCR with primers derived from a non-coding region of the human TT virus (TTV) genome, the TTV sequence in serum samples obtained from pigs (Sus domesticus), dogs (Canis familiaris) and cats (Felis catus) was identified and the entire genomic sequence was determined for each representative isolate. Three TTV isolates (Sd-TTV31 from a pig, Cf-TTV10 from a dog and Fc-TTV4 from a cat) comprising 2878, 2797 and 2064 nucleotides, respectively, each had three open reading frames (ORFs) encoding 436–635 (ORF1), 73–105 (ORF2) and 224–243 (ORF3) aa but lacked ORF4, similar to tupaia TTV. ORF3 was presumed to arise from a splicing of TTV mRNA, similar to human prototype TTV. Although the nucleotide sequence of Sd-TTV31, Cf-TTV10 and Fc-TTV4 differed by more than 50% from each other and from previously reported TTVs of 3·4–3·9 kb and TTV-like mini viruses (TLMVs) of 2·8–3·0 kb isolated from humans and non-human primates as well as tupaia TTVs of 2·2 kb, they resembled known TTVs and TLMVs with regard to genomic organization and presumed transcriptional profile rather than animal circoviruses of 1·7–2·3 kb. Phylogenetic analysis revealed that Sd-TTV31, Cf-TTV10 and Fc-TTV4 were closer to TTVs from lower-order primates and tupaias than to TTVs from higher-order primates and TLMVs. These results indicate that domestic pigs, cats and dogs are naturally infected with species-specific TTVs with small genomic size and suggest a wide distribution of TTVs with extremely divergent genomic sequence and length in animals.
Circulating and cell-bound antibodies increase coxsackievirus B4-induced production of IFN-α by peripheral blood mononuclear cells from patients with type 1 diabetes
Authors: Hober Didier , Chehadeh Wassim , Weill Jacques , Hober Christine , Vantyghem Marie-Christine , Gronnier Pascale , Wattré Pierre 
Published: August 2015

Increased levels of IFN-α have been found in patients with type 1 diabetes who have detectable levels of coxsackievirus B4 (CVB4) RNA in their blood. The IFN-α-inducing activity of CVB4in vitrois weak but can be enhanced by human IgGs. Therefore, it was investigatedin vitrowhether a preferential IFN-α response of peripheral blood mononuclear cells (PBMCs) to CVB4 exists in patients with type 1 diabetes (n=56) compared with healthy subjects (n=20) and whether antibodies play a role. In patients, the levels of IFN-α obtained after stimulation by PBMCs with CVB4 were higher (P=0·008), an individual IFN-α response by PBMCs to CVB4 was more frequent (P=0·0004) and increased levels of IFN-α were observed in CVB4-infected whole blood cultures. The IFN-α-inducing activity of patients plasma and IgGs mixed with CVB4 and then added to PBMCs was high in comparison with healthy subjects (P<0·001) and was inhibited by preincubating the cells with anti-FcγRII, anti-FcγRIII and anti-CAR (coxsackievirus and adenovirus receptor) antibodies. The strong IFN-α responsiveness of PBMCs to CVB4 suggested that IgGs bound to the cell surface might play a role. A short 56 °C incubation of PBMCs from patients responsive to CVB4 generated supernatants, which, when added to cells, exhibited IFN-α-enhancing activity in combination with CVB4, whereas those of controls did not. Specific antibodies for FcγRI, FcγRII and CAR inhibited this activity. These studies demonstrate that CVB4, through interactions with circulating and/or cell-bound IgGs, can strongly induce the production of IFN-α by PBMCs from patients with type 1 diabetes.
Natural genetic recombination between co-circulating heterotypic enteroviruses
Authors: Oprisan Gabriela , Combiescu Mariana , Guillot Sophie , Caro Valerie , Combiescu Andrei , Delpeyroux Francis , Crainic Radu 
Published: August 2015

Natural recombination in poliovirus is a frequent phenomenon. In practice, whenever different genotypes have the opportunity to infect the same individual, a high proportion of viruses with recombinant genomes are excreted. To determine whether enteroviruses other than poliovirus can naturally produce viable virions with recombinant genomes, we studied the molecular features of two distant regions of the viral genomes – the VP1 coding region and the 3D polymerase coding region – of the echovirus serotypes associated with a large outbreak of aseptic meningitis. Nucleotide sequences of nine epidemic strains [belonging to echovirus serotypes 4 (E4), 7 (E7) and 30 (E30)] in the two genomic regions (300 nt of VP1 and 520 nt of 3D polymerase) were compared to prototype and field strains, and phylogenetic trees were generated from alignments. In the VP1 region, each of the three epidemic serotypes clustered with the homotypic prototype strain, whereas in the 3D polymerase region, E7 and E30 grouped as a single cluster, distant from the two corresponding prototype strains. This suggests that one of these two E7 and E30 strains has evolved through recombination with the other or that both have acquired the 3D polymerase coding region from a common ancestor. Our results suggest that such genetic recombinations between different echovirus serotypes are possible when multiple epidemic strains are circulating simultaneously.
Kinetics of binding, uptake and degradation of live fluorescent (DsRed) bacteria by Dictyostelium discoideum
Authors: Maselli Andrew , Laevsky Gary , Knecht David A 
Published: August 2015

The kinetics of binding, uptake and degradation of bacteria by vegetativeDictyosteliumamoeba usingEscherichia coliexpressing the recombinant fluorescent protein DsRed have been characterized. There are significant advantages to using DsRed-expressing bacteria for phagocytosis assays. Stable expression of the fluorescent protein, DsRed, provides living bacteria with a bright internal fluorescent signal that is degradable in the phagolysosomal pathway. Unlike assays with chemically labelled bacteria or latex beads, the bacteria are alive and possess a natural, unaltered external surface for receptor interaction.Dictyosteliumcells rapidly bind and phagocytose DsRed bacteria. Pulse–chase experiments show that the signal derived from DsRed is degraded with a half-life of approximately 45 min. To distinguish internalized bacteria from those bound to the surface, an assay was developed in which sodium azide was used to release surface-bound particles. Surprisingly, surface particle release appears to be independent of myosin II function. Using this assay it was shown that the uptake of bacteria into cells is extremely rapid. After 1 min incubation, 20% of the signal is derived from internalized bacteria. The proportion of the signal from internalized bacteria increases gradually and reaches 50% at steady state. This assay will be useful in investigations of the molecular machinery of phagocytosis and post-internalization vesicle trafficking.
A novel recombinant DNA system for high efficiency affinity purification of proteins inSaccharomyces cerevisiae
Authors: Carrick Brian H. , Hao Lixuan , Smaldino Philip J. , Engelke David R. 
Published: August 2015

AbstractIsolation of endogenous proteins fromSaccharomyces cerevisiaehas been facilitated by inserting encoding polypeptide affinity tags at the C-termini of chromosomal open reading frames (ORFs) using homologous recombination of DNA fragments. The tagged protein isolation is limited by a number of factors, including high cost of affinity resins for bulk isolation and low concentration of ligands on the resin surface, leading to low isolation efficiencies and trapping of contaminants. To address this we have created a recombinant “CelTag” DNA construct from which PCR fragments can be created to easily tag C-termini ofS. cerevisiaeORFs using selection for anat1marker. The tag has a C-terminal cellulose binding module to be used in the first affinity step. Microgranular cellulose is very inexpensive and has an effectively continuous ligand on its surface, allowing rapid, highly efficient purification with minimal background in a single step. Cellulose-bound proteins are released by specific cleavage of an included site for TEV protease, giving nearly pure product. The tag can be lifted from the recombinant DNA construct either with or without a 13x myc epitope tag between the target ORF and the TEV protease site. Binding of CelTag protein fusions to cellulose is stable to high salt, nonionic detergents, and 1 M urea, allowing stringent washing conditions to remove loosely associated components, as needed, before specific elution. It is anticipated that this reagent will allow isolation of rare or unstable protein complexes from large quantities of yeast extract, including soluble, membrane-bound, or chromatin-associated assemblies.
Missing Data and Technical Variability in Single-Cell RNA-Sequencing Experiments
Authors: Hicks Stephanie C. , Townes F. William , Teng Mingxiang , Irizarry Rafael A. 
Published: August 2015

AbstractUntil recently, high-throughput gene expression technology, such as RNA-Sequencing (RNA-seq) required hundreds of thousands of cells to produce reliable measurements. Recent technical advances permit genome-wide gene expression measurement at the single-cell level. Single-cell RNA-Seq (scRNA-seq) is the most widely used and numerous publications are based on data produced with this technology. However, RNA-Seq and scRNA-seq data are markedly different. In particular, unlike RNA-Seq, the majority of reported expression levels in scRNA-seq are zeros, which could be either biologically-driven, genes not expressing RNA at the time of measurement, or technically-driven, gene expressing RNA, but not at a sufficient level to detected by sequencing technology. Another difference is that the proportion of genes reporting the expression level to be zero varies substantially across single cells compared to RNA-seq samples. However, it remains unclear to what extent this cell-to-cell variation is being driven by technical rather than biological variation. Furthermore, while systematic errors, including batch effects, have been widely reported as a major challenge in high-throughput technologies, these issues have received minimal attention in published studies based on scRNA-seq technology. Here, we use an assessment experiment to examine data from published studies and demonstrate that systematic errors can explain a substantial percentage of observed cell-to-cell expression variability. Specifically, we present evidence that some of these reported zeros are driven by technical variation by demonstrating that scRNA-seq produces more zeros than expected and that this bias is greater for lower expressed genes. In addition, this missing data problem is exacerbated by the fact that this technical variation varies cell-to-cell. Then, we show how this technical cell-to-cell variability can be confused with novel biological results. Finally, we demonstrate and discuss how batch-effects and confounded experiments can intensify the problem.
Fines, fees and funding: makerspaces standing apart
Authors: Crumpton Michael A 
Published: August 2015

Purpose
– The purpose of this article is to discuss operational components associated with creating a makerspace unit or department within a library.

Design/methodology/approach
– Several considerations are discussed that should be considered for successful implementation of a makerspace in a library.

Findings
– Makerspaces add a unique and fresh element to libraries and should be provided a sustainable model up front.

Originality/value
– The ideas and concepts expressed are those of the author.
Furthering the librarian’s journey: predicting terrorism?
Authors: Steele Kirstin 
Published: August 2015

Purpose
– The purpose of this paper is to compare the traditional librarian positions with intelligence analyst positions.

Design/methodology/approach
– Opinion.

Findings
– Similarities outnumber differences, and borrowing vocabulary and skills could benefit both, especially regarding long-term planning and spending in academic libraries.

Research limitations/implications
– Comparing salaries, management structure and possibilities for advancement would be interesting points of study.

Originality/value
– A literature search for comparing librarians with intelligence analysts revealed, in part, a 2013 lecture at the annual Special Libraries Association conference by Edna Reid, and a 2012 article from the Journal of Education for Library and Information Science on incorporating aspects of intelligence analysis into library school curricula.
Library savings through student labor
Authors: Cottrell Terrance Luther , Bell Brigitte 
Published: August 2015

Purpose
– The purpose of this article is to briefly present current research and insight into the subject of student labor as a sharp cost-saving measure in the management of today’s library personnel budgets.

Design/methodology/approach
– Drawing from a recent empirical study on the subject, this article adds commentary from other researchers on the pitfalls and benefits of student library labor versus paraprofessionals and librarians.

Findings
– Although library student workers are commonly not seen as “ideal” employees, their demonstrated performance on many library tasks is compelling enough to consider hiring more of them in place of existing staff.

Originality/value
– This subject can be provocative for managers to simply mention to their staff or professional colleagues. There is little research in this area, and this article helps to broach the subject in a candid manor to spark more discussion among library staff looking to improve their bottom line.
Health risks, social security, and religious choice of rural residents
Authors: Jiang Jinqi , Zheng Fengtian 
Published: August 2015

Purpose
– The reform and opening up have triggered a “revival” of religious belief in rural China. The purpose of this paper is to explain why rural residents are increasingly becoming religious, by analysing the inherent relationship between their risks and religious choice, and conducts a preliminary investigation of the common characteristics of rural believers and the determinants of their religious choice.

Design/methodology/approach
– The authors applied a logit model to test the determinants of rural residents’ religious choice. The authors used sample survey data collected in 2008 from the rural area of Songxian County, Henan Province.

Findings
– The results suggest that age, sex, political status, health risks, and social security have a significant effect on rural residents’ religious choice. On this basis, the authors have discussed the inherent logic of “disease-related religious practice”. From these results, the paper points out that lack of basic public services such as medical care due to the government’s withdrawal from these fields has increased the health risks of rural residents, triggering a “revival” of religious belief in rural China.

Originality/value
– This paper has improved on previous research in two ways. First, it analyses the relationship between health risk and religious choice, shedding light on the underlying causes of the religious revival in rural China. Second, the methodology involves an analysis of household survey data, thus filling the gap created by less-rigorous quantitative analysis in rural China-based religious research.
Unpacking the perceived opportunity to misbehave
Authors: Daunt (née Reynolds) Kate L. , Greer Dominique A. 
Published: August 2015

Purpose
– This study aims to use opportunity as a theoretical lens to investigate how the spatio-temporal and social dimensions of the consumption environment create perceived opportunities for consumers to misbehave.

Design/methodology/approach
– Drawing on routine activity theory and social impact theory, the authors use two experiments to demonstrate that spatio-temporal and social dimensions can explain consumer theft in retail settings.

Findings
– Study 1 reveals mixed empirical support for the basic dimensions of routine activity theory, which posits that the opportunity to thieve is optimised when a motivated offender, suitable target and the absence of a capable formal guardian transpire in time and space. Extending the notion of guardianship, Study 2 tests social impact theory and shows that informal guardianship impacts the likelihood of theft under optimal routine activity conditions.

Originality/value
– The study findings highlight important implications for academicians and retail managers: rather than focusing on the uncontrollable characteristics of thieving offenders, more controllable spatio-temporal and social factors of the retail environment can be actively monitored and manipulated to reduce perceived opportunities for consumer misbehaviour.