niryuu/sni-each-converted huggingface dataset:
Background: Influenza surveillance systems do not allow the identification of the true burden of illness caused by influenza in the community because they are restricted to consulting cases. A study was conducted to estimate the incidence and the burden of self-defined influenza, and to describe healthcare seeking behavior for self-defined influenza during the A(H1N1)2009 pandemic in the French population. Methods: We conducted a random-based retrospective cross-sectional telephone survey between May 2009 and April 2010 among a random sample of the French population.
Output: Burden of influenza, healthcare seeking behaviour and hygiene measures during the A (H1N1)2009 pandemic in France: a population based study
Background: Pseudomonas aeruginosa is the most common bacterial pathogen in patients with cystic fibrosis (CF). Current infection control guidelines aim to prevent transmission via contact and respiratory droplet routes and do not consider the possibility of airborne transmission. It was hypothesised that subjects with CF produce viable respirable bacterial aerosols with coughing. Methods: A cross-sectional study was undertaken of 15 children and 13 adults with CF, 26 chronically infected with P aeruginosa. A cough aerosol sampling system enabled fractioning of respiratory particles of different sizes and culture of viable Gram-negative non-fermentative bacteria. Cough aerosols were collected during 5 min of voluntary coughing and during a sputum induction procedure when tolerated. Standardised quantitative culture and genotyping techniques were used. Results: P aeruginosa was isolated in cough aerosols of 25 subjects (89%), 22 of whom produced sputum samples. P aeruginosa from sputum and paired cough aerosols were indistinguishable by molecular typing. In four cases the same genotype was isolated from ambient room air. Approximately 70% of viable aerosols collected during voluntary coughing were of particles (3.3 mm aerodynamic diameter. P aeruginosa, Burkholderia cenocepacia, Stenotrophomonas maltophilia and Achromobacter xylosoxidans were cultivated from respiratory particles in this size range. Positive room air samples were associated with high total counts in cough aerosols (p = 0.003). The magnitude of cough aerosols was associated with higher forced expiratory volume in 1 s (r = 0.45, p = 0.02) and higher quantitative sputum culture results (r = 0.58, p = 0.008). Conclusion: During coughing, patients with CF produce viable aerosols of P aeruginosa and other Gram-negative bacteria of respirable size range, suggesting the potential for airborne transmission.
Output: Cough-generated aerosols of Pseudomonas aeruginosa and other Gram-negative bacteria from patients with cystic fibrosis
Mouse hepatitis virus (MHV), a murine coronavirus, replicates in the cytoplasm and synthesizes 7 viral mRNAs containing an identical stretch of leader RNA sequences at the 5'-end of each RNA. The leader-coding sequences at the 5'-end of genomic RNA are at least 72 nucleotides in length and are joined to the viral mRNAs by a unique mechanism. Utilizing a leader-specific cDNA probe, we have detected several free leader RNA species ranging from 70 to 82 nucleotides in length. The predominant leader RNA was approximately 75 nucleotides. In addition, larger distinct leader-containing RNAs were also detected ranging from 130 to 250 nucleotides in length. The 70-82-nucleotide leader-related RNAs were present in both the cytosol and membrane fractions of infected cells. They were also detected only in the small RNA fractions but not associated with the replicative-intermediate RNA. These data suggest that the leader RNAs were associated with the membrane-bound transcription complex but at least part of them were dissociated from the RNA template. We have also identified a temperature-sensitive mutant, which synthesizes only leader RNA but not mRNAs at nonpermissive temperature, indicating that leader RNA synthesis is distinct from the transcription of mRNAs. These data support the leader-primed mechanism for coronavirus transcription and suggest that one or more free leader RNAs are used as primers of mRNA synthesis. Mouse hepatitis virus, transcription, small leader related RNAs, coronavirus, temperature-sensitive mutant 0168-1702/85/$03.30 0 1985 Elsevier Science Publishers B.V. (Biomedical Division)
Output: Characterization of leader-related small RNAs in coronavirus-infected cells: Further evidence for leader-primed mechanism of transcription
Porcine reproductive and respiratory syndrome (PRRS) has been one of the most economically important diseases affecting swine industry worldwide and causes great economic losses each year. PRRS virus (PRRSV) replicates mainly in porcine alveolar macrophages (PAMs) and dendritic cells (DCs) and develops persistent infections, antibody-dependent enhancement (ADE), interstitial pneumonia and immunosuppression. But the molecular mechanisms of PRRSV infection still are poorly understood. Here we report on the first genome-wide host transcriptional responses to classical North American type PRRSV (N-PRRSV) strain CH 1a infection using Solexa/Illumina's digital gene expression (DGE) system, a tagbased high-throughput transcriptome sequencing method, and analyse systematically the relationship between pulmonary gene expression profiles after N-PRRSV infection and infection pathology. Our results suggest that N-PRRSV appeared to utilize multiple strategies for its replication and spread in infected pigs, including subverting host innate immune response, inducing an anti-apoptotic and anti-inflammatory state as well as developing ADE. Upregulation expression of virus-induced pro-inflammatory cytokines, chemokines, adhesion molecules and inflammatory enzymes and inflammatory cells, antibodies, complement activation were likely to result in the development of inflammatory responses during N-PRRSV infection processes. N-PRRSV-induced immunosuppression might be mediated by apoptosis of infected cells, which caused depletion of immune cells and induced an anti-inflammatory cytokine response in which they were unable to eradicate the primary infection. Our systems analysis will benefit for better understanding the molecular pathogenesis of N-PRRSV infection, developing novel antiviral therapies and identifying genetic components for swine resistance/susceptibility to PRRS.
Output: Understanding PRRSV Infection in Porcine Lung Based on Genome-Wide Transcriptome Response Identified by Deep Sequencing
The human coronaviruses (CoV) include HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1, some of which have been known for decades. The severe acute respiratory syndrome (SARS) CoV briefly emerged into the human population but was controlled. In 2012, another novel severely human pathogenic CoV-the Middle East Respiratory Syndrome (MERS)-CoV-was identified in the Kingdom of Saudi Arabia; 80% of over 2000 human cases have been recorded over five years. Targeted research remains key to developing control strategies for MERS-CoV, a cause of mild illness in its camel reservoir. A new therapeutic toolbox being developed in response to MERS is also teaching us more about how CoVs cause disease. Travel-related cases continue to challenge the world's surveillance and response capabilities, and more data are needed to understand unexplained primary transmission. Signs of genetic change have been recorded, but it remains unclear whether there is any impact on clinical disease. How camels came to carry the virus remains academic to the control of MERS. To date, human-to-human transmission has been inefficient, but virus surveillance, characterisation, and reporting are key to responding to any future change. MERS-CoV is not currently a pandemic threat; it is spread mainly with the aid of human habit and error.
Output: An Opportunistic Pathogen Afforded Ample Opportunities: Middle East Respiratory Syndrome Coronavirus
On the assumption that depho~phoryiation of the n~urotropic.coronavirus J HM (JHMV) nuclcocap~ld protein (NI may be connected with initiation or the infectiaas cycle we ~arehed for a relevant host enxyme activity, Analysi~ of ~ubccllular fractions from L-2 murin© flhrt~bla~ts, ~parate¢l t ~ dual Percoll density g, tadieats, revealed the presence of a pho~phoprotei~ phosphatase (PPPaseL co.~cdimcntinll with the endososomai/prelyso. s~im.I material, which possesses high activity alainxt N, With purified pZPJN as substratc it was demonstrated that this PPPase. d stinilaishable from acid and tdkalin~ phosph~tascs, acts optimalb, at neutral pl'{ in th© pres©nc¢ of Mn ]" following treatment with a detergent, Complete inhibition wi:h okadaic acid at 0.9.-4,$ tIM but not at b, d0 nM relegates thi~ PPPasc ton type I protein phosphatase. Similar PPPase activily for N was present in the endosome fraction of at rat Roc. 1 astrocytoma.olijlodendroc~cte cell line and in homc~lenates of brain and cultured OliltOdendrocytes. Oar d~ta sul/gest that the phosphorylatcd N of the inoculum may be modified by the endosomal PPPa~e in hosl ¢©11~, incladinil tho~c from the CNS so a~ to factlitale the .II.IMV infectious process. In this paper, we present data regarding partial characterization of a phosphoprotein phosphatase, associated with the endosomal fraction of host cells (PPPase), which is highly active against the nucleocapsid protein IN) of JHMV. Among the 3 major structural proteins of JHMV, N is phosphorylated [91 and has the capacity to bind nucleic acid [10]. Implications of dephosphorylation of N on early host-virus interactions are discussed. EXPERIMENTAL Okadaic acid was purchased from Monna Bioproducts0 Hawaii. Acid phosphatase of potato was obtained from Nutritional Bioclaemical Corporation, Ohio, alkaline phosphatase of E. colt from Sigma, St, Louis and Percoll from Pharnaacia, Propagation of L-2 murine fibroblasts [11] as monolayers and coronavirus JHMV, including plaque assays (pfu), followed procedures described previously [5] , Susper~sior, cultures of L-2 cells for biochemical studies were grown in MEM supplemented with 8% Nu-Serum plus 2% FBS, The immortalized Roe.1 cell-cell hybrid fine, of rat C~ glioma x primary oligodendrocyte (a kind gift from Dr. F.A, McMorris, The Wistar Institute, Philadelphia, PAl, was grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10070 FBS, 1.2 g/l NaHCOa and I xHAT supplement (Gibco), Primary cultures enriched for rat oligodendrocytes (95a70 pure) were isolated and cultured for 10 days as described previously [12] . Homogenates obtained by a Dounce homogeniser of oligodendrocyte and whole brain from 2-day-old rats were suspended in Published by Elsevier Science Publishers B. V.
Output: Endosomal association of a protein phosphatase with high dephosphorylating activity against a coronavirus nucleocapsid protein
Mink enteritis virus (MEV) is one of the most important pathogens in the mink industry. Recent studies have shed light into the role of microRNAs (miRNAs), small noncoding RNAs of length ranging from 18-23 nucleotides (nt), as critical modulators in the host-pathogen interaction networks. We previously showed that miRNA miR-181b can inhibit MEV replication by repression of viral non-structural protein 1 expression. Here, we report that two other miRNAs (miR-320a and miR-140) inhibit MEV entry into feline kidney (F81) cells by downregulating its receptor, transferrin receptor (TfR), by targeting the 3′ untranslated region (UTR) of TfR mRNA, while being themselves upregulated.
Output: MicroRNA miR-320a and miR-140 inhibit mink enteritis virus infection by repression of its receptor, feline transferrin receptor
In this review, we report that the receptor of mouse hepatitis virus (MHV), carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), is an important determinant of mouse susceptibility to MHV infection. This finding was revealed by using mouse strains with two different allelic forms of the MHV receptor, Ceacam1a and Ceacam1b. Although previous studies indicated that susceptibility is determined by a single gene, Ceacam1, our recent work in gene-replaced mice with chimeric Ceacam1 pointed toward the involvement of other host factors (genes) in the susceptibility. Studies on mouse susceptibility to MHV, as well as the factors involved in their susceptibility, are overviewed.
Output: MINI REVIEW ARTICLE Mouse hepatitis virus receptor as a determinant of the mouse susceptibility to MHV infection
We need to apply lessons learned from previous influenza pandemics to continuously update preparedness and response plans. It has become evident that strengthening networks of international referral laboratories coupled with scaling-up efforts to expand epidemiological surveillance networks is critical for responding and mitigating the impact of influenza pandemics. The current swine-related influenza A (H1N1) pandemic has also shown that international collaboration remains a critical component to effectively respond to influenza pandemics in the current globalized world. Ó 2009 IMSS. Published by Elsevier Inc.
Output: What Have We Learned from the Novel Influenza A (H1N1) Pandemic in 2009 for Strengthening Pandemic Influenza Preparedness?
The burden of unsafe drinking water is responsible for millions of deaths each year. To relieve this burden, we are in search of an inexpensive material that can adsorb pathogens from drinking water. In this pursuit, we have studied the natural carbohydrate, chitosan. To impart virus removal features, chitosan has been functionalized with a quaternary amine to form quaternized chitosan N-[(2-hydroxyl-3-trimethylammonium) propyl] chitosan (HTCC). HTCC can be electrospun into nanofibers with the non-ionogenic polyvinyl alcohol (PVA), creating a high surface area mat. High surface area is a major requirement for effective adsorption processes. HTCC is antiviral and antimicrobial, making it a good material for water purification. However, HTCC dissolves in water. We have explored the parameters to crosslink the nanofibers with glutaraldehyde. We have imparted water stability so there is a maximum of 30% swelling of the fibers after 6 h in water. The water stable fibers retain their ability to adsorb virus, as shown for an enveloped and nonenveloped virus. HTCC now has the potential to be incorporated into a microfiltration membrane that can remove viruses. This could create an inexpensive, low pressure filtration membrane for drinking water purification.
Output: Virus adsorption of water-stable quaternized chitosan nanofibers
Some single-stranded positive-sense RNA [ssRNA(+)] viruses, including Flavivirus, generate specific organelle-like structures in the host endoplasmic reticulum (ER). These structures are called virus replication organelles and consist of two distinct subdomains, the vesicle packets (VPs) and the convoluted membranes (CMs). The VPs are clusters of small vesicle compartments and are considered to be the site of viral genome replication. The CMs are electron-dense amorphous structures observed in proximity to the VPs, but the exact roles of CMs are mostly unknown. Several recent studies have revealed that flaviviruses recruit several host factors that are usually used for the biogenesis of other conventional organelles and usurp their function to generate virus replication organelles. In the current review, we summarize recent studies focusing on the role of host factors in the formation of virus replication organelles and discuss how these intricate membrane structures are organized.
Output: Molecular Sciences Review Flavivirus Replication Organelle Biogenesis in the Endoplasmic Reticulum: Comparison with Other Single-Stranded Positive-Sense RNA Viruses
Recent advances in understanding different RNAs and unique features of their biology have revealed a wealth of information. However, approaches to identify small molecules that target these newly discovered regulatory elements have been lacking. The application of new biochemical screening and design-based technologies, coupled with a resurgence of interest in phenotypic screening, has resulted in several compelling successes in targeting RNA. A number of recent advances suggest that achieving the long-standing goal of developing drug-like, biologically active small molecules that target RNA is possible. This review highlights advances and successes in approaches to targeting RNA with diverse small molecules, and the potential for these technologies to pave the way to new types of RNA-targeted therapeutics.
Output: The Emerging Role of RNA as a Therapeutic Target for Small Molecules
A combination of comparative sequence analysis and thermodynamic methods reveals the conservation of tertiary structure elements in the 5' untranslated region (UTR) of human enteroviruses and rhinoviruses. The predicted common structural elements occur in the 3' end of a segment that is critical for internal ribosome binding, termed "ribosome landing pad" (RLP), of polioviruses. Base pairings between highly conserved 17-nucleotide (nt) and 21 -nt sequences in the 5' UTR of human enteroviruses and rhinoviruses constitute a predicted pseudoknot that is significantly more stable than those that can be formed from a large set of randomly shuffled sequences. A conserved singlestranded polypyrimidine tract is located between two conserved tertiary elements. R. Nicholson, J. Pelletier, S.-Y. Le, and N. Sonenberg (1991, J. l&o/. 65, 5886-5894) demonstrated that the point mutations of 3-nt UUU out of an essential 4-nt pyrimidine stretch sequence UUUC abolished translation. Structural analysis of the mutant sequence indicates that small point mutations within the short polypyrimidine sequence would destroy the tertiary interaction in the predicted, highly ordered structure. The proposed common tertiary structure can offer experimentalists a model upon which to extend the interpretations for currently available data. Based on these structural features possible base-pairing models between human enteroviruses and 18 S rRNA and between human rhinoviruses and 18 S rRNA are proposed. The proposed common structure implicates a biological function for these sequences in translational initiation.
Output: Conserved Tertiary Structure Elements in the 5' Untranslated Region of Human Enteroviruses and Rhinoviruses
Immunochromatography (IC) is an antigen-detection assay that plays an important role in the rapid diagnosis of influenza virus because the protocol is short time and easy to use. Despite the usability of IC, the sensitivity is approximately 10 3 pfu per reaction. In addition, antigen-antibody interaction-based method cannot be used for the detection of influenza viruses with major antigenic change. In this study, we established the use of fluorescent immunochromatography (FLIC) to detect a broad spectrum of H5 subtype influenza A viruses. This method has improved sensitivity 10-100 fold higher than traditional IC because of the use of fluorescent conjugated beads. Our Type-E FLIC kit detected all of the H5 subtype influenza viruses that were examined, as well as recombinant hemagglutinin (HA) proteins (rHAs) belonging to the Eurasian H5 subtype viruses and the Type-N diagnosed North American H5 subtype influenza A viruses. Thus, this kit has the improved potential to detect H5 subtype influenza viruses of different clades with both Type-E and Type-N FLIC kits. Compared with PCR-based diagnosis, FLIC has a strong advantage in usability, because the sample preparation required for FLIC is only mix-and-drop without any additional steps such as RNA extraction. Our results can provide new strategies against the spread and transmission of HPAI H5N1 viruses in birds and mammals including humans.
Output: Broad-Spectrum Detection of H5 Subtype Influenza A Viruses with a New Fluorescent Immunochromatography System
The NIC in Lyon has been involved in the virological diagnosis of suspect severe acute respiratory syndrome (SARS) patients. In March, the French medical authorities organized a medical surveillance of the medical staff who had returned from the French hospital in Hanoi. Each person presenting or not with respiratory symptoms was sampled systematically by the nearest general practitioner (GP) belonging to the influenza network surveillance in the community called GROG and the samples were sent to the NICs located either in Paris or in Lyon. We also received samples from patients hospitalized in the south of France suffering from acute respiratory infection soon after a journey in Asia. We implemented a PCR diagnosis for the human respiratory viruses: influenza A and B, Parainfluenza (Type 1 to Type 4), Metapneumovirus, RSV, Rhinovirus, Enterovirus, Adenovirus. In April, we set up the PCR detection of the SARS-associated coronavirus Urbani strain. The practitioners performed respiratory samples. From 14 March to 15 May we received and tested 88 respiratory samples, respectively, 19 were realized by GPs from the community network and 69 came from hospitalized patients. We never detected the urbani coronavirus strain. However, we detected respiratory viruses in 24% of the cases: the most frequent virus was influenza A H3N2 (11%) and Parainfluenza type 3 (8%). RSV, influenza A H1N1 and Rhinovirus were also detected 2, 1 and 1 cases, respectively. All the positive samples except the rhinovirus came from hospitalized patients. The patients were sampled once and all of them recovered rapidly. D
Output: Differential virological diagnosis of acute respiratory infections in suspect SARS patients I. GROG Collective Name of the GROG Network: Groupes Régionaux d'Observation de la Grippe, France
The recent 2014-2016 West African Ebola virus epidemic underscores the need for the development of novel anti-Ebola therapeutics, due to the high mortality rates of Ebola virus infections and the lack of FDA-approved vaccine or therapy that is available for the prevention and treatment. Traditional Chinese medicines (TCMs) represent a huge reservoir of bioactive chemicals and many TCMs have been shown to have antiviral activities. 373 extracts from 128 TCMs were evaluated using a high throughput assay to screen for inhibitors of Ebola virus cell entry. Extract of Rhodiola rosea displayed specific and potent inhibition against cell entry of both Ebola virus and Marburg virus. In addition, twenty commercial compounds that were isolated from Rhodiola rosea were evaluated using the pseudotyped Ebola virus entry assay, and it was found that ellagic acid and gallic acid, which are two structurally related compounds, are the most effective ones. The activity of the extract and the two pure compounds were validated using infectious Ebola virus. The time-of-addition experiments suggest that, mechanistically, the Rhodiola rosea extract and the effective compounds act at an early step in the infection cycle following initial cell attachment, but prior to viral/cell membrane fusion. Our findings provide evidence that Rhodiola rosea has potent anti-filovirus properties that may be developed as a novel anti-Ebola treatment.
Output: Identification of Ellagic Acid from Plant Rhodiola rosea L. as an Anti-Ebola Virus Entry Inhibitor
Middle East respiratory syndrome coronavirus (MERS-CoV) has infected at least 2040 patients and caused 712 deaths since its first appearance in 2012, yet neither pathogen-specific therapeutics nor approved vaccines are available. To address this need, we are developing a subunit recombinant protein vaccine comprising residues 377-588 of the MERS-CoV spike protein receptor-binding domain (RBD), which, when formulated with the AddaVax adjuvant, it induces a significant neutralizing antibody response and protection against MERS-CoV challenge in vaccinated animals. To prepare for the manufacture and first-in-human testing of the vaccine, we have developed a process to stably produce the recombinant MERS S377-588 protein in Chinese hamster ovary (CHO) cells. To accomplish this, we transfected an adherent dihydrofolate reductase-deficient CHO cell line (adCHO) with a plasmid encoding S377-588 fused with the human IgG Fc fragment (S377-588-Fc). We then demonstrated the interleukin-2 signal peptide-directed secretion of the recombinant protein into extracellular milieu. Using a gradually increasing methotrexate (MTX) concentration to 5 lM, we increased protein yield by a factor of 40. The adCHO-expressed S377-588-Fc recombinant protein demonstrated functionality and binding specificity identical to those of the protein from transiently transfected HEK293T cells. In addition, hCD26/ dipeptidyl peptidase-4 (DPP4) transgenic mice vaccinated with AddaVax-adjuvanted S377-588-Fc could produce neutralizing antibodies against MERS-CoV and survived for at least 21 days after challenge with live MERS-CoV with no evidence of immunological toxicity or eosinophilic immune enhancement. To prepare for large scale-manufacture of the vaccine antigen, we have further developed a high-yield monoclonal suspension CHO cell line.
Output: Engineering a stable CHO cell line for the expression of a MERS-coronavirus vaccine antigen
Infectious disease nucleic acid amplification technologies (NAAT) have superior sensitivity, specificity, and rapid time to result compared to traditional microbiological methods. Recovery of concentrated, high quality pathogen nucleic acid (NA) from complex specimen matrices is required for optimal performance of several NA amplification/detection technologies such as polymerase chain reaction (PCR). Fully integrated NAAT platforms that enable rapid sample-to-result workflows with minimal user input are generally restricted to larger reference lab settings, and their complexity and cost are prohibitive to widespread implementation in resource limited settings (RLS). Identification of component technologies for incorporation of reliable and affordable sample preparation with pathogen NA amplification/ detection into an integrated platform suitable for RLS, is a necessary first step toward achieving the overarching goal of reducing infectious disease-associated morbidity and mortality globally. In the current study, we evaluate the performance of six novel NA extraction technologies from different developers using blinded panels of stool, sputum and blood spiked with variable amounts of quality-controlled DNA-and/or RNA-based microbes. The extraction efficiencies were semi-quantitatively assessed using validated real-time reverse transcription (RT)-PCR assays specific for each microbe and comparing target-specific RT-PCR results to those obtained with reference NA extraction methods. The technologies were ranked based on overall diagnostic accuracy (analytical sensitivity and specificity). Sample input and output volumes, total processing time, user-required manual steps and cost estimates were also examined for suitability in RLS. Together with the performance analysis, these metrics were used to select the more suitable candidate technologies for further optimization of integrated NA amplification and detection technologies for RLS.
Output: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings
The red-crowned crane is one of the rarest crane species, and its population is decreasing due to loss of habitat, poisoning, and infections. Using a viral metagenomics approach, we analyzed the virome of feces from wild and captive red-crowned cranes, which were pooled separately. Vertebrate viruses belonging to the families Picornaviridae, Parvoviridae, Circoviridae, and Caliciviridae were detected. Among the members of the family Picornaviridae, we found three that appear to represent new genera. Six nearly complete genomes from members of the family Parvoviridae were also obtained, including four new members of the proposed genus "Chapparvovirus", and two members of the genus Aveparvovirus. Six small circular DNA genomes were also characterized. One nearly complete genome showing a low level of sequence identity to caliciviruses was also characterized. Numerous viruses believed to infect insects, plants, and crustaceans were also identified, which were probably derived from the diet of red-crowned cranes. This study increases our understanding of the enteric virome of red-crowned cranes and provides a baseline for comparison to those of other birds or following disease outbreaks.
Output: The fecal virome of red-crowned cranes
Pulmonary gene delivery is thought to play an important role in treating genetically related diseases and may induce immunity towards pathogens entering the body via the airways. In this study we prepared poly (D,L-lactide-co-glycolide) (PLGA) nanoparticles bearing polyethyleneimine (PEI) on their surface and characterized them for their potential in serving as non-viral gene carriers to the pulmonary epithelium. Particles that were synthesized at different PLGA-PEI ratios and loaded with DNA in several PEI -DNA ratios, exhibited narrow size distribution in all formulations, with mean particle sizes ranging between 207 and 231 nm. Zeta potential was strongly positive (above 30 mV) for all the PEI -DNA ratios examined and the loading efficiency exceeded 99% for all formulations. Internalization of the DNA-loaded PLGA -PEI nanoparticles was studied in the human airway submucosal epithelial cell line, Calu-3, and DNA was detected in the endo-lysosomal compartment 6 h after particles were applied. Cytotoxicity of these nanoparticles was dependent on the PEI -DNA ratio and best cell viability was achieved by PEI -DNA ratios 1:1 and 0.5:1. These findings demonstrate that PLGA-PEI nanoparticles are a potential new delivery system to carry genes to the lung epithelium. q
Output: PLGA -PEI nanoparticles for gene delivery to pulmonary epithelium
Antibody profiles have the potential to revolutionize personalized medicine by providing important information related to autoimmunity against self-proteins and exposure to infectious agents. One immunoassay technology, Luciferase Immunoprecipitation Systems (LIPS), harnesses light emitting recombinant proteins to generate robust, high quality antibody data often spanning a large dynamic range of detection. Here we describe the general format of LIPS and discuss studies using the technology to measure autoantibodies in several human autoimmune diseases including type I diabetes, Sjögren's syndrome, systemic lupus erythematosus, and immunodeficiencies secondary to anti-cytokine autoantibodies. We also describe the usefulness of evaluating antibodies against single or multiple antigens from infectious agents for diagnosis, pathogen discovery and for obtaining individual exposure profiles. These diverse findings support the notion that LIPS is a useful technology for generating antibody profiles for personalized diagnosis and monitoring of human health.
Output: Luciferase Immunoprecipitation Systems for Measuring Antibodies in Autoimmune and Infectious Diseases
Genome Biology 2006, 7:R110 comment reviews reports deposited research refereed research interactions information Abstract Protein microarrays provide a versatile method for the analysis of many protein biochemical activities. Existing DNA microarray analytical methods do not translate to protein microarrays due to differences between the technologies. Here we report a new approach, ProCAT, which corrects for background bias and spatial artifacts, identifies significant signals, filters nonspecific spots, and normalizes the resulting signal to protein abundance. ProCAT provides a powerful and flexible new approach for analyzing many types of protein microarrays.
Output: Article R110
Repurposing antimalarials as dengue antivirals Chloroquine Primaquine Stable replicon cell lines for dengue and West Nile viruses Inhibition of dengue virus replication and infectivity Amodiaquine therapeutic index a b s t r a c t Dengue virus serotypes 1-4 (DENV1-4) are transmitted by mosquitoes which cause most frequent arboviral infections in the world resulting in $390 million cases with $25,000 deaths annually. There is no vaccine or antiviral drug currently available for human use. Compounds containing quinoline scaffold were shown to inhibit flavivirus NS2B-NS3 protease (NS2B-NS3pro) with good potencies. In this study, we screened quinoline derivatives, which are known antimalarial drugs for inhibition of DENV2 and West Nile virus (WNV) replication using the corresponding replicon expressing cell-based assays. Amodiaquine (AQ), one of the 4-aminoquinoline drugs, inhibited DENV2 infectivity measured by plaque assays, with EC 50 and EC 90 values of 1.08 ± 0.09 lM and 2.69 ± 0.47 lM, respectively, and DENV2 RNA replication measured by Renilla luciferase reporter assay, with EC 50 value of 7.41 ± 1.09 lM in the replicon expressing cells. Cytotoxic concentration (CC 50 ) in BHK-21 cells was 52.09 ± 4.25 lM. The replication inhibition was confirmed by plaque assay of the extracellular virions as well as by qRT-PCR of the intracellular and extracellular viral RNA levels. AQ was stable for at least 96 h and had minor inhibitory effect on entry, translation, and post-replication stages in the viral life cycle. DENV protease, 5 0 -methyltransferase, and RNA-dependent RNA polymerase do not seem to be targets of AQ. Both p-hydroxyanilino and diethylaminomethyl moieties are important for AQ to inhibit DENV2 replication and infectivity. Our results support AQ as a promising candidate for anti-flaviviral therapy.
Output: Amodiaquine, an antimalarial drug, inhibits dengue virus type 2 replication and infectivity
Transmissible gastroenteritis virus was administered orally to cats. No clinical disease resulted but infectious virus was isolated from faeces for up to 22 days after infection and serum antibody was detected by neutralisation and immunofluorescence tests. . The spread of transmissible gastroenteritis virus (TGEV) from infected pig herds and the recrudescence of infection after long periods have not been adequately explained. Experiments on the host range of the virus have indicated that nonporcine hosts could have a role in the epidemiology of TGE (2, 4, 7, 8, 9, t6). Indirect immunofluorescence (IIF) and virus neutralisation (V1N!) tests have been used recently to demonstrate antibody to TGEV in cats. In Holland and Great Britain samples from cats with clinical feline infectious peritonitis (FIP) frequently have antibody to TGEV in the I I F test (10). However, neutralising antibody has not been found in sera from Dutch cats with FIP. American and Dutch studies have recently demonstrated that sera from cats experimentally infected with F I P will cross-react, at low titre, with TGEV-infected pig cells by immunofluoreseence but will not neutralise TGEV in vitro (10, 12) . This evidence has been used to suggest that an antigenic relationship exists between TGEV and F I P virus. The potential of the cat to excrete TGEV was studied by virus reisolation and the serological responses to TGEV and F I P were monitored; thus the possible epidemiological role of the cat in TGE could be assessed. In addition information was obtained on the possible origin and relationship of VN and I I F antibodies to TGEV which occur naturally in cats, often at high titres (10, 13). TGEV strain KN63, used as inoculum in this experiment, was prepared as a clarified 50 per cent suspension of small intestine from an infected gnotobiotic piglet. I t had a titre of i.7 × 107 PFU/ml.
Output: Archives of Virology Virus Isolation and Serum, Antibody Responses After Infection of Cats With Transmissible Gastroenteritis Virus BrieiReport
Background. Community-acquired pneumonia (CAP) remains an important cause of morbidity and mortality. Polymerase chain reaction (PCR) has been shown to be more sensitive than current standard microbiological methods and, therefore, may improve the accuracy of microbiological diagnosis for patients with CAP. Methods. Conventional detection techniques and multiplex real-time PCR for atypical bacteria and respiratory viruses were performed on samples collected from 105 adults enrolled in a prospective study. An infiltrate was visible on each patient's chest radiograph, and a pneumonia severity index score was determined for each patient. Results. Microbiological diagnoses were determined for 52 (49.5%) of 105 patients by conventional techniques and for 80 (76%) of 105 patients by real-time PCR. The time to obtain the result of real-time PCR could be reduced to 6 h. PCR methodology was significantly more sensitive for the detection of atypical pathogens and viruses ( ). Respiratory viral infections and mixed infections were detected in 15 (14.2%) and 3 (2.8%) of P р .001 105 patients, respectively, by conventional methods, but were detected in 59 (56.2%) and 28 (26.5%) of 105, respectively, by real-time PCR. Presence of a mixed infection was significantly associated with severe pneumonia ( ). Human rhinoviruses and coronaviruses, OC43 and 229E, were frequently identified pathogens. P p .002 Conclusions. The combined real-time PCR assay is more sensitive for diagnosis of the main viruses and atypical bacteria that cause CAP compared with conventional methods, and obtains results in a clinically relevant time period.
Output: Etiology of CAP Identified with Real-Time PCR • CID 2005:41 (1 August) • 345 Improved Diagnosis of the Etiology of Community-Acquired Pneumonia with Real-Time Polymerase Chain Reaction
strains of infectious bronchitis virus (IBV) were isolated from the vaccinated chicken flocks in Sichuan province, China. The S1 genes of the isolates were amplified and sequenced. Phylogenetic analysis revealed that the 19 isolates and 37 reference IBV strains can be grouped into eight genotypes. Although IBVs of Taiwan-I type, massachusetts type, and proventriculitis type were isolated, but most isolates were LX4 genotype. Homology analysis of the sequences of S1 genes of the 19 isolates and 37 reference IBV strains revealed that the identity of the nucleotides and amino acid sequences of the S1 genes between the 15 LX4-type isolates and other IBV strains were 71.9-99.3% and 72.1-99.1%, respectively, while those of the analyzed IBV of LX4 type were 96.0-99.9% and 94.3-99.8%, respectively. The results from this study and other published results in the GenBank database showed that isolates circulating in Sichuan province in recent years were mainly LX4 genotype, which is the predominant genotype circulated in China in recent years.
Output: Genetic analysis revealed LX4 genotype strains of avian infectious bronchitis virus became predominant in recent years in Sichuan area, China
Maintenance of epigenetic modifiers is of utmost importance to preserve the epigenome and consequently appropriate cellular functioning. Here, we analyzed Polycomb group protein (PcG) complex integrity in response to heat shock (HS). Upon HS, various Polycomb Repressive Complex (PRC)1 and PRC2 subunits, including CBX proteins, but also other chromatin regulators, are found to accumulate in the nucleolus. In parallel, binding of PRC1/2 to target genes is strongly reduced, coinciding with a dramatic loss of H2AK119ub and H3K27me3 marks. Nucleolar-accumulated CBX proteins are immobile, but remarkably both CBX protein accumulation and loss of PRC1/2 epigenetic marks are reversible. This post-heat shock recovery of pan-nuclear CBX protein localization and reinstallation of epigenetic marks is HSP70 dependent. Our findings demonstrate that the nucleolus is an essential protein quality control center, which is indispensable for recovery of epigenetic regulators and maintenance of the epigenome after heat shock.
Output: Protein quality control in the nucleolus safeguards recovery of epigenetic regulators after heat shock
A prospective cohort study was undertaken to determine calf-level factors that affected calf health status between birth and 6 months of age. A convenience sample of approximately 3300 female Holstein calves born in 1991 on two large Florida dairy farms was used for the study. Data collected on each calf at birth included farm of origin, weight, height at the pelvis, birth date, and serum total protein (a measure of colostral immunoglobulin absorption). Birth season was dichotomized into summer and winter using meteorological data collected by University of Florida Agricultural Research Stations. Health data including date of initial treatment and number of treatments were collected for the diseases diarrhea, omphalitis, septicemia and pneumonia. All calves were followed for 6 months. Cumulative incidences of mortality and occurrence of diarrhea, omphalitis, septicemia and pneumonia were 0.12, 0.35, 0.11, 0.24 and 0.21, respectively. Serum total protein (TP) was a significant risk factor for mortality. The association of TP and mortality was quadratic and showed a dramatic decrease in mortality as TP increased from 4.0 to 5.0 g/dl, a small improvement from 5.0 to 6.0 g/d1 and virtually no improvement in mortality rates as TP increased over 6.0 g/dl. The hazard mortality ratio was constant from birth to six months, indicating that the increased risk of mortality associated with low levels of TP was evident through six months of age. No interactions between TP, farm, season, or birth weight were found in these analyses. Serum total protein concentration was a significant risk factor for the 32 G. A. Donovan et al. /Preventive Veterinary Medicine 34 (1998) 31-46 occurrences, age of onset and severity of septicemia and pneumonia. The association between TP and septicemia was linear and an interaction with birth season was found. The association between TP and pneumonia was quadratic, and in contrast to the TP-and-septicemia relationship, the morbidity hazard ratio for pneumonia was not constant over the time measured; that is, colostral immunity protected the calf from developing pneumonia early in life, but this effect disappeared as the calf got older. Total protein was not a significant risk factor for diarrhea or omphalitis. 0 1998 Elsevier Science B.V.
Output: PREVENTIVE Associations between passive immunity and morbidity and mortality in dairy heifers in Florida, USA
Recombinant vesicular stomatitis virus (VSV) is widely used as a vaccine platform. However, the capacity of VSV-based vaccines to induce mucosal immunity has not been fully investigated. In the present study, a recombinant VSV expressing coxsackievirus B3 (CVB3) major immunogen VP1 has been generated and the immune protection elicited by VSV-VP1 was evaluated. We demonstrated that intranasal delivery of VSV-VP1 can induce a potent antigen-specific mucosal immune response as well as a systemic immune response, particularly the induction of polyfunctional T cells. Importantly, mice immunized with VSV-VP1 were better protected against CVB3-induced viral myocarditis than those receiving a chitosan-formulated DNA vaccine. Increased dendritic cell (DC) maturation in the mesenteric lymph node (MLN) was observed in the mice vaccinated with VSV-VP1, which could be a potential mechanism for the protective immune response. These findings support VSV as a viral delivery vector that can induce robust mucosal immunity that should be considered for further vaccine development.
Output: A vesicular stomatitis virus-based mucosal vaccine promotes dendritic cell maturation and elicits preferable immune response against coxsackievirus B3 induced viral myocarditis
This paper presents a label-free affinity-based capacitive biosensor using interdigitated electrodes. Using an optimized process of DNA probe preparation to minimize the effect of contaminants in commercial thiolated DNA probe, the electrode surface was functionalized with the 24-nucleotide DNA probes based on the West Nile virus sequence (Kunjin strain). The biosensor has the ability to detect complementary DNA fragments with a detection limit down to 20 DNA target molecules (1.5 aM range), making it suitable for a practical point-of-care (POC) platform for low target count clinical applications without the need for amplification. The reproducibility of the biosensor detection was improved with efficient covalent immobilization of purified single-stranded DNA probe oligomers on cleaned gold microelectrodes. In addition to the low detection limit, the biosensor showed a dynamic range of detection from 1 µL -1 to 10 5 µL -1 target molecules (20 to 2 million targets), making it suitable for sample analysis in a typical clinical application environment. The binding results presented in this paper were validated using fluorescent oligomers.
Output: A Sensitive DNA Capacitive Biosensor Using Interdigitated Electrodes (BIOS-D-16-01739, Revised) Affinity-based Capacitive Biosensor Interdigitated Electrodes Nucleic Acid-based Biosensor Viral Diagnostics Pathogen Detection Point-of-care Diagnostics
Plasmacytoid dendritic cells (pDCs) mediate type I interferon (IFN-I) responses to viruses that are recognized through the Toll-like receptor 7 (TLR7) or TLR9 signaling pathway. However, it is unclear how pDCs regulate the antiviral responses via innate and adaptive immune cells. We generated diphtheria toxin receptor transgenic mice to selectively deplete pDCs by administration of diphtheria toxin. pDC-depleted mice were challenged with viruses known to activate pDCs. In murine cytomegalovirus (MCMV) infection, pDC depletion reduced early IFN-I production and augmented viral burden facilitating the expansion of natural killer (NK) cells expressing the MCMV-specific receptor Ly49H. During vesicular stomatitis virus (VSV) infection, pDC depletion enhanced early viral replication and impaired the survival and accumulation of virusspecific cytotoxic T lymphocytes. We conclude that pDCs mediate early antiviral IFN-I responses and influence the accrual of virus-specific NK or CD8 + T cells in a virus-dependent manner.
Output: Plasmacytoid Dendritic Cell Ablation Impacts Early Interferon Responses and Antiviral NK and CD8 + T Cell Accrual
Charley, B., McCullough, K. and Martinod, S., 1988. Antiviral and antigenic properties of recombinant porcine interferon gamma. Vet. Immunol. Immunopathol., Recombinant porcine interferon gamma (rPoIFN7) induced a dose-dependent inhibition of the cytopathic effect produced by vesicular stomatitis virus (VSV) challenge of both homologous and heterologous (bovine) cell lines. In addition, an antiviral effect of rPoIFN7 was demonstrable against the coronavirus transmissible gastroenteritis virus (TGEV) infection of porcine epithelial cells and of pulmonary macrophages. A rabbit anti-PoIFN7 antiserum was prepared and shown to specifically neutralize the antiviral effects of natural and recombinant porcine IFN7 preparations. This antiserum could also neutralize recombinant bovine IFN7 but not recombinant human IFNT. These results suggest antigenic homology of porcine and bovine IFN~ but antigenic differences between these molecules and human IFNT.
Output: Antiviral and Antigenic Properties of Recombinant Porcine Interferon Gamma
Rhubarb (Rheum emodi, family Polygonaceae) has been traditionally used as diuretic, liver stimulant, purgative/cathartic, stomachic, anticholesterolaemic, antitumour, antiseptic and tonic. A number of anthraquinone derivatives including emodin, aloe-emodin, physcion, chrysophanol, rhein, emodin glycoside and chrysophanol glycoside occur as the main chemical constituents. In the past few years, new components such as sulfemodin 8-O-b-D-glucoside, revandchinone-1, revandchinone-2, revandchinone-3, revandchinone-4, 6-methyl-rhein and 6-methyl aloe-emodin have been reported from the same species. Anthraquinone derivatives show evidence of antifungal, anti-microbial, anti-Parkinson's, anti-proliferative, immuno-enhancing, antiviral and antioxidant activities. This review covers published work on botany, chemistry and therapeutic uses of different components from rhubarb.
Output: Phytoconstituents and therapeutic uses of Rheum emodi wall. ex Meissn