niryuu/sni-each-converted huggingface dataset:
The ability to use double-stranded RNA to inhibit gene expression sequence-specifically (RNA interference, or RNAi) is currently revolutionizing science and medicine alike. Numerous pre-clinical studies are evaluating RNAi as a novel therapeutic modality in the battle against gain-of-function autosomal dominant diseases, cancer, and viral infections. One emerging concern is that RNAi mono-therapies might ultimately fail to control viruses that can escape silencing by mutation and/or RNAi suppression. Thus, sophisticated strategies are being developed that aim to avert viral resistance by combining RNAi effectors with each other or with further gene expression inhibitors. Several reports already validate this new concept of "combinatorial RNAi" (coRNAi) and illustrate its versatility by describing co-expression of RNAi triggers directed against single or multiple, viral or cellular, targets. Other studies document the successful delivery of these triggers with additional RNA-or protein-based silencers. Moreover, vectors have been engineered to blend RNAi-mediated gene inhibition with conventional gene replacement strategies. Collectively, these efforts open up exciting new therapeutic avenues but could also augment the inherent risks of RNAi technology, including immune responses, off-targeting, and oversaturation of endogenous pathways. Here, we critically review all coRNAi strategies and discuss the requirements for their transition into clinical application.
Output: review 878 Combinatorial RNAi: A Winning Strategy for the Race Against Evolving Targets?
The interferon-inducible transmembrane proteins (IFITMs) are a family of small transmembrane proteins belonging to the interferon (IFN)-stimulated gene (ISG) superfamily and strongly induced by IFNs. In this paper, we studied the expression profile of IFITMs in 32 organ tissues. The IFITM mRNA expression profile showed that IFITM1, IFITM2 and IFITM3 were expressed in each tissue, especially, in spermatophore, spermaduct, testicle and epididymis. The expression of IFITM1, IFITM2 and IFITM3 showed a trend from high to low. Except for IFITM3 and IFITM6, the others IFITMs were highly expressed in the bone marrow, and the expression level of them was higher in the tibia than that in other parts of the long bones. In liver, the relative expression of IFITM1 and IFITM3 was higher than that of other members. The expression level of IFITM5 was the highest in bone marrow, successively in pancreas, and it was low in skin, smooth muscle and fat. Interestingly, the expression profile of IFITM2 and IFITM7 in tissues was similar to IFITM5. The expression of IFITM2, IFITM5 and IFITM10 were higher in smooth muscle than that in skeletal muscle. IFITM2, IFITM5, IFITM7 and IFITM10 were both highly expressed in esophagus and trachea. In addition, the expression of IFITM6 in eyes was high, and also in pancreas, gallbladder and bone. In the present study, we systematically analyzed the mRNA expression profile of IFITMs in 32 organ tissues, providing the foundation for the study of the function of the IFITMs.
Output: Intractable & Rare Diseases Research
Angiotensin-converting enzyme 2 (ACE2) is a protein consisting of two domains, the N-terminus is a carboxypeptidase homologous to ACE and the C-terminus is homologous to collectrin and responsible for the trafficking of the neutral amino acid transporter B(0)AT1 to the plasma membrane of gut epithelial cells. The carboxypeptidase domain not only metabolizes angiotensin II to angiotensin-(1-7), but also other peptide substrates, such as apelin, kinins and morphins. In addition, the collectrin domain regulates the levels of some amino acids in the blood, in particular of tryptophan. Therefore it is of no surprise that animals with genetic alterations in the expression of ACE2 develop a diverse pattern of phenotypes ranging from hypertension, metabolic and behavioural dysfunctions, to impairments in serotonin synthesis and neurogenesis. This review summarizes the phenotypes of such animals with a particular focus on the central nervous system.
Output: ACE2 in Brain Physiology and Pathophysiology: Evidence from Transgenic Animal Models
Astroviruses are small, non-enveloped, positive sense, single-stranded RNA viruses first identified in 1975 in children suffering from diarrhea and then described in a wide variety of animals. To date, the list of animal species susceptible to astrovirus infection has expanded to 22 animal species or families, including domestic, synantropic and wild animals, avian, and mammalian species in the terrestrial and aquatic environments. Astrovirus infections are considered among the most common cause of gastroenteritis in children, second only to rotavirus infections, but in animals their association with enteric diseases is not well documented, with the exception of turkey and mink astrovirus infection. Genetic variability has been described in almost all astrovirus species sufficiently examined infecting mammals and birds; however, antigenic variability has been demonstrated for human astroviruses but is far less investigated in animal viruses. Interestingly, there is an increasing evidence of recombination events occurring in astroviruses, which contributes to increase the genetic variability of this group of viruses. A wide variety of species infected, the evident virus genetic diversity and the occurrence of recombination events indicate or imply either cross-species transmission and subsequent virus adaptation to new hosts or the co -infection of the same host with different astroviruses. This can also favor the emergence of novel astroviruses infecting animals or with a zoonotic potential. After more than 30 years from their first description in humans, there are many exciting streams of research to be explored and intriguing questions that remain to be answered about the relatively under-studied Astroviridae family. In the present work, we will review the existing knowledge concerning astrovirus infections in humans and animals, with particular focus on the molecular biology, interspecies transmission and zoonotic potential of this group of viruses.
Output: Astrovirus infections in humans and animals -Molecular biology, genetic diversity, and interspecies transmissions
Infectious diseases due to microbes of high pathogenic potential remain a constant and variable threat for human and animal health. The emergence of new diseases or the re-emergence of diseases that were previously under control complicates the situation to date. Infectious disease research, which has undergone a dramatic progress in understanding disease mechanisms such as host-pathogen interactions, is now focusing increasingly on new strategies for prevention and therapy. Significant progress has been achieved in the development of delivery systems for protective heterologous protein antigens and in veterinary vaccinology. A landmark of infectious diseases research is the chemical synthesis of genomes, a major new field of research referred to as ''synthetic biology'', that to date has resulted in the chemical synthesis of the poliovirus and of phage fX174 genomes and their expression as infectious viruses. On the molecular level the evolution of pathogens and mechanisms of genome flexibility, which account for several pathogenic properties of infectious agents, have received increased attention. Bacterial toxins are an additional threat to human health and their interference with host cells and cellular functions is receiving more attention.
Output: MEETING REPORT Threat of infection: Microbes of high pathogenic potential -strategies for detection, control and eradication
Virus pseudotyping is a useful and safe technique for studying entry of emerging strains of influenza virus. However, few studies have compared different reassortant combinations in pseudoparticle systems, or compared entry kinetics of native viruses and their pseudotyped analogs. Here, vesicular stomatitis virus (VSV)-based pseudovirions displaying distinct influenza virus envelope proteins were tested for fusion activity. We produced VSV pseudotypes containing the prototypical X-31 (H3) HA, either alone or with strain-matched or mismatched N2 NAs. We performed single-particle fusion assays using total internal reflection fluorescence microscopy to compare hemifusion kinetics among these pairings. Results illustrate that matching pseudoparticles behaved very similarly to native virus. Pseudoparticles harboring mismatched HA-NA pairings fuse at significantly slower rates than native virus, and NA-lacking pseudoparticles exhibiting the slowest fusion rates. Relative viral membrane HA density of matching pseudoparticles was higher than in mismatching or NA-lacking pseudoparticles. An equivalent trend of HA expression level on cell membranes of HA/NA co-transfected cells was observed and intracellular trafficking of HA was affected by NA co-expression. Overall, we show that specific influenza HA-NA combinations can profoundly affect the critical role played by HA during entry, which may factor into viral fitness and the emergence of new pandemic influenza viruses.
Output: Viral fusion efficacy of specific H3N2 influenza virus reassortant combinations at single-particle level
Over the past decade, outbreaks of new or reemergent viruses such as severe acute respiratory syndrome (SARS) virus, Middle East respiratory syndrome (MERS) virus, and Zika have claimed thousands of lives and cost governments and healthcare systems billions of dollars. Because the appearance of new or transformed diseases is likely to continue, the detection and characterization of emergent diseases is an important problem. We describe a Bayesian statistical model that can detect and characterize previously unknown and unmodeled diseases from patient-care reports and evaluate its performance on historical data.
Output: A Bayesian approach for detecting a disease that is not being modeled
The newly identified 2019 novel coronavirus (2019-nCoV) has caused more than 11,900 laboratory-confirmed human infections, including 259 deaths, posing a serious threat to human health. Currently, however, there is no specific antiviral treatment or vaccine. Considering the relatively high identity of receptor-binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Here, we report for the first time that a SARS-CoV-specific human monoclonal antibody, CR3022, could bind potently with 2019-nCoV RBD (KD of 6.3 nM). The epitope of CR3022 does not overlap with the ACE2 binding site within 2019-nCoV RBD. These results suggest that CR3022 may have the potential to be developed as candidate therapeutics, alone or in combination with other neutralizing antibodies, for the prevention and treatment of 2019-nCoV infections. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g. m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, implying that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD.
Output: Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus- specific human monoclonal antibody
As the human lung is exposed to a variety of microbial pathogens in the environment, a first line of defense is built up by pulmonary cells like bronchial/ alveolar epithelial cells and alveolar macrophages. These cells express several pattern recognition receptors (PRRs) recognizing highly conserved microbial motifs and initiating the production of chemokines and pro-and anti-inflammatory cytokines acting as transmembrane or intracellular receptors. This might not only lead to acute but also to chronic inflammation which is discussed as an underlying mechanism in the pathogenesis of different lung diseases.
Output: Innate immunity in the human lung: pathogen recognition and lung disease
A biotinylated-oligonucleotide-based method was used to isolate the subgenomic mRNAs of the coronavirus transmissible gastroenteritis virus (TGEV) to investigate the amounts of the mRNAs produced at early, middle and late times in the replication cycle. TGEV mRNA 6, which encodes the N protein, was observed to be the most abundant species throughout the replication cycle. The ratios of mRNA 6 to the other mRNAs were 1:0.11 (mRNA 2), 1:0.16 (mRNAs 3 and 4) and 1:0.37 (mRNA 5) at 12 h post-infection. All the mRNA species were differentially regulated throughout the replication cycle, although the rate of accumulation of mRNAs 4, 5 and 6, but not mRNA 3, increased markedly towards the end of the replication cycle, mRNA 7 was not detected in the system used. There was no observable correlation between the amounts of each mRNA synthesised and the potential degree of base pairing between the 3' end of the leader sequence and the transcription associated sequences on the genomic RNA at any time during the replication cycle. This indicates that the extent of base pairing was not the only factor involved in the control of subgenomic mRNA synthesis.
Output: Quantification of individual subgenomic mRNA species during replication of the coronavirus transmissible gastroenteritis virus
Influenza infection and pneumonia are known to cause much of their mortality by inducing acute respiratory distress syndrome (ARDS), which is the most severe form of acute lung injury (ALI). Angiotensin-converting enzyme 2 (ACE2), which is a negative regulator of angiotensin II in the renin-angiotensin system, has been reported to have a crucial role in ALI. Downregulation of ACE2 is always associated with the ALI or ARDS induced by avian influenza virus, severe acute respiratory syndrome-coronavirus, respiratory syncytial virus and sepsis. However, the molecular mechanism of the decreased expression of ACE2 in ALI is unclear. Here we show that avian influenza virus H5N1 induced the upregulation of miR-200c-3p, which was then demonstrated to target the 3′-untranslated region of ACE2. Then, we found that nonstructural protein 1 and viral RNA of H5N1 contributed to the induction of miR-200c-3p during viral infection. Additionally, the synthetic analog of viral double-stranded RNA (poly (I:C)), bacterial lipopolysaccharide and lipoteichoic acid can all markedly increase the expression of miR-200c-3p in a nuclear factor-κB-dependent manner. Furthermore, markedly elevated plasma levels of miR-200c-3p were observed in severe pneumonia patients. The inhibition of miR-200c-3p ameliorated the ALI induced by H5N1 virus infection in vivo, indicating a potential therapeutic target. Therefore, we identify a shared mechanism of viral and bacterial lung infection-induced ALI/ARDS via nuclear factor-κB-dependent upregulation of miR-200c-3p to reduce ACE2 levels, which leads increased angiotensin II levels and subsequently causes lung injury.
Output: miRNA-200c-3p is crucial in acute respiratory distress syndrome
Theiler's murine encephalomyelitis virus (TMEV) and other neurotropic virus infections result in degeneration of each component of the neuron: apoptosis of the cell body, axonal (Wallerian) degeneration, and dendritic and synaptic pathology. In general, axonal degeneration is detrimental for hosts. However, axonal degeneration can be beneficial in the case of infection with neurotropic viruses that spread in the CNS using axonal transport. C57BL/Wld S (Wld S , Wallerian degeneration slow mutant) mice are protected from axonal degeneration. Wld S mice infected with the neurovirulent GDVII strain of TMEV are more resistant to virus infection than wild-type mice, suggesting that axonal preservation contributes to the resistance. By contrast, infection with the less virulent Daniels strain of TMEV results in high levels of virus propagation in the CNS, suggesting that prolonged survival of axons in Wld S mice favors virus spread. Thus, axonal degeneration might be a beneficial self-destruct mechanism that limits the spread of neurotropic viruses, in the case of less virulent virus infection. We hypothesize that neurons use 'built-in' self-destruct protection machinery (compartmental neurodegeneration) against neurotropic virus infection, since the CNS is an immunologically privileged site. Early induction of apoptosis in the neuronal cell body limits virus replication. Wallerian degeneration of the axon prevents axonal transport of virus. Dendritic and synaptic degeneration blocks virus transmission at synapses. Thus, the balance between neurodegeneration and virus propagation may be taken into account in the future design of neuroprotective therapy. Neurons are the transmitting cells of the nervous system and communicate by chemical and electrical means. A neuron can be divided into different components: cell body (soma), a longer cell process called an axon, branching processes called dendrites and synapses. A neuron transmits information via the axon, which terminates at a synapse for conveying ongoing signals, while dendrites integrate incoming signals. Since axons as well as their neuronal cell bodies do not usually regenerate in the CNS, axonal damage often results in permanent neurological deficits. Axonal degeneration in the CNS can be seen in several neurological conditions, such as neurodegenerative diseases (e.g., amyotrophic lateral sclerosis and neuroaxonal dystrophy) [1], traumatic lesions and infections [2] [3] [4] [5] .
Output: Axonal degeneration as a self-destructive defense mechanism against neurotropic virus infection NIH Public Access
Interest in the potential of monoclonal antibodies (mAbs) to serve as therapeutic agents has surged in the past decade with a major emphasis on human viral diseases. There has been much attention in this area directed towards the human immunodeficiency virus type-1 (HIV-1) and promising research developments have emerged on the inhibition of HIV-1 infection by mAbs and the identification of several highly conserved neutralizing epitopes. More recently, potent fully-human neutralizing mAbs have been developed against a variety of important human viral disease agents including the paramyxoviruses Hendra virus and Nipah virus, and human or humanized mAbs have been developed against severe acute respiratory syndrome coronavirus (SARS CoV), and West Nile virus, among others. Most of these more recently developed antiviral mAbs have come from the use of antibody phage-display technologies and the implementation of simplified, inexpensive yet efficient methods, for expressing and purifying the initially selected fragment antibodies is of prime importance in further facilitating this area of research.
Output: Chapter 25 Antibody Fragment Expression and Purification
pilgrimages and sporting events are linked to numerous health hazards, including the transmission of infectious diseases, physical injuries, and an impact on local and global health systems and services. As with other forms of disaster, mass gathering-related disasters are the product of the management of different hazards, levels of exposure, and vulnerability of the population and environment, and require comprehensive risk management that looks beyond single hazards and response. Incorporating an all-hazard, prevention-driven, evidence-based approach that is multisectoral and multidisciplinary is strongly advocated by the Sendai Framework for Disaster Risk Reduction 2015-2030. This paper reviews some of the broader impacts of mass gatherings, the opportunity for concerted action across policy sectors and scientific disciplines offered by the year 2015 (including through the Sendai Framework), and the elements of a 21 st century approach to mass gatherings.
Output: Reducing risks to health and wellbeing at mass gatherings: the role of the Sendai Framework for Disaster Risk Reduction
Transmissible gastroenteritis virus (TGEV) of pigs and porcine epidemic diarrhea virus (PEDV) are two porcine coronaviruses in the genus Alphacoronavirus of the Coronavirinae subfamily in the Coronaviridae family within the order Nidovirales. Based on sequence heterogeneity, PED viruses are tentatively categorized as "classical" and "emerging" strains. The classical strains include PED viruses identified between 1970s to 2010, whereas PED viruses isolated after 2010 are referred to as emerging strains. The emerging strains are further divided into "non-S INDEL (insertions and deletions)" and "S INDEL" strains on the basis of the spike (S) protein sequences and virulence in piglets. Another proposal classifies PED viruses into up to five genotypes. The enveloped virions of coronaviruses are spherical and/or pleomorphic with diameters of 144.8 ± 7.2 nm for TGEV (PUR46-MAD strain) and 95-190 nm for PEDV (CV777 strain). Viral envelope contains the spike (S), membrane (M), and envelope (E) proteins. Homotrimeric S protein complexes form the distinctive "corona-like" structure on the surface of the virions. Within the envelope, there exists a nucleocapsid consisting of the nucleocapsid (N) protein and viral genomic RNA. Both TGEV and PEDV have a typical genomic organization of coronaviruses. The positive-sense, single-stranded RNA genome is approximately 28 kb in length with a 5′ cap structure and a 3′ polyadenylated tail. The coding sequence is flanked by untranslated regions (UTRs) at 5′ and 3′ ends. The N-terminal two-thirds of the genome contain one major open reading frame ORF1a encoding replicase polyprotein pp1a. A -1 frameshift just 5′ to the stop codon of ORF1a gives rise to ORF1b encoding a much longer replicase polyprotein pp1ab. These polyproteins are cleaved into 16 nonstructural proteins (nsps) mostly involved in viral RNA replication. The rest 10-kb genome codes for structural proteins S, M, E, and N, as well as accessory proteins with various functions (Fig. 1) . TGEV encodes three accessory proteins, whereas PEDV encodes one.
Output: Transmissible Gastroenteritis Virus of Pigs and Porcine Epidemic Diarrhea Virus
Mannan-containing products are capable of modulating immune responses in animals. However, different products may have diverse immunomodulation. The experiment was conducted to examine effects of mannan oligosaccharide (Actigen; ACT) on growth performance and serum concentrations of antibodies and infl ammatory mediators in weanling pigs (Sus scrofa) experimentally infected with porcine reproductive and respiratory syndrome virus (PRRSV). A total of 32 PRRSV-negative pigs (3 wk old) were randomly assigned from within blocks to 1 of 4 treatments in a 2 by 2 factorial arrangement [2 types of diet: control (0%) and ACT addition (0.04%); and with and without PRRSV] in a randomized complete block design. Pigs were blocked by initial BW within sex. Ancestry was equalized across treatments. Pigs (8/treatment) were kept individually in each pen. After 2 wk of an 8-wk period of feeding the treatments, pigs received an intranasal inoculation of PRRSV or sham medium at 5 wk of age. Infection by PRRSV decreased ADG, ADFI, and G:F throughout the experiment (P < 0.01). Actigen did not affect ADG (P = 0.450), but decreased (P = 0.047) ADFI from 28 to 42 days postinoculation (DPI). During that time, ACT improved G:F in infected pigs but not in sham controls
Output: Mannan oligosaccharide increases serum concentrations of antibodies and infl ammatory mediators in weanling pigs experimentally infected with porcine reproductive and respiratory syndrome virus 1,2
MBP-tagged TRIM25 protein was expressed in E.coli Rosetta 2 (DE3) TM cells (Millipore). Transformed cells were grown in LB broth containing 0.2% glucose at 37 °C. Then, 0.2 mM IPTG was added and the cells were incubated under shaking conditions for 18 h at 25 °C, after which the cells were harvested by centrifugation. The pellet was resuspended in T1 buffer (20 mM Tris/Cl(pH 7.4), 1 mM EDTA, 1 mM sodium azide, and 1 mM DTT) and sonicated. After centrifugation, the supernatant was loaded onto a DEAE ion-exchange column (GE healthcare) and the flow throw was collected. Next, the pooled sample was applied to amylose resin (NEB). The column was washed with T2 buffer (T1 buffer + 200 mM NaCl) and eluted with T3 buffer (T2 buffer + 10 mM maltose). The purity of the proteins was analyzed by 10% SDS-PAGE. The final yield of MBP-TRIM25 was determined by the Bradford assay with BSA as the standard and the samples were stored at �80 °C. His-tagged RIG-I was expressed in E. coli BL21(DE3) cells. The transformed cells were grown in LB broth at 37 °C and then further incubated at 4 °C for 3 h. Subsequently, 0.25 mM IPTG was added and the cells were incubated under shaking conditions for 18 h at 25 °C, after which the cells were harvested by centrifugation. The pellet was resuspended in R1 buffer (50 mM HEPES; pH 7.4, 10% glycerol, 500 mM NaCl, 0.2% NP-40, 10 mM imidazole, 1 mM PMSF, 0.5 mg/ml lysozyme, and protease inhibitor cocktail) and sonicated. After centrifugation, the supernatant was applied to a Ni-NTA chelating agarose (Incospham). The column was washed with R2 buffer (50 mM HEPES; pH 7.4, 10% glycerol, 500 mM NaCl, 0.2% NP-40, and 50 mM imidazole) and the His-tagged RIG-I was eluted by increasing the imidazole concentration. The purest fractions were applied to a heparin-Sepharose column (GE healthcare), and the resin was washed with R3 buffer (50 mM Tris/Cl(pH 7.4), 10% glycerol, 0.2% NP-40, and 20 mM NaCl) and eluted with increasing concentrations of NaCl (up to 500 mM). The final yield of His-RIG-I was determined by the Bradford assay (Bio-Rad) with BSA as the standard. RNA Aptamers Specific to NS1 Protein of Influenza Virus Hye-Min Woo et al.
Output: Molecules and Cells Supplementary Materials
Acute pharyngitis is a common illness in both children and adults, caused by a wide variety of microbial agents. In children, approximately 20% of pharyngitis is caused by group A beta-hemolytic streptococci (GABHS); in adults, 5% of pharyngitis is due to GABHS. The signs and symptoms of infection are variable, ranging from mild sore throat with minimal physical findings to high fever and severe pain. The differential diagnosis of GABHS pharyngitis is extensive. Most cases of acute pharyngitis in both children and adults are caused by viruses. The gold standard diagnostic test for GABHS remains the throat culture. It is important to select appropriate candidates for culture to maintain the sensitivity of the test. Penicillin is still recommended as first-line treatment for documented GABHS infections. Prompt treatment is important to prevent serious sequelae of infection. (Prim Care Update Ob/Gyns 2002; 9:222-225. © 2002 Elsevier Science Inc. All rights reserved.)
Output: GROUP A STREPTOCOCCAL PHARYNGITIS
The Mediterranean diet is rich in fruits and vegetables, monounsaturated fatty acids from olive oil, and is complemented with the traditional use of culinary and medicinal herbs and spices. An important feature of this diet is the negative association with the incidence of metabolic syndrome, which is characterized by increased risk of cardiovascular disease. Conformity to the Mediterranean diet has also been linked to a decreased risk of cardiovascular disease and cancer in US populations. Plants that originated in the Mediterranean basin have been used for centuries in botanical therapies. Many of these plants are believed to prevent and/or cure a wide spectrum of ailments based on their content in bioactive components that exert anti-oxidant, anti-infl ammatory, anticarcinogenic, anti-diabetic, and anti-thrombotic functions. This chapter underlines the health benefi ts that may derive from utilization through dietary assumption or medicinal applications of a selected group of plant products including extracts and specifi c bioactive components found in rosemary, licorice, chamomile, and olive oil. Each section provides a scientifi c analysis of the most recent literature and attempts to highlight the mechanisms of action and molecular targets of bioactive components derived from these plants.
Output: Health Benefi ts of Traditional Culinary and Medicinal Mediterranean Plants
Severe acute respiratory syndrome (SARS) is characterized by acute respiratory distress syndrome (ARDS) and pulmonary fibrosis, and monocytes/macrophages are the key players in the pathogenesis of SARS. In this study, we compared the transcriptional profiles of SARS coronavirus (SARS-CoV)-infected monocytic cells against that infected by coronavirus 229E (CoV-229E). Total RNA was extracted from infected DC-SIGN-transfected monocytes (THP-1-DC-SIGN) at 6 and 24 h after infection, and the gene expression was profiled in oligonucleotide-based microarrays. Analysis of immune-related gene expression profiles showed that at 24 h after SARS-CoV infection: (1) IFN-a/b-inducible and cathepsin/proteasome genes were downregulated; (2) hypoxia/ hyperoxia-related genes were upregulated; and (3) TLR/TLR-signaling, cytokine/cytokine receptor-related, chemokine/chemokine receptor-related, lysosome-related, MHC/chaperon-related, and fibrosis-related genes were differentially regulated. These results elucidate that SARS-CoV infection regulates immune-related genes in monocytes/macrophages, which may be important to the pathogenesis of SARS.
Output: SARS-CoV Regulates Immune Function-Related Gene Expression in Human Monocytic Cells
Therapeutic recombinant human catalase (rhCAT) can quench infection-induced reactive oxygen species (ROS), thereby alleviating the associated tissue damage. Although the intranasal route is efficient to deliver native rhCAT to the lung, the therapeutic effect is limited by rapid elimination from the blood. In this study, we modified rhCAT with the active polymer, polyethylene glycol monomethyl ether (PEG)-5000, and analyzed the pharmacokinetics of PEGylated rhCAT in mice. The high tetra-PEGylation ratio was about 60 %, and PEGylation prolonged the half-life of rhCAT in serum (75 vs. 13.5 min for native rhCAT). The protective effects of PEG-rhCAT were investigated in a mouse model of influenza virus A (H1N1)-associated pneumonia. PEG-rhCAT was more effectively delivered than native rhCAT and was associated with higher survival ratio, less extensive lung injuries, reduced ROS levels, and lower viral replication. Collectively, these findings indicate that PEGylation can enhance the therapeutic efficacy of native rhCAT and suggest that PEGylated rhCAT may represent a novel complement therapy for H1N1 influenza-induced pneumonia.
Output: PEGylated human catalase elicits potent therapeutic effects on H1N1 influenza-induced pneumonia in mice
Theoretically, homogeneous environments favor the evolution of specialists whereas heterogeneous environments favor generalists. Canine distemper is a multi-host carnivore disease caused by canine distemper virus (CDV). The described cell receptor of CDV is SLAM (CD150). Attachment of CDV hemagglutinin protein (CDV-H) to this receptor facilitates fusion and virus entry in cooperation with the fusion protein (CDV-F). We investigated whether CDV strains co-evolved in the large, homogeneous domestic dog population exhibited specialist traits, and strains adapted to the heterogeneous environment of smaller populations of different carnivores exhibited generalist traits. Comparison of amino acid sequences of the SLAM binding region revealed higher similarity between sequences from Canidae species than to sequences from other carnivore families. Using an in vitro assay, we quantified syncytia formation mediated by CDV-H proteins from dog and non-dog CDV strains in cells expressing dog, lion or cat SLAM. CDV-H proteins from dog strains produced significantly higher values with cells expressing dog SLAM than with cells expressing lion or cat SLAM. CDV-H proteins from strains of non-dog species produced similar values in all three cell types, but lower values in cells expressing dog SLAM than the values obtained for CDV-H proteins from dog strains. By experimentally changing one amino acid (Y549H) in the CDV-H protein of one dog strain we decreased expression of specialist traits and increased expression of generalist traits, thereby confirming its functional importance. A virus titer assay demonstrated that dog strains produced higher titers in cells expressing dog SLAM than cells expressing SLAM of non-dog hosts, which suggested possible fitness benefits of specialization post-cell entry. We provide in vitro evidence for the expression of specialist and generalist traits by CDV strains, and fitness trade-offs across carnivore host environments caused by antagonistic pleiotropy. These findings extend knowledge on CDV molecular epidemiology of particular relevance to wild carnivores.
Output: Antagonistic Pleiotropy and Fitness Trade-Offs Reveal Specialist and Generalist Traits in Strains of Canine Distemper Virus
Engineering vaccine-based therapeutics for infectious diseases is highly challenging, as trial formulations are often found to be nonspecific, ineffective, thermally or hydrolytically unstable, and/or toxic. Vaccines have greatly improved the therapeutic landscape for treating infectious diseases and have significantly reduced the threat by therapeutic and preventative approaches. Furthermore, the advent of recombinant technologies has greatly facilitated growth within the vaccine realm by mitigating risks such as virulence reversion despite making the production processes more cumbersome. In addition, seroconversion can also be enhanced by recombinant technology through kinetic and nonkinetic approaches, which are discussed herein. Recombinant technologies have greatly improved both amino acid-based vaccines and DNA-based vaccines. A plateau of interest has been reached between 2001 and 2010 for the scientific community with regard to DNA vaccine endeavors. The decrease in interest may likely be attributed to difficulties in improving immunogenic properties associated with DNA vaccines, although there has been research demonstrating improvement and optimization to this end. Despite improvement, to the extent of our knowledge, there are currently no regulatory body-approved DNA vaccines for human use (four vaccines approved for animal use). This article discusses engineering DNA vaccines against infectious diseases while discussing advantages and disadvantages of each, with an emphasis on applications of these DNA vaccines. This review paper summarizes the state of the engineered/recombinant DNA vaccine field, with a scope entailing ''Engineering DNA vaccines against infectious diseases". We endeavor to emphasize recent advances, recapitulating the current state of the field. In addition to discussing DNA therapeutics that have already been clinically translated, this review also examines current research developments, and the challenges thwarting further progression. Our review covers: recombinant DNA-based subunit vaccines; internalization and processing; enhancing immune protection via adjuvants; manufacturing and engineering DNA; the safety, stability and delivery of DNA vaccines or plasmids; controlling gene expression using plasmid engineering and gene circuits; overcoming immunogenic issues; and commercial successes. We hope that this review will inspire further research in DNA vaccine development.
Output: Engineering DNA vaccines against infectious diseases
To establish a characteristic host response to predict the pathogenicity and tissue tropism of infectious bronchitis viruses (IBV), we investigated innate immune responses (IIR) and apoptosis in chicken embryo kidney cells (CEKC) and tracheal organ cultures (TOC) infected with three IBV strains. Results showed nephropathogenic IBV strains 885 and QX induced greater apoptosis in CEKC than M41, which induced greater apoptosis in TOCs compared to 885 and QX. Elevated IIR is associated with tissue tropism of different IBV strains. Compared to M41, 885 and QX caused greater induction of toll like receptor 3 (TLR3), melanoma differentiation associated protein 5 (MDA5) and interferon beta (IFN-β) in CEKC. In contrast, M41 infection caused greater expression of these genes than 885 or QX in TOCs. In summary, greater levels of apoptosis and elevated levels of TLR3, MDA5 and IFN-β expression are associated with increased pathogenicity of IBV strains in renal and tracheal tissues.
Output: Pathogenicity and tissue tropism of infectious bronchitis virus is associated with elevated apoptosis and innate immune responses
In this study, the results of an airflow investigation conducted on 7 June 2015 as part of a series of epidemiologic investigations at Pyeongtaek St. Mary's Hospital, South Korea, were investigated. The study involved 38 individuals who were infected directly and indirectly with Middle East Respiratory Syndrome (MERS), by a super-spreader patient. Tracer gas experiments conducted on the eighth floor, where the initial patient was hospitalized, confirmed that the tracer gas spread to adjacent patient rooms and rooms across corridors. In particular, the experiment with an external wind direction and speed similar to those during the hospitalization of the initial patient revealed that the air change rate was 17-20 air changes per hour (ACH), with air introduced through the window in the room of the infected patient (room 8104). The tracer gas concentration of room 8110, which was the farthest room, was 7.56% of room 8104, indicating that a high concentration of gas has spread from room 8104 to rooms across the corridor. In contrast, the tracer gas was barely detected in a maternity ward to the south of room 8104, where there was no secondary infected patient. Moreover, MERS is known to spread mainly by droplets through close contact, but long-distance dispersion is probable in certain environments, such as that of a super-spreader patient hospitalized in a room without ventilation, hospitals with a central corridor type, and indoor airflow dispersion due to external wind.
Output: Airflow as a Possible Transmission Route of Middle East Respiratory Syndrome at an Initial Outbreak Hospital in Korea
For epidemic control, rapid identification and characterization of the responsible unknown agent are crucial. To address this critical question, a method was developed for virus discovery based on a flexible nested-PCR subtraction hybridization. As a positive control, we used hepatitis C virus as a hypothetical unrecognized virus and "discover" it in the sample. Using template-switching universal long-PCR to produce large quantities of cDNA, our nested-PCR-based subtractive hybridization coupled with a single-strand deletion technology removed most of the common cDNA. Following subtraction hybridization, a cDNA library was constructed and displayed by differential reverse dot blot hybridization. This new genomic subtraction hybridization method will be ideally suited to identify rapidly any previously unrecognized viral agent. Published by Elsevier B.V.
Output: Rapid approach to identify an unrecognized viral agent
Background. Chronic lung allograft dysfunction (CLAD) is a major cause of allograft loss post-lung transplantation. Prior studies have examined the association between respiratory virus infection (RVI) and CLAD were limited by older diagnostic techniques, study design, and case numbers. We examined the association between symptomatic RVI and CLAD using modern diagnostic techniques in a large contemporary cohort of lung transplant recipients (LTRs). Methods. We retrospectively assessed clinical variables including acute rejection, cytomegalovirus pneumonia, upper and lower RVI, and the primary endpoint of CLAD (determined by 2 independent reviewers) in 250 LTRs in a single university transplantation program. Univariate and multivariate Cox models were used to analyze the relationship between RVI and CLAD in a time-dependent manner, incorporating different periods of risk following RVI diagnosis. Results. Fifty patients (20%) were diagnosed with CLAD at a median of 95 weeks post-transplantation, and 79 (32%) had 114 episodes of RVI. In multivariate analysis, rejection and RVI were independently associated with CLAD (adjusted hazard ratio [95% confidence interval]) 2.2 (1.2-3.9), P = .01 and 1.9 (1.1-3.5), P = .03, respectively. The association of RVI with CLAD was stronger the more proximate the RVI episode: 4.8 (1.9-11.6), P < .01; 3.4 (1.5-7.5), P < .01; and 2.4 (1.2-5.0), P = .02 in multivariate analysis for 3, 6, and 12 months following RVI, respectively. Conclusions. Symptomatic RVI is independently associated with development of CLAD, with increased risk at shorter time periods following RVI. Prospective studies to characterize the virologic determinants of CLAD and define the underlying mechanisms are warranted.
Output: Clinical Infectious Diseases Symptomatic Respiratory Virus Infection and Chronic Lung Allograft Dysfunction
Scrub typhus is the most common febrile disease in Korea during the autumn. Jeju Island is the largest island in South Korea and has a distinctive oceanic climate. This study aimed to identify epidemiologic characteristics of scrub typhus on Jeju Island. From January 2011 to December 2016, 446 patients were diagnosed with scrub typhus on Jeju Island. The patients' personal data and the environmental factors that might be related to scrub typhus were investigated and retrospectively analyzed. The median age of the patients was 58-years-old (range, 8 to 91) and 43% of them worked in the agricultural, forestry or livestock industry. Regardless of their job, 87% of the patients had a history of either working outdoors or of other activities before developing scrub typhus. The south and southeast regions of Jeju Island, especially Namwon-eup, showed the highest incidence of scrub typhus. Workers in mandarin orange orchards seemed to be the highest risk group for scrub typhus infection. Scrub typhus on Jeju Island showed unique characteristics. To efficiently prevent scrub typhus, each year individual regional approaches should be developed based on the epidemiologic characteristics of the disease.
Output: 제주도 쯔쯔가무시증의 역학적 특성 Epidemiologic characteristics of scrub typhus in Jeju Island
Attenuated viral vaccines can be generated by targeting essential pathogenicity factors. We report here the rational design of an attenuated recombinant coronavirus vaccine based on a deletion in the coding sequence of the nonstructural protein 1 (nsp1). In cell culture, nsp1 of mouse hepatitis virus (MHV), like its SARS-coronavirus homolog, strongly reduced cellular gene expression. The effect of nsp1 on MHV replication in vitro and in vivo was analyzed using a recombinant MHV encoding a deletion in the nsp1-coding sequence. The recombinant MHV nsp1 mutant grew normally in tissue culture, but was severely attenuated in vivo. Replication and spread of the nsp1 mutant virus was restored almost to wild-type levels in type I interferon (IFN) receptor-deficient mice, indicating that nsp1 interferes efficiently with the type I IFN system. Importantly, replication of nsp1 mutant virus in professional antigen-presenting cells such as conventional dendritic cells and macrophages, and induction of type I IFN in plasmacytoid dendritic cells, was not impaired. Furthermore, even low doses of nsp1 mutant MHV elicited potent cytotoxic T cell responses and protected mice against homologous and heterologous virus challenge. Taken together, the presented attenuation strategy provides a paradigm for the development of highly efficient coronavirus vaccines.
Output: Coronavirus Non-Structural Protein 1 Is a Major Pathogenicity Factor: Implications for the Rational Design of Coronavirus Vaccines
Both porcine reproductive and respiratory syndrome and swine influenza are acute, highly contagious swine diseases. These diseases pose severe threats for the swine industry and cause heavy economic losses worldwide. In this study, we have developed a chimeric viruslike particle (VLP) vaccine candidate for porcine reproductive and respiratory syndrome virus (PRRSV) and H3N2 influenza virus and investigated its immunogenicity in mice. The HA and M1 proteins from the H3N2 influenza virus and the PRRSV GP5 protein fused to the cytoplasmic and transmembrane domains of the NA protein were both incorporated into the chimeric VLPs. Analysis of the immune responses showed that the chimeric VLPs elicited serum antibodies specific for both PRRSV GP5 and the H3N2 HA protein, and they stimulated cellular immune responses compared to the responses to equivalent amounts of inactivated viruses. Taken together, the results suggested that the chimeric VLP vaccine represents a potential strategy for the development of a safe and effective vaccine to control PRRSV and H3N2 influenza virus. C. Xue and W. Wang contributed equally to this work.
Output: Chimeric influenza-virus-like particles containing the porcine reproductive and respiratory syndrome virus GP5 protein and the influenza virus HA and M1 proteins
(n = 83) and medical staff (n = 12) had to undergo dialysis treatment in an isolated environment. This study was performed to investigate the effects of stress caused by dialysis treatment under isolation. Plasma samples from the HD patients and medical staff were collected at the time of isolation(M0), the following month(M1), and three months after isolation(M3). Parameters for stress included circulating cell-free genomic DNA(ccf-gDNA), circulating cell-free mitochondria DNA(ccf-mtDNA), and pentraxin-3(PTX-3). Decreased values of Hct, kt/v and ca x p were recovered after the end of two weeks of isolation. The levels of ccf-gDNA and ccf-mtDNA were the highest at M0 and decreased gradually in both HD patients and the medical staff. The normalization of ccf-gDNA and ccf-mtDNA was significantly delayed in HD patients compared with the response in the medical staff. PTX-3 increased only in HD patients and was highest at M0, and it then gradually decreased. Medical isolation and subnormal quality of care during the MERS outbreak caused extreme stress in HD patients. Plasma cell-free DNA and PTX-3 seems to be good indicators of stress and quality of care in HD patients. Measurement of plasma cell-free genomic DNA and cell-free mitochondria DNA. Circulating cf-DNA was extracted from 200 μL of plasma using a QIAamp DNeasy Blood and Tissue kit (Qiagen, Valencia, Calif). The ccf-gDNA and ccf-mtDNA were amplified using a StepOnePlus real-time PCR system (Applied Biosystems, Massachusetts). Primers for the human NADH1 dehydrogenase 1 gene (ND1) were used for mtDNA, and primers for the human lipoprotein lipase gene (LPL) were used for gDNA. Standard DNA fragments of ND1 and LPL were synthesized using an Integrated DNA Technologies kit (IDT, Coralville, IA) for absolute quantification. The fragment solutions were 10-fold serially diluted. The concentrations of DNA were converted to copy number using the Andrew Staroscik Calculator for the absolute copy number from a template 33 . All samples were analyzed in duplicate, and a no-template negative control was included in every analysis. Pentraxin-3 (PTX-3) ELIZA. The level of PTX-3 in plasma was measured using a Quantikine ELISA Human Pentraxin 3/TSG-13 kit (R&D Systems, Minneapolis) according to the manufacturer's protocol. The detection range was 0.31-20.00 ng/mL. Concentrations were determined using a standard curve generated from specific standards provided by the manufacturer. Each sample was measured in duplicate. Statistics. Statistical analyses were conducted using SPSS software (version 20 SPSS, Inc., Chicago, IL). For normally distributed variables, Student's t-test and one-way ANOVA were used for comparisons, and the data are presented as the mean ± SE. The Mann-Whitney U and Kruskal-Wallis tests were used for comparisons of variables that were not normally distributed. Correlations were assessed with Pearson's correlation coefficient for parametric distributions. Statistical significance was set at P < 0.05.
Output: Inevitable isolation and the change of stress markers in hemodialysis patients during the 2015 MERS- CoV outbreak in Korea OPEN