niryuu/sni-each-converted huggingface dataset:
a b s t r a c t Coronaviruses (CoVs) are an important cause of illness in humans and animals. Most human coronaviruses commonly cause relatively mild respiratory illnesses; however two zoonotic coronaviruses, SARS-CoV and MERS-CoV, can cause severe illness and death. Investigations over the past 35 years have illuminated many aspects of coronavirus replication. The focus of this review is the functional analysis of conserved RNA secondary structures in the 5 and 3 of the betacoronavirus genomes. The 5 350 nucleotides folds into a set of RNA secondary structures which are well conserved, and reverse genetic studies indicate that these structures play an important role in the discontinuous synthesis of subgenomic RNAs in the betacoronaviruses. These cis-acting elements extend 3 of the 5 UTR into ORF1a. The 3 UTR is similarly conserved and contains all of the cis-acting sequences necessary for viral replication. Two competing conformations near the 5 end of the 3 UTR have been shown to make up a potential molecular switch. There is some evidence that an association between the 3 and 5 UTRs is necessary for subgenomic RNA synthesis, but the basis for this association is not yet clear. A number of host RNA proteins have been shown to bind to the 5 and 3 cis-acting regions, but the significance of these in viral replication is not clear. Two viral proteins have been identified as binding to the 5 cis-acting region, nsp1 and N protein. A genetic interaction between nsp8 and nsp9 and the region of the 3 UTR that contains the putative molecular switch suggests that these two proteins bind to this region.
Output: The structure and functions of coronavirus genomic 3 and 5 ends
This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1-507) from strains detected worldwide and chicken tissuespecific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC 9 GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.
Output: Avian coronavirus Spike Glycoprotein Ectodomain Shows a Low Codon Adaptation to Gallus gallus with Virus-Exclusive Codons in Strategic Amino Acids Positions
Severe acute respiratory syndrome virus (SARS-CoV) that lacks the envelope (E) gene (rSARS-CoV-DE) is attenuated in vivo. To identify factors that contribute to rSARS-CoV-DE attenuation, gene expression in cells infected by SARS-CoV with or without E gene was compared. Twenty-five stress response genes were preferentially upregulated during infection in the absence of the E gene. In addition, genes involved in signal transduction, transcription, cell metabolism, immunoregulation, inflammation, apoptosis and cell cycle and differentiation were differentially regulated in cells infected with rSARS-CoV with or without the E gene. Administration of E protein in trans reduced the stress response in cells infected with rSARS-CoV-DE or with respiratory syncytial virus, or treated with drugs, such as tunicamycin and thapsigargin that elicit cell stress by different mechanisms. In addition, SARS-CoV E protein down-regulated the signaling pathway inositol-requiring enzyme 1 (IRE-1) of the unfolded protein response, but not the PKR-like ER kinase (PERK) or activating transcription factor 6 (ATF-6) pathways, and reduced cell apoptosis. Overall, the activation of the IRE-1 pathway was not able to restore cell homeostasis, and apoptosis was induced probably as a measure to protect the host by limiting virus production and dissemination. The expression of proinflammatory cytokines was reduced in rSARS-CoV-DE-infected cells compared to rSARS-CoV-infected cells, suggesting that the increase in stress responses and the reduction of inflammation in the absence of the E gene contributed to the attenuation of rSARS-CoV-DE.
Output: Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Regulates Cell Stress Response and Apoptosis
A rapid review was performed to determine (1) the number and causes of reported laboratory-acquired infections (LAI) in the Asia-Pacific region; (2) their significance and threat to the community; (3) the primary risk factors associated with LAIs; (4) the consequences in the event of a LAI or pathogen escape; and (5) to make general recommendations regarding biosafety practices for diagnosis and research in the Asia-Pacific region. A search for LAI and zoonoses in the Asia-Pacific region using online search engines revealed a relatively low number of reports. Only 27 LAI reports were published between 1982 and 2016. The most common pathogens associated with LAIs were dengue virus, Arthroderma spp., Brucella spp., Mycobacterium spp., Rickettsia spp., and Shigella spp. Seventy-eight percent (21 out of 27 LAI reports) occurred in high-income countries (i.e., Australia, Japan, South Korea, Singapore, and Taiwan) where laboratories were likely to comply with international biosafety standards. Two upper-middle income countries (China (2), and Malaysia (2)) and one lower-middle income country (India (2)) reported LAI incidents. The majority of the reports (fifty-two percent (14/27)) of LAIs occurred in research laboratories. Five LAI reports were from clinical or diagnostic laboratories that are considered at the frontier for zoonotic disease detection. Governments and laboratories in the Asia-Pacific region should be encouraged to report LAI cases as it provides a useful tool to monitor unintended release of zoonotic pathogens and to further improve laboratory biosafety. Non-reporting of LAI events could pose a risk of disease transmission from infected laboratory staff to communities and the environment. The international community has an important and continuing role to play in supporting laboratories in the Asia-Pacific region to ensure that they maintain the safe working environment for the staff and their families, and the wider community.
Output: Tropical Medicine and Infectious Disease A Review of Laboratory-Acquired Infections in the Asia-Pacific: Understanding Risk and the Need for Improved Biosafety for Veterinary and Zoonotic Diseases
Plasmodium falciparum-infected erythrocytes (IEs) that bind to chondroitin sulphate A (CSA) in the placenta by PAM-associated clonally variant surface antigens (VSA). Pregnancy-specific VSA (VSAPAM), which include the PfEMP1 variant VAR2CSA, are targets of IgG-mediated protective immunity to PAM. Here, we report an investigation of the specificity of naturally acquired immunity to PAM, using eight human monoclonal IgG1 antibodies that react exclusively with intact CSA-adhering IEs expressing VSAPAM. Four reacted in Western blotting with high-molecularweight (> 200 kDa) proteins, while seven reacted with either the DBL3-X or the DBL5-e domains of VAR2CSA expressed either as Baculovirus constructs or on the surface of transfected Jurkat cells. We used a panel of recombinant antigens representing DBL3-X domains from P. falciparum field isolates to evaluate B-cell epitope diversity among parasite isolates, and identified the binding site of one monoclonal antibody using a chimeric DBL3-X construct. Our findings show that there is a high-frequency memory response to VSA PAM, indicating that VAR2CSA is a primary target of naturally acquired PAM-specific protective immunity, and demonstrate the value of human monoclonal antibodies and conformationally intact recombinant antigens in VSA characterization.
Output: Human pregnancy-associated malaria-specific B cells target polymorphic, conformational epitopes in VAR2CSA
Transmissible gastroenteritis virus (TGEV) is a coronavirus that causes villus atrophy, followed by crypt hyperplasia, reduces the activities of intestinal digestive enzymes, and disrupts the absorption of intestinal nutrients. In vivo, TGEV primarily targets and infects intestinal epithelial cells, which play an important role in glucose absorption via the apical and basolateral transporters Na + -dependent glucose transporter 1 (SGLT1) and facilitative glucose transporter 2 (GLUT2), respectively. In this study, we therefore sought to evaluate the effects of TGEV infection on glucose uptake and SGLT1 and GLUT2 expression. Our data demonstrate that infection with TGEV resulted in increased glucose uptake and augmented expression of EGFR, SGLT1 and GLUT2. Moreover, inhibition studies showed that EGFR modulated glucose uptake in control and TGEV infected cells. Finally, high glucose absorption was subsequently found to promote TGEV replication. Competing Interests: The authors have declared that no competing interests exist. EGFR and SGLT1 protein was dynamic. (A) Cells were treated with PBS, DMSO (100 nM), or AG1478 (100 nM) at 37˚C for 48 h. The culture medium from each group was then assayed. (B) Western blot analysis of the expression levels of p-EGFR, EGFR, SGLT1, GLUT2, and β-tubulin. Experiments were performed separately three times. (C) The intensities of protein bands were quantified using Quantity One and SPSS software. (D) Cells were transfected with shEGFR, shEGFR control, pLVX-EGFR, or pLVX-EGFR control. After 48 h of incubation, culture medium from each group and from mock-infected cells was assayed. (E) The expression levels of p-EGFR, EGFR, SGLT1, GLUT2, and β-tubulin proteins were evaluated by western blot analysis. Experiments were performed separately three times. (F) The intensities of protein bands were quantified using Quantity One and SPSS software. (G) IPEC-J2 cells were treated with phlorizin (500 μM) at 37˚C for 48 h, and culture medium from each group was assayed. (H) The expression levels of SGLT1, EGFR, and β-tubulin were evaluated by western blot analysis. (I) The intensities of protein bands were quantified using Quantity One and SPSS software. (J) IPEC-J2 cells were treated with three SGLT1-specific siRNA molecules for 48 h, and culture medium from each group was assayed. (K) Western blot analysis of the expression levels of SGLT1, EGFR, and β-tubulin. (L) The intensities of protein bands were quantified using Quantity One and SPSS software. Each experiment was performed separately three times.
Output: Transmissible Gastroenteritis Virus Infection Enhances SGLT1 and GLUT2 Expression to Increase Glucose Uptake
Acute respiratory failure contributes significantly to nonrelapse mortality after allogeneic hematopoietic stem cell transplantation. Although there is a trend of improved survival over time, mortality remains unacceptably high. An understanding of the pathophysiology of early respiratory failure, opportunities for targeted therapy, assessment of the patient at risk, optimal use of noninvasive positive pressure ventilation, strategies to improve alveolar recruitment, appropriate fluid management, care of the patient with chronic lung disease, and importantly, a team approach between critical care and transplantation services may improve outcomes. Ó
Output: A Critical Care and Transplantation-Based Approach to Acute Respiratory Failure after Hematopoietic Stem Cell Transplantation in Children
| The renin-angiotensin system (RAS) has pivotal roles in the regulation of normal physiology and the pathogenesis of cardiovascular disease. Angiotensin-converting enzyme (ACE) 2, and its product angiotensin 1-7, are thought to have counteracting effects against the adverse actions of other, better known and understood, members of the RAS. The physiological and pathological importance of ACE2 and angiotensin 1-7 in the cardiovascular system are not completely understood, but numerous experimental studies have indicated that these components have protective effects in the heart and blood vessels. Here, we provide an overview on the basic properties of ACE2 and angiotensin 1-7 and a summary of the evidence from experimental and clinical studies of various pathological conditions, such as hypertension, atherosclerosis, myocardial remodelling, heart failure, ischaemic stroke, and diabetes mellitus. ACE2mediated catabolism of angiotensin II is likely to have a major role in cardiovascular protection, whereas the relevant functions and signalling mechanisms of actions induced by angiotensin 1-7 have not been conclusively determined. The ACE2-angiotensin 1-7 pathway, however, might provide a useful therapeutic target for the treatment of cardiovascular disease, especially in patients with overactive RAS.
Output: Angiotensin-converting enzyme 2 and angiotensin 1-7: novel therapeutic targets
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) has been recognized as an invariant internal control for various gene expression studies due to its classical housekeeping role in the glycolytic metabolism. However recently, this enzyme has been proven to be a multifunctional protein involved in diverse non-glycolytic activities. In the present study, two paralogue isoforms of GAPDH mRNAs were characterized from a marine teleost species, rockbream (Oplegnathus fasciatus; Perciformes) and their transcriptional responses to bacterial and viral infections were examined. Rockbream GAPDH1 and GAPDH2 cDNAs encoded 333 and 335 amino acids, respectively, and the amino acid sequence identity between those two isoforms was 74%. Two isoform GAPDH mRNAs were detected ubiquitously in all of tissues examined, but their expression levels were quite variable among tissues. Based on the real-time RT-PCR analysis, the transcription of rbGAPDH1 was affected by neither bacterial (Escherichia coli, Edwardsiella tarda, Vibrio anguillarum or Streptococcus iniae) nor viral (rockbream iridovirus; RBIV) challenges. However on the contrary, the mRNA expression of rbGAPDH2 was significantly up-regulated in liver resulting from the bacterial infections (up to 25-fold), and in both liver (more than sixfold) and kidney (up to fivefold) from the viral infection. Results in the present study suggest that teleost GAPDH isoforms may also be potentially involved in immune modulations especially with respect to inflammatory responses, which is distinct from its classical glycolytic function.
Output: Differential modulations of two glyceraldehyde 3-phosphate dehydrogenase mRNAs in response to bacterial and viral challenges in a marine teleost Oplegnathus fasciatus (Perciformes)
Background. Kawasaki disease (KD) is characterized by systemic vasculitis of unknown etiology. Our previous studies showed expression of CD40 ligand on CD4+ T cells correlated to the coronary artery lesion (CAL) and disease progress in KD. Other studies from Japan suggested the role of CD40L in the pathogenesis of CAL, and this might help explain the excessive number of males affected with KD but cannot be reproduced by Taiwanese population. This study was conducted to investigate the CD40 polymorphism in KD and CAL formation. Methods. A total of 950 subjects (381 KD patients and 569 controls) were investigated to identify 2 tagging single-nucleotide polymorphisms (tSNPs) of CD40 (rs4810485 and rs1535045) by using the TaqMan allelic discrimination assay. Results. A significant association was noted with regards to CD40 tSNPs (rs1535045) between controls and KD patients (P = 0.0405, dominant model). In KD patients, polymorphisms of CD40 (rs4810485) showed significant association with CAL formation (P = 0.0436, recessive model). Haplotype analysis did not yield more significant results between polymorphisms of CD40 and susceptibility/disease activity of KD. Conclusions. This study showed for the first time that polymorphisms of CD40 are associated with susceptibility to KD and CAL formation, in the Taiwanese population.
Output: The cientificWorldJOURNAL Clinical Study CD40 Gene Polymorphisms Associated with Susceptibility and Coronary Artery Lesions of Kawasaki Disease in the Taiwanese Population
Martinez, M.L. and Weiss, R.C., 1993. Detection of feline infectious peritonitis virus in cell cultures and peripheral blood mononuclear leukocytes of experimentally infected cats using a biotinylated eDNA probe. Vet. Microbiol. 34: 259-271. A dot blot hybridization assay, using a biotinylated cDNA probe, was able to detect feline infectious peritonitis virus (F1PV) RNA in Felis catus whole fetus (fcwf-4) cells infected with the F1PV isolates DF2, 79-1146, UCDI, and UCD2. The probe cross-hybridized in the dot blot assay with nucleic acid of a closely related feline coronavirus, feline enteric coronavirus (FECV)-79-1683. To construct the probe, a 2.5 kilobase cDNA, prepared from FIPV-DF2 genomic RNA, was molecularly cloned. The recombinant cDNA clone was digested with the restriction endonuclease Rsa I, and an 870 basepair Rsa 1 fragment was isolated from vector DNA by agarose electrophoresis and glassmilk purification. This fragment was complementary to the 3' three fourths of the nucleocapsid gene. The hybridization probe was prepared by random primed labeling in the presence of biotin-I 1-dUTP. Using an avidinalkaline phosphatase conjugate and chemilumineseent substrate detection system, virus could be detected in as few as 3000 infected cells. In an in vivo study, the probe was used to detect FIPV RNA in peripheral blood mononuclear leukocytes (PBML) isolated at various post-infection days (PID) from cats experimentally infected with the FIP-producing coronavirus isolate FIPV-79-1146 or FIPV-DF2. Viral RNA could be detected in as few as 12 000 PBML isolated from cats at PID 7 and in 50 000 PBML at PID 22. There was no consistent pattern, however, between hybridization results and prognosis or severity of disease at the time of sampling. Despite some cross-hybridization with FECV RNA, this probe should be useful for diagnosis of FIP, because cats infected with FECV most likely do not become viremic.
Output: Detection of feline infectious peritonitis virus infection in cell cultures and peripheral blood mononuclear leukocytes of experimentally infected cats using a biotinylated eDNA probe
This study examines the impact of HSR services on the tourism spatial interactions between Beijing and Tianjin in China. Data were collected from official statistical reports. A method of derivation was developed and several indexes, such as tourism mean center, and tourism standard distance are further applied to measure temporalspatial changes between the two adjoining cities. The results reveal the dynamic tourism spatial interaction between Beijing and Tianjin has been influenced by a range of factors including population, destination attractiveness, disposable income and income elasticity, changes in the domestic and international spatial structure of tourist flows and how destination management organizations react to the changes. The study has implications for both the research and practice of city transportation and tourism development.
Output: The impact of high-speed railway on tourism spatial structures between two adjoining metropolitan cities in China: Beijing and Tianjin
Pathological, immunocytochemical and microbiological findings in 32 cases of calf pneumonia associated with Haemophilus somnus infection are described. The majority of cases were "found dead" or died after a sudden onset pneumonia of less than 24h duration. Lesions of exudative bronchopneumonia were present and the cases could be divided into two main groups on the basis ofhistopathological and immunocytochemical features. In group A, cases were dominated by necrotizing bronchiolitis, degeneration and necrosis of airway and alveolar exudates, severe alveolitis with accumulations of degenerate basophilic cells, interstitial inflammatory changes and the widespread distribution ofH. somnus antigen in airways and alveoli. In Group B, necrotizing and degenerative changes were much less extensive and less severe and the overall appearance was of suppurative bronchopneumonia with H. somnus antigen much less widespread within the lungs. Alveolar oedema, hyaline membrane formation and alveolar epithelial hyperplasia were present in caudodorsal lung areas of several calves. No major differences were seen between the histopathology of lungs where H. somnus was' the sole isolate and that of lungs where H. somnus was isolated along with other bacterial pathogens.
Output: Pathological, Immunocytochemlcal and Microbiological Findings in Calf Pneumonias associated with Haernophilus sornnus infection
Equine coronavirus (ECoV) is considered an enteric pathogen of foals and has only recently been associated with infections in adult horses. Seroprevalence data is needed to better understand the epidemiology of ECoV in adult horses, evaluate diagnostic modalities and develop preventive measures. The objective of this study was to investigate the seroprevalence and selective risk factors for ECoV in 5247 healthy adult horses in the USA, using a recently established and validated IgG enzyme-linked immunosorbent assay. Prevalence factors analysed in this study included geographic region, age, breed, sex and use. A total of 504/5247 horses (9.6%) horses tested seropositive. Geographic region (Mid-West; P = 0.008), breed (Draft horses; P = 0.003) and specific uses of horses (ranch/farm, P = 0.034; breeding use, P = 0.016) were all statistically significant risk factors for seropositivity.
Output: Seroprevalence and risk factors for infection with equine coronavirus in healthy horses in the USA
The L protein of mononegaviruses harbours all catalytic activities for genome replication and transcription. It contains six conserved domains (CR-I to -VI; Fig. 1a ). CR-III has been linked to polymerase and polyadenylation activity, CR-V to mRNA capping and CR-VI to cap methylation. However, how these activities are choreographed is poorly understood. Here we present the 2.2-Å X-ray structure and activities of CR-VI þ , a portion of human Metapneumovirus L consisting of CR-VI and the poorly conserved region at its C terminus, the þ domain. The CR-VI domain has a methyltransferase fold, which besides the typical S-adenosylmethionine-binding site ( SAM P) also contains a novel pocket ( NS P) that can accommodate a nucleoside. CR-VI lacks an obvious cap-binding site, and the SAM P-adjoining site holding the nucleotides undergoing methylation ( SUB P) is unusually narrow because of the overhanging þ domain. CR-VI þ sequentially methylates caps at their 2 0 O and N7 positions, and also displays nucleotide triphosphatase activity.
Output: ARTICLE X-ray structure and activities of an essential Mononegavirales L-protein domain
A series of novel ketoprofen derivatives 4aj bearing both amide and carbamate functionalities were prepared using the benzotriazole method of carboxylic and hydroxy group activation. Selective reduction of ketoprofen produced hydroxy derivative 2, which in the reaction with one or two moles of 1-benzotriazole carboxylic acid chloride (1) gave benzotriazole derivatives 3a and 3b, respectively. Compounds 3a and 3b with various amines afforded amidocarbamates 4a-j. Antioxidative screenings revealed that the prepared compounds 3b and 4a-j possess excellent lipid peroxidation inhibition at 0.1 mM concentration, higher than 95% for the derivatives bearing aromatic, cycloalkyl or heterocyclic substituents. Two of the compounds, 3b and 4g, also show high soybean lipoxygenase inhibition activity (95 and 83.5%, respectively). On the other hand, the amidocarbamate derivatives of ketoprofen show only weak reducing activity against 1,1diphenyl-2-picrylhydrazyl radicals. No selective antiviral effects were noted for the tested compounds against a broad variety of DNA and RNA viruses. Most compounds were endowed with a moderate (IC 50 : 10-25 lM) cytostatic activity.
Output: The novel amidocarbamate derivatives of ketoprofen: synthesis and biological activity
The epidemic caused by the novel coronavirus in Wuhan at the end of 2019 has become an urgent public event of worldwide concern. However, due to the changing data of the epidemic, there is no scientific estimate of the cure rate and case fatality rate of the epidemic. This study proposes a method to estimate the cure rate and case fatality rate of COVID-19. The ratio of cumulative discharges on a given day to the sum of cumulative discharges on a given day and cumulative deaths before j days is used to estimate the cure rate. Moreover, the case fatality ratio can also be estimated. After simulation calculations, j is statistically appropriate when it is 8-10, and it is also clinically appropriate. When j is 9, based on the available data, it is inferred that the cure rate of this epidemic is about 93% and the case fatality rate is about 7%. This method of estimating the cure rate can be used to evaluate the effectiveness of treatment in different medical schemes and different regions, and has great value and significance for decision-making in the epidemic. improvement of medical conditions, and rich experience in treatment, patients with COVID-19 will be treated more effectively. Consequently, the CR will increase, and the CFR will decrease. The authors declare no conflict of interest.
Output: Estimating the cure rate and case fatality rate of the ongoing epidemic COVID-19
Background: The relation between weather conditions, viral transmission and seasonal activity of respiratory viruses is not fully understood. Objectives: To investigate the impact of outdoor weather in a temperate climate setting on the seasonal epidemiology of viruses causing respiratory tract infections, particularly influenza A (IFA). Study design: In total, 20,062 clinical nasopharyngeal swab samples referred for detection of respiratory pathogens using a multiplex PCR panel, between October 2010 and July 2013, were included. Results of PCR detection were compared with local meteorological data for the same period. Results: Low temperature and vapor pressure (VP) were associated with weekly incidence of IFA, respiratory syncytial virus, metapneumovirus, bocavirus and adenovirus but no association with relative humidity was found. The incidence of human rhinovirus and enterovirus was independent of temperature. During seasonal IFA outbreaks, the weekly drop of average temperature (compared with the week before) was strongly associated with the IFA incidence recorded the following week. Conclusion: A sudden drop in outdoor temperature might activate the annual influenza epidemic in a temperate climate by facilitating aerosol spread in dry air. These conditions also seem to affect the incidence of other respiratory pathogens but not human rhino-or enterovirus, suggesting that routes of infection other than aerosol may be relevant for these agents.
Output: A four year seasonal survey of the relationship between outdoor climate and epidemiology of viral respiratory tract infections in a temperate climate
Rationale: After lung transplantation, insults to the allograft generally result in one of four histopathologic patterns of injury: (1) acute rejection, (2) lymphocytic bronchiolitis, (3) organizing pneumonia, and (4) diffuse alveolar damage (DAD). We hypothesized that DAD, the most severe form of acute lung injury, would lead to the highest risk of chronic lung allograft dysfunction (CLAD) and that a type I immune response would mediate this process. Objectives: Determine whether DAD is associated with CLAD and explore the potential role of CXCR3/ligand biology. Methods: Transbronchial biopsies from all lung transplant recipients were reviewed. The association between the four injury patterns and subsequent outcomes were evaluated using proportional hazards models with time-dependent covariates. Bronchoalveolar lavage (BAL) concentrations of the CXCR3 ligands (CXCL9/MIG, CXCL10/ IP10, and CXCL11/ITAC) were compared between allograft injury patterns and "healthy" biopsies using linear mixed-effects models. The effect of these chemokine alterations on CLAD risk was assessed using Cox models with serial BAL measurements as time-dependent covariates. Measurements and Main Results: There were 1,585 biopsies from 441 recipients with 62 episodes of DAD. An episode of DAD was associated with increased risk of CLAD (hazard ratio, 3.0; 95% confidence interval, 1.9-4.7) and death (hazard ratio, 2.3; 95% confidence interval, 1.7-3.0). There were marked elevations in BAL CXCR3 ligand concentrations during DAD. Furthermore, prolonged elevation of these chemokines in serial BAL fluid measurements predicted the development of CLAD. Conclusions: DAD is associated with marked increases in the risk of CLAD and death after lung transplantation. This association may be mediated in part by an aberrant type I immune response involving CXCR3/ligands.
Output: CXCR3 Ligands Are Associated with the Continuum of Diffuse Alveolar Damage to Chronic Lung Allograft Dysfunction
Background: The 5′-triphosphorylated, 2′-5′-linked oligoadenylate polyribonucleotides (2-5As) are central to the interferon-induced antiviral 2-5A system. The 2-5As bind and activate the RNase L, an endoRNase degrading viral and cellular RNA leading to inhibition of viral replication. The 2-5A system is tightly controlled by synthesis and degradation of 2-5As. Whereas synthesis is mediated by the 2′-5′ oligoadenylate synthetase family of enzymes, degradation seems to be orchestrated by multiple enzyme nucleases including phosphodiesterase 12, the ectonucleotide pyrophosphatase/phosphodiesterase 1 and the A-kinase anchoring protein 7. Results: Here we present assay tools for identification and characterization of the enzymes regulating cellular 2-5A levels. A procedure is described for the production of 2′-5′ oligoadenylates, which are then used as substrates for development and demonstration of enzyme assays measuring synthetase and nuclease activities, respectively. The synthetase assays produce only a single reaction product allowing for very precise kinetic assessment of the enzymes. We present an assay using dATP and the A(pA) 3 tetramer core as substrates, which requires prior isolation of A(pA) 3 . A synthetase assay using either of the dNTPs individually together with NAD + as substrates is also presented. The nuclease reactions make use of the isolated 2′-5′ oligoadenylates in producing a mixture of shorter reaction products, which are resolved by ion-exchange chromatography to determine the enzyme activities. A purified human 2′-5′ oligoadenylate synthetase and a purified human phosphodiesterase 12 along with crude extracts expressing those proteins, are used to demonstrate the assays. Conclusions: This paper comprises an assay toolbox for identification and characterization of the synthetases and nucleases regulating cellular 2-5A levels. Assays are presented for both enzyme families. The assays can also be used to address a broader cellular role of the OAS enzymes, based on the multiple substrate specificity intrinsic to these proteins. Keywords: 2′-5′ oligoadenylate synthetase (OAS), 2′-5′ oligoadenylate nuclease, 5′-triphosphorylated, 2′-5′-linked oligoadenylate polyribonucleotides (2-5As), 5′-dephosphorylated forms of 2-5As (2-5A core molecules), Enzyme assays
Output: Enzyme assays for synthesis and degradation of 2-5As and other 2′-5′ oligonucleotides
Background: Feline infectious peritonitis (FIP) is a lethal immune-mediated disease caused by feline coronavirus (FCoV). Currently, no therapy with proven efficacy is available. In searching for agents that may prove clinically effective against FCoV infection, five analogous overlapping peptides were designed and synthesized based on the putative heptad repeat 2 (HR2) sequence of the spike protein of FCoV, and the antiviral efficacy was evaluated. Methods: Plaque reduction assay and MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) cytotoxicity assay were performed in this study. Peptides were selected using a plaque reduction assay to inhibit Feline coronavirus infection. The results demonstrated that peptide (FP5) at concentrations below 20 μM inhibited viral replication by up to 97%. The peptide (FP5) exhibiting the most effective antiviral effect was further combined with a known anti-viral agent, human interferon-α (IFN-α), and a significant synergistic antiviral effect was observed. Our data suggest that the synthetic peptide FP5 could serve as a valuable addition to the current FIP prevention methods.
Output: Peptides Corresponding to the Predicted Heptad Repeat 2 Domain of the Feline Coronavirus Spike Protein Are Potent Inhibitors of Viral Infection
Avian infectious bronchitis virus (IBV) is a member of the family Coronaviridae. A binding domain that mediates the attachment of the virus to its receptor has been identified in the S1 protein of prototype IBV strain M41. In this study, we identified this binding domain in a different strain, as well as the cellular proteins that interact with it. First, we expressed the S1 N proteins (residues 19-270) of M41 and another isolate, SCZJ3, and compared the binding capacities of recombinant S1 N -M41 and S1 N -SCZJ3 to host tissues. Protein histochemistry showed that both S1 N -M41 and S1 N -SCZJ3 could bind to lung and kidney, and that recombinant S1 N -SCZJ3 displayed a distinctive staining pattern in the proventriculus. Recombinant S1 N -SCZJ3 was then employed to purify binding-associated proteins in lung, kidney, and proventriculus. Using an affinity chromatography assay, two common bands of about 60 kDa and 70 kDa were obtained from the total tissue proteins. These protein bands were identified by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) as protein disulfide isomerase (PDI) and heat shock protein 70 (HSP70). Finally, infection of chicken embryo kidney (CEK) cells by SCZJ3 was found to be inhibited by anti-HSP70 but not anti-PDI polyclonal antibody. These data indicate that HSP70 is part of the receptor complex of IBV and might help to understand the mechanism of S-mediated cell entry of IBV.
Output: Heat shock protein 70 in lung and kidney of specific-pathogen-free chickens is a receptor-associated protein that interacts with the binding domain of the spike protein of infectious bronchitis virus
Meliacine (MA), an antiviral principle present in partially purified leaf extracts of Melia azedarach L., prevents the development of herpetic stromal keratitis (HSK) in mice by diminishing the viral load in the eye and the severity of lesions caused by a virus-induced immunopathological reaction. The tetranortriterpenoid 1-cinnamoyl-3,11-dihydroxymeliacarpin (CDM), obtained from MA purification, displays anti-herpetic activity and impedes nuclear factor B (NF-B) activation in HSV-1 infected conjunctival cells. To extend our understanding about CDM biological properties, we investigated its anti-HSV-1 activity as well as the effect on NF-B activation and cytokine secretion induced by viral (HSV-1) and no-viral (LPS) stimuli, in corneal cells and macrophages. CDM exerted a potent anti-HSV-1 effect on corneal cells and inhibited NF-B translocation to the nucleus, leading to a decrease in IL-6 production. Besides, CDM seemed to modulate IL-6 and TNF-␣ responses in macrophages, whether they were infected with HSV-1 or stimulated with LPS. However, CDM did not affect NF-B activation in these cells, suggesting that an alternative NF-B cell signaling pathway would be involved in the modulation of cytokine production. We conclude that, in addition to its antiviral effect, CDM would be acting as an immunomodulating compound which would be responsible for the improvement of murine HSK already reported.
Output: A natural tetranortriterpenoid with immunomodulating properties as a potential anti-HSV agent
We report on a study conducted in Guangdong Province, China, to characterize behaviors and perceptions associated with transmission of pathogens with pandemic potential in highly exposed human populations at the animal-human interface. A risk factor/exposure survey was administered to individuals with high levels of exposure to wildlife. Serological testing was performed to evaluate prior infection with several wildlife viral pathogens. Follow up serology was performed on a subset of the cohort as well as close contacts of individuals. 1,312 individuals were enrolled in the study. Contact with a wide range of wildlife species was reported in both occupational and occasional contexts. The overall proportion of individuals seropositive to any of the tested wildlife pathogens was approximately 4.0%. However, persons employed as butchers demonstrated a seropositivity of 9.0% to at least one pathogen of interest. By contrast, individuals working as hunters had lower rates of seropositivity. Among the study population, a number of other behaviors showed correlation with seropositivity, including contact with particular wildlife species such as field rats. These results demonstrate the need to further explore zoonotic risks of particular activities regarding wildlife contact, and to better understand risks of persons working as butchers with wildlife species.
Output: Serologic and behavioral risk survey of workers with wildlife contact in China
Host responses can contribute to the severity of viral infection, through the failure of innate antiviral mechanisms to recognize and restrict the pathogen, the development of intense systemic inflammation leading to circulatory failure or through tissue injury resulting from overly exuberant cell-mediated immune responses. High-throughput genomics methods are now being used to identify the biochemical pathways underlying ineffective or damaging host responses in a number of acute and chronic viral infections. This article reviews recent gene-expression studies of 1918 H1N1 influenza and Ebola hemorrhagic fever in cell culture and animal models, focusing on how genomics experiments can be used to increase our understanding of the mechanisms that permit those viruses to cause rapidly overwhelming infection. Particular attention is paid to how evasion of type I IFN responses in infected cells might contribute to over-activation of inflammatory responses. Reviewing recent research and describing how future studies might be tailored to understand the relationship between the infected cell and its environment, this article discusses how the rapidly growing field of high-throughput genomics can contribute to a more complete understanding of severe, acute viral infections and identify novel targets for therapeutic intervention.
Output: Applications of high-throughput genomics to antiviral research: evasion of antiviral responses and activation of inflammation during fulminant RNA virus infection
Interest in bat-related viruses has increased considerably during the last decade, leading to the discovery of a rising number of new viruses in several bat species. Poxviridae are a large, diverse family of DNA viruses that can infect a wide range of vertebrates and invertebrates. To date, only a few documented detections of poxviruses have been described in bat populations on three different continents (America, Africa, and Australia). These viruses are phylogenetically dissimilar and have diverse clinical impacts on their hosts. Herein, we report the isolation, nearly complete genome sequencing, and annotation of a novel poxvirus detected from an insectivorous bat (Hypsugo savii) in Northern Italy. The virus is tentatively named Hypsugopoxvirus (HYPV) after the bat species from which it was isolated. The nearly complete genome size is 166,600 nt and it encodes 161 genes. Genome analyses suggest that HYPV belongs to the Chordopoxvirinae subfamily, with the highest nucleotide identity (85%) to Eptesipoxvirus (EPTV) detected from a microbat Eptesicus fuscus in WA, USA, in 2011. To date, HYPV represents the first poxvirus detected in bats in Europe; thus, its viral ecology and disease associations should be investigated further.
Output: Hypsugopoxvirus: A Novel Poxvirus Isolated from Hypsugo savii in Italy
Clinical data on MERS-CoV infections are scarce. We report epidemiological, demographic, clinical, and laboratory characteristics of 47 cases of MERS-CoV infections, identify knowledge gaps, and defi ne research priorities. We abstracted and analysed epidemiological, demographic, clinical, and laboratory data from confi rmed cases of sporadic, household, community, and health-care-associated MERS-CoV infections reported from Saudi Arabia between Sept 1, 2012, and June 15, 2013. Cases were confi rmed as having MERS-CoV by real-time RT-PCR. Findings 47 individuals (46 adults, one child) with laboratory-confi rmed MERS-CoV disease were identifi ed; 36 (77%) were male (male:female ratio 3·3:1). 28 patients died, a 60% case-fatality rate. The case-fatality rate rose with increasing age. Only two of the 47 cases were previously healthy; Interpretation Disease caused by MERS-CoV presents with a wide range of clinical manifestations and is associated with substantial mortality in admitted patients who have medical comorbidities. Major gaps in our knowledge of the epidemiology, community prevalence, and clinical spectrum of infection and disease need urgent defi nition. Funding None. 13: 752-61
Output: Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study
The photocatalytic activity of TiO 2 was enhanced by Ag metal doping. TiO 2 and Ag-doped TiO 2 were coated on porous polyurethane (PU) using C-Si-O-Ti bonds. Increased adsorption ability of the photocatalyst was due to the porosity of the PU. Removal of E. coli from an aerosol was only by adsorption with PU and TiO 2 /PU. Under visible light, E. coli was removed by adsorption and photo-oxidation with Ag-TiO 2 /PU. We investigated a novel approach by synthesizing an integrated material, which could act as both adsorbent and photocatalytic material, for bioaerosol purification under visible light conditions. Ag was used as a dopant agent to enhance photocatalytic activity of TiO 2 , leading to high photocatalytic activity of the doped TiO 2 even under visible light. Under visible light, the doped TiO 2 photocatalyst could produce oxy radicals, oxidative agents, that participate in oxidation reactions to decompose important organic components of bacteria, leading to death or removal of bacteria from an aerosol. Adsorption property was integrated into the enhanced TiO 2 photocatalyst by using polyurethane (PU), a honeycomb structure material, as a substrate for coating process of the doped TiO 2 . Three materials including pristine PU, TiO 2 coating on PU (TiO 2 /PU), and Ag-doped TiO 2 coating on PU (Ag-TiO 2 /PU) were used to remove Escherichia coli in an aerosol under visible light. Under dark conditions, the removal capacities of E. coli in the aerosol by PU, TiO 2 /PU, and Ag-TiO 2 /PU were 1.2 Â 10 5 , 2.7 Â 10 5 , and 6.2 Â 10 5 (CFU/cm 3 ), respectively. Under visible light irradiation, the removal capacities of E. coli in an aerosol by PU, TiO 2 /PU, and Ag-TiO 2 /PU were 1.2 Â 10 5 , 2.7 Â 10 5 , and 1.8 Â 10 6 (CFU/cm 3 ), respectively. The improvement of the removal capacity by TiO 2 /PU and Ag-TiO 2 /PU, versus PU, is due to adsorption alone and the combination of adsorption plus photocatalytic activity, respectively.
Output: Novel integrated approach of adsorption and photo-oxidation using Ag-TiO 2 /PU for bioaerosol removal under visible light
Computer analysis of the intrinsic membrane protein, myelin proteolipid, shows strong sequence similarities between the putative extramembranc segments of the proteolipid protein and a number of viral proteins, several of which infect humans. These similarities are even more striking than those reported previously between viral proteins and the encephalitogenic myelin basic protein (MBP). These findings, along with other reports of molecular mimicry by viruses, suggest that immunological cross-reactions between virusinduced antibodies or T-cells and analogous antigenic determinants (epitopes) in myelin protcolipid could be involved in the pathophysiology of multiple sclerosis or post-infectious dcmyclinating syndromes. Proteolipid prolein Multiple sclerosis Viral protein Myelin basic protein Amino acid sequenee Sequence homology
Output: Analogous amino acid sequences in myelin protcolipid and viral proteins
Understanding how disease affects commercial production is imperative for pig producers to quantify its full impact on pig performance, carcass quality, and net returns. The objective of this experiment was to assess the productivity and economic importance of naturally occurring health challenges (HC) under commercial conditions. Three 1,000 pig grow-finish facilities received 936 pigs each. The experimental period started approximately 34 d post placement at an average start BW of 13.1 ± 0.2 kg.
Output: Impact of health challenges on pig growth performance, carcass characteristics, and net returns under commercial conditions
The Scutellaria species (Lamiaceae) is used as a source of flavonoids to treat a variety of diseases in traditional medicine. In spite of many reports about the cytotoxic and antitumor effects of some species of this genus, anticancer researches on one of the Iranian species S. litwinowii have not yet been conducted. The cytotoxic properties of total methanol extract of S. litwinowii and its fractions were investigated on different cancer cell lines including AGS, HeLa, MCF-7, PC12 and NIH 3T3. Meanwhile, the role of apoptosis in this toxicity was explored. The cells were cultured in DMEM medium and incubated with different concentrations of herb plant extracts. Cell viability was quantitated by MTT assay. Apoptotic cells were determined using propidium iodide staining of DNA fragmentation by flow cytometry (sub-G1 peak). Scutellaria litwinowii inhibited the growth of malignant cells in a dose-dependent manner. Among solvent fractions of S. litwinowii, the methylene chloride fraction was found to be more toxic compared to other fractions. The IC 50 values of this fraction against AGS, HeLa, MCF-7 and PC12 cell lines after 24 h were determined, 121.2 ± 3.1, 40.9 ± 2.5, 115.9 ± 3.5 and 64.5 ± 3.4 μg/ml, respectively. Scutellaria litwinowii induced a sub-G1 peak in the flow cytometry histogram of treated cells compared to control cells indicating that apoptotic cell death is involved in S. litwinowii toxicity. Scutellaria litwinowii exerts cytotoxic and proapototic effects in a variety of malignant cell lines and could be considered as a potential chemotherapeutic agent in cancer treatment.
Output: Original Article Analyzing Cytotoxic and Apoptogenic Properties of Scutellaria litwinowii Root Extract on Cancer Cell Lines