niryuu/sni-each-converted huggingface dataset:
The avalanche of newly found protein sequences in the postgenomic era has motivated and challenged us to develop an automated method that can rapidly and accurately predict the localization of an uncharacterized protein in cells because the knowledge thus obtained can greatly speed up the process in finding its biological functions. However, it is very difficult to establish such a desired predictor by acquiring the key statistical information buried in a pile of extremely complicated and highly variable sequences. In this paper, based on the concept of the pseudo amino acid composition (Chou, K. C. PROTEINS: Structure, Function, and Genetics, 2001, 43: 246-255), the approach of cellular automata image is introduced to cope with this problem. Many important features, which are originally hidden in the long amino acid sequences, can be clearly displayed through their cellular automata images. One of the remarkable merits by doing so is that many image recognition tools can be straightforwardly applied to the target aimed here. High success rates were observed through the self-consistency, jackknife, and independent dataset tests, respectively.
Output: Using cellular automata images and pseudo amino acid composition to predict protein subcellular location
Phenomenon of RNA-induced gene silencing is a highly conservative mechanism among eukaryotic organisms. Several classes of small RNAs (siRNAs and miRNAs) 21-25 nt in length, which play a significant role in the processes of development of an organism, occurred important components of antiviral defence in animals and plants. This review shortly describes the main stages of gene silencing mechanism, features of antiviral RNA silencing in plants, invertebrates, mammals, ways of suppression of RNA-interference by viruses, as well as possible approaches of utilization of abovementioned phenomenon for struggling against viral infections.
Output: 63 1 Abbreviations: PTGS-posttranscriptional gene silencing dsRNA-double stranded RNA nt-nucleotide siRNA-small interfering RNA miRNA-micro RNA RISC-RNA-induced silencing complex RdRP-RNA-dependent RNA polymerase TMV-tobacco mosaic virus VIGS-virus induced gene silencing CP-coat protein TEV-tobacco etch virus VSV-vesicular stomatitis virus PFV-1-primate foamy virus 1 GFP-green fluorescent protein EBV-Epstein-Barr virus PVY-potato virus Y PVX-potato virus X ORSV-Odontoglossum rings pot virus HIV-Human immunodeficiency virus HBV-Hepatitis B virus HCV-Hepatitis C virus SARS-CoV-Severe Acute Respiratory Syndrome- Coronavirus CMV-Cucumber mosaic virus ZYMV-Zucchini mosaic virus WMV-2-Watermelon mosaic virus-2 TSWV-Tomato wilt spot virus TCSV-Tomato chlorotic spot virus PRSV-Peanut ring spot virus Role of siRNAs and miRNAs in the Processes of RNA-Mediated Gene Silencing during Viral Infections 1
The worldwide outbreak of the swine-origin 2009 H1N1 influenza A virus (IAV) and an increasing number of influenza cases caused by a highly pathogenic avian influenza (HPAI) H5N1 have accelerated the need to develop vaccines and antiviral agents against IAVs. Among various antivirals, neutralizing monoclonal antibodies (mAbs) are considered important passive therapeutics having an immediate effect against viral pathogens. Here we report a pseudovirus neutralization assay for rapid screening of neutralizing mAbs targeting hemagglutinin (HA) of H5N1 and H1N1 IAV. In this study, we generated six pseudoviruses with an HIV-1 backbone, respectively, expressing HA of four clades of H5N1 IAV and the 2009 epidemic H1N1 IAV. The resulting pseudoviruses were able to infect a variety of human and non-human cells, with 293T cells from human kidney as the most susceptible target cells. Using the established pseudovirus neutralization assay, we showed that three of ten selected mAbs specific to HA could potently neutralize infection of a pseudovirus bearing HA from the homologous IAV A/VietNam/1194/ 2004(H5N1) strain. This was highly consistent with the result of a microneutralization assay testing the same strain of a live IAV. Since the pseudovirus neutralization assay does not involve an infectious virus and can be performed without the requirement of a biosafety-3 laboratory, it may be applied for safe and rapid screening of neutralizing mAbs and antiviral agents targeting HA of IAVs.
Output: Development of a safe and convenient neutralization assay for rapid screening of influenza HA-specific neutralizing monoclonal antibodies
induced host immune response , but the relative contribution of each remains largely unknown. For example , C57BL/6 (B6) mice infected with mouse hepatitis virus (JHM strain , JHMV) develop severe encephalitis , with death occurring within 7 days. Here, we show that the host response to a single JHMVspecific immunodominant CD4 T-cell epitope is critical for severe disease. We engineered a recombinant JHMV with mutations in the immunodominant CD4 T-cell epitope (rJ.M Y135Q ). Infection of naïve B6 mice with this virus resulted in mild disease with no mortality. However , introduction of a CD4 T-cell epitope from Listeria monocytogenes into rJ.M Y135Q generated a highly virulent virus. The decrease in disease severity was not due to a switch from Th1 to Th2 predominance in rJ.M Y135Q -infected mice , an effect on CD8 T-cell function , or differential expression of tumor necrosis factor-␣ by JHMV-specific CD4 T cells. These results show that the response to a single virus-specific CD4 T-cell epitope may contribute to a pathogenic host response in the setting of acute viral disease and that abrogation of this response ameliorates clinical disease without diminishing virus clearance.
Output: Pathogenic Role for Virus-Specific CD4 T Cells in Mice with Coronavirus-Induced Acute Encephalitis
Alphaviruses are members of the Togaviridae family and are grouped into two categories: arthritogenic and encephalitic. Arthritogenic alphavirus infections, as the name implies, are associated with arthritic outcomes while encephalitic alphavirus infections can lead to encephalitic outcomes in the infected host. Of the non-structural proteins (nsPs) that the viruses code for, nsP3 is the least understood in terms of function. Alphavirus nsP3s are characterized by regions with significantly conserved domain structure along with regions of high variability. Interactions of nsP3 with several host proteins have been documented including, stress granule-related proteins, dead box proteins, heat shock proteins, and kinases. In some cases, in addition to the interaction, requirement of the interaction to support infection has been demonstrated. An understanding of the proteomic network of nsP3 and the mechanisms by which these interactions support the establishment of a productive infection would make alphavirus nsP3 an interesting target for design of effective medical countermeasures.
Output: Interactions of Alphavirus nsP3 Protein with Host Proteins
The methods of repeated immunization with inactivated vaccines have been used widely to increase antibody protection against infectious bronchitis virus (IBV). However, compared with DNA vaccines, these methods usually induce poor cellular responses. In the present study, specific pathogen-free (SPF) chickens were immunized intramuscularly with a DNA vaccine carrying the main IBV structural genes (pVAX1-S1, pVAX1-M, and pVAX1-N, respectively) and boosted with the IBV M41 strain inactivated vaccine to assess whether such a new strategy could enhance the immune responses against IBV. The protection efficacy of the DNA vaccine carrying different structural genes for priming was evaluated further. The chickens were immunized primely on day 7 and boosted 2 weeks later. After that, distribution of the DNA vaccine in vivo, the percentage of CD4+CD3+ and CD8+CD3+ subgroups of peripheral blood T-lymphocytes, and the specific IgG and virus neutralizing antibodies were measured. Chickens were then challenged by the nasal-ocular route with the IBV M41 strain 4 weeks after booster immunization. The results demonstrated that priming with a DNA vaccine encoding nucleocapsid protein (pVAX1-N) and boosting with the inactivated IBV vaccine led to the dramatic augmentation of humoral and cellular responses, and provided up to 86.7% rate of immune protection, providing an effective approach to protect chickens from IBV.
Output: Priming with a DNA vaccine and boosting with an inactivated vaccine enhance the immune response against infectious bronchitis virus
Natural human exhalation flows such as coughing, sneezing and breathing can be considered as 'jet-like' airflows in the sense that they are produced from a single source in a single exhalation effort, with a relatively symmetrical, conical geometry. Although coughing and sneezing have garnered much attention as potential, explosive sources of infectious aerosols, these are relatively rare events during daily life, whereas breathing is necessary for life and is performed continuously. Real-time shadowgraph imaging was used to visualise and capture high-speed images of healthy volunteers sneezing and breathing (through the nose -nasally, and through the mouth -orally). Six volunteers, who were able to respond to the pepper sneeze stimulus, were recruited for the sneezing experiments (2 women: 27.566.36 years; 4 men: 29.25610.53 years). The maximum visible distance over which the sneeze plumes (or puffs) travelled was 0.6 m, the maximum sneeze velocity derived from these measured distances was 4.5 m/s. The maximum 2-dimensional (2-D) area of dissemination of these sneezes was 0.2 m 2 . The corresponding derived parameter, the maximum 2-D area expansion rate of these sneezes was 2 m 2 /s. For nasal breathing, the maximum propagation distance and derived velocity were 0.6 m and 1.4 m/s, respectively. The maximum 2-D area of dissemination and derived expansion rate were 0.11 m 2 and 0.16 m 2 /s, respectively. Similarly, for mouth breathing, the maximum propagation distance and derived velocity were 0.8 m and 1.3 m/ s, respectively. The maximum 2-D area of dissemination and derived expansion rate were 0.18 m 2 and 0.17 m 2 /s, respectively. Surprisingly, a comparison of the maximum exit velocities of sneezing reported here with those obtained from coughing (published previously) demonstrated that they are relatively similar, and not extremely high. This is in contrast with some earlier estimates of sneeze velocities, and some reasons for this difference are discussed.
Output: Airflow Dynamics of Human Jets: Sneezing and Breathing -Potential Sources of Infectious Aerosols
Background. Human coronavirus NL63 (HCoV-NL63) is a globally endemic pathogen causing mild and severe respiratory tract infections with reinfections occurring repeatedly throughout a lifetime. Methods. Nasal samples were collected in coastal Kenya through community-based and hospital-based surveillance. HCoV-NL63 was detected with multiplex real-time reverse transcription PCR, and positive samples were targeted for nucleotide sequencing of the spike (S) protein. Additionally, paired samples from 25 individuals with evidence of repeat HCoV-NL63 infection were selected for whole-genome virus sequencing. Results. HCoV-NL63 was detected in 1.3% (75/5573) of child pneumonia admissions. Two HCoV-NL63 genotypes circulated in Kilifi between 2008 and 2014. Full genome sequences formed a monophyletic clade closely related to contemporary HCoV-NL63 from other global locations. An unexpected pattern of repeat infections was observed with some individuals showing higher viral titers during their second infection. Similar patterns for 2 other endemic coronaviruses, HCoV-229E and HCoV-OC43, were observed. Repeat infections by HCoV-NL63 were not accompanied by detectable genotype switching. Conclusions. In this coastal Kenya setting, HCoV-NL63 exhibited low prevalence in hospital pediatric pneumonia admissions. Clade persistence with low genetic diversity suggest limited immune selection, and absence of detectable clade switching in reinfections indicates initial exposure was insufficient to elicit a protective immune response.
Output: Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya
Individuals use social network sites (SNSs) as an effective tool for communicating relevant information with others during the outbreak of infectious diseases. However, little is known about the underlying mechanism through which communicative behaviors influence preventive behaviors. Thus, in the context of Middle East respiratory syndrome (MERS) in South Korea, this study investigated how two communicative behaviors (message expression and reception) in SNSs affected the communicators' intentions to engage in MERS-preventive behaviors. Using data collected from a nationally representative panel survey of 1000 Korean adults aged 19 or older, we examined a theoretical expression and reception effects model. Results support the presence of effects from expressing and receiving MERS-related information via SNSs and their underlying mechanism during South Korea's MERS outbreak. Public health officials and communication professionals should actively use SNS communication in coping with public health crisis caused by emerging infectious diseases.
Output: The effects of SNS communication: How expressing and receiving information predict MERS-preventive behavioral intentions in South Korea
Chemokines have been demonstrated to serve an important role in a variety of diseases, particularly in tumor progression. There have been numerous studies that have reported that T cells serve major roles in tumor progression. However, the function of CXC motif chemokine ligand 9 (CXCL9) in prostate cancer remains unknown. The present study aimed to investigate the role of CXCL9 in prostate cancer. A prostate cancer mouse model was generated by treating C57/BL-6 and B6.Cg-Selplgtm1Fur/J mice with 3,2'-dimethyl 4-aminobiphenyl (DMAB). Hematoxylin and eosin staining detected the histopathological alterations of mouse prostate tissues. Immunohistochemistry (IHC) staining determined cell proliferation of the mice. Flow cytometry was used to detect the alterations of T cells in C57+DMAB or CXCL9+DMAB mice. Immunofluorescence revealed that there was positive expression of interleukin-6 (IL-6) and transforming growth factor (TGF)-β in the mouse tissues. The survival rates of C57+DMAB and CXCL9+DMAB mice was analyzed. The association of CXCL9 expression and clinical stages was also evaluated. Results revealed that prostate cancer pathology and cell proliferation in CXCL9+DMAB mice were significantly greater compared with the C57+DMAB mice. Compared with C57+DMAB mice, the number of T cells in peripheral blood and spleen of CXCL9+DMAB mice was significantly reduced. IHC demonstrated that the expression of IL-6 and TGF-β was significantly downregulated in the CXCL9+DMAB mice. The survival rate of CXCL9+DMAB mice was significantly decreased compared with the C57+DMAB mice. In addition, reverse transcription-quantitative polymerase chain reaction analysis demonstrated that CXCL9 mRNA expression in clinical samples was positively associated with clinical pathological stages of prostate cancer. In conclusion, CXCL9 may promote prostate cancer progression via inhibition of cytokines from T cells. ST and YG conceived and designed the experiments; ST, FS, YL and YG performed the experiments; ST, KW and YG analyzed the data; ST, KW, FS and YG contributed reagents/materials/analysis tools and ST and YG wrote the manuscript. Animal experiments were approved by the Medical Ethics Committee of Linyi People's Hospital. These tissue samples were collected with the consent of the patients and the study was approved by the Medical Ethics Committee of the Linyi People's Hospital.
Output: CXCL9 promotes prostate cancer progression through inhibition of cytokines from T cells
Coronavirus Autophagy ER stress Unfolded protein response Mitogen-activated protein kinase A B S T R A C T Coronavirus infection induces the generation of autophagosomes, and certain host proteins regulating cellular autophagy are hijacked by some coronaviruses to facilitate the formation of double membrane vesicles. However, mechanisms underlying coronavirus-induced autophagy remain largely unknown. In this study, we demonstrate that autophagosome formation and apparent autophagic flux are induced in cells infected with infectious bronchitis virus (IBV)a gammacoronavirus. Notably, IBV-induced autophagy was dependent on autophagy related 5 (ATG5) but not beclin1 (BECN1), although both are essential proteins in the canonical autophagy pathway. Moreover, the ER stress sensor inositol requiring enzyme 1 (IRE1), but not its substrate Xbox protein 1 (XBP1), was also essential for the induction of autophagy during IBV infection. Finally, the antiapoptotic extracellular signal-regulated kinase 1/2 (ERK1/2) also contributed to IBV-induced autophagy. Our findings add new knowledge to the regulatory mechanisms governing coronavirus-induced autophagy, highlighting an extensive cross-talk among cellular signaling pathways during coronavirus infection.
Output: The ER stress sensor IRE1 and MAP kinase ERK modulate autophagy induction in cells infected with coronavirus infectious bronchitis virus
We describe here the design, synthesis, molecular modeling, and biological evaluation of a series of small molecule, nonpeptide inhibitors of SARS-CoV PLpro. Our initial lead compound was identified via high-throughput screening of a diverse chemical library. We subsequently carried out structure-activity relationship studies, and optimized the lead structure to potent inhibitors that have shown antiviral activity against SARS-CoV infected Vero E6 cells. Based upon the X-ray crystal structure of one of the potent inhibitors 24-bound to SARS-CoV PLpro, a drug-design template was created. Our structure-based modification led to the design of a more potent inhibitor, 2 (enzyme IC 50 = 0.46 μM; antiviral EC 50 = 12.5 μM). Interestingly, its methylamine derivative 49 displayed good enzyme inhibitory potency (IC 50 = 1.3 μM) and most potent SARS antiviral activity (EC 50 = 2.5 μM) in the series. We have carried out computational docking studies and generated a predictive 3D-QSAR model for SARS-CoV PLpro inhibitors.
Output: Structure-Based Design, Synthesis, and Biological Evaluation of a Series of Novel and Reversible Inhibitors for the Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease
Most biological activities of antibodies depend on their ability to engage Receptors for the Fc portion of immunoglobulins (FcRs) on a variety of cell types. As FcRs can trigger positive and negative signals, as these signals control several biological activities in individual cells, as FcRs are expressed by many cells of hematopoietic origin, mostly of the myeloid lineage, as these cells express various combinations of FcRs, and as FcR-expressing cells have different functional repertoires, antibodies can exert a wide spectrum of biological activities. Like B and T Cell Receptors (BCRs and TCRs), FcRs are bona fide immunoreceptors. Unlike BCRs and TCRs, however, FcRs are immunoreceptors with an adaptive specificity for antigen, with an adaptive affinity for antibodies, with an adaptive structure and with an adaptive signaling. They induce adaptive biological responses that depend on their tissue distribution and on FcR-expressing cells that are selected locally by antibodies. They critically determine health and disease. They are thus exquisitely adaptive therapeutic tools.
Output: Fc Receptors as Adaptive Immunoreceptors
Controlling airborne microorganisms has become increasingly important with increase in human indoor activities, epidemic disease outbreaks, and airborne pathogen transmission. Treatments using antimicrobial nanoparticles have shown promise because of the high surface-to-volume ratio of nanoparticles compared to their bulk counterparts, and their unique physical and chemical properties. In this study, hybrid nanostructures of multiwalled carbon nanotubes (MWCNTs) coated with antimicrobial, natural product (NP) nanoparticles were synthesized using a twin-head electrospray system (THES). The coated nanoparticles were then used in antimicrobial air filters to increase their antimicrobial efficiency. Electrosprayed droplets were converted to NP nanoparticles and MWCNTs through ethanol evaporation. Oppositely charged NP nanoparticles and MWCNTs were coagulated via Coulombic collisions to form hybrid nanoparticles that were deposited continuously onto an air filter medium. The size distribution and composition of the hybrid NP/MWCNT particles were characterized using a wide-range particle spectrometer (WPS) and transmission electron microscope (TEM). The concentration of hybrid NP/MWCNT nanoparticles was lower than that of NP nanoparticles but higher than that of MWCNTs and showed a bimodal size distribution with peak diameters of 21.1 and 49 nm. TEM analyses confirmed that the NP nanoparticles were attached to the MWCNT surface with a density of $ 4-9 particles/MWCNT. When deposited onto the filter medium, NP/MWCNT particles formed dendrites on the filter's fiber surface. The filtration efficiency and pressure drop of the NP/MWCNT-coated filters were higher than those of pristine, NP nanoparticles-coated or MWCNTs-coated filters. The hybrid filter also exhibited stronger antimicrobial activity than those of NP or MWCNT-coated filters at identical deposited volumes (1.1 Â 10 -2 cm 3 / cm 2 filter ). Ninety-five percent of the tested bacterial aerosols were inactivated on the NP/ MWCNTs filter while only o70% were inactivated on NP-or MWCNT-coated filters.
Output: Synthesis of hybrid carbon nanotube structures coated with Sophora flavescens nanoparticles and their application to antimicrobial air filtration
We introduce a new approach to investigate problem of DNA sequence alignment. The method consists of three parts: (i) simple alignment algorithm, (ii) extension algorithm for largest common substring, (iii) graphical simple alignment tree (GSA tree). The approach firstly obtains a graphical representation of scores of DNA sequences by the scoring equation R 0 Ã RÀS 0 Ã SÀT 0 Ã ða þ bkÞ. Then a GSA tree is constructed to facilitate solving the problem for global alignment of 2 DNA sequences. Finally we give several practical examples to illustrate the utility and practicality of the approach. Crown
Output: New method for global alignment of 2 DNA sequences by the tree data structure
Delineation of the intricacies of protein function from macromolecular structure constitutes a continual obstacle in the study of cell and pathogen biology. Structure-based phylogenetic analysis has emerged as a powerful tool for addressing this challenge, allowing the detection and quantification of conserved architectural properties between proteins, including those with low or no detectable sequence homology. With a focus on viral protein structure, we highlight how a number of investigations have utilized this powerful method to infer common functionality and ancestry.
Output: Unraveling virus relationships by structure-based phylogenetic classification
Background: Severe pneumonia is responsible for great mortality and morbidity worldwide, and early-applied effective antiinfective therapy can improve the prognosis of patients. However, identification of infectious agents in severe pneumonia remains a major challenge so far. In this study, the potential utility of transmission electron microscopy (TEM) in detecting nonbacterial pathogens in patients with severe pneumonia was retrospectively evaluated. Materials and Methods: A total of 106 patients diagnosed with severe pneumonia at our hospital from September 2015 to December 2017 were included, and their baseline clinical characteristics were collected. Nonbacterial infectious agents detected by TEM in bronchoalveolar lavage fluid (BALF) and serological tests were summarized. The detection rates were further compared between TEM and serological tests. Results: BALF examination under the transmission electron microscope revealed 24 viruses, 16 mycoplasmas, 18 chlamydia, 2 fungi and 74 bacteria in 99 samples, among which 61 samples were mixed infections. The combined use of serological tests and TEM significantly improved the detection rate of nonbacterial infectious agents in patients with severe pneumonia. Conclusions: Our data support that implementation of TEM could improve the sensitivity for detecting viruses, atypical pathogens and mixed infections in BALF from patient of severe pneumonia. Therefore, TEM may be used as an auxiliary diagnostic method of other microbiological tests in severe pneumonia.
Output: Transmission Electron Microscopy Improves the Diagnostic Sensitivity in Nonbacterial Etiology of Severe Pneumonia: A Retrospective Study
Porcine epidemic diarrhea, a disastrous gastrointestinal disease, causes great financial losses due to its high infectivity, morbidity and mortality in suckling piglets despite the development and application of various vaccines. In this study, high-throughput sequencing was used to explore differences in the intestinal microbiota between uninfected piglets and piglets infected with porcine epidemic diarrhea virus (PEDV). The results revealed that the small intestinal microbiota of suckling piglets infected with PEDV showed low diversity and was dominated by Proteobacteria (49.1%). Additionally, the composition of the small intestinal microbiota of sucking piglets infected with PEDV showed marked differences from that of the uninfected piglets. Some of the taxa showing differences in abundance between uninfected piglets and piglets infected with PEDV were associated with cellular transport and catabolism, energy metabolism, the biosynthesis of other secondary metabolites, and amino acid metabolism as determined through the prediction of microbial function based on the bacterial 16S rRNA gene. Therefore, adjusting the intestinal microbiota might be a promising method for the prevention or treatment of PEDV.
Output: Differences in the intestinal microbiota between uninfected piglets and piglets infected with porcine epidemic diarrhea virus
a b s t r a c t Background: Coronavirus 229E (HCoV-229E), one of the causes of the common cold, exacerbates chronic obstructive pulmonary disease (COPD) and bronchial asthma. Longacting muscarinic antagonists and b 2 -agonists and inhaled corticosteroids inhibit the exacerbation of COPD and bronchial asthma caused by infection with viruses, including Please cite this article as: Yamaya M et al., Inhibitory effects of glycopyrronium, formoterol, and budesonide on coronavirus HCoV-229E replication and cytokine production by primary cultures of human nasal and tracheal epithelial cells, Respiratory Investigation, https:// Available online xxx Keywords: Airway epithelial cells HCoV-229E CD13 Long-acting b 2 agonist Long-acting muscarinic antagonist HCoV-229E. However, the effects of these drugs on HCoV-229E replication and infectioninduced inflammation in the human airway are unknown. Methods: Primary human nasal (HNE) and tracheal (HTE) epithelial cell cultures were infected with HCoV-229E. Results: Pretreatment of HNE and HTE cells with glycopyrronium or formoterol decreased viral RNA levels and/or titers, the expression of the HCoV-229E receptor CD13, the number and fluorescence intensity of acidic endosomes where HCoV-229E RNA enters the cytoplasm, and the infection-induced production of cytokines, including IL-6, IL-8, and IFN-b. Treatment of the cells with the CD13 inhibitor 2 0 2 0 -dipyridyl decreased viral titers. Pretreatment of the cells with a combination of three drugs (glycopyrronium, formoterol, and budesonide) exerted additive inhibitory effects on viral titers and cytokine production. Pretreatment of HNE cells with glycopyrronium or formoterol reduced the susceptibility to infection, and pretreatment with the three drugs inhibited activation of nuclear factorkappa B p50 and p65 proteins. Pretreatment with formoterol increased cAMP levels and treatment with cAMP decreased viral titers, CD13 expression, and the fluorescence intensity of acidic endosomes. Conclusions: These findings suggest that glycopyrronium, formoterol, and a combination of glycopyrronium, formoterol, and budesonide inhibit HCoV-229E replication partly by inhibiting receptor expression and/or endosomal function and that these drugs modulate infection-induced inflammation in the airway.
Output: Inhibitory effects of glycopyrronium, formoterol, and budesonide on coronavirus HCoV-229E replication and cytokine production by primary cultures of human nasal and tracheal epithelial cells
After infecting the Vero E6 cells by nasal/throat swabs collected from SARS patients, we studied the SARS-associated virus by electron microscopy and molecular biological technique. The results show that the diameter of newly isolated virus is about 50nm without envelope or 100 nm with envelope. The virus was proved to be a new coronavirus by RT-PCR and it responded positively to convalescent-phase serum specimen from SARS patients, which is the evidence that this new virus is etiologically linked to the outbreak of SARS. The morphogenesis and distribution of the virus are also discussed in this article.
Output: Morphology and Morphogenesis of Severe Acute Respiratory Syndrome (SARS)-associated Virus
MRNA2 of the arteriviruses lactate dehydrogenase-elevating virus (LDV) and equine arteritis virus (EAV) encodes two proteins that are read in different frames, an about 26 kDa minor envelope glycoprotein and an about 8 kDa protein that lacks N-glycosylation sites and a signal peptide, but possesses a central hydrophobic segment. Recent studies have shown that both proteins of EAV are translated from mRNA 2 in EAV infected BHK cells, that the 8 kDa protein is membrane associated and that small amounts of it are recovered in purified virions (Snijder, E.J., van Tol, H., Pederson, K.W., Raamsman, M.J.B., de Vries, A.A.F., 1999. Identification of a novel structural protein of arteriviruses. J. Virol. 73, 6335-6345). The authors concluded that the 8 kDa protein is another arterivirus envelope protein and designated it E protein. However, we have not detected a significant level of an 8 kDa protein in LDV virions and thus conclude that it is not a structural virion component.
Output: An ORF-2a protein is not present at a significant level in virions of the arterivirus lactate dehydrogenase-elevating virus
Dengue is the commonest arboviral disease of humans. An early and accurate diagnosis of dengue can support clinical management, surveillance and disease control and is central to achieving the World Health Organisation target of a 50% reduction in dengue case mortality by 2020. Methods 5729 children with fever of <72hrs duration were enrolled into this multicenter prospective study in southern Vietnam between 2010-2012. A composite of gold standard diagnostic tests identified 1692 dengue cases. Using statistical methods, a novel Early Dengue Classifier (EDC) was developed that used patient age, white blood cell count and platelet count to discriminate dengue cases from non-dengue cases. The EDC had a sensitivity of 74.8% (95%CI: 73.0-76.8%) and specificity of 76.3% (95%CI: 75.2-77.6%) for the diagnosis of dengue. As an adjunctive test alongside NS1 rapid testing, sensitivity of the composite test was 91.6% (95%CI: 90.4-92.9%). We demonstrate that the early diagnosis of dengue can be enhanced beyond the current standard of care using a simple evidence-based algorithm. The results should support patient management and clinical trials of specific therapies. Dengue is a very common acute infectious disease in the tropical world. Health care professionals are able to better care for dengue patients if they can make an early diagnosis and make a plan for case management. This current study investigated fever in 5729 children in Vietnam with 3 days or less of fever and identified 1692 dengue cases using advanced, gold standard methods. We systematically collected a range of medical and laboratory findings on each patient when they entered the study and used statistical tools to determine if these medical and laboratory findings could enable early diagnosis, independent of sophisticated, gold-standard laboratory tests. Our results, called the Early Dengue Classifier, had performance characteristics suggesting it could improve the diagnostic proficiency of health care professionals. However the performance of the Early Dengue Classifier is not perfect and likely will not change the practice of experienced doctors in dengue endemic settings. Our study highlights the need for 2 nd generation, easy-to-use rapid diagnostic tests that can accurately diagnose dengue in the first few days of fever.
Output: Tien Giang Provincial Hospital, My Tho, Tien Giang Province, Vietnam, 6 Dong Nai Children's Hospital
Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell environment and enhance human health. Synthetic biology devices contribute not only to improve our understanding of disease mechanisms, but also provide novel diagnostic tools. Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs. The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already pointed out during a lecture delivered at Kuwait University in 2005. Of two approaches to synthetic biology, top-down and bottom-up, the latter is more relevant to the development of personalized medicines as it provides more flexibility in constructing a partially synthetic cell from basic building blocks for a desired task.
Output: E-Mail Synthetic Biology and Personalized Medicine
To identify the potential B-cell antigenic epitopes within the N-terminus of SARS-CoV (SARSassociated coronavirus, SARS-CoV) M protein and characterize monoclonal antibody (MAb) against the protein as well as its recognizing region, we expressed and purified a portion of SARS-CoV M protein (amino acid 1-43) in Escherichia coli (E. coli). By using Western blot and enzyme-linked immunosorbent assay (ELISA), we showed that the purified recombinant M protein could be recognized by four SARS-CoV-positive human sera even when those sera were 12,800-fold diluted. Furthermore, we characterized one representative IgG2 MAb, 3H9, which exhibited a strong immunoreaction to both recombinant M protein and native viral protein of SARS-CoV. We found a B-cell antigenic epitope located between amino acid 1-15 and defined the MAb recognizing region within amino acid 16-28 of M. These findings not only suggest that both recombinant M protein and its specific MAbs may be used as the diagnostic reagents for SARS, but also provide a potential target site for the design of an epitope-based vaccine against SARS.
Output: Identification of a B-cell antigenic epitope at the N-terminus of SARS-CoV M protein and characterization of monoclonal antibody against the protein
Mice aged 1, 4 or 8 weeks were inoculated with haemagglutinating encephalomyelitis virus (HEV), strain 67N, by the intracerebral (i.c.), intranasal (i.n.), intraperitoneal (i.p.), subcutaneous (s.c.), intravenous (i.v.) or oral route, with different doses. In 1-week-old mice, mortality and mean time to death were mostly the same regardless of the inoculation route, except for the oral route, which appeared to be the least effective. The virus killed 4-week-old mice readily by all routes of inoculation except the oral, and 8-weekold mice by i.c., i.n. or s.c. inoculation. In descending order of efficacy, the routes of HEV infection were: i.c., i.n., s.c., i.p., i.v. and oral. To follow the spread of HEV from peripheral nerves to the central nervous system (CNS), the virus was inoculated subcutaneously into the right hind leg of 4-week-old mice. The virus was first detected in the spinal cord on day 2, and in the brain on day 3. The brain titres became higher than those of the spinal cord, reaching a maximum of 10 7 PFU/0.2 g when the animals were showing CNS signs. Viral antigen was first detected immunohistochemically in the lumbar spinal cord and the dorsal root ganglion ipsilateral to the inoculated leg; it was detected later in the pyramidal cells of the hippocampus and cerebral cortex, and in the Purkinje cells of the cerebellum but not in the ependymal cells, choroid plexus cells or other glial cells. The infected neurons showed no cytopathological changes. q
Output: Neurotropism of Swine Haemagglutinating Encephalomyelitis Virus (Coronavirus) in Mice Depending upon Host Age and Route of Infection
Purpose: Wheezing following viral lower respiratory tract infections (LRTIs) in children <2 years of age is an important risk factor for the development of asthma later in life; however, not all children with viral LRTIs develop wheezing. This study investigated risk factors for the development of wheezing during viral LRTIs requiring hospitalization. Methods: The study included 142 children <2 years of age hospitalized for LRTIs with at least one virus identified as the cause and classified them into children diagnosed with LRTIs with wheezing (n=70) and those diagnosed with LRTIs without wheezing (n=72). Results: There were no significant differences in the viruses detected between the two groups. Multivariate logistic regression analysis showed that, after adjusting for potentially confounding variables including sex and age, the development of wheezing was strongly associated with parental history of allergic diseases (adjusted odds ratio [aOR], 20.19; 95% confidence interval [CI], 3.22-126.48), past history of allergic diseases (aOR, 13.95; 95% CI, 1.34-145.06), past history of hospitalization for respiratory illnesses (aOR, 21.36; 95% CI, 3.77-120.88), exposure to secondhand smoke at home (aOR, 14.45; 95% CI, 4.74-44.07), and total eosinophil count (aOR, 1.01; 95% CI, 1.01-1.02). Conclusion: Past and parental history of allergic diseases, past history of hospitalization for respiratory illnesses, exposure to secondhand smoke at home, and total eosinophil count were closely associated with the development of wheezing in children <2 years of age who required hospitalization for viral LRTIs. Clinicians should take these factors into consideration when treating, counseling, and monitoring young children admitted for viral LRTIs.
Output: Clinical risk factors associated with the develop ment of wheezing in children less than 2 years of age who required hospitalization for viral lower respiratory tract infections
The major histocompatibility complex (MHC) is one of the most diverse genetic regions under pathogen-driven selection because of its central role in antigen binding and immunity. The highest MHC variability, both in terms of the number of individual alleles and gene copies, has so far been found in passerine birds; this is probably attributable to passerine adaptation to both a wide geographic range and a diverse array of habitats. If extraordinary high MHC variation and duplication rates are adaptive features under selection during the evolution of ecologically and taxonomically diverse species, then similarly diverse MHC architectures should be found in bats. Bats are an extremely species-rich mammalian group that is globally widely distributed. Many bat species roost in multitudinous groups and have high contact rates with pathogens, conspecifics, and allospecifics. We have characterized the MHC class I diversity in 116 Panamanian Seba's short-tailed bats (Carollia perspicillata), a widely distributed, generalist, neotropical species. We have detected a remarkable individual and population-level diversity of MHC class I genes, with between seven and 22 alleles and a unique genotype in each individual. This diversity is comparable with that reported in passerine birds and, in both taxonomic groups, further variability has evolved through length polymorphisms. Our findings support the hypothesis that, for species with a geographically broader range, high MHC class I variability is particularly adaptive. Investigation of the details of the underlying adaptive processes and the role of the high MHC diversity in pathogen resistance are important next steps for a better understanding of the role of bats in viral evolution and as carriers of several deadly zoonotic viruses.
Output: Can extreme MHC class I diversity be a feature of a wide geographic range? The example of Seba's short-tailed bat (Carollia perspicillata)
Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the genomes, allowing for identification of known viruses and full genome sequencing, while the second set targets regions conserved among viral families or genera, providing the ability to detect both known and potentially novel members of those virus groups. Efficiency of enrichment was assessed by NGS testing reference virus and clinical samples with known infection. We show significant improvement in viral identification using enriched NGS compared to unenriched NGS. Without enrichment, we observed an average of 0.3% targeted viral reads per sample. However, after enrichment, 50%-99% of the reads per sample were the targeted viral reads for both the reference isolates and clinical specimens using both probe sets. Importantly, dramatic improvements on genome coverage were also observed following virus-specific probe enrichment. The methods described here provide improved sensitivity for virus identification by NGS, allowing for a more comprehensive analysis of disease etiology.
Output: Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing
This study was conducted to determine the perceptions of zoonotic disease risk among Australian veterinarians, the infection control practices they use to protect themselves from zoonotic diseases, and the factors influencing their use of these protective practices. A questionnaire was designed and piloted prior to its administration to veterinarians at the annual Australian Veterinary Association Conference in May 2011. The questionnaire comprised 21 closed, semi-closed and open questions. Data from the questionnaire were analyzed using ordinal logistic regression analyses to determine significant factors for veterinarians' use of personal protective equipment (PPE). A total of 344 veterinarians completed the questionnaire of which 63.7% were women, 63.2% worked in small/companion animal practice, and 79.9% worked in private veterinary practice. Of the respondents, 44.9% reported contracting a zoonosis during their careers with 19.7% reporting a suspected case and 25.2% reporting a confirmed incidence. Around 40-60% of veterinarians perceived exposure to zoonosis likely or very likely in a variety of situations. With reference to current national industry guidelines, the reported use of PPE was less than "adequate" for most scenarios except for performing postmortems, surgery or dental procedures. No PPE was used by 60-70% of veterinarians for treating respiratory and neurological cases and by 40-50% when treating gastrointestinal and dermatological cases. Workplace conditions need improvement as 34.8% of workplaces did not have isolation units for infected animals, 21.1% did not have separate eating areas for staff, and 57.1% did not have complete PPE kits for use. Veterinarians were more likely to use PPE if they had undertaken postgraduate education, perceived that zoonosis exposure from animals and procedures was likely, consciously considered PPE use for every case they dealt with and believed that liability issues and risks encouraged use of PPE. In contrast, those working in private practices, those who tended to 'just hope for the best' when trying to avoid zoonotic diseases, and those who were not aware of industry guidelines were less likely to use PPE. The results suggest that veterinarians' perceptions and workplace policies and culture substantially influence their use of PPE. Efforts should be made to encourage veterinarians and their workplaces to use infection control practices to protect themselves and their staff from zoonotic diseases.
Output: Zoonotic disease risk perceptions and infection control practices of Australian veterinarians: Call for change in work culture
RATIONALE: In infancy, rhinovirus illnesses and severe RSV bronchiolitis indicate increased risk for recurrent wheezing and asthma, but there is less information about other viruses. We evaluated the frequency and severity of metapneumovirus (HMPV) and coronavirus (HCV) infections in a high-risk group of infants. METHODS: Nasal lavage samples were obtained in the first year of life during scheduled study visits and symptomatic respiratory illnesses as part of the Childhood Origins of Asthma Project (COAST). Samples (n 5 567) were analyzed by Respiratory Multicode Assay (RMA) for HMPV, HCV-229E, HCV-OC43, HCV-NL63 and HCV-SARS. RESULTS: HMPV was isolated in 10.7% of samples during illnesses (n 5 291), and also occurred with other respiratory viruses (4.8%). 47.8% of HMPV illnesses included wheezing. HCV were isolated in 19.2% of the samples during illnesses and included HCV-OC43 (10.0%) and HCV-NL63 (9.6%). In addition, HCV was commonly detected together with other respiratory viruses (6.5%). Of all HCV illnesses (n 5 42), 33.3% included wheezing; however, HCV-NL63 had a significantly higher wheezing rate compared to HCV-OC43 (37.5% vs. 4.5%, p 5 0.028). Children who had at least one HCV-NL63 illness during infancy were significantly more likely to have asthma at age 6 compared to those without HCV-NL63 illnesses (52.2% vs. 25.0%, p 5 0.007). Having either HCV-OC43 or HMPV was not a risk factor for asthma at age 6. CONCLUSIONS: Improvements in viral diagnostics has allowed for identification of viruses that are difficult to culture. In infancy, HCV-NL63, HCV-OC43 and HMPV were significant causes of wheezing illnesses, however, only HCV-NL63 was significantly associated with asthma development at age six.
Output: 574 Coronavirus NL63 Illnesses in Infancy are a Risk Factor for Asthma at Age Six 575 Seasonal Distribution Of Respiratory Viruses In Pediatric