niryuu/sni-each-converted huggingface dataset:
Background: The spread of an novel coronavirus (SARS-CoV-2, previously named 2019-nCoV) has already taken on pandemic proportions, affecting over 100 countries in a matter of weeks. Elucidating the diagnostic value of different methods, especially the auxiliary diagnosis value of antibodies assays for SARS-CoV-2 infection is helpful for improving the sensitivities of pathogenic-diagnosis, providing timely treatment, and differentiating the infected cases from the healthy, thus preventing further epidemics. Methods: Medical records from 38 patients with confirmed SARS-CoV-2 infection in the Second People's Hospital of Fuyang from January 22, 2020 to February 28, 2020 were collected and retrospectively analyzed. Specimens including throat swabs, sputum and serum were collected during the hospitalization period, viral RNAs and serum IgM-IgG antibodies to SARS-CoV-2 were measured respectively. The detectability of different methods as well as the auxiliary diagnosis value of antibodies test for SARS-CoV-2 infection were analyzed. Results: Among 38 patients, the total seropositive rate for IgM and IgG was 50.0% and 92.1%, respectively. Two patients remained seronegative throughout the course of illness. In the early phase of illness, the RNA test for sputum specimens possessed the highest detectability(92.3%), followed by the the RNA test for throat swabs (69.2%), and the antibodies assays presented lower positive rates(IgM, 23.0%, IgG, 53.8%). While, the sensitivity of antibodies assays overtook that of RNA test since day 8 after onset (IgM, 50.0%; IgG, 87.5%). Of note, the positive rate of throat swabs was only 13.0% for cases in later phase(≥15 d.a.o), and the sensitivities of IgM and IgG rose to 52.2% and 91.3%, respectively. Combined use of antibodies assay and qRT-PCR at the same time was able to improve the sensitivities of pathogenic-diagnosis, especially for the throat swabs group at the later stage of illness. Moreover, most of these cases with undetectable viral RNA in throat swabs specimens at the early stage of illness were able to be IgM/IgG seropositive after 7 days. The antibodies detection against SARS-CoV-2 offers vital clinical information for physicians, and could be used as an effective supplementary indicator . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) The copyright holder for this preprint .
Output: Evaluation of the auxiliary diagnosis value of antibodies assays for the detection of novel coronavirus (SARS-Cov-2)
Sprague-Dawley rats were injected intraperitoneally with a suspension of Trypanosoma brucei brucei. An early induction of major histocompatibility complex (MHC) class I antigens as well as an infiltration of macrophage-like cells and cytotoxic T-cells was detected with immunohistochemical techniques in circumventricular organs, such as the median eminence, neurohypophysis, subfornical organ, pineal gland and area postrema. These areas, which lack a blood-brain barrier, correspond to those showing early invasion of trypanosomes. In addition, there was a marked induction of MHC class I in neurons in two hypothalamic nuclei, the paraventricular and supraoptic nuclei. Neurons in these two nuclei are located behind the blood-brain barrier, but project to the neurohypophysis and to the median eminence, thereby exposing their axon terminals to factors circulating in the blood or released locally from invading trypanosomes or from macrophages or cytotoxic T-cells. It is suggested that the alteration in the nerve cell bodies in the hypothalamic nuclei is caused by retrograde axonal signals from these target areas.
Output: Early major histocompatibility complex (MHC) class I antigen induction in hypothalamic supraoptic and paraventricular nuclei in trypanosome-infected rats
Objectives. Assess how people perceive the risks of coronavirus infection, whether people take preventive measures, and which (pre-outbreak) factors contribute to the perceived risks and measures taken, such as (pre-outbreak) respiratory problems, heart problems, diabetes, anxiety and depression symptoms, loneliness, age, gender, marital status and education level. Methods. Data were collected in the longitudinal LISS panel, based on a random sample of the Dutch population. The coronavirus survey started on March 2, and the data collection ended on March 17 2020. Data were linked with surveys on health and social integration conducted at the end of 2019 (N study sample =3,540). Results. About 15% perceived the risk of infection as high, and 11% the risk becoming ill when infected. Multivariate logistic regression analyses showed the following. Older age-groups perceived the risk for coronavirus infection as lower (all adjusted Odd Ratio's [aOR] ≤ .058). In total, 43.8% had taken preventive measures, especially females (aOR=1.47, 95% CI=1.27-1.69). Those with lower education levels less often used preventive measures (aOR=0.56, 95% CI=0.46-0.69). Those with preoutbreak respiratory problems (aOR=2.89, 95% CI=2.24-3.73), heart problems (aOR=2.17, 95% CI=1.49-3.16) and diabetes (aOR=3.10, 95% CI=2.02-4.74) perceived the risk becoming ill when infected as higher than others. However, respondents with pre-outbreak respiratory problems and diabetes did not more often take preventive measures. Vulnerable patients more often recognize that they are at risk becoming ill when infected by the coronavirus, but many do not take preventive measures. Interventions to stimulate the use of preventive measures should pay additional attention to physically vulnerable patients, men and those with lower education levels.
Output: Pre-outbreak determinants of perceived risks of corona infection and preventive measures taken. A prospective population-based study Perceived risks and preventive measures corona outbreak
Ten reference genes were investigated for normalization of gene expression data in the shell gland of laying hens. Analyses performed with geNorm revealed that hypoxanthine phosphoribosyltransferase 1 (HPRT1) and hydroxymethylbilane synthase (HMBS) were the two most stable reference genes in response to post-oviposition time alone (POT) or with nicarbazin treatment (POT+N) of laying hens. NormFinder analyses showed that the two most stable reference genes in response to POT and POT+N were 18S ribosomal RNA (18S rRNA), ribosomal protein L4 (RPL4) and HMBS, RPL4, respectively. BestKeeper analyses showed that 18S rRNA, RPL4 and HPRT1, HMBS were the two most stable reference genes for POT, and POT+N, respectively. Of the ten reference genes, all except B2M showed geNorm M <0.5, suggesting that they were stably expressed in the shell gland tissue. Consensus from these three programs suggested HPRT1 and HMBS could be used as the two most stable reference genes in the present study. Expression analyses of four candidate target genes with the two most and the two least stable genes showed that a combination of stable reference genes leads to more discriminable quantification of expression levels of target genes, while the least stable genes failed to do so. Therefore, HMBS and HPRT1 are recommended as the two most stable reference genes for the normalization of gene expression data at different stages of eggshell formation in brown-egg laying hens. Available statistical programs for reference gene ranking should include more robust analysis capability to analyse the gene expression data generated from factorial design experiments. Citation: Samiullah S, Roberts J, Wu S-B (2017) Reference gene selection for the shell gland of laying hens in response to time-points of eggshell formation and nicarbazin. PLoS ONE 12(7): e0180432. https://doi.org/10.
Output: Reference gene selection for the shell gland of laying hens in response to time-points of eggshell formation and nicarbazin
Canine distemper virus (CDV) is the cause of a severe and highly contagious disease in dogs. The unpredictable and variable course of CDV-related disease may hamper correct diagnosis of infection and makes it crucial the collection of samples suitable for laboratory confirmation. In the present study we were able to follow the disease in two dogs infected naturally, collecting different biological matrices during the entire period of infection. By real time RT-PCR, viral RNA was detected and quantified, suggesting that urine and rectal swabs would be useful for ante-mortem diagnosis of distemper in dogs, regardless of the clinical stage and form of the illness.
Output: Virological and serological findings in dogs with naturally occurring distemper
Most epidemiological studies of acute respiratory distress syndrome (ARDS) have been conducted in western countries, and studies in Asia are limited. The aim of our study was to evaluate the incidence, in-hospital mortality, and 1-year mortality of ARDS in Taiwan. We conducted a nationwide inpatient cohort study based on the Taiwan National Health Insurance Research Database between 1997 and 2011. A total of 40,876 ARDS patients (68% male; mean age 66 years) were identified by International Classification of Diseases, 9th edition coding and further analyzed for clinical characteristics, medical costs, and mortality. The overall crude incidence of ARDS was 15.74 per 100,000 person-years, and increased from 2.53 to 19.26 per 100,000 personyears during the study period. The age-adjusted incidence of ARDS was 15.19 per 100,000 person-years. The overall in-hospital mortality was 57.8%. In-hospital mortality decreased from 59.7% in 1997 to 47.5% in 2011 (P < 0.001). The in-hospital mortality rate was lowest (33.5%) in the youngest patients (age 18-29 years) and highest (68.2%) in the oldest patients (>80 years, P < 0.001). The overall 1-year mortality rate was 72.1%, and decreased from 75.8% to 54.7% during the study period. Patients who died during hospitalization were older (69 AE 17 versus 62 AE 19, P < 0.001) and predominantly male (69.8% versus 65.3%, P < 0.001). In addition, patients who died during hospitalization had significantly higher medical costs (6421 versus 5825 US Dollars, P < 0.001) and shorter lengths of stay (13 versus 19 days, P < 0.001) than patients who survived. We provide the first large-scale epidemiological analysis of ARDS incidence and outcomes in Asia. Although the overall incidence was lower than has been reported in a prospective US study, this may reflect underdiagnosis by International Classification of Diseases, 9th edition code and identification of only patients with more severe ARDS in this analysis. Overall, there has been a decreasing trend in in-hospital and 1year mortality rates in recent years, likely because of the implementation of lung-protective ventilation. (Medicine 94(43):e1849) Abbreviations: ARDS = acute respiratory distress syndrome, ICD-9 = International Classification of Diseases, 9th edition, ICU = intensive care unit. Editor: Levent Dalar. FIGURE 3. In-hospital mortality rates of ARDS in Taiwan. (A) In-hospital mortality rates of ARDS over the study period 1997-2011; (B) Age-specific in-hospital mortality rates of ARDS. Blue diamonds: male; red squares: female; green triangles: total population. FIGURE 4. One-year mortality rates of ARDS between 1997 and 2011 in Taiwan. Blue diamonds: male; red squares: female; green triangles: total population.
Output: Incidence and Outcomes of Acute Respiratory Distress Syndrome A Nationwide Registry-Based Study in Taiwan, 1997 to 2011
The original scientifi c strategy behind vaccinology has historically been to "isolate, inactivate, and inject," fi rst invoked by Louis Pasteur. The recombinant DNA and nanotechnology did much enlarge the repertoire on vaccines, which is today based on three adjusted principles, attenuation, inactivation, and recombination, as shown in Fig. 9 .1 . The three principles are regarded as equal, and all experimental possibilities for a new vaccine development against a pathogen should be studied in detail. The recombinant DNA and nanotechnology did not change the basic scientifi c strategy: live and non-live vaccines. Live vaccines are non-adjuvanted, and non-live vaccines are generally adjuvanted. New developments against tuberculosis (TB) highlight this broad experimental approach: Today, it estimated that about one-third of the world population is infected with the TB bacillus. Approximately 54 million people are infected every year, 9.4 million develop the disease, and 1.7 million die from this curable disease. The TB bacillus kills more people than any other infectious agent alone. Currently, BCG (Bacillus Calmette-Guérin) is the only vaccine recommended by the WHO, with more than three billion doses administered since its introduction in 1921. BCG is prepared from a strain of the attenuated live bovine tuberculosis bacillus, Mycobacterium bovis , which lost its virulence in humans by being specially subcultured in an artifi cial medium. However, although it protects newborns and children from severe forms of TB, its effi cacy against pulmonary TB in adolescents and adults is far from optimal, with protection rates varying between 0 and 80 % according to the geographical area. Contents Live and Non-live Vaccines
Output: Types of Recombinant Vaccines 9.1 Live and Non-live Vaccines
Background: Acute exacerbation of chronic bronchitis (AECB) is a common condition, with substantial associated costs and morbidity. Research efforts have focused on innovations that will reduce the morbidity associated with AECB. Health care payers increasingly expect that the results of evidence-based economic evaluations will guide practitioners in their choice of cost-effective interventions. Objectives: To provide a framework on which to base effective and efficient antimicrobial therapy for AECB, we present a concise clinical review of AECB, followed by an assessment of the available data on the economic impact of this disease. We then address several AECB-specific issues that must be considered in cost-effectiveness analyses of AECB antimicrobial interventions. Methods: Published literature on the clinical and economic impact of AECB was identified using MEDLINE@, pre-MEDLlNE@, HealthSTAR, ClNAHL, Current Contents/All Editions, EMBASE, and International Pharmaceutical Abstracts databases. Other potential sources were identified by searching for references in retrieved articles, review articles, consensus statements, and articles written by selected authorities. Results: In evaluating cost-effectiveness analyses of AECB antimicrobial therapy it is critical to (1) use the disease-free interval as an outcome measure, (2) evaluate the sequence of multiple therapies, (3) address the impact of both current and future antibiotic resistance, and (4) measure all appropriate AECB-associated costs, both direct and indirect. Incorporating these approaches in economic analyses of AECB antimicrobial therapy can help health care organizations make evidence-based decisions regarding the cost-effective management of AECB.
Output: Acute Exacerbation of Chronic Bronchitis: Disease-Specific Issues That Influence the Cost-Effectiveness of Antimicrobial Therapy
Vesicle-mediated transport is a process carried out by virtually every cell and is required for the proper targeting and secretion of proteins. As such, there are numerous players involved to ensure that the proteins are properly localized. Overall, transport requires vesicle budding, recognition of the vesicle by the target membrane and fusion of the vesicle with the target membrane resulting in delivery of its contents. The initial interaction between the vesicle and the target membrane has been referred to as tethering. Because this is the first contact between the two membranes, tethering is critical to ensuring that specificity is achieved. It is therefore not surprising that there are numerous 'tethering factors' involved ranging from multisubunit complexes, coiled-coil proteins and Rab guanosine triphosphatases. Of the multisubunit tethering complexes, one of the best studied at the molecular level is the evolutionarily conserved TRAPP complex. There are two forms of this complex: TRAPP I and TRAPP II. In yeast, these complexes function in a number of processes including endoplasmic reticulum-to-Golgi transport (TRAPP I) and an ill-defined step at the trans Golgi (TRAPP II). Because the complex was first reported in 1998 (1), there has been a decade of studies that have clarified some aspects of its function but have also raised further questions. In this review, we will discuss recent advances in our understanding of yeast and mammalian TRAPP at the structural and functional levels and its role in disease while trying to resolve some apparent discrepancies and highlighting areas for future study.
Output: The TRAPP Complex: Insights into its Architecture and Function NIH Public Access Author Manuscript
For over 30 years, HIV/AIDS has wreaked havoc in the world. In the absence of an effective vaccine for HIV, development of new anti-HIV agents is urgently needed. We previously identified the antiviral activities of the scorpion-venom-peptidederived mucroporin-M1 for three RNA viruses (measles viruses, SARS-CoV, and H5N1). In this investigation, a panel of scorpion venom peptides and their derivatives were designed and chosen for assessment of their anti-HIV activities. A new scorpion venom peptide derivative Kn2-7 was identified as the most potent anti-HIV-1 peptide by screening assays with an EC 50 value of 2.76 mg/ml (1.65 mM) and showed low cytotoxicity to host cells with a selective index (SI) of 13.93. Kn2-7 could inhibit all members of a standard reference panel of HIV-1 subtype B pseudotyped virus (PV) with CCR5-tropic and CXCR4tropic NL4-3 PV strain. Furthermore, it also inhibited a CXCR4-tropic replication-competent strain of HIV-1 subtype B virus. Binding assay of Kn2-7 to HIV-1 PV by Octet Red system suggested the anti-HIV-1 activity was correlated with a direct interaction between Kn2-7 and HIV-1 envelope. These results demonstrated that peptide Kn2-7 could inhibit HIV-1 by direct interaction with viral particle and may become a promising candidate compound for further development of microbicide against HIV-1.
Output: Anti-HIV-1 Activity of a New Scorpion Venom Peptide Derivative Kn2-7
lung transplantation and thought to represent chronic rejection. Increased expression of Pentraxin 3 (PTX3), an acute phase protein, was associated with worse outcome in lung transplant patients. To determine the role of recipient PTX3 in development of chronic rejection, we used a minor alloantigen-mismatched murine orthotopic single lung transplant model. Male C57BL/10 mice were used as donors. Male PTX3 knockout (KO) mice and their wild type (WT) littermates on 129/SvEv/C57BL6/J background were used as recipients. In KO recipients, 7/13 grafted lungs were consolidated without volume recovery on CT scan, while only 2/9 WT mice showed similar graft consolidation. For grafts where lung volume could be reliably analyzed by CT scan, the lung volume recovery was significantly reduced in KO mice compared to WT. Interstitial inflammation, parenchymal fibrosis and bronchiolitis obliterans scores were significantly higher in KO mice. Presence of myofibroblasts and lymphoid aggregation was significantly enhanced in the grafts of PTX3 KO recipients. Recipient PTX3 deficiency enhanced chronic rejection-like lesions by promoting a fibrotic process in the airways and lung parenchyma. The underlying mechanisms and potential protective role of exogenous PTX3 as a therapy should be further explored.
Output: Pentraxin 3 deficiency enhances features of chronic rejection in a mouse orthotopic lung transplantation model
The current emergence of the novel coronavirus pandemic caused by SARS-CoV-2 demands the development of new therapeutic strategies to prevent rapid progress of mortalities. The coronavirus spike (S) protein, which facilitates viral attachment, entry and membrane fusion is heavily glycosylated and plays a critical role in the elicitation of the host immune response. The spike protein is comprised of two protein subunits (S1 and S2), which together possess 22 potential N-glycosylation sites. Herein, we report the glycosylation mapping on spike protein subunits S1 and S2 expressed on human cells through high resolution mass spectrometry. We have characterized the quantitative N-glycosylation profile on spike protein and interestingly, observed unexpected O-glycosylation modifications on the receptor binding domain (RBD) of spike protein subunit S1. Even though O-glycosylation has been predicted on the spike protein of SARS-CoV-2, this is the first report of experimental data for both the site of O-glycosylation and identity of the O-glycans attached on the subunit S1. Our data on the N-and O-glycosylation is strengthened by extensive manual interpretation of each glycopeptide spectra in addition to using bioinformatics tools to confirm the complexity of glycosylation in the spike protein. The elucidation of the glycan repertoire on the spike protein provides insights into the viral binding studies and more importantly, propels research towards the development of a suitable vaccine candidate. author/funder. All rights reserved. No reuse allowed without permission.
Output: Deducing the N-and O-glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2
A tryptophan-rich octapeptide, C8 (Ac-Trp-Glu-Asp-Trp-Val-Gly-Trp-Ile-NH 2 ), modelled on the membrane-proximal external region of the feline immuno-deWciency virus (FIV) gp36 glycoprotein ectodomain, exhibits potent antiviral activity against FIV. A mechanism has been proposed by which the peptide, being positioned on the surface of the cell membrane, inhibits its fusion with the virus. In the present work, peptide-lipid interactions of C8 with dimyristoyl phosphatidylcholine liposomes are investigated using electron spin resonance spectroscopy of spin-labelled lipids. Three other peptides, obtained from modiWcations of C8, have also been investigated, in an attempt to clarify the essential molecular features of the interactions involving the tryptophan residues. The results show that C8 adsorbs strongly on the bilayer surface. Membrane binding requires not only the presence of the Trp residues in the sequence, but also their common orientation on one side of the peptide that is engendered by the WX 2 WX 2 W motif. Membrane interaction correlates closely with peptide antiviral activity, indicating that the membrane is essential in stabilizing the peptide conformation that will be able to inhibit viral infection.
Output: Interaction of short modiWed peptides deriving from glycoprotein gp36 of feline immunodeWciency virus with phospholipid membranes
The porcine epidemic diarrhoea virus (PEDV), a member of the Coronaviridae family, causes acute diarrhoea and dehydration in pigs. Although it was first identified in Europe, it has become increasingly problematic in many Asian countries, including Korea, China, Japan, the Philippines, and Thailand. The economic impacts of the PEDV are substantial, given that it results in significant morbidity and mortality in neonatal piglets and is associated with increased costs related to vaccination and disinfection. Recently, progress has been made in understanding the molecular epidemiology of PEDV, thereby leading to the development of new vaccines. In the current review, we first describe the molecular and genetic characteristics of the PEDV. Then we discuss its molecular epidemiology and diagnosis, what vaccines are available, and how PEDV can be treated.
Output: Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines
General agreement exists effective disaster management faces constraints related to knowledge sharing and a need for real-time research responses. Extreme case examples of disasters especially vulnerable to these challenges are global pandemics, or disease outbreaks, in which data required for research response are only available after the start of an outbreak. This paper argues the developing field of probabilistic innovation (innovation increasing probability of solving societal problems through radically increasing coordination of volumes of problem-solving inputs and analysis), and its methodologies, such as those drawing from crowdsourced R&D and social media, may offer useful insights into enabling real time research capabilities, with important implications for disaster and crisis management. Three paradigms of disaster research are differentiated, as literature is related to theory offered by post normal science, Kuhnian 'normal science' and Lakatosian 'structural science,' and the goal of achieving real time research problem solving capacity in disaster crisis situations. Global collaborative innovation platforms and large-scale investments in emerging crowdsourced R&D and social media technologies together with synthesis of appropriate theory may contribute to improved real time disaster response and resilience across contexts, particularly in instances where data required to manage response is only available after disasters unfold.
Output: Disaster management, crowdsourced R&D and probabilistic innovation theory: Toward real time disaster response capability
Recombinant proteins are traditionally limited to linear configuration. Herein, we report in vivo protein topology engineering using highly efficient, mechanically interlocking SpyX modules named AXB and BXA. SpyX modules are protein domains composed of p53dim (X), SpyTag (A), and SpyCatcher (B). The p53dim guides the intertwining of the two nascent protein chains followed by autocatalytic isopeptide bond formation between SpyTag and SpyCatcher to fulfill the interlocking, leading to a variety of backbone topologies. Direct expression of AXB or BXA produces protein catenanes with distinct ring sizes. Recombinant proteins containing SpyX modules are obtained either as mechanically interlocked obligate dimers if the protein of interest is fused to the N-or C-terminus of SpyX modules, or as star proteins if the protein is fused to both N-and C-termini. As examples, cellular syntheses of dimers of (GB1) 2 (where GB1 stands for immunoglobulin-binding domain B1 of streptococcal protein G) and of four-arm elastin-like star proteins were demonstrated. Comparison of the catenation efficiencies in different constructs reveals that BXA is generally much more effective than AXB, which is rationalized by the arrangement of three domains in space. Mechanical interlocking induces considerable stability enhancement. Both AXB and BXA have a melting point ∼20°C higher than the linear controls and the BXA catenane has a melting point~2°C higher than the cyclic control BX'A. Notably, four-arm elastin-like star proteins demonstrate remarkable tolerance against trypsin digestion. The SpyX modules provide a convenient and versatile approach to construct unconventional protein topologies via the "assembly-reaction" synergy, which opens a new horizon in protein science for stability enhancement and function reinforcement via topology engineering.
Output: Topology Engineering of Proteins in Vivo Using Genetically Encoded, Mechanically Interlocking SpyX Modules for Enhanced Stability
A 1,7-bis(alkylamino)diazachrysene-based small molecule was previously identified as an inhibitor of the botulinum neurotoxin serotype A light chain metalloprotease. Subsequently, a variety of derivatives of this chemotype were synthesized to develop structure-activity relationships, and all are inhibitors of the BoNT/A LC. Three-dimensional analyses indicated that half of the originally discovered 1,7-DAAC structure superimposed well with 4-amino-7-chloroquinolinebased antimalarial agents. This observation led to the discovery that several of the 1,7-DAAC derivatives are potent in vitro inhibitors of Plasmodium falciparum and, in general, are more efficacious against CQ-resistant strains than against CQ-susceptible strains. In addition, by inhibiting β-hematin formation, the most efficacious 1,7-DAAC-based antimalarials employ a mechanism of action analogous to that of 4,7-ACQ-based antimalarials and are well tolerated by normal cells. One candidate was also effective when administered orally in a rodent-based malaria model. Finally, the 1,7-DAAC-based derivatives were examined for Ebola filovirus inhibition in an assay employing Vero76 cells, and three provided promising antiviral activities and acceptably low toxicities.
Output: A Chemotype That Inhibits Three Unrelated Pathogenic Targets: The Botulinum Neurotoxin Serotype A Light Chain, P. falciparum Malaria, and the Ebola Filovirus
Paramyxovirus entry into cells requires fusion of the viral and cell membranes mediated by one of the major virus glycoproteins, the fusion (F) glycoprotein which transits from a metastable pre-fusion conformation to a highly stable post-fusion structure during the membrane fusion process. F protein refolding involves large conformational changes of the protein trimer. One of these changes results in assembly of two heptad repeat sequences (HRA and HRB) from each protomer into a six-helix bundle (6HB) motif. To assist in distinguishing pre-and post-fusion conformations of the Pneumovirinae F proteins, and as extension of previous work , a general strategy was designed to obtain polyclonal and particularly monoclonal antibodies specific of the 6HB motif of the Pneumovirinae fusion protein. The antibodies reported here should assist in the characterization of the structural changes that the F protein of human metapneumovirus or respiratory syncytial virus experiences during the process of membrane fusion.
Output: Generation of monoclonal antibodies specific of the postfusion conformation of the Pneumovirinae fusion (F) protein
Canine distemper virus (CDV) invades the nervous system and replicates in neurons and glial cell of the white matter during a period of severe viral induced immunosuppression. Demyelination occurs in infected white matter areas in the absence of inflammation. The mechanism of demyelination is not apparent because there is no ultrastructural evidence of viral replication in the oligodendrocytes, the myelin producing cells. However, brain tissue culture studies have shown that oligodendrocytes support transcription of all CDV genes and later on degenerate, although no viral proteins can be found in these cells. It remains to be shown how such a restricted infection leads to demyelination. Concomitant with immunologic recovery during the further course of the disease, inflammation occurs in the demyelinating lesions with progression of the lesions in some animals. A series of experiments in vitro suggested that chronic demyelination is due to a bystander mechanism associated with the virus-induced immune response in which antibody dependent cell-mediated reactions play an important role. The progressive, or even relapsing, course of the disease is associated with viral persistence in the nervous system. Persistence of CDV in the brain appears to be due to non-cytolytic selective spread of the virus with very limited budding. In this way CDV escapes immune surveillance. * Corresponding author. Fax: 41 31 63125 38. 0378-l 135/95/$09.50 0 1995 Elsevier Science B.V. All rights reserved SSDZO378-1135(95)00021-6
Output: The neurobiology of canine distemper virus infection
A unique subline of BALB/c mice, designated BALB/cV, exhibits an intermediate mammary tumor incidence (47%) and harbors a distinct milk-transmitted mouse mammary tumor virus (MMTV). The BALB/cV subline was used to study the molecular basis of potential virus-host interactions involving cell surface-expressed MMTV proteins. Cell surface iodination identified virus-specific proteins expressed on BALB/cV primary mammary tumor cells grown in culture. In contrast to (C3H)MMTV-producing cell lines which expressed MMTV gp52, BALB/cV tumor cells lacked gp52 and expressed instead a 68K, env-related protein. The 68K"" protein was also detected on the surface of metabolically labeled BALB/cV tumor cells by an external immunoprecipitation technique. The expression of 68Kp"" was restricted to mammary tissues of BALB/cV mice that also expressed other MMTV proteins. Biochemical analysis established that 68K"" was not modified by N-linked glycosylation. '%I-labeled 68K"" was rapidly released into the media of tumor cell cultures and was recovered both in the form of a soluble protein and in a 100,OOOg pellet. The biologic function of this cell surface-expressed viral protein remains unknown.
Output: Identification and Characterization of a Mouse Mammary Tumor Virus Protein Uniquely Expressed on the Surface of BALB/cV Mammary Tumor Cells
Supplementary Text 1: Details of specimen collection, processing, polymerase chain reaction 34 assays, quality control measures, and assay parameters used to identify respiratory viruses. Specimen collection 36 All swabs were collected using a plastic-shaft, rayon-budded swab in a transport tube with a foam 37 pad reservoir soaked with viral transport medium (Virocult MW950, Medical Wire & Equipment, 38 Wiltshire, England). A single swab was used to sample both nostrils. 39 Quality Control measures 40 A known amount of whole equine herpesvirus (EHV) spiked into each sample assessed nucleic 41 acid extraction quality and presence of polymerase chain reaction (PCR) inhibitors. 1 Any extract 42 having a >3 cycle-threshold (Ct) difference to that of the expected value by EHV real-time PCR 43 assays was considered to have failed quality control and the sample was re-extracted. Specimen quality was assessed by testing for a marker of human genomic DNA, endogenous 46 retrovirus-3 (ERV-3). 2 We have demonstrated previously that among specimens with an ERV-3 Ct a adjusted for clustering using sandwich estimators to account for within-infant correlation between observations; b Individual rhinovirus species do not add up to 'All rhinovirus' detections because of a combination of more than one rhinovirus species detected within the same ARI episode, or single new virus detection episodes where HRV positive specimens could not be sequenced.
Output: Viruses causing lower respiratory symptoms in children younger than 2-years of age: 1 findings from the ORChID birth cohort. 2
Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems level analysis. Current genome annotation programs do not identify all of the functional elements of the genome, especially small non-coding RNAs (sRNAs). Whole genome transcriptome analysis is a complementary method to identify ''novel'' genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. In particular, the identification of non-coding RNAs has revealed their widespread occurrence and functional importance in gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Histophilus somni, one of the causative agents of Bovine Respiratory Disease (BRD) as well as bovine infertility, abortion, septicemia, arthritis, myocarditis, and thrombotic meningoencephalitis. In this study, we report a single nucleotide resolution transcriptome map of H. somni strain 2336 using RNA-Seq method. The RNA-Seq based transcriptome map identified 94 sRNAs in the H. somni genome of which 82 sRNAs were never predicted or reported in earlier studies. We also identified 38 novel potential protein coding open reading frames that were absent in the current genome annotation. The transcriptome map allowed the identification of 278 operon (total 730 genes) structures in the genome. When compared with the genome sequence of a non-virulent strain 129Pt, a disproportionate number of sRNAs (,30%) were located in genomic region unique to strain 2336 (,18% of the total genome). This observation suggests that a number of the newly identified sRNAs in strain 2336 may be involved in strain-specific adaptations.
Output: RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen ''Histophilus somni 2336
The surveillance and prevention of pathogenic microbiological contamination are the most important tasks of biosafety management in the lab. There is an urgent need to establish an effective and unbiased method to evaluate and monitor such contamination. This study aims to investigate the utility of next generation sequencing (NGS) method to detect possible contamination in the microbiology laboratory. Environmental samples were taken at multiple sites at the lab including the inner site of centrifuge rotor, the bench used for molecular biological tests, the benches of biosafety cabinets used for viral culture, clinical sample pre-treatment and nucleic acids extraction, by scrubbing the sites using sterile flocked swabs. The extracted total nucleic acids were used to construct the libraries for deep sequencing according to the protocol of Ion Torrent platform. At least 1G raw data was obtained for each sample. The reads of viruses and bacteria accounted for 0.01 ± 0.02%, and 77.76 ± 12.53% of total reads respectively. The viral sequences were likely to be derived from gene amplification products, the nucleic acids contaminated in fetal bovine serum. Reads from environmental microorganisms were also identified. Our results suggested that NGS method was capable of monitoring the nucleic acids contaminations from different sources in the lab, demonstrating its promising utility in monitoring and assessing the risk of potential laboratory contamination. The risk of contamination from reagents, remnant DNA and environment should be considered in data analysis and results interpretation.
Output: Application of next generation sequencing technology on contamination monitoring in microbiology laboratory
The seventh novel human infecting Betacoronavirus that causes pneumonia (2019 novel coronavirus, 2019-nCoV) originated in Wuhan, China. The evolutionary relationship between 2019-nCoV and the other human respiratory illness-causing coronavirus is not closely related. We sought to characterize the relationship of the translated proteins of 2019-nCoV with other species of Orthocoronavirinae. A phylogenetic tree was constructed from the genome sequences. A cluster tree was developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The combined data were used to characterize the relationship of the translated proteins of 2019-nCoV to other species of Orthocoronavirinae. Our analysis reliably suggests that 2019-nCoV is most closely related to BatCoV RaTG13 and belongs to subgenus Sarbecovirus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus. The phylogenetic profiling cluster of homolog proteins of one annotated 2019-nCoV protein against other genome sequences revealed two clades of ten 2019-nCoV proteins. Clade 1 consisted of a group of conserved proteins in Orthocoronavirinae comprising Orf1ab polyprotein, Nucleocapsid protein, Spike glycoprotein, and Membrane protein. Clade 2 comprised six proteins exclusive to Sarbecovirus and Hibecovirus. Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. Thus, we speculated that knowledge of the functional changes in the NS7b and NS8 proteins during evolution may provide important information to explore the human infective property of 2019-nCoV.
Output: Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV
Aim: An epidemiological study of canine parvovirus infection in dogs in and around Bhubaneswar, Odisha was conducted between December 2012 to March 2013 and prevalence rate was studied on the basis of age, breed, and sex. Materials and Methods: A total of 71 fecal samples from suspected diarrheic dogs were collected in sterile phosphate buffer saline (10% W/V) and examined by polymerase chain reaction (PCR) for detection of canine parvo virus infection, followed by epidemiological study in relation to age, breed, and sex. Results: Of 71 samples analyzed, 29 (40.85%) were found to be positive by PCR assay. The infection was higher in Deshi/ local breeds (34.48%), followed by German shepherd (17.24%), equal incidences in mixed and Labrador retriever (10.34%), Rottweiler and German spitz showed 6.90% each and finally lower incidences in four breeds (3.45%) such as Dalmatians, Nea politan mastiff, Pug and Great Dane. Age-wise prevalence study revealed the infection being more in the age group of 3-6 months (41.37%), followed by equal incidences of 27.59% in 1-3 months and 6-12 months age group, and a low incidence in age groups above 12 months (3.45%). The incidence was predominantly higher in males (86.21%) than females (13.79%). The epidemiological analysis revealed that the breed wise prevalence was found to be more in Deshi breeds as compared to others, age groups below 6 months were found to be more prone to parvovirus infection and males were mostly infected.
Output: Epidemiological study of canine parvovirus infection in and around Bhubaneswar, Odisha, India
We discuss crisis prevention and management during the first 3 months of the severe acute respiratory syndrome (SARS) outbreak in Singapore. Four public health issues were considered: prevention measures, self-health evaluation, SARS knowledge, and appraisal of crisis management. We conducted telephone interviews with a representative sample of 1,201 adults, >21 years of age. We found that sex, age, and attitude (anxiety and perception of open communication with authorities) were associated with practicing preventive measures. Analysis of Singapore's outbreak improves our understanding of the social dimensions of infectious disease outbreaks.
Output: EMERGENCE OF SARS
The world was shocked in early 2003 when a pandemic of severe acute respiratory syndrome (SARS) was imminent. The outbreak of this novel disease, caused by a novel coronavirus (the SARS-coronavirus), hit hardest in the Asian Pacific region, though eventually it spread to five continents. The speed of the spread of the SARS epidemic was unprecedented due to the highly efficient intercontinental transportation. An international collaborative effort through the World Health Organization (WHO) has helped to identify the aetiological agent about 1 month after the onset of the epidemic. The power of molecular biology and bioinformatics has enabled the complete decoding of the viral genome within weeks. Over 1000 publications on the phylogeny, epidemiology, genomics, laboratory diagnostics, antiviral, immunization, pathogenesis, clinical disease, and management accumulated within just 1 year. Although the exact animal reservoir of virus and how it evolved into a human pathogen are still obscure, accurate diagnosis and epidemiological control of the disease are now possible. This article reviews what is currently known about the virus and the disease. Journal of NeuroVirology (2005) 11, 455-468.
Output: The severe acute respiratory syndrome (SARS)
Daniel, S.L., Legendre, A.M., Moore, R.N. and Rouse, B.T., 1993. Isolation and functional studies on feline bone marrow derived macrophages. Vet. lmmunol. Immunopathol., In this report, we describe an in vitro culture method for feline bone marrow cells, which yields large numbers of quiescent macrophages after 14 days of culture. The bulk of the cultured cell population consists of macrophages as assessed by morphology, macrophage specific cytochemistry, and phagocytosis. The remaining cells were lymphocytes, bone marrow stromal cells, fibroblasts and occasional polymorphonuclear leukocytes. While resting cells produced no detectable interleukin 1, stimulation with lipopolysaccharide (LPS) induced the production of biologically active interleukin 1. After 6 h LPS stimulation, mRNA for tumor necrosis factor a and interleukin lfl was detectable. The absence of mRNA in unstimulated cells indicates cultured macrophages were not activated until stimulated by LPS or plastic adherence. This approach provides a useful means to measure potential modulatory effects by virus infections or other agents upon feline macrophage gene expression. ABBREVIATIONS BM, bone marrow; FeLV, feline leukemia virus; FIV, feline immunodeficiency virus; HIV, human immunodefieiency virus; IL-I, interleukin 1; LPS, lipopolysaccharide; PHA-P, phytohemagglutinin P; PMN, polymorphonuclear ieukocytes; TNF, tumor necrosis factor.
Output: Isolation and functional studies on feline bone marrow derived macrophages
Coronavirus envelope (E) protein is a small integral membrane protein with multi-functions in virion assembly, morphogenesis and virus-host interaction. Different coronavirus E proteins share striking similarities in biochemical properties and biological functions, but seem to adopt distinct membrane topology. In this report, we study the membrane topology of the SARS-CoV E protein by immunofluorescent staining of cells differentially permeabilized with detergents and proteinase K protection assay. It was revealed that both the N-and C-termini of the SARS-CoV E protein are exposed to the cytoplasmic side of the membranes (N cyto C cyto ). In contrast, parallel experiments showed that the E protein from infectious bronchitis virus (IBV) spanned the membranes once, with the N-terminus exposed luminally and the C-terminus exposed cytoplasmically (N exo(lum) -C cyto ). Intriguingly, a minor proportion of the SARS-CoV E protein was found to be modified by N-linked glycosylation on Asn 66 and inserted into the membranes once with the C-terminus exposed to the luminal side. The presence of two distinct membrane topologies of the SARS-CoV E protein may provide a useful clue to the pathogenesis of SARS-CoV.
Output: Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells
Background: Cytokines play important roles in antiviral action. We examined whether polymorphisms of IFN-γ,TNF-α and IL-10 affect the susceptibility to and outcome of severe acute respiratory syndrome (SARS). A case-control study was carried out in 476 Chinese SARS patients and 449 healthy controls. We tested the polymorphisms of IFN-γ,TNF-α and IL-10 for their associations with SARS. Results: IFN-γ +874A allele was associated with susceptibility to SARS in a dose-dependent manner (P < 0.001). Individuals with IFN-γ +874 AA and AT genotype had a 5.19-fold (95% Confidence Interval [CI], 2.78-9.68) and 2.57-fold (95% CI, 1.35-4.88) increased risk of developing SARS respectively. The polymorphisms of IL-10 and TNF-α were not associated with SARS susceptibility. Conclusion: IFN-γ +874A allele was shown to be a risk factor in SARS susceptibility.
Output: BMC Infectious Diseases The interferon gamma gene polymorphism +874 A/T is associated with severe acute respiratory syndrome