niryuu/sni-each-converted huggingface dataset:
C ell-to-cell spread of retroviruses via virological synapse (VS) contributes to overall progression of disease. VS are specialized pathogen-induced cellular structures that facilitate cell-to-cell transfer of HIV-1 and HTLV-1. VS provide a mechanistic explanation for cell-associated retroviral replication. While VS share some common features with neurological or immunological synapses, they also exhibit important differences. The role of VS might not be limited to human retroviruses and the emerging role of a plant synapse suggests that VS might well be conserved structures for cell-cell spreading of both animal and plant viruses. Dissection of the VS is just at its beginning, but already offers ample information and fascinating insights into mechanisms of viral replication and cell-to-cell communication. The complex functioning of biological systems requires the capacity of cells to interact in a synchronized manner. The capacity of cells to come in close contact with one another enables rapid exchange of information through directed secretion. In complex systems such as the nervous and immune systems, characteristic rearrangements of plasma membrane proteins appear at the cell-cell junction, called synapse. A synapse is defined as "a stable adhesive junction across which information is relayed by directed secretion".^ The concept of the neural synapse (NS) was first introduced over a century ago and was depicted as a stable structure organized and specialized in intercellular signaling between neurons. Plasma membranes of the pre and post-synaptic neurons are contiguous and information is conveyed to the downstream cell via secretion of neurotransmitters. In order to generate a favorable microenvironment, stabilization of synapse by scaffolding proteins, mainly cadherins and other adhesion molecules, is required (reviewed in re£ 1). In the immune system, interactions between T cells and antigen presenting cells (APC) are essential for an effective adaptive immune response. By analogy with the nervous system, these specialized interactions occur via an immunological synapse (IS). The concept of the IS has been extended to several types of cell-cell interactions within the context of the immune system (signaling via receptor engagement, lytic granules, directed secretion of cytokines) since its first description 20 years ago (reviewed in refs. 2,3) . Although the IS shares many similarities with the NS, it also differs in two aspects. First, the panel of receptors and adhesion proteins recruited to the IS diverges from those in the neural synapse: integrins play the central role in stabilizing IS. Second, the establishment of an IS is a dynamic process between moving cells, whereas the neural synapse is long-lived. Therefore, in
Output: Virological Synapse for Cell-Cell Spread of Viruses
Development of effective vaccines, in particular, subunit-based vaccines, against emerging Middle East respiratory syndrome (MERS) caused by the MERS coronavirus (MERS-CoV) will provide the safest means of preventing the continuous spread of MERS in humans and camels. This review briefly describes the structure of the MERS-CoV spike (S) protein and its receptor-binding domain (RBD), discusses the current status of MERS vaccine development, and illustrates the strategies used to develop RBD-based subunit vaccines against MERS. It also summarizes currently available animal models for MERS-CoV and proposes a future direction for MERS vaccines. Taken together, this review will assist researchers working to develop effective and safe subunit vaccines against MERS-CoV and any other emerging coronaviruses that might cause future pandemics.
Output: Receptor-binding domain-based subunit vaccines against MERS-CoV
Four truncated porcine aminopeptidase N (pAPN, a cellular receptor for porcine coronaviruses) proteins were expressed in prokaryotic cells. The recognizing of a specific serum against pAPN to these proteins was investigated by enzyme-linked immunosorbent assay (ELISA) and immunoblotting. The binding ability of the proteins to transmissible gastroenteritis virus (TGEV), a porcine coronavirus, was analyzed by ELISA. The inhibitory effect of these proteins to cell infection by TGEV was analyzed using plaque assays. Our data indicate that three truncated pAPNs positively reacted with the specific antiserum and the major binding regions of pAPN were limited in regions 36aa-223aa, 349aa-591aa and 592-963aa. The proteins showed discrepant binding activity to either pAPN antibody or TGE virions. Moreover, the truncated proteins blocked the infection of cells by TGEV to different extent. The results suggest that the major antibody-binding domains of pAPN may associate with the receptor-binding determinants. The role of APN is discussed in the context of virus receptor usage.
Output: Binding characterization of determinants in porcine aminopeptidase N, the cellular receptor for transmissible gastroenteritis virus
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is the cause of an atypical pneumonia that affected Asia, North America and Europe in 2002-2003. The viral spike (S) glycoprotein is responsible for mediating receptor binding and membrane fusion. Recent studies have proposed that the carboxyl terminal portion (S2 subunit) of the S protein is a class I viral fusion protein. The Wimley and White interfacial hydrophobicity scale was used to identify regions within the CoV S2 subunit that may preferentially associate with lipid membranes with the premise that peptides analogous to these regions may function as inhibitors of viral infectivity. Five regions of high interfacial hydrophobicity spanning the length of the S2 subunit of SARS-CoV and murine hepatitis virus (MHV) were identified. Peptides analogous to regions of the N-terminus or the pretransmembrane domain of the S2 subunit inhibited SARS-CoV plaque formation by 40-70% at concentrations of 15-30 μM. Interestingly, peptides analogous to the SARS-CoV or MHV loop region inhibited viral plaque formation by >80% at similar concentrations. The observed effects were dose-dependent (IC50 values of 2-4 μM) and not a result of peptide-mediated cell cytotoxicity. The antiviral activity of the CoV peptides tested provides an attractive basis for the development of new fusion peptide inhibitors corresponding to regions outside the fusion protein heptad repeat regions.
Output: Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein NIH Public Access
TiO 2 photocatalysts were prepared and coated on surfaces. Ultrathin TiO 2 coatings were obtained by wash-coating and screen-printing techniques. The latter provides films of excellent adhesion that could tolerate washing under water jet. The scratch-proof coatings were characterized, and X-ray diffraction (XRD), atomic force microscopy (AFM) and N 2 physisorption indicated that the addition of polyethylene glycol (PEG) not only improved the coating properties of TiO 2 but also served as poragen to produce high surface area, mesoporous TiO 2 . The coated TiO 2 displayed better activity than the commercial P25 TiO 2 for photocatalytic oxidation of ethylene, ethanol, acetaldehyde, isopropanol and acetone. The catalyst also exhibited excellent bactericidal, fungicidal and virucidal activities against a wide variety of Gram-positive and Gram-negative bacteria, fungal spores and T2 bacterial phage. A simple photoreactor with tangential air flow was designed and tested in a chamber, before incorporating in a prototype air purifier. The study showed that there is good agreement between laboratory catalyst reaction data (i.e., 110 mmol h −1 for acetone) and the prototype test results (69 mmol h −1 ).
Output: Investigation of the performance of TiO 2 photocatalytic coatings
We have produced a new Ebola virus pseudotype, E-S-FLU, that can be handled in biosafety level 1/2 containment for laboratory analysis. The E-S-FLU virus is a single-cycle influenza virus coated with Ebolavirus glycoprotein, and it encodes enhanced green fluorescence protein as a reporter that replaces the influenza virus hemagglutinin. MDCK-SIAT1 cells were transduced to express Ebolavirus glycoprotein as a stable transmembrane protein for E-S-FLU virus production. Infection of cells with the E-S-FLU virus was dependent on the Niemann-Pick C1 protein, which is the well-characterized receptor for Ebola virus entry at the late endosome/lysosome membrane. The E-S-FLU virus was neutralized specifically by an anti-Ebolavirus glycoprotein antibody and a variety of small drug molecules that are known to inhibit the entry of wild-type Ebola virus. To demonstrate the application of this new Ebola virus pseudotype, we show that a single laboratory batch was sufficient to screen a library (LOPAC 1280 ; Sigma) of 1,280 pharmacologically active compounds for inhibition of virus entry. A total of 215 compounds inhibited E-S-FLU virus infection, while only 22 inhibited the control H5-S-FLU virus coated in H5 hemagglutinin. These inhibitory compounds have very dispersed targets and mechanisms of action, e.g., calcium channel blockers, estrogen receptor antagonists, antihistamines, serotonin uptake inhibitors, etc., and this correlates with inhibitor screening results obtained with other pseudotypes or wild-type Ebola virus in the literature. The E-S-FLU virus is a new tool for Ebola virus cell entry studies and is easily applied to highthroughput screening assays for small-molecule inhibitors or antibodies. IMPORTANCE Ebola virus is in the Filoviridae family and is a biosafety level 4 pathogen. There are no FDA-approved therapeutics for Ebola virus. These characteristics warrant the development of surrogates for Ebola virus that can be handled in more convenient laboratory containment to study the biology of the virus and screen for inhibitors. Here we characterized a new surrogate, named E-S-FLU virus, that is based on a disabled influenza virus core coated with the Ebola virus surface protein but does not contain any genetic information from the Ebola virus itself. We show that E-S-FLU virus uses the same cell entry pathway as wild-type Ebola virus. As an example of the ease of use of E-S-FLU virus in biosafety level 1/2 containment, we showed that a single production batch could provide enough surrogate virus to screen a standard small-molecule library of 1,280 candidates for inhibitors of viral entry.
Output: Characterization of Influenza Virus Pseudotyped with Ebolavirus Glycoprotein VACCINES AND ANTIVIRAL AGENTS crossm
This article describes methods of treatment for avian zoonoses, modern antibiotic therapy and drug resistance of selected pathogens, which pose a threat to the population's health. A tabular form has been used to present the current data from the European Union from 2011 to 2017 regarding human morbidity and mortality and the costs incurred by national health systems for the treatment of zoonoses occurring in humans and animals. Moreover, the paper includes descriptions of selected diseases, which indirectly affect birds. Scientists can obtain information regarding the occurrence of particular diseases, their aetiology, epidemiology, incubation period and symptoms caused by dangerous microorganisms and parasites. This information should be of particular interest for people who have frequent contact with birds, such as ornithologists, as well as veterinarians, farm staff, owners of accompanying animals and zoological workers. This paper presents a review used for identification and genetic characterization of bacterial strains isolated from a variety of environmental sources, e.g., bird feathers along with their practical application. We describe the bacterial, viral and fungal serotypes present on avian feathers after the slaughter process. This review also enables us to effectively identify several of the early stages of infectious diseases from heterogeneous avian research material.
Output: Bird feathers as potential sources of pathogenic microorganisms: a new look at old diseases
Many of the studies on emerging epidemics (such as SARS and pandemic flu) use mass action models to estimate reproductive numbers and the needed control measures. In reality, transmission patterns are more complex due to the presence of various social networks. One level of complexity can be accommodated by considering a community of households. Our study of transmission dynamics in a community of households emphasizes five types of reproductive numbers for the epidemic spread: household-to-household reproductive number, leaky vaccine-associated reproductive numbers, perfect vaccine reproductive number, growth rate reproductive number, and the individual reproductive number. Each of those carries different information about the transmission dynamics and the required control measures, and often some of those can be estimated from the data while others cannot. Simulations have shown that under certain scenarios there is an ordering for those reproductive numbers. We have proven a number of ordering inequalities under general assumptions about the individual infectiousness profiles. Those inequalities allow, for instance, to estimate the needed vaccine coverage and other control measures without knowing the various transmission parameters in the models. Along the way, we've also shown that in choosing between increasing vaccine efficacy and increasing coverage levels by the same factor, preference should go to efficacy.
Output: REPRODUCTIVE NUMBERS, EPIDEMIC SPREAD AND CONTROL IN A COMMUNITY OF HOUSEHOLDS
Successful vaccine development remains a huge challenge for infectious diseases such as malaria, HIV and influenza. As a novel way to present antigenic epitopes to the immune system, we have developed icosahedral self-assembling protein nanoparticles (SAPNs) to serve as a prototypical vaccine platform for infectious diseases. Here we examine some biophysical factors that affect the self-assembly of these nanoparticles, which have as basic building blocks coiled-coil oligomerization domains joined by a short linker region. Relying on in silico computer modeling predictions, we selected five different linker regions from the RCSB protein database that connect oligomerization domains, and then further studied the self-assembly and stability of in vitro produced nanoparticles through biophysical characterization of formed particles. One design in particular, T2i88, revealed excellent self-assembly and homogeneity thus paving the way toward a more optimized nanoparticle for vaccine applications. From the Clinical Editor: Despite the widespread use of vaccines worldwide, successful development of vaccines against some diseases remains a challenge still. In this article, the authors investigated the physic-chemical and biological properties of icosahedral self-assembling protein nanoparticles (SAPNs), which mimic viral particles, in order to utilize this technology as potential platform for future design of vaccines.
Output: Optimizing the design of protein nanoparticles as carriers for vaccine applications
The COVID-19 pandemic has shown a markedly low proportion of cases among children. Age disparities in observed cases could be explained by assortative mixing patterns and reactive school closures which decrease mixing between children, or by children exhibiting lower susceptibility to infection, or by children having a lower propensity to show clinical symptoms. We formally test these hypotheses by fitting an age-structured mathematical model to epidemic data from six countries, finding 1 . CC-BY 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. The copyright holder for this preprint . https://doi.org/10.1101/2020.03.24.20043018 doi: medRxiv preprint / strong age dependence in the probability of developing clinical symptoms, rising from around 20% in under 10s to over 70% in older adults. We find that interventions aimed at halting transmission in children may have minimal effects on preventing cases depending on the relative transmissibility of subclinical infections. Our estimated age-specific clinical fraction has implications for the expected global burden of clinical cases because of demographic differences across settings. In younger populations, the expected clinical attack rate would be lower, although it is likely that comorbidities in low-income countries will affect disease severity. Without effective control measures, regions with older populations may see disproportionally more clinical cases, particularly in the later stages of the pandemic.
Output: Age-dependent effects in the transmission and control of COVID-19 epidemics
Only a few years ago, viral diagnosis was largely an exercise for academic researchers and public health practitioners with focus on epidemiologic analyses and outbreak prevention, detection, and control. Opportunities for therapeutic intervention were limited to only a few applications such as herpesvirus infections, infl uenza, and HIV/AIDS; hence, once a bacterial or fungal infection was excluded, clinicians were limited to providing supportive care for what was presumed to be a viral syndrome. Public health organizations tracked the incidence of viral infections and the development of resistance to the few antiviral drugs in use and provided input to governments and the pharmaceutical industry regarding selection of vaccine targets. More recently, interest in viral diagnostics has burgeoned with the advent of new tools for detection and discovery, global recognition of pandemic risk, high-throughput drug screening, rational drug design, and immunotherapeutics. An additional impetus has been the implication of viruses in chronic illnesses not previously attributed to infection. The objective of this chapter is to review the factors responsible for the rise in awareness of viral infections, methods for diagnosis and monitoring viral infections, and future prospects for improvements in discovery, detection, and response to the challenges of clinical virology.
Output: Diagnosis, Discovery and Dissection of Viral Diseases
medRxiv preprint Effect of pre-existing immunity on seroconversion to recent strains Pre-existing, homologous titer to circulating strains is a well-described predictor of risk of seroconversion (14), which is confirmed in our study (Table 1 and tables S5 and S6). However, we hypothesized that including metrics of antibody profiles that integrate previous exposure history would further improve predictions of the risk of seroconversion. Therefore, we examined the association between the risk of seroconversion with age at baseline sampling, pre-existing, homologous titer to outcome strains (the ith strain), titer to the i-1th strain, and summary metrics . CC-BY-NC 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint .
Output: Life course exposures continually shape antibody profile and risk of seroconversion to influenza
Background: Influenza virus is responsible for annual deaths due to seasonal epidemics and is the cause of major pandemics which have claimed millions of human lives over the last century. Knowledge about respiratory virus transmission is advancing. Spread is likely through the air, but much work remains to be done to characterize the aerosols produced by infected individuals, including viral particle survival and infectivity. Although coughs have been characterized, little work has been done to examine coughs from infected individuals. The WeCoF project aims at providing evidence to support prevention measures to mitigate person-to-person influenza transmission in critical locations, such as hospitals, and during pandemics. Findings: A novel experimental cough chamber facilitythe FLUGIEhas been developed to study the far-field aerodynamics and aerosol transport of droplets produced by the coughs from humans naturally-infected with influenza. The flow field of each cough is measured using Particle Image Velocimetry (PIV). A preliminary study involving 12 healthy individuals has been carried out in order to quantify the strengths of their coughs at a distance of 1 m from the mouth. The spatially averaged maximum velocity was determined and the average value was 0.41 m/s across 27 coughs of good data quality. The peak value of velocity was also extracted and compared with the average velocity. Conclusions: Preliminary results show that there is significant air motion associated with a cough (on the order of 0.5 m/s) as far away as 1 m from the mouth of the healthy person who coughs. The results from this pilot study provide the framework for a more extensive participant recruitment campaign that will encompass a statisticallysignificant cohort.
Output: Western Cold and Flu (WeCoF) aerosol study - preliminary results
Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA-RNA interactions, often spanning thousands of nucleotides. The plus-strand RNA genomes of tombusviruses exemplify this concept by possessing different long-range RNA-RNA interactions that regulate both viral translation and transcription. Here we report that a third fundamental tombusvirus process, viral genome replication, requires a long-range RNA-based interaction spanning ,3000 nts. In vivo and in vitro analyses suggest that the discontinuous RNA platform formed by the interaction facilitates efficient assembly of the viral RNA replicase. This finding has allowed us to build an integrated model for the role of global RNA structure in regulating the reproduction of a eukaryotic RNA virus, and the insights gained have extended our understanding of the multifunctional nature of viral RNA genomes.
Output: A Discontinuous RNA Platform Mediates RNA Virus Replication: Building an Integrated Model for RNA-based Regulation of Viral Processes A Discontinuous RNA Platform Mediates RNA Virus Replication: Building an Integrated Model for RNA-based Regulation of Viral Processes
In the past decade, clinical microbiology laboratories have undergone important changes with the introduction of molecular biology techniques and laboratory automation. In the future, there will be a need for more rapid diagnoses, increased standardization of testing and greater adaptability to cope with new threats from infectious microorganisms, such as agents of bioterrorism and emerging pathogens. The combination of the new tools that are now being developed in research laboratories, the general reorganization of clinical laboratories and improved communication between physicians and clinical microbiologists should lead to profound changes in the way that clinical microbiologists work. The following terms in this article are linked online to: Entrez: http://www.ncbi.nlm.nih.gov/entrez mecA Infectious Disease Information: http://www.cdc.gov/ncidod/diseases/index.htm: Bacillus anthracis | cytomegalovirus | group A streptococcus | group B streptococci | hepatitis C | HIV | influenza | Lyme disease | Plasmodium spp. | pneumonia | Q fever | rotavirus | rubella | SARS | Staphylococcus aureus | Toxoplasma gondii FURTHER INFORMATION GenBank: http://www.ncbi.nih.gov/Genbank/ Access to this interactive links box is free online.
Output: WHAT DOES THE FUTURE HOLD FOR CLINICAL MICROBIOLOGY?
Background: The prevalence and risk factors for infection with enteropathogens in dogs frequenting dog parks have been poorly documented, and infected dogs can pose a potential zoonotic risk for owners. Hypothesis/Objectives: To determine the prevalence and risk factors of infection with enteropathogens and zoonotic Giardia strains in dogs attending dog parks in Northern California and to compare results of fecal flotation procedures performed at a commercial and university parasitology laboratory. Animals: Three-hundred dogs attending 3 regional dog parks in Northern California. Methods: Prospective study. Fresh fecal specimens were collected from all dogs, scored for consistency, and owners completed a questionnaire. Specimens were analyzed by fecal centrifugation flotation, DFA, and PCR for detection of 11 enteropathogens. Giardia genotyping was performed for assemblage determination. Results: Enteropathogens were detected in 114/300 dogs (38%), of which 62 (54%) did not have diarrhea. Frequency of dog park attendance correlated significantly with fecal consistency (P = .0039), but did not correlate with enteropathogen detection. Twenty-seven dogs (9%) were infected with Giardia, and genotyping revealed nonzoonotic assemblages C and D. The frequency of Giardia detection on fecal flotation was significantly lower at the commercial laboratory versus the university laboratory (P = .013), and PCR for Giardia was negative in 11/27 dogs (41%) that were positive on fecal flotation or DFA. Conclusions and Clinical Importance: Enteropathogens were commonly detected in dogs frequenting dog parks, and infection with Giardia correlated with fecal consistency. PCR detection of Giardia had limited diagnostic utility, and detection of Giardia cysts by microscopic technique can vary among laboratories.
Output: Prevalence of Enteropathogens in Dogs Attending 3 Regional Dog Parks in Northern California
Background: Glycyrrhiza uralensis is one of the most popular medicinal plants in the world and is also widely used in the flavoring of food and tobacco. Due to limited genomic and transcriptomic data, the biosynthetic pathway of glycyrrhizin, the major bioactive compound in G. uralensis, is currently unclear. Identification of candidate genes involved in the glycyrrhizin biosynthetic pathway will significantly contribute to the understanding of the biosynthetic and medicinal chemistry of this compound. We used the 454 GS FLX platform and Titanium regents to produce a substantial expressed sequence tag (EST) dataset from the vegetative organs of G. uralensis. A total of 59,219 ESTs with an average read length of 409 bp were generated. 454 ESTs were combined with the 50,666 G. uralensis ESTs in GenBank. The combined ESTs were assembled into 27,229 unique sequences (11,694 contigs and 15,535 singletons). A total of 20,437 unique gene elements representing approximately 10,000 independent transcripts were annotated using BLAST searches (e-value ≤ 1e-5) against the SwissProt, KEGG, TAIR, Nr and Nt databases. The assembled sequences were annotated with gene names and Gene Ontology (GO) terms. With respect to the genes related to glycyrrhizin metabolism, genes encoding 16 enzymes of the 18 total steps of the glycyrrhizin skeleton synthesis pathway were found. To identify novel genes that encode cytochrome P450 enzymes and glycosyltransferases, which are related to glycyrrhizin metabolism, a total of 125 and 172 unigenes were found to be homologous to cytochrome P450s and glycosyltransferases, respectively. The cytochrome P450 candidate genes were classified into 32 CYP families, while the glycosyltransferase candidate genes were classified into 45 categories by GO analysis. Finally, 3 cytochrome P450 enzymes and 6 glycosyltransferases were selected as the candidates most likely to be involved in glycyrrhizin biosynthesis through an organ-specific expression pattern analysis based on real-time PCR. Conclusions: Using the 454 GS FLX platform and Titanium reagents, our study provides a high-quality EST database for G. uralensis. Based on the EST analysis, novel candidate genes related to the secondary metabolite pathway of glycyrrhizin, including novel genes encoding cytochrome P450s and glycosyltransferases, were found. With the assistance of organ-specific expression pattern analysis, 3 unigenes encoding cytochrome P450s and 6 unigenes encoding glycosyltransferases were selected as the candidates most likely to be involved in glycyrrhizin biosynthesis.
Output: EST analysis reveals putative genes involved in glycyrrhizin biosynthesis
The burden of vector-borne diseases (Dengue, Zika virus, yellow fever, etc.) gradually increased in the past decade across the globe. Mathematical modelling on infectious diseases helps to study the transmission dynamics of the pathogens. Theoretically, the diseases can be controlled and eventually eradicated by maintaining the effective reproduction number, (R eff ), strictly less than 1. We established a vector-host compartmental model, and derived (R eff ) for vector-borne diseases. The analytic form of the (R eff ) was found to be the product of the basic reproduction number and the geometric average of the susceptibilities of the host and vector populations. The (R eff ) formula was demonstrated to be consistent with the estimates of the 2015-2016 yellow fever outbreak in Luanda, and distinguished the second minor epidemic wave. For those using the compartmental model to study the vector-borne infectious disease epidemics, we further remark that it is important to be aware of whether one or two generations is considered for the transition ''from host to vector to host'' in reproduction number calculation.
Output: Distributed under Creative Commons CC-BY 4.0 Modelling the effective reproduction number of vector-borne diseases: the yellow fever outbreak in Luanda, Angola 2015-2016 as an example
The genome organization and expression strategy of the newly identified severe acute respiratory syndrome coronavirus (SARS-CoV) were predicted using recently published genome sequences. Fourteen putative open reading frames were identified, 12 of which were predicted to be expressed from a nested set of eight subgenomic mRNAs. The synthesis of these mRNAs in SARS-CoV-infected cells was confirmed experimentally. The 4382-and 7073 amino acid residue SARS-CoV replicase polyproteins are predicted to be cleaved into 16 subunits by two viral proteinases (bringing the total number of SARS-CoV proteins to 28). A phylogenetic analysis of the replicase gene, using a distantly related torovirus as an outgroup, demonstrated that, despite a number of unique features, SARS-CoV is most closely related to group 2 coronaviruses. Distant homologs of cellular RNA processing enzymes were identified in group 2 coronaviruses, with four of them being conserved in SARS-CoV. These newly recognized viral enzymes place the mechanism of coronavirus RNA synthesis in a completely new perspective. Furthermore, together with previously described viral enzymes, they will be important targets for the design of antiviral strategies aimed at controlling the further spread of SARS-CoV.
Output: Unique and Conserved Features of Genome and Proteome of SARS-coronavirus, an Early Split-off From the Coronavirus Group 2 Lineage
Recent advances in the diagnostic and metagenomic investigations of the feline enteric environment have allowed the identification of several novel viruses that have been associated with gastroenteritis in cats. In the last few years, noroviruses, kobuviruses, and novel parvoviruses have been repetitively detected in diarrheic cats as alone or in mixed infections with other pathogens, raising a number of questions, with particular regards to their pathogenic attitude and clinical impact. In the present article, the current available literature on novel potential feline enteric viruses is reviewed, providing a meaningful update on the etiology, epidemiologic, pathogenetic, clinical, and diagnostic aspects of the infections caused by these pathogens.
Output: Feline Virome-A Review of Novel Enteric Viruses Detected in Cats
The present study aimed to investigate the effects of levodopa (LEV) on cellular apoptosis in a rabbit model of steroid-associated necrosis of the femoral head (SANFH). A total of 44 healthy adult Chinese rabbits were randomly divided into three groups: Group A (n=15), administered a combination of lipopolysaccharide and hormone to establish the SANFH animal model; group B (n=15), SANFH animal model as in group A orally administered LEV (0.4 g/kg/day) on the day of injection; and group C (n=14), the control group. On the 6th and 8th week of modeling, seven rabbits from each group were sacrificed to harvest bilateral femoral head specimens for hematoxylin and eosin staining and apoptosis detection by terminal deoxynucleotidyl transferase dUTP nick-end labeling assay analysis, as well as for observing pathological changes and analyzing cellular apoptosis. Eight weeks after modeling, the serum insulin-like growth factor (IGF)-1 levels of the three groups were measured. The empty lacunae rate and apoptosis index of bone cells in the treatment group were significantly lower than that of the model group (P<0.01). Eight weeks after treatment, the serum levels of IGF-1 were significantly higher than that of the model group (P<0.01). These findings suggested that LEV was able to reduce steroid-induced bone cellular apoptosis, reduce the occurrence of necrosis of the femoral head and, through in vivo metabolism, it may promote the synthesis and release of IGF-1, which could be one of its biological pathways to prevent and treat SANFH. Levodopa attenuates cellular apoptosis in steroid-associated necrosis of the femoral head
Output: EXPERIMENTAL AND THERAPEUTIC MEDICINE
Marine sponges and their associated bacteria have been proven to be a rich source of novel secondary metabolites with therapeutic usefulness in cancer, infection, and autoimmunity. In this study, 79 strains belonging to 20 genera of the order Actinomycetales and seven strains belonging to two genera of the order Sphingomonadales were cultivated from 18 different Caribbean sponges and identified by 16S rRNA gene sequencing. Seven of these strains are likely to represent novel species. Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. These results highlight the significance of marine sponge-associated bacteria to produce bioactive secondary metabolites with therapeutic potential in the treatment of infectious diseases and disorders of the immune system.
Output: Anti-protease and Immunomodulatory Activities of Bacteria Associated with Caribbean Sponges
Chitin is a linear polysaccharide of N-acetylglucosamine, which is highly abundant in nature and mainly produced by marine crustaceans. Chitosan is obtained by hydrolytic deacetylation. Both polysaccharides are renewable resources, simply and cost-effectively extracted from waste material of fish industry, mainly crab and shrimp shells. Research over the past five decades has revealed that chitosan, in particular, possesses unique and useful characteristics such as chemical versatility, polyelectrolyte properties, gel-and film-forming ability, high adsorption capacity, antimicrobial and antioxidative properties, low toxicity, and biocompatibility and biodegradability features. A plethora of chemical chitosan derivatives have been synthesized yielding improved materials with suggested or effective applications in water treatment, biosensor engineering, agriculture, food processing and storage, textile additives, cosmetics fabrication, and in veterinary and human medicine. The number of studies in this research field has exploded particularly during the last two decades. Here, we review recent advances in utilizing chitosan and chitosan derivatives in different technical, agricultural, and biomedical fields. A large number of chitosan-based composites were investigated for removal of metal ions from aqueous solutions. They include chitosan-polymer macromolecular complexes (as cellulose, cellulosic matrix like cotton fibers, alginate, polyvinyl alcohol, polyvinyl chloride), chitosan ceramics, as well as clay and silicate composites (bentonite, montmorillonite, perlite, and zeolite) (Wan Ngah et al. 2011) . Due to the vast number of scientific publications on chitosan-based adsorption that have been published, only a representative sample is depicted for Cr(VI) and Cu(II). Cognate composites were devised as adsorbents of other metal ions (Cd, As, Fe, Pb, Co, Pb, Hg, Ni, Zn, U) that can be found in the detailed reviews of Reddy and Lee (
Output: Chitin/Chitosan: Versatile Ecological, Industrial, and Biomedical Applications
have set up a public forum on www.LAMP-Seq.org. The ongoing COVID-19 pandemic has already caused devastating losses. Early evidence shows that the exponential spread of COVID-19 can be slowed by restrictive isolation measures, but these place a tremendous burden on society. Moreover, once these restrictions are lifted, the exponential spread is likely to re-emerge. It has been suggested that populationscale testing can help break the cycle of isolation and spread, but current detection methods are not capable of such large-scale processing. Here we propose LAMP-Seq, a barcoded Reverse-Transcription Loop-mediated Isothermal Amplification (RT-LAMP) protocol that could dramatically reduce the cost and complexity of population-scale testing. In this approach, individual samples are processed in a single heat step, producing barcoded amplicons that can be shipped to a sequencing center, pooled, and analyzed en masse. Using unique barcode combinations per sample from a compressed barcode space enables extensive pooling, significantly reducing cost and organizational efforts. Given the low cost and scalability of next-generation sequencing, we believe that this method can be affordably scaled to analyze millions of samples per day using existing sequencing infrastructure.
Output: LAMP-Seq: Population-Scale COVID-19 Diagnostics Using a Compressed Barcode Space
Calves fed soya proteins may develop severe gastrointestinal disorders. Whether these are predominantly associated with particular Ig subclasses and (or) dietary proteins remains unclear. Therefore, antibody responses to soyabean protein were analysed by dot-and blot-immunobinding in plasma and intestinal mucous secretions. One-month-old calves were fed for 2.5 months liquid diets based on skim milk powder (SMP) or a mixture (2:3, protein basis) of whey and soyabean products including a low antigenic hydrolysed soya protein isolate (HSPI) and a highly antigenic heated soya flour ( HSF), Specific antibodies ( Abs) of the main isotypes (IgM, IgA, IgGl, IgG2) were characterised by immunostaining of samples which had been previously incubated with nitrocellulose sheets coated with SMP, HSPI or HSF extracts. Plasma collected before feeding experimental diets showed very little specific Abs. By contrast, 2.5 months later, a three-fold increase (P < 0.05) in IgGl and IgA titres against HSF antigens was observed in calves fed HSF compared with those fed the control or HSPI diet. IgGl immunoblotting revealed many protein bands from soya in the molecular range of 22-32 and 38-42 kDa. Immunorecognition of specific proteins from SMP and HSPI remained low and similar among animal groups. Specific IgM, IgA and IgGl titres against HSF, and to a lesser extent HSPI, were significantly higher (P <0.05) in jejunal mucous secretion of calves fed HSF compared with other groups. Secretions from calves fed HSF bound to many soyabean proteins in the range of 17-23 and 26-38 kDa, with similar patterns for IgA and lgG1. By contrast, only weak bands were found for IgM and IgG2 in all groups of calves. Thus. calves fed antigenic HSF do present specific Abs including IgGl and IgA isotypes. both systemically and locally. Therefore, IgG I and( or) IgA rather than IgM and IgG2 Abs may be preferred for assessing the immunogenicity of soyabean products in calves. interestingly. soyabean immunogenicity was drastically reduced by adequate proteolysis.
Output: + I ) 704 355 8254; Fax. ( + I
The entry mechanism of Junin virus (JV) into Vero cells was studied analyzing the effect of lysosomotropic compounds and acid pH on JV infection. Ammonium chloride, amantadine, chlorpheniramine and procaine inhibited JV production. The action of ammonium chloride was exerted at early times of infection. Virus internalization was inhibited and viral protein expression was not detected. When the extracellular medium was buffered at low pH, the ammonium chloride induced block on JV infection was overcome. Furthermore, JV was able to induce fusion of infected cells at pH 5.5 leading to polykaryoctye formation. Taken together, these results demonstrate that JV entry occurs through an endocytic mechanism requiring a low pH dependent membrane fusion.
Output: The entry of Junin virus into Vero cells
BACKGROUND: Single-nucleotide polymorphisms (SNPs) that impact on the differential expression of interleukin 28B (IL28B) are implicated in the progression of viral-induced diseases. In this prospective longitudinal cohort study, we evaluated the association between IL28B SNPs rs12979860 and rs8099917 and the clinical outcome of bronchiolitis in pediatric patients. METHODS: A total of 682 infants suffering from bronchiolitis, categorized based on the final clinical outcome as mild or severe, were genotyped for IL28B SNPs rs12979860 and rs8099917. RESULTS: When infants were categorized exclusively based on the final clinical outcome, no association was established between IL28B SNPs and the severity of bronchiolitis. However, when stratified by sex, the homozygotes for the minor alleles of rs12979860 (T) and rs8099917 (G) were associated with a mild disease in girls but not in boys. CONCLUSION: SNPs rs12979860 and rs8099917 correlate with the severity of bronchiolitis and display a sex bias, where GG rs8099917 and TT rs12979860 genotypes are associated with a mild disease in girls but not in boys. These findings suggest that innate immunity and female sex links with the outcome of the diseases induced by respiratory viruses, such as RSV.
Output: Correlation between female sex, IL28B genotype, and the clinical severity of bronchiolitis in pediatric patients
Eight accessory proteins have been identified in severe acute respiratory syndrome-associated coronavirus (SARS-CoV). They are believed to play roles in the viral life cycle and may contribute to the pathogenesis and virulence. ORF9b as one of these accessory proteins is located in subgenomic mRNA9 and encodes a 98 amino acid protein. However, whether 9b protein is a structural component of SARS-CoV particles remains unknown. In this study, we demonstrate that 9b protein is translated from bicistronic mRNA9 via leaky ribosome scanning and it is incorporated into both virus-like particles (VLPs) and purified SARS-CoV virions. Further analysis shows that sufficient incorporation of 9b protein into VLPs is dependent upon the coexpression of E and M proteins, but not upon the presence of either S or N protein. Our data indicate that 9b protein of SARS-CoV is another virion-associated accessory protein. This finding will lead to a better understanding of the properties of the SARS-CoV 9b protein.
Output: Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein
Newcastle disease virus (NDV) are both important viruses seriously affecting poultry industry worldwide. In this study, reverse-transcription LAMP (RT-LAMP) was combined with lateral flow dipstick (LFD) forming a novel detection tool which could simultaneously detect IBV and NDV visually. Primers targeted the 5 -untranslated region (5 -UTR) of IBV genome and the conserved region of NDV large polymerase gene (LP). The specificity and sensitivity of this multiple reverse transcription-LAMP-LFD (mRT-LAMP-LFD) assay were compared with those of conventional RT-PCR, nested RT-PCR (nRT-PCR), quantification RT-PCR (qRT-PCR), and RT-LAMP monitored by electrophoresis. No non-specific amplifications were observed when the assays were tested with unrelated viruses. According to the sensitivity study, when detecting IBV or NDV alone, the lowest detection limits of mRT-LAMP-LFD were 10 0.8 IBV RNA copies/reaction and 10 0.7 NDV RNA copies/reaction. Furthermore, when detecting IBV and NDV simultaneously, the lowest detection limit was the same as that of the single detection assays. In the clinical sample study, mRT-LAMP-LFD performed the best among these assays. When tested with IBV or NDV single infected samples, the mean detection rates were 98.65% and 97.25%, respectively. In the IBV and NDV co-infected sample study, the mean detection rates of IBV and NDV were both 95%. This study showed that mRT-LAMP-LFD was a promising qualitative detection tool suitable for field single or multiple IBV and NDV detection.
Output: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick
Background: Canine adenovirus 2, parainfluenza, and Bordetella bronchiseptica cause respiratory disease in dogs, and each has a modified live intranasal vaccine available. Molecular diagnostic assays to amplify specific nucleic acids are available for each of these agents. If positive molecular diagnostic assay results are common after vaccination, the positive predictive value of the diagnostic assays for disease would be decreased. Objective: To determine the impact of administration of commercially available modified live topical adenovirus 2, B. bronchiseptica, and parainfluenza vaccine has on the results of a commercially available PCR panel. Animals: Eight puppies from a research breeding facility negative for these pathogens. Methods: Blinded prospective pilot study. Puppies were vaccinated with a single dose of modified live topical adenovirus 2, B. bronchiseptica, and parainfluenza and parenteral dose of adenovirus 2, canine distemper virus, and parvovirus. Nasal and pharyngeal swabs were collected on multiple days and submitted for PCR assay. Results: Nucleic acids of all 3 organisms contained in the topical vaccine were detected from both samples multiple times through 28 days after vaccination with higher numbers of positive samples detected between days 3 and 10 after vaccination. Conclusions and Clinical Importance: Vaccine status should be considered when interpreting respiratory agent PCR results if modified live vaccines have been used. Development of quantitative PCR and wild-type sequencing are necessary to improve positive predictive value of these assays by distinguishing vaccinate from natural infection.
Output: Adenovirus 2, Bordetella bronchiseptica, and Parainfluenza Molecular Diagnostic Assay Results in Puppies After vaccination with Modified Live Vaccines