niryuu/sni-each-converted huggingface dataset:
Human astrovirus nonstructural protein nsP1a/4, located at the C-terminal end of 17 nsP1a, is thought to be involved in the regulation of RNA replication and capsid 18 maturation;however, its rolesviral growth and virulence are not well understood. 19 We investigated the intracellular host proteins that interact with nsP1a and 20 explored the potential roles of the interaction in the pathogenesis of human 21 astrovirus infection. We screened 14 independent proteins with a cDNA library 22 a nonstructural protein located at the C-terminal end of the human astrovirus 38 nsP1a polyprotein, interacts with the host protein CD63. Over expression of 39 CD63 promoted viral RNA replication, whereas knockdown of CD63 decreased 40 virus RNA replication, indicating that CD63 plays a critical role in the human 41 astrovirus life cycle. 42 43 KEYWORDS: human astrovirus, HAstV, protein-protein interaction, nsP1a, 44 nsP1a/4, CD63, virus replication 45 46 author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/331835 doi: bioRxiv preprint Viruses are obligate intracellular pathogens thatutilize host-cell machinery to 47 infect cells, replicate themselves, and then exit the cells for another round of 48 infection. Human astroviruses (HAstVs) are a group of non-enveloped, 49 single-stranded, and positive-sense RNA viruses in the family Astroviridae. 50 HAstVs are causative agents of viral diarrhea in young children, 51 immunocompromised patients, and elderly individuals (1-5). The astrovirus 52 genome has three open reading frames (ORFs); ORF1a and ORF1b encode two 53 nonstructural polyproteins (nsPs), and ORF2 encodes the capsid protein (6). The 54 nsP1a polyprotein, transcribed from ORF1a, is involved in viral transcription 55 and replication. When HAstV infects a host cell, nsP1a is cleaved into at least 56 four products, named nsP1a/1, nsP1a/2, nsP1a/3 (protease), and nsP1a/4. The 57 nsP1a/4 protein is located at the C-terminal end of nsP1a.Several domains have 58 been identified in nsP1a/4, including two coiled-coil regions, a death domain 59 (DD), a nuclear localization signal (NLS), a putative viral genome-linked 60 protein(VPg), and a hypervariable region (HVR)(7-12). It was confirmed that 61 nsP1a/4 plays important roles in the activation of capsid maturation and the 62 regulation of RNA replication (13, 14). To better understand the roles of nsP1a 63 and nsP1a/4 in HAstV infection and replication, we characterized host proteins 64 that interact with nsP1a or nsP1a/4 by utilizing a yeast two-hybrid approach. We 65 identified at least 14 host proteins that could bind to nsP1a, one of which was 66 CD63. CD63, a member of the tetraspan transmembrane protein family, is a 68 author/funder. All rights reserved. No reuse allowed without permission.
Output: Host protein CD63 enhances viral RNA replication by interacting with human astrovirus nonstructural protein nsP1a/4 2
Thank you for the submission of your manuscript to EMBO Molecular Medicine. We have now heard back from two of the three referees whom we asked to evaluate your manuscript. As these two referees have very similar recommendations, we decided to go ahead and make a decision now. Although referees do find the study suitable for publication in principle, referee 2 suggested expanding the discussion and providing additional explanations here and there. We would welcome the submission of a revised version for further consideration and depending on the nature of the revisions, this may be sent back or not to the referees for another round of review.
Output: Development of broad-spectrum human monoclonal antibodies for rabies post-exposure prophylaxis Transaction Report
Swine influenza virus and Streptococcus suis are two important contributors to the porcine respiratory disease complex, and both have significant economic impacts. Clinically, influenza virus and Streptococcus suis co-infections in pigs are very common, which often contribute to severe pneumonia and can increase the mortality. However, the co-infection pathogenesis in pigs is unclear. In the present study, co-infection experiments were performed using swine H1N1 influenza virus and Streptococcus suis serotype 2 (SS2). The H1N1-SS2 co-infected pigs exhibited more severe clinical symptoms, serious pathological changes, and robust apoptosis of lungs at 6 days post-infection compared with separate H1N1 and SS2 infections. A comprehensive gene expression profiling using a microarray approach was performed to investigate the global host responses of swine lungs against the swine H1N1 infection, SS2 infection, co-infection, and phosphate-buffered saline control. Results showed 457, 411, and 844 differentially expressed genes in the H1N1, SS2, and H1N1-SS2 groups, respectively, compared with the control. Noticeably, genes associated with the immune, inflammatory, and apoptosis responses were highly overexpressed in the co-infected group. Pathway analysis indicated that the cytokine-cytokine receptor interactions, MAPK, toll-like receptor, complement and coagulation cascades, antigen processing and presentation, and apoptosis pathway were significantly regulated in the coinfected group. However, the genes related to these were less regulated in the separate H1N1 and SS2 infection groups. This observation suggested that a certain level of synergy was induced by H1N1 and SS2 co-infection with significantly stronger inflammatory and apoptosis responses, which may lead to more serious respiratory disease syndrome and pulmonary pathological lesion.
Output: Investigation of Pathogenesis of H1N1 Influenza Virus and Swine Streptococcus suis Serotype 2 Co-Infection in Pigs by Microarray Analysis a11111 OPEN ACCESS
B cell hybridomas are an important source of monoclonal antibodies. In this paper, we developed a high-throughput method to characterize mouse IgG antibodies using surface plasmon resonance technology. This assay rapidly determines their sub-isotypes, whether they bind native antigen and their approximate affinities for the antigen using only 50 μl of hybridoma cell culture supernatant. Moreover, we found that mouse hybridomas secreting IgG antibodies also have membrane form IgG expression without Igα. Based on this surface IgG, we used flow cytometry to isolate rare γ2a isotype switched variants from a γ2b antibody secreting hybridoma cell line. Also, we used fluorescent antigen to single cell sort antigen binding hybridoma cells from bulk mixture of fused hybridoma cells instead of the traditional multi-microwell plate screening and limiting dilution sub-cloning thus saving time and labor. The IgG monoclonal antibodies specific for the native antigen identified with these methods are suitable for in vivo therapeutic uses, but also for sandwich ELISA assays, histology, flow cytometry, immune precipitation and x-ray crystallography. Fig 5. Isolation of IgG ɣ2a antibody secreting cells from an IgG ɣ2b hybridoma cell line. (A) Detection of IgG ɣ2a antibody secreting hybridoma cells in S212, an IgG ɣ2b hybridoma cell line with ELISPOT. (B) Cell surface IgG staining of S212 cells. (C) Enrichment of IgG ɣ2a secreting cells by MACS and single cell sorting of these heavy chain switched cells. (D) Biacore testing of S212 IgG ɣ2b antibody and the switched IgG ɣ2a antibody. Fig 6. Sorting of native antigen binding IgG hybridomas from a fusion bulk mixture. (A) Staining of OVA specific hybridoma cell line with fluorescent OVA. (B) Sorting of OVA specific hybridoma clls from a fusion bulk mixture.
Output: A Rapid Method to Characterize Mouse IgG Antibodies and Isolate Native Antigen Binding IgG B Cell Hybridomas
Glycans are multi-branched sugars that are displayed from lipids and proteins. Through their diverse polysaccharide structures they can potentiate a myriad of cellular signaling pathways involved in development, growth, immuno-communication and survival. Not surprisingly, disruption of glycan synthesis is fundamental to various human diseases; including cancer, where aberrant glycosylation drives malignancy. Here, we report the discovery of a novel mannose-binding lectin, ML6, which selectively recognizes and binds to these irregular tumor-specific glycans to elicit potent and rapid cancer cell death. This lectin was engineered from gene models identified in a tropical rainforest tree root transcriptome and is unusual in its six canonical mannose binding domains (QxDxNxVxY), each with a unique amino acid sequence. Remarkably, ML6 displays antitumor activity that is >10 5 times more potent than standard chemotherapeutics, while being almost completely inactive towards non-transformed, healthy cells. This activity, in combination with results from glycan binding studies, suggests ML6 differentiates healthy and malignant cells by exploiting divergent glycosylation pathways that yield naïve and incomplete cell surface glycans in tumors. Thus, ML6 and other high-valence lectins may serve as novel biochemical tools to elucidate the glycomic signature of different human tumors and aid in the rational design of carbohydratedirected therapies. Further, understanding how nature evolves proteins, like ML6, to combat the changing defenses of competing microorganisms may allow for fundamental advances in the way we approach combinatorial therapies to fight therapeutic resistance in cancer. OPEN ACCESS Citation: Lawanprasert A, Guinan CA, Langford EA, Hawkins CE, Sloand JN, Fescemyer HW, et al. (2020) Discovery of antitumor lectins from rainforest tree root transcriptomes. PLoS ONE 15 (2): e0229467. https://doi.org/10.
Output: Discovery of antitumor lectins from rainforest tree root transcriptomes
Dysfunction of CFTR in cystic fibrosis (CF) airway epithelium perturbs the normal regulation of ion transport, leading to a reduced volume of airway surface liquid (ASL), mucus dehydration, decreased mucus transport, and mucus plugging of the airways. CFTR is normally expressed in ciliated epithelial cells of the surface and submucosal gland ductal epithelium and submucosal gland acinar cells. Critical questions for the development of gene transfer strategies for CF airway disease are what airway regions require CFTR function and how many epithelial cells require CFTR expression to restore normal ASL volume regulation and mucus transport to CF airway epithelium? An in vitro model of human CF ciliated surface airway epithelium (CF HAE) was used to test whether a human parainfluenza virus (PIV) vector engineered to express CFTR (PIVCFTR) could deliver sufficient CFTR to CF HAE to restore mucus transport, thus correcting the CF phenotype. PIVCFTR delivered CFTR to .60% of airway surface epithelial cells and expressed CFTR protein in CF HAE approximately 100-fold over endogenous levels in non-CF HAE. This efficiency of CFTR delivery fully corrected the basic bioelectric defects of Cl 2 and Na + epithelial ion transport and restored ASL volume regulation and mucus transport to levels approaching those of non-CF HAE. To determine the numbers of CF HAE surface epithelial cells required to express CFTR for restoration of mucus transport to normal levels, different amounts of PIVCFTR were used to express CFTR in 3%-65% of the surface epithelial cells of CF HAE and correlated to increasing ASL volumes and mucus transport rates. These data demonstrate for the first time, to our knowledge, that restoration of normal mucus transport rates in CF HAE was achieved after CFTR delivery to 25% of surface epithelial cells. In vivo experimentation in appropriate models will be required to determine what level of mucus transport will afford clinical benefit to CF patients, but we predict that a future goal for corrective gene transfer to the CF human airways in vivo would attempt to target at least 25% of surface epithelial cells to achieve mucus transport rates comparable to those in non-CF airways.
Output: CFTR Delivery to 25% of Surface Epithelial Cells Restores Normal Rates of Mucus Transport to Human Cystic Fibrosis Airway Epithelium
The World Health Organization (WHO), like many other organisations around the world, has recognised the need to use more rigorous processes to ensure that health care recommendations are informed by the best available research evidence. This is the thirteenth of a series of 16 reviews that have been prepared as background for advice from the WHO Advisory Committee on Health Research to WHO on how to achieve this. We reviewed the literature on applicability, transferability, and adaptation of guidelines. We searched five databases for existing systematic reviews and relevant primary methodological research. We reviewed the titles of all citations and retrieved abstracts and full text articles if the citations appeared relevant to the topic. We checked the reference lists of articles relevant to the questions and used snowballing as a technique to obtain additional information. We used the definition "coming from, concerning or belonging to at least two or all nations" for the term international. Our conclusions are based on the available evidence, consideration of what WHO and other organisations are doing and logical arguments. We did not identify systematic reviews addressing the key questions. We found individual studies and projects published in the peer reviewed literature and on the Internet. • Resources for developing high quality recommendations are limited. Internationally developed recommendations can facilitate access to and pooling of resources, reduce unnecessary duplication, and involve international scientists. • Priority should be given to international health problems and problems that are important in low and middle-income countries, where these advantages are likely to be greatest. • Factors that influence the transferability of recommendations across different settings should be considered systematically and flagged, including modifying factors, important variation in needs, values, costs and the availability of resources.
Output: Improving the use of research evidence in guideline development: 13. Applicability, transferability and adaptation
In the face of the worldwide threat of severe acute respiratory syndrome (SARS) to human life, some of the most urgent challenges are to develop fast and accurate analytical methods for early diagnosis of this disease as well as to create a safe anti-viral vaccine for prevention. To these ends, we investigated the antigenicity of the spike protein (S protein), a major structural protein in the SARS-coronavirus (SARS-CoV). Based upon the theoretical analysis for hydrophobicity of the S protein, 18 peptides were synthesized. Using Enzyme-Linked Immunosorbent Assay (ELISA), these peptides were screened in the sera from SARS patients. According to these results, two fragments of the S gene were amplified by PCR and cloned into pET-32a. Both S fragments were expressed in the BL-21 strain and further purified with an affinity chromatography. These recombinant S fragments were confirmed to have positive cross-reactions with SARS sera, either by Western blot or by ELISA. Our results demonstrated that the potential epitope regions were located at Codons 469-882 in the S protein, and one epitope site was located at Codons 599-620. Identification of antigenic regions in the SARS-CoV S protein may be important for the functional studies of this virus or the development of clinical diagnosis.
Output: A Strategy for Searching Antigenic Regions in the SARS-CoV Spike Protein
Newcastle disease virus (NDV) causes morbidities and mortalities in wild and domestic birds globally. For humans, exposure to infected birds can cause conjunctivitis and influenza-like symptoms. NDV infections in mammals are rarely reported. In this study, using next-generation sequencing, an NDV was identified and isolated from Vero cells inoculated with the nasal swab of an aborted dromedary fetus in Dubai, during the time when an NDV outbreak occurred in a pigeon farm located in close proximity to the dairy camel farm where the mother of the aborted dromedary fetus resided, and there were a lot of pigeons in the camel farm. Genome analysis revealed that the structurally and functionally important features of other NDVs were also present in this dromedary NDV genome. Phylogenetic analysis based on the nucleotide sequences of fusion protein (F), hemagglutinin-neuraminidase protein (HN) and complete polyprotein showed that the virus belonged to sub-genotype VIg of class II NDV and is most closely related to pigeon NDVs in Egypt in the same year. The present study is the first that demonstrated isolation of NDV in dromedaries. Further study is warranted to investigate the relationship between NDV infection and abortion.
Output: First Isolation and Rapid Identification of Newcastle Disease Virus from Aborted Fetus of Dromedary Camel Using Next-Generation Sequencing
The complexities of the dynamic processes and their control associated with biological and ecological systems offer many challenges for the control engineer. Over the past decades the application of dynamic modelling and control has aided understanding of their complexities. At the same time using such complex systems as test-beds for new control methods has highlighted their limitations (e.g. in relation to system identification) and has thus acted as a catalyst for methodological advance. This paper continues the theme of exploring opportunities and achievements in applying modelling and control in the bio-and ecological domains.
Output: DEALING WITH BIO-AND ECOLOGICAL COMPLEXITY: CHALLENGES AND OPPORTUNITIES "Status report prepared by the IFAC Coordinating committee on Bio-and Ecological Systems" by
Chloroquine is a 9-aminoquinolone with well-known anti-malarial effects. It has biochemical properties that could be applied to inhibit viral replication. We report here that chloroquine is able to inhibit influenza A virus replication, in vitro, and the IC50s of chloroquine against influenza A viruses H1N1 and H3N2 are lower than the plasma concentrations reached during treatment of acute malaria. The potential of chloroquine to be added to the limited range of anti-influenza drugs should be explored further, particularly since antiviral drugs play a vital role in influenza pandemic preparedness.
Output: In vitro inhibition of human influenza A virus replication by chloroquine
Purpose: Activation of Toll-like receptor 2 (TLR2) present on circulating monocytes in patients with Kawasaki disease (KD) can lead to the production of proinflammatory cytokines and interleukin-10 (IL-10). We aimed to determine the association of the frequency of circulating TLR2+/ CD14+ monocytes (FTLR2%) with the outcomes of KD, as well as to compare FTLR2% to the usefulness of sIL-10. Methods: The FTLR2% in patients with KD was measured by flow cytometry. Serum levels of IL-10 (sIL-10) were determined in 31 patients with KD before the initial treatment with intravenous immunoglobulin (IVIG) and in 21 febrile controls by using enzyme-linked immunosorbent assay. Patients were classified as having coronary artery lesions (CALs) based on the maximal internal diameters of the proximal right coronary artery and proximal left anterior descending coronary artery one month after the initial diagnosis. Results: We found that FTLR2% greater than 92.62% predicted CALs with 80% sensitivity and 68.4% specificity, whereas FTLR2% more than 94.61% predicted IVIG resistance with 66.7% sensitivity and 71.4% specificity. Moreover, sIL-10 more than 15.52 pg/mL predicted CALs and IVIG resistance with 40% and 66.7% sensitivity, respectively, and 73.7% and 76.2% specificity, respectively. Conclusion: We showed that measuring FTLR2% before the initial treatment could be useful in predicting CAL development with better sensitivity than sIL-10 and with results comparable to sIL-10 results for the prediction of IVIG resistance in patients with KD. However, further studies are necessary to validate FTLR2% as a marker of prognosis and severity of KD.
Output: Kang SJ and Kim NS • Circulating Toll-like receptor 2-positive monocytes in Kawasaki disease Association of Toll-like receptor 2-positive mo- no cytes with coronary artery lesions and treat- ment nonresponse in Kawasaki disease
Free or low-cost sources of unstructured information, such as Internet news and online discussion sites, provide detailed local and near real-time data on disease outbreaks, even in countries that lack traditional public health surveillance. To improve public health surveillance and, ultimately, interventions, we examined 3 primary systems that process event-based outbreak information: Global Public Health Intelligence Network, HealthMap, and EpiSPIDER. Despite similarities among them, these systems are highly complementary because they monitor different data types, rely on varying levels of automation and human analysis, and distribute distinct information. Future development should focus on linking these systems more closely to public health practitioners in the fi eld and establishing collaborative networks for alert verifi cation and dissemination. Such development would further establish event-based monitoring as an invaluable public health resource that provides critical context and an alternative to traditional indicator-based outbreak reporting.
Output: Use of Unstructured Event-Based Reports for Global Infectious Disease Surveillance
Like most positive-strand RNA viruses, hepatitis C virus (HCV) forms a membrane-associated replication complex consisting of replicating RNA, viral and host proteins anchored to altered cell membranes. We used a combination of qualitative and quantitative electron microscopy (EM), immuno-EM, and the 3D reconstruction of serial EM sections to analyze the host cell membrane alterations induced by HCV. Three different types of membrane alteration were observed: vesicles in clusters (ViCs), contiguous vesicles (CVs), and double-membrane vesicles (DMVs). The main ultrastructural change observed early in infection was the formation of a network of CVs surrounding the lipid droplets. Later stages in the infectious cycle were characterized by a large increase in the number of DMVs, which may be derived from the CVs. These DMVs are thought to constitute the membranous structures harboring the viral replication complexes in which viral replication is firmly and permanently established and to protect the virus against double-stranded RNA-triggered host antiviral responses. Keywords HCV Á Host cell membranes Á Membranous web Á Electron microscopy Á 3D reconstruction Abbreviations BSA Bovine serum albumin CM Convoluted membranes CV Contiguous vesicles DENV Dengue virus DMEM Dulbecco's modified Eagle medium DMV Double-membrane vesicle EM Electron microscopy FFU Focus forming unit HCV Hepatitis C virus KUNV Kunjin virus LD Lipid droplet MAbs Mouse monoclonal antibody MMV Multimembrane vesicles MVB Multivesicular bodies ViC Vesicles in cluster VP Vesicle packets WNV West Nile virus E. Blanchard and P. Roingeard are co-last authors. Electronic supplementary material The online version of this article (
Output: Sequential biogenesis of host cell membrane rearrangements induced by hepatitis C virus infection
Chemical compounds studied in this article: Formaldehyde (PubChem CID: 712) Ethanol (PubChem CID: 702) Dexamethasone (PubChem CID: 5743) Polymyxin B (PubChem CID: 49800004). Ethnopharmacological relevance: Houttuynia cordata (HC) has been used as a folk therapy to treat pulmonary infections. This study aimed to determine the role and mechanism of action of polysaccharides isolated from HC (HCP) in lipopolysaccharide (LPS)-induced ALI in the mice. Materials and methods: LPS was delivered by the intratracheal route to Balb/c mice 2 h before HCP (40, 80 and 160 mg/kg) administration. Results: The number of total cells, protein and tumor necrosis factor-α (TNF-α) concentrations in bronchoalveolar lavage fluid, the wet/dry weight ratio (w/d) of lungs and pulmonary pathology of each mouse were analyzed, it was found that HCP significantly alleviated ALI induced by LPS. Moreover, in lungs of mice, it was found that the infiltration of inflammatory cells, the expression of Toll-like receptor 4 and complement deposition were significantly decreased by HCP treatment. In vitro assays showed that C5a, a complement activation product, induced significant macrophage migration and treatment with HCP prevented it. The in vitro results also proved that LPS increased nitric oxide and pro-inflammatory cytokines (TNF-α, interleukin-6, and interleukin-1β) production, and HCP antagonized these effects of LPS. It was also found that HCP alone augmented secretion of some pro-inflammatory cytokines. Conclusion: These results indicate that HCP may alleviate LPS induced lung inflammatory injury, which may be associated with its inhibitory effect on the over activation of complement and macrophages. This suggests a potential role to treat ALI.
Output: Houttuynia cordata Thunb. polysaccharides ameliorates lipopolysaccharide-induced acute lung injury in mice
Respiratory fi lters (also known as bacterial or microbial fi lters) are devices with a high capacity to prevent the passage of microorganisms [ 1 ] and are placed in the breathing circuit in order to protect the patient from possible respiratory infections carried by the respirator. The use of respiratory fi lters was proposed after the reports between 1952 and 1972 of several outbreaks of respiratory infection attributed to contamination of anesthesia machines [2] [3] [4] . However, the results of later studies showed no contamination of patients by anesthesia machines, and vice versa [5] [6] [7] [8] [9] , and that they could have undesirable effects [ 10 ] and did not decrease the incidence of ventilator-associated pneumonia (VAP) in clinical studies [11] [12] [13] ; therefore, its usefulness is questioned. The internal component of the fi lters can be composed of different materials [ 1 ] : wool, foam, paper, polypropylene, polysulfone, ceramics or glass fi bers. Filters can have different mechanisms of microbial fi ltration [ 1 ] : (1) mechanical fi ltration, (2) electrostatic fi ltration and (3) fi ltration bactericides.
Output: 20 Respiratory Filters and Ventilator-Associated Pneumonia: Composition, Efficacy Tests and Advantages and Disadvantages
Camels have cultural value in the Arab society and are considered one of the most important animals in the Arabian Peninsula and arid environments, due to the distinct characteristics of their meat and milk. Moreover, there is a great interest in camel racing and beauty shows. Therefore, treatment of elite animals, increasing the number of camels as well as genetic improvement is an essential demand. Because there are unique camels for milk production, meat, or in racing, the need to propagate genetically superior camels is urgent. Recent biotechnological approaches such as stem cells hold great promise for biomedical research, genetic engineering, and as a model for studying early mammalian developmental biology. Establishment of stem cells lines from camels would tremendously facilitate regenerative medicine for genetically superior camels, permit the gene targeting of the camel genome and the generation of genetically modified animal and be a mean for genome conservation for the elite breeds. In this mini-review, we show the current research, future horizons and potential applications for camel stem cells.
Output: The current perspectives of dromedary camel stem cells research
Shigella species are a common cause of acute diarrheal disease in China. In this study, we characterized the changing trends and serotype distribution of Shigella species in Beijing from 1994 to 2010. A total of 5999 Shigella strains were isolated and serotyped from the 302nd Hospital in Beijing. The annual number of Shigella isolates reached a peak (n = 1192; 19.84%) in 1996 and then decreased annually, reaching the lowest point (n = 24; 0.41%) in 2010. S. flexneri 2a and S. sonnei were the most frequently isolated Shigella, with their respective isolates making up 53.3% and 27.6% of the total. Isolates of S. flexneri 4c, 4a, and x made up 3% respectively of the total isolates. Significant decreases in percentage of S. flexneri over time were observed. S. sonnei surpassed S. flexneri 2a as the predominant serotype in 2000. Most isolates were recovered from July to September; 13.6% of the isolates were recovered from children aged 0 to 5 years, and 16% were recovered from those aged 21 to 25 years. S. flexneri 2a and 5 were recovered mostly from males (33.41%, p < 0.001; and 0.46%, p < 0.001%; respectively), whereas S. flexneri 2b and 6, and S. sonnei were most often isolated from females. Continuous monitoring of Shigella showed that all 4 species and 27 serotypes were present in Beijing, China, during the study period. The emergence of S. sonnei and the overall decreasing isolation rate of Shigella in Beijing can potentially aid in the development of vaccine and control strategies for shigellosis in the city.
Output: Changing trends and serotype distribution of Shigella species in Beijing from 1994 to 2010
To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of 13 C α chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue α/β protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed 13 C α chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical 13 C α chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed 13 C α chemical shifts, Δ ca,i , for the individual residues along the sequence. This indicates that the Δ ca,i -values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.
Output: Sequential nearest-neighbor effects on computed 13 C α chemical shifts NIH Public Access
Murine norovirus-1 (MNV-1) is known to subvert host cell division inducing an accumulation of cells in the G 0 /G 1 phase, creating conditions where viral replication is favored. This study identified that NS5 (VPg), is capable of inducing cell cycle arrest in the absence of viral replication or other viral proteins in an analogous manner to MNV-1 infection. NS5 expression induced an accumulation of cells in the G 0 /G 1 phase in an asynchronous population by inhibiting progression at the G 1 /S restriction point. Furthermore, NS5 expression resulted in a down-regulation of cyclin A expression in asynchronous cells and inhibited cyclin A expression in cells progressing from G 1 to S phase. The activity of NS5 on the host cell cycle occurs through an uncharacterized function. Amino acid substitutions of NS5(Y26A) and NS5(F123A) that inhibit the ability for NS5 to attach to RNA and recruit host eukaryotic translation initiation factors, respectively, retained the ability to induce an accumulation of cells in the G 0 /G 1 phase as identified for wild-type NS5. To the best of our knowledge, this is the first report of a VPg protein manipulating the host cell cycle.
Output: Expression of the NS5 (VPg) Protein of Murine Norovirus Induces a G1/S Phase Arrest
Porcine epidemic diarrhea virus (PEDV) is a causative agent of porcine epidemic diarrhea; consequently, the small intestine was believed to be its only target organ. In this study, we found that PEDV infected not only the small intestines, but also the respiratory tract. Infection and replication of PEDV in the respiratory tract from naturally PEDV-infected piglets were examined by reverse transcription polymerase chain reaction, immunohistochemistry, and virus re-isolation. Our observations were confirmed by experimental inoculation, and we found that PEDV infection in the respiratory tract was specifically associated with alveolar macrophages in the lung. Vero cell-adapted PEDV was able to replicate in both primary alveolar macrophages and continuous porcine alveolar macrophage cells. Sequencing analysis of the spike (S) glycoprotein revealed that mutations in S might be a potential determinant of auxiliary targets for PEDV. The discovery that PEDV infects and replicates in alveolar macrophages provides new insights into its pathogenesis.
Output: Porcine epidemic diarrhea virus infects and replicates in porcine alveolar macrophages
Ebola virus (EboV) belongs to the Filoviridae family of viruses that causes severe and fatal hemhorragic fever. Infection by EboV involves fusion between the virus and host cell membranes mediated by the envelope glycoprotein GP2 of the virus. Similar to the envelope glycoproteins of other viruses, the central feature of the GP2 ectodomain postfusion structure is a six-helix bundle formed by the protein's N-and C-heptad repeat regions (NHR and CHR, respectively). Folding of this six-helix bundle provides the energetic driving force for membrane fusion; in other viruses, designed agents that disrupt formation of the six-helix bundle act as potent fusion inhibitors. To interrogate determinants of EboV GP2-mediated membrane fusion, we designed model proteins that consist of the NHR and CHR segments linked by short protein linkers. Circular dichroism and gel filtration studies indicate that these proteins adopt stable ahelical folds consistent with design. Thermal denaturation indicated that the GP2 six-helix bundle is highly stable at pH 5.3 (melting temperature, T m , of 86.8 6 2.0°C and van't Hoff enthalpy, DH vH , of 228.2 6 1.0 kcal/mol) and comparable in stability to other viral membrane fusion six-helix bundles. We found that the stability of our designed a-helical bundle proteins was dependent on buffering conditions with increasing stability at lower pH. Small pH differences (5.3-6.1) had dramatic effects (DT m 5 37°C) suggesting a mechanism for conformational control that is dependent on environmental pH. These results suggest a role for low pH in stabilizing six-helix bundle formation during the process of GP2-mediated viral membrane fusion.
Output: Designed protein mimics of the Ebola virus glycoprotein GP2 a-helical bundle: Stability and pH effects
In May 2014, a traveler from the Kingdom of Saudi Arabia was the first person identified with Middle East respiratory syndrome coronavirus (MERS-CoV) infection in the United States. To evaluate transmission risk, we determined the type, duration, and frequency of patient contact among health care personnel (HCP), household, and community contacts by using standard questionnaires and, for HCP, global positioning system (GPS) tracer tag logs. Respiratory and serum samples from all contacts were tested for MERS-CoV. Of 61 identified contacts, 56 were interviewed. HCP exposures occurred most frequently in the emergency department (69%) and among nurses (47%); some HCP had contact with respiratory secretions. Household and community contacts had brief contact (e.g., hugging). All laboratory test results were negative for MERS-CoV. This contact investigation found no secondary cases, despite case-patient contact by 61 persons, and provides useful information about MERS-CoV transmission risk. Compared with GPS tracer tag recordings, self-reported contact may not be as accurate.
Output: Lack of Transmission among Close Contacts of Patient with Case of Middle East Respiratory Syndrome Imported into the United States, 2014
Hepatitis C is a serious health issue and cause liver disorders in millions of people. Available therapeutic agents require long term administration with numerous side effects. Therefore, there is a dire need to find alternative treatment options for this disease. Since ancient times, medicinal plants are widely used to cure various diseases with no or less harmful effects. Therefore, this study was designed to find out phytochemicals and investigate antiviral activity of methanol extract of Ajuga bracteosa, Ajuga parviflora, Berberis lycium and Citrus lemon against Hepatitis C Virus (HCV infection). Phytochemical analysis of the plant extract was performed using various chemical tests. Toxicity of the plant extract was determined against using trypan blue exclusion method. Antiviral activity of the selected plant extract was find out against HCV infected HepG2 cells. For this purpose, HepG2 cells were seeded with HCV positive and negative serum and nontoxic doses of plant extract for 24 and 48 h. After this RNA was extracted and viral load was determined using Real-time PCR. Phytochemical analysis showed the presence of flavonoids and phenols in all plant extracts while amino acids, alkaloids and tannins were present in B. lycium and saponins were detected in C. lemon. Toxicity assay showed that all plant extracts were nontoxic at maximum concentration of 200 μg/ml except B. lycium, which showed mild toxicity at 40 μg/ml and were extremely toxic at 60 μg/ml and above doses. Real-time PCR quantitation result revealed that after 24 h treatments A. parviflora showed highest antiviral activity, followed by A. bracteosa, while B. lycium extract had low (35%) and C. lemon has no antiviral effects. The 48 h treatments showed an increase antiviral activity by A. bracteosa followed by A. parviflora and B. lycium while C. lemon showed negative effect. Our results depicted that mentioned plants might be used as an alternative therapeutic regime or in combination with existing treatments against HCV.
Output: Phytochemical profiling and antiviral activity of Ajuga bracteosa, Ajuga parviflora, Berberis lycium and Citrus lemon against Hepatitis C Virus
A cross-classified and multiple membership Cox model was applied to calf mortality data from Western Canada, where 23,409 calves from 174 herds were followed for up to 180 days after calving. The herds were cross-classified by 49 veterinary clinics and 9 ecological regions and in a multiple membership relation to the veterinary clinics, resulting in a 3level cross-classified and multiple membership data structure. The model was formulated in a mixed-effects Poisson model framework with normally distributed random effects, and was fitted to the data by Bayesian Markov Chain Monte Carlo (MCMC) estimation. Important fixed effects included whether the calf was a twin, calf gender, assistance at calving, cow age, average temperature the first week after calving, the percentage of the herd that had already calved, whether calf shelters were provided, whether cow-calf pairs were moved to a nursery area, and whether any animals were purchased into the herd at or near the time of calving. The analysis demonstrated a greater variation among herds than among both ecological regions and veterinary clinics. Further, a simulation study for a setting similar to the real data gave evidence that the used approach provides valid estimates.
Output: A cross-classified and multiple membership Cox model applied to calf mortality data
The unfolded protein response (UPR) is a stress-induced cyto-protective mechanism elicited towards an influx of large amount of proteins in the endoplasmic reticulum (ER). In the present study, we evaluated if AAV manipulates the UPR pathways during its infection. We first examined the role of the three major UPR axes, namely, endoribonuclease inositolrequiring enzyme-1 (IRE1a), activating transcription factor 6 (ATF6) and PKR-like ER kinase (PERK) in AAV infected cells. Total RNA from mock or AAV infected HeLa cells were used to determine the levels of 8 different ER-stress responsive transcripts from these pathways. We observed a significant up-regulation of IRE1a (up to 11 fold) and PERK (up to 8 fold) genes 12-48 hours after infection with self-complementary (sc)AAV2 but less prominent with single-stranded (ss)AAV2 vectors. Further studies demonstrated that scAAV1 and scAAV6 also induce cellular UPR in vitro, with AAV1 vectors activating the PERK pathway (3 fold) while AAV6 vectors induced a significant increase on all the three major UPR pathways [6-16 fold]. These data suggest that the type and strength of UPR activation is dependent on the viral capsid. We then examined if transient inhibition of UPR pathways by RNA interference has an effect on AAV transduction. siRNA mediated silencing of PERK and IRE1a had a modest effect on AAV2 and AAV6 mediated gene expression (,1.5-2 fold) in vitro. Furthermore, hepatic gene transfer of scAAV2 vectors in vivo, strongly elevated IRE1a and PERK pathways (2 and 3.5 fold, respectively). However, when animals were pre-treated with a pharmacological UPR inhibitor (metformin) during scAAV2 gene transfer, the UPR signalling and its subsequent inflammatory response was attenuated concomitant to a modest 2.8 fold increase in transgene expression. Collectively, these data suggest that AAV vectors activate the cellular UPR pathways and their selective inhibition may be beneficial during AAV mediated gene transfer.
Output: Associated Virus Vectors
This study investigates and compares the virucidal performances of photocatalytic (PC) and photoelectrocatalytic (PEC) treatments in the presence and absence of halides, such as Br À and Cl À , under comparable experimental conditions. The results confirm that the PC virucidal efficiency can be enhanced in the presence of low halide concentrations (e.g., X = Br À or Cl À ) and further enhanced by applying potential bias onto the photoanode in a PEC system. The PEC treatment in the presence of 1.0 mM Br (PEC-Br) shows the highest virucidal efficiency, enabling complete inactivation of a $1000 TCID50 replication-deficient recombinant adenovirus (RDRADS) population within 31.7 s. The superior virucidal performances of PEC-X treatments can be attributed to the increased production of active oxygen species and additional viricides resulting from the PEC halide oxidation, as well as prolonged lifetime of photoholes (h + ) for direct inactivation. The findings of this work confirm that new forms of active species generated in situ via a PC or PEC process are effective for viruses.
Output: Adenovirus inactivation by in situ photocatalytically and photoelectrocatalytically generated halogen viricides
Acute Hemorrhagic Edema (AHE) is a rare form of leukocytoclastic vasculitis with an unknown etiology. There are various possible triggers associated with the development of AHE such as Upper Respiratory Tract related infections which have been reported in the literature. A typical case of AHE is a child less than 2 years of age having the symptoms of fever, Acral Targetoid Purpura, and Edema. The course of this illness is benign with a complete resolution within few weeks. This case report involves a patient having the classical symptoms of fever, Purpura and Edema, but with an unusual extensive truncal involvement. Moreover, Rhinovirus infection testing was positive in the child's case. The presence of the virus gives a suspicion of being the possible trigger for the boy's AHE. In the previous hospital, the treatment started with steroid for a course of one week without a significant improvement which brought the patients to the Emergency department. A decision of continuing a supportive treatment led to a complete resolution. After 3 weeks the AHE symptoms were gone without any complications.
Output: Acute Hemorrhagic Edema with extensive truck involvement and Rhinovirus infection association- NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Programmed cell death-1 (PD-1) receptor signaling dampens the functionality of T cells faced with repetitive antigenic stimulation from chronic infections or tumors. Using intracerebral (i.c.) inoculation with mouse polyomavirus (MuPyV), we have shown that CD8 T cells establish a PD-1 hi , tissue-resident memory population in the brains (bT RM ) of mice with a low-level persistent infection. In MuPyV encephalitis, PD-L1 was expressed on infiltrating myeloid cells, microglia and astrocytes, but not on oligodendrocytes. Engagement of PD-1 on anti-MuPyV CD8 T cells limited their effector activity. NanoString gene expression analysis showed that neuroinflammation was higher in PD-L1 −/− than wild type mice at day 8 post-infection, the peak of the MuPyV-specific CD8 response. During the persistent phase of infection, however, the absence of PD-1 signaling was found to be associated with a lower inflammatory response than in wild type mice. Genetic disruption and intracerebroventricular blockade of PD-1 signaling resulted in an increase in number of MuPyV-specific CD8 bT RM and the fraction of these cells expressing CD103, the αE integrin commonly used to define tissue-resident T cells. However, PD-L1 −/− mice persistently infected with MuPyV showed impaired virus control upon i.c. re-infection with MuPyV. Collectively, these data reveal a temporal duality in PD-1-mediated regulation of MuPyV-associated neuroinflammation. PD-1 signaling limited the severity of neuroinflammation during acute infection but sustained a level of inflammation during persistent infection for maintaining control of virus re-infection.
Output: a section of the journal Frontiers in Immunology PD-1 Dynamically Regulates Inflammation and Development of Brain-Resident Memory CD8 T Cells During Persistent Viral Encephalitis
Background: Proteolytic processing of the Lassa virus envelope glycoprotein precursor GP-C by the host proprotein convertase site 1 protease (S1P) is a prerequisite for the incorporation of the subunits GP-1 and GP-2 into viral particles and, hence, essential for infectivity and virus spread. Therefore, we tested in this study the concept of using S1P as a target to block efficient virus replication. We demonstrate that stable cell lines inducibly expressing S1P-adapted a 1 -antitrypsin variants inhibit the proteolytic maturation of GP-C. Introduction of the S1P recognition motifs RRIL and RRLL into the reactive center loop of a 1 -antitrypsin resulted in abrogation of GP-C processing by endogenous S1P to a similar level observed in S1P-deficient cells. Moreover, S1P-specific a 1 -antitrypsins significantly inhibited replication and spread of a replication-competent recombinant vesicular stomatitis virus expressing the Lassa virus glycoprotein GP as well as authentic Lassa virus. Inhibition of viral replication correlated with the ability of the different a 1 -antitrypsin variants to inhibit the processing of the Lassa virus glycoprotein precursor. Conclusions/Significance: Our data suggest that glycoprotein cleavage by S1P is a promising target for the development of novel anti-arenaviral strategies. Citation: Maisa A, Strö her U, Klenk H-D, Garten W, Strecker T (2009) Inhibition of Lassa Virus Glycoprotein Cleavage and Multicycle Replication by Site 1 Protease-Adapted a 1 -Antitrypsin Variants. PLoS Negl Trop Dis 3(6): e446.
Output: Inhibition of Lassa Virus Glycoprotein Cleavage and Multicycle Replication by Site 1 Protease-Adapted a 1 - Antitrypsin Variants