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Adverse Events Post Smallpox-Vaccination: Insights from Tail Scarification Infection in Mice with Vaccinia virus  [PDF]
Bruno E. F. Mota,Nadia Gallardo-Romero,Giliane Trindade,M. Shannon Keckler,Kevin Karem,Darin Carroll,Marco A. Campos,Leda Q. Vieira,Flávio G. da Fonseca,Paulo C. P. Ferreira,Cláudio A. Bonjardim,Inger K. Damon,Erna G. Kroon
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0018924
Abstract: Adverse events upon smallpox vaccination with fully-replicative strains of Vaccinia virus (VACV) comprise an array of clinical manifestations that occur primarily in immunocompromised patients leading to significant host morbidity/mortality. The expansion of immune-suppressed populations and the possible release of Variola virus as a bioterrorist act have given rise to concerns over vaccination complications should more widespread vaccination be reinitiated. Our goal was to evaluate the components of the host immune system that are sufficient to prevent morbidity/mortality in a murine model of tail scarification, which mimics immunological and clinical features of smallpox vaccination in humans. Infection of C57BL/6 wild-type mice led to a strictly localized infection, with complete viral clearance by day 28 p.i. On the other hand, infection of T and B-cell deficient mice (Rag1?/?) produced a severe disease, with uncontrolled viral replication at the inoculation site and dissemination to internal organs. Infection of B-cell deficient animals (μMT) produced no mortality. However, viral clearance in μMT animals was delayed compared to WT animals, with detectable viral titers in tail and internal organs late in infection. Treatment of Rag1?/? with rabbit hyperimmune anti-vaccinia serum had a subtle effect on the morbidity/mortality of this strain, but it was effective in reduce viral titers in ovaries. Finally, NUDE athymic mice showed a similar outcome of infection as Rag1?/?, and passive transfer of WT T cells to Rag1?/? animals proved fully effective in preventing morbidity/mortality. These results strongly suggest that both T and B cells are important in the immune response to primary VACV infection in mice, and that T-cells are required to control the infection at the inoculation site and providing help for B-cells to produce antibodies, which help to prevent viral dissemination. These insights might prove helpful to better identify individuals with higher risk of complications after infection with poxvirus.
Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources
Sem Genini, Bouabid Badaoui, Gert Sclep, Stephen C Bishop, Dave Waddington, Marie-Hélène Pinard van der Laan, Christophe Klopp, Cédric Cabau, Hans-Martin Seyfert, Wolfram Petzl, Kirsty Jensen, Elizabeth J Glass, Astrid de Greeff, Hilde E Smith, Mari A Smits, Ingrid Olsaker, Guro M Boman, Giuliano Pisoni, Paolo Moroni, Bianca Castiglioni, Paola Cremonesi, Marcello Del Corvo, Eliane Foulon, Gilles Foucras, Rachel Rupp, Elisabetta Giuffra
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-225
Abstract: Ingenuity Pathway Analysis of affected genes showed that the four meta-analysis combinations share biological functions and pathways (e.g. protein ubiquitination and polyamine regulation) which are intrinsic to the general disease response. In the overall response, pathways related to immune response and inflammation, as well as biological functions related to lipid metabolism were altered. This latter observation is consistent with the milk fat content depression commonly observed during mastitis infection. Complementarities between early and late stage responses were found, with a prominence of metabolic and stress signals in the early stage and of the immune response related to the lipid metabolism in the late stage; both mechanisms apparently modulated by few genes, including XBP1 and SREBF1.The cattle-specific response was characterized by alteration of the immune response and by modification of lipid metabolism. Comparison of E. coli and S. aureus infections in cattle in vivo revealed that affected genes showing opposite regulation had the same altered biological functions and provided evidence that E. coli caused a stronger host response.This meta-analysis approach reinforces previous findings but also reveals several novel themes, including the involvement of genes, biological functions, and pathways that were not identified in individual studies. As such, it provides an interesting proof of principle for future studies combining information from diverse heterogeneous sources.In the last decade, gene expression profiling microarrays have been widely used in animal genomics and this technique has enabled researchers to monitor, on a broad scale, the effects of pathogens on host cells and tissues, aiming to gain insight into the molecular mechanisms that are involved in the host-pathogen interactions. Mastitis is one of the most costly diseases of the dairy industry, which makes it among the major concerns for the livestock sector [1]. As a consequence, numero
Infection of Burkholderia cepacia Induces Homeostatic Responses in the Host for Their Prolonged Survival: The Microarray Perspective  [PDF]
Vanitha Mariappan, Kumutha Malar Vellasamy, Jaikumar Thimma, Onn Haji Hashim, Jamuna Vadivelu
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0077418
Abstract: Burkholderia cepacia?is an opportunistic human pathogen associated with life-threatening pulmonary infections in immunocompromised individuals. Pathogenesis of B. cepacia infection involves adherence, colonisation, invasion, survival and persistence in the host. In addition, B. cepacia are also known to secrete?factors, which are associated with virulence in the pathogenesis of the infection. In this study, the host factor that may be the cause of the infection was elucidated in human epithelial cell line, A549, that was exposed to live?B. cepacia?(mid-log phase) and its secretory proteins (mid-log and early-stationary phases) using the Illumina Human Ref-8 microarray platform. The non-infection A549 cells were used as a control. Expression of the host genes that are related to apoptosis, inflammation and cell cycle as well as metabolic pathways were differentially regulated during the infection. Apoptosis of the host cells and secretion of pro-inflammatory cytokines were found to be inhibited by both live?B. cepacia?and its secretory proteins. In contrast, the host cell cycle and metabolic processes, particularly glycolysis/glycogenesis and fatty acid metabolism were transcriptionally up-regulated during the infection. Our microarray analysis provided preliminary insights into mechanisms of?B. cepacia?pathogenesis. The understanding of host response to an infection would provide novel therapeutic targets both for enhancing the host’s defences and repressing detrimental responses induced by the invading pathogen.
Microarray data analysis: Gaining biological insights  [PDF]
Rumdeep Kaur Grewal, Sampa Das
Journal of Biomedical Science and Engineering (JBiSE) , 2013, DOI: 10.4236/jbise.2013.610124
Abstract: DNA microarray is a widely used technique which allows one to identify the genes that are similarly or differentially expressed in different cell types or conditions, to learn how their expression levels change in different developmental stages or disease states, and to identify the cellular processes in which they participate. This technology produces a large amount of complex data, necessitating employment of multiple bioinformatics and computational tools and techniques to provide a comprehensive view of the underlying biology. This review overviews methods and techniques which may be employed to analyze and interpret microarray data. The focus is primarily on analysis of gene expression matrices to obtain biological insights to this end. Both supervised and unsupervised methods commonly used for expression data analysis have been discussed. Data visualization techniques which may be used to comprehend biological relevance of the data has also been discussed in brief.

Microarray Analysis of the Intestinal Host Response in Giardia duodenalis Assemblage E Infected Calves  [PDF]
Leentje Dreesen, Manuela Rinaldi, Koen Chiers, Robert Li, Thomas Geurden, Wim Van den Broeck, Bruno Goddeeris, Jozef Vercruysse, Edwin Claerebout, Peter Geldhof
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0040985
Abstract: Despite Giardia duodenalis being one of the most commonly found intestinal pathogens in humans and animals, little is known about the host-parasite interactions in its natural hosts. Therefore, the objective of this study was to investigate the intestinal response in calves following a G. duodenalis infection, using a bovine high-density oligo microarray to analyze global gene expression in the small intestine. The resulting microarray data suggested a decrease in inflammation, immune response, and immune cell migration in infected animals. These findings were examined in more detail by histological analyses combined with quantitative real-time PCR on a panel of cytokines. The transcription levels of IL-6, IL-8, IL-13, IL-17, and IFN-γ showed a trend of being downregulated in the jejunum of infected animals compared to the negative controls,.No immune cell recruitment could be seen after infection, and no intestinal pathologies, such as villus shortening or increased levels of apoptosis. Possible regulators of this intestinal response are the nuclear peroxisome proliferator-activated receptors alpha (PPARα), and gamma (PPARγ) and the enzyme adenosine deaminase (ADA), all for which an upregulated expression was found in the microarray and qRT-PCR analyses.
Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events
Sónia S Albuquerque, Céline Carret, Ana Grosso, Alice S Tarun, Xinxia Peng, Stefan HI Kappe, Miguel Prudêncio, Maria M Mota
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-270
Abstract: To gain new insights into the molecular host-parasite interactions that take place during malaria liver infection, we have used high-throughput microarray technology to determine the transcriptional profile of P. berghei-infected hepatoma cells. The data analysis shows differential expression patterns for 1064 host genes starting at 6 h and up to 24 h post infection, with the largest proportion correlating specifically with the early stages of the infection process. A considerable proportion of those genes were also found to be modulated in liver cells collected from P. yoelii-infected mice 24 and 40 h after infection, strengthening the data obtained with the in vitro model and highlighting genes and pathways involved in the host response to rodent Plasmodium parasites.Our data reveal that host cell infection by Plasmodium sporozoites leads to a coordinated and sequential set of biological events, ranging from the initial stage of stress response up to the engagement of host metabolic processes and the maintenance of cell viability throughout infection.Malaria remains a major health problem worldwide with 35% of the human population being at risk of becoming infected [1]. The disease is caused by parasitic protozoa of the genus Plasmodium, which reach their mammalian host through the bite of an infected female Anopheles mosquito. The biological events that occur between the bite of a malaria-infected mosquito and the release of Plasmodium merozoites into the bloodstream are obligatory steps in the establishment of a malaria infection. Recently, our knowledge of the initial steps occurring in the skin immediately after mosquito bite increased (reviewed in [2]). We now also have a greater understanding not only of how sporozoites traverse the liver sinusoids and reach the hepatocytes before invading a final cell and forming a parasitophorous vacuole [3,4], but also of how, inside hepatocytes, the so-called exoerythrocytic forms (EEFs) of the Plasmodium parasite develo
Transcriptional Interactions During Smallpox Infection and Identification of Early Infection Biomarkers  [PDF]
Willy A. Valdivia-Granda,Maricel G. Kann,Jose Malaga
Quantitative Biology , 2006,
Abstract: Smallpox is a deadly disease that can be intentionally reintroduced into the human population as a bioweapon. While host gene expression microarray profiling can be used to detect infection, the analysis of this information using unsupervised and supervised classification techniques can produce contradictory results. Here, we present a novel computational approach to incorporate molecular genome annotation features that are key for identifying early infection biomarkers (EIB). Our analysis identified 58 EIBs expressed in peripheral blood mononuclear cells (PBMCs) collected from 21 cynomolgus macaques (Macaca fascicularis) infected with two variola strains via aerosol and intravenous exposure. The level of expression of these EIBs was correlated with disease progression and severity. No overlap between the EIBs co-expression and protein interaction data reported in public databases was found. This suggests that a pathogen-specific re-organization of the gene expression and protein interaction networks occurs during infection. To identify potential genome-wide protein interactions between variola and humans, we performed a protein domain analysis of all smallpox and human proteins. We found that only 55 of the 161 protein domains in smallpox are also present in the human genome. These co-occurring domains are mostly represented in proteins involved in blood coagulation, complement activation, angiogenesis, inflammation, and hormone transport. Several of these proteins are within the EIBs category and suggest potential new targets for the development of therapeutic countermeasures.
Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray
Ilanit Samolski, Alberto de Luis, Juan Vizcaíno, Enrique Monte, M Belén Suárez
BMC Microbiology , 2009, DOI: 10.1186/1471-2180-9-217
Abstract: Global microarray analysis revealed 1,617 probe sets showing differential expression in T. harzianum mycelia under at least one of the culture conditions tested as compared with one another. Hierarchical clustering and heat map representation showed that the expression patterns obtained in glucose medium clustered separately from the expression patterns observed in the presence of tomato plants and chitin. Annotations using the Blast2GO suite identified 85 of the 257 transcripts whose probe sets afforded up-regulated expression in response to tomato plants. Some of these transcripts were predicted to encode proteins related to Trichoderma-host (fungus or plant) associations, such as Sm1/Elp1 protein, proteases P6281 and PRA1, enchochitinase CHIT42, or QID74 protein, although previously uncharacterized genes were also identified, including those responsible for the possible biosynthesis of nitric oxide, xenobiotic detoxification, mycelium development, or those related to the formation of infection structures in plant tissues.The effectiveness of the Trichoderma HDO microarray to detect different gene responses under different growth conditions in the fungus T. harzianum strongly indicates that this tool should be useful for further assays that include different stages of plant colonization, as well as for expression studies in other Trichoderma spp. represented on it. Using this microarray, we have been able to define a number of genes probably involved in the transcriptional response of T. harzianum within the first hours of contact with tomato plant roots, which may provide new insights into the mechanisms and roles of this fungus in the Trichoderma-plant interaction.The ability of some fungal species of the genus Trichoderma to suppress disease and stimulate the growth and development of plants explains the wide and long-term use of these organisms in many crops [1]. Traditionally, the beneficial effects of Trichoderma spp. on plants have been attributed to their
Microarray Analysis of Human Monocytes Infected with Francisella tularensis Identifies New Targets of Host Response Subversion  [PDF]
Jonathan P. Butchar, Thomas J. Cremer, Corey D. Clay, Mikhail A. Gavrilin, Mark D. Wewers, Clay B. Marsh, Larry S. Schlesinger, Susheela Tridandapani
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002924
Abstract: Francisella tularensis is a gram-negative facultative bacterium that causes the disease tularemia, even upon exposure to low numbers of bacteria. One critical characteristic of Francisella is its ability to dampen or subvert the host immune response. In order to help understand the mechanisms by which this occurs, we performed Affymetrix microarray analysis on transcripts from blood monocytes infected with the virulent Type A Schu S4 strain. Results showed that expression of several host response genes were reduced such as those associated with interferon signaling, Toll-like receptor signaling, autophagy and phagocytosis. When compared to microarrays from monocytes infected with the less virulent F. tularensis subsp. novicida, we found qualitative differences and also a general pattern of quantitatively reduced pro-inflammatory signaling pathway genes in the Schu S4 strain. Notably, the PI3K / Akt1 pathway appeared specifically down-regulated following Schu S4 infection and a concomitantly lower cytokine response was observed. This study identifies several new factors potentially important in host cell subversion by the virulent Type A F. tularensis that may serve as novel targets for drug discovery.
Differential Expression of microRNAs in the Non-Permissive Schistosome Host Microtus fortis under Schistosome Infection  [PDF]
Hongxiao Han, Jinbiao Peng, Yanhui Han, Min Zhang, Yang Hong, Zhiqiang Fu, Jianmei Yang, Jianping Tao, Jiaojiao Lin
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0085080
Abstract: The reed vole Microtus fortis is the only mammal known in China in which the growth, development and maturation of schistosomes (Schistosoma japonicum) is prevented. It might be that the anti-schistosomiasis mechanisms of M. fortis associate with microRNA-mediated gene expression, given that the latter has been found to be involved in gene regulation in eukaryotes. In the present study, the difference between pathological changes in tissues of M. fortis and of mice (Mus musculus) post-schistosome infection were observed by using hematoxylin-eosin staining. In addition, microarray technique was applied to identify differentially expressed miRNAs in the same tissues before and post-infection to analyze the potential roles of miRNAs in schistosome infection in these two different types of host. Histological analyses showed that S. japonicum infection in M. fortis resulted in a more intensive inflammatory response and pathological change than in mice. The microarray analysis revealed that 162 miRNAs were expressed in both species, with 12 in liver, 32 in spleen and 34 in lung being differentially expressed in M. fortis. The functions of the differentially expressed miRNAs were mainly revolved in nutrient metabolism, immune regulation, etc. Further analysis revealed that important signaling pathways were triggered after infection by S. japonicum in M. fortis but not in the mice. These results provide new insights into the general mechanisms of regulation in the non-permissive schistosome host M. fortis that exploits potential miRNA regulatory networks. Such information will help improve current understanding of schistosome development and host–parasite interactions.
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