A murine model for neuropsychiatric disorders associated with group A β-hemolytic streptococcal infection

A syndrome of motoric and neuropsychiatric symptoms comprising various elements, including chorea, hyperactivity, tics, emotional lability, and obsessive-compulsive symptoms, can occur in association with group A β-hemolytic streptococcal (GABHS) infection. We tested the hypothesis that an immune response to GABHS can result in behavioral abnormalities. Female SJL/J mice were immunized and boosted with a GABHS homogenate in Freund's adjuvant, whereas controls received Freund's adjuvant alone. When sera from GABHS-immunized mice were tested for immunoreactivity to mouse brain, a subset was found to be immunoreactive to several brain regions, including deep cerebellar nuclei (DCN), globus pallidus, and thalamus. GABHS-immunized mice having serum immunoreactivity to DCN also had increased IgG deposits in DCN and exhibited increased rearing behavior in open-field and hole-board tests compared with controls and with GABHS-immunized mice lacking serum anti-DCN antibodies. Rearing and ambulatory behavior were correlated with IgG deposits in the DCN and with serum immunoreactivity to GABHS proteins in Western blot. In addition, serum from a GABHS mouse reacted with normal mouse cerebellum in nondenaturing Western blots and immunoprecipitated C4 complement protein and α-2-macroglobulin. These results are consistent with the hypothesis that immune response to GABHS can result in motoric and behavioral disturbances and suggest that anti-GABHS antibodies cross-reactive with brain components may play a role in their pathophysiology

Nonparametric methods for the analysis of single-color pathogen microarrays

<p>Abstract</p> <p>Background</p> <p>The analysis of oligonucleotide microarray data in pathogen surveillance and discovery is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied.</p> <p>Results</p> <p>Positive predictive value and false positive rates were examined to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney <it>U</it>, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, the chi-square proved most useful.</p> <p>Conclusions</p> <p>The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy.</p

Molecular characterization of severe and mild cases of Influenza A (H1N1) 2009 strain from Argentina

While worldwide pandemic influenza A(H1N1) pdm case fatality rate (CFR) was 0.4%, Argentina's was 4.5%. A total of 34 strains from mild and severe cases were analyzed. A full genome sequencing was carried out on 26 of these, and a partial sequencing on the remaining eight. We observed no evidence that the high CFR can be attributed to direct virus changes. No evidence of re-assortment, mutations associated with resistance to antiviral drugs, or genetic drift that might contribute to virulence was observed. Although the mutation D225G associated with severity in the latest reports from the Ukraine and Norway is not observed among the Argentine strains, an amino acid change in the area (S206T) surrounding the HA receptor binding domain was observed, the same previously established worldwide

Comprehensive viral oligonucleotide probe design using conserved protein regions

Oligonucleotide microarrays have been applied to microbial surveillance and discovery where highly multiplexed assays are required to address a wide range of genetic targets. Although printing density continues to increase, the design of comprehensive microbial probe sets remains a daunting challenge, particularly in virology where rapid sequence evolution and database expansion confound static solutions. Here, we present a strategy for probe design based on protein sequences that is responsive to the unique problems posed in virus detection and discovery. The method uses the Protein Families database (Pfam) and motif finding algorithms to identify oligonucleotide probes in conserved amino acid regions and untranslated sequences. In silico testing using an experimentally derived thermodynamic model indicated near complete coverage of the viral sequence database

MassTag polymerase chain reaction for differential diagnosis of viral hemorrhagic fevers

Viral hemorrhagic fevers are associated with high rates of illness and death. Although therapeutic options are limited, early differential diagnosis has implications for containment and may aid in clinical management. We describe a diagnostic system for rapid, multiplex polymerase chain reaction identification of 10 different causes of viral hemorrhagic fevers

Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments

Polymerase chain reaction (PCR) is widely applied in clinical and environmental microbiology. Primer design is key to the development of successful assays and is often performed manually by using multiple nucleic acid alignments. Few public software tools exist that allow comprehensive design of degenerate primers for large groups of related targets based on complex multiple sequence alignments. Here we present a method for designing such primers based on tree building followed by application of a set covering algorithm, and demonstrate its utility in compiling Multiplex PCR primer panels for detection and differentiation of viral pathogens

Caracterización molecular de cepas de influenza A (H1N1) 2009 de casos leves y graves de la Argentina

Fil: Cisterna, Daniel. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Campos, Ana. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Pontoriero, Andrea. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Alonio, Virginia. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Molina, Viviana. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Palacios, Gustavo. Columbia University. Center for Infection and Immunity; Estados Unidos.Fil: Solovyov, Alexander. Columbia University. Center for Infection and Immunity; Estados Unidos.Fil: Hui, Jeffrey. Columbia University. Center for Infection and Immunity; Estados Unidos.Fil: Savji, Nazir. Columbia University. Center for Infection and Immunity; Estados Unidos.Fil: Bussetti, Ana Valeria. Columbia University. Center for Infection and Immunity; Estados Unidos.Fil: Jabado, Omar J. Columbia University. Center for Infection and Immunity; Estados Unidos.Fil: Street, Craig. Columbia University. Center for Infection and Immunity; Estados Unidos.Fil: Hirschberg, David L. Columbia University. Center for Infection and Immunity; Estados Unidos.Fil: Rabadan, Raul. Columbia University. Department of Biomedical Informatics; Estados UnidosFil: Hutchison, Stephen. 454 Life Sciences; Estados UnidosFil: Egholm, Michael. 454 Life Sciences; Estados Unidos.Fil: Lipkin, W. Ian. Columbia University. Center for Infection and Immunity; Estados Unidos.Fil: Baumeister, Elsa. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; ArgentinaWhile worldwide pandemic influenza A(H1N1) pdm case fatality rate (CFR) was 0.4%, Argentina’s was 4.5%. A total of 34 strains from mild and severe cases were analyzed. A full genome sequencing was carried out on 26 of these, and a partial sequencing on the remaining eight. We observed no evidence that the high CFR can be attributed to direct virus changes. No evidence of re-assortment, mutations associated with resistance to antiviral drugs, or genetic drift that might contribute to virulence was observed. Although the mutation D225G associated with severity in the latest reports from the Ukraine and Norway is not observed among the Argentine strains, an amino acid change in the area (S206T) surrounding the HA receptor binding domain was observed, the same previously established worldwide. (ES) Mientras que la tasa de letalidad (CFR) para (H1N1)pdm en todo el mundo era del 0.4%, en la Argentina la mortalidad observada fue de 4.5%. La secuenciación del genoma completo de 26 cepas de virus argentinos de influenza A (H1N1)pdm de casos leves y graves y de 8 cepas secuenciadas parcialmente no mostró evidencia de que la elevada tasa de letalidad se pueda atribuir directamente a cambios en el virus. No se encontraron hallazgos de recombinación, de mutaciones asociadas con la resistencia a los medicamentos antivirales ni de variaciones genéticas que puedan contribuir a la virulencia observada. Si bien la mutación D225G asociada con la gravedad, comunicada en informes procedentes de Ucrania y Noruega, no se ha encontrado en las cepas argentinas estudiadas, se ha observado un cambio aminoacídico en la región (S206T) en torno al dominio del sitio de unión al receptor en la HA, el mismo hallado en cepas distribuidas alrededor del mundo

Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases

To facilitate rapid, unbiased, differential diagnosis of infectious diseases, we designed GreeneChipPm, a panmicrobial microarray comprising 29,455 sixty-mer oligonucleotide probes for vertebrate viruses, bacteria, fungi, and parasites. Methods for nucleic acid preparation, random primed PCR amplification, and labeling were optimized to allow the sensitivity required for application with nucleic acid extracted from clinical materials and cultured isolates. Analysis of nasopharyngeal aspirates, blood, urine, and tissue from persons with various infectious diseases confirmed the presence of viruses and bacteria identified by other methods, and implicated Plasmodium falciparum in an unexplained fatal case of hemorrhagic feverlike disease during the Marburg hemorrhagic fever outbreak in Angola in 2004–2005

Detection of Respiratory Viruses and Subtype Identification of Influenza A Viruses by GreeneChipResp Oligonucleotide Microarray

Acute respiratory infections are significant causes of morbidity, mortality, and economic burden worldwide. An accurate, early differential diagnosis may alter individual clinical management as well as facilitate the recognition of outbreaks that have implications for public health. Here we report on the establishment and validation of a comprehensive and sensitive microarray system for detection of respiratory viruses and subtyping of influenza viruses in clinical materials. Implementation of a set of influenza virus enrichment primers facilitated subtyping of influenza A viruses through the differential recognition of hemagglutinins 1 through 16 and neuraminidases 1 through 9. Twenty-one different respiratory virus species were accurately characterized, including a recently identified novel genetic clade of rhinovirus.Fil: Quan, Phenix-Lan. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Palacios, Gustavo. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Jabado, Omar J. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Conlan, Sean. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Hirschberg, David L. Stanford School of Medicine; Estados Unidos.Fil: Pozo, Francisco. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Jack, Philippa J. M. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: Cisterna, Daniel. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Renwick, Neil. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Hui, Jeffrey. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Drysdale, Andrew. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Amos-Ritchie, Rachel. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: Baumeister, Elsa. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Savy, Vilma. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Lager, Kelly M. USDA. National Animal Disease Center; Estados Unidos.Fil: Richt, Jürgen A. USDA. National Animal Disease Center; Estados Unidos.Fil: Boyle, David B. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: García-Sastre, Adolfo. Mount Sinai School of Medicine. Department of Microbiology and Emerging Pathogens Institute; Estados Unidos.Fil: Casas, Inmaculada. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Perez-Breña, Pilar. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Briese, Thomas. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Lipkin, W. Ian. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos

Detection of Respiratory Viruses and Subtype Identification of Influenza A Viruses by GreeneChipResp Oligonucleotide Microarray

Acute respiratory infections are significant causes of morbidity, mortality, and economic burden worldwide. An accurate, early differential diagnosis may alter individual clinical management as well as facilitate the recognition of outbreaks that have implications for public health. Here we report on the establishment and validation of a comprehensive and sensitive microarray system for detection of respiratory viruses and subtyping of influenza viruses in clinical materials. Implementation of a set of influenza virus enrichment primers facilitated subtyping of influenza A viruses through the differential recognition of hemagglutinins 1 through 16 and neuraminidases 1 through 9. Twenty-one different respiratory virus species were accurately characterized, including a recently identified novel genetic clade of rhinovirus.Fil: Quan, Phenix-Lan. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Palacios, Gustavo. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Jabado, Omar J. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Conlan, Sean. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Hirschberg, David L. Stanford School of Medicine; Estados Unidos.Fil: Pozo, Francisco. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Jack, Philippa J. M. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: Cisterna, Daniel. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Renwick, Neil. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Hui, Jeffrey. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Drysdale, Andrew. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Amos-Ritchie, Rachel. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: Baumeister, Elsa. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Savy, Vilma. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Lager, Kelly M. USDA. National Animal Disease Center; Estados Unidos.Fil: Richt, Jürgen A. USDA. National Animal Disease Center; Estados Unidos.Fil: Boyle, David B. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: García-Sastre, Adolfo. Mount Sinai School of Medicine. Department of Microbiology and Emerging Pathogens Institute; Estados Unidos.Fil: Casas, Inmaculada. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Perez-Breña, Pilar. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Briese, Thomas. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Lipkin, W. Ian. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos