ABSTRACT
The quadrupolar interaction experienced by the spin-1 14N nucleus is known to be extremely sensitive to local structure and dynamics. Furthermore, the 14N isotope is 99.6% naturally abundant, making it an attractive target for characterisation of nitrogen-rich biological molecules by solid-state NMR. In this study, dynamic nuclear polarization (DNP) is used in conjunction with indirect 14N detected solid-state NMR experiments to simultaneously characterise the quadrupolar interaction at multiple 14N sites in the backbone of the microcrystalline protein, GB3. Considerable variation in the quadrupolar interaction (>700 kHz) is observed throughout the protein backbone. The distribution in quadrupolar interactions observed reports on the variation in local backbone conformation and subtle differences in hydrogen-bonding; demonstrating a new route to the structural and dynamic analysis of biomolecules.
Subject(s)
Nitrogen/chemistry , Nuclear Magnetic Resonance, Biomolecular , Proteins/chemistry , Bacterial Proteins/chemistry , Hydrogen BondingABSTRACT
Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish, implicated in skin and gill disease, often causing high mortality. The aim of this study was the isolation and characterization of Flavobacterium columnare in tropical fish in Brazil. Piracanjuba (Brycon orbignyanus), pacu (Piaractus mesopotamicus), tambaqui (Colossoma macropomum) and cascudo (Hypostomus plecostomus) were examined for external lesions showing signs of colunmaris disease such as greyish white spots, especially on the head, dorsal part and caudal fin of the fish. The sampling comprised 50 samples representing four different fish species selected for study. Samples for culture were obtained by skin and kidney scrapes with a sterile cotton swabs of columnaris disease fish and streaked onto Carlson and Pacha (1968) artificial culture medium (broth and solid) which were used for isolation. The strains in the liquid medium were Gram negative, long, filamentous, exhibited flexing movements (gliding motility), contained a large number of long slender bacteria and gathered into columns'. Strains on the agar produced yellow-pale colonies, rather small, flat that had rhizoid edges. A total of four Flavobacterium columnare were isolated: 01 Brycon orbignyanus strain, 01 Piaractus mesopotamicus strain, 01 Colossoma macropomum strain, and 01 Hypostomus plecostomus strain. Biochemical characterization, with its absorption of Congo red dye, production of flexirubin-type pigments, H2S production and reduction of nitrates proved that the isolate could be classified as Flavobacterium columnare.
Subject(s)
Fish Diseases/microbiology , Flavobacteriaceae Infections/veterinary , Flavobacterium/isolation & purification , Animals , Brazil , Fish Diseases/diagnosis , Flavobacteriaceae Infections/diagnosis , Flavobacteriaceae Infections/microbiology , Flavobacterium/classificationABSTRACT
Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish, implicated in skin and gill disease, often causing high mortality. The aim of this study was the isolation and characterization of Flavobacterium columnare in tropical fish in Brazil. Piracanjuba (Brycon orbignyanus), pacu (Piaractus mesopotamicus), tambaqui (Colossoma macropomum) and cascudo (Hypostomus plecostomus) were examined for external lesions showing signs of colunmaris disease such as greyish white spots, especially on the head, dorsal part and caudal fin of the fish. The sampling comprised 50 samples representing four different fish species selected for study. Samples for culture were obtained by skin and kidney scrapes with a sterile cotton swabs of columnaris disease fish and streaked onto Carlson and Pacha (1968) artificial culture medium (broth and solid) which were used for isolation. The strains in the liquid medium were Gram negative, long, filamentous, exhibited flexing movements (gliding motility), contained a large number of long slender bacteria and gathered into columns'. Strains on the agar produced yellow-pale colonies, rather small, flat that had rhizoid edges. A total of four Flavobacterium columnare were isolated: 01 Brycon orbignyanus strain, 01 Piaractus mesopotamicus strain, 01 Colossoma macropomum strain, and 01 Hypostomus plecostomus strain. Biochemical characterization, with its absorption of Congo red dye, production of flexirubin-type pigments, H2S production and reduction of nitrates proved that the isolate could be classified as Flavobacterium columnare.
Flavobacterium columnare é o agente etiológico da columnariose em peixes de água doce, ocasionando enfermidade na pele e nas brânquias, provocando freqüentemente um grande número de mortalidade. O objetivo deste estudo foi o isolamento e a caracterização de Flavobacterium columnare em peixes tropicais no Brasil. Piracanjuba (Brycon orbignyanus), pacu (Piaractus mesopotamicus), tambaqui (Colossoma macropomum) e cascudo (Hypostomus plecostomus) foram examinados externamente com relação a sinais característicos de columnariose, como manchas acinzentadas na cabeça, região dorsal e pedúnculo caudal dos peixes. A amostragem compreendeu a coleta de 50 exemplares de peixes, representando as quatro diferentes espécies escolhidas para este estudo. Amostras para o isolamento foram obtidas através de raspado com swab estéril das lesões e do rim dos peixes clinicamente diagnosticados como acometidos por columnarios e imediatamente semeados em meios de culturas artificiais (líquido e sólido) próprios para o estudo de Flavobacterium segundo Carlson e Pacha (1968). No meio líquido, houve o desenvolvimento de microrganismos que observados em gota pendente apresentaram a forma de bacilos finos, longos, móveis por deslizamento. Através da coloração de Gram, apresentaram morfologia de bacilos finos, Gram negativos, agrupados em colunas. Em meio sólido, as colônias eram pequenas, cinza-amareladas, com borda em forma de raiz. No total, foram obtidos quatro isolamentos: 01 cepa de Brycon orbignyanus; 01 cepa de Piaractus mesopotamicus; 01 cepa de Colossoma macropomum; e 01 cepa de Hypostomus plecostomus. A caracterização bioquímica das amostras, como absorção do vermelho Congo, produção de flexirrubina, produção de H2S e redução do nitrato, sugere que os isolamentos poderiam ser classificados como Flavobacterium columnare.
Subject(s)
Animals , Fish Diseases/microbiology , Flavobacteriaceae Infections/veterinary , Flavobacterium/isolation & purification , Brazil , Fish Diseases/diagnosis , Flavobacteriaceae Infections/diagnosis , Flavobacteriaceae Infections/microbiology , Flavobacterium/classificationABSTRACT
The HIV pandemic is a pressing threat to global public health; HIV vaccine development is critical. Clinical evaluation of HIV vaccine candidates differs from the standard therapeutics trial framework primarily due to the fact that healthy individuals are studied. We present an early stage evaluation program developed for the HIV Vaccine Trials Network (HVTN) motivated by characteristics unique to the vaccine setting. The program consists of 3 prototypical stages (Phase I, Ib, II) that provide a unified yet flexible approach to the safety and immunogenicity evaluation of diverse vaccine regimens. The goal of these early trials is to narrow the number of candidate vaccines to the most promising candidates worthy of further study in efficacy trials.
Subject(s)
AIDS Vaccines/therapeutic use , Clinical Trials, Phase I as Topic/methods , Clinical Trials, Phase II as Topic/methods , Data Interpretation, Statistical , AIDS Vaccines/immunology , Enzyme-Linked Immunosorbent Assay/methods , HIV Antibodies/blood , HIV Infections/prevention & control , HIV-1/immunology , Humans , T-Lymphocytes/immunologyABSTRACT
Consider a study of two groups of individuals infected with a population of a genetically related heterogeneous mixture of viruses, and multiple viral sequences are sampled from each person. Based on estimates of genetic distances between pairs of aligned viral sequences within individuals, we develop four new tests to compare intra-individual genetic sequence diversity between the two groups. This problem is complicated by two levels of dependency in the data structure: (i) Within an individual, any pairwise distances that share a common sequence are positively correlated; and (ii) for any two pairings of individuals which share a person, the two differences in intra-individual distances between the paired individuals are positively correlated. The first proposed test is based on the difference in mean intra-individual pairwise distances pooled over all individuals in each group, standardized by a variance estimate that corrects for the correlation structure using U-statistic theory. The second procedure is a nonparametric rank-based analog of the first test, and the third test contrasts the set of subject-specific average intra-individual pairwise distances between the groups. These tests are very easy to use and solve correlation problem (i). The fourth procedure is based on a linear combination of all possible U-statistics calculated on independent, identically distributed sequence subdatasets, over the two levels (i) and (ii) of dependencies in the data, and is more complicated than the other tests but can be more powerful. Although the proposed methods are empirical and do not fully utilize knowledge from population genetics, the tests reflect biology through the evolutionary models used to derive the pairwise sequence distances. The new tests are evaluated theoretically and in a simulation study, and are applied to a dataset of 200 HIV sequences sampled from 21 children.
Subject(s)
Genetic Variation , Sequence Alignment/methods , Virus Diseases/virology , Viruses/genetics , Base Sequence , Biometry , Child , Empirical Research , Genome, Viral , HIV Infections/virology , HIV-1/genetics , Humans , Statistics, NonparametricABSTRACT
This paper presents the implementation of a model for expression array annotation (EAA) using the BioMediator biological data integration system along with BioConductor, an analytic tools platform. The model presented addresses the need for annotation sources identified during BioConductor inverted exclamation mark s development. Annotation provides us with well-curated genomic background knowledge for expression array analysis and interpretation. Annotation requests are constructed and posted to the query interface of the EAA package (the EAA model implemented as a component of BioConductor). The software enumerates all possible annotation paths for queries. These are then transformed to PQL queries and processed by BioMediator. Annotation entities returned from the EAA package answer the annotation request.
Subject(s)
Computational Biology , Databases, Genetic , Gene Expression Profiling , Software , Information Storage and Retrieval , Oligonucleotide Array Sequence AnalysisABSTRACT
The location shift model is commonly used to quantify the difference between groups in a two-arm study. Nonparametric inference procedures for the location shift parameter with censored observations have recently been extensively studied. However, the validity of these procedures depends heavily on the model assumption. In this article, a class of graphical and numerical methods are proposed for checking the adequacy of the location shift model. Our graphical procedures are much less subjective than the eye-ball method based on the standard Q-Q plot. The proposed methods are illustrated with real-life examples.
Subject(s)
Life Tables , Models, Statistical , Acquired Immunodeficiency Syndrome/drug therapy , Acquired Immunodeficiency Syndrome/mortality , Antiviral Agents/administration & dosage , Data Interpretation, Statistical , Humans , Survival Analysis , Zidovudine/administration & dosageABSTRACT
Em amostras de sangue colhidas de 60 fêmeas adultas, criadas no Estado de Säo Paulo, realizou-se o exame sorológico visando a detecçäo de anticorpos contra o vírus da Artrite-Encefalite Caprina (VAEC) e Mycoplasma mycoides. O índice clínico (IC) foi obtido pelo uso de uma fita métrica. Näo foram encontradas diferenças estatísticas significativas entre as médias dos IC encontrados em animais sorologicamente positivos e negativos. Considerando-se como 6,0 cm o valor crítico do IC, encontrou-se uma sensibilidade relativa de 57 por cento e uma especificidade relativa de 61 por cento no emprego do IC para o diagnóstico da infecçäo pelo VAEC e Mycoplasma mycoides. Os resultados encontrados mostram que o IC, isoladamente, näo é um critério satisfatório para o diagnóstico da infecçäo pelo VAEC
Subject(s)
Animals , Female , Arthritis-Encephalitis Virus, Caprine , Goat Diseases , GoatsABSTRACT
Mycoplasma pneumoniae isolation was attempted in respiratory fluids from 64 patients with respiratory infection Complement fixation test (CF) and counterimmunoelectrophoresis (CIE) were used for Mycoplasma antibody detection using the patient sera. Mycoplasma pneumoniae was not isolated. Serologic diagnosis were positives in 3.1% (2/64) by CF test and 1.6% (1/64) by CIE. Serologic tests done in 200 health controls showed 4% (8/200) positives by CIE and 1% (2/200) by CF. The results showed differences in sensitivity among the serologic tests. CF seems to be more indicated for Mycoplasma infection diagnosis while, CIE could be used for Mycoplasmas serosurveys. The prevalence of Mycoplasma pneumoniae infections was low (3.1%) in the 64 patients during our study period.
Subject(s)
Lung Diseases/microbiology , Mycoplasma pneumoniae/isolation & purification , Acute Disease , Adolescent , Adult , Brazil , Child , Child, Preschool , Female , Humans , MaleABSTRACT
Os autores analisaram um lote de oito bezerros da raca Holandesa preta e branca, pertencentes a um mesmo plantel e criados em sistema de confinamento, que apresentavam um quadro de pneumonia. De quatro deles, foram isolados e caracterizados microrganismos do genero Mycoplasma atraves do cultivo "in vitro" e estudo da ultra estrutura eletronica, sendo uma das especies identificada como Mycoplasma bovis pelo "Mycoplasma Reference Laboratory-Colindale, England"
