Publication bias in animal research: a systematic review protocol.

BACKGROUND: Systematic reviews and meta-analyses of pre-clinical studies, in vivo animal experiments in particular, can influence clinical care. Publication bias is one of the major threats of validity in systematic reviews and meta-analyses. Previous empirical studies suggested that systematic reviews and meta-analyses have become more prevalent until 2010 and found evidence for compromised methodological rigor with a trend towards improvement. We aim to comprehensively summarize and update the evidence base on systematic reviews and meta-analyses of animal studies, their methodological quality and assessment of publication bias in particular. METHODS/DESIGN: The objectives of this systematic review are as follows: âeuro¢To investigate the epidemiology of published systematic reviews of animal studies until present. âeuro¢To examine methodological features of systematic reviews and meta-analyses of animal studies with special attention to the assessment of publication bias. âeuro¢To investigate the influence of systematic reviews of animal studies on clinical research by examining citations of the systematic reviews by clinical studies. Eligible studies for this systematic review constitute systematic reviews and meta-analyses that summarize in vivo animal experiments with the purpose of reviewing animal evidence to inform human health. We will exclude genome-wide association studies and animal experiments with the main purpose to learn more about fundamental biology, physical functioning or behavior. In addition to the inclusion of systematic reviews and meta-analyses identified by other empirical studies, we will systematically search Ovid Medline, Embase, ToxNet, and ScienceDirect from 2009 to January 2013 for further eligible studies without language restrictions. Two reviewers working independently will assess titles, abstracts, and full texts for eligibility and extract relevant data from included studies. Data reporting will involve a descriptive summary of meta-analyses and systematic reviews. DISCUSSION: Results are expected to be publicly available later in 2013 and may form the basis for recommendations to improve the quality of systematic reviews and meta-analyses of animal studies and their use with respect to clinical care.

Oligogalacturonide defense signals in plants: large fragments interact with the plasma membrane in vitro.

Oligogalacturonides are plant cell wall-derived regulatory molecules which stimulate defense gene expression during pathogenesis. In vitro, these compounds enhance the phosphorylation of an approximately 34-kDa protein (pp34) in purified plasma membranes from potato and tomato leaves. We now show that polygalacturonate-enhanced phosphorylation of pp34 occurs in plasma membranes purified from tomato roots, hypocotyls, and stems and from undifferentiated potato cells. Furthermore, a similar phosphorylation is detected in leaf plasma membranes from soybean, a plant distantly related to tomato. Purified oligogalacturonides 13 to at least 26 residues long stimulate pp34 thiophosphorylation in vitro. This stimulation pattern differs from the induction of many known defense responses in vivo, where a narrower range of smaller fragments, between approximately 10 and 15 residues long, are active. On the basis of these differences we suggest that observed effects of applied exogenous oligogalacturonides on defense responses may not necessarily reflect the situation during pathogenesis. The cell wall could act as a barrier to many exogenous oligo- and polygalacturonides as well as other large regulatory ligands.

Genetic diversity in soybean germplasm identified by SSR and EST-SSR markers

The objectives of this work were to investigate the genetic variation in 79 soybean (Glycine max) accessions from different regions of the world, to cluster the accessions based on their similarity, and to test the correlation between the two types of markers used. Simple sequence repeat markers present in genomic (SSR) and in expressed regions (EST-SSR) were used. Thirty SSR primer-pairs were selected (20 genomic and 10 EST-SSR) based on their distribution on the 20 genetic linkage groups of soybean, on their trinucleotide repetition unit and on their polymorphism information content. All analyzed loci were polymorphic, and 259 alleles were found. The number of alleles per locus varied from 2-21, with an average of 8.63. The accessions exhibit a significant number of rare alleles, with genotypes 19, 35, 63 and 65 carrying the greater number of exclusive alleles. Accessions 75 and 79 were the most similar and accessions 31 and 35, and 40 and 78, were the most divergent ones. A low correlation between SSR and EST-SSR data was observed, thus genomic and expressed microsatellite markers are required for an appropriate analysis of genetic diversity in soybean. The genetic diversity observed was high and allowed the formation of five groups and several subgroups. A moderate relationship between genetic divergence and geographic origin of accessions was observed.

Crystal size distribution of periclase in contact metamorphic dolomite marbles from the southern Adamello Massif, Italy

Crystal size distributions (CSD) of periclase in contact metamorphic dolomite marbles are presented for two profiles near the Cima Uzza summit in the southern Adamello Massif (Italy). The database was combined with geochemical and petrological information to deduce the controls on the periclase-forming reaction. The contact metamorphic dolomite marbles are exposed at the contact of mafic intrusive rocks and are partially surrounded by them. Brucite is retrograde and pseudomorphs spherical periclase crystals. Prograde periclase growth is the consequence of limited infiltration of water-rich fluid at T near 605C. Stable isotope data show depletion in (13)C and (18)O over a narrow region (40 cm) near the magmatic contact, whereas the periclase-forming reaction front extends up to 4 m from the contact. CSD analyses along the two profiles show that the median grain size of the periclase crystals does not change, but that there is a progressively greater distribution of grain sizes, including a greater proportion of larger grains, with increasing distance from the contact. A qualitative model, based on the textural and geochemical data, attributes these variations in grain size to changing reaction affinities along a kinetically dispersed infiltration front. This study highlights the need to invoke disequilibrium processes for metamorphic mineral growth and expands the use of CSDs to systems of mineral formation driven by fluid infiltration.

Stability of Citrus tristeza virus protective isolates in field conditions

The objective of this work was to monitor the maintenance of Citrus tristeza virus (CTV) protective isolates stability in selected clones of 'Pêra' sweet orange (Citrus sinensis), preimmunized or naturally infected by the virus, after successive clonal propagations. The work was carried out in field conditions in the north of Paraná State, Brazil. Coat protein gene (CPG) analysis of 33 isolates collected from 16 clones of 'Pêra' sweet orange was performed using single strand conformational polymorphism (SSCP). Initially, the isolates were characterized by symptoms of stem pitting observed in clones. Then viral genome was extracted and used as template for the amplification of CPG by reverse transcription polimerase chain reaction (RTPCR). RTPCR products electrophoretic profiles were analyzed using the Jaccard coefficient and the UPGMA method. The majority of the clones had weak to moderate stem pitting symptoms and its CTV isolates showed alterations in the SSCP profiles. However, the stability of the protective complex has been maintained, except for isolates from two analised clones. Low genetic variability was observed within the isolates during the studied years.

Feasibility of direct mapping of cerebral fluorodeoxy-D-glucose metabolism in situ at subcellular resolution using soft X-ray fluorescence.

Glucose metabolism is difficult to image with cellular resolution in mammalian brain tissue, particularly with (18) fluorodeoxy-D-glucose (FDG) positron emission tomography (PET). To this end, we explored the potential of synchrotron-based low-energy X-ray fluorescence (LEXRF) to image the stable isotope of fluorine (F) in phosphorylated FDG (DG-6P) at 1 μm(2) spatial resolution in 3-μm-thick brain slices. The excitation-dependent fluorescence F signal at 676 eV varied linearly with FDG concentration between 0.5 and 10 mM, whereas the endogenous background F signal was undetectable in brain. To validate LEXRF mapping of fluorine, FDG was administered in vitro and in vivo, and the fluorine LEXRF signal from intracellular trapped FDG-6P over selected brain areas rich in radial glia was spectrally quantitated at 1 μm(2) resolution. The subsequent generation of spatial LEXRF maps of F reproduced the expected localization and gradients of glucose metabolism in retinal Müller glia. In addition, FDG uptake was localized to periventricular hypothalamic tanycytes, whose morphological features were imaged simultaneously by X-ray absorption. We conclude that the high specificity of photon emission from F and its spatial mapping at ≤1 μm resolution demonstrates the ability to identify glucose uptake at subcellular resolution and holds remarkable potential for imaging glucose metabolism in biological tissue. © 2012 Wiley Periodicals, Inc.

Aclimatação ao frio e dano por geada em canola

O objetivo deste trabalho foi avaliar a influência da aclimatação ao frio sobre o dano causado pela geada em diferentes estádios fenológicos de genótipos de canola. Foram realizados cinco experimentos em ambiente controlado, em 2006, 2007 e 2008. Os fatores avaliados foram: genótipos, aclimatação (com; sem), intensidades de geada, estádios de desenvolvimento de plantas, regimes de aclimatação e regimes de geada. As variáveis avaliadas foram: queima de folhas, massa de matéria seca, estatura de plantas, duração de subperíodo, componentes de rendimento e rendimento de grãos. A aclimatação ao frio, antes da geada, resultou em menor queima de folhas e maior massa de matéria seca, em comparação a plantas não aclimatadas. As geadas foram prejudiciais a partir de -6°C no início do ciclo de desenvolvimento, principalmente em plantas não aclimatadas, e a partir de -4ºC na floração, com redução do número de síliquas e do número de grãos por síliqua. A aclimatação após as geadas não contribuiu para a tolerância da canola a esse evento. Geadas consecutivas não acarretaram maior prejuízo à canola. A aclimatação de plantas de canola antes da geada reduz os danos, principalmente quando a geada ocorre no início do desenvolvimento das plantas.

Desempenho de frangos de corte alimentados com ingrediente de alta digestibilidade nas fases de criação pré-inicial e inicial

O objetivo deste trabalho foi avaliar o efeito de dieta, com inclusão de um núcleo energético-proteico (NEP) de alta digestibilidade, no desempenho produtivo e características de carcaça de frangos de corte. O NEP constituiu-se de composto de óleo degomado de soja, milho pré-gelatinizado, soja biprocessada, mananoligossacarídeos e peptídeos. O total de 864 pintainhos machos, da linhagem AgRoss 508, com um dia de idade, foram pesados individualmente e distribuídos em blocos ao acaso. Os tratamentos consistiram de suplementos com diferentes teores de NEP, com oito repetições com 27 aves cada: T1, controle, 0% de NEP; T2, 7% de NEP (1-7 dias) e 3,5% de NEP (8-21 dias); T3, 14% de NEP (1-7 dias) e 7% de NEP (8-21 dias); e T4, 21% de NEP (1-7 dias) e 10,5% de NEP (8-21 dias). Aos 21 dias de idade, o peso corporal, ganho de peso, consumo médio de ração, conversão alimentar e rendimento de carcaça e cortes não foram afetados significativamente pelos tratamentos experimentais. A utilização de NEP na dieta de frangos de corte não altera o desempenho das aves e não interfere nas variáveis de características de carcaça.

Atmosfera modificada e refrigeração para conservação pós-colheita de uva 'Niagara Rosada'

O objetivo deste trabalho foi avaliar os efeitos da atmosfera modificada na conservação pós-colheita da uva 'Niagara Rosada' armazenada sob refrigeração, em dois experimentos. No primeiro experimento avaliou-se o acondicionamento de cachos nas seguintes embalagens: papelão ondulado (testemunha); tereftalato de polietileno (PET); cloreto de polivinila (PVC) 17 μm; polietileno linear de baixa densidade (PELBD) 25 μm; e PELBD 50 μm. Em outro experimento, avaliaram-se os sistemas de acondicionamento: sacolas de plástico abertas (testemunha); polietileno de baixa densidade (PEBD) 25 μm; PEBD 25 μm, com injeção de mistura gasosa (21% O2/5% CO2); PEBD 25 μm (21% O2/10% CO2); PEBD 25 μm (21% O2/20% CO2). Os cachos foram armazenados a 1±1°C e 90±5% de umidade relativa (UR) por 28 dias, seguido de armazenamento em condições do ambiente (25±2°C e 80±5% UR). Os cachos foram avaliados quanto à perda de massa de matéria fresca, firmeza, cor das bagas, esbagoamento, sólidos solúveis totais (SST), acidez titulável (AT), relação SST/AT e incidência de podridões. O filme PELBD 50 μm, a partir do 14º dia a 1°C, seguido por mais três dias a 25°C, causou a fermentação dos cachos. As embalagens PELBD 25 μm, com ou sem injeção de mistura gasosa, e PVC 17 μm reduzem a perda de massa de matéria fresca dos cachos, mas não reduzem o esbagoamento e a incidência de podridões.

The histone-interacting domain of nuclear factor I activates simian virus 40 DNA replication in vivo.

Efficient initiation of SV40 DNA replication requires transcription factors that bind auxiliary sequences flanking the minimally required origin. To evaluate the possibility that transcription factors may activate SV40 replication by acting on the chromatin structure of the origin, we used an in vivo replication system in which we targeted GAL4 fusion proteins to the minimally required origin. We found that the proline-rich transcriptional activation domain of nuclear factor I (NF-I), which has been previously shown to interact with histone H3, specifically activates replication. Evaluation of a series of deletion and point mutants of NF-I indicates that the H3-binding domain and the replication activity coincide perfectly. Assays with other transcription factors, such as Sp1, confirmed the correlation between the interaction with H3 and the activation of replication. These findings imply that transcription factors such as NF-I can activate SV40 replication via direct interaction with chromatin components, thereby contributing to the relief of nucleosomal repression at the SV40 origin.