The use of flow microfluorimetry in the analysis of the phenotype expression of mouse histocompatibility antigens

Quantitation of the expression of cell surface antigens has hitherto been limited to analysis by either cytotoxicity tests or radioimmune assays (5, 15). We report here the use of a new methodology to analyze and quantitate the expression of mouse histocompabililty antigens (H-2 locus) in hybrid clones and parental cell types. The binding of fluorescein-tagged antibody is measured on a cell-to-cell basis in large viable cell populations using flow microfluorimetric techniques. These techniques have been used to measure hapten and immunoglobulin binding to lymphocyte populations (8, 9, 14). However, this is the first report in which these techniques have been used to examine the expression of the H-2 locus. The advantage of this approach is twofold: first, a large and statistically significant sample population may be analyzed one cell at a time, thus revealing the fine detail of heterogeneity in the expression of the cell surface markers within a population. Second, as has been demonstrated for analysis of specific components of the immune system, this method does permit fluorescence-activated sorting of cell types according to their different surface populations (8, 9, 14).     

Genome analysis reveals insights of the endophytic <Emphasis Type="Italic">Bacillus toyonensis</Emphasis> BAC3151 as a potentially novel agent for biocontrol of plant pathogens

Diseases caused by phytopathogenic microorganisms account for enormous losses for agribusiness. Although Bacillus species are recognized as being antimicrobial producers and some may provide benefits to plants, the association between Bacillus toyonensis and plants has not been studied. In this study, the whole-genome sequenced endophytic B. toyonensis BAC3151, which has demonstrated antimicrobial activity and quorum sensing inhibition of phytopathogenic bacteria, was investigated for its potential for the production of compounds for biocontrol of plant pathogens. Four whole-genome sequenced B. toyonensis strains shared 3811 protein-coding DNA sequences (CDSs), while strain-specific CDSs, such as biosynthetic gene clusters of antimicrobials, were associated with specific chromosomal regions and mobile genetic elements of the strains. B. toyonensis strains had a higher frequency of putative bacteriocins gene clusters than that of Bacillus species traditionally used for the production of antimicrobials. In addition, gene clusters potentially involved in the production of novel bacteriocins were found in BAC3151, as well as biosynthetic genes of several other compounds, including non-ribosomal peptides, N-acyl homoserine lactonase and chitinases, revealing a genetic repertoire for antimicrobial synthesis greater than that of other Bacillus strains that have demonstrated effective activity against phytopathogens. This study showed for the first time that B. toyonensis has potential to produce various antimicrobials, and the analyses performed indicated that the endophytic strain BAC3151 can be useful for the development of new strategies to control microbial diseases in plants that are responsible for large damages in agricultural crops.     

Land Surface Phenology in the Tropics: The Role of Climate and Topography in a Snow-Free Mountain

Leaf phenology represents a major temporal component of ecosystem functioning, and understanding the drivers of seasonal variation in phenology is essential to understand plant responses to climate change. We assessed the patterns and drivers of land surface phenology, a proxy for leafing phenology, for the meridional Espinhaço Range, a South American tropical mountain comprising a mosaic of savannas, dry woodlands, montane vegetation and moist forests. We used a 14-year time series of MODIS/NDVI satellite images, acquired between 2001 and 2015, and extracted phenological indicators using the TIMESAT algorithm. We obtained precipitation data from the Tropical Rainfall Measuring Mission, land surface temperature from the MODIS MOD11A2 product, and cloud cover frequency from the MODIS MOD09GA product. We also calculated the topographic wetness index and simulated clear-sky radiation budgets based on the SRTM elevation model. The relationship between phenology and environmental drivers was assessed using general linear models. Temporal displacement in the start date of the annual growth season was more evident than variations in season length among vegetation types, indicating a possible temporal separation in the use of resources. Season length was inversely proportional to elevation, decreasing 1.58 days per 100 m. Green-up and senescence rates were faster where annual temperature amplitude was higher. We found that water and light availability, modulated by topography, are the most likely drivers of land surface phenology in the region, determining the start, end and length of the growing season. Temperature had an important role in determining the rates of leaf development and the strength of vegetation seasonality, suggesting that tropical vegetation is also sensitive to latitudinal temperature changes, regardless of the elevational gradient. Our work improves the current understanding of phenological strategies in the seasonal tropics and emphasizes the importance of topography in shaping light and water availability for leaf development in snow-free mountains.     

Rethinking tropical phenology: insights from long‐term monitoring and novel analytical methods

Here, we introduce the Special Section (SS) on long‐term monitoring and new analytical methods in tropical phenology. The SS puts together nine original papers plus a synthesis, bringing significant advances and new insights into our understanding of tropical phenology across Africa and tropical America. The papers address environmental cues, methodological shortcomings, and provide innovative analytical approaches, opening new pathways, perspective and applications of tropical phenology for forest management and environmental monitoring. The SS is a substantial step toward a more comprehensive overview of trends in tropical phenology, as seven of nine studies evaluate >10‐yr data sets applying new methods of analysis such as hierarchical Bayesian models, generalized additive models, and Fourier analysis. We argue that it is essential to maintain ongoing monitoring programs and build a tropical phenology network at least for long‐term (>10 yr) study sites, providing the means for national and international financial support. Cross‐continental comparisons are now a primary goal, as we work toward a global vision of trends and shifts in tropical phenology in the Anthropocene.     

Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain 1/06-A, Isolated from a Horse in North America

Corynebacterium pseudotuberculosis causes disease in several animal species, although distinct biovars exist that appear to be restricted to specific hosts. In order to facilitate a better understanding of the differences between biovars, we report here the complete genome sequence of the equine pathogen Corynebacterium pseudotuberculosis strain 1/06-A.     

Reproductive phenology of a northeast Brazilian mangrove community: Environmental and biotic constraints

Brazil has the third largest area of mangrove in the world, which is widely threatened by anthropogenic pressures. We carried out the first long-term phenological study investigating whether environment and competition for pollinators shape the reproduction of a western mangrove community in Brazil, and provide new information for mangrove conservation. We monitored monthly the flowering and fruiting of Avicennia schaueriana, Conocarpus erectus, Laguncularia racemosa and Rhizophora mangle, the only species composing this mangrove community. We applied circular statistics to detect seasonal trends, null models to test for aggregated, staggered or random flowering patterns, performed correlations between phenophases and climate, and calculated intra-specific phenological synchrony. Each species presented a different flowering pattern, from brief annual to continuous and from regular to irregular, resulting in a bimodal pattern at community level. Fruiting was annual or continuous and seasonally unimodal at community level. Precipitation showed the strongest correlation with reproduction for all species, except L. racemosa. Flowering was randomly distributed among species sharing pollinators and each species presented high intra-specific synchrony. The studied mangrove showed a diversity of flowering patterns despite the low number of species. Annual to sub-annual sequential flowering were prevalent, sustaining the pollinators of species all the year long, while the wind-pollinated species flowered continuously. We provide strong evidence that daylength, rainfall and temperature are driving the flowering and fruiting rhythm of these mangrove species.     

The Virological and Immunological Characteristics of the HIV-1-Infected Population in Brazil: From Initial Diagnosis to Impact of Antiretroviral Use

BackgroundImmunological and virological status of HIV-infected individuals entering the Brazilian public system over time was analyzed. We evaluated the impact of ART on virological, immunological and antiretroviral resistance over time.MethodsCD4+ T cell counts, viral loads and genotypes from patients over 13 years old from 2001–2011 were analyzed according to demographic data. We compared groups using parametric t-tests and linear regression analysis in the R statistical software language.ResultsMean baseline CD4+ T cell counts varied from 348 (2003) to 389 (2009) and was higher among women (p = 1.1 x 10⁻⁸), lower in older patients (p< 1 x 10⁻⁸) and lower in less developed regions (p = 1.864 x 10⁻⁵). Percentage of treated patients with undetectable viral loads increased linearly from 46% (2001) to 77% (2011), was lower among women (p = 2.851 x 10⁻⁶), younger ages (p = 1 x 10⁻³), and in less developed regions (p = 1.782 x 10⁻⁴). NRTI acquired resistance was 86% in 2001–3 and decreased over time. NNRTI resistance increased from 2001-3(50%) to 2006–9 (60%), PI resistance decreased from 2001–3 (60%) to 2009 (40%), and 3-class resistance was stable over time around 25%. Subtype prevalence comprised B (75.3%), B/F recombinants (12.2%), C (5.7%), F (5.3%) and B/C recombinants (1.5%), with regional variations. Three-class resistance was 26.5% among Bs, 22.4% among Fs and 17.2% among Cs.ConclusionsHIV diagnosis occurs late, especially among elderly Brazilians. Younger individuals need special attention due to poor virological response to treatment. Antiretroviral Resistance profile is subtype related.     

Mathematical contributions to link biota with environment

Hutchinson's pioneering work on the niche concept, dating from 1957, inspired the development of many ecological models. The first proposals, BIOCLIM and HABITAT, were simple geometric approximations to the shape of the niche. Despite their simplicity, they combine two features that make them adequate for the purpose of exploring the niche: they fit a predefined shape to the empirical data; and produce binary or ordinal predictions rather than continuous predictions. Thus, both explicitly delineate a precise boundary for the niche. However, the two methods present some limitations: BIOCLIM assumes that the variables are independent in their action on the species; and HABITAT, although not having that limitation, only delineates the boundaries of the niches without distinguishing levels of suitability for the species. We propose, discuss and illustrate: (1) the use of depth functions to identify regions with distinct suitability inside the niche; and (2) a general framework to assess overlap of the niches of two species, which can be applied to predictions from models that decompose the niche into a finite number of measurable regions.