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31.
Rommel Thiago Jucá Ramos Adriana Ribeiro Carneiro Vasco Azevedo Maria Paula Schneider Debmalya Barh Artur Silva 《Bioinformation》2012,8(20):996-999
Modern genomic sequencing technologies produce a large amount of data with reduced cost per base; however, this data consists
of short reads. This reduction in the size of the reads, compared to those obtained with previous methodologies, presents new
challenges, including a need for efficient algorithms for the assembly of genomes from short reads and for resolving repetitions.
Additionally after abinitio assembly, curation of the hundreds or thousands of contigs generated by assemblers demands
considerable time and computational resources. We developed Simplifier, a stand-alone software that selectively eliminates
redundant sequences from the collection of contigs generated by ab initio assembly of genomes. Application of Simplifier to data
generated by assembly of the genome of Corynebacterium pseudotuberculosis strain 258 reduced the number of contigs generated by
ab initio methods from 8,004 to 5,272, a reduction of 34.14%; in addition, N50 increased from 1 kb to 1.5 kb. Processing the contigs of
Escherichia coli DH10B with Simplifier reduced the mate-paired library 17.47% and the fragment library 23.91%. Simplifier removed
redundant sequences from datasets produced by assemblers, thereby reducing the effort required for finalization of genome
assembly in tests with data from Prokaryotic organisms.
Availability
Simplifier is available at http://www.genoma.ufpa.br/rramos/softwares/simplifier.xhtmlIt requires Sun jdk 6 or higher. 相似文献32.
María C. Ortiz María F. Albertoni Borghese Sabrina E. Balonga Agustina Lavagna Ana L. Filipuzzi Rosana Elesgaray María A. Costa Mónica P. Majowicz 《PloS one》2014,9(8)
The aim of this study was to evaluate whether L-Arginine (L-Arg) supplementation modifies nitric oxide (NO) system and consequently aquaporin-2 (AQP2) expression in the renal outer medulla of streptozotocin-diabetic rats at an early time point after induction of diabetes. Male Wistar rats were divided in four groups: Control, Diabetic, Diabetic treated with L-Arginine and Control treated with L-Arginine. Nitric oxide synthase (NOS) activity was estimated by [14C] L-citrulline production in homogenates of the renal outer medulla and by NADPH-diaphorase staining in renal outer medullary tubules. Western blot was used to detect the expression of AQP2 and NOS types I and III; real time PCR was used to quantify AQP2 mRNA. The expression of both NOS isoforms, NOS I and NOS III, was decreased in the renal outer medulla of diabetic rats and L-Arg failed to prevent these decreases. However, L-Arg improved NO production, NADPH-diaphorase activity in collecting ducts and other tubular structures, and NOS activity in renal homogenates from diabetic rats. AQP2 protein and mRNA were decreased in the renal outer medulla of diabetic rats and L-Arg administration prevented these decreases. These results suggest that the decreased NOS activity in collecting ducts of the renal outer medulla may cause, at least in part, the decreased expression of AQP2 in this model of diabetes and constitute additional evidence supporting a role for NO in contributing to renal water reabsorption through the modulation of AQP2 expression in this pathological condition. However, we cannot discard that another pathway different from NOS also exists that links L-Arg to AQP2 expression. 相似文献
33.
Characterization of Lipids and Proteins Associated to the Cell Wall of the Acapsular Mutant Cryptococcus neoformans Cap 67 下载免费PDF全文
Jhon H. S. Pires Felipe Gazos‐Lopes Milene C. Vallejo Tiago J. P. Sobreira Igor C. Almeida Rosana Puccia 《The Journal of eukaryotic microbiology》2015,62(5):591-604
Cryptococcus neoformans is an opportunistic human pathogen that causes life‐threatening meningitis. In this fungus, the cell wall is exceptionally not the outermost structure due to the presence of a surrounding polysaccharide capsule, which has been highly studied. Considering that there is little information about C. neoformans cell wall composition, we aimed at describing proteins and lipids extractable from this organelle, using as model the acapsular mutant C. neoformans cap 67. Purified cell wall preparations were extracted with either chloroform/methanol or hot sodium dodecyl sulfate. Total lipids fractionated in silica gel 60 were analyzed by electrospray ionization tandem mass spectrometry (ESI‐MS/MS), while trypsin digested proteins were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC‐MS/MS). We detected 25 phospholipid species among phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, and phosphatidic acid. Two glycolipid species were identified as monohexosyl ceramides. We identified 192 noncovalently linked proteins belonging to different metabolic processes. Most proteins were classified as secretory, mainly via nonclassical mechanisms, suggesting a role for extracellular vesicles (EV) in transwall transportation. In concert with that, orthologs from 86% of these proteins have previously been reported both in fungal cell wall and/or in EV. The possible role of the presently described structures in fungal–host relationship is discussed. 相似文献
34.
Simone V. Generoso Mirelle Viana Rosana Santos Flaviano S. Martins José A. N. Machado Rosa M. E. Arantes Jacques R. Nicoli Maria I. T. D. Correia Valbert N. Cardoso 《Archives of microbiology》2010,192(6):477-484
Probiotic is a preparation containing microorganisms that confers beneficial effect to the host. This work assessed whether
oral treatment with viable or heat-killed yeast Saccharomyces cerevisiae strain UFMG 905 prevents bacterial translocation (BT), intestinal barrier integrity, and stimulates the immunity, in a murine
intestinal obstruction (IO) model. Four groups of mice were used: mice undergoing only laparotomy (CTL), undergoing intestinal
obstruction (IO) and undergoing intestinal obstruction after previous treatment with viable or heat-killed yeast. BT, determined
as uptake of 99mTc-E. coli in blood, mesenteric lymph nodes, liver, spleen and lungs, was significantly higher in IO group than in CTL group. Treatments
with both yeasts reduced BT in blood and all organs investigated. The treatment with both yeasts also reduced intestinal permeability
as determined by blood uptake of 99mTc-DTPA. Immunological data demonstrated that both treatments were able to significantly increase IL-10 levels, but only viable
yeast had the same effect on sIgA levels. Intestinal lesions were more severe in IO group when compared to CTL and yeasts
groups. Concluding, both viable and heat-killed cells of yeast prevent BT, probably by immunomodulation and by maintaining
gut barrier integrity. Only the stimulation of IgA production seems to depend on the yeast viability. 相似文献
35.
Azevedo NF Jardim T Almeida C Cerqueira L Almeida AJ Rodrigues F Keevil CW Vieira MJ 《Antonie van Leeuwenhoek》2011,100(3):463-470
Staphylococcus epidermidis is considered to be one of the most common causes of nosocomial bloodstream infections, particularly in immune-compromised
individuals. Here, we report the development and application of a novel peptide nucleic acid probe for the specific detection
of S. epidermidis by fluorescence in situ hybridization. The theoretical estimates of probe matching specificity and sensitivity were 89 and
87%, respectively. More importantly, the probe was shown not to hybridize with closely related species such as Staphylococcus aureus. The method was subsequently successfully adapted for the detection of S. epidermidis in mixed-species blood cultures both by microscopy and flow cytometry. 相似文献
36.
Salt Tolerant and Sensitive Rice Varieties Display Differential Methylome Flexibility under Salt Stress 总被引:1,自引:0,他引:1
Liliana J. Ferreira Vanessa Azevedo Jo?o Maroco M. Margarida Oliveira Ana Paula Santos 《PloS one》2015,10(5)
DNA methylation has been referred as an important player in plant genomic responses to environmental stresses but correlations between the methylome plasticity and specific traits of interest are still far from being understood. In this study, we inspected global DNA methylation levels in salt tolerant and sensitive rice varieties upon salt stress imposition. Global DNA methylation was quantified using the 5-methylcytosine (5mC) antibody and an ELISA-based technique, which is an affordable and quite pioneer assay in plants, and in situ imaging of methylation sites in interphase nuclei of tissue sections. Variations of global DNA methylation levels in response to salt stress were tissue- and genotype-dependent. We show a connection between a higher ability of DNA methylation adjustment levels and salt stress tolerance. The salt-tolerant rice variety Pokkali was remarkable in its ability to quickly relax DNA methylation in response to salt stress. In spite of the same tendency for reduction of global methylation under salinity, in the salt-sensitive rice variety IR29 such reduction was not statistically supported. In ‘Pokkali’, the salt stress-induced demethylation may be linked to active demethylation due to increased expression of DNA demethylases under salt stress. In ‘IR29’, the induction of both DNA demethylases and methyltransferases may explain the lower plasticity of DNA methylation. We further show that mutations for epigenetic regulators affected specific phenotypic parameters related to salinity tolerance, such as the root length and biomass. This work emphasizes the role of differential methylome flexibility between salt tolerant and salt sensitive rice varieties as an important player in salt stress tolerance, reinforcing the need to better understand the connection between epigenetic networks and plant responses to environmental stresses. 相似文献
37.
Jafelice RM de Barros LC Bassanezi RC Gomide F 《Bulletin of mathematical biology》2004,66(6):1597-1620
This paper introduces a model for the evolution of positive HIV population and manifestation of AIDS (acquired immunideficiency
syndrome). The focus is on the nature of the transference rate of HIV to AIDS. Expert knowledge indicates that the transference
rate is uncertain and depends strongly on the viral load and the CD4+ level of the infected individuals. Here, we suggest to view the transference rate as a fuzzy set of the viral load and
CD4+ level values. In this case the dynamic model results in a fuzzy model that preserves the biological meaning and nature
of the transference rate λ. Its behavior fits the natural history of HIV infection reported in the medical science domain. The paper also includes a
comparison between the fuzzy model and a classic Anderson’s model using data reported in the literature. 相似文献
38.
Carvalho RF Aidar ST Azevedo RA Dodd IC Peres LE 《Plant biology (Stuttgart, Germany)》2011,13(3):546-550
Tomato high pigment (hp) mutants represent an interesting horticultural resource due to their enhanced accumulation of carotenoids, flavonoids and vitamin C. Since hp mutants are known for their exaggerated light responses, the molecules accumulated are likely to be antioxidants, recruited to deal with light and others stresses. Further phenotypes displayed by hp mutations are reduced growth and an apparent disturbance in water loss. Here, we examined the impact of the hp1 mutation and its near isogenic line cv Micro-Tom (MT) on stomatal conductance (gs), transpiration (E), CO(2) assimilation (A) and water use efficiency (WUE). Detached hp1 leaves lost water more rapidly than control leaves, but this behaviour was reversed by exogenous abscisic acid (ABA), indicating the ability of hp1 to respond to this hormone. Although attached hp1 leaves had enhanced gs, E and A compared to control leaves, genotypic differences were lost when water was withheld. Both instantaneous leaf-level WUE and long-term whole plant WUE did not differ between hp1 and MT. Our results indicate a link between exaggerated light response and water loss in hp1, which has important implications for the use of this mutant in both basic and horticultural research. 相似文献
39.
Sousa AF Andrade PZ Pirzgalska RM Galhoz TM Azevedo AM da Silva CL Aires-Barros MR Cabral JM 《Biotechnology letters》2011,33(12):2373-2377
A novel cell separation process based on immunoaffinity aqueous two phase systems is presented to isolate and purify CD34+ stem/progenitor cells directly from the whole umbilical cord blood (UCB). A system, composed of polyethylene glycol and dextran,
was evaluated for the selective recovery of CD34+ cells from UCB. A monoclonal antibody against the CD34 surface antigen was used for the direct partitioning of CD34+ cells in UCB to the PEG-rich phase. The initial population of CD34+ cells (0.2% of the initial sample) was enriched to values up to 42% in a single partitioning step, while the majority of
contaminant cells were partitioned to the dextran-rich phase (1.37 × 10−2 < KP < 2.76 × 10−2). This novel selection method allowed a recovery yield of 95% of CD34+ cells with a purification factor of 245 and is expected to pave a new way to purify hematopoietic stem/progenitor cells for
use in a variety of clinical settings. 相似文献
40.
A. Ghelfi S.A. Gaziola M.C. Cia S.M. Chabregas M.C. Falco P.R. Kuser‐Falcão R.A. Azevedo 《The Annals of applied biology》2011,159(2):267-280
Sugarcane yield and quality are affected by a number of biotic and abiotic stresses. In response to such stresses, plants may increase the activities of some enzymes such as glutathione transferase (GST), which are involved in the detoxification of xenobiotics. Thus, a sugarcane GST was modelled and molecular docked using the program LIGIN to investigate the contributions of the active site residues towards the binding of reduced glutathione (GSH) and 1‐chloro‐2,4‐dinitrobenzene (CDNB). As a result, W13 and I119 were identified as key residues for the specificity of sugarcane GSTF1 (SoGSTF1) towards CDNB. To obtain a better understanding of the catalytic specificity of sugarcane GST (SoGSTF1), two mutants were designed, W13L and I119F. Tertiary structure models and the same docking procedure were performed to explain the interactions between sugarcane GSTs with GSH and CDNB. An electron‐sharing network for GSH interaction was also proposed. The SoGSTF1 and the mutated gene constructions were cloned and expressed in Escherichia coli and the expressed protein purified. Kinetic analyses revealed different Km values not only for CDNB, but also for GSH. The Km values were 0.2, 1.3 and 0.3 mM for GSH, and 0.9, 1.2 and 0.5 mM for CDNB, for the wild type, W13L mutant and I119F mutant, respectively. The Vmax values were 297.6, 224.5 and 171.8 µmol min?1 mg?1 protein for GSH, and 372.3, 170.6 and 160.4 µmol min?1 mg?1 protein for CDNB. 相似文献