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  • 1
    Electronic Resource
    Electronic Resource
    Relaxation processes following excitation and ionization of SiF4 in the vicinity of the silicon 2p threshold. II. Dissociation of the molecular ions (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 90 (1989), S. 7078-7086 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Partial ion yields from photoionization of SiF4 have been measured with time-of-flight mass spectrometry, photoion–photoion coincidence and triple photoion coincidence techniques using synchrotron radiation from 100 to 136 eV, in the region of the silicon 2p edge where strong resonances are found. From the photon energy dependence of positive ion pairs and of doubly charged fragment intensities, with a suitable normalization procedure, we have estimated the total double photoionization cross section. Below the Si2p edge, the double to single dissociative ionization branching ratio follows the resonance behavior, and is consistent with the photoelectron results of de Souza et al. (Paper I) and discussed in terms of multibond breaking dissociation pathways of residual excited ions (singly and doubly charged) produced by resonant Auger decay processes. Above the Si2p edge, the fragmentation is found to originate from dissociative double ionization occurring after normal Auger processes. The small additional contribution of triple dissociative ionization is consistent with a second order Auger process. In contrast, the underlying valence ionization continuum is responsible for all parent intensity and most of the SiF+3 fragment expected from the normal dissociative ionization channels. The measurement of appearance energies of fragment ion pairs by the photoion–photoion coincidence method, offers a direct measurement of the first direct double ionization onset in SiF4 and new values for other dissociative SiF2+4 states which complement those found by Auger spectroscopy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456236
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  • 2
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    Genetic variation in polyploid forage grass: Assessing the molecular genetic variability in the Paspalum genus (2013)
    BioMed Central
    Details
    Publication Date: 2013-06-09
    Description: Background: Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct identification of germplasms and quantification of their variability are necessary for the proper development of conservation and breeding programs. Evaluation of microsatellite markers in different species of Paspalum conserved in a germplasm bank allowed assessment of the genetic differences among them and assisted in their proper botanical classification. Results: Seventeen new polymorphic microsatellites were developed for Paspalum atratum Swallen and Paspalum notatum Flugge, twelve of which were transferred to 35 Paspalum species and used to evaluate their variability. Variable degrees of polymorphism were observed within the species. Based on distance-based methods and a Bayesian clustering approach, the accessions were divided into three main species groups, two of which corresponded to the previously described Plicatula and Notata Paspalum groups. In more accurate analyses of P. notatum accessions, the genetic variation that was evaluated used thirty simple sequence repeat (SSR) loci and revealed seven distinct genetic groups and a correspondence of these groups to the three botanical varieties of the species (P. notatum var. notatum, P. notatum var. saurae and P. notatum var. latiflorum). Conclusions: The molecular genetic approach employed in this study was able to distinguish many of the different taxa examined, except for species that belong to the Plicatula group, which has historically been recognized as a highly complex group. Our molecular genetic approach represents a valuable tool for species identification in the initial assessment of germplasm as well as for characterization, conservation and successful species hybridization.
    Electronic ISSN: 1471-2156
    Topics: Biology
    Published by BioMed Central
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  • 3
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    Genetic variation in polyploid forage grass: Assessing the molecular genetic variability in the Paspalumgenus (2013)
    BioMed Central
    Details
    Publication Date: 2013-06-08
    Description: Background Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct identification of germplasms and quantification of their variability are necessary for the proper development of conservation and breeding programs. Evaluation of microsatellite markers in different species of Paspalum conserved in a germplasm bank allowed assessment of the genetic differences among them and assisted in their proper botanical classification. Results Seventeen new polymorphic microsatellites were developed for Paspalum atratum Swallen and Paspalum notatum Flüggé, twelve of which were transferred to 35 Paspalum species and used to evaluate their variability. Variable degrees of polymorphism were observed within the species. Based on distance-based methods and a Bayesian clustering approach, the accessions were divided into three main species groups, two of which corresponded to the previously described Plicatula and Notata Paspalum groups. In more accurate analyses of P. notatum accessions, the genetic variation that was evaluated used thirty simple sequence repeat (SSR) loci and revealed seven distinct genetic groups and a correspondence of these groups to the three botanical varieties of the species (P. notatum var. notatum, P. notatum var. saurae and P. notatum var. latiflorum). Conclusions The molecular genetic approach employed in this study was able to distinguish many of the different taxa examined, except for species that belong to the Plicatula group, which has historically been recognized as a highly complex group. Our molecular genetic approach represents a valuable tool for species identification in the initial assessment of germplasm as well as for characterization, conservation and successful species hybridization.
    Electronic ISSN: 1471-2156
    Topics: Biology
    Published by BioMed Central
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  • 4
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    Liver and blood cytokine microenvironment in HCV patients is associated to liver fibrosis score: a proinflammatory cytokine ensemble orchestrated by TNF and tuned by IL-10 (2016)
    BioMed Central
    Details
    Publication Date: 2016-01-09
    Description: In this study, we have evaluated the immunological status of hepatitis C virus (HCV)-infected patients aiming at identifying putative biomarkers associated with distinct degrees of liver fibrosis. Peripheral b...
    Electronic ISSN: 1471-2180
    Topics: Biology
    Published by BioMed Central
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  • 5
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    NPHS2 mutations account for only 15 % of nephrotic syndrome cases (2015)
    BioMed Central
    Details
    Publication Date: 2015-09-30
    Description: Background: Nephrotic syndrome is traditionally classified on the basis of the response to standard steroid treatment. Mutations in more than 24 genes have been associated with nephrotic syndrome in children, although the great majority of steroid-resistant cases have been attributed to mutations in three main genes: NPHS1, NPHS2 and WT1. The aims of this study were to identify mutations in these genes more frequently reported as mutated and to characterize each variation using different in silico prediction algorithms in order to understand their biological functions. Methods: We performed direct sequence analysis of exons 8 and 9 of WT1, 8 exons of NPHS2 and 29 exons of NPHS1, including NPHS2 and NPHS1 intron–exon boundary sequences, as well as 700 bp of the 5′ UTR from both genes in 27 steroid-resistant patients aged between 3 months and 18 years. Results: Analysis of the NPHS2 gene revealed four missense mutations, one frameshift mutation and three variations in the 5′ UTR. Four patients presented compound heterozygosis, and four other patients presented one heterozygous alteration only. WT1 and NPHS1 gene analysis did not reveal any mutations.DiscussionThis is the first study focusing on genetics of SRNS in Brazilian children. Identification of mutations is important because it could influence physicians’ decision on patient treatment, as patients carrying mutations can be spared the side effects of immunosuppressive therapy and ultimately could be considered for kidney transplantation from a living donor. Conclusions: After molecular analysis of the genes more frequently reported as mutated in 27 steroid-resistant nephrotic syndrome patients, we identified NPHS2 mutations confirming the hereditary character of the kidney disease in only 14.8 % of patients. Therefore, the next step is to perform a next generation sequencing based analysis of glomeluropathy-related panel of genes for the remaining patients in order to search for mutations in other genes related to steroid-resistant nephrotic syndrome.
    Electronic ISSN: 1471-2350
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 6
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    Microsatellite marker development for the rubber tree (Hevea brasiliensis): characterization and cross-amplification in wild Hevea species. (2012)
    BioMed Central
    Details
    Publication Date: 2012-06-26
    Description: Background: 〉The rubber tree (Hevea brasiliensis) is native to the Amazon region and it is the major source of natural rubber in the world. Rubber tree breeding is time-consuming and expensive. However, molecular markers such as microsatellites can reduce the time required for these programs. This study reports new genomic microsatellite markers developed and characterized in H. brasiliensis and the evaluation of their transferability to other Hevea species.FindingsWe constructed di- and trinucleotide-enriched libraries. From these two libraries, 153 primer pairs were designed and initially evaluated using 9 genotypes of H. brasiliensis. A total of 119 primer pairs had a good amplification product, 90 of which were polymorphic. We chose 46 of the polymorphic markers and characterized them in 36 genotypes of H. brasiliensis. The expected and observed heterozygosities ranged from 0.1387 to 0.8629 and 0.0909 to 0.9167, respectively. The polymorphism information content (PIC) values ranged from 0.097 to 0.8339, and the mean number of alleles was 6.4 (2¿17). These 46 microsatellites were also tested in 6 other Hevea species. The percentage of transferability ranged from 82% to 87%. Locus duplication was found in H. brasiliensis and also in 5 of other species in which transferability was tested. Conclusions: This study reports new microsatellite markers for H. brasiliensis that can be used for genetic linkage mapping, quantitative trait loci identification and marker- assisted selection. The high percentage of transferability may be useful in the evaluations of genetic variability and to monitor introgression of genetic variability from different Hevea species into breeding programs.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 7
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    Antitumor and anti-cachectic effects of shark liver oil and fish oil: comparison between independent or associative chronic supplementation in Walker 256 tumor-bearing rats (2013)
    BioMed Central
    Details
    Publication Date: 2013-10-17
    Description: Background: Shark liver oil (SLOil) and fish oil (FOil), which are respectively rich in alkylglycerols (AKGs) and n-3 polyunsaturated fatty acids (PUFAs), are able to reduce the growth of some tumors and the burden of cachexia. It is known that FOil is able to reduce proliferation rate and increase apoptotic cells and lipid peroxidation of tumor cells efficiently. However, there are few reports revealing the influence of SLOil on these parameters. In the current study, effects of FOil chronic supplementation on tumor growth and cachexia were taken as reference to compare the results obtained with SLOil supplementation. Also, we evaluated if the association of SLOil and FOil was able to promote additive effects. Methods: Weanling male Wistar rats were divided into 4 groups: fed regular chow (C), supplemented (1g/kg body weight) with SLOil (CSLO), FOil (CFO) and both (CSLO + FO). After 8 weeks half of each group was inoculated with Walker 256 cells originating new groups (W, WSLO, WFO and WSLO + FO). Biochemical parameters of cachexia, tumor weight, hydroperoxide content, proliferation rate and percentage of apoptotic tumor cells were analysed. Fatty acids and AKG composition of tumor and oils were obtained by high performance liquid chromatography and gas chromatography -- mass spectrometry, respectively. Statistical analysis was performed by unpaired t-test and one-way ANOVA followed by a post hoc Tukey test. Results: Fourteen days after inoculation, SLOil was able to restore cachexia parameters to control levels, similarly to FOil. WSLO rats presented significantly lower tumor weight (40%), greater tumor cell apoptosis (~3-fold), decreased tumor cell proliferation (35%), and higher tumor content of lipid hydroperoxides (40%) than observed in W rats, but FOil showed more potent effects. Supplementation with SLOil + FOil did not promote additive effects. Additionally, chromatographic results suggested a potential incorporation competition between the n-3 fatty acids and the AKGs in the tumor cells' membranes. Conclusions: SLOil is another marine source of lipids with similar FOil anti-cachectic capacity. Furthermore, despite being less potent than FOil, SLOil presented significant in vivo antitumor effects. These results suggest that the chronic supplementation with SLOil may be adjuvant of the anti-cancer therapy.
    Electronic ISSN: 1476-511X
    Topics: Biology
    Published by BioMed Central
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  • 8
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    Functional expression and activity of the recombinant antifungal defensin PvD1r from Phaseolus vulgaris L. (common bean) seeds (2014)
    BioMed Central
    Details
    Publication Date: 2014-04-02
    Description: Background: Defensins are basic, cysteine-rich antimicrobial peptides that are important components of plant defense against pathogens. Previously, we isolated a defensin, PvD1, from Phaseolus vulgaris L. (common bean) seeds. Results: The aim of this study was to overexpress PvD1 in a prokaryotic system, verify the biologic function of recombinant PvD1 (PvD1r) by comparing the antimicrobial activity of PvD1r to that of the natural defensin, PvD1, and use a mutant Candida albicans strain that lacks the gene for sphingolipid biosynthesis to unravel the target site of the PvD1r in C. albicans cells. The cDNA encoding PvD1, which was previously obtained, was cloned into the pET-32 EK/LIC vector, and the resulting construct was used to transform bacterial cells (Rosetta Gami 2 (DE3) pLysS) leading to recombinant protein expression. After expression had been induced, PvD1r was purified, cleaved with enterokinase and repurified by chromatographic steps. N-terminal amino acid sequencing showed that the overall process of the recombinant production of PvD1r, including cleavage with the enterokinase, was successful. Additionally, modeling revealed that PvD1r had a structure that was similar to the defensin isolated from plants. Purified PvD1 and PvD1r possessed inhibitory activity against the growth of the wild-type pathogenic yeast strain C. albicans. Both defensins, however, did not present inhibitory activity against the mutant strain of C. albicans. Antifungal assays with the wild-type C. albicans strains showed morphological changes upon observation by light microscopy following growth assays. PvD1r was coupled to FITC, and the subsequent treatment of wild type C. albicans with DAPI revealed that the labeled peptide was intracellularly localized. In the mutant strain, no intracellular labeling was detected. Conclusion: Our results indicate that PvD1r retains full biological activity after recombinant production, enterokinase cleavage and purification. Additionally, our results from the antimicrobial assay, the microscopic analysis and the PvD1r-FITC labeling assays corroborate each other and lead us to suggest that the target of PvD1 in C. albicans cells is the sphingolipid glucosylceramide.
    Electronic ISSN: 1471-2091
    Topics: Chemistry and Pharmacology
    Published by BioMed Central
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  • 9
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    Probing the antisymmetric Fano interference assisted by a Majorana fermion (2014)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2014-11-04
    Description: As the Fano effect is an interference phenomenon where tunneling paths compete for the electronic transport, it becomes a probe to catch fingerprints of Majorana fermions lying on condensed matter systems. In this work, we benefit of this mechanism by proposing as a route for that an Aharonov-Bohm-like interferometer composed by two quantum dots, being one of them coupled to a Majorana bound state, which is attached to one of the edges of a semi-infinite Kitaev wire within the topological phase. By changing the Fermi energy of the leads and the symmetric detuning of the levels for the dots, we show that opposing Fano regimes result in a transmittance characterized by distinct conducting and insulating regions, which are fingerprints of an isolated Majorana quasiparticle. Furthermore, we show that the maximum fluctuation of the transmittance as a function of the detuning is half for a semi-infinite wire, while it corresponds to the unity for a finite system. The setup proposed here constitutes an alternative experimental tool to detect Majorana excitations.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 10
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    Building the sugarcane genome for biotechnology and identifying evolutionary trends (2014)
    BioMed Central
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    Publication Date: 2014-07-01
    Description: Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome. Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences. Conclusion: This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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