Antioxidant activity and absorption of cyanidin-3-O-glucoside liposomes in GES-1 cells in vitro

ABSTRACT

The use of anthocyanins are limited by their chemical properties. Recent evidence suggests Cyanidin-3-O-glucoside (C3 G) liposomes via the ethanol injection method exhibit improved stability. In the current study, the characterization and cell absorption of C3 G liposomes were explored via transmission electron microscopy and flow cytometry. The internalization of the C3 G liposomes across the gastric epithelial cell monolayer (GES-1 cells) were investigated. Results showed that the particle size and encapsulation efficiency were 234 ± 9.35 nm and 75.0% ± 0.001, respectively. The total antioxidant capacity (T-AOC) and malondialdehyde (MDA) content were used to evaluate the antioxidant activity of C3 G liposomes. The C3 G liposomes can obviously increased T-AOC and decreased the MDA content.Collectively, C3 G liposomes protected human GES-1 cells from gastric mucosal injury induced by H₂O₂ by activating the related antioxidant pathway. Our research could provide a new effective treatment strategy for the absorption of stomach drugs.

Abbreviations: C3G: Cyanidin-3-O-glucoside; LP: Liposome; GES-1 cells: Human gastric epithelial cell lines; FBS: Fetal Bovine Serum; PBS: Phosphate-buffered saline; PC: Phosphatidylcholine; CH: Cholesterol; MDA: Malondialdehyde; TEM: Transmission electron microscope; FCM: Flow cytometry; FITC: Fluorescein isothiocyanate; DAPI: 4′, 6-diamidino-2phenylidole; FT-IR: Fourier Transform infrared spectroscopy; PFA: Paraformaldehyde     

Understanding the genetic and molecular constitutions of heterosis for developing hybrid rice

The wide adoption of hybrid rice has greatly increased rice yield in the last several decades. The utilization of heterosis facilitated by male sterility has been a common strategy for hybrid rice development. Here, we summarize our efforts in the genetic and molecular understanding of heterosis and male sterility together with the related progress from other research groups. Analyses of F1 diallel crosses show that strong heterosis widely exists in hybrids of diverse germplasms, and inter-subsp...     

Mapping the d1 and d2 dwarfing genes and the purple foliage color locus P in pearl millet

The d(1) and d(2) dwarfing genes and the P purple foliage color gene were placed on the restriction fragment length polymorphism (RFLP)-based molecular marker linkage map of pearl millet [Pennisetum glaucum (L.) R. Br.] using a mapping population based on a cross of inbred lines IP 18293 (D(1)/D(1), d(2)/d(2), P/P) and Tift 238D1 (d(1)/d(1) D(2)/D(2) p/p). A skeleton genetic linkage map of 562 cM (Haldane function) was constructed using 33 RFLP markers and these three morphological markers. The D(1)/d(1) plant height locus mapped to pearl millet linkage group 1, while the D(2)/d(2) plant height locus and the P/p foliage color locus mapped to pearl millet linkage group 4. Loose genetic linkage was observed between the D(2)/d(2) and P/p loci, with 42% repulsion-phase recombination corresponding to 92 cM (Haldane). This loose linkage of morphological marker loci detected on pearl millet LG4 can likely find use in applied pearl millet breeding programs, as host plant resistances to both downy mildew and rust have previously been identified in this genomic region. Such exploitation of these morphological markers in an applied disease resistance breeding program would require development of appropriate genetic stocks, but the relatively loose genetic linkage between d(2) and P suggests that this should not be difficult.     

The molecular basis of white pericarps in African domesticated rice: novel mutations at the Rc gene

Repeated phenotypic evolution can occur at both the inter- and intraspecific level and is especially prominent in domesticated plants, where artificial selection has favoured the same traits in many different species and varieties. The question of whether repeated evolution reflects changes at the same or different genes in each lineage can now be addressed using the domestication and improvement genes that have been identified in a variety of crops. Here, we document the genetic basis of nonpigmented ('white') pericarps in domesticated African rice (Oryza glaberrima) and compare it with the known genetic basis of the same trait in domesticated Asian rice (Oryza sativa). In some cases, white pericarps in African rice are apparently caused by unique mutations at the Rc gene, which also controls pericarp colour variation in Asian rice. In one case, white pericarps appear to reflect changes at a different gene or potentially a cis-regulatory region.     

Identification and linkage mapping of complementary recessive genes causing hybrid breakdown in an intraspecific rice cross

One outcome of hybrid breakdown is poor growth, which we observed as a reduction in the number of panicles per plant and in culm length in an F₂ population derived from a cross between the genetically divergent rice (Oryza sativa L.) cultivars ‘Sasanishiki’ (japonica) and ‘Habataki’ (indica). Quantitative trait locus (QTL) analysis of the two traits and two-way ANOVA of the detected QTLs suggested that the poor growth was due mainly to an epistatic interaction between genes at QTLs located on chromosomes 2 and 11. The poor growth was likely to result when a plant was homozygous for the ‘Habataki’ allele at the QTL on chromosome 2 and homozygous for the ‘Sasanishiki’ allele at the QTL on chromosome 11. The results suggest that the poor growth found in the F₂ population was due to hybrid breakdown of a set of complementary genes. To test this hypothesis and determine the precise chromosomal location of the genes causing the hybrid breakdown, we performed genetic analyses using a chromosome segment substitution line, in which a part of chromosome 2 from ‘Habataki’ was substituted into the genetic background of ‘Sasanishiki’. The segregation patterns of poor growth in plants suggested that both of the genes underlying the hybrid breakdown were recessive. The gene on chromosome 2, designated hybrid breakdown 2 (hbd2), was mapped between simple sequence repeat markers RM3515 and RM3730. The gene on chromosome 11, hbd3, was mapped between RM5824 and RM1341. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The LAX1 and FRIZZY PANICLE 2 genes determine the inflorescence architecture of rice by controlling rachis-branch and spikelet development

We have analyzed two mutants that exhibit altered panicle architecture in rice (Oryza sativa L.). In lax1-2, which is a new and stronger allele of the previously reported lax mutant, initiation and/or maintenance of rachis-branches, lateral spikelets, and terminal spikelets was severely prevented. In situ hybridization analysis using OSH1, a rice knotted1 (kn1) ortholog, confirmed the absence of lateral meristems in lax1-2 panicles. These defects indicate that the LAX1 gene is required for the initiation/maintenance of axillary meristems in the rice panicle. In addition to its role in forming lateral meristems, the wild-type LAX1 gene acts as a floral meristem identity gene which specifies the terminal spikelet meristem. A comparison of the defects in lax1-1 and lax1-2 plants suggested that the sensitivities to reduced LAX1 activity were not uniform among different types of meristems. In the fzp2 mutant panicle, the basic branching pattern of the panicle was indistinguishable from that of the wild type; however, specification of both terminal and lateral spikelet meristems was blocked, and sequential rounds of branching occurred at the point where the spikelet meristems are initiated in the wild-type panicle. This resulted in the generation of a panicle composed of excessive ramification of rachis-branches. The lax1-1 fzp2 double mutants exhibited a novel, basically additive, phenotype, which suggests that LAX1 and FZP2 function in genetically independent pathways.     

Population history and natural selection shape patterns of genetic variation in 132 genes

Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may facilitate the identification of complex disease genes. Although the signature that natural selection imparts on DNA sequence variation is difficult to disentangle from the effects of neutral processes such as population demographic history, selective and demographic forces can be distinguished by analyzing multiple loci dispersed throughout the genome. We studied the molecular evolution of 132 genes by comprehensively resequencing them in 24 African-Americans and 23 European-Americans. We developed a rigorous computational approach for taking into account multiple hypothesis tests and demographic history and found that while many apparent selective events can instead be explained by demography, there is also strong evidence for positive or balancing selection at eight genes in the European-American population, but none in the African-American population. Our results suggest that the migration of modern humans out of Africa into new environments was accompanied by genetic adaptations to emergent selective forces. In addition, a region containing four contiguous genes on Chromosome 7 showed striking evidence of a recent selective sweep in European-Americans. More generally, our results have important implications for mapping genes underlying complex human diseases.     

Association of genetic variation in co-stimulatory molecule genes with outcome of liver transplant in Iranian patients

CD28, cytotoxic T-lymphocyte associated antigen 4 (CTLA4), inducible costimulator (ICOS) and programmed cell death 1 are closely-linked genes located on chromosome 2q and encode co-stimulatory molecules, which are T-cell activity regulators. The principal assignment of T-cell mediated immune response in allograft rejection is an interesting topic of multiple studies. Although the variation in these genes may influence the graft survival and the amount of immunosuppression needed, the studies so far have been restricted solely to the CTLA4 gene. In 145 patients who underwent liver allograft transplantation, 10 single nucleotide polymorphisms of CD28, CTLA4, ICOS, and PD.1 genes were defined. To distinguish the polymorphisms of all 10 SNPs, PCR-RFLP method was used and according to the standard criteria, acute rejection episodes were determined. CTLA4-1661, AA genotype was significantly more frequent in the patients with acute rejection and AG genotype was significantly more frequent in the patients without rejection. Frequencies of CTLA4+49 AG A allele and CTLA4-1661AG A allele were significantly higher than those of CTLA4+49 AG and CTLA4-1661AG, G allele in the patients with acute rejection. ICOS+693, GG genotype and G allele were significantly less frequent in the patients with acute rejection and CD28 CT genotype was significantly more in patients with acute rejection. The present results demonstrate that potentially functional genetic variation in T-cell co-stimulatory molecules including ICOS, CTLA4 and CD28 can influence liver transplant outcome.     

A revision of the systematics of panther worms (Hofstenia spp., Acoela), with notes on color variation and genetic variation within the genus

Species of the genus Hofstenia are voracious predators and among the largest and most colorful of the Acoela. They are known from Japan, the Red Sea, the North Atlantic islands of Bermuda and the Bahamas, and the Caribbean and in a variety of habitats including the rocky intertidal, among Thalassia sea grass, on filamentous algae and decaying mangrove leaves. Certain color morphs associated with each of these habitats seem to have confused the taxonomy of the group. While brown-and-white banding and spotting patterns of Hofstenia miamia and Hofstenia giselae are distinctive for species associated with mangrove leaves and Thallasia sp. and are likely to be cryptic for these specific environments, we find some evidence to suggest that the coloration is mimicry of a nudibranch with aposematic coloration. The common plan in these patterns is one with three variously solid or spotted lighter cross bands on a dark background. Our examination of museum type material and live specimens of Hofstenia collected from Bahamas, Belize, Bermuda, and Panama revealed no internal morphological differences between the Hofstenia species occurring in the Caribbean. Similarly, our analyses of 18S and 28S molecular sequence data revealed no significant differences among specimens. Accordingly, we declare that Hofstenia giselae is a junior synonym of Hofstenia miamia, the three-banded panther worm. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users. Handling editor: K. Martons     

Biodegradation of 3-chlorobenzoate and formation of black color in the presence and absence of benzoate

Summary Four isolates of Pseudomonas from soil and sewage utilized 3-chlorobenzoate (3-CBA) adaptively as sole source of carbon and energy. Two of these were studied in detail. Their doubling times in batch culture were about twice as long on chlorobenzoate as on benzoate or glucose. Both isolates showed oxygen uptake on catechol, without lag, when grown on either benzoate or 3-CBA. One strain, designated Pseudomonas H1, could oxidize a key intermediate, 4-chlorocatechol, only when grown on 3-CBA. Pseudomonas H2 could oxidize the chlorocatechol not only when grown on 3-CBA but also when grown on benzoate. Benzoate-adapted P. H1 therefore accumulated chlorocatechols when incubated with a mixture of 3-CBA and benzoate, whereas P. H2 under the same conditions did not. The accumulated chlorocatechols inhibited further oxygen uptake, and in alkaline media they polymerized to a black, melanin-like pigment. Intense black pigment, similar to that formed by P. I, was formed if raw sewage was incubated with a mixture of 3-CBA and benzoate. The pigment was not formed if the sewage was first adapted by incubation with 3-CBA.     

Population genetic analysis of the genes APOE, APOB(3'VNTR) and ACE in some black and Amerindian communities from Colombia

A population genetic study was carried out with the APOE, APOB and ACE loci in 17 Colombian human populations. Ten of them were Amerindian communities coming from the northeastern part of Colombia, Pacific region, Eastern Plains and Amazonia. Six were black populations from Providence Island, Caribbean and Pacific coasts. Finally, the Mestizo population of Bogota was studied as well. The APOE and ACE loci were in Hardy-Weinberg equilibrium, whereas the APOB locus was not studied in all populations. The genetic heterogeneity was substantially greater among the Amerindian populations (G(ST) = 0.059) than in the Afrocolombian populations (G(ST) = 0.009). Also the gene flow population pair estimates were so much higher among the Afrocolombian populations (Nm = 49.08 +/- 43.07) than among Amerindian populations (Nm = 9.66 +/- 18.04). Different phylogenetic and multivariant analyses showed that the Amerindian populations analyzed were clustered in three different arrays: one constituted by the Colombian northeastern and Pacific populations, the second one by the two Amazon populations (Coreguaje and Nukak) and the last one by the Yuco (the unique Caribbe-speaking population among those studied). The latter population was highly divergent from a genetic point of view from the remainder Amerindian populations studied. By using the Mantel test, the existence of a positive and significant correlation between the genetic and geographical distances found among Amerindian populations was demonstrated. This fact was not observed among the Afrocolombian populations. Nevertheless, an isolation-by-distance Slatkin analysis test did not show a significant clear structure of this special pattern among the Indian tribes studied.     

Hierarchical analysis of population genetic variation in mitochondrial and nuclear genes of Daphnia pulex

The geographic structure of Daphnia pulex populations from the central United States is analyzed with respect to isozyme and mitochondrial DNA variation. The species complex consists of cyclic and obligate parthenogens. A hierarchical analysis of population structure in the cyclic parthenogens by using a fixation-index approach indicates that this is one of the most extremely subdivided species yet studied. This genetic structure, much of which accrues within 100 km, is certainly due in part to the limited dispersal ability of Daphnia. However, previous work has shown that fluctuating selection can account for the spatial heterogeneity in isozyme frequencies in these populations. This may explain why the population subdivision for the mitochondrial genome increases approximately three times as rapidly with distance as does that for nuclear genes, which is slower than the neutral expectation. The obligate parthenogens are shown to be polyphyletic in origin, evolutionarily young, and, in some cases, geographically widespread.     

Partitioning of genetic variation between regulatory and coding gene segments: the predominance of software variation in genes encoding introvert proteins

Summary  In considering genetic variation in eukaryotes, a fundamental distinction can be made between variation in regulatory (software) and coding (hardware) gene segments. For quantitative traits the bulk of variation, particularly that near the population mean, appears to reside in regulatory segments. The main exceptions to this rule concern proteins which handle extrinsic substances, here termed extrovert proteins. The immune system includes an unsually large proportion of this exceptional category, but even so its chief source of variation may well be polymorphism in regulatory gene segments. The main evidence for this view emerges from genome scanning for quantitative trait loci (QTL), which in the case of the immune system points to a major contribution of pro-inflammatory cytokine genes. Further support comes from sequencing of major histocompatibility complex (Mhc) class II promoters, where a high level of polymorphism has been detected. These Mhc promoters appear to act, in part at least, by gating the back-signal from T cells into antigen-presenting cells. Both these forms of polymorphism are likely to be sustained by the need for flexibility in the immune response. Future work on promoter polymorphism is likely to benefit from the input from genome informatics.     

Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes

The major histocompatibility complex (MHC) forms an integral component of the vertebrate immune response and, due to strong selection pressures, is one of the most polymorphic regions of the entire genome. Despite over 15 years of research, empirical studies offer highly contradictory explanations of the relative roles of different evolutionary forces, selection and genetic drift, acting on MHC genes during population bottlenecks. Here, we take a meta-analytical approach to quantify the results of studies into the effects of bottlenecks on MHC polymorphism. We show that the consequences of selection acting on MHC loci prior to a bottleneck event, combined with drift during the bottleneck, will result in overall loss of MHC polymorphism that is ～15% greater than loss of neutral genetic diversity. These results are counter to general expectations that selection should maintain MHC polymorphism, but do agree with the results of recent simulation models and at least two empirical studies. Notably, our results suggest that negative frequency-dependent selection could be more important than overdominance for maintaining high MHC polymorphism in pre-bottlenecked populations.     

Ecological genetics of adaptive color polymorphism in pocket mice: geographic variation in selected and neutral genes

Patterns of geographic variation in phenotype or genotype may provide evidence for natural selection. Here, we compare phenotypic variation in color, allele frequencies of a pigmentation gene (the melanocortin-1 receptor, Mc1r), and patterns of neutral mitochondrial DNA (mtDNA) variation in rock pocket mice (Chaetodipus intermedius) across a habitat gradient in southern Arizona. Pocket mice inhabiting volcanic lava have dark coats with unbanded, uniformly melanic hairs, whereas mice from nearby light-colored granitic rocks have light coats with banded hairs. This color polymorphism is a presumed adaptation to avoid predation. Previous work has demonstrated that two Mc1r alleles, D and d, differ by four amino acids, and are responsible for the color polymorphism: DD and Dd genotypes are melanic whereas dd genotypes are light colored. To determine the frequency of the two Mc1r allelic classes across the dark-colored lava and neighboring light-colored granite, we sequenced the Mc1r gene in 175 individuals from a 35-km transect in the Pinacate lava region. We also sequenced two neutral mtDNA genes, COIII and ND3, in the same individuals. We found a strong correlation between Mc1r allele frequency and habitat color and no correlation between mtDNA markers and habitat color. Using estimates of migration from mtDNA haplotypes between dark- and light-colored sampling sites and Mc1r allele frequencies at each site, we estimated selection coefficients against mismatched Mc1r alleles, assuming a simple model of migration-selection balance. Habitat-dependent selection appears strong but asymmetric: selection is stronger against light mice on dark rock than against melanic mice on light rock. Together these results suggest that natural selection acts to match pocket mouse coat color to substrate color, despite high levels of gene flow between light and melanic populations.     

The red and the black: bioluminescence and the color of animals in the deep sea

The colors of deep-sea species are generally assumed to be cryptic,but it is not known how cryptic they are and under what conditions.This study measured the color of approximately 70 deep-sea species,both pelagic and benthic, and compared the results with twosets of predictions: 1) optimal crypsis under ambient light,2) optimal crypsis when viewed by bioluminescent "searchlights."The reflectances of the pelagic species at the blue-green wavelengthsimportant for deep-sea vision were far lower than the predictedreflectances for crypsis under ambient light and closer to thezero reflectance prediction for crypsis under searchlights.This suggests that bioluminescence is more important than ambientlight for the visual detection of pelagic species at mesopelagicdepths. The reflectances of the benthic species were highlyvariable and a relatively poor match to the substrates on whichthey were found. However, estimates of the contrast sensitivityof deep-sea visual systems suggest that even approximate matchesmay be sufficient for crypsis in visually complex benthic habitats.Body coloration was generally uniform, but many crabs had strikingpatterns that may serve to disrupt the outlines of their bodies.     

Investigating the potential role of genetic and epigenetic variation of DNA methyltransferase genes in hyperplastic polyposis syndrome

Background

Hyperplastic Polyposis Syndrome (HPS) is a condition associated with multiple serrated polyps, and an increased risk of colorectal cancer (CRC). At least half of CRCs arising in HPS show a CpG island methylator phenotype (CIMP), potentially linked to aberrant DNA methyltransferase (DNMT) activity. CIMP is associated with methylation of tumor suppressor genes including regulators of DNA mismatch repair (such as MLH1, MGMT), and negative regulators of Wnt signaling (such as WIF1). In this study, we investigated the potential for interaction of genetic and epigenetic variation in DNMT genes, in the aetiology of HPS.

Methods

We utilized high resolution melting (HRM) analysis to screen 45 cases with HPS for novel sequence variants in DNMT1, DNMT3A, DNMT3B, and DNMT3L. 21 polyps from 13 patients were screened for BRAF and KRAS mutations, with assessment of promoter methylation in the DNMT1, DNMT3A, DNMT3B, DNMT3L MLH1, MGMT, and WIF1 gene promoters.

Results

No pathologic germline mutations were observed in any DNA-methyltransferase gene. However, the T allele of rs62106244 (intron 10 of DNMT1 gene) was over-represented in cases with HPS (p<0.01) compared with population controls. The DNMT1, DNMT3A and DNMT3B promoters were unmethylated in all instances. Interestingly, the DNMT3L promoter showed low levels of methylation in polyps and normal colonic mucosa relative to matched disease free cells with methylation level negatively correlated to expression level in normal colonic tissue. DNMT3L promoter hypomethylation was more often found in polyps harbouring KRAS mutations (p = 0.0053). BRAF mutations were common (11 out of 21 polyps), whilst KRAS mutations were identified in 4 of 21 polyps.

Conclusions

Genetic or epigenetic alterations in DNMT genes do not appear to be associated with HPS, but further investigation of genetic variation at rs62106244 is justified given the high frequency of the minor allele in this case series.     

Further support to the uncoupling-to-survive theory: the genetic variation of human UCP genes is associated with longevity

In humans Uncoupling Proteins (UCPs) are a group of five mitochondrial inner membrane transporters with variable tissue expression, which seem to function as regulators of energy homeostasis and antioxidants. In particular, these proteins uncouple respiration from ATP production, allowing stored energy to be released as heat. Data from experimental models have previously suggested that UCPs may play an important role on aging rate and lifespan. We analyzed the genetic variability of human UCPs in cohorts of subjects ranging between 64 and 105 years of age (for a total of 598 subjects), to determine whether specific UCP variability affects human longevity. Indeed, we found that the genetic variability of UCP2, UCP3 and UCP4 do affect the individual's chances of surviving up to a very old age. This confirms the importance of energy storage, energy use and modulation of ROS production in the aging process. In addition, given the different localization of these UCPs (UCP2 is expressed in various tissues including brain, hearth and adipose tissue, while UCP3 is expressed in muscles and Brown Adipose Tissue and UCP4 is expressed in neuronal cells), our results may suggest that the uncoupling process plays an important role in modulating aging especially in muscular and nervous tissues, which are indeed very responsive to metabolic alterations and are very important in estimating health status and survival in the elderly.     

Regions outside the leucine-rich repeat domain determine the distinct resistance specificities of the rice blast resistance genes Pik and Pik-m

Two alleles of the rice blast resistance (R) Pik locus, Pik-m and Pik, are each composed of a pair of nucleotide-binding site–leucine-rich repeat (NBS–LRR) genes, referred to as the first gene and the second gene. Pik-m and Pik are unique in that many of the amino acid substitutions between them are distributed in or near the N-terminal coiled-coil (CC) domain of the first gene, suggesting that the CC domain of the first gene plays an important role in determinating their R specificity. To examine this hypothesis, I investigated resistance phenotypes of transgenic plants carrying each of two kinds of domain-swapped Pik-m-based recombinant first genes. Replacement of the LRR domain of Pik-m with the equivalent region of Pik did not change the Pik-m-type specificity, indicating that regions outside the LRR domain are responsible for differentiating the R specificity of Pik-m from Pik. In contrast, replacement of both the NBS and LRR domains of Pik-m with the corresponding region of Pik resulted in loss of blast resistance, suggesting that co-adaptation of polymorphisms in the CC and NBS domains is necessary to maintain resistance.