Effects of genetics and environment on isoflavone content of soybean from different regions of Brazil

The effects of genetics and environmental factors on isoflavone content of soybean (Glycine max L.) cultivars grown in different locations in Brazil in 1993/94 were evaluated. Seeds of different cultivars were analised by high performance liquid chromatography (HPLC). In Rio Grande do Sul (RS), Paraná (PR), and Mato Grosso do Sul (MS) States, a significant difference in the isoflavone total content average of the cultivars IAS 5 and FT-Abyara (163.9, 116.4 and 79.5 mg/100 g, respectively) was observed. In general, IAS 5 contained higher isoflavone than FT-Abyara. Cultivars IAS 5 and FT-Abyara grown at Vacaria, RS (28°30' S latitude) with temperature average of 19°C, had the highest isoflavone concentrations (218.7 and 163.8 mg/100 g, respectively). In Palotina, PR (24°27' S latitude), where temperature average was 24°C, the isoflavone concentrations were 105.9 and 86.8 mg/100 g, respectively. The lowest isoflavone contents were observed for FT-Estrela and FT-Cristalina, (27.6 and 46.5 mg/100 g, repectively) at Rondonópolis, MT (16°20' S latitude), where the temperature was 27°C.

DNA knots and DNA supercoiling.

Comment on: Witz G, et al. Proc Natl Acad Sci USA 2011; 108:3608-11.

Host genetics and HIV-1: the final phase?

This is a crucial transition time for human genetics in general, and for HIV host genetics in particular. After years of equivocal results from candidate gene analyses, several genome-wide association studies have been published that looked at plasma viral load or disease progression. Results from other studies that used various large-scale approaches (siRNA screens, transcriptome or proteome analysis, comparative genomics) have also shed new light on retroviral pathogenesis. However, most of the inter-individual variability in response to HIV-1 infection remains to be explained: genome resequencing and systems biology approaches are now required to progress toward a better understanding of the complex interactions between HIV-1 and its human host.

Nuclear translocation and DNA recognition signals colocalized within the bZIP domain of cyclic adenosine 3',5'-monophosphate response element-binding protein CREB.

CREB is a cAMP-responsive nuclear DNA-binding protein that binds to cAMP response elements and stimulates gene transcription upon activation of the cAMP signalling pathway. The protein consists of an amino-terminal transcriptional transactivation domain and a carboxyl-terminal DNA-binding domain (bZIP domain) comprised of a basic region and a leucine zipper involved in DNA recognition and dimerization, respectively. Recently, we discovered a testis-specific transcript of CREB that contains an alternatively spliced exon encoding multiple stop codons. CREB encoded by this transcript is a truncated protein lacking the bZIP domain. We postulated that the antigen detected by CREB antiserum in the cytoplasm of germinal cells is the truncated CREB that must also lack its nuclear translocation signal (NTS). To test this hypothesis we prepared multiple expression plasmids encoding carboxyl-terminal deletions of CREB and transiently expressed them in COS-1 cells. By Western immunoblot analysis as well as immunocytochemistry of transfected cells, we show that CREB proteins truncated to amino acid 286 or shorter are sequestered in the cytoplasm, whereas a CREB of 295 amino acids is translocated into the nucleus. Chimeric CREBs containing a heterologous NTS fused to the first 248 or 261 amino acids of CREB are able to drive the translocation of the protein into the nucleus. Thus, the nine amino acids in the basic region involved in DNA recognition between positions 287 and 295 (RRKKKEYVK) of CREB contain the NTS. Further, mutation of the lysine at position 290 in CREB to an asparagine diminishes nuclear translocation of the protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Linking the population genetics and ecology of arbuscular mycorrhizal fungi

Résumé Les champignons endomycorhiziens arbusculaires (CEA) ont co-évolué avec les plantes terrestres depuis plus de 400 millions d'années. De nos jours, les CEA forment une symbiose avec les racines de la majorité des plantes terrestres. Les CEA sont écologiquement importants parce qu'ils influencent non seulement la croissance des plantes, mais aussi leur diversité. Les CEA sont des biotrophes obligatoires qui reçoivent leur énergie sous forme de glucides issus de la photosynthèse des plantes. En contrepartie, les CEA apportent à leurs hôtes du phospore. Les CEA croissent et se reproduisent clonalement en formant des hyphes et des spores. De plus, les CEA sont coenocytiques et multigénomiques; le cytoplasme d'un CEA contient des noyeaux génétiquement différents. De nombreuses études ont démontré que différentes espèces de CEA agissent différentiellement sur la croissance des plantes. Malgré une conscience de plus en plus forte de l'existence d'une variabilité intraspécifique, la question de savoir si les populations de CEA sont génétiquement variables a été largement négligée. Dans le Chapitre 2, j'ai cherché à savoir si une population de CEA provenant d'un seul champ possède une diversité génétique. Cette étude a mis en évidence une importante variation génétique et phénotypique au sein d'individus de la même population. Des différences au niveau de traits de croissance, héritables et liés à la valeur sélective, indiquent que la variation génétique observée entre isolats n'est pas entièrement neutre. Dans le Chapitre 3, je montre que les différences génétiques entre isolats de CEA d'une population provoquent de la variation dans la croissance des plantes. L'effet des isolats dépend des conditions environnementales et varie de bénéfique à parasitique. Dans le Chapitre 4, je montre que des traits de croissance de CEA varient significativement dans des environnements contrastés. J'ai détecté de fortes interactions entre différents génotypes de CEA et différentes espèces de plantes. Ceci suggère que dans un environnement hétérogène, la sélection pourrait localement favoriser différents génotypes de CEA, maintenant ainsi la diversité génétique dans la population. Les résultats de ce travail aident à mieux comprendre l'importance écologique de la variation intraspécifique des CEA. La possibilité de pouvoir cultiver des individus d'une population de CEA au laboratoire nous a permis une meilleure compréhension de la génétique de ces champignons. De plus, ce travail est une base pour de futures expériences visant à comprendre l'importance évolutive de la diversité intraspécifique des CEA. Abstract Arbuscular mycorrhizal fungi (A1VIF) have co-evolved with land plants -for over 400 million years. Today, AMF form symbioses with roots of most land plants and are ecologically important because they alter plant growth and affect plant diversity. AMF are obligate biotrophs, obtaining their energy in form of plant-derived photosynthates. In return,- they supply their host plants with phosphorous. These fungi grow and reproduce clonally by hyphae and spores. They are coenocytic and multigenomic, harbouring genetically different nuclei in a common cytoplasm. Many studies have shown different AMF species differentially alter plant growth. Despite the increasing awareness of intraspecific variability the question whether there is any genetic variation among different individuals of the same population has been largely neglected. In Chapter 2, we investigated whether there is genetic diversity in a field population of the AMF G. intraradices. This work revealed that large genetic and heritable phenotypic variation exists in this AMF population. Differences in fitness-related growth traits among isolates suggest that some of the observed genetic variation is not selectively neutral. In Chapter 3, we show that genetic differences among isolates from the same population also cause variation in plant growth. The isolate effects on plant growth depended on the environmental conditions and varied from beneficial to detrimental. In Chapter 4, fitnessrelated growth traits of genetically different isolates were significantly altered in contrasting environments. we detected strong AMF isolate by host species interacfions which suggests that in a heterogeneous environment selection could locally favour different AMF genotypes, thereby maintaining high genetic diversity in the population. The results of this work contribute to the understanding of the ecological importance of intraspecific diversity in AMF. The possibility of culturing individuals of an AMF field population under laboratory condition gave new insights into AMF genetics and lays a foundation for future studies to analyse the evolutionary significance of intraspecific genetic diversity in AMF.

Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma.

BACKGROUND: HOX genes are a family of developmental genes that are expressed neither in the developing forebrain nor in the normal brain. Aberrant expression of a HOX-gene dominated stem-cell signature in glioblastoma has been linked with increased resistance to chemo-radiotherapy and sustained proliferation of glioma initiating cells. Here we describe the epigenetic and genetic alterations and their interactions associated with the expression of this signature in glioblastoma. RESULTS: We observe prominent hypermethylation of the HOXA locus 7p15.2 in glioblastoma in contrast to non-tumoral brain. Hypermethylation is associated with a gain of chromosome 7, a hallmark of glioblastoma, and may compensate for tumor-driven enhanced gene dosage as a rescue mechanism by preventing undue gene expression. We identify the CpG island of the HOXA10 alternative promoter that appears to escape hypermethylation in the HOX-high glioblastoma. An additive effect of gene copy gain at 7p15.2 and DNA methylation at key regulatory CpGs in HOXA10 is significantly associated with HOX-signature expression. Additionally, we show concordance between methylation status and presence of active or inactive chromatin marks in glioblastoma-derived spheres that are HOX-high or HOX-low, respectively. CONCLUSIONS: Based on these findings, we propose co-evolution and interaction between gene copy gain, associated with a gain of chromosome 7, and additional epigenetic alterations as key mechanisms triggering a coordinated, but inappropriate, HOX transcriptional program in glioblastoma.

Life-course socioeconomic status and DNA methylation of genes regulating inflammation

BACKGROUND: In humans, low socioeconomic status (SES) across the life course is associated with greater diurnal cortisol production, increased inflammatory activity and higher circulating antibodies for several pathogens, all suggesting a dampened immune response. Recent evidence suggests that DNA methylation of pro-inflammatory genes may be implicated in the biological embedding of the social environment. METHODS: The present study examines the association between life-course SES and DNA methylation of candidate genes, selected on the basis of their involvement in SES-related inflammation, in the context of a genome-wide methylation study. Participants were 857 healthy individuals sampled from the EPIC Italy prospective cohort study. RESULTS: Indicators of SES were associated with DNA methylation of genes involved in inflammation. NFATC1, in particular, was consistently found to be less methylated in individuals with low vs high SES, in a dose-dependent manner. IL1A, GPR132 and genes belonging to the MAPK family were also less methylated among individuals with low SES. In addition, associations were found between SES and CXCL2 and PTGS2, but these genes were consistently more methylated among low SES individuals. CONCLUSIONS: Our findings support the hypothesis that the social environment leaves an epigenetic signature in cells. Although the functional significance of SES-related DNA methylation is still unclear, we hypothesize that it may link SES to chronic disease risk.

Geographic assignment of seabirds to their origin: combining morphology, genetics and biogeochemical analyses

Longline fisheries, oil spills, and offshore wind farms are some of the major threats increasing seabird mortality at sea, but the impact of these threats on specific populations has been difficult to determine so far. We tested the use of molecular markers, morphometric measures, and stable isotope (δ15N and δ13C) and trace element concentrations in the first primary feather (grown at the end of the breeding period) to assign the geographic origin of Calonectris shearwaters. Overall, we sampled birds from three taxa: 13 Mediterranean Cory's Shearwater (Calonectris diomedea diomedea) breeding sites, 10 Atlantic Cory's Shearwater (Calonectris diomedea borealis) breeding sites, and one Cape Verde Shearwater (C. edwardsii) breeding site. Assignment rates were investigated at three spatial scales: breeding colony, breeding archipelago, and taxa levels. Genetic analyses based on the mitochondrial control region (198 birds from 21 breeding colonies) correctly assigned 100% of birds to the three main taxa but failed in detecting geographic structuring at lower scales. Discriminant analyses based on trace elements composition achieved the best rate of correct assignment to colony (77.5%). Body measurements or stable isotopes mainly succeeded in assigning individuals among taxa (87.9% and 89.9%, respectively) but failed at the colony level (27.1% and 38.0%, respectively). Combining all three approaches (morphometrics, isotopes, and trace elements on 186 birds from 15 breeding colonies) substantially improved correct classifications (86.0%, 90.7%, and 100% among colonies, archipelagos, and taxa, respectively). Validations using two independent data sets and jackknife cross-validation confirmed the robustness of the combined approach in the colony assignment (62.5%, 58.8%, and 69.8% for each validation test, respectively). A preliminary application of the discriminant model based on stable isotope δ15N and δ13C values and trace elements (219 birds from 17 breeding sites) showed that 41 Cory's Shearwaters caught by western Mediterranean long-liners came mainly from breeding colonies in Menorca (48.8%), Ibiza (14.6%), and Crete (31.7%). Our findings show that combining analyses of trace elements and stable isotopes on feathers can achieve high rates of correct geographic assignment of birds in the marine environment, opening new prospects for the study of seabird mortality at sea.

RNA and DNA aptamers as potential tools to prevent cell adhesion in disease

Recent research has shown that receptor-ligand interactions between surfaces of communicating cells are necessary prerequisites for cell proliferation, cell differentiation and immune defense. Cell-adhesion events have also been proposed for pathological conditions such as cancer growth, metastasis, and host-cell invasion by parasites such as Trypanosoma cruzi. RNA and DNA aptamers (aptus = Latin, fit) that have been selected from combinatorial nucleic acid libraries are capable of binding to cell-adhesion receptors leading to a halt in cellular processes induced by outside signals as a consequence of blockage of receptor-ligand interactions. We outline here a novel approach using RNA aptamers that bind to T. cruzi receptors and interrupt host-cell invasion in analogy to existing procedures of blocking selectin adhesion and function in vitro and in vivo.

Effects of lipopolysaccharide on low- and high-density cultured rabbit vascular smooth muscle cells: differential modulation of nitric oxide release, ERK1/ERK2 MAP kinase activity, protein tyrosine phosphatase activity, and DNA synthesis

Previous studies have shown that exogenously generated nitric oxide (NO) inhibits smooth muscle cell proliferation. In the present study, we stimulated rabbit vascular smooth muscle cells (RVSMC) with E. coli lipopolysaccharide (LPS), a known inducer of NO synthase transcription, and established a connection between endogenous NO, phosphorylation/dephosphorylation-mediated signaling pathways, and DNA synthesis. Non-confluent RVSMC were cultured with 0, 5, 10, or 100 ng/ml of the endotoxin. NO release was increased by 86.6% (maximum effect) in low-density cell cultures stimulated with 10 ng/ml LPS as compared to non-stimulated controls. Conversely, LPS (5 to 100 ng/ml) did not lead to enhanced NO production in multilayered (high density) RVSMC. DNA synthesis measured by thymidine incorporation showed that LPS was mitogenic only to non-confluent RVSMC; furthermore, the effect was prevented statistically by aminoguanidine (AG), a potent inhibitor of the inducible NO synthase, and oxyhemoglobin, an NO scavenger. Finally, there was a cell density-dependent LPS effect on protein tyrosine phosphatase (PTP) and ERK1/ERK2 mitogen-activated protein (MAP) kinase activities. Short-term transient stimulation of ERK1/ERK2 MAP kinases was maximal at 12 min in non-confluent RVSMC and was prevented by preincubation with AG, whereas PTP activities were inhibited in these cells after 24-h LPS stimulation. Conversely, no significant LPS-mediated changes in kinase or phosphatase activities were observed in high-density cells. LPS-induced NO generation by RVSMC may switch on a cell density-dependent proliferative signaling cascade, which involves the participation of PTP and the ERK1/ERK2 MAP kinases.

Cytotoxic and DNA-topoisomerase effects of lapachol amine derivatives and interactions with DNA

The cytotoxic activity of amino (3a-e), aza-1-antraquinone (4a-e) lapachol derivatives against Ehrlich carcinoma and human K562 leukemia cells was investigated. Cell viability was determined using MTT assay, after 48 (Ehrlich) or 96 h (K562) of culture, and vincristine (for K562 leukemia) and quercetin (for Ehrlich carcinoma) were used as positive controls. The results showed dose-dependent growth-inhibiting activities and that the amino derivatives were active against the assayed cells, whereas the 4a-e derivatives were not. The allylamine derivative 3a was the most active against Ehrlich carcinoma, with IC50 = 16.94 ± 1.25 µM, and against K562 leukemia, with IC50 = 14.11 ± 1.39 µM. The analogous lawsone derivative, 5a, was also active against Ehrlich carcinoma (IC50 = 23.89 ± 2.3 µM), although the 5d and 5e derivatives showed lower activity. The interaction between 3a-d and calf thymus DNA was investigated by fluorimetric titration and the results showed a hyperchromic effect indicating binding to DNA as presented of ethidium bromide, used as positive control. The inhibitory action on DNA-topoisomerase II-a was also evaluated by a relaxation assay of supercoiled DNA plasmid, and the etoposide (200 µM) was used as positive control. Significant inhibitory activities were observed for 3a-d at 200 µM and a partial inhibitory action was observed for lapachol and methoxylapachol.

Association between the c.910A>G genetic variant of the XRCC1 gene and susceptibility to esophageal cancer in the Chinese Han population

Esophageal cancer (EC) is a common malignancy worldwide. The X-ray repair cross-complementing 1 gene (XRCC1) is one of the most important candidate genes for influencing susceptibility to EC. This study aimed to investigate the effect of XRCC1 genetic variants on susceptibility to EC. A total of 383 EC patients (males: 239, females: 144, mean age: 56.62) and 387 cancer-free controls (males: 251, females: 136, mean age: 58.23) were enrolled in this study. The c.910A>G genetic variant of theXRCC1 gene was determined by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing methods. The allele and genotype frequencies indicated statistical differences between EC patients and cancer-free controls. The c.910A>G genetic variant was statistically associated with increased susceptibility to EC [GGvs AA: odds ratio (OR)=1.79, 95% confidence interval (CI)=1.12-2.86, P=0.014; GG vs AG/AA: OR=1.76, 95%CI=1.13-2.75, P=0.013; G vs A: OR=1.25, 95%CI=1.01-1.55, P=0.041]. The allele G and genotype GG could contribute to the increased susceptibility to EC. Our findings suggest that the c.910A>G genetic variant is associated with susceptibility to EC in the Chinese Han population, and might be used as a molecular marker for detecting susceptibility to EC.

Desiccation tolerance and DNA integrity in Eugenia pleurantha O. Berg. (myrtaceae) seeds

The aim of this study was to assess the desiccation tolerance and DNA integrity in Eugenia pleurantha seeds dehydrated to different moisture contents (MCs). Seeds extracted from mature fruits were submmited to drying in silica gel and evaluated at every five percentual points of decrease from the initial MC (35.5%, fresh weight basis). The effects of dehydration on seeds were verified through germination tests and DNA integrity assessment. Undried seeds achieved 87% germination, value reduced to 36% after being dried to 9.8% MC. When dried slightly more, to 7.4% MC, seeds were no longer able to germinate, suggesting an intermediate behavior in relation to desiccation tolerance. It was observed DNA degradation in seeds with 7.4% MC, which might have contributed to the loss of seed germination.