Analysis of allelic differential expression in the human genome using allele-specific serial analysis of gene expression tags

Recent reports have demonstrated that a significant proportion of human genes display allelic differential expression (ADE). ADE is associated with phenotypic variability and may contribute to complex genetic diseases. Here, we present a computational analysis of ADE using allele-specific serial analysis of gene expression (SAGE) tags representing 1295 human genes. We identified 472 genes for which unequal representation (>3-fold) of allele-specific SAGE tags was observed in at least one SAGE library, suggesting the occurrence of ADE. For 235 out of these 472 genes, the difference in the expression level between both allele-specific SAGE tags was statistically significant (p < 0.05). Eleven candidate genes were then subjected to experimental validation and ADE was confirmed for 8 out of these 11 genes. Our results suggest that at least 25% of the human genes display ADE and that allele-specific SAGE tags can be efficiently used for the identification of such genes.     

Classical and alternative components of the mitochondrial respiratory chain in pathogenic fungi as potential therapeutic targets

The frequency of opportunistic fungal infection has increased drastically, mainly in patients who are immunocompromised due to organ transplant, leukemia or HIV infection. In spite of this, only a few classes of drugs with a limited array of targets, are available for antifungal therapy. Therefore, more specific and less toxic drugs with new molecular targets is desirable for the treatment of fungal infections. In this context, searching for differences between mitochondrial mammalian hosts and fungi in the classical and alternative components of the mitochondrial respiratory chain may provide new potential therapeutic targets for this purpose.     

Are all sex chromosomes created equal?

Three principal types of chromosomal sex determination are found in nature: male heterogamety (XY systems, as in mammals), female heterogamety (ZW systems, as in birds), and haploid phase determination (UV systems, as in some algae and bryophytes). Although these systems share many common features, there are important biological differences between them that have broad evolutionary and genomic implications. Here we combine theoretical predictions with empirical observations to discuss how differences in selection, genetic properties and transmission uniquely shape each system. We elucidate how the differences among these systems can be exploited to gain insights about general evolutionary processes, genome structure, and gene expression. We suggest directions for research that will greatly increase our general understanding of the forces driving sex-chromosome evolution in diverse organisms.     

The Influence of <Emphasis Type="Italic">P. fluorescens</Emphasis> Cell Morphology on the Lytic Performance and Production of Phage ϕIBB-PF7A

This study aims at assessing the influence of Pseudomonas fluorescence cell morphology on the effectiveness and production of the lytic bacteriophage ϕIBB-PF7A. P. fluorescens were cultured as rods or as elongated cells by varying the temperature and rotary agitation conditions. Cells presented rod shape when grown at temperatures up to 25°C and also at 30°C under static conditions, and elongated morphology only at 30°C when cultures were grown under agitation. Elongated cells were 0.4 up to 27.9 μm longer than rod cells. Rod-shaped hosts were best infected by phages at 25°C which resulted in an 82% cell density reduction. Phage infection of elongated cells was successful, and the cell density reductions achieved was statistically similar (P > 0.05) to those obtained at the optimum growth temperature of P. fluorescens. Phage burst size varied with the cell growth conditions and was approximately 58 and 153 PFU per infected rod and elongated cells, grown at 160 rpm, at 25°C (the optimal temperature) and 30°C, respectively. Phage adsorption was faster to elongated cells, most likely due to the longer length of the host. The surface composition of rod and elongated cells is similar in terms of outer membrane proteins and lipopolysaccharide profiles. The results of this study suggest that the change of rod cells to an elongated morphology does not prevent cells from being attacked by phages and also does not impair the phage infection.     

Investigation of biota associated and natural infection by sporulated bacteria in Culicidae larvae from São Paulo state, Brazil

The aim of this study was to investigate the naturally occurring bacteria from Culicidae larvae found in São Paulo state between 2006 and 2008 from the Tiete Ecological Park in the municipality of Caraguatatuba. Bacterial strains were obtained after surface sterilization of larvae followed by thermal treatment and incubation in bacteriological media under laboratory conditions. Identification was determined using cytomorphology, biochemical and physiological tests. Strains were characterized by qualitative evaluation of biological activity against Culicidae larvae, comparing protein profiles obtained by electrophoresis of crystal protoxins, electrophoresis of Lysinibacillus sphaericus isoenzymes, detection of the L₂ fraction of Hemolytic BL enterotoxin and amplification of DNA using Multiplex-PCR to detect HBL, NHE, CytK, BceT and EntFM enterotoxins. The results obtained in this study demonstrated that the endosymbiotic bacterial diversity belonging to Bacillus and related genera associated with Culicidae larvae is limited to a number of species that does not vary throughout the seasons.     

Prevalence and molecular characterization of Mycoplasma ovis in selected free-ranging Brazilian deer populations

Mycoplasma ovis is a hemoplasma that may cause anemia and mortality in small ruminants. Our aim was to determine whether M. ovis infects populations of free-ranging deer in Brazil. Buffy coat samples from 64 Blastocerus dichotomus from Porto Primavera, 18 Ozotocerus bezoarticus from Pantanal, and 21 O. bezoarticus from Emas National Park were tested. Using a M. ovis PCR protocol to amplify extracted DNA, 46/64 (72%) of deer from Porto Primavera, 10/18 (56%) from Pantanal, and 4/21 (19%) from Emas National Park were positive, giving an overall positive rate of 58% for hemoplasma in these wild deer. Sequencing and phylogenetic analysis of the 16S rRNA gene revealed 3 genetically distinct hemoplasmas including M. ovis, 'Candidatus Mycoplasma erythrocervae', and a hemoplasma most closely related to M. ovis. Phylogenetic analysis of the 23S rRNA gene from selected sequences confirmed these relationships.     

Micronuclei as biomarkers for evaluating the risk of malignant transformation in the uterine cervix

We evaluated micronucleus and apoptosis occurrence among women with normal smears and women with different kinds of cervical abnormalities, i.e., inflammatory processes and low- and high-grade squamous intraepithelial lesions (N = 12, N = 10 and N = 27, respectively). The sample included 59 women who were seen at a public medical service for cervical cancer prevention in Feira de Santana, Bahia, Brazil. The diagnosis was established by means of cytological, colposcopic, and histopathological examination. Cytogenetic analysis was performed on 2000 cells from each woman and included assessment of micronuclei and nuclear degenerative abnormalities indicative of apoptosis (karyorrhexis, pyknosis and condensed chromatin). Micronucleus frequency was significantly higher in the women with high-grade squamous intraepithelial lesions than in the women without cervical abnormalities or inflammatory processes (P< 0.001) or in the women with low-grade squamous intraepithelial lesions (P < 0.005). The frequency of apoptosis was similar in women without cervical abnormalities and women showing high-grade squamous intraepithelial lesions (P > 0.50), and significantly lower in women without cervical abnormalities and in women showing high-grade squamous intraepithelial lesions than in women showing inflammatory processes or low-grade squamous intraepithelial lesions (P < 0.0001). These results indicate that, in addition to Papanicolaou cervical cytological analysis, it would be useful to use micronucleus analysis to screen women who are at risk of developing cervical cancer. The assessment of nuclear degenerative abnormalities indicative of apoptosis increased the sensitivity of this test.     

Involvement of catalase in the apoptotic mechanism induced by apigenin in HepG2 human hepatoma cells

Apigenin has been reported to inhibit proliferation of cancer cells; however, the mechanism underlying its action is not completely understood. Here, we evaluated the effects of apigenin on the levels of expression and activity of antioxidant enzymes, and the involvement of ROS in the mechanism of cell death induced by apigenin in HepG2 human hepatoma cells. Upon treatment with apigenin, HepG2 cells displayed a reduction in cell viability in a dose- and time-dependent manner, and some morphological changes. In addition, apigenin treatment induced ROS generation and significantly decreased the mRNA levels and activity of catalase and levels of intracellular GSH. On the other hand, apigenin treatment did not alter the expression or activity levels of other antioxidant enzymes. Addition of exogenous catalase significantly reduced the effects of apigenin on HepG2 cell death. We also demonstrated that HepG2 cells are more sensitive to apigenin-mediated cell death than are primary cultures of mouse hepatocytes, suggesting a differential toxic effect of this agent in tumor cells. Our results suggest that apigenin-induced apoptosis in HepG2 cells may be mediated by a H₂O₂-dependent pathway via reduction of the antioxidant defenses.