Selection of endogenous genes for gene expression studies in Eucalyptus under biotic (Puccinia psidii) and abiotic (acibenzolar-S-methyl) stresses using RT-qPCR

Background: Rust caused by Puccinia psidii Winter has been limiting for the establishment of new Eucalyptus plantations, as well as for resprouting of susceptible genetic materials. Identifying host genes involved in defense responses is important to elucidate resistance mechanisms. Reverse transcription-quantitative PCR is the most common method of mRNA quantitation for gene expression analysis. This method generally employs a reference gene as an internal control to normalize results. A good endogenous control transcript shows minimal variation due to experimental conditions. Findings. We analyzed the expression of 13 genes to identify transcripts with minimal variation in leaves of 60-day-old clonal seedlings of two Eucalyptus clones (rust-resistant and susceptible) subjected to biotic (P. psidii) and abiotic (acibenzolar-S-methyl, ASM) stresses. Conclusions. For tissue samples of clones that did not receive any stimulus, a combination of the eEF2 and EglDH genes was the best control for normalization. When pathogen-inoculated and uninoculated plant samples were compared, eEF2 and UBQ together were more appropriate as normalizers. In ASM-treated and untreated leaves of both clones, transcripts of the CYP and elF4B genes combined were the ones with minimal variation. Finally, when comparing expression in both clones for ASM-treated leaves, P. psidii-inoculated leaves, ASM-treated plus P. psidii-inoculated leaves, and their respective controls, the genes with the most stable expression were EgIDH and UBQ. The chitinase gene, which is highly expressed in studies on plant resistance to phytopathogens, was used to confirm variation in gene expression due to the treatments. © 2010 Laia et al; licensee BioMed Central Ltd.

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Background. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions. Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas. © 2010 Moreira et al; licensee BioMed Central Ltd.

Oral lichen planus: A retrospective study of 110 Brazilian patients

Background. Oral lichen planus (OLP) is a chronic autoimmune disease characterized by multiple clinical presentations and a relatively high prevalence in the population. This retrospective patient record study investigated the profile of OLP in a group of Brazilian patients seen between 1989 and 2009. Findings. The clinical records were analyzed and data such as gender, age, race, clinical presentation of OLP, site affected, presence of symptoms and extraoral manifestations of the disease, smoking habit, and consumption of alcoholic beverages were obtained. Among the 1822 records of patients with oral mucosal lesions, OLP was identified in 6.03%. Of these, 76.36% were females, with a mean age of 54 years, and 85% were whites. The reticular form was the most frequent (81.81%). Extraoral lesions were observed in 32.72% of the patients and painful symptoms were reported by 50.90%. The cheek mucosa was the site most affected (92.72%) and multiple oral lesions were observed in 77.27% of the patients. Among patients with OLP, 18.18% reported a smoking habit and 29.09% the consumption of alcoholic beverages. Conclusions. This retrospective study showed a relatively high prevalence of OLP in the population studied, with a predominance of the disease among middle-aged white women and bilateral involvement of the cheek mucosa. Reticular lesions were the most frequent, followed by the erosive form which is mainly associated with painful symptoms. No relationship with tobacco or alcohol consumption was observed. © 2010 Almeida et al; licensee BioMed Central Ltd.

Structural studies of Helicase NS3 variants from Hepatitis C virus genotype 3 in virological sustained responder and non-responder patients

Background. About 130 million people are infected with the hepatitis C virus (HCV) worldwide, but effective treatment options are not yet available. One of the most promising targets for antiviral therapy is nonstructural protein 3 (NS3). To identify possible changes in the structure of NS3 associated with virological sustained response or non-response of patients, a model was constructed for each helicase NS3 protein coding sequence. From this, the goal was to verify the interaction between helicases variants and their ligands. Findings. Evidence was found that the NS3 helicase portion of non-responder patients contained substitutions in its ATP and RNA binding sites. K210E substitution can cause an imbalance in the distribution of loads, leading to a decrease in the number of ligations between the essential amino acids required for the hydrolysis of ATP. W501R substitution causes an imbalance in the distribution of loads, leading and forcing the RNA to interact with the amino acid Thr269, but not preventing binding of ribavirin inhibitor. Conclusions. Useful information is provided on the genetic profiling of the HCV genotype 3, specifically the coding region of the NS3 protein, improving our understanding of the viral genome and the regions of its protein catalytic site. © 2010 Rahal et al; licensee BioMed Central Ltd.

Comparison of methods for the detection of biofilm production in coagulase-negative staphylococci

Background: The ability of biofilm formation seems to play an essential role in the virulence of coagulase-negative staphylococci (CNS). The most clearly characterized component of staphylococcal biofilms is the polysaccharide intercellular adhesin (PIA) encoded by the icaADBC operon. Biofilm production was studied in 80 coagulase-negative staphylococci (CNS) strains isolated from clinical specimens of newborns with infection hospitalized at the Neonatal Unit of the University Hospital, Faculty of Medicine of Botucatu, and in 20 isolates obtained from the nares of healthy individuals without signs of infection. The objective was to compare three phenotypic methods with the detection of the icaA, icaD and icaC genes by PCR. Findings: Among the 100 CNS isolates studied, 82% tested positive by PCR, 82% by the tube test, 81% by the TCP assay, and 73% by the CRA method. Using PCR as a reference, the tube test showed the best correlation with detection of the ica genes, presenting high sensitivity and specificity. Conclusions: The tube adherence test can be indicated for the routine detection of biofilm production in CNS because of its easy application and low cost and because it guarantees reliable results with excellent sensitivity and specificity. © 2010 Cunha et al; licensee BioMed Central Ltd.

Epidemiology of vampire bat-transmitted rabies virus in Goiaαs, central Brazil: Re-evaluation based on G-L intergenic region

Background. Vampire bat related rabies harms both livestock industry and public health sector in central Brazil. The geographical distributions of vampire bat-transmitted rabies virus variants are delimited by mountain chains. These findings were elucidated by analyzing a high conserved nucleoprotein gene. This study aims to elucidate the detailed epidemiological characters of vampire bat-transmitted rabies virus by phylogenetic methods based on 619-nt sequence including unconserved G-L intergenic region. Findings. The vampire bat-transmitted rabies virus isolates divided into 8 phylogenetic lineages in the previous nucleoprotein gene analysis were divided into 10 phylogenetic lineages with significant bootstrap values. The distributions of most variants were reconfirmed to be delimited by mountain chains. Furthermore, variants in undulating areas have narrow distributions and are apparently separated by mountain ridges. Conclusions. This study demonstrates that the 619-nt sequence including G-L intergenic region is more useful for a state-level phylogenetic analysis of rabies virus than the partial nucleoprotein gene, and simultaneously that the distribution of vampire bat-transmitted RABV variants tends to be separated not only by mountain chains but also by mountain ridges, thus suggesting that the diversity of vampire bat-transmitted RABV variants was delimited by geographical undulations. © 2010 Itou et al; licensee BioMed Central Ltd.

Characterization of the genetic diversity of Mycobacterium tuberculosis in São Paulo city, Brazil

Background: Tuberculosis is a major health problem in São Paulo, Brazil, which is the most populous and one of the most cosmopolitan cities in South America. To characterize the genetic diversity of Mycobacterium tuberculosis in the population of this city, the genotyping techniques of spoligotyping and MIRU were applied to 93 isolates collected in two consecutive years from 93 different tuberculosis patients residing in São Paulo city and attending the Clemente Ferreira Institute (the reference clinic for the treatment of tuberculosis). Findings. Spoligotyping generated 53 different spoligotype patterns. Fifty-one isolates (54.8%) were grouped into 13 spoligotyping clusters. Seventy- two strains (77.4%) showed spoligotypes described in the international databases (SpolDB4, SITVIT), and 21 (22.6%) showed unidentified patterns. The most frequent spoligotype families were Latin American Mediterranean (LAM) (26 isolates), followed by the T family (24 isolates) and Haarlem (H) (11 isolates), which together accounted for 65.4% of all the isolates. These three families represent the major genotypes found in Africa, Central America, South America and Europe. Six Spoligo-International- types (designated SITs by the database) comprised 51.8% (37/72) of all the identified spoligotypes (SIT53, SIT50, SIT42, SIT60, SIT17 and SIT1). Other SITs found in this study indicated the great genetic diversity of M. tuberculosis, reflecting the remarkable ethnic diversity of São Paulo city inhabitants. The MIRU technique was more discriminatory and did not identify any genetic clusters with 100% similarity among the 93 isolates. The allelic analysis showed that MIRU loci 26, 40, 23 and 10 were the most discriminatory. When MIRU and spoligotyping techniques were combined, all isolates grouped in the 13 spoligotyping clusters were separated. Conclusions: Our data indicated the genomic stability of over 50% of spoligotypes identified in São Paulo and the great genetic diversity of M. tuberculosis isolates in the remaining SITs, reflecting the large ethnic mix of the São Paulo city inhabitants. The results also indicated that in this city, M. tuberculosis isolates acquired drug resistance independently of genotype and that resistance was more dependent on the selective pressure of treatment failure and the environmental circumstances of patients. © 2011 Leite et al; licensee BioMed Central Ltd.

Birth defects in newborns and stillborns: An example of the Brazilian reality

Background: This study constitutes a clinical and genetic study of all newborn and stillborn infants with birth defects seen in a period of one year in a medical school hospital located in Brazil. The aims of this study were to estimate the incidence, causes and consequences of the defects. Methods. For all infants we carried out physical assessment, photographic records, analysis of medical records and collection of additional information with the family, besides the karyotypic analysis or molecular tests in indicated cases. Result: The incidence of birth defects was 2.8%. Among them, the etiology was identified in 73.6% (ci95%: 64.4-81.6%). Etiology involving the participation of genetic factors single or associated with environmental factors) was more frequent 94.5%, ci95%: 88.5-98.0%) than those caused exclusively by environmental factors (alcohol in and gestational diabetes mellitus). The conclusive or presumed diagnosis was possible in 85% of the cases. Among them, the isolated congenital heart disease (9.5%) and Down syndrome (9.5%) were the most common, followed by gastroschisis (8.4%), neural tube defects (7.4%) and clubfoot (5.3%). Maternal age, parental consanguinity, exposure to teratogenic agents and family susceptibility were some of the identified risk factors. The most common observed consequences were prolonged hospital stays and death. Conclusions: The current incidence of birth defects among newborns and stillbirths of in our population is similar to those obtained by other studies performed in Brazil and in other underdeveloped countries. Birth defects are one of the major causes leading to lost years of potential life. The study of birth defects in underdeveloped countries should continue. The identification of incidence, risk factors and consequences are essential for planning preventive measures and effective treatments. © 2011 Fett-Conte et al; licensee BioMed Central Ltd.

Differences in dietary pattern between obese and eutrophic children

Background: Excessive consumption of energy is a decisive factor of obesity, but a simple quantitative assessment of consumption between obese and eutrophic individuals not always explains the problem, raising questions about the importance of the qualitative aspects of food. Therefore, the purpose of this study was to evaluate the differences in nutrient composition and meal patterns between eutrophic and obese schoolchildren. Methods. The diet of 83 children (42 obese and 41 eutrophic), aged between 7 and 11 years of age, was assessed by two non-consecutive dietary recalls. After the software analysis of macro and micronutrients composition, the different types and amount of legumes, fruits and vegetables were analyzed to verify the dietary patterns. Results: No differences were verified in energy consumption between the groups (eutrophic = 1934.2 672.7 kcal, obese = 1835.8 621.2 kcal). In general, children showed consumption within the recommended ranges of carbohydrates, lipids and proteins. The average consumption of fiber was higher in the eutrophic group (20.7 g) when compared to the obese group (14.8 g). The dietary fiber was strongly correlated with the number of servings of beans (r = 0.77), when compared to fruits (r = 0.44) and leafy vegetables (r = 0.13). It was also observed that the higher the consumption of fiber and beans, the lower the proportion of dietary fat (r = -0.22) in the diet. Generally, there was a low consumption of fiber (20.7 g = eutrophic group/14.8 g = obese group), beans (1.1 portions in the eutrophic and obese groups), fruits (0.7 portions eutrophic group and 0.6 obese group) and vegetables (1.3 eutrophic group and 1.1 obese group). Conclusions: It is concluded that the obesity was more related to a dietary pattern of low intake of dietary fiber than excessive energy consumption and macronutrients imbalance. © 2011 de Oliveira et al; licensee BioMed Central Ltd.

Risk factors for low birth weight in Botucatu city, SP state, Brazil: A study conducted in the public health system from 2004 to 2008

Background: Low birth weight (LBW), defined as birth weight less than 2500 g, has a complex etiology and may be a result of premature interruption of pregnancy or intrauterine growth restriction. The objective of this study was to provide information on determinants of LBW and contribute to the understanding of the problem in Brazil. Methods. A case-control study was conducted in Botucatu city, SP state, Brazil. The study population consisted of 2 groups with 860 newborns in each group as follows: low weight newborns (LWNB) and a control group (weight ≤ 2500 g). Secondary data from 2004 to 2008 were collected using the Live Birth Certificate (LBC) and records from medical charts of pregnant women in Basic Health Units (BHU) and in the Public University Hospital (UH). Variables were as follows: maternal socio-demographic characteristics, pregnancy and birth conditions including quality of prenatal care according to 3 criteria. They were based on parameters established by the Ministry of Health (MH), one of them, the modified Kessner Index. The multivariable analysis by logistic regression was used to evaluate the association between variables and LBW. Results: According to the analysis, the factors associated with LBW were as follows: prematurity (OR = 56.98, 95% CI 29.52-109.95), twin pregnancy (OR = 20.00, 95% CI 6.25-100.00), maternal smoking (OR = 2.12, 95% CI 1.33-3.45), maternal malnourishment (OR = 2.30, 95% CI 1.08-5.00), maternal obesity (OR = 2.30, 95% IC 1.18-4.48), weight gain during pregnancy less than 5 kg (OR = 2.63, 95% CI 1.35-5.00) and weight gain during pregnancy more than 15 kg (OR = 2.26, 95% CI 1.16-4.41). Adequacy of prenatal care visits adjusted to gestational age was less frequent in the LBW group than in the control group (68.7% vs. 80.5%, x 2 p < 0.001). According to the modified Kessner Index, 64.4% of prenatal visits in the LWNB group were adequate. Conclusion: LWNB are a quite heterogeneous group of infants concerning their determinants and prevention actions against LBW and the follow-up of these infants have also been very complex. Therefore, improvement in the quality of care provided should be given priority through concrete actions for prevention of LBW. © 2012 Fonseca et al; licensee BioMed Central Ltd.

Peripheral calcifying cystic odontogenic tumour of the maxillary gingiva

Background: Odontogenic tumors are lesions that are derived from remnants of the components of the developing tooth germ. The calcifying cystic odontogenic tumor or calcifying odontogenic cyst is a benign cystic neoplasm of odontogenic origin that is characterized by an ameloblastoma-like epithelium and ghost cells. Calcifying cystic odontogenic tumor may be centrally or peripherally located, and its ghost cells may exhibit calcification, as first described by Gorlin in 1962. Most peripheral calcifying cystic odontogenic tumors are located in the anterior gingiva of the mandible or maxilla. Case presentation. Authors report a rare case of a peripheral calcifying cystic odontogenic tumor of the maxillary gingiva. A 39-year-old male patient presented with a fibrous mass on the attached buccal gingiva of the upper left cuspid teeth. It was 0.7-cm-diameter, painless and it was clinically diagnosed as a peripheral ossifying fibroma. After an excisional biopsy, the diagnosis was peripheric calcifying cystic odontogenic tumor. The patient was monitored for five years following the excision, and no recurrence was detected. Conclusions: All biopsy material must be sent for histological examination. If the histological examination of gingival lesions with innocuous appearance is not performed, the frequency of peripheral calcifying cystic odontogenic tumor and other peripheral odontogenic tumors may be underestimated. © 2012 Lima et al.; licensee BioMed Central Ltd.

Dietary intake and blood lipid profile in overweight and obese schoolchildren

Abstract. Background: The high blood lipid levels and obesity are one of the main risk factors for cardiovascular diseases, and the atherosclerotic process begins in childhood. Some environmental factors are supposed to be involved in this relationship, such as dietary factors. This study aimed to investigate the relationship between dietary intake and blood lipids levels in overweight and obese schoolchildren. Methods. This is a cross-sectional study with 147 overweight and obese schoolchildren in Botucatu city, Brazil. The anthropometric measurements (body weight, height, body mass index, waist circumference and skinfolds), pubertal staging evaluation and biochemical tests were taken in all children. Three 24h-recall were applied in order to estimate the dietary intake and its relationship with blood lipid levels. The Student t test and multiple linear regression analysis were used for statistical analysis. Statistical significance was assessed at the level of 0.05. The data were processed in SAS software (version 9.1.3; SAS Institute). Results: At this study, 63% of children were obese (body mass index higher than 95§ssup§th§esup§ percentile) and 80% showed high body fat percentage. The percentage of children with abnormal total cholesterol and triglycerides was 12% and 10%, respectively, and 28% presented at least one abnormal lipid levels. The average values of anthropometric measurements were higher in children with elevated lipid levels. Total cholesterol levels were positively related to full-fat dairy products and triglycerides levels to saturated fat percentage. Conclusions: Saturated fat was positively associated with elevated lipid levels in overweight and obese schoolchildren. These results reinforce the importance of healthy dietary habits since childhood in order to reduce the risks of cardiovascular diseases in adulthood. © 2012 Rinaldi et al.; licensee BioMed Central Ltd.

Indices of body fat distribution for assessment of lipodysthrophy in people living with HIV/AIDS

Background: Metabolic and morphological changes associated with excessive abdominal fat, after the introduction of Antiretroviral Therapy, increase the risk of cardiovascular disease in people living with HIV/AIDS(PLWHA). Accurate methods for body composition analysis are expensive and the use of anthropometric indices is an alternative. However the investigations about this subject in PLWHA are rare, making this research very important for clinical purpose and to advance scientific knowledge. The aim of this study is to correlate results of anthropometric indices of evaluation of body fat distribution with the results obtained by Dual-energy X-Ray Absorptiometry(DEXA) , in people living with HIV/AIDS. Methods. The sample was of 67 PLWHA(39 male and 28 female), aged 43.6+7.9 years. Body mass index, conicity index, waist/hip ratio, waist/height ratio and waist/thigh were calculated. Separated by sex, each index/ratio was plotted in a scatter chart with linear regression fit and their respective Pearson correlation coefficients. Analyses were performed using Prism statistical program and significance was set at 5%. Results: The waist/height ratio presented the highest correlation coefficient, for both male (r=0.80, p<0.001) and female (r=0.87, p <001), while the lowest were in the waist/thigh also for both: male group (r=0.58, p<0.001) and female group (r=0.03, p=0.86). The other indices also showed significant positive correlation with DEXA. Conclusion: Anthropometric indices, especially waist/height ratio may be a good alternative way to be used for evaluating the distribution of fat in the abdominal region of adults living with HIV/ADIS. © 2012 Segatto et al.; licensee BioMed Central Ltd.

Immunohistochemical features of multifocal melanoacanthoma in the hard palate: A case report

Background: Melanoacanthoma (MA) has been described in the oral mucosa as a solitary lesion or, occasionally, as multiple lesions. MA mainly affects dark skinned patients and grows rapidly, showing a plane or slightly raised appearance and a brown to black color. The differential diagnosis includes oral nevi, amalgam tattoos, and melanomas. We report here the case of a 58-year-old black woman who presented multiple pigmented lesions on the hard palate. Case presentation. Based on the differential diagnosis of melanoma, a punch biopsy (4 mm in diameter) was performed. The material was fixed in 10% formalin, embedded in paraffin, and stained with hematoxylin-eosin or submitted to immunohistochemical analysis. Immunohistochemistry using antibodies against protein S-100, melan-A, HMB-45, MCM-2, MCM-5, Ki-67 and geminin was performed. Immunohistochemical analysis revealed strong cytoplasmic immunoreactivity of dendritic melanocytes for proteinS-100, HMB-45 and melan-A.Positive staining for proliferative markers (MCM-2, MCM-5, Ki-67) was only observed in basal and suprabasal epithelial cells, confirming the reactive etiology of the lesion. The diagnosis was oral Melanoacanthoma (MA). Conclusion: The patient has been followed up for 30 months and shows no clinical alterations. MA should be included in the differential diagnosis of pigmented lesions of the oral cavity. © 2013 das Chagas e Silva de Carvalho et al.; licensee BioMed Central Ltd.

Undesirable effect of cosmetic lip augmentation with autologous fat tissue

Background: Facial cosmetic procedures are commonplace nowadays, especially techniques that aim to increase lip volume. Full lips provide a youthful, healthy, feminine and sensual appearance. There are many techniques and materials used to recover the loss of contour that occurs with age. Case presentation. An unusual case of fat tissue accumulation following cosmetic upper lip augmentation in a 61 year-old female was reported. Surgical treatment was performed for esthetic concerns. Microscopically, the tissue removed was composed of muscle fibers and mature adipocytes. Conclusion: Undesirable effects of esthetic treatment can occur and the clinician should be familiar with such complications to diagnose and manage them. © 2013 Kaminagakura et al.; licensee BioMed Central Ltd.