Estimating the Influence of Physicochemical and Biochemical Property Indexes on Selection for Amino Acids Usage in Eukaryotic Cells.

Proteins can evolve by accumulating changes on amino acid sequences. These changes are mainly caused by missense mutations on its DNA coding sequences. Mutations with neutral or positive effects on fitness can be maintained while deleterious mutations tend to be eliminated by natural selection. Amino acid changes are influenced by the biophysical, chemical, and biological properties of amino acids. There is a multiplicity of amino acid properties that can influence the function and expression of proteins. Amino acid properties can be expressed into numerical indexes, which can help to predict functional and structural aspects of proteins and allow statistical inferences of selection pressure on amino acid usage. The accuracy of these analyses may be compromised by the existence of several numerical indexes that measure the same amino acid property, and the lack of objective parameters to determine the most accurate and biologically relevant index. In the present study, the gradient consistency test was used in order to estimate the magnitude of directional selection imparted by amino acid biochemical and biophysical properties on protein evolution.

Effects of Pamidronate on Dental Enamel Formation Assessed by Light Microscopy, Energy-Dispersive X-Ray Analysis, Scanning Electron Microscopy, and Microhardness Testing.

The aim of the present work was to investigate birefringence and morphology of the secretory-stage enamel organic extracellular matrix (EOECM), and structural and mechanical properties of mature enamel of upper incisors from adult rats that had been treated with pamidronate disodium (0.5 mg/kg/week for 56 days), using transmitted polarizing and bright-field light microscopies (TPLM and BFLM), energy-dispersive X-ray (EDX) analysis, scanning electron microscopy (SEM) and microhardness testing. BFLM showed no morphological changes of the EOECM in pamidronate and control groups, but TPLM revealed a statistically significant reduction in optical retardation values of birefringence brightness of pamidronate-treated rats when compared with control animals (p0.05). The present study indicates that pamidronate can affect birefringence of the secretory-stage EOECM, which does not seem to be associated with significant changes in morphological and/or mechanical properties of mature enamel.

HaCaT anchorage blockade leads to oxidative stress, DNA damage and DNA methylation changes.

Cell adhesion plays an important role in neoplastic transformation. Thus, anchorage-independent growth and epithelial-mesenchymal transition, which are features associated to anoikis-resistance, are vital steps in cancer progression and metastatic colonization. Cell attachment loss may induce intracellular oxidative stress, which triggers DNA damage as methylation changes. HaCaT lineage cells were submitted to periods of 1, 3, 5 and 24 h of anchorage blockage with the purpose of study of oxidative stress effect on changes in the DNA methylation pattern, derived from attachment blockade. Through this study, HaCaT anchorage blockage-induced oxidative stress was reported to mediate alterations in global DNA methylation changes and into TP53 gene promoter pattern during anoikis-resistance acquisition. Furthermore, at the first experimental time-periods (1, 3 and 5 h), genome hypermethylation was found; however, genome hypomethylation was observed in later time-periods (24 h) of attachment impediment. The TP 53 methylation analyses were performed after 24 h of replated anoikis-resistance cells and same methylation pattern was observed, occurring an early (1 and 3 h) hypermethylation that was followed by late (5 and 24 h) hypomethylation. However, LINE-1, a marker of genomic instability, was perceived in time-dependent hypomethylation. The mRNA levels of the DNMTs enzymes were influenced by cell attachment blockage, but non-conclusive results were obtained in order to match DNMTs transcription to pattern methylation results. In conclusion, DNA damage was found, leaded by oxidative stress that has come up from HaCaT anchorage blockade, which rises a global genome hypomethylation tendency as consequence, which might denote genomic instability.

Translational signatures and mRNA levels are highly correlated in human stably expressed genes.

BACKGROUND: Gene expression is one of the most relevant biological processes of living cells. Due to the relative small population sizes, it is predicted that human gene sequences are not strongly influenced by selection towards expression efficiency. One of the major problems in estimating to what extent gene characteristics can be selected to maximize expression efficiency is the wide variation that exists in RNA and protein levels among physiological states and different tissues. Analyses of datasets of stably expressed genes (i.e. with consistent expression between physiological states and tissues) would provide more accurate and reliable measurements of associations between variations of a specific gene characteristic and expression, and how distinct gene features work to optimize gene expression. RESULTS: Using a dataset of human genes with consistent expression between physiological states we selected gene sequence signatures related to translation that can predict about 42% of mRNA variation. The prediction can be increased to 51% when selecting genes that are stably expressed in more than 1 tissue. These genes are enriched for translation and ribosome biosynthesis processes and have higher translation efficiency scores, smaller coding sequences and 3' UTR sizes and lower folding energies when compared to other datasets. Additionally, the amino acid frequencies weighted by expression showed higher correlations with isoacceptor tRNA gene copy number, and smaller absolute correlation values with biosynthetic costs. CONCLUSION: Our results indicate that human gene sequence characteristics related to transcription and translation processes can co-evolve in an integrated manner in order to optimize gene expression.

The role of modularity in the evolution of primate postcanine dental formula: integrating jaw space with patterns of dentition.

The assembly of a phenotype into modules or developmental fields, which are semiautonomous units in development and function, seems to be one of the strategies to increase the capacity to produce phenotypic variation. In mammals the upper dentition is formed on two distinct developmental units, wherein incisors are formed on the primary palate, which is derived from the embryonic frontonasal process, and the other teeth (canine, premolar, and molar) are formed on the alveolar bone, which is derived from the maxillary process (termed herein as PALATE2). The aim of the present work was to analyze the variations in size and number of premolar and molar teeth in primate dentition and to correlate these morphometrical parameters with the relative size of these tooth classes with respect to PALATE2. Furthermore, we seek to understand to what extent the changes in the relative size of premolar and molar fields can influence the size of each tooth within its respective field, and how these parameters connect with the variations in the dental formula that occurred during primate evolution. The data presented here not only indicate that premolar and molar fields can be seen as submodules of a larger and hierarchically superior module (i.e., PALATE2) but also present quantitative parameters that allow us to understand how variations in the relative size of premolar and molar teeth connect with the variations in the dental formula that occurred during primate evolution.

Association of matrix metalloproteinase gene polymorphism with temporomandibular joint degeneration.

Temporomandibular joint (TMJ) degeneration is a frequent cause of orofacial pain. Matrix metalloproteinases (MMPs) degrade extracellular matrix components and play an important role in TMJ degeneration. We investigated the frequency of the MMP1 1G/2G polymorphism (rs1799750), the MMP3 5A/6A polymorphism (rs3025058), and the MMP9 C/T polymorphism (rs3918242) in individuals with TMJ degeneration, in order to analyze the association of polymorphisms in these genes with TMJ degeneration. The population studied comprised 117 healthy controls and 115 individuals diagnosed with TMJ degeneration upon examination of magnetic resonance imaging (MRI) and computed tomography (CT) images. Genotypes were determined using PCR restriction fragment length polymorphism (RFLP). Logistic regression analyses revealed an association between the MMP1 2G/2G genotype and degeneration; in contrast, there was no association between either the MMP3 or the MMP9 genotype and degeneration. Our results may indicate a role for the MMP1 polymorphism in TMJ degeneration.

Interleukin-8 gene promoter polymorphism (rs4073) may contribute to chronic periodontitis.

BACKGROUND: The proinflammatory chemokine interleukin (IL)-8 is important in the regulation of the inflammatory response. Analyses of the single nucleotide polymorphism (SNP) reference sequence (rs) 4073 showed that the A allele upregulated IL-8 levels after stimulation with lipopolysaccharides. We investigated the association of the SNP rs4073 with chronic periodontitis. METHODS: Genotyping was performed by a standard polymerase chain reaction-restriction fragment length polymorphism assay in 289 genomic DNA samples of healthy control subjects and patients with chronic periodontitis; analyses were adjusted by multivariate logistic regression modeling. A real-time polymerase chain reaction performance was used to detect levels of the IL-8 mRNA. RESULTS: The analysis pointed to a statistically significant association of chronic periodontitis with the heterozygous TA genotype (P = 0.001); the results showed an increase in the frequency of the A allele in the diseased group (36% in the control group versus 48% in the periodontitis group). The higher levels of the IL-8 mRNA were found in the periodontitis group, mainly in individuals who presented the TA genotype (P = 0.03). CONCLUSION: The SNP rs4073 was associated with chronic periodontitis in non-smoker Brazilian subjects because the frequency of the A allele was higher in the disease group than in the control group, and the TA genotype was associated with increased levels of IL-8 mRNA transcripts.

Association of IL1 gene polymorphisms with chronic periodontitis in Brazilians.

UNLABELLED: Chronic periodontal disease (PD) is an infectious immune-inflammatory illness. Polymorphisms in IL1 genes play a role in inflammatory diseases through the modulation of cytokine levels. OBJECTIVE: this study aimed to investigate the association between polymorphisms in the IL1 gene cluster and chronic periodontitis in a Brazilian population. DESIGN: a sample of 113 subjects over 25 years (mean age 41.2) were grouped into: 44 healthy individuals, 31 subjects with moderate and 38 with severe periodontitis. DNA was obtained through a mouthwash and oral mucosa scraping. PCR-RFLP was used to identify the following polymorphisms: IL1A C-889T (rs1800587), IL1B C-511T (rs16944), IL1B C+3954T (rs11436340), IL1RN intron 2 (rs2234663). Differences in the allele/genotype/haplotype frequencies were assessed by Chi-square test (p<0.05). The risk associated with alleles, genotypes and haplotypes was calculated as odds ratio (OR) with 95% confidence intervals (CI). RESULTS: neither IL1A (C-889T) nor IL1B (C+3954T) polymorphisms was associated with chronic PD. Allele T for IL1B (C-511T) only associated with PD in the group of blacks and mulattos. Moreover, genotype 2/2 for IL1RN (intron 2) was associated with severe PD. CONCLUSIONS: genotype 2/2 of IL1RN for the whole Brazilian population and allele T of IL1B (C-511T) in a subgroup of Afro-Americans and mulattos were suggested as putative risk indicators for chronic periodontitis.

Transcriptional activity analysis of promoter region of human PAX9 gene under dexamethasone, retinoic acid, and ergocalciferol treatment in MCF-7 and MDPC23.

PAX9 gene is a member of the family homeobox of transcription factors and performs important function in development and organogenesis. Mutations in PAX9 coding sequences have been implicated in autosomal dominant oligodontia affecting predominantly permanent molars and second premolars. Previous studies have shown that PAX9 is required for secondary palate development and teratogens have been identified as inducers of a tooth and craniofacial malformations. This work focused on the analysis on the 5'-flanking region of the PAX9 gene studying the influence of retinoic acid, dexamethasone, and vitamin D on the expression of PAX9 by expression constructs that carry the reporter gene luciferase. As results, retinoic acid and dexamethasone showed progressive decrease of PAX9 expression. PAX9-pGL3B1 and PAX9-pGL3B2 promoter was inhibited under the treatment of dexamethasone and ergocalciferol. Retinoic acid and dexamethasone did not alter PAX9-pGL3B3 behavior indicating that sequences present between -1106 and +92 were important for the transcriptional activity of PAX9 promoter. In this study, we characterized the transcriptional activity of specific regions of the PAX9 promoter gene and we demonstrated that retinoic acid and ergocalciferol can modulate the transcriptional activity of PAX9 gene.

DNA methylation status of the IL8 gene promoter in aggressive periodontitis.

BACKGROUND: Studies evaluating the methylation status of cytokine genes may have relevance for inflammatory diseases in which the expression of some cytokines is altered, such as periodontitis. This study observes the DNA methylation status in the interleukin-8 (IL8) gene promoter in cells of the oral epithelium of subjects affected by generalized aggressive periodontitis (AgP) and compares it to those of control subjects. METHODS: Genomic DNA from epithelial oral cells of 37 generalized AgP patients and 37 controls were purified and modified by sodium bisulphite. Modified DNA was submitted by methylation-specific polymerase chain reaction, electrophoresed on 10% polyacrylamide gels, and stained. RESULTS: Subjects who presented generalized AgP have a higher frequency of hypomethylation of the IL8 gene promoter in oral epithelium cells than that of controls (86.5% in the generalized AgP group versus 62% in the control group; P = 0.016; chi(2) test). CONCLUSIONS: A marked hypomethylated status is found in the oral epithelial cells of subjects presenting with generalized AgP, compared to controls, in the promoter region of the IL8 gene. This hypomethylated status may reflect a generalized condition of oral epithelial cells, including gingival epithelium, because gingival epithelial cells were also collected during mouthwash use.

Birefringence of the secretory-stage enamel organic extracellular matrix from rats submitted to successive injections of bisphosphonates.

The aim of the present study was to assess birefringence of the secretory-stage enamel organic extracellular matrix (ECM) and mechanical properties of mature enamel from rats treated with bisphosphonates. Longitudinal sections were obtained from upper incisors of rats that had been submitted to injections of bisodic etidronate (8 mg/Kg/day), sodium alendronate (30 microg/Kg/day), or sodium chloride as control (8 mg/Kg/day) for 42 days. Sections were immersed in 80% glycerin for 30 min and optical retardation of birefringence brightness in the secretory-stage enamel organic ECM was determined in nanometers. Etidronate-treated rats exhibited extensive morphological changes in the secretory-stage enamel organic ECM inclusive nonbirefringent conspicuous incremental lines, but presented optical retardation values similar to those showed by control rats (p > 0.05). Birefringence of secretory enamel organic ECM from etidronate rats presented an irregular aspect. Alendronate-treated rats did not show morphological alterations in the secretory-stage enamel organic ECM, however, they presented significant reduction in optical retardation of birefringence brightness when compared with control and etidronate rats (p < 0.01). Alendronate and etidronate groups exhibited reductions of approximately 6-10% in mature enamel cross-sectional microhardness when compared with control group (p < 0.01). Scanning electron microscopy analysis showed extensive alterations in mature enamel only from etidronate group with absence of enamel rods. The present work shows that bisphosphonates can affect the birefringence of the secretory-stage enamel organic ECM. The results presented here suggest that alterations in the supramolecular organization of the secretory-stage enamel organic ECM are a plausible mechanism by which environmental factors may cause enamel defects.

DNA methylation status of the IL8 gene promoter in oral cells of smokers and non-smokers with chronic periodontitis.

AIM: This study analysed the status of DNA methylation in the promoter region of the IL8 gene in oral mucosa cells from healthy, smoker and non-smoker subjects with chronic periodontitis and compared these findings among groups with mRNA levels. MATERIAL AND METHODS: Genomic DNA from epithelial oral cells of 41 healthy subjects, 30 smokers with chronic periodontitis and 40 non-smokers with chronic periodontitis were purified and modified by sodium bisulphite. Genomic DNA from blood leucocytes and gingival cells from biopsies of 13 subjects of each group were also purified and modified by sodium bisulphite. Modified DNA was submitted by methylation-specific polymerase chain reaction (PCR) (MSP), electrophoresed on 10% polyacrylamide gels and stained with SYBR Gold. Total RNA from gingival cells was also isolated using the TRIzol reagent, and real-time PCR performance was used to detect the levels of interleukin-8 mRNA. RESULTS: Our results indicate that individuals with chronic periodontitis, independent of smoking habit, have a higher percentage of hipomethylation of the IL8 gene than those controls in epithelial oral cells (p<0.0001), and expression of higher levels of interleukin-8 (IL-8) mRNA than controls in gingival cells (p=0.007). No significant differences among groups were observed in gingival cells and blood cells. CONCLUSION: We conclude that inflammation in the oral mucosa might lead to changes in the DNA methylation status of the IL8 gene in epithelial oral cells.

2-hydroxyethyl methacrylate as an inhibitor of matrix metalloproteinase-2.

This study evaluated the effect of different concentrations of 2-hydroxyethyl methacrylate (HEMA) on the inhibition of matrix metalloproteinase-2 (MMP-2) in vitro. Mouse gingival explants were cultured overnight in Dulbecco's modified Eagle's minimal essential medium, following which the expression of secreted enzymes was analyzed by gelatin zymography and the effects of different amounts of HEMA on enzyme activity were investigated. The gelatinolytic proteinases present in the conditioned media were characterized as being matrix metalloproteinases (MMPs) by means of specific chemical inhibition. The MMPs present in the conditioned media were identified, using immunoprecipitation, as MMP-2. Three major bands were detected in the zymographic assays and were characterized, according to their respective molecular weights, into the following forms of MMP-2: zymogene (72 kDa), intermediate (66 kDa), and active (62 kDa). All forms of MMP-2 were inhibited by HEMA in a dose-dependent manner, implying that MMP-2 may be inhibited by HEMA in vivo.

Novel mutations in the IRF6 gene in Brazilian families with Van der Woude syndrome.

Van der Woude Syndrome (VWS) is an autosomal craniofacial disorder characterized by lower lip pits and cleft lip and/or palate. Mutations in the interferon regulatory factor 6 (IRF6) gene have been identified in patients with VWS. To identify novel IRF6 mutations in patients affected by VWS, we screened 2 Brazilian families, sequencing the entire IRF6-coding region and flanking intronic boundaries. Two novel heterozygous mutations were identified: a frame shift mutation with deletion of G at the nucleotide position 520 in the exon 6 (520delG), and a missense single nucleotide substitution from T to A at nucleotide position 1135 in exon 8 (T1135A). By using restriction enzyme analysis, we were able to demonstrate the lack of similar mutations in unrelated healthy individuals and non-syndromic cleft lip and palate patients. Our results further confirmed that haploinsufficiency of the IRF6 gene results in VWS.

Osseointegrated implant failure associated with MMP-1 promotor polymorphisms (-1607 and -519).

PURPOSE: Two polymorphisms in the promoter region of human MMP-1 gene, an insertion of a guanine at position -1607 and A-519G substitution, have been shown to increase the transcriptional activity of these matrix metalloproteinases (MMPs). The objective of this study was to investigate the possible relationship between these polymorphisms and early implant failure. MATERIALS AND METHODS: A sample of 104 nonsmokers was divided into 2 groups: a test group comprising 44 patients with 1 or more early failed implants and a control group consisting of 60 individuals with 1 or more healthy implants. Genomic DNA from oral mucosa was amplified by polymerase chain reaction and analyzed by restriction endonucleases. The significance of the differences in observed frequencies of polymorphisms were assessed by chi2 tests. RESULTS: The G-1607GG polymorphism with the genotype G/G was observed at a frequency of 62% in the control group, while in the test group this genotype was noted in 34% of the individuals (P = .011). The allele G was found at a frequency of 75% in control group and 61.66% in the test group (P = .05). No significant differences were seen in the genotypes and allele frequencies in the A-519G polymorphism among the groups (P = .064 and P = .124, respectively). The distribution of the haplotypes arranged as alleles and genotypes showed a significant difference between control and test groups (P = .031 and P = .002, respectively). CONCLUSION: On the basis of this study of 60 patients who experienced no implant failure and 44 patients who experienced implant failure, the results suggest that G-1607GG polymorphism in MMP-1 gene is associated with early implant failure, while A-519G polymorphism in MMP-1 gene does not show a significant relationship with implant loss. This study also suggests that haplotypes G-1607GG and A-519G of MMP-1 may be associated with the osseointegration process.

Extraction of genomic DNA from paraffin-embedded tissue sections of human fetuses fixed and stored in formalin for long periods.

The advent of polymerase chain reaction (PCR) technology has increased the interest in fetal specimens housed in anatomy museums, as they may represent a unique source of genetic material for the study of uncommon or rare pathological conditions such as congenital malformations, neoplastic processes and parasitic as well as other infectious diseases. The aim of this study is to evaluate the quality of genomic DNA extracted from paraffin-embedded tissue sections of human fetuses that have been maintained in formalin for several years. Fetal tissues were embedded in paraffin, and tissue sections were submitted to ethanol/xylene dewaxing, followed by DNA extraction with ammonium acetate. DNA fragments were amplified from DNA extracted from formalin-fixed tissue sections, but not from Bouin-fixed tissues (average yield of 13.7 microg/ml from 10 umbilical cord sections of 10 microm; A(260):A(280)=1.55,). The addition of bovine serum albumim increased the yield of PCR amplification. Genomic DNA can be reliably amplified from paraffin-embedded human fetal tissues that had been fixed in formalin during 19 years and used for microdissection studies. This simple, cost-effective, and non-laborious method should facilitate the molecular analysis of a large number of specimens fixed for long periods of time.

Amelogenin- and enamelysin (Mmp-20)-deficient mice display altered birefringence in the secretory-stage enamel organic extracellular matrix.

Dental enamel is the most mineralized tissue of vertebrate organisms. Enamel biosynthesis is initiated by the secretion, processing, and self-assembly of a complex mixture of proteins. The formation of an ordered enamel organic extracellular matrix (ECM) seems be a crucial step for the proper formation of mineral phase. Polarizing microscopy demonstrates that the ordered supramolecular structure of the secretory-stage enamel organic ECM is strongly birefringent. In the present work we analyzed the birefringence of secretory-stage enamel organic ECM in amelogenin (Amelx)- and enamelysin (Mmp20)-deficient mice. Female Amelx+/- animals showed significant reduction in optical retardation values when compared with the Amelx+/+ subgroup (p=0.0029). The secretory-stage enamel organic ECM of the Amelx-/- subgroup did not exhibit birefringence. The secretory-stage enamel organic ECM of Mmp20-/- mice showed a significant decrease in optical retardation as compared with Mmp20+/+ and Mmp20+/- mice (p=0.0000). Mmp20+/- and Mmp20+/+ mice exhibited similar birefringence (p=1.0000). The results presented here support growing evidence for the idea that the birefringence of secretory-stage enamel organic ECM is influenced by the ordered supramolecular organization of its components.

Exclusion of known gene for enamel development in two Brazilian families with amelogenesis imperfecta.

Amelogenesis imperfecta (AI) is a genetically heterogeneous group of diseases that result in defective development of tooth enamel. Mutations in several enamel proteins and proteinases have been associated with AI. The object of this study was to evaluate evidence of etiology for the six major candidate gene loci in two Brazilian families with AI. Genomic DNA was obtained from family members and all exons and exon-intron boundaries of the ENAM, AMBN, AMELX, MMP20, KLK4 and Amelotin gene were amplified and sequenced. Each family was also evaluated for linkage to chromosome regions known to contain genes important in enamel development. The present study indicates that the AI in these two families is not caused by any of the known loci for AI or any of the major candidate genes proposed in the literature. These findings indicate extensive genetic heterogeneity for non-syndromic AI.

A new locus for autosomal dominant amelogenesis imperfecta on chromosome 8q24.3.

Amelogenesis imperfecta (AI) is a collective term used to describe phenotypically diverse forms of defective tooth enamel development. AI has been reported to exhibit a variety of inheritance patterns, and several loci have been identified that are associated with AI. We have performed a genome-wide scan in a large Brazilian family segregating an autosomal dominant form of AI and mapped a novel locus to 8q24.3. A maximum multipoint LOD score of 7.5 was obtained at marker D8S2334 (146,101,309 bp). The disease locus lies in a 1.9 cM (2.1 Mb) region according to the Rutgers Combined Linkage-Physical map, between a VNTR marker (at 143,988,705 bp) and the telomere (146,274,826 bp). Ten candidate genes were identified based on gene ontology and microarray-facilitated gene selection using the expression of murine orthologues in dental tissue, and examined for the presence of a mutation. However, no causative mutation was identified.

Comparison of three methods for enamel protein extraction in different developmental phases of rat lower incisors.

Protein extraction methods [urea, trichloroacetic acid (TCA), and acetic acid] were compared for protein recovery from rat incisor developing enamel in the S phase (intermediate/late secretion), M1 phase (early maturation), M2 phase (intermediate maturation), and M3 phase (final maturation). We compared the protein recoveries with the percentage of enamel matrix dry weight burnt off by incineration. Our results indicate that TCA and urea were equally efficient for the extraction of S-stage proteins (85% and 90% recovery, respectively), while urea was the best for M1-stage proteins (92% recovery), and TCA the best for M2-stage (99% recovery) and M3-stage (60% recovery) proteins. The other methods yielded less than 30% recovery in comparison to incineration for M2 and M3 stages. The fact that urea extraction works well in the S and M1 stages and not thereafter is probably related to the changes in the proteins during enamel development and the amount of mineral that needs to be dissolved. TCA is the single method that effectively recovered proteins from all developmental stages of the rat incisor enamel.