Extensive cross-talk and global regulators identified from an analysis of the integrated transcriptional and signaling network in Escherichia coli

To understand the regulatory dynamics of transcription factors (TFs) and their interplay with other cellular components we have integrated transcriptional, protein-protein and the allosteric or equivalent interactions which mediate the physiological activity of TFs in Escherichia coli. To study this integrated network we computed a set of network measurements followed by principal component analysis (PCA), investigated the correlations between network structure and dynamics, and carried out a procedure for motif detection. In particular, we show that outliers identified in the integrated network based on their network properties correspond to previously characterized global transcriptional regulators. Furthermore, outliers are highly and widely expressed across conditions, thus supporting their global nature in controlling many genes in the cell. Motifs revealed that TFs not only interact physically with each other but also obtain feedback from signals delivered by signaling proteins supporting the extensive cross-talk between different types of networks. Our analysis can lead to the development of a general framework for detecting and understanding global regulatory factors in regulatory networks and reinforces the importance of integrating multiple types of interactions in underpinning the interrelationships between them.

MRI analysis of the relationship between bone changes in the temporomandibular joint and articular disc position in symptomatic patients

Objectives: The aim of this study was to investigate bone changes in the condyle, articular eminence and glenoid fossa in relation to the position of the articular disc. Methods: 148 temporomandibular joints (TMJs) of 74 symptomatic patients who underwent MRI were evaluated. The position of the disc was classified as either normal (N), disc displacement with reduction (DDwR), disc displacement without reduction (DDwoR) and posterior displacement (PD). Bone changes were investigated in the condyle and temporal components of the TMJ and classified as osteophytosis, sclerosis or erosion. Results: There were no bone changes in the glenoid fossa of the temporal bone. Of the total number of TMJs studied, 94 (63.5%) were N, 34 (23%) presented DDwoR, 19 (12.8%) presented DDwR and 1 (0.7%) presented PD. The bone changes in the condyle and posterior aspect of the articular eminence were associated with the position of the disc. The bone changes in the anterior aspect of the articular eminence were not associated with the position of the disc. Conclusion: In cases of DDwoR, bone changes in the condyles were more common. The combination of erosion and osteophytosis in the condyle and the bone changes of the posterior aspect of the articular eminence were associated with disc position. Dentomaxillofacial Radiology (2012) 41, 367-372. doi: 10.1259/dmfr/79317853

Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions

Nicotinamide adenine dinucleotide (NAD) is a ubiquitous cofactor participating in numerous redox reactions. It is also a substrate for regulatory modifications of proteins and nucleic acids via the addition of ADP-ribose moieties or removal of acyl groups by transfer to ADP-ribose. In this study, we use in-depth sequence, structure and genomic context analysis to uncover new enzymes and substrate-binding proteins in NAD-utilizing metabolic and macromolecular modification systems. We predict that Escherichia coli YbiA and related families of domains from diverse bacteria, eukaryotes, large DNA viruses and single strand RNA viruses are previously unrecognized components of NAD-utilizing pathways that probably operate on ADP-ribose derivatives. Using contextual analysis we show that some of these proteins potentially act in RNA repair, where NAD is used to remove 2'-3' cyclic phosphodiester linkages. Likewise, we predict that another family of YbiA-related enzymes is likely to comprise a novel NAD-dependent ADP-ribosylation system for proteins, in conjunction with a previously unrecognized ADP-ribosyltransferase. A similar ADP-ribosyltransferase is also coupled with MACRO or ADP-ribosylglycohydrolase domain proteins in other related systems, suggesting that all these novel systems are likely to comprise pairs of ADP-ribosylation and ribosylglycohydrolase enzymes analogous to the DraG-DraT system, and a novel group of bacterial polymorphic toxins. We present evidence that some of these coupled ADP-ribosyltransferases/ribosylglycohydrolases are likely to regulate certain restriction modification enzymes in bacteria. The ADP-ribosyltransferases found in these, the bacterial polymorphic toxin and host-directed toxin systems of bacteria such as Waddlia also throw light on the evolution of this fold and the origin of eukaryotic polyADP-ribosyltransferases and NEURL4-like ARTs, which might be involved in centrosomal assembly. We also infer a novel biosynthetic pathway that might be involved in the synthesis of a nicotinate-derived compound in conjunction with an asparagine synthetase and AMPylating peptide ligase. We use the data derived from this analysis to understand the origin and early evolutionary trajectories of key NAD-utilizing enzymes and present targets for future biochemical investigations.

Multivariate analysis of fresh-cut carambola slices stored under different temperatures

Quality of fresh-cut carambola (Averrhoa carambola L) is related to many chemical and biochemical variables especially those involved with softening and browning, both influenced by storage temperature. To study these effects, a multivariate analysis was used to evaluate slices packaged in vacuum-sealed polyolefin bags, and stored at 2.5 degrees C, 5 degrees C and 10 degrees C, for up to 16 d. The quality of slices at each temperature was correlated with the duration of storage, O(2) and CO(2) concentration in the package, physical chemical constituents, and activity of enzymes involved in softening (PG) and browning (PPO) metabolism. Three quality groups were identified by hierarchical cluster analysis, and the classification of the components within each of these groups was obtained from a principal component analysis (PCA). The characterization of samples by PCA clearly distinguished acceptable and non-acceptable slices. According to PCA, acceptable slices presented higher ascorbic acid content, greater hue angles ((o)h) and final lightness (L-5) in the first principal component (PC1). On the other hand, non-acceptable slices presented higher total pectin content. PPO activity in the PC1. Non-acceptable slices also presented higher soluble pectin content, increased pectin solubilisation and higher CO(2) concentration in the second principal component (PC2) whereas acceptable slices showed lower total sugar content. The hierarchical cluster and PCA analyses were useful for discriminating the quality of slices stored at different temperatures. (C) 2011 Elsevier B.V. All rights reserved.

Phylogenetic and Similarity Analysis of HTLV-1 Isolates from HIV-Coinfected Patients from the South and Southeast Regions of Brazil

HTLV-1 is endemic in Brazil and HIV/ HTLV-1 coinfection has been detected, mostly in the northeast region. Cosmopolitan HTLV-1a is the main subtype that circulates in Brazil. This study characterized 17 HTLV-1 isolates from HIV coinfected patients of southern (n = 7) and southeastern (n = 10) Brazil. HTLV-1 provirus DNA was amplified by nested PCR (env and LTR) and sequenced. Env sequences (705 bp) from 15 isolates and LTR sequences (731 bp) from 17 isolates showed 99.5% and 98.8% similarity among sequences, respectively. Comparing these sequences with ATK (HTLV-1a) and Mel5 (HTLV-1c) prototypes, similarities of 99% and 97.4%, respectively, for env and LTR with ATK, and 91.6% and 90.3% with Mel5, were detected. Phylogenetic analysis showed that all sequences belonged to the transcontinental subgroup A of the Cosmopolitan subtype, clustering in two Latin American clusters.

Risk factors for hepatitis C virus infection in Inland Brazil: An analysis of pooled epidemiological sectional studies

In order to assess the contribution of different parenteral routes as risk exposure to the hepatitis C virus (HCV), samples from nine surveys or cross-sectional studies conducted in two Brazilian inland regions were pooled, including a total of 3,910 subjects. Heterogeneity among the study results for different risk factors was tested and the results were shown to be homogeneous. Anti-HCV antibodies were observed in 241 individuals, of which 146 (3.7%, 95% CI?=?3.24.4) had HCV exposure confirmed by immunoblot analysis or PCR test. After adjustment for relevant variables, a correlation between confirmed HCV exposure and injection drug use, tattooing, and advance age was observed. In a second logistic model that included exposures not searched in all nine studies, a smaller sample was analyzed, revealing an independent HCV association with past history of surgery and males who have sex with other males, in addition to repeated injection drug use. Overall, these analyses corroborate the finding that injection drug use is the main risk factor for HCV exposure and spread, in addition to other parenteral routes. J. Med. Virol. 84:756762, 2012. (C) 2012 Wiley Periodicals, Inc.

Phylogenetic analysis of Codium species from Brazil, with the description of the new species C. pernambucensis (Bryopsidales, Chlorophyta)

The genus Codium comprises c. 125 species widely distributed in marine coastal environments throughout the world. Due to morphological plasticity, the taxonomic delimitation of Codium species can be difficult. Sequences of the first exon of the large subunit of RUBISCO (rbcL) have been used in the molecular delimitation of species and for phylogenetic purposes. In the present study, we complement previous morphological work on Brazilian Codium species with molecular systematics. Based on the partial rbcL sequences, seven species are recognized along the Brazilian coast: C. decorticatum, C. intertextum, C. isthmocladum, C. profundum, C. spongiosum, C. taylorii and the new species Codium pernambucensis. Ten unique sequences were obtained among the samples examined, which we used in combination with previously published sequences to infer molecular phylogenies using various methods. The resulting trees showed three principal monophyletic groupings: Clade A with species having a prostrate habit, not branched, and mostly with small, grouped utricles; Clade B primarily consisting of upright species with cylindrical branches and large individual utricles; and Clade C composed of upright species with cylindrical branches that are slightly flattened, and have intermediate-sized individual utricles. The Brazilian species grouped with morphologically similar taxa from other geographic localities, and are present in all three main clades. A new sprawling species, Codium pernambucensis is described based on morphology and molecular analyses.

Expression Analysis of Wound Healing Genes in Human Periapical Granulomas of Progressive and Stable Nature

Introduction: Wound healing process involves the activation of extracellular matrix components, remodeling enzymes, cellular adhesion molecules, growth factors, cytokines and chemokines genes. However, the molecular patterns underlying the healing process periapical environment remain unclear. Here we hypothesized that endodontic infection might result in an imbalance in the expression of wound healing genes involved in the pathogenesis of periapical lesions. Furthermore, we suggest that differential expression of wound healing markers in active and latent granulomas could account for different clinical outcomes for such lesions. Methods: Study samples consisted of 93 periapical granulomas collected after endodontic surgeries and 24 healthy periodontal ligament tissues collected from premolars extracted for orthodontic purposes as control samples. Of these, 10 periapical granulomas and 5 healthy periapical tissues were used for expression analysis of 84 wound healing genes by using a pathway-specific real-time polymerase chain reaction array. The remaining 83 granulomas and all 24 control specimens were used to validate the obtained array data by real-time polymerase chain reaction. Observed variations in expression of wound healing genes were analyzed according to the classification of periapical granulomas as active/progressive versus inactive/stable (as determined by receptor activator for nuclear factor kappa B ligand/osteoprotegerin expression ratio). Results: We observed a marked increase of 5-fold or greater in SERPINE1, TIMP1, COL1A1, COL5A1, VTN, CTGF, FGF7, TGFB1, TNF, CXCL11, ITGA4, and ITGA5 genes in the periapical granulomas when compared with control samples. SERPINE1, TIMP1, COL1A1, TGFB1, and ITGA4 mRNA expression was significantly higher in inactive compared with active periapical granulomas (P < .001), whereas TNF and CXCL11 mRNA expression was higher in active lesions (P < .001). Conclusions: The identification of novel gene targets that curb the progression status of periapical lesions might contribute to a more accurate diagnosis and lead to treatment modalities more conducive to endodontic success. (J Endod 2012;38:185-190)

Molecular analysis of Aspergillus section Flavi isolated from Brazil nuts

Brazil nuts are an important export market in its main producing countries, including Brazil, Bolivia, and Peru. Approximately 30,000 tons of Brazil nuts are harvested each year. However, substantial nut contamination by Aspergillus section Flavi occurs with subsequent production of aflatoxins. In our study, Aspergillus section Flavi were isolated from Brazil nuts (Bertholletia excelsa), and identified by morphological and molecular means. We obtained 241 isolates from nut samples, 41% positive for aflatoxin production. Eighty-one isolates were selected for molecular investigation. Pairwise genetic distances among isolates and phylogenetic relationships were assessed. The following Aspergillus species were identified: A. flavus, A. caelatus, A. nomius, A. tamarii, A. bombycis, and A. arachidicola. Additionally, molecular profiles indicated a high level of nucleotide variation within beta-tubulin and calmodulin gene sequences associated with high genetic divergence from RAPD data. Among the 81 isolates analyzed by molecular means, three of them were phylogenetically distinct from all other isolates representing the six species of section Flavi. A putative novel species was identified based on molecular profiles.

Parametric Analysis of Effective Material Properties of Thickness-Shear Piezoelectric Macro-Fibre Composites

A previous study on the characterization of effective material properties of a d(15) thickness-shear piezoelectric Macro-Fibre Composite (MFC) made of seven layers (Kapton, Acrylic, Electrode, Piezoceramic Fibre and Epoxy Composite, Electrode, Acrylic, Kapton) using a finite element homogenization method has shown that the packaging reduces significantly the shear stiffness of the piezoceramic material and, thus, leads to significantly smaller effective electromechanical coupling coefficient k(15) and piezoelectric stress constant e(15) when compared to the piezoceramic fibre properties. Therefore, the main objective of this work is to perform a parametric analysis in which the effect of the variations of fibre volume fraction, Epoxy elastic modulus, electrode thickness and active layer thickness on the MFC effective material properties is evaluated. Results indicate that an effective d(15) MFC should use relatively thick fibres having relatively high shear modulus and relatively stiff epoxy filler. On the other hand, the electrode thickness does not affect significantly the MFC performance.

Longitudinal familial analysis of blood pressure involving parametric (co)variance functions

Abstract Background For analyzing longitudinal familial data we adopted a log-linear form to incorporate heterogeneity in genetic variance components over the time, and additionally a serial correlation term in the genetic effects at different levels of ages. Due to the availability of multiple measures on the same individual, we permitted environmental correlations that may change across time. Results Systolic blood pressure from family members from the first and second cohort was used in the current analysis. Measures of subjects receiving hypertension treatment were set as censored values and they were corrected. An initial check of the variance and covariance functions proposed for analyzing longitudinal familial data, using empirical semi-variogram plots, indicated that the observed trait dispersion pattern follows the assumptions adopted. Conclusion The corrections for censored phenotypes based on ordinary linear models may be an appropriate simple model to correct the data, ensuring that the original variability in the data was retained. In addition, empirical semi-variogram plots are useful for diagnosis of the (co)variance model adopted.

Finite element analysis of stress distribution in anchor teeth in surgically assisted rapid palatal expansion

The treatment of a transverse maxillary deficiency in skeletally mature individuals should include surgically assisted rapid palatal expansion. This study evaluated the distribution of stresses that affect the expander's anchor teeth using finite element analysis when the osteotomy is varied. Five virtual models were built and the surgically assisted rapid palatal expansion was simulated. Results showed tension on the lingual face of the teeth and alveolar bone, and compression on the buccal side of the alveolar bone. The subtotal Le Fort I osteotomy combined with intermaxillary suture osteotomy seemed to reduce the dissipation of tensions. Therefore, subtotal Le Fort I osteotomy without a step in the zygomaticomaxillary buttress, combined with intermaxillary suture osteotomy and pterygomaxillary disjunction may be the osteotomy of choice to reduce tensions on anchor teeth, which tend to move mesiobuccally (premolar) and distobuccally (molar)

Comparative analysis of Enterococcus Faecalis biofilm formation on different substrates

Introduction: The aim of this study was to compare Enterococcus faecalis biofilm formation on different substrates. Methods: Cell culture plates containing growth medium and E. faecalis (ATCC 29212) were used to grow biofilm on bovine dentin, gutta-percha, hydroxyapatite, or bovine bone. Substrates were incubated at 37 C for 14 or 21 days, and the medium was changed every 48 hours. After the growth induction periods, specimens (n = 5 per group and per induction period) were stained by using Live/Dead, and the images were analyzed under a confocal microscope. The total biovolume (mm3), live bacteria biovolume (mm3), and substrate coverage (%) were quantified by using the BioImage_L software. Results obtained were analyzed by nonparametric tests (P = .05). Results: Biofilm formation was observed in all groups. Gutta-percha had the lowest total biovolume at 14 days (P < .05) and hydroxyapatite the highest at 21 days (P < .05). No significant difference was observed in green biovolume at 14 days. At 21 days, however, hydroxyapatite had the highest volume (P < .05). The percentages of coverage were similar among all substrates at 21 days (P > .05), but at 14 days, bovine bone presented the highest coverage (P < .05). Conclusions: E. faecalis was capable of forming biofilm on all substrates during both growth periods; hydroxyapatite presented the highest rates of biofilm formation. The type of substrate influenced the biofilm characteristics, according to the parameters evaluated

Morphologic micro–computed tomography analysis of mandibular premolars with three root canals

Introduction: This study aimed to describe the anatomy of mandibular premolars with type IX canal configuration by using micro–computed tomography. Methods: Mandibular premolars with radicular grooves (n = 105) were scanned, and 16 teeth with type IX configuration were selected. Number and location of canals, distances between anatomic landmarks, occurrence of apical delta, root canal fusion, and furcation canals, as well as 2-dimensional (area, perimeter, roundness, major and minor diameters) and 3-dimensional (volume, surface area, and structuremodel index) analysis were performed. Data were statistically compared by using analysis of variance and Kruskal-Wallis tests (a = 0.05). Results: Overall, specimens had 1 root with a main canal that divided into mesiobuccal, distobuccal, and lingual canals at the furcation level. Mean length of the teeth was 22.9 2.06 mm, and the configuration of the pulp chamber was mostly triangle-shaped. Mean distances from the furcation to the apex and cementoenamel junction were 9.14 2.07 and 5.59 2.19 mm, respectively. Apical delta, root canal fusion, and furcation canals were present in 4, 5, and 10 specimens, respectively. No statistical differences were found in the 2-dimensional and 3-dimensional analyses between root canals (P > .05). Conclusions: Type IX configuration of the root canal system was found in 16 of 105 mandibular premolars with radicular grooves. Most of the specimens had a triangle-shaped pulp chamber. Within this anatomic configuration, complexities of the root canal systems such as the presence of furcation canals, fusion of canals, oval-shaped canals in the apical third, small orifices at the pulp chamber level, and apical delta were also observed

Analysis of the biofilm proteome of Xylella fastidiosa

Abstract Background Xylella fastidiosa is limited to the xylem of the plant host and the foregut of insect vectors (sharpshooters). The mechanism of pathogenicity of this bacterium differs from other plant pathogens, since it does not present typical genes that confer specific interactions between plant and pathogens (avr and/or hrp). The bacterium is injected directly into the xylem vessels where it adheres and colonizes. The whole process leads to the formation of biofilms, which are considered the main mechanism of pathogenicity. Cells in biofilms are metabolically and phenotypically different from their planktonic condition. The mature biofilm stage (phase of higher cell density) presents high virulence and resistance to toxic substances such as antibiotics and detergents. Here we performed proteomic analysis of proteins expressed exclusively in the mature biofilm of X. fastidiosa strain 9a5c, in comparison to planktonic growth condition. Results We found a total of 456 proteins expressed in the biofilm condition, which correspond to approximately 10% of total protein in the genome. The biofilm showed 37% (or 144 proteins) different protein than we found in the planktonic growth condition. The large difference in protein pattern in the biofilm condition may be responsible for the physiological changes of the cells in the biofilm of X. fastidiosa. Mass spectrometry was used to identify these proteins, while real-time quantitative polymerase chain reaction monitored expression of genes encoding them. Most of proteins expressed in the mature biofilm growth were associated with metabolism, adhesion, pathogenicity and stress conditions. Even though the biofilm cells in this work were not submitted to any stress condition, some stress related proteins were expressed only in the biofilm condition, suggesting that the biofilm cells would constitutively express proteins in different adverse environments. Conclusions We observed overexpression of proteins related to quorum sensing, proving the existence of communication between cells, and thus the development of structuring the biofilm (mature biofilm) leading to obstruction of vessels and development of disease. This paper reports a first proteomic analysis of mature biofilm of X. fastidiosa, opening new perspectives for understanding the biochemistry of mature biofilm growth in a plant pathogen.