SIS: a program to generate draft genome sequence scaffolds for prokaryotes

Background: Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome. Results: We present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversion signature pair is present in contigs and no inversion signatures have been overwritten in evolution. The algorithm is also capable of generating scaffolds in the presence of any kind of inversion, even though in this general case there is no guarantee that all scaffolds in the scaffold set will be correct. We compare the performance of SIS, the program that implements the algorithm, to seven other scaffold-generating programs. The results of our tests show that SIS has overall better performance. Conclusions: SIS is a new easy-to-use tool to generate contig scaffolds, available both as stand-alone and as a web server. The good performance of SIS in our tests adds evidence that large-scale inversions are widespread in prokaryotic genomes.

Edible films from alginate-acerola puree reinforced with cellulose whiskers

Fruit purees, combined or not with polysaccharides, have been used in some studies to elaborate edible films. The present study was conducted to evaluate tensile properties and water vapor barrier of alginate-acerola puree films plasticized with corn syrup, and to study the influence of cellulose whiskers from different origins (cotton fiber or coconut husk fiber, the latter submitted to one- or multi-stage bleaching) on the film properties. The whiskers improved the overall tensile properties (except by elongation) and the water vapor barrier of the films. The films with coconut whiskers, even those submitted only to a one-stage bleaching, presented similar properties to those of films with cotton whiskers, despite the low compatibility between the matrix and the remaining lignin in coconut whiskers. This was probably ascribed to a counterbalancing effect of the higher aspect ratios of the coconut whiskers. (C) 2011 Elsevier Ltd. All rights reserved.

Pore size regulates cell and tissue interactions with PLGA-CaP scaffolds used for bone engineering

A common subject in bone tissue engineering is the need for porous scaffolds to support cell and tissue interactions aiming at repairing bone tissue. As poly(lactide-co-glycolide)calcium phosphate (PLGACaP) scaffolds can be manufactured with different pore sizes, the aim of this study was to evaluate the effect of pore diameter on osteoblastic cell responses and bone tissue formation. Scaffolds were prepared with 85% porosity, with pore diameters in the ranges 470590, 590850 and 8501200 mu m. Rat bone marrow stem cells differentiated into osteoblasts were cultured on the scaffolds for up to 10 days to evaluate cell growth, alkaline phosphatase (ALP) activity and the gene expression of the osteoblast markers RUNX2, OSX, COL, MSX2, ALP, OC and BSP by real-time PCR. Scaffolds were implanted in critical size rat calvarial defects for 2, 4, and 8 weeks for histomorphometric analysis. Cell growth and ALP activity were not affected by the pore size; however, there was an increase in the gene expression of osteoblastic markers with the increase in the pore sizes. At 2 weeks all scaffolds displayed a similar amount of bone and blood vessels formation. At 4 and 8 weeks much more bone formation and an increased number of blood vessels were observed in scaffolds with pores of 470590 mu m. These results show that PLGACaP is a promising biomaterial for bone engineering. However, ideally, combinations of larger (similar to 1000 mu m) and smaller (similar to 500 mu m) pores in a single scaffold would optimize cellular and tissue responses during bone healing. Copyright (C) 2011 John Wiley & Sons, Ltd.

Hybrid Scaffolds Built From PET and Collagen as a Model For Vascular Graft Architecture

A hybrid material with excellent mechanical and biological properties is produced by electrospinning a co-solution of PET and collagen. The fibers are mapped using SEM, confocal Raman microscopy and collagenase digestion assays. Fibers of different compositions and morphologies are intermingled within the same membrane, resulting in a heterogeneous scaffold. The collagen distribution and exposure are found to depend on the PET/collagen ratio. The materials are chemically and mechanically characterized and biologically tested with fibroblasts (3T3-L1) and a HUVEC culture in vitro. All of the hybrid scaffolds show better cell attachment and proliferation than PET. These materials are potential candidates to be used as vascular grafts.

Sodium Alginate-Based Ionic Conducting Membranes

The present study investigates gel polymer electrolytes (GPEs) based on sodium alginate plasticized with glycerol containing either CH3COOH or LiClO4. The membranes showed ionic conductivity results of 3.1 x 10(-4) S/cm for the samples with LiClO4 and 8.7x10(-5) S/cm for the samples with CH3COOH at room temperature. The samples also showed thermal stability up to 160 degrees C, transparency of up to 90%, surface uniformity and adhesion to glass and steel. Moreover, Dynamic Mechanical Analysis revealed two relaxations for both samples and the Ea values were between 18 and 36 kJ/mol. All the results obtained indicate that alginate-based GPEs can be used as electrolytes in electrochemical devices.

Raman and XRD study on brookite-anatase coexistence in cathodic electrosynthesized titania

Among the many methods developed for the synthesis of titanium dioxide, cathodic electrosynthesis has not received much attention because the resulting amorphous oxy-hydroxide matrix demands a further thermal annealing step to be transformed into crystalline titania. However, the possibility of filling deep recessed templates by the control of the solidliquid interface makes it a potentially suitable technique for the fabrication of porous scaffolds for photovoltaics and photocatalysis. Furthermore, a careful control of the crystallization process enables the growth of larger grains with lower density of grain boundaries, which act as electron traps that slow down electronic transport and promote charge recombination. In this report, well crystallized titania deposits were obtained by thermal annealing of amorphous deposits fabricated by cathodically assisted electrosynthesis on indium-tin oxide (ITO)substrates. The combined use of Raman spectroscopy and X-ray diffraction showed that the crystallization process is more intricate than previously assumed. It is shown that the amorphous matrix evolves into a rutile-free mixture of brookite and anatase at temperatures as low as 200 degrees C that persists up to 800 degrees C, when pure anatase dominates. The amount of brookite in the brookiteanatase mixture reaches a maximum at 400 degrees C. This very simple method for obtaining a brookiteanatase mixture and the ability to tune their proportions by thermal annealing is a promising alternative whose potential for solar cells and photocatalysis deserves a careful evaluation. Copyright (C) 2011 John Wiley & Sons, Ltd.

Characterization and in vitro evaluation of bacterial cellulose membranes functionalized with osteogenic growth peptide for bone tissue engineering

The aim of this study was to characterize the physicochemical properties of bacterial cellulose (BC) membranes functionalized with osteogenic growth peptide (OGP) and its C-terminal pentapeptide OGP[10-14], and to evaluate in vitro osteoinductive potential in early osteogenesis, besides, to evaluate cytotoxic, genotoxic and/or mutagenic effects. Peptide incorporation into the BC membranes did not change the morphology of BC nanofibers and BC crystallinity pattern. The characterization was complemented by Raman scattering, swelling ratio and mechanical tests. In vitro assays demonstrated no cytotoxic, genotoxic or mutagenic effects for any of the studied BC membranes. Culture with osteogenic cells revealed no difference in cell morphology among all the membranes tested. Cell viability/proliferation, total protein content, alkaline phosphatase activity and mineralization assays indicated that BC-OGP membranes enabled the highest development of the osteoblastic phenotype in vitro. In conclusion, the negative results of cytotoxicity, genotoxicity and mutagenicity indicated that all the membranes can be employed for medical supplies, mainly in bone tissue engineering/regeneration, due to their osteoinductive properties.

Anion dopant effects on the structure and performance of polyethersulfone membranes

In this work, the effect of various casting solution salt dopants with similar cations, but different anions: (NaPO3)(6), Na2SO4, Na2CO3, NaCl, and NaF, on the morphology and performance of polyethersulfone ultrafiltration membranes was evaluated. The phase inversion process was used to produce all membranes using an 18% polyethersulfone in n-methylpyrrolidone casting solution and water as the non-solvent. Scanning electron microscopy (SEM) images of the membrane cross-section and surface pores were used to determine the specific anion effects on membrane morphology. The SEM images depicted significant changes to the membrane internal structure and pore size with respect to the type and concentration of the casting solution anion dopant. Membrane permeability, molecular weight cut-off, alginate retention, and susceptibility to fouling were evaluated using ultrapure water dead-end and ultrapure water, aqueous polyethylene glycol, aqueous sodium alginate, and natural surface water cross-flow filtration tests. Among the anions evaluated, hexametaphosphate doped at 1% w/w to the polymer resulted in the membrane with highest dead-end permeability at 490 LMH-bar (2- to 3-fold greater than the control), greatest alginate retention at 96.5%, and lowest susceptibility to fouling. The significant increase in membrane performance indicates that the hexametaphosphate anion has great potential to be used as a membrane casting solution dopant. It was also clearly demonstrated that membrane pore morphological characteristics can be effectively used to predict drinking water treatment performance. (C) 2012 Elsevier B.V. All rights reserved.

Effect of pre-flaring and file size on the accuracy of two electronic apex locators

Objective: This ex vivo study evaluated the effect of pre-flaring and file size on the accuracy of the Root ZX and Novapex electronic apex locators (EALs). Material and methods: The actual working length (WL) was set 1 mm short of the apical foramen in the palatal root canals of 24 extracted maxillary molars. The teeth were embedded in an alginate mold, and two examiners performed the electronic measurements using #10, #15, and #20 K-files. The files were inserted into the root canals until the "0.0" or "APEX" signals were observed on the LED or display screens for the Novapex and Root ZX, respectively, retracting to the 1.0 mark. The measurements were repeated after the pre-flaring using the S1 and SX Pro-Taper instruments. Two measurements were performed for each condition and the means were used. Intra-class correlation coefficients (ICCs) were calculated to verify the intra-and inter-examiner agreement. The mean differences between the WL and electronic length values were analyzed by the three-way ANOVA test (p<0.05). Results: ICCs were high (>0.8) and the results demonstrated a similar accuracy for both EALs (p>0.05). Statistically significant accurate measurements were verified in the pre-flared canals, except for the Novapex using a #20 K-file. Conclusions: The tested EALs showed acceptable accuracy, whereas the pre-flaring procedure revealed a more significant effect than the used file size.

Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection

The major cause of athlete's foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response. IMPORTANCE Athlete's foot, jock itch, ringworm, and nail infections are common fungal infections, all caused by fungi known as dermatophytes (fungi that infect skin). This report presents the genome sequences of Trichophyton rubrum, the most frequent cause of athlete's foot, as well as four other common dermatophytes. Dermatophyte genomes are enriched for four gene classes that may contribute to the ability of these fungi to cause disease. These include (i) proteases secreted to degrade skin; (ii) kinases, including pseudokinases, that are involved in signaling necessary for adapting to skin; (iii) secondary metabolites, compounds that act as toxins or signals in the interactions between fungus and host; and (iv) a class of proteins (LysM) that appear to bind and mask cell wall components and carbohydrates, thus avoiding the host's immune response to the fungi. These genome sequences provide a strong foundation for future work in understanding how dermatophytes cause disease.

Diversity of propanil-degrading bacteria isolated from rice rhizosphere and their potential for plant growth promotion

The herbicide propanil has long been used in rice production in southern Brazil. Bacteria isolated from contaminated soils in Massaranduba, Santa Catarina, Brazil, were found to be able to grow in the presence of propanil, using this compound as a carbon source. Thirty strains were identified as Pseudomonas (86.7%), Serratia (10.0%), and Acinetobacter (3.3%), based on phylogenetic analysis of 16S rDNA. Little genetic diversity was found within species, more than 95% homology, suggesting that there is selective pressure to metabolize propanil in the microbial community. Two strains of Pseudomonas (AF7 and AF1) were selected in bioreactor containing chemotactic growth medium, with the highest degradation activity of propanil exhibited by strain AF7, followed by AF1 (60 and 40%, respectively). These strains when encapsulated in alginate exhibited a high survival rate and were able to colonize the rice root surfaces. Inoculation with Pseudomonas strains AF7 and AF1 significantly improved the plant height of rice. Most of the Pseudomonas strains produced indoleacetic acid, soluble mineral phosphate, and fixed nitrogen. These bacterial strains could potentially be used for the bioremediation of propanil-contaminated soils and the promotion of plant growth.

In vitro and in vivo evaluation of the biocompatibility of a calcium phosphate/poly(lactic-co-glycolic acid) composite

This study assess the effects of bioceramic and poly(lactic-co-glycolic acid) composite (BCP/PLGA) on the viability of cultured macrophages and human dental pulp fibroblasts, and we sought to elucidate the temporal profile of the reaction of pulp capping with a composite of bioceramic of calcium phosphate and biodegradable polymer in the progression of delayed dentine bridge after (30 and 60 days) in vivo. Histological evaluation of inflammatory infiltrate and dentin bridge formation were performed after 30 and 60 days. There was similar progressive fibroblast growth in all groups and the macrophages showed viability. The in vivo study showed that of the three experimental groups: BCP/PLGA composite, BCP and calcium hydroxide (Ca(OH)(2)) dentin bridging was the most prevalent (90 %) in the BCP/PLGA composite after 30 days, mild to moderate inflammatory response was present throughout the pulp after 30 days. After 60 days was observed dentine bridging in 60 % and necrosis in 40 %, in both groups. The results indicate that understanding BCP/PLGA composite is biocompatible and by the best tissue response as compared to calcium hydroxide in direct pulp capping may be important in the mechanism of delayed dentine bridge after 30 and 60 days.

Cytocompatibility of Porous Biphasic Calcium Phosphate Granules With Human Mesenchymal Cells by a Multiparametric Assay

This work aims to evaluate the cytocompatibility of injectable and moldable restorative biomaterials based on granules of dense or porous biphasic calcium phosphates (BCPs) with human primary mesenchymal cells, in order to validate them as tools for stem cell-induced bone regeneration. Porous hydroxyapatite (HA) and HA/beta-tricalcium phosphate (beta-TCP) (60: 40) granules were obtained by the addition of wax spheres and pressing at 20 MPa, while dense materials were compacted by pressing at 100 MPa, followed by thermal treatment (1100 degrees C), grinding, and sieving. Extracts were prepared by 24-h incubation of granules on culture media, with subsequent exposition of human primary mesenchymal cells. Three different cell viability parameters were evaluated on the same samples. Scanning electron microscopy analysis of the granules revealed distinct dense and porous surfaces. After cell exposition to extracts, no significant differences on mitochondrial activity (2,3-bis(2-methoxy-4-nitro-5-sulfophenly)-5-[(phenylamino) carbonyl]-2H-tetrazolium hydroxide) or cell density (Crystal Violet Dye Elution) were observed among groups. However, Neutral Red assay revealed that dense materials extracts induced lower levels of total viable cells to porous HA/beta-TCP (P < 0.01). Calcium ion content was also significantly lower on the extracts of dense samples. Porogenic treatments on BCP composites do not affect cytocompatibility, as measured by three different parameters, indicating that these ceramics are well suited for further studies on future bioengineering applications.

The influence of pore size on osteoblast phenotype expression in cultures grown on porous titanium

This study investigated the effect of pore size on osteoblastic phenotype development in cultures grown on porous titanium (Ti). Porous Ti discs with three different pore sizes, 312 mu m (Ti 312), 130 mu m (Ti 130) and 62 mu m (Ti 62) were fabricated using a powder metallurgy process. Osteoblastic cells obtained from human alveolar bone were cultured on porous Ti samples for periods of up to 14 days. Cell proliferation was affected by pore size at day 3 (p = 0.0010), day 7 (p = 0.0005) and day 10 (p = 0.0090) in the following way: Ti 62 < Ti 130 < Ti 312. Gene expression of bone markers evaluated at 14 days was affected, RUNX2 (p = 0.0153), ALP (p = 0.0153), BSP (p = 0.0156), COL (p = 0.0156), and OPN (p = 0.0156) by pore size as follows: Ti 312 < Ti 130 < Ti 62. Based on these results, the authors suggest that porous Ti surfaces with pore sizes near 62 mu m, compared with those of 312 mu m and 130 mu m, yield the highest expression of osteoblast phenotype as indicated by the lower cell proliferation rate and higher gene expression of bone markers.

Application of Polysaccharide Hydrogels in Adsorption and Controlled-Extended Release of Fertilizers Processes

This article studied the applicability of poly(acrylamide) and methylcellulose (PAAm-MC) hydrogels as potential delivery vehicle for the controlled-extended release of ammonium sulfate (NH(4))(2)SO(4) and potassium phosphate (KH(2)PO(4)) fertilizers. PAAm-MC hydrogels with different acrylamide (AAm) and MC concentrations were prepared by a free radical polymerization method. The adsorption and desorption kinetics of fertilizers were determined using conductivity measurements based on previously built analytical curve. The addition of MC in the PAAm chains increased the quantities of (NH(4))(2)SO(4) and KH(2)PO(4) loaded and extended the time and quantities of fertilizers released. Coherently, both loading and releasing processes were strongly influenced by hydrophilic properties of hydrogels (AAm/MC mass proportion). The best sorption (124.0 mg KH(2)PO(4)/g hydrogel and 58.0 mg (NH(4))(2)SO(4)/g hydrogel) and desorption (54.9 mg KH(2)PO(4)/g hydrogel and 49.5 mg (NH(4))(2)SO(4)/g hydrogel) properties were observed for 6.0% AAm-1.0% MC hydrogels (AAm/MC mass proportion equal 6), indicating that these hydrogels are potentially viable to be used in controlled-extended release of fertilizers systems. (C) 2011 Wiley Periodicals, Inc. J Appl Polym Sci 123: 2291-2298, 2012