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1.  Development of a Multiplex PCR Assay Targeting O-Antigen Modification Genes for Molecular Serotyping of Shigella flexneri ▿  
Journal of Clinical Microbiology  2011;49(11):3766-3770.
Shigella flexneri is the major Shigella species that causes diarrheal disease in developing countries. It is further subdivided into 15 serotypes based on O-antigen structure. Serotyping of S. flexneri is important for epidemiological purposes. In this study, we developed a multiplex PCR assay targeting the O-antigen synthesis gene wzx and the O-antigen modification genes gtrI, gtrIC, gtrII, oac, gtrIV, gtrV, and gtrX for molecular serotyping of S. flexneri. The multiplex PCR assay contained eight sets of specific PCRs in a single tube and can identify 14 of the 15 serotypes (the exception being serotype Xv) of S. flexneri recognized thus far. A nearly perfect concordance (97.8%) between multiplex PCR assay and slide agglutination was observed when 358 S. flexneri strains of various serotypes were analyzed, except that 8 strains were carrying additional cryptic and/or defective serotype-specific genes. The multiplex PCR assay provides a rapid and specific method for the serotype identification of S. flexneri.
doi:10.1128/JCM.01259-11
PMCID: PMC3209073  PMID: 21880974
2.  A Novel Glucosyltransferase Involved in O-Antigen Modification of Shigella flexneri Serotype 1c▿ † 
Journal of Bacteriology  2009;191(21):6612-6617.
The O antigen of serotype 1c differs from the unmodified O antigen of serotype Y by the addition of a disaccharide (two glucosyl groups) to the tetrasaccharide repeating unit. It was shown here that addition of the first glucosyl group is mediated by the previously characterized gtrI cluster, which is found within a cryptic prophage at the proA locus in the bacterial chromosome. Transposon mutagenesis was performed to disrupt the gene responsible for addition of the second glucosyl group, causing reversion to serotype 1a. Colony immunoblotting was used to identify the desired revertants, and subsequent sequencing, cloning, and functional expression successfully identified the gene encoding serotype 1c-specific O-antigen modification. This gene (designated gtrIC) was present as part of a three-gene cluster, similar to other S. flexneri glucosyltransferase genes. Relative to the other S. flexneri gtr clusters, the gtrIC cluster is more distantly related and appears to have arrived in S. flexneri from outside the species. Analysis of surrounding sequence suggests that the gtrIC cluster arrived via a novel bacteriophage that was subsequently rendered nonfunctional by a series of insertion events.
doi:10.1128/JB.00628-09
PMCID: PMC2795301  PMID: 19717593
3.  Identification and Characterization of a Novel Shigella flexneri Serotype Yv in China 
PLoS ONE  2013;8(7):e70238.
Shigella flexneri is the major cause of bacterial shigellosis in developing countries. S. flexneri is divided into at least 19 serotypes, the majority of which are modifications of the same basic O-antigen by glucosylation and/or O-acetylation of its sugar residues by phage encoded serotype-converting genes. Recently, a plasmid encoded phosphoethanolamine (PEtN) modification of the O-antigen has been reported, which is responsible for the presence of the MASF IV-1 determinant and results in conversion of traditional serotypes X, 4a and Y to novel serotypes Xv, 4av and Yv, respectively. In this study, we characterized 19 serotype Yv strains isolated in China. A variant of the O-antigen phosphoethanolamine transferase gene opt (formerly called lpt-O) carried by a pSFxv_2-like plasmid was found in serotype Yv strains, which specifies the phosphorylation pattern on the O-antigen of this serotype. For the majority of the O-antigen units, the PEtN modification occurs on RhaIII, while for a minority, modifications occur on both RhaII and RhaIII. Serotype-specific gene detection and PFGE analysis suggested that these serotype Yv isolates were originated from serotypes Y, Xv and 2a by acquisition of an opt-carrying plasmid and/or inactivation of serotype-specific gene gtrII or gtrX. These data, combined with those of serotypes Xv and 4av reported earlier, demonstrate that the plasmid-encoded PEtN modification is an important serotype conversion mechanism in S. flexneri, in addition to glucosylation and O-acetylation.
doi:10.1371/journal.pone.0070238
PMCID: PMC3728103  PMID: 23936172
4.  Sequence of the Genome of Salmonella Bacteriophage P22 
Journal of Bacteriology  2000;182(22):6472-6481.
The sequence of the nonredundant region of the Salmonella enterica serovar Typhimurium temperate, serotype-converting bacteriophage P22 has been completed. The genome is 41,724 bp with an overall moles percent GC content of 47.1%. Numerous examples of potential integration host factor and C1-binding sites were identified in the sequence. In addition, five potential rho-independent terminators were discovered. Sixty-five genes were identified and annotated. While many of these had been described previously, we have added several new ones, including the genes involved in serotype conversion and late control. Two of the serotype conversion gene products show considerable sequence relatedness to GtrA and -B from Shigella phages SfII, SfV, and SfX. We have cloned the serotype-converting cassette (gtrABC) and demonstrated that it results in Salmonella serovar Typhimurium LT2 cells which express antigen O1. Many of the putative proteins show sequence relatedness to proteins from a great variety of other phages, supporting the hypothesis that this phage has evolved through the recombinational exchange of genetic information with other viruses.
PMCID: PMC94795  PMID: 11053393
5.  Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence 
Gut Pathogens  2014;6:7.
Background
Public Health England (PHE) holds a collection of Shigella flexneri Type strains isolated between 1949 and 1972 representing 15 established serotypes and one provisional type, E1037. In this study, the genomes of all 16 PHE Type strains were sequenced using the Illumina HiSeq platform. The relationship between core genome phylogeny and serotype was examined.
Results
The most common target gene for the detection of Shigella species in clinical PCR assays, ipaH, was detected in all genomes. The type-specific target genes were correctly identified in each genome sequence. In contrast to the S. flexneri in serotype 5 strain described by Sun et al. (2012), the two PHE serotype 5 Type strains possessed an additional oac gene and were differentiated by the presence (serotype 5b) or absence (serotype 5a) of gtrX. The somatic antigen structure and phylogenetic relationship were broadly congruent for strains expressing serotype specific antigens III, IV and V, but not for those expressing I and II. The whole genome phylogenies of the 15 isolates sequenced showed that the serotype 6 Type Strain was phylogenetically distinct from the other S. flexneri serotypes sequenced. The provisional serotype E1037 fell within the serotype 4 clade, being most closely related to the Serotype 4a Type Strain.
Conclusions
The S. flexneri genome sequences were used to evaluate phylogenetic relationships between Type strains and validate genotypic and phenotypic assays. The analysis confirmed that the PHE S. flexneri Type strains are phenotypically and genotypically distinct. Novel variants will continue to be added to this archive.
doi:10.1186/1757-4749-6-7
PMCID: PMC3972513  PMID: 24684748
Shigella flexneri type strains; Next generation sequencing technology; Molecular serotyping
6.  Emergence of a New Multidrug-Resistant Serotype X Variant in an Epidemic Clone of Shigella flexneri▿ †  
Journal of Clinical Microbiology  2009;48(2):419-426.
Shigella spp. are the causative agent of shigellosis with Shigella flexneri serotype 2a being the most prevalent in developing countries. Epidemiological surveillance in China found that a new serotype of S. flexneri appeared in 2001 and replaced serotype 2a in 2003 as the most prevalent serotype in Henan Province. The new serotype also became the dominant serotype in 7 of the 10 other provinces under surveillance in China by 2007. The serotype was identified as a variant of serotype X. It differs from serotype X by agglutination to the monovalent anti-IV type antiserum and the group antigen-specific monoclonal antibody MASF IV-I. Genome sequencing of a serotype X variant isolate, 2002017, showed that it acquired a Shigella serotype conversion island, also as an SfX bacteriophage, containing gtr genes for type X-specific glucosylation. Multilocus sequence typing of 15 genes from 37 serotype X variant isolates and 69 isolates of eight other serotypes, 1a, 2a, 2b, 3a, 4a, 5b, X, and Y, found that all belong to a new sequence type (ST), ST91. Pulsed-field gel electrophoresis revealed 154 pulse types with 655 S. flexneri isolates analyzed and identified 57 serotype switching events. The data suggest that S. flexneri epidemics in China have been caused by a single epidemic clone, ST91, with frequent serotype switching to evade infection-induced immunity to serotypes to which the population was exposed previously. The clone has also acquired resistance to multiple antibiotics. These findings underscore the challenges to the current vaccine development and control strategies for shigellosis.
doi:10.1128/JCM.00614-09
PMCID: PMC2815595  PMID: 19955273
7.  Genomic analysis of bacteriophage ε34 of Salmonella enterica serovar Anatum (15+) 
BMC Microbiology  2008;8:227.
Background
The presence of prophages has been an important variable in genetic exchange and divergence in most bacteria. This study reports the determination of the genomic sequence of Salmonella phage ε34, a temperate bacteriophage that was important in the early study of prophages that modify their hosts' cell surface and is of a type (P22-like) that is common in Salmonella genomes.
Results
The sequence shows that ε34 is a mosaically related member of the P22 branch of the lambdoid phages. Its sequence is compared with the known P22-like phages and several related but previously unanalyzed prophage sequences in reported bacterial genome sequences.
Conclusion
These comparisons indicate that there has been little if any genetic exchange within the procapsid assembly gene cluster with P22-like E. coli/Shigella phages that are have orthologous but divergent genes in this region. Presumably this observation reflects the fact that virion assembly proteins interact intimately and divergent proteins can no longer interact. On the other hand, non-assembly genes in the "ant moron" appear to be in a state of rapid flux, and regulatory genes outside the assembly gene cluster have clearly enjoyed numerous and recent horizontal exchanges with phages outside the P22-like group. The present analysis also shows that ε34 harbors a gtrABC gene cluster which should encode the enzymatic machinery to chemically modify the host O antigen polysaccharide, thus explaining its ability to alter its host's serotype. A comprehensive comparative analysis of the known phage gtrABC gene clusters shows that they are highly mobile, having been exchanged even between phage types, and that most "bacterial" gtrABC genes lie in prophages that vary from being largely intact to highly degraded. Clearly, temperate phages are very major contributors to the O-antigen serotype of their Salmonella hosts.
doi:10.1186/1471-2180-8-227
PMCID: PMC2629481  PMID: 19091116
8.  Horizontally Acquired Glycosyltransferase Operons Drive Salmonellae Lipopolysaccharide Diversity 
PLoS Genetics  2013;9(6):e1003568.
The immunodominant lipopolysaccharide is a key antigenic factor for Gram-negative pathogens such as salmonellae where it plays key roles in host adaptation, virulence, immune evasion, and persistence. Variation in the lipopolysaccharide is also the major differentiating factor that is used to classify Salmonella into over 2600 serovars as part of the Kaufmann-White scheme. While lipopolysaccharide diversity is generally associated with sequence variation in the lipopolysaccharide biosynthesis operon, extraneous genetic factors such as those encoded by the glucosyltransferase (gtr) operons provide further structural heterogeneity by adding additional sugars onto the O-antigen component of the lipopolysaccharide. Here we identify and examine the O-antigen modifying glucosyltransferase genes from the genomes of Salmonella enterica and Salmonella bongori serovars. We show that Salmonella generally carries between 1 and 4 gtr operons that we have classified into 10 families on the basis of gtrC sequence with apparent O-antigen modification detected for five of these families. The gtr operons localize to bacteriophage-associated genomic regions and exhibit a dynamic evolutionary history driven by recombination and gene shuffling events leading to new gene combinations. Furthermore, evidence of Dam- and OxyR-dependent phase variation of gtr gene expression was identified within eight gtr families. Thus, as O-antigen modification generates significant intra- and inter-strain phenotypic diversity, gtr-mediated modification is fundamental in assessing Salmonella strain variability. This will inform appropriate vaccine and diagnostic approaches, in addition to contributing to our understanding of host-pathogen interactions.
Author Summary
Bacterial pathogens frequently evolve mechanisms to vary the composition of their surface structures. The consequence is enhanced long-term survival by facilitating persistence and evasion of the host immune system. Salmonella sp., cause severe infections in a range of mammalian hosts and guard themselves with a protective coat, termed the O-antigen. Through genome sequence analyses we found that Salmonella have acquired an unprecedented repertoire of genetic sequences for modifying their O-antigen coat. There is strong evidence that these genetic factors have a dynamic evolutionary history and are spread through the bacterial population by bacteriophage. In addition to this genetic repertoire, we determined that Salmonella can and often do employ stochastic mechanisms for expression of these genetic factors. This means that O-antigen coat diversity can be generated within a Salmonella population that otherwise has a common genome. Our data significantly enhance our appreciation of the genetic and regulatory characteristics underpinning Salmonella O-antigen diversity. The role attributed to bacteriophage in generating this diversity highlights that Salmonella are acquiring an extensive repertoire of O-antigen modifying traits that may enhance the pathogen's ability to persist and cause disease in mammalian hosts. Such genetic traits may make useful markers for defining new epidemiological and diagnostic tools.
doi:10.1371/journal.pgen.1003568
PMCID: PMC3688519  PMID: 23818865
9.  Glutamyl-tRNA Reductase of Chlorobium vibrioforme Is a Dissociable Homodimer That Contains One Tightly Bound Heme per Subunit 
Journal of Bacteriology  2005;187(13):4444-4450.
δ-Aminolevulinic acid, the biosynthetic precursor of tetrapyrroles, is synthesized from glutamate via the tRNA-dependent five-carbon pathway in the green sulfur bacterium Chlorobium vibrioforme. The enzyme glutamyl-tRNA reductase (GTR), encoded by the hemA gene, catalyzes the first committed step in this pathway, which is the reduction of tRNA-bound glutamate to produce glutamate 1-semialdehyde. To characterize the GTR protein, the hemA gene from C. vibrioforme was cloned into expression plasmids that added an N-terminal His6 tag to the expressed protein. The His-tagged GTR protein was purified using Ni affinity column chromatography. GTR was observable as a 49-kDa band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels. The native molecular mass, as determined by gel filtration chromatography, appeared to be approximately 40 kDa, indicating that native GTR is a monomer. However, when the protein was mixed with 5% (vol/vol) glycerol, the product had an apparent molecular mass of 95 kDa, indicating that the protein is a dimer under these conditions. Purified His6-GTR was catalytically active in vitro when it was incubated with Escherichia coli glutamyl-tRNAGlu and purified recombinant Chlamydomonas reinhardtii glutamate-1-semialdehyde aminotransferase. The expressed GTR contained 1 mol of tightly bound heme per mol of pep tide subunit. The heme remained bound to the protein throughout purification and was not removed by anion- or cation-exchange column chromatography. However, the bound heme was released during SDS-PAGE if the protein was denatured in the presence of β-mercaptoethanol. Added heme did not inhibit the activity of purified expressed GTR in vitro. However, when the GTR was expressed in the presence of 3-amino-2,3- dihydrobenzoic acid (gabaculine), an inhibitor of heme synthesis, the purified GTR had 60 to 70% less bound heme than control GTR, and it was inhibited by hemin in vitro.
doi:10.1128/JB.187.13.4444-4450.2005
PMCID: PMC1151790  PMID: 15968053
10.  Phase variation controls expression of Salmonella lipopolysaccharide modification genes by a DNA methylation-dependent mechanism 
Molecular Microbiology  2010;77(2):337-353.
The O-antigen of Salmonella lipopolysaccharide is a major antigenic determinant and its chemical composition forms the basis for Salmonella serotyping. Modifications of the O-antigen that can affect the serotype include those carried out by the products of glycosyltransferase operons (gtr), which are present on specific Salmonella and phage genomes. Here we show that expression of the gtr genes encoded by phage P22 that confers the O1 serotype is under the control of phase variation. This phase variation occurs by a novel epigenetic mechanism requiring OxyR in conjunction with the DNA methyltransferase Dam. OxyR is an activator or a repressor of the system depending on which of its two binding sites in the gtr regulatory region is occupied. Binding is decreased by methylation at Dam target sequences in either site, and this confers heritability of the expression state to the system. Most Salmonella gtr operons share the key regulatory elements that are identified here as essential for this epigenetic phase variation.
doi:10.1111/j.1365-2958.2010.07203.x
PMCID: PMC2909390  PMID: 20487280
11.  The intrinsic GTPase activity of the Gtr1 protein from Saccharomyces cerevisiae 
BMC Biochemistry  2012;13:11.
Background
The Gtr1 protein of Saccharomyces cerevisiae is a member of the RagA subfamily of the Ras-like small GTPase superfamily. Gtr1 has been implicated in various cellular processes. Particularly, the Switch regions in the GTPase domain of Gtr1 are essential for TORC1 activation and amino acid signaling. Therefore, knowledge about the biochemical activity of Gtr1 is required to understand its mode of action and regulation.
Results
By employing tryptophan fluorescence analysis and radioactive GTPase assays, we demonstrate that Gtr1 can adopt two distinct GDP- and GTP-bound conformations, and that it hydrolyses GTP much slower than Ras proteins. Using cysteine mutagenesis of Arginine-37 and Valine-67, residues at the Switch I and II regions, respectively, we show altered GTPase activity and associated conformational changes as compared to the wild type protein and the cysteine-less mutant.
Conclusions
The extremely low intrinsic GTPase activity of Gtr1 implies requirement for interaction with activating proteins to support its physiological function. These findings as well as the altered properties obtained by mutagenesis in the Switch regions provide insights into the function of Gtr1 and its homologues in yeast and mammals.
doi:10.1186/1471-2091-13-11
PMCID: PMC3477016  PMID: 22726655
Gtr1; GTPase; Intrinsic tryptophan fluorescence; Rag GTPase; Cysteine mutagenesis; Switch region
12.  Chemoheterotrophic Growth of the Cyanobacterium Anabaena sp. Strain PCC 7120 Dependent on a Functional Cytochrome c Oxidase 
Journal of Bacteriology  2012;194(17):4601-4607.
Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium commonly used as a model organism for studying cyanobacterial cell differentiation and nitrogen fixation. For many decades, this cyanobacterium was considered an obligate photo-lithoautotroph. We now discovered that this strain is also capable of mixotrophic, photo-organoheterotrophic, and chemo-organoheterotrophic growth if high concentrations of fructose (at least 50 mM and up to 200 mM) are supplied. Glucose, a substrate used by some facultatively organoheterotrophic cyanobacteria, is not effective in Anabaena sp. PCC 7120. The gtr gene from Synechocystis sp. PCC 6803 encoding a glucose carrier was introduced into Anabaena sp. PCC 7120. Surprisingly, the new strain containing the gtr gene did not grow on glucose but was very sensitive to glucose, with a 5 mM concentration being lethal, whereas the wild-type strain tolerated 200 mM glucose. The Anabaena sp. PCC 7120 strain containing gtr can grow mixotrophically and photo-organoheterotrophically, but not chemo-organoheterotrophically with fructose. Anabaena sp. PCC 7120 contains five respiratory chains ending in five different respiratory terminal oxidases. One of these enzymes is a mitochondrial-type cytochrome c oxidase. As in almost all cyanobacteria, this enzyme is encoded by three adjacent genes called coxBAC1. When this locus was disrupted, the cells lost the capability for chemo-organoheterotrophic growth.
doi:10.1128/JB.00687-12
PMCID: PMC3415483  PMID: 22730128
13.  A comparative evaluation of the effectiveness of guided tissue regeneration by using a collagen membrane with or without decalcified freeze-dried bone allograft in the treatment of infrabony defects: A clinical and radiographic study 
Background:
The present, randomized, controlled clinical and radiographic study was undertaken to compare the effectiveness of guided tissue regeneration (GTR) by using a collagen membrane barrier with or without decalcified freeze-dried bone allograft (DFDBA) in the treatment of periodontal infrabony defects characterized by unfavorable architecture.
Materials and Methods:
Sixteen systemically healthy patients with 20 periodontal infrabony defects were selected for the study. Each patient had at least ≥ 5 mm clinical probing pocket depth (PPD) at the selected site and depth of intrabony component ≥ 3 mm as assessed by clinical and radiographic measurements. Baseline measurements included plaque index, papillary bleeding index, PPD, gingival recession, clinical attachment level and radiographic defect depth (DD). At the time of surgery, the defects were randomly assigned to either the test group (collagen membrane plus DFDBA) or the control group (collagen membrane only).
Results:
At the 6-month examination, PPPD reduction was significantly greater in the GTR + DFDBA group (4.06 ± 0.38 mm) compared with the GTR group (3.2 ± 0.74 mm). The mean gains of clinical attachment were 3.54 ± 0.36 mm in the test group and 2.50 ± 0.74 mm in the control group. Radiographic DD reduction was similarly greater in the GTR + DFDBA group (2.40 ± 0.51 mm) compared with the GTR group (1.60 ± 0.51 mm).
Conclusions:
The results of the present study indicate that the use of a GTR membrane with bone graft has significantly improved all clinical parameters tested as compared with the use of bioresorbable membrane alone in the treatment of infrabony defects characterized by unfavorable architecture.
doi:10.4103/0972-124X.118321
PMCID: PMC3800412  PMID: 24174729
Bone graft; guided tissue regeneration; infrabony defect
14.  Putative GTP-binding protein, Gtr1, associated with the function of the Pho84 inorganic phosphate transporter in Saccharomyces cerevisiae. 
Molecular and Cellular Biology  1992;12(7):2958-2966.
We have found an open reading frame which is 1.1 kb upstream of PHO84 (which encodes a Pi transporter) and is transcribed from the opposite strand. In Saccharomyces cerevisiae, this gene is distal to the TUB3 locus on the left arm of chromosome XIII and is named GTR1. GTR1 encodes a protein consisting of 310 amino acid residues containing, in its N-terminal region, the characteristic tripartite consensus elements for binding GTP conserved in GTP-binding proteins, except for histidine in place of a widely conserved aspargine residue in element III. Disruption of the GTR1 gene resulted in slow growth at 30 degrees C and no growth at 15 degrees C; other phenotypes resembled those of pho84 mutants and included constitutive synthesis of repressible acid phosphatase, reduced Pi transport activity, and resistance to arsenate. The latter phenotypes were shown to be due to a defect in Pi uptake, and the Gtr1 protein was found to be functionally associated with the Pho84 Pi transporter. Recombination between chromosome V (at the URA3 locus) and chromosome XIII (in the GTR1-PHO84-TUB3 region) by using a plasmid-encoded site-specific recombination system indicated that the order of these genes was telomere-TUB3-PHO84-GTR1-CENXIII.
Images
PMCID: PMC364509  PMID: 1620108
15.  Cloning and sequence analysis of a cDNA for a rat liver glutathione S-transferase Yb subunit. 
Nucleic Acids Research  1986;14(15):6101-6114.
We have isolated a Yb-subunit cDNA clone from a GSH S-transferase (GST) cDNA library made from rat liver polysomal poly(A) RNAs. Sequence analysis of one of these cDNA, pGTR200, revealed an open reading frame of 218 amino acids of Mr = 25,915. The deduced sequence is in agreement with the 19 NH2-terminal residues for GST-A. The sequence of pGTR200 differs from another Yb cDNA, pGTA/C44 by four nucleotides and two amino acids in the coding region, thus revealing sequence microheterogeneity. The cDNA insert in pGTR200 also contains 36 nucleotides in the 5' noncoding region and a complete 3' noncoding region. The Yb subunit cDNA shares very limited homology with those of the Ya or Yc cDNAs, but has relatively higher sequence homology to the placental subunit Yp clone pGP5. The mRNA of pGTR200 is not expressed abundantly in rat hearts and seminal vesicles. Therefore, the GST subunit sequence of pGTR200 probably represents a basic Yb subunit. Genomic DNA hybridization patterns showed a complexity consistent with having a multigene family for Yb subunits. Comparison of the amino acid sequences of the Ya, Yb, Yc, and Yp subunits revealed significant conservation of amino acids (approximately 29%) throughout the coding sequences. These results indicate that the rat GSTs are products of at least four different genes that may constitute a supergene family.
Images
PMCID: PMC311624  PMID: 2875437
16.  Materials and prognostic factors of bone regeneration in periapical surgery: A systematic review 
Objectives: Analyse the effectiveness of different materials and techniques used in guided tissue regeneration (GTR) applied in periapical surgery, comparing the success rate obtained in 4-wall defects and in through-and-through bone lesions as well as to establish prognostic factors. Material and Methods: A Cochrane, PubMed-MEDLINE and Scopus database search (October 2012 to March 2013) was conducted with the search terms “periapical surgery”, “surgical endodontic treatment”, “guided tissue regeneration”, “bone regeneration”, “bone grafts”, “barrier membranes” and “periapical lesions” individually and next, using the Boolean operator “AND”. The inclusion criteria were the use of GTR (bone graft and/or membrane barrier), clinical studies including at least 10 patients, 10 years aged articles published in English or French. The exclusion criteria were case reports and nonhuman studies. Results: 34 publications were selected from a total of 483. 9 of the 34 were excluded. Finally, the systematic review included 25 articles: 2 metaanalysis, 8 reviews, 13 prospective studies and 2 retrospective studies. They were stratified according to their level of scientific evidence using the SORT criteria. The 4-wall periapical and through-and-through lesions improve more their prognosis by combining bone grafts and barrier membranes than using these materials exclusively, respect to the control groups. The results show lower failure rates in 4-wall lesions than in through-and-through lesions using GTR. Conclusions: The combined GTR technique (filling material and membranes) obtains a greater success rate both in 4-wall lesions and in through-and-through lesions, respect to the control groups. The use of regeneration materials seems to be more necessary in through-and-through lesions,> 5mm lesions, lower teeth and apicomarginal lesions as they have the worst healing prognosis. In function of the articles scientific quality, a type B recommendation is given in favour to the use of GTR in association of periapical surgery in case of 4-wall and through-and-through lesions.
Key words:Periapical surgery, surgical endodontic treatment, guided tissue regeneration, bone regeneration, bone grafts, barrier membranes.
doi:10.4317/medoral.19453
PMCID: PMC4119321  PMID: 24608211
17.  Autologous glioma cell vaccine admixed with interleukin-4 gene transfected fibroblasts in the treatment of patients with malignant gliomas 
Background
The prognosis for malignant gliomas remains dismal. We addressed the safety, feasibility and preliminary clinical activity of the vaccinations using autologous glioma cells and interleukin (IL)-4 gene transfected fibroblasts.
Methods
In University of Pittsburgh Cancer Institute (UPCI) protocol 95-033, adult participants with recurrent glioblastoma multiforme (GBM) or anaplastic astrocytoma (AA) received gross total resection (GTR) of the recurrent tumors, followed by two vaccinations with autologous fibroblasts retrovirally transfected with TFG-IL4-Neo-TK vector admixed with irradiated autologous glioma cells. In UPCI 99-111, adult participants with newly diagnosed GBM or AA, following GTR and radiation therapy, received two intradermal vaccinations with the TFG-IL4-Neo-TK-transfected fibroblasts admixed with type-1 dendritic cells (DC) loaded with autologous tumor lysate. The participants were evaluated for occurrence of adverse events, immune response, and clinical response by radiological imaging.
Results and Discussion
In UPCI 95-033, only 2 of 6 participants received the vaccinations. Four other participants were withdrawn from the trial because of tumor progression prior to production of the cellular vaccine. However, both participants who received two vaccinations demonstrated encouraging immunological and clinical responses. Biopsies from the local vaccine sites from one participant displayed IL-4 dose-dependent infiltration of CD4+ as well as CD8+ T cells. Interferon (IFN)-γ Enzyme-Linked Immuno-SPOT (ELISPOT) assay in another human leukocyte antigen (HLA)-A2+ participant demonstrated systemic T-cell responses against an HLA-A2-restricted glioma-associated antigen (GAA) epitope EphA2883–891. Moreover, both participants demonstrated clinical and radiological improvement with no evidence of allergic encephalitis, although both participants eventually succumbed with the tumor recurrence. In 99-111, 5 of 6 enrolled participants received scheduled vaccinations with no incidence of major adverse events. Monocyte-derived DCs produced high levels of IL-12 p70. Treatment was well tolerated; however, we were unable to observe detectable IFN-γ post-vaccine responses or prolonged progression-free survival in these participants.
Conclusion
Feasibility challenges inherent in the generation of a patient-specific gene transfection-based vaccine strongly suggests the need for more practical formulations that would allow for the timely administration of vaccines. Nevertheless, successful generation of type-1 DCs and preliminary safety in the current study provide a strong rationale for further efforts to develop novel glioma vaccines.
doi:10.1186/1479-5876-5-67
PMCID: PMC2254376  PMID: 18093335
18.  Effect of Autogenous Cortical Bone Grafting in Conjunction with Guided Tissue Regeneration in the Treatment of Intraosseous Periodontal Defects 
European Journal of Dentistry  2010;4(4):403-411.
Objectives:
The aim of this clinical trial was to evaluate the additional benefit of using guided tissue regeneration (GTR) with autogenous cortical bone (ACB) grafting versus ACB grafting alone for the regenerative treatment of intraosseous periodontal defects.
Methods:
Via a split-mouth design, 12 patients with chronic periodontitis (five men, seven women; mean age, 45.3±4.6 years) who had probing pocket depths (PPDs) of ≥6 mm following initial periodontal therapy were randomly assigned to two treatments in contralateral areas of the dentition: a combination of ACB grafting and GTR (with a absorbable membrane of polylactic acid) or ACB grafting alone. The compared parameters were preoperative and 6-month postoperative PPDs, clinical attachment levels (CALs), and radiographic alveolar bone heights.
Results:
Both treatment modalities resulted in significant changes in the postoperative measurements from the preoperative values (P<.01). The reduction in the PPDs, gain in the CALs, and gain in the radiographic alveolar bone heights were 4.58±1.08, 4.25±1.06, and 5.50±2.24 mm in the patients treated with ACB grafting and GTR and 4.92±1.00, 4.50±0.80, and 5.92±1.83 mm in those treated with ACB grafting alone, respectively. The differences between the treatments were not statistically significant (P>.05).
Conclusions:
Within the study limitations, both ACB grafting with GTR and ACB grafting alone lead to significant improvements in clinical and radiographic parameters at 6 months postoperatively. The combined approach does not provide any additional benefit for treating intraosseous periodontal defects.
PMCID: PMC2948748  PMID: 20922160
Autogenous bone graft; Guided tissue regeneration; Intraosseous defects; Periodontal regeneration
19.  Recurrence following neurosurgeon-determined gross-total resection of adult supratentorial low-grade glioma: results of a prospective clinical trial 
Journal of neurosurgery  2008;109(5):10.3171/JNS/2008/109/11/0835.
Object
In 1998, the Radiation Therapy Oncology Group initiated a Phase II study of observation for adults < 40 years old with cerebral low-grade glioma who underwent a neurosurgeon-determined gross-total resection (GTR).
Methods
Patient eligibility criteria included the presence of a World Health Organization Grade II astrocytoma, oligodendroglioma, or mixed oligoastrocytoma confirmed histologically; age 18–39 years; Karnofsky Performance Scale score ≥ 60; Neurologic Function Scale score ≤ 3; supratentorial tumor location; neurosurgeon-determined GTR; and pre- and postoperative MR imaging with contrast enhancement available for central review by the principal investigator. Patients were observed following GTR and underwent MR imaging every 6 months. Prognostic factors analyzed for their contribution to patient overall survival, progression-free survival (PFS), and tumor recurrence included age, sex, Karnofsky Performance Scale score, Neurologic Function Scale score, histological type, contrast enhancement on preoperative MR imaging, preoperative tumor diameter, residual disease based on postoperative MR imaging, and baseline Mini-Mental State Examination score.
Results
Between 1998 and 2002, 111 eligible patients were entered into the study. In these 111 patients, the overall survival rates at 2 and 5 years were 99 and 93%, respectively. The PFS rates in these 111 patients at 2 and 5 years were 82 and 48%, respectively. Three prognostic factors predicted significantly poorer PFS in univariate and multivariate analyses: 1) preoperative tumor diameter ≥ 4 cm; 2) astrocytoma/oligoastrocytoma histological type; and 3) residual tumor ≥ 1 cm according to MR imaging. Review of the postoperative MR imaging results revealed that 59% of patients had < 1 cm residual disease (with a subsequent 26% recurrence rate), 32% had 1–2 cm residual disease (with a subsequent 68% recurrence rate), and 9% had > 2 cm residual disease (with a subsequent 89% recurrence rate).
Conclusions
These data suggest that young adult patients with low-grade glioma who undergo a neurosurgeon-determined GTR have a > 50% risk of tumor progression 5-years postoperatively, warranting close follow-up and consideration for adjuvant treatment.
doi:10.3171/JNS/2008/109/11/0835
PMCID: PMC3833272  PMID: 18976072
gross-total resection; low-grade glioma; progression-free survival; surgery
20.  Reduced Heme Levels Underlie the Exponential Growth Defect of the Shewanella oneidensis hfq Mutant 
PLoS ONE  2014;9(10):e109879.
The RNA chaperone Hfq fulfills important roles in small regulatory RNA (sRNA) function in many bacteria. Loss of Hfq in the dissimilatory metal reducing bacterium Shewanella oneidensis strain MR-1 results in slow exponential phase growth and a reduced terminal cell density at stationary phase. We have found that the exponential phase growth defect of the hfq mutant in LB is the result of reduced heme levels. Both heme levels and exponential phase growth of the hfq mutant can be completely restored by supplementing LB medium with 5-aminolevulinic acid (5-ALA), the first committed intermediate synthesized during heme synthesis. Increasing expression of gtrA, which encodes the enzyme that catalyzes the first step in heme biosynthesis, also restores heme levels and exponential phase growth of the hfq mutant. Taken together, our data indicate that reduced heme levels are responsible for the exponential growth defect of the S. oneidensis hfq mutant in LB medium and suggest that the S. oneidensis hfq mutant is deficient in heme production at the 5-ALA synthesis step.
doi:10.1371/journal.pone.0109879
PMCID: PMC4214671  PMID: 25356668
21.  Clinical evaluation of subepithelial connective tissue graft and guided tissue regeneration for treatment of Miller’s class 1 gingival recession (comparative, split mouth, six months study) 
Objectives: The present study aims to clinically compare and evaluate subepithelial connective tissue graft and the GTR based root coverage in treatment of Miller’s Class I gingival recession. Study Design: 30 patients with at least one pair of Miller’s Class I gingival recession were treated either with Subepithelial connective tissue graft (Group A) or Guided tissue regeneration (Group B). Clinical parameters monitored included recession RD, width of keratinized gingiva (KG), probing depth (PD), clinical attachment level (CAL), attached gingiva (AG), residual probing depth (RPD) and % of Root coverage(%RC). Measurements were taken at baseline, three months and six months. A standard surgical procedure was used for both Group A and Group B. Data were recorded and statistical analysis was done for both intergroup and intragroup. Results: At end of six months % RC obtained were 84.47% (Group A) and 81.67% (Group B). Both treatments resulted in statistically significant improvement in clinical parameters. When compared, no statistically significant difference was found between both groups except in RPD, where it was significantly greater in Group A. Conclusions: GTR technique has advantages over subepithelial connective tissue graft for shallow Miller’s Class I defects and this procedure can be used to avoid patient discomfort and reduce treatment time.
Key words:Collagen membrane, comparative split mouth study, gingival recession, subepithelial connective tissue graft, guided tissue regeneration (GTR).
doi:10.4317/jced.51302
PMCID: PMC4134848  PMID: 25136420
22.  GtrS and GltR form a two-component system: the central role of 2-ketogluconate in the expression of exotoxin A and glucose catabolic enzymes in Pseudomonas aeruginosa 
Nucleic Acids Research  2014;42(12):7654-7665.
In the human pathogen Pseudomonas aeruginosa, the GltR regulator is required for glucose transport, whereas GtrS is a sensor kinase that plays a key role in mediating bacteria–host interaction and pathogen dissemination in the host. We show that GtrS and GltR form a two-component system that regulates the expression from the promoters Pedd/gap-1, PoprB and Pglk, which control the expression of genes involved in glucose metabolism and transport. In addition, the GtrS/GltR pair regulates the expression of toxA that encodes exotoxin A, the primary virulence factor. Microcalorimetry-based ligand screening of the recombinant GtrS ligand-binding domain revealed specific binding of 2-ketogluconate (2-KG) (KD = 5 μM) and 6-phosphogluconate (KD = 98 μM). These effectors accelerate GtrS autophosphorylation, with concomitant transphosphorylation of GltR leading to a three-fold increase in transcription. Surprisingly, in vivo a similar increase in expression from the above promoters was observed for the mutant deficient in GltR regardless of the presence of effectors. The GltR operator site was found to contain the consensus sequence 5′-tgGTTTTTc-3′. We propose that 2-KG is a key metabolite in the stringent transcriptional control of genes involved in virulence and glucose metabolism. We show that GltR is a transcriptional repressor that is released from DNA upon phosphorylation.
doi:10.1093/nar/gku496
PMCID: PMC4081096  PMID: 24920832
23.  Clinical evaluation of regenerative potential of type I collagen membrane along with xenogenic bone graft in the treatment of periodontal intrabony defects assessed with surgical re-entry and radiographic linear and densitometric analysis 
Background and Objectives:
The primary goal of periodontal therapy is to restore the tooth supporting tissues lost due to periodontal disease. The aim of the present study was to compare the efficacy of combination of type I collagen (GTR membrane) and xenogenic bone graft with open flap debridement (OFD) in treatment of periodontal intrabony defects.
Materials and Methods:
Twenty paired intrabony defects were surgically treated using split mouth design. The defects were randomly assigned to treatment with OFD + collagen membrane + bone graft (Test) or OFD alone (Control). The clinical efficacy of two treatment modalities was evaluated at 9 month postoperatively by clinical, radiographical, and intrasurgical (re-entry) parameters. The measurements included probing pocket depth (PD), clinical attachment level (CAL), gingival recession (GR), bone fill (BF), bone density (BD) and intra bony component (INTRA).
Results:
The mean reduction in PD at 0–9 month was 3.3±0.82 mm and CAL gain of 3.40±1.51 mm occurred in the collagen membrane + bone graft (Test) group; corresponding values for OFD (Control) were 2.20±0.63 mm and 1.90±0.57 mm. Similar pattern of improvement was observed when radiographical and intra-surgical (re-entry) post operative evaluation was made. All improvement in different parameters was statistically significant (P< 0.01).
Interpretation and Conclusion:
Treatment with a combination of collagen membrane and bone graft led to a significantly more favorable clinical outcome in intrabony defects as compared to OFD alone.
doi:10.4103/0972-124X.65432
PMCID: PMC2933525  PMID: 20922075
Bone grafts; collagen membrane; guided tissue regeneration; periodontal regeneration
24.  PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination 
BMC Bioinformatics  2011;12:10.
Background
We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by 'Pairwise Identity and Cost Scores Ordination' (PICS-Ord). The method works via ordination of sequence identity or cost scores matrices by means of Principal Coordinates Analysis (PCoA). After identification of ambiguous regions, the method computes pairwise distances as sequence identities or cost scores, ordinates the resulting distance matrix by means of PCoA, and encodes the principal coordinates as ordered integers. Three biological and 100 simulated datasets were used to assess the performance of the new method.
Results
Including ambiguous regions coded by means of PICS-Ord increased topological accuracy, resolution, and bootstrap support in real biological and simulated datasets compared to the alternative of excluding such regions from the analysis a priori. In terms of accuracy, PICS-Ord performs equal to or better than previously available methods of ambiguous region coding (e.g., INAASE), with the advantage of a practically unlimited alignment size and increased analytical speed and the possibility of PICS-Ord scores to be analyzed together with DNA data in a partitioned maximum likelihood model.
Conclusions
Advantages of PICS-Ord over step matrix-based ambiguous region coding with INAASE include a practically unlimited number of OTUs and seamless integration of PICS-Ord codes into phylogenetic datasets, as well as the increased speed of phylogenetic analysis. Contrary to word- and frequency-based methods, PICS-Ord maintains the advantage of pairwise sequence alignment to derive distances, and the method is flexible with respect to the calculation of distance scores. In addition to distance and maximum parsimony, PICS-Ord codes can be analyzed in a Bayesian or maximum likelihood framework. RAxML (version 7.2.6 or higher that was developed for this study) allows up to 32-state ordered or unordered characters. A GTR, MK, or ORDERED model can be applied to analyse the PICS-Ord codes partition, with GTR performing slightly better than MK and ORDERED.
Availability
An implementation of the PICS-Ord algorithm is available from http://scit.us/projects/ngila/wiki/PICS-Ord. It requires both the statistical software, R http://www.r-project.org and the alignment software Ngila http://scit.us/projects/ngila.
doi:10.1186/1471-2105-12-10
PMCID: PMC3024941  PMID: 21214904
25.  Assessment of Hyperactive Reflexes in Patients with Spinal Cord Injury 
BioMed Research International  2015;2015:149875.
Hyperactive reflexes are commonly observed in patients with spinal cord injury (SCI) but there is a lack of convenient and quantitative characterizations. Patellar tendon reflexes were examined in nine SCI patients and ten healthy control subjects by tapping the tendon using a hand-held instrumented hammer at various knee flexion angles, and the tapping force, quadriceps EMG, and knee extension torque were measured to characterize patellar tendon reflexes quantitatively in terms of the tendon reflex gain (Gtr), contraction rate (Rc), and reflex loop time delay (td). It was found that there are significant increases in Gtr and Rc and decrease in td in patients with spinal cord injury as compared to the controls (P < 0.05). This study presented a convenient and quantitative method to evaluate reflex excitability and muscle contraction dynamics. With proper simplifications, it can potentially be used for quantitative diagnosis and outcome evaluations of hyperreflexia in clinical settings.
doi:10.1155/2015/149875
PMCID: PMC4310310  PMID: 25654084

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