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author:("hemmings, S")
1.  Rupture of the cell envelope by induced intracellular gas phase expansion in gas vacuolate bacteria. 
Journal of Bacteriology  1980;143(2):841-846.
Using a new approach, we estimated the physical strength of the cell envelopes of three species of gram-negative, gas vacuolate bacteria (Microcyclus aquaticus, Prosthecomicrobium pneumaticum, and Meniscus glaucopis). Populations of cells were slowly (0.5 to 2.9 h) saturated with argon, nitrogen, or helium to final pressures up to 100 atm (10, 132 kPa). The gas phases of the vesicles remained intact and, upon rapid (1 to 2 s) decompression to atmospheric pressure, expanded and ruptured the cells; loss of colony-forming units was used as an index of rupture. Because the cell envelope is the cellular component most likely to resist the expanding intracellular gas phase, its strength can be estimated from the minimum gas pressures that produce rupture. The viable counts indicated that these minimum pressures were between 25 and 50 atm; the majority of the cell envelopes were ruptured at pressures between 50 and 100 atm. Cells in which the gas vesicles were collapsed and the gas phases were effectively dissolved by rapid compression tolerated decompression from much higher gas saturations. Cells that do not normally possess gas vesicles (Escherichia coli) or that had been prevented from forming them by addition of L-lysine to the medium (M. aquaticus) were not harmed by decompression from gas saturation pressures up to 300 atm.
PMCID: PMC294375  PMID: 7204336
2.  Intensive glycaemic control for patients with type 2 diabetes: systematic review with meta-analysis and trial sequential analysis of randomised clinical trials 
Objective To assess the effect of targeting intensive glycaemic control versus conventional glycaemic control on all cause mortality and cardiovascular mortality, non-fatal myocardial infarction, microvascular complications, and severe hypoglycaemia in patients with type 2 diabetes.
Design Systematic review with meta-analyses and trial sequential analyses of randomised trials.
Data sources Cochrane Library, Medline, Embase, Science Citation Index Expanded, LILACS, and CINAHL to December 2010; hand search of reference lists and conference proceedings; contacts with authors, relevant pharmaceutical companies, and the US Food and Drug Administration.
Study selection Randomised clinical trials comparing targeted intensive glycaemic control with conventional glycaemic control in patients with type 2 diabetes. Published and unpublished trials in all languages were included, irrespective of predefined outcomes.
Data extraction Two reviewers independently assessed studies for inclusion and extracted data related to study methods, interventions, outcomes, risk of bias, and adverse events. Risk ratios with 95% confidence intervals were estimated with fixed and random effects models.
Results Fourteen clinical trials that randomised 28 614 participants with type 2 diabetes (15 269 to intensive control and 13 345 to conventional control) were included. Intensive glycaemic control did not significantly affect the relative risks of all cause (1.02, 95% confidence interval 0.91 to 1.13; 28 359 participants, 12 trials) or cardiovascular mortality (1.11, 0.92 to 1.35; 28 359 participants, 12 trials). Trial sequential analyses rejected a relative risk reduction above 10% for all cause mortality and showed insufficient data on cardiovascular mortality. The risk of non-fatal myocardial infarction may be reduced (relative risk 0.85, 0.76 to 0.95; P=0.004; 28 111 participants, 8 trials), but this finding was not confirmed in trial sequential analysis. Intensive glycaemic control showed a reduction of the relative risks for the composite microvascular outcome (0.88, 0.79 to 0.97; P=0.01; 25 600 participants, 3 trials) and retinopathy (0.80, 0.67 to 0.94; P=0.009; 10 793 participants, 7 trials), but trial sequential analyses showed that sufficient evidence had not yet been reached. The estimate of an effect on the risk of nephropathy (relative risk 0.83, 0.64 to 1.06; 27 769 participants, 8 trials) was not statistically significant. The risk of severe hypoglycaemia was significantly increased when intensive glycaemic control was targeted (relative risk 2.39, 1.71 to 3.34; 27 844 participants, 9 trials); trial sequential analysis supported a 30% increased relative risk of severe hypoglycaemia.
Conclusion Intensive glycaemic control does not seem to reduce all cause mortality in patients with type 2 diabetes. Data available from randomised clinical trials remain insufficient to prove or refute a relative risk reduction for cardiovascular mortality, non-fatal myocardial infarction, composite microvascular complications, or retinopathy at a magnitude of 10%. Intensive glycaemic control increases the relative risk of severe hypoglycaemia by 30%.
doi:10.1136/bmj.d6898
PMCID: PMC3223424  PMID: 22115901
3.  mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences 
Microbiome  2013;1:23.
Background
Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database.
Results
Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure.
Conclusions
mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.
doi:10.1186/2049-2618-1-23
PMCID: PMC3971603  PMID: 24451012
Operational taxonomic unit; Assembly; Automated sequence analysis pipeline; 60 kDa chaperonin; Cpn60; Barcode; Microbial profiling; Microbiota; Microbiota analysis
4.  The Role of Paracrine and Autocrine Signaling in the Early Phase of Adipogenic Differentiation of Adipose-derived Stem Cells 
PLoS ONE  2013;8(5):e63638.
Introduction
High cell density is known to enhance adipogenic differentiation of mesenchymal stem cells, suggesting secretion of signaling factors or cell-contact-mediated signaling. By employing microfluidic biochip technology, we have been able to separate these two processes and study the secretion pathways.
Methods and results
Adipogenic differentiation of human adipose-derived stem cells (ASCs) cultured in a microfluidic system was investigated under perfusion conditions with an adipogenic medium or an adipogenic medium supplemented with supernatant from differentiating ASCs (conditioned medium). Conditioned medium increased adipogenic differentiation compared to adipogenic medium with respect to accumulation of lipid-filled vacuoles and gene expression of key adipogenic markers (C/EBPα, C/EBPβ, C/EBPδ, PPARγ, LPL and adiponectin). The positive effects of conditioned medium were observed early in the differentiation process.
Conclusions
Using different cell densities and microfluidic perfusion cell cultures to suppress the effects of cell-released factors, we have demonstrated the significant role played by auto- or paracrine signaling in adipocyte differentiation. The cell-released factor(s) were shown to act in the recruitment phase of the differentiation process.
doi:10.1371/journal.pone.0063638
PMCID: PMC3665830  PMID: 23723991
5.  The Correlation of 113Cd NMR and 111mCd PAC Spectroscopies Provides a Powerful Approach for the Characterization of the Structure of CdII-Substituted ZnII Proteins** 
CdII has been used as a probe of zinc metalloenzymes and proteins because of the spectroscopic silence of ZnII. One of the most commonly used spectroscopic techniques is 113Cd NMR; however, in recent years 111mCd Perturbed Angular Correlation spectroscopy (111mCd PAC) has also been shown to provide useful structural, speciation and dynamics information on CdII complexes and biomolecules. In this article, we show how the joint use of 113Cd NMR and 111mCd PAC spectroscopies can provide detailed information about the CdII environment in thiolate-rich proteins. Specifically we show that the 113Cd NMR chemical shifts observed for CdII in the designed TRI series (TRI = Ac-G-(LKALEEK)4G-NH2) of peptides vary depending on the proportion of trigonal planar CdS3 and pseudotetrahedral CdS3O species present in the equilibrium mixture. PAC spectra are able to quantify these mixtures. When one compares the chemical shift range for these peptides (from δ = 570 to 700 ppm), it is observed that CdS3 species have δ 675–700 ppm, CdS3O complexes fall in the range δ 570–600 ppm and mixtures of these forms fall linearly between these extremes. If one then determines the pKa2 values for CdII complexation [pKa2 is for the reaction Cd[(peptide–H)2(peptide)]+→Cd-(peptide)3− + 2H+ and compares these to the observed chemical shift for the Cd(peptide)3− complexes, one finds that there is also a direct linear correlation. Thus, by determining the chemical shift value of these species, one can directly assess the metal-binding affinity of the construct. This illustrates how proteins may be able to fine tune metal-binding affinity by destabilizing one metallospecies with respect to another. More important, these studies demonstrate that one may have a broad 113Cd NMR chemical shift range for a chemical species (e.g., CdS3O) which is not necessarily a reflection of the structural diversity within such a four-coordinate species, but rather a consequence of a fast exchange equilibrium between two related species (e.g., CdS3O and CdS3). This could lead to reinterpretation of the assignments of cadmium–protein complexes and may impact the application of CdII as a probe of ZnII sites in biology.
doi:10.1002/chem.200802105
PMCID: PMC3598615  PMID: 19229934
cadmium; metallopeptides; NMR spectroscopy; zinc proteins
6.  The Chaperonin-60 Universal Target Is a Barcode for Bacteria That Enables De Novo Assembly of Metagenomic Sequence Data 
PLoS ONE  2012;7(11):e49755.
Barcoding with molecular sequences is widely used to catalogue eukaryotic biodiversity. Studies investigating the community dynamics of microbes have relied heavily on gene-centric metagenomic profiling using two genes (16S rRNA and cpn60) to identify and track Bacteria. While there have been criteria formalized for barcoding of eukaryotes, these criteria have not been used to evaluate gene targets for other domains of life. Using the framework of the International Barcode of Life we evaluated DNA barcodes for Bacteria. Candidates from the 16S rRNA gene and the protein coding cpn60 gene were evaluated. Within complete bacterial genomes in the public domain representing 983 species from 21 phyla, the largest difference between median pairwise inter- and intra-specific distances (“barcode gap”) was found from cpn60. Distribution of sequence diversity along the ∼555 bp cpn60 target region was remarkably uniform. The barcode gap of the cpn60 universal target facilitated the faithful de novo assembly of full-length operational taxonomic units from pyrosequencing data from a synthetic microbial community. Analysis supported the recognition of both 16S rRNA and cpn60 as DNA barcodes for Bacteria. The cpn60 universal target was found to have a much larger barcode gap than 16S rRNA suggesting cpn60 as a preferred barcode for Bacteria. A large barcode gap for cpn60 provided a robust target for species-level characterization of data. The assembly of consensus sequences for barcodes was shown to be a reliable method for the identification and tracking of novel microbes in metagenomic studies.
doi:10.1371/journal.pone.0049755
PMCID: PMC3506640  PMID: 23189159
7.  Controlling and Fine Tuning the Physical Properties of Two Identical Metal Coordination Sites in De Novo Designed Three Stranded Coiled Coil Peptides 
Herein we report how de novo designed peptides can be used to investigate whether the position of a metal site along a linear sequence that folds into a three stranded α-helical coiled coil defines the physical properties of Cd(II) ions in either CdS3 or CdS3O (O-being an exogenous water molecule) coordination environments. Peptides are presented that bind Cd(II) into two identical coordination sites that are located at different topological positions at the interior of these constructs. The peptide grandL16PenL19IL23PenL26I binds two Cd(II) as trigonal planar 3-coordinate CdS3 structures whereas grandL12AL16CL26AL30C sequesters two Cd(II) as pseudotetrahedral 4-coordinate CdS3O structures. We demonstrate how for the first peptide, having a more rigid structure, the location of the identical binding sites along the linear sequence does not affect the physical properties of the two bound Cd(II). However, because these are rigid aggregates, the sites are not completely independent as Cd(II) bound to one of the sites (113Cd NMR chemical shift of 681 ppm) is perturbed by the metallation state (apo or [Cd(pep)(Hpep)2]+ or [Cd(pep)3]−) of the second center (113Cd NMR chemical shift of 686 ppm). grandL12AL16CL26AL30C shows a completely different behavior. The physical properties of the two bound Cd(II) ions indeed depend on the position of the metal center, having pKa2 values for the equilibrium [Cd(pep)(Hpep)2]+ → [Cd(pep)3]− + 2H+ (corresponding to deprotonation and coordination of cysteine thiols) that range from 9.9 to 13.9. In addition, the L26AL30C site shows dynamic behavior, which is not observed for the L12AL16C site. These results indicate that for these systems one cannot simply assign a “4-coordinate structure” and assume certain physical properties for that site since important factors such as packing of the adjacent Leu, size of the intended cavity (endo vs exo) and location of the metal site play crucial roles in determining the final properties of the bound Cd(II).
doi:10.1021/ja104433n
PMCID: PMC3149768  PMID: 21162521
9.  Development of a New Type of Prolonged Release Hydrocodone Formulation Based on Egalet® ADPREM Technology Using In Vivo–In Vitro Correlation 
Pharmaceutics  2011;3(1):73-87.
A novel abuse deterrent, prolonged release tablet formulation of Hydrocodone for once-daily dosing has been developed, based on the novel proprietary Egalet® ADPREM technology. The tablet is an injection molded polymer system consisting of an erodible matrix in which the Active Pharmaceutical Ingredient (API), such as Hydrocodone, is dispersed. The matrix is partly covered with a water-impermeable, non-erodible shell which leaves both ends of the cylindrical tablet exposed to erosion by the gastrointestinal (GI) fluid. In vivo–in vitro correlation (IVIVC) was initiated and validated with three formulations. A good internal predictability was observed for the three formulations. How the changing conditions in the GI tract influenced in vivo performance of an erosion based product was discussed. The validated IVIVC could be used to optimize the tablet formulation and to obtain a desired profile. In addition, this technique could help to establish the dissolution limits in which a certainty of bioequivalence is calculated. Based on this validated level A IVIVC, dissolution can be used as surrogate of bioequivalence for development, but also scale up post approval changes.
doi:10.3390/pharmaceutics3010073
PMCID: PMC3857038  PMID: 24310426
hydrocodone; controlled release; opioid; pain management; IVIVC; dissolution; Abuse Deterrent Erodible Matrix technology; oral solid dosage form
10.  Design of Thiolate Rich Metal Binding Sites within a Peptidic Framework 
Inorganic chemistry  2008;47(23):10875-10888.
A de novo protein design strategy provides a powerful tool to elucidate how heavy metals interact with proteins. Cysteine derivatives of the TRI peptide family (Ac-G(LKALEEK)4G-NH2) have been shown to bind heavy metals in an unusual trigonal geometry. Our present objective was to design binding sites in α-helical scaffolds that are able to form higher coordination number complexes with Cd(II) and Hg(II). Herein, we evaluate the binding of Cd(II) and Hg(II) to double cysteine substituted TRI peptides lacking intervening leucines between sulfurs in the heptads. We compare a -Cysd-X-X-X-Cysa- binding motif found in TRIL12CL16C to the more common -Cysa-X-X-Cysd- sequence of native proteins found in TRIL9CL12C. Compared to TRI, these substitutions destabilize the helical aggregates, leading to mixtures of two and three stranded bundles. The three stranded coiled coils are stabilized by the addition of metals. TRIL9CL12C forms distorted tetrahedral complexes with both Cd(II) and Hg(II), as supported by UV-vis, CD, 113Cd NMR, 199Hg NMR and 111mCd PAC spectroscopy. Additionally, these signatures are very similar to those found for heavy metal substituted rubredoxin. These results suggest that in terms of Hg(II) binding, TRIL9CL12C can be considered as a good mimic of the metallochaperone HAH1, that has previously been shown to form protein dimers. TRIL12CL16C has limited ability to generate homoleptic tetrahedral complexes (Cd(SR)42−). These type of complexes were identified only for Hg(II). However, the spectroscopic signatures suggest a different geometry around the metal ion, demonstrating that effective metal sequestration into the hydrophobic interior of the bundle requires more than simply adding two sulfur residues in adjacent layers of the peptide core. Thus, proper design of metal binding sites must also consider the orientation of cysteine sidechains in a vs d positions of the heptads.
doi:10.1021/ic8009817
PMCID: PMC2650386  PMID: 18959366
11.  Essential Role for Schizosaccharomyces pombe pik1 in Septation 
PLoS ONE  2009;4(7):e6179.
Background
Schizosaccharomyces pombe pik1 encodes a phosphatidylinositol 4-kinase, reported to bind Cdc4, but not Cdc4G107S.
Principal Findings
Gene deletion revealed that pik1 is essential. In cells with pik1 deleted, ectopic expression of a loss-of-function allele, created by fusion to a temperature-sensitive dihydrofolate reductase, allowed normal cell proliferation at 25°C. At 36°C, cells arrested with abnormally thick, misplaced or supernumerary septa, indicating a defect late in septation. In addition to being Golgi associated, ectopically expressed GFP-tagged Pik1 was observed at the medial cell plane late in cytokinesis. New alleles, created by site-directed mutagenesis, were expressed ectopically. Lipid kinase and Cdc4-binding activity assays were performed. Pik1D709A was kinase-dead, but bound Cdc4. Pik1R838A did not bind Cdc4, but was an active kinase. Genomic integration of these substitutions in S. pombe and complementation studies in Saccharomyces cerevisiae pik1-101 cells revealed that D709 is essential in both cases while R838 is dispensable. In S. pombe, ectopic expression of pik1 was dominantly lethal; while, pik1D709A,R838A was innocuous, pik1R838A was almost innocuous, and pik1D709A produced partial lethality and septation defects. The pik1 ectopic expression lethal phenotype was suppressed in cdc4G107S. Thus, D709 is essential for kinase activity and septation.
Conclusions
Pik1 kinase activity is required for septation. The Pik1 R838 residue is required for important protein-protein interactions, possibly with Cdc4.
doi:10.1371/journal.pone.0006179
PMCID: PMC2704394  PMID: 19587793
12.  A CuI-sensing ArsR family Metal Sensor Protein with a Relaxed Metal Selectivity Profile 
Biochemistry  2008;47(40):10564-10575.
ArsR (or ArsR/SmtB) family metalloregulatory homodimeric repressors collectively respond to a wide range of metal ion inducers in regulating homeostasis and resistance of essential and nonessential metal ions in bacteria. BxmR from the cyanobacterium Osciliatoria brevis is the first characterized ArsR protein that senses both CuI/AgI and divalent metals ZnII/CdII in cells by regulating the expression of a P-type ATPase efflux pump (Bxa1) and an intracellular metallothionein (BmtA). We show here that both pairs of predicted α3N and α5 sites bind metal ions, but with distinct physicochemical and functional metal specificities. Inactivation of the thiophilic α3N site via mutation (C77S) abolishes regulation by both CdII and CuI, while ZnII remains a potent allosteric negative effector of operator/promoter binding (ΔGc≥+3.2 kcal mol−1). In contrast, α5 site mutant retains regulation by all four metal ions, albeit with a smaller coupling free energy (ΔGc≈+1.7 (±0.1) kcal mol−1). Unlike the other metals ions, the BxmR dimer binds four mol•equiv CuI to form an α3N binuclear CuI2S4 cluster by x-ray absorption spectroscopy. BxmR is thus distinguishable from other closely-related ArsR family sensors, in having evolved a metalloregulatory α3N site that can adopt an expanded range of coordination chemistries, while maintaining redundancy in the response to ZnII. The evolutionary implications of these findings for the ArsR metal sensor family are discussed.
doi:10.1021/bi801313y
PMCID: PMC2599807  PMID: 18795800
13.  Effect of 1,25-dihydroxy-vitamin D3 in experimental sepsis 
Background: In addition to the regulation of calcium homeostasis, vitamin D affects the cellular immune system, targets the TNF-α pathway and increases vasoconstrictor response to angiotensin II. We therefore examined the effect of 1,25-dihydroxy-vitamin D3 on coagulation and organ failure in experimental sepsis in the rat.
Methods: Three series of placebo-controlled studies were conducted. All rats were pre-treated with daily SC injections of 1,25-dihydroxy-vitamin D3 100 ng/kg or placebo vehicle for 3 days. In study 1, sepsis was accomplished by abdominal surgery comprising a coecal ligation and puncture with a 1,2 mm needle, or sham surgery. In study 2, the rats had a single IP injection of lipopolysaccharide from E. Coli 0111:B4 (LPS) 8 mg/kg, or placebo. In study 3, an hour-long IV infusion of LPS 7 mg/kg, or placebo was given.
Results: All three models of sepsis showed significant effects on coagulation and liver function with reduced thrombocyte count and prothrombin time together with elevated ALT and bilirubin (p<0.05) as compared to controls. In study 1, the vitamin D treated rats maintained normal platelet count, whereas the vehicle treated rats showed a significant reduction (p<0.05). This effect of vitamin D on platelets was not found in the LPS-treated groups. We found no significant differences between vitamin D and placebo-treated rats with regards to liver function.
Conclusion: The present data suggest a positive modulating effect of 1,25-dihydroxy-vitamin D3 supplementation on sepsis-induced coagulation disturbances in the coecal ligation and puncture model. No such effect was found in LPS-induced sepsis.
PMCID: PMC1925152  PMID: 17657282
1; 25 Vitamin D; calcitriol; sepsis; rats; coagulation; thrombocytes
14.  Characterization of Intestinal Microbiota and Response to Dietary Virginiamycin Supplementation in the Broiler Chicken†  
The inclusion of antibiotic growth promoters, such as virginiamycin, at subtherapeutic levels in poultry feeds has a positive effect on health and growth characteristics, possibly due to beneficial effects on the host gastrointestinal microbiota. To improve our understanding of the chicken gastrointestinal microbiota and the effect of virginiamycin on its composition, we characterized the bacteria found in five different gastrointestinal tract locations (duodenal loop, mid-jejunum, proximal ileum, ileocecal junction, and cecum) in 47-day-old chickens that were fed diets excluding or including virginiamycin throughout the production cycle. Ten libraries (five gastrointestinal tract locations from two groups of birds) of approximately 555-bp chaperonin 60 PCR products were prepared, and 10,932 cloned sequences were analyzed. A total of 370 distinct cpn60 sequences were identified, which ranged in frequency of recovery from 1 to 2,872. The small intestinal libraries were dominated by sequences from the Lactobacillales (90% of sequences), while the cecum libraries were more diverse and included members of the Clostridiales (68%), Lactobacillales (25%), and Bacteroidetes (6%). To assess the effects of virginiamycin on the gastrointestinal microbiota, 15 bacterial targets were enumerated using quantitative, real-time PCR. Virginiamycin was associated with increased abundance of many of the targets in the proximal gastrointestinal tract (duodenal loop to proximal ileum), with fewer targets affected in the distal regions (ileocecal junction and cecum). These findings provide improved profiling of the composition of the chicken intestinal microbiota and indicate that microbial responses to virginiamycin are most significant in the proximal small intestine.
doi:10.1128/AEM.72.4.2815-2823.2006
PMCID: PMC1448984  PMID: 16597987
15.  Comparison of Ileum Microflora of Pigs Fed Corn-, Wheat-, or Barley-Based Diets by Chaperonin-60 Sequencing and Quantitative PCR 
We have combined the culture-independent methods of high-throughput sequencing of chaperonin-60 PCR product libraries and quantitative PCR to profile and quantify the small-intestinal microflora of pigs fed diets based on corn, wheat, or barley. A total of 2,751 chaperonin-60 PCR product clones produced from samples of ileum digesta were examined. The majority (81%) of these clones contained sequences independently recovered from all three libraries; 372 different nucleotide sequences were identified, but only 14% of the 372 different sequences were recovered from all three libraries. Taxonomic assignments of the library sequences were made by comparison to a reference database of chaperonin-60 sequences combined with phylogenetic analysis. The taxa identified are consistent with previous reports of pig ileum microflora. Frequencies of each sequence in each library were calculated to identify taxa that varied in frequency between the corn, barley, and wheat libraries. The chaperonin-60 sequence inventory was used as a basis for designing PCR primer sets for taxon-specific quantitative PCR. Results of quantitative PCR analysis of ileum digesta confirmed the relative abundances of targeted taxa identified with the library sequencing approach. The results of this study indicate that chaperonin-60 clone libraries can be valid profiles of complex microbial communities and can be used as the basis for producing quantitative PCR assays to measure the abundance of taxa of interest during experimentally induced or natural changes in a community.
doi:10.1128/AEM.71.2.867-875.2005
PMCID: PMC546709  PMID: 15691942
16.  Impact of Irradiation and Polycyclic Aromatic Hydrocarbon Spiking on Microbial Populations in Marine Sediment for Future Aging and Biodegradability Studies 
Experiments were carried out to develop methods to generate well-characterized, polycyclic aromatic hydrocarbon (PAH)-spiked, aged but minimally altered sediments for fate, biodegradation, and bioavailability experiments. Changes in indigenous bacterial populations were monitored in mesocosms constructed of relatively clean San Diego Bay sediments, with and without exposure to gamma radiation, and then spiked with five different PAHs and hexadecane. While phenanthrene and chrysene degraders were present in the unspiked sediments and increased during handling, PAH spiking of nonirradiated sediments led to dramatic increases in their numbers. Phenotypic characterization of isolates able to grow on phenanthrene or chrysene placed them in several genera of marine bacteria: Vibrio, Marinobacter or Cycloclasticus, Pseudoalteromonas, Marinomonas, and Halomonas. This is the first time that marine PAH degraders have been identified as the latter two genera, expanding the diversity of marine bacteria with this ability. Even at the highest irradiation dose (10 megarads), heterotrophs and endospore formers reappeared within weeks. However, while bacteria from the unirradiated sediments had the capacity to both grow on and mineralize 14C-labeled phenanthrene and chrysene, irradiation prevented the reappearance of PAH degraders for up to 4 months, allowing spikes to age onto the sediments, which can be used to model biodegradation in marine sediments.
doi:10.1128/AEM.68.6.2858-2868.2002
PMCID: PMC123915  PMID: 12039743
17.  Extensive Profiling of a Complex Microbial Community by High-Throughput Sequencing 
Complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. Attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. The availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. Here we describe the application of an established molecular diagnostic method based on the chaperonin-60 sequence, in combination with high-throughput sequencing, to the profiling of a microbial community: the pig intestinal microbial community. Four libraries of cloned cpn60 sequences were generated by two genomic DNA extraction procedures in combination with two PCR protocols. A total of 1,125 cloned cpn60 sequences from the four libraries were sequenced. Among the 1,125 cloned cpn60 sequences, we identified 398 different nucleotide sequences encoding 280 unique peptide sequences. Pairwise comparisons of the 398 unique nucleotide sequences revealed a high degree of sequence diversity within the library. Identification of the likely taxonomic origins of cloned sequences ranged from imprecise, with clones assigned to a taxonomic subclass, to precise, for cloned sequences with 100% DNA sequence identity with a species in our reference database. The compositions of the four libraries were compared and differences related to library construction parameters were observed. Our results indicate that this method is an alternative to 16S rRNA sequence-based studies which can be scaled up for the purpose of performing a potentially comprehensive assessment of a given microbial community or for comparative studies.
doi:10.1128/AEM.68.6.3055-3066.2002
PMCID: PMC123911  PMID: 12039767
18.  Arabidopsis thaliana type I and II chaperonins 
Cell Stress & Chaperones  2001;6(3):190-200.
An examination of the Arabidopsis thaliana genome sequence led to the identification of 29 predicted genes with the potential to encode members of the chaperonin family of chaperones (CPN60 and CCT), their associated cochaperonins, and the cytoplasmic chaperonin cofactor prefoldin. These comprise the first complete set of plant chaperonin protein sequences and indicate that the CPN family is more diverse than previously described. In addition to surprising sequence diversity within CPN subclasses, the genomic data also suggest the existence of previously undescribed family members, including a 10-kDa chloroplast cochaperonin. Consideration of the sequence data described in this review prompts questions about the complexities of plant CPN systems and the evolutionary relationships and functions of the component proteins, most of which have not been studied experimentally.
PMCID: PMC434400  PMID: 11599560
19.  Streptococcus suis Serotypes Characterized by Analysis of Chaperonin 60 Gene Sequences 
Applied and Environmental Microbiology  2001;67(10):4828-4833.
Streptococcus suis is an important pathogen of swine which occasionally infects humans as well. There are 35 serotypes known for this organism, and it would be desirable to develop rapid methods methods to identify and differentiate the strains of this species. To that effect, partial chaperonin 60 gene sequences were determined for the 35 serotype reference strains of S. suis. Analysis of a pairwise distance matrix showed that the distances ranged from 0 to 0.275 when values were calculated by the maximum-likelihood method. For five of the strains the distances from serotype 1 were greater than 0.1, and for two of these strains the distances were were more than 0.25, suggesting that they belong to a different species. Most of the nucleotide differences were silent; alignment of protein sequences showed that there were only 11 distinct sequences for the 35 strains under study. The chaperonin 60 gene phylogenetic tree was similar to the previously published tree based on 16S rRNA sequences, and it was also observed that strains with identical chaperonin 60 gene sequences tended to have identical 16S rRNA sequences. The chaperonin 60 gene sequences provided a higher level of discrimination between serotypes than the 16S RNA sequences provided and could form the basis for a diagnostic protocol.
doi:10.1128/AEM.67.10.4828-4833.2001
PMCID: PMC93237  PMID: 11571190
20.  Simultaneous identification of GSTP1 Ile105→Val105 and Ala114→Val114 substitutions using an amplification refractory mutation systempolymerase chain reactionassay: studies in patients with asthma 
Respiratory Research  2001;2(4):255-260.
Background
The glutathione S-transferase (GST) enzyme GSTP1 utilizes byproducts of oxidative stress. We previously showed that alleles of GSTP1 that encode the Ile105→Val105 substitution are associated with the asthma phenotypes of atopy and bronchial hyperresponsiveness (BHR). However, a further polymorphic site (Ala114→Val114) has been identified that results in the following alleles: GSTP1*A (wild-type Ile105→Ala114), GSTP1*B (Val105→Ala114), GSTP1*C (Val105→Val114) and GSTP1*D (Ile105→Val114).
Methods
Because full identification of GSTP1 alleles may identify stronger links with asthma phenotypes, we describe an amplification refractory mutation system (ARMS) assay that allows identification of all genotypes. We explored whether the GSTP1 substitutions influence susceptibility to asthma, atopy and BHR.
Results
Among 191 atopic nonasthmatic, atopic asthmatic and nonatopic nonasthmatic individuals, none had the BD, CD, or DD genotypes. GSTP1 BC was significantly associated with reduced risk for atopy (P = 0.031). Compared with AA, trend test analysis identified a significant decrease in the frequency of GSTP1 BC with increasing severity of BHR (P = 0.031). Similarly, the frequency of GSTP1 AA increased with increasing BHR.
Conclusion
These data suggest that GSTP1*B and possibly GSTP1*C are protective against asthma and related phenotypes.
doi:10.1186/rr64
PMCID: PMC56208  PMID: 11686891
amplification refractory mutation system; asthma; bronchial hyperresponsiveness; GSTP1
21.  Identification of Enterococcus Species and Phenotypically Similar Lactococcus and Vagococcus Species by Reverse Checkerboard Hybridization to Chaperonin 60 Gene Sequences 
Journal of Clinical Microbiology  2000;38(11):3953-3959.
Data from four recent studies (S. H. Goh et al., J. Clin. Microbiol. 36:2164–2166, 1998; S. H. Goh et al., J. Clin. Microbiol. 34:818–823, 1996; S. H. Goh et al., J. Clin. Microbiol. 35:3116–3121, 1997; A. Y. C. Kwok et al., Int. J. Syst. Bacteriol. 49:1181–1192, 1999) suggest that an approximately 600-bp region of the chaperonin 60 (Cpn60) gene, amplified by PCR with a single pair of degenerate primers, has utility as a potentially universal target for bacterial identification (ID). This Cpn60 gene ID method correctly identified isolates representative of numerous staphylococcal species and Streptococcus iniae, a human and animal pathogen. We report herein that this method enabled us to distinguish clearly between 17 Enterococcus species (Enterococcus asini, Enterococcus rattus, Enterococcus dispar, Enterococcus gallinarum, Enterococcus hirae, Enterococcus durans, Enterococcus cecorum, Enterococcus faecalis, Enterococcus mundtii, Enterococcus casseliflavus, Enterococcus faecium, Enterococcus malodoratus, Enterococcus raffinosus, Enterococcus avium, Enterococcus pseudoavium, Enterococcus new sp. strain Facklam, and Enterococcus saccharolyticus), and Vagococcus fluvialis, Lactococcus lactis, and Lactococcus garvieae. From 123 blind-tested samples, only two discrepancies were observed between the Facklam and Collins phenotyping method (R. R. Facklam and M. D. Collins, J. Clin. Microbiol. 27:731–734, 1989) and the Cpn60 ID method. In each case, the discrepancies were resolved in favor of the Cpn60 ID method. The species distributions of the 123 blind-tested isolates were Enterococcus new sp. strain Facklam (ATCC 700913), 3; E. asini, 1; E. rattus, 4; E. dispar, 2; E. gallinarum, 20; E. hirae, 9; E. durans, 9; E. faecalis, 12; E. mundtii, 3; E. casseliflavus, 8; E. faecium, 25; E. malodoratus, 3; E. raffinosus, 8; E. avium, 4; E. pseudoavium, 1; an unknown Enterococcus clinical isolate, sp. strain R871; Vagococcus fluvialis, 4; Lactococcus garvieae, 3; Lactococcus lactis, 3; Leuconostoc sp., 1; and Pediococcus sp., 1. The Cpn60 gene ID method, coupled with reverse checkerboard hybridization, is an effective method for the identification of Enterococcus and related organisms.
PMCID: PMC87524  PMID: 11060051
22.  Streptococcus iniae, a Human and Animal Pathogen: Specific Identification by the Chaperonin 60 Gene Identification Method 
Journal of Clinical Microbiology  1998;36(7):2164-2166.
It was recently reported that Streptococcus iniae, a bacterial pathogen of aquatic animals, can cause serious disease in humans. Using the chaperonin 60 (Cpn60) gene identification method with reverse checkerboard hybridization and chemiluminescent detection, we identified correctly each of 12 S. iniae samples among 34 aerobic gram-positive isolates from animal and clinical human sources.
PMCID: PMC105023  PMID: 9650992
23.  Identification of Staphylococcus species and subspecies by the chaperonin 60 gene identification method and reverse checkerboard hybridization. 
Journal of Clinical Microbiology  1997;35(12):3116-3121.
A previous study (S. H. Goh et al., J. Clin. Microbiol. 34:818-823, 1996) demonstrated that a 600-bp region of the chaperonin 60 (Cpn60) genes from various bacterial isolates could be amplified by PCR with a pair of degenerate primers and that the products could be used as species-specific probes for Staphylococcus aureus, S. epidermidis, S. haemolyticus, S. lugdunensis, S. saprophyticus, and S. schleiferi. To further validate the utility of bacterial Cpn60 genes as universal targets for bacterial identification (ID), reverse checkerboard chemiluminescent hybridization experiments were performed with DNA probes from 34 different Staphylococcus species and subspecies. With the exception of probes from the Cpn60 genes of S. intermedius and S. delphini, which cross hybridized, all were species specific. Two subspecies of both S. capitis and S. cohnii were differentiated from one another, while DNAs from the two S. schleiferi subspecies cross hybridized. When 40 known Staphylococcus isolates were tested in a blind experiment by the Cpn60 gene method, 36 strains, representing six species and one subspecies (S. sciuri, S. caseolyticus, S. hominis, S. warneri, S. hyicus, S. haemolyticus, and S. capitis subsp. ureolyticus), were correctly identified. DNA from the four remaining isolates, known to be S. hyicus bovine strains, failed to hybridize to DNA from the S. hyicus target strain or any other Staphylococcus species. However, DNAs from these S. hyicus isolates did cross hybridize with each other. New DNA sequence data and evidence from previous studies suggest some genetic divergence between the two groups of S. hyicus isolates. Our results demonstrate that this Cpn60 gene-based ID method has the potential to be a basic method for bacterial ID. Studies are in progress to further validate the utility of this Cpn60 gene system for ID of Staphylococcus and other genera, including those of slow-growing microorganisms.
PMCID: PMC230133  PMID: 9399505
24.  HSP60 gene sequences as universal targets for microbial species identification: studies with coagulase-negative staphylococci. 
Journal of Clinical Microbiology  1996;34(4):818-823.
A set of universal degenerate primers which amplified, by PCR, a 600-bp oligomer encoding a portion of the 60-kDa heat shock protein (HSP60) of both Staphylococcus aureus and Staphylococcus epidermidis were developed. However, when used as a DNA probe, the 600-bp PCR product generated from S. epidermidis failed to cross-hybridize under high-stringency conditions with the genomic DNA of S. aureus and vice versa. To investigate whether species-specific sequences might exist within the highly conserved HSP60 genes among different staphylococci, digoxigenin-labelled HSP60 probes generated by the degenerate HSP60 primers were prepared from the six most commonly isolated Staphylococcus species (S. aureus 8325-4, S. epidermidis 9759, S. haemolyticus ATCC 29970, S. schleiferi ATCC 43808, S. saprophyticus KL122, and S. lugdunensis CRSN 850412). These probes were used for dot blot hybridization with genomic DNA of 58 reference and clinical isolates of Staphylococcus and non-Staphylococcus species. These six Staphylococcus species HSP60 probes correctly identified the entire set of staphylococcal isolates. The species specificity of these HSP60 probes was further demonstrated by dot blot hybridization with PCR-amplified DNA from mixed cultures of different Staphylococcus species and by the partial DNA sequences of these probes. In addition, sequence homology searches of the NCBI BLAST databases with these partial HSP60 DNA sequences yielded the highest matching scores for both S. epidermidis and S. aureus with the corresponding species-specified probes. Finally, the HSP60 degenerate primers were shown to amplify an anticipated 600-bp PCR product from all 29 Staphylococcus species and from all but 2 of 30 other microbial species, including various gram-positive and gram-negative bacteria, mycobacteria, and fungi. These preliminary data suggest the presence of species-specific sequence variation within the highly conserved HSP60 genes of staphylococci. Further work is required to determine whether these degenerate HSP60 primers may be exploited for species-specific microbic identification and phylogenetic investigation of staphylococci and perhaps other microorganisms in general.
PMCID: PMC228899  PMID: 8815090
25.  Enumeration of phenanthrene-degrading bacteria by an overlayer technique and its use in evaluation of petroleum-contaminated sites. 
Bacteria that are capable of degrading polycyclic aromatic hydrocarbons were enumerated by incorporating soil and water dilutions together with fine particles of phenanthrene, a polycyclic aromatic hydrocarbon, into an agarose overlayer and pouring the mixture over a mineral salts underlayer. The phenanthrene-degrading bacteria embedded in the overlayer were recognized by a halo of clearing in the opaque phenanthrene layer. Diesel fuel- or creosote-contaminated soil and water that were undergoing bioremediation contained 6 x 10(6) to 100 x 10(6) phenanthrene-degrading bacteria per g and ca. 5 x 10(5) phenanthrene-degrading bacteria per ml, respectively, whereas samples from untreated polluted sites contained substantially lower numbers. Unpolluted soil and water contained no detectable phenanthrene degraders (desert soil) or only very modest numbers of these organisms (garden soil, municipal reservoir water).
PMCID: PMC195824  PMID: 1514804

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