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PubMed2006

Urban aerosols harbor diverse and dynamic bacterial populations.

Considering the importance of its potential implications for human health, agricultural productivity, and ecosystem stability, surprisingly little is known regarding the composition or dynamics of the atmosphere's microbial inhabitants. Using a custom high-density DNA microarray, we detected and monitored bacterial populations in two U.S. cities over 17 weeks. These urban aerosols contained at least 1,800 diverse bacterial types, a richness approaching that of some soil bacterial communities. We also reveal the consistent presence of bacterial families with pathogenic members including environmental relatives of select agents of bioterrorism significance. Finally, using multivariate regression techniques, we demonstrate that temporal and meteorological influences can be stronger factors than location in shaping the biological composition of the air we breathe.

Aerosols↗
PubMed2003

Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment.

Bacterial communication via quorum sensing (QS) has been reported to be important in the production of virulence factors, antibiotic sensitivity, and biofilm development. Two QS systems, known as the las and rhl systems, have been identified previously in the opportunistic pathogen Pseudomonas aeruginosa. High-density oligonucleotide microarrays for the P. aeruginosa PAO1 genome were used to investigate global gene expression patterns modulated by QS regulons. In the initial experiments we focused on identifying las and/or rhl QS-regulated genes using a QS signal generation-deficient mutant (PAO-JP2) that was cultured with and without added exogenous autoinducers [N-(3-oxododecanoyl) homoserine lactone and N-butyryl homoserine lactone]. Conservatively, 616 genes showed statistically significant differential expression (P </= 0.05) in response to the exogenous autoinducers and were classified as QS regulated. A total of 244 genes were identified as being QS regulated at the mid-logarithmic phase, and 450 genes were identified as being QS regulated at the early stationary phase. Most of the previously reported QS-promoted genes were confirmed, and a large number of additional QS-promoted genes were identified. Importantly, 222 genes were identified as being QS repressed. Environmental factors, such as medium composition and oxygen availability, eliminated detection of transcripts of many genes that were identified as being QS regulated.

4-Butyrolactone↗
PubMed2002

Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition.

Bacterivorous protists are known to induce changes in bacterial community composition (BCC). We hypothesized that changes in BCC could be related quantitatively to a measure of grazing: the ratio of bacterial mortality to growth rate. To test this hypothesis, we analyzed time-course changes in BCC, protistan grazing rate, and bacterial production from 3 in situ studies conducted in a freshwater reservoir and three laboratory studies. In the field experiments, samples were manipulated to yield different levels of protistan bacterivory and incubated in dialysis bags. Laboratory investigations were continuous cultivation studies in which different bacterivorous protists were added to bacterial communities. BCC was assessed using 4-6 different rRNA-targeted oligonucleotide probes for community analysis. Change in BCC (delta BCC) was estimated as the sum of changes in the proportions of the two phylogenetic groups that showed the largest shifts. Analysis of a set of 22 estimates of shifts in the ratio of grazing to production rate over periods of 48-72 h and A BCC showed that delta BCC was positively and tightly correlated (r2 = 0.784) with shifts in the ratio of grazing mortality to cell production. While the nature of a shift in BCC is unpredictable, the magnitude of the change can be related to changes in the balance between bacterial production and protistan grazing. bacterial community composition

Animals↗
PubMed1992

Extraction and partial characterization of non-histone nuclear proteins of Schistosoma mansoni.

A pool of nuclear proteins from adult worms of Schistosoma mansoni was analyzed for amino acid composition and found to be compatible with high mobility group (HMG) proteins. One of the schistosome HMG proteins was identified as HMG 2 by one-dimensional and two-dimensional PAGE. Stage-specific differences in the HMG-like protein composition were encountered when adult worms were compared to schistosomula, the larval form. Immobilization of the adult male and female nuclear proteins onto nitrocellulose, followed by hybridization against 32P-F-10, a schistosome sex specific gene encoding a major egg shell protein, revealed distinct banding patterns. On the other hand, a synthetic oligonucleotide, derived from the 3' untranslated end of the F-10 gene and possibly containing one regulatory element of the gene, bound mainly to male low MW proteins.

Aging↗
PubMed2005

Differentially expressed cortical genes contribute to perivascular deposition in transgenic mice with inducible neuron-specific expression of TGF-beta1.

In the brain the expression of transforming growth factor beta1 (TGF-beta1) is involved both in neuroprotective and neurodegenerative processes. Recently, we have established a transgenic mouse model with inducible neuron-specific expression of TGF-beta1 based on the tetracycline-regulated gene expression system. A long-term expression of TGF-beta1 results in persisting perivascular thioflavin-positive depositions, which did not disappear even though the transgene synthesis was repressed completely by administration of doxycycline. Formation and composition of these depositions are hardly elucidated. The aim of this study was to identify TGF-beta1 responding genes potentially participating in forming these depositions. To address this problem we have compared the cortical mRNA expression pattern of TGF-beta1 expressing mice with mice impeded to express the transgenic protein using oligonucleotide microarray analysis. Differential gene expression was further characterized by quantitative real-time reverse transcription-polymerase chain reaction including animals, where the long-lasting TGF-beta1 expression was repressed. While no change of amyloid precursor protein RNA expression level was detected, various genes strongly involved in calcium homeostasis, tissue mineralization or vascular calcification were identified differentially expressed. It is suggested, that these genes might contribute to the perivascular depositions in the TGF-beta1 expressing mice.

Animals↗
PubMed2004

Isolation, properties and partial amino acid sequence of a new actinoporin from the sea anemone Radianthus macrodactylus.

A new cytolytic toxin, actinoporin RTX-S II, was isolated from the sea anemone Radianthus macrodactylus with a high degree of purity by a combination of gel filtration, ion-exchange and reverse-phase chromatography. RTX-S II has molecular mass of 19,280 Da and isoelectric point of 10.0. The hemolytic activity of RTX-S II is inhibited by sphingomyelin. RTX-S II had an LD(50) of 70 mg/kg, and is lacking in phospholipase activity. The amino acid composition of this protein contains a high amount of basic and non-polar amino acids and no cysteine. The N-terminal sequence of RTX-S II was determined. The partial amino acid sequence (141 aa) of RTX-S II was deduced based on the cDNA sequence obtained with two oligonucleotides encoding the N-terminal portion of RTX-S II and the internal conserved cytolysin peptide by PCR. A comparison of the RTX-S II cDNA sequence and the rtx-s II gene obtained with the same PCR primers indicates that they are 100% identical at the nucleotide level. It shows that no introns are present in the corresponding region of the rtx-s II gene. Multiple alignments of RTX-S II with known sequences of actinoporins show that RTX-S II is highly homologous to magnificalysin II from Heteractis magnifica. The predicted secondary structure of RTX-S II is predominantly anti-parallel beta-structure, which is in good agreement with experimental data obtained from other sea anemones-actinoporins.

Amino Acid Sequence↗
PubMed2003

The signature of selection mediated by expression on human genes.

As the efficacy of natural selection is expected to be a function of population size, in humans it is usually presumed that selection is a weak force and hence that gene characteristics are mostly determined by stochastic forces. In contrast, in species with large population sizes, selection is expected to be a much more effective force. Evidence for this has come from examining how genic parameters vary with expression level, which appears to determine many of a gene's features, such as codon bias, amino acid composition, and size. However, not until now has it been possible to examine whether human genes show the signature of selection mediated by expression level. Here, then, to investigate this issue, we gathered expression data for >10,000 human genes from public data sets obtained by different technologies (SAGE and high-density oligonucleotide chip arrays) and compared them with gene parameters. We find that, even after controlling for regional effects, highly expressed genes code for smaller proteins, have less intronic DNA, and higher codon and amino acid biases. We conclude that, contrary to the usual supposition, human genes show signatures consistent with selection mediated by expression level.

Chromosome Mapping↗
PubMed2005

Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease.

The composition and spatial organization of the mucosal flora in biopsy specimens from patients with inflammatory bowel disease (IBD; either Crohn's disease or ulcerative colitis), self-limiting colitis, irritable-bowel syndrome (IBS), and healthy controls were investigated by using a broad range of fluorescent bacterial group-specific rRNA-targeted oligonucleotide probes. Each group included 20 subjects. Ten patients who had IBD and who were being treated with antibiotics were also studied. Use of nonaqueous Carnoy fixative to preserve the mucus layer was crucial for detection of bacteria adherent to the mucosal surface (mucosal bacteria). No biofilm was detectable in formalin-fixed biopsy specimens. Mucosal bacteria were found at concentrations greater than 10(9)/ml in 90 to 95% of IBD patients, 95% of patients with self-limiting colitis, 65% of IBS patients, and 35% of healthy controls. The mean density of the mucosal biofilm was 2 powers higher in IBD patients than in patients with IBS or controls, and bacteria were mostly adherent. Bacteroides fragilis was responsible for >60% of the biofilm mass in patients with IBD but for only 30% of the biofilm mass in patients with self-limiting colitis and <15% of the biofilm mass in patients with IBS. In contrast, bacteria which positively hybridized with the probe specific for Eubacterium rectale-Clostridium coccoides accounted for >40% of the biofilm in IBS patients but for <15% of the biofilm in IBD patients. In patients treated with (5-ASA) or antibiotics, the biofilm could be detected with 4,6-diamidino-2-phenylindole but did not hybridize with fluorescence in situ hybridization probes. A Bacteroides fragilis biofilm is the main feature of IBD. This was not previously recognized due to a lack of appropriate tissue fixation. Both 5-ASA and antibiotics suppress but do not eliminate the adherent biofilm.

Adult↗
PubMed2004

[Determination of antisense phosphorothioate oligonucleotide drug Cantide by capillary gel electrophoresis].

Cantide is a 20-mer antisense phosphorothioate oligonucleotide that inhibits telomerase catalytic subunit hTERT. A capillary gel electrophoresis (CGE) method with internal standard was used for the determination of Cantide. Cantide and the phosphorothioate internal standard were prepared on a solid-phase DNA synthesizer and purified by preparative strong anion-exchange chromatography and reversed-phase high performance liquid chromatography. Cantide and the internal standard had approximately equal percentage of base composition. Cantide was determined with capillary electrophoresis instrument and ssDNA kit. The size of the capillary column was 31 cm x 100 microm i.d. with an effective length of 20 cm. Samples were electrokinetically injected using -10 kV voltage for a duration of 1 s. The column temperature and sample storage temperature was 40 degrees C and 30 degrees C, respectively. The detection wavelength was 254 nm. The running buffer was a mixture of 7 mol/L urea-tris-boric acid (pH 8.5). The calibration curve was linear in the range of 12.5-800 mg/L with correlation coefficient of 0.99997. The limit of detection of Cantide was 0.220 mg/L. Intra-day and inter-day relative standard deviations (RSDs) for Cantide were 0.449%-1.89%, and 1.01%-1.48%, respectively. The average recovery was 96.95% with RSD of 6.88%. The assay validation study and the characterization of CGE revealed that the method can be used in quantitative analysis of Cantide for pharmacokinetic characterization, and the results are accurate and reproducible.

Chromatography, High Pressure Liquid↗
PubMed1997

Pharmacokinetics and tissue distribution of a DNA-methyltransferase antisense (MT-AS) oligonucleotide and its catabolites in tumor-bearing nude mice.

The pharmacokinetics of a 20-mer phosphorothioate antisense oligodeoxynucleotide was investigated in nude mice bearing a s.c. human lung carcinoma. The oligodeoxynucleotide, referred to as DNA-methyltransferase antisense (MT-AS) was designed to bind to the mRNA that coded for DNA-methyltransferase, an enzyme that controls the extent of methylation of 5'-cytosine. MT-AS was administered at four different doses (10, 30, 100 and 300 mg/kg) as an i.v. bolus in a composite study design. A maximum of four blood samples were collected from any single animal, followed by sacrifice to obtain tissues. The plasma and tissue samples were collected from 5 min to 48 h after dosing and were processed by anion-exchange HPLC (high performance liquid chromatography) and by capillary gel electrophoresis. On the basis of total (i.e., 15-mer to 20-mer species) MT-AS plasma concentrations as determined by HPLC, total clearance ranged from 7.9 ml/min/kg at the 30-mg/kg dose level to 15.2 ml/min/kg at 10 mg/kg; however, there were no definitive dose-dependent changes in clearance. The volume of distribution at steady state increased from a low value of 379 ml/kg at 30 mg/kg to a high of 1983.0 ml/kg at 300 mg/kg, a result that suggests saturable protein binding. In vitro plasma protein binding data supported this possibility, because the percentage of MT-AS bound decreased at high MT-AS concentrations. MT-AS distributed into most tissues, with a general rank order of kidney > liver > tumor > lung > muscle > brain. Analysis of plasma samples by capillary gel electrophoresis from 2 h to 8 h revealed that about 50% of the total oligodeoxynucleotides were due to the parent 20-mer MT-AS; the remainder consisted of 15-mer to 19-mer catabolites. Of particular interest was the relatively high tumor uptake of MT-AS. These results will support future studies designed to characterize the pharmacological action of MT-AS and its efficacy in preclinical models.

Animals↗
PubMed1998

The stability of duplexes involving AT and/or G4EtC base pairs is not dependent on their AT/G4EtC ratio content. Implication for DNA sequencing by hybridization.

Sequencing by the recently reported hybridization technique requires the formation of DNA duplexes with similar stabilities. In this paper we describe a new strategy to obtain DNA duplexes with a thermal stability independent of their AT/GC ratio content. Melting data were acquired on 35 natural and 27 modified duplexes of a given length and of varying base compositions. Duplexes built with AT and/or G4EtC base pairs exhibit a thermal stability restrained to a lower range of temperature than that of the corresponding natural compounds (16 instead of 51 degrees C). The 16 degrees C difference in thermal stability observed between the least stable and the most stable duplex built with AT and/or G4EtC base pairs is mainly due to the sequence effect and not to their AT/G4EtC ratio content. Thus N -4-ethyl-2'-deoxycytidine (d4EtC) hybridizes specifically with natural deoxyguanosine leading to a G4EtC base pair whose stability is very close to that of the natural AT base pair. Oligonucleotide probes involving d4EtC can be easily prepared by chemical synthesis with phosphoramidite chemistry. Modified DNA targets were successfully amplified by random priming or PCR techniques using d4EtCTP, dATP, dGTP and dTTP in the presence of DNA polymerase. This new system might be very useful for DNA sequencing by hybridization.

Adenine↗
PubMed2002

Unique condensation patterns of triplex DNA: physical aspects and physiological implications.

Triple-stranded DNA structures can be formed in living cells, either by native DNA sequences or following the application of antigene strategies, in which triplex-forming oligonucleotides are targeted to the nucleus. Recent studies imply that triplex motifs may play a role in DNA transcription, recombination and condensation processes in vivo. Here we show that very short triple-stranded DNA motifs, but not double-stranded segments of a comparable length, self-assemble into highly condensed and ordered structures. The condensation process, studied by circular dichroism and polarized-light microscopy, occurs under conditions that mimic cellular environments in terms of ionic strength, ionic composition and crowding. We argue that the unique tendency of triplex DNA structures to self-assemble, a priori unexpected in light of the very short length and the large charge density of these motifs, reflects the presence of strong attractive interactions that result from enhanced ion correlations. The results provide, as such, a direct experimental link between charge density, attractive interactions between like-charge polymers and DNA packaging. Moreover, the observations strongly support the notion that triple-stranded DNA motifs may be involved in the regulation of chromosome organization in living cells.

Chromosomes↗
PubMed2001

Changes in the Epilimnetic Bacterial Community Composition, Production, and Protist-Induced Mortality along the Longitudinal Axis of a Highly Eutrophic Reservoir.

We studied changes in the epilimnetic bacterial community composition (BCC), bacterial biomass and production, and protistan succession and bacterivory along the longitudinal axis of the canyon-shaped, highly eutrophic Sau Reservoir (NE Spain) during two sampling campaigns, in April and July 1997. Longitudinal changes in BCC from the river inflow to the dam area of the reservoir were detected by using oligonucleotide probes targeted to the kingdom Bacteria, to the alpha, beta, and gamma subclasses (ALFA, BETA, and GAMA) of the class Proteobacteria, and to the Cytophaga/Flavobacterium (CF) cluster. In general, the inflow of the organically loaded Ter river, with highly abundant allochthonous bacterial populations, induced a clearly distinguishable longitudinal succession of the structure of the microbial food web. The most dynamic changes in microbial parameters occurred at the plunge point, the mixing area of river water and the reservoir epilimnion. Changes within members of BETA and CF were the most important in determining changes in BCC, bacterial abundance and biomass. Much less relevant changes occurred within the less abundant ALFA and GAMA bacteria. From the plunge point downstream, we described a significant shift in BCC in the form of decreased proportions of BETA and CF. This shift spatially coincided with the highest values of heterotrophic nanoflagellate bacterivory (roughly doubled the bacterial production). CF numerically dominated throughout the reservoir without any marked longitudinal changes in their mean cell volume. In contrast, very large cells affiliated to BETA clearly dominated in the allochthonous bacterial biomass brought by the river. BETA showed a marked downstream trend of decreasing mean cell volume. We conclude that the observed BCC shift and the longitudinal shift in food web structure (bacteria-heterotrophic nanoflagellates-ciliates) resulted from highly complex interactions brought about by several major factors: varying hydrology, the high localized allochthonous input of organic matter brought by the river, downstream changing substrate availability, and selective protistan bacterivory.

Journal Article↗
PubMed1980

Nucleotide sequence heterogeneity of the RNA from a natural population of foot-and-mouth-disease virus.

The genomic RNA from isolates of foot-and-mouth-disease virus (FMDV) of serological types O or C obtained during epizootic outbreaks have been analysed by two-dimensional gel electrophoresis of the T1 RNase-generated oligonucleotides (T1 fingerprinting). Among virus isolates that are closely related serologically, 4-12 oligonucleotide changes were detected constitute the genome, the variations affect 0.7%-2.2% positions in FMDV RNA. Higher nucleotide-sequence divergence exists between the genomic RNAs from serologically unrelated viruses, while a 100-fold lower RNA sequence heterogeneity has been detected by analysis of individual clones derived from one viral isolate. Oligonucleotide mapping indicates that the variant oligonucleotides are scattered throughout the FMDV genome. We suggest that extensive genetic variability at many RNA sites is the basis for the antigenic diversity of FMDV.

Antigens, Viral↗
PubMed1993

Structure and thermodynamics of nonalternating C.G base pairs in Z-DNA: the 1.3-A crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG).d(m5CGCCm5CG).

We have solved the single-crystal X-ray structure of the complementary hexanucleotides d(m5-CGGGm5CG) and d(m5CGCCm5CG). The hexamer duplex was crystallized as Z-DNA, but contains a single C.G base pair that does not follow the alternating pyrimidine/purine rule for Z-DNA formation. This is the first crystal structure which serves to illustrate the structural consequences of placing a cytosine in the sterically disfavored syn conformation. In addition, since these sequences are not self-complementary, the individual strands of this asymmetric hexamer are unique in sequence and therefore distinguishable in the crystal lattice. Nevertheless, the crystal of this duplex is isomorphous with other Z-DNA hexamer structures. The asymmetry of this hexamer sequence required that the structure be solved using two unique models, which are distinguished by the orientation of hexanucleotides in the crystal lattice. In one model (the GG model) the cytosine in the syn conformation is packed against the terminal guanine base of a symmetry-related hexamer, while in the alternative model (the CC model) this cytosine sits exposed in a solvent channel of the lattice. We find that neither model alone can completely account for the observed electron densities. The two models ultimately were refined together. A composite structure consisting of 65% GG model and 35% CC model refined to an R-factor of 19.3%, which was significantly lower than refinements using either model alone. A detailed analysis of these two structures shows that, in spite of the out-of-alternation C.G base pair, the features characteristic of Z-DNA have been maintained. Both models, however, show significant local structural adjustments to accommodate the single cytosine base which is forced to adopt the syn conformation in each hexamer. In general, it appears that in order to relieve the energetically unfavorable steric contacts between the cytosine base in the syn conformation and the deoxyribose sugar, the base is forced into a highly buckled conformation, and that this large buckle in turn alters the conformation of neighboring residues. This unusual conformation also significantly weakens base-stacking interactions between the cytosine in syn and the adjacent residues in the helix and affects the exposure of the bases to solvent. We conclude that this crystal structure provides a molecular rationale for why nonalternating bases are energetically disfavored in Z-DNA.

Base Composition↗
PubMed1985

Analysis of products formed during bleomycin-mediated DNA degradation.

By the use of DNA, copolymers of defined nucleotide composition, and a synthetic dodecanucleotide having putative bleomycin cleavage sites in proximity to the 5'- and 3'-termini, the products formed concomitant with DNA strand scission have been isolated and subjected to structural identification and quantitation via direct comparison with authentic synthetic samples. The products of DNA strand scission by Fe(II)-bleomycin include oligonucleotides having each of the four possible nucleoside 3'-(phosphoro-2''-O-glycolates) at their 3'-termini, as well as the four possible base propenals. At least for 3-(adenin-9'-yl)propenal and 3-(thymin-1'-yl)propenal, the products formed were exclusively of the trans configuration.

Base Sequence↗
PubMed1990

Polarity of annealing and structural analysis of the RNase H resistant alpha-5'-d[TACACA].beta-5'-r[AUGUGU] hybrid determined by high-field 1H, 13C, and 31P NMR analysis.

The novel hybrid duplex alpha-5'-d[TACACA]-3'.beta-5'-r[AUGUGU]-3' was analyzed extensively by 1D and 2D NMR methods. Two forms of the duplex exist in about an 80:20 ratio. Analysis of the exchangeable imino protons of the major component revealed that three AU and one AT base pair are present in addition to two GC base pairs, confirming that the duplex anneals in parallel orientation. The presence of the AT base pair, which can only be accounted for by a parallel duplex, was confirmed by a selective INEPT experiment, which correlated the thymidine imino proton to its C5 carbon. The lesser antiparallel form could be detected by exchangeable and nonexchangeable proton resonances in both strands. An exchange peak was observed in the NOESY spectrum for the thymidine methyl group resonance in both the predominant and lesser conformations, indicating the lifetime of the individual structures was on the millisecond time scale. The nonexchangeable protons of the predominant duplex were assigned by standard methods. The sugar pucker of the ribonucleosides was determined to be of the "S" type by a pseudorotation analysis according to Altona, with the J-couplings measured from the multiplet components of the phase-sensitive COSY experiment. The NOE pattern observed for the alpha-deoxynucleosides also suggested an S-type sugar pucker. The adoption of an S-type sugar pucker for both strands indicates that, in contrast to RNA.DNA duplexes formed exclusively from beta-nucleotides, the alpha-DNA.beta-RNA duplex may form a B-type helix. The 31P resonances of the alpha and beta strands have very different chemical shifts in the hybrid duplex and the difference persists above the helix melting temperature, indicating an intrinsic difference in 31P chemical shift for nucleotides differing only in the configuration about the glycosidic bond.

Base Composition↗
PubMed2003

Unified description of electrophoresis and diffusion for DNA and other polyions.

The electrophoretic mobilities and diffusion coefficients of single- and double-stranded DNA molecules up to 50,000 bases or base pairs in size have been analyzed, using mobilities and diffusion coefficients either measured by capillary electrophoresis or taken from the literature. The Einstein equation suggests that the electrophoretic mobilities (mu) and diffusion coefficients (D) should be related by the expression mu/D = Q/k(B)T, where Q is the charge of the polyion (Q = ze(o), where z is the number of charged residues and e(o) is the fundamental electronic charge), k(B) is Boltzmann's constant, and T is the absolute temperature. If this equation were true, the ratio mu/zD should be a constant equal to e(o)/k(B)T (39.6 V(-1)) at 20 degrees C. However, the ratio mu/zD decreases with an increase in molecular weight for both single- and double-stranded DNAs. The mobilities and diffusion coefficients are better described by the modified Einstein equation mu/N(m)D = e(o)/k(B)T, where N is the number of repeat units (bases or base pairs) in the DNA and m is a constant equal to the power law dependence of the diffusion coefficients on molecular weight. The average value of the ratio mu/N(m)D is 40 +/- 4 V(-1) for 36 single- and double-stranded DNA molecules of different sizes, close to the theoretically expected value. The generality of the modified Einstein equation is demonstrated by analyzing literature values for sodium polystyrenesulfonate (PSS). The average value of the ratio mu/N(m)D is 35 +/- 6 V(-1) for 14 PSS samples containing up to 855 monomers.

Base Composition↗