Template-assisted synthesis of adenine-mutagenized cDNA by a retroelement protein complex.

Diversity-generating retroelements (DGRs) create unparalleled levels of protein sequence variation through mutagenic retrohoming. Sequence information is transferred from an invariant template region (TR), through an RNA intermediate, to a protein-coding variable region. Selective infidelity at adenines during transfer is a hallmark of DGRs from disparate bacteria, archaea, and microbial viruses. We recapitulated selective infidelity in vitro for the prototypical Bordetella bacteriophage DGR. A complex of the DGR reverse transcriptase bRT and pentameric accessory variability determinant (Avd) protein along with DGR RNA were necessary and sufficient for synthesis of template-primed, covalently linked RNA-cDNA molecules, as observed in vivo. We identified RNA-cDNA molecules to be branched and most plausibly linked through 2'-5' phosphodiester bonds. Adenine-mutagenesis was intrinsic to the bRT-Avd complex, which displayed unprecedented promiscuity while reverse transcribing adenines of either DGR or non-DGR RNA templates. In contrast, bRT-Avd processivity was strictly dependent on the template, occurring only for the DGR RNA. This restriction was mainly due to a noncoding segment downstream of TR, which specifically bound Avd and created a privileged site for processive polymerization. Restriction to DGR RNA may protect the host genome from damage. These results define the early steps in a novel pathway for massive sequence diversification.

Microbial diversity and composition in different gut locations of hyperlipidemic mice receiving krill oil.

Low-dose (LD, 100 mg kg-1 day-1), moderate-dose (MD, 200 mg kg-1 day-1), and high-dose (HD, 600 mg kg-1 day-1) krill oil treatments have a stepwise, enhanced effect on alleviating hyperlipidemia, and 16S rRNA sequencing of the fecal samples demonstrates that krill oil treatment alters microbial communities. Feces may not represent all microbial communities in the gastrointestinal (GI) tract. Therefore, in this study, the stored ileal and colon samples collected from LD and HD groups were sequenced, and the location-specific modulations of microbial communities were observed after krill oil treatments. The 16S rRNA sequencing of the ileal samples showed that the LD and HD groups have similar patterns between control and high-fat diet (HFD) treatments, and six most abundant genera and 40 operational taxonomic units that respond to krill oil treatment were identified. However, the 16S rRNA sequencing of the colon samples showed that LD krill oil shifts the structure from the HFD to that of the control, whereas the HD group was distributed between the control and HFD groups. The corresponding most abundant genera and responsive OTUs totaled 4 and 45, respectively. In conclusion, different gastrointestinal tract locations contain different microbial communities. These results will help to provide a comprehensive understanding of the role of dietary krill oil in modulating the gut microbiota and alleviating hyperlipidemia.

Impact of alkaline dust pollution on genetic variation of Usnea subfloridana populations.

Very little is known whether and how air pollution impacts genetic diversity of lichenized fungi that are well-known indicators of environmental quality. We studied the genetic variation of eight Usnea subfloridana populations in Pinus sylvestris-dominated boreal forest stands in southern Estonia, Northern Europe; four of these populations were exposed to long-term dust pollution released from unpaved road. The mean bark pH of lichen phorophyte differed considerably between polluted and unpolluted forest stands. We genotyped 274 Usnea thalli using nine specific fungal microsatellite markers. Genetic variation measures were calculated and compared between populations from different habitats. Allelic richness, Shannon's information index, and genetic diversity of lichen populations were significantly higher in unpolluted forest sites than in polluted forest sites. We conclude that environmental disturbances caused by alkaline dust pollution had negative impact on the genetic variation of U. subfloridana, a common species of lichenized fungi.

[Study of drug intervention in diversity changes of TCRVbeta gene in AIDS patients with incomplete immune reconstitution].

OBJECTIVE: To discuss the drug intervention in diversity changes of TCRVbeta gene in AIDS patients with incomplete immune reconstitution. METHOD: PBMCs were isolated from 37 cases of AIDS patients failure to immune reconstitution before and after treatment with immune 2 and 15 cases of HIV negative healthy donors. The human gene TCRVbeta CDR3 diversity quantitative detection reagent box were used, and mapped the distribution of gene scanning and calculated different CDR3 fragme of each Vbeta family size. RESULT: Compared with the normal group, there appeared some single or oligoclonal amplification of Vbeta CDR3 region in the patients, which were improved or recovered after treatment. Among them, D value of four families (9, 11, 21, 22 ) decreased after treatment in both groups. The decrease in family 21 and 22 was significant (P < 0.05) in treatment group compared with the control group. And family 18 was decreased in treatment group and increased significantly in control group (P < 0.05). CONCLUSION: Study of the mechanism showed oligoclonal of TCRVbeta family can get recovery in some degrees after treated by Immune 2 plus HAART, suggesting that the medicine may promote T-cell receptor gene rearrangement, helping immune cells to effectively identify the virus to reduce T-cell apoptosis.

[Diversity changes of TCRVbeta gene in AIDS patients with incomplete immune reconstitution and influence of drug].

OBJECTIVE: To discuss the drug intervention in diversity changes of TCRVbeta gene in AIDS patients with incomplete immune reconstitution. METHOD: PBMCs were isolated from 37 cases of AIDS patients failure to immune reconstitution before and after treatment with Immune 2 and 15 cases of HIV negative healthy donors. The human gene TCRVbeta CDR3 diversity quantitative detection reagent box were used, and mapped the distribution of gene scanning and calculated different CDR3 fragme of each Vbeta family size. RESULT: (1) Gaussian distribution of TCRVbeta families in patients with incomplete immune reconstitution after one year of HAART, had been broken with the occurrence of the offset TCR lineage. After six months of treatment of traditional Chinese medicine combined HAART, the TCR lineage has been partially restored. (2) Evaluated by the D (distance) value calculated by a quantitative analysis software which the kit provides, there were no significant difference in D value change between the two groups, but with traditional Chinese medicine can reduce the data variability. (3) CD4+ T cell counts had a significant correlation (r = -0.772, P = 0.000) with TCRVbeta genetic diversity. CONCLUSION: Study of the mechanism showed oligoclonal of TCRVbeta family can get recovery in some degrees after treated by Immune 2 plus HAART, suggesting that the medicine may promote T-cell receptor gene rearrangement, helping immune cells to effectively identify the virus to reduce T-cell apoptosis.

Genetic diversity of Oenoccoccus oeni isolated from wines treated with phenolic extracts as antimicrobial agents.

Molecular techniques have been applied to study the evolution of wine-associated lactic acid bacteria from red wines produced in the absence and presence of antimicrobial phenolic extracts, eucalyptus leaves and almond skins, and to genetically characterize representative Oenococcus oeni strains. Monitoring microbial populations by PCR-DGGE targeting the rpoB gene revealed that O. oeni was, as expected, the species responsible for malolactic fermentation (MLF). Representative strains from both extract-treated and not-treated wines were isolated and all were identified as O. oeni species, by 16S rRNA sequencing. Typing of isolated O. oeni strains based on the mutation of the rpoB gene suggested a more favorable adaptation of L strains (n = 63) than H strains (n = 3) to MLF. Moreover, PFGE analysis of the isolated O. oeni strains revealed 27 different genetic profiles, which indicates a rich biodiversity of indigenous O. oeni species in the winery. Finally, a higher number of genetic markers were shown in the genome of strains from control wines than strains from wines elaborated with phenolic extracts. These results provide a basis for further investigation of the molecular and evolutionary mechanisms leading to the prevalence of O. oeni in wines treated with polyphenols as inhibitor compounds.

Could contaminant induced mutations lead to a genetic diversity overestimation?

Contaminant driven genetic erosion reported through the inspection of selectable traits can be underestimated using neutral markers. This divergence was previously reported in the aquatic system of an abandoned pyrite mine. The most sensitive genotypes of the microcrustacean cladoceran Daphnia longispina were found to be lacking in the impacted reservoir near the entrance of the metal rich acid mine drainage (AMD). Since that divergence could be, at least partially, accounted for by mutagenicity and genotoxicity of the AMD, the present study aimed at providing such a characterization. The Allium cepa chromosomal aberration assay, using root meristematic cells, was carried out, by exposing seeds to 100, 10, 1, and 0.1 % of the local AMD. Chromosomal aberrations, cell division phases and cell death were quantified after the AMD exposure and after 24 and 48 h recovery periods. The AMD revealed to be mutagenic and genotoxic, even after diluting it to 1 and 0.1 %. Dilutions within this range were previously found to be below the lethality threshold and to elicit sublethal effects on reproduction of locally collected D. longispina clonal lineages Significant mutagenic effects (micronuclei and chromosomal breaks) were also found at 0.1 % AMD, supporting that exposure may induce permanent genetic alterations. Recovery tests showed that AMD genotoxic effects persisted after the exposure.

Genetics, phosphorus availability, and herbivore-derived induction as sources of phenotypic variation of leaf volatile terpenes in a pine species.

Oleoresin produced and stored in pine tree leaves provides direct resistance to herbivores, while leaf volatile terpenes (LVT) in the resin are also powerful airborne infochemicals. Resin concentration and profile show considerable spatial and temporal phenotypic variation within and among pine populations. LVT biochemistry is known to be under genetic control, and although LVT should be plastic to diverse abiotic and biotic environmental factors such as nutrient availability and herbivore attack, little is known about their relative contributions and interactive effects. The aim of this paper was to clarify whether reduced phosphorus availability could increase the LVT concentration and affect the expression of herbivore-derived induced defences, and how plasticity would contribute to the phenotypic variation of LVT. The constitutive and methyl-jasmonate (MeJa) induced LVT concentration and profile were analysed in 17 half-sib Pinus pinaster families growing under two levels of P-availability (complete and P-limited fertilization). Individual terpene concentrations showed large additive genetic variation, which was more pronounced in the control than in MeJa-induced pines. MeJa application did not affect the LVT concentration, but significantly modified the LVT profile by depleting the α-pinene content and reducing the sesquiterpene fraction. Low P-availability strongly reduced plant growth and foliar nutrient concentrations, but did not affect LVT concentration and profile, and did not interact with MeJa-induction. Results indicate a strong homeostasis of LVT concentration to P-availability, and minor changes in the LVT profile due to MeJa-induction. Genetic variation appears to be the main source of phenotypic variation affecting the LVT concentration in this pine species.

Arsenic influence on genetic variation in grain trace-element nutrient content in Bengal delta grown rice.

It has previously been shown that across different arsenic (As) soil environments, a decrease in grain selenium (Se), zinc (Zn), and nickel (Ni) concentrations is associated with an increase in grain As. In this study we aim to determine if there is a genetic element for this observation or if it is driven by the soil As environment. To determine the genetic and environmental effect on grain element composition, multielement analysis using ICP-MS was performed on rice grain from a range of rice cultivars grown in 4 different field sites (2 in Bangladesh and 2 in West Bengal). At all four sites a negative correlation was observed between grain As and grain Ni, while at three of the four sites a negative correlation was observed between grain As and grain Se and grain copper (Cu). For manganese, Ni, Cu, and Se there was also a significant genetic interaction with grain arsenic indicating some cultivars are more strongly affected by arsenic than others.

Intra- and inter-individual variation of BIS-index and Entropy during controlled sedation with midazolam/remifentanil and dexmedetomidine/remifentanil in healthy volunteers: an interventional study.

INTRODUCTION: We studied intra-individual and inter-individual variability of two online sedation monitors, BIS and Entropy, in volunteers under sedation. METHODS: Ten healthy volunteers were sedated in a stepwise manner with doses of either midazolam and remifentanil or dexmedetomidine and remifentanil. One week later the procedure was repeated with the remaining drug combination. The doses were adjusted to achieve three different sedation levels (Ramsay Scores 2, 3 and 4) and controlled by a computer-driven drug-delivery system to maintain stable plasma concentrations of the drugs. At each level of sedation, BIS and Entropy (response entropy and state entropy) values were recorded for 20 minutes. Baseline recordings were obtained before the sedative medications were administered. RESULTS: Both inter-individual and intra-individual variability increased as the sedation level deepened. Entropy values showed greater variability than BIS(R) values, and the variability was greater during dexmedetomidine/remifentanil sedation than during midazolam/remifentanil sedation. CONCLUSIONS: The large intra-individual and inter-individual variability of BIS and Entropy values in sedated volunteers makes the determination of sedation levels by processed electroencephalogram (EEG) variables impossible. Reports in the literature which draw conclusions based on processed EEG variables obtained from sedated intensive care unit (ICU) patients may be inaccurate due to this variability. TRIAL REGISTRATION: clinicaltrials.gov Nr. NCT00641563.

Influence of oral doxycycline therapy on the diversity and antibiotic susceptibility of human intestinal bifidobacterial population.

AIM: To evaluate the influence of doxycycline therapy on the composition and antibiotic susceptibility of intestinal bifidobacteria. METHODS AND RESULTS: Faecal samples were collected from nine subjects receiving doxycycline therapy and ten control subjects, and analysed for bifidobacteria by culturing and PCR-DGGE (denaturing gradient gel electrophoresis). A marked decrease in the diversity (average number of amplicons detected by PCR-DGGE 0.8 in the antibiotic vs 4.3 in the control group) of Bifidobacterium populations was observed during doxycycline therapy. The proportion of a tetracycline-resistant bifidobacterial population was higher in the antibiotic group than in the control group (83%vs 26%). Based on the tet gene PCR, resistance could be associated with the presence of tet(W). In two subjects, strains representing highly similar genetic fingerprints but different tetracycline susceptibilities were detected. A mutation causing lack of functionality in the tet(W) was observed in one of the susceptible strains. CONCLUSIONS: Doxycycline therapy had a drastic effect on the diversity and tetracycline susceptibility of intestinal Bifidobacterium populations. SIGNIFICANCE AND IMPACT OF THE STUDY: The use of broad-spectrum antibiotics increased the pool of tetracycline-resistant commensal bacteria in the intestine. The detection of resistance genes alone is not sufficient for the evaluation of bacterial antibiotic resistance.

Genetic impact of the Prestige oil spill in wild populations of a poor dispersal marine snail from intertidal rocky shores.

In November 2002, the sinking of the Prestige cargo ship produced an oil spill of 60,000 tons that affected many areas along the Galician coast (in the northwest of Spain). In a number of rocky shore sites, most organisms (particularly marine mollusks) were nearly extinct at a local scale. We tested whether the local bottleneck/extinction that occurred in affected localities caused any detectable reduction of the genetic diversity in the marine snail Littorina saxatilis, an ovoviviparous rocky shore model species characterized by a low dispersal ability, high population density, and wide distribution range. We compared the level of genetic variation and population differentiation between affected (polluted) and control sites located in seven geographical areas (three sites per area, one impacted and two controls, and two replicates per site) one and a half years after the spill. The analysis included molecular marker variation (microsatellite and AFLP loci) and quantitative trait genetic variation for shell variables in embryos extracted from pregnant females. Our results indicate that the affected populations did not show a significant overall reduction in genetic diversity when compared to the controls, suggesting that the species is highly resistant to losing genetic variability as a consequence of a local short-term pollution process in spite of its low dispersal ability and direct development. However, some genetic effects were detected in the polluted populations, particularly for quantitative shell traits and AFLPs, consistent with local adaptations resulting from the fuel contamination.

The effect of medicated diets and level of feeding on caecal microbiota of lactating rabbit does.

AIMS: To study the effect of the type of antibiotic used in medicated diets against pathogens and the feeding level on the microbial biodiversity in the rabbit caecum. METHODS AND RESULTS: Three groups of eight does were given a diet unsupplemented (NAB) or with 100 ppm of bacitracin (BAC) or tiamulin (TIA). Litter sizes of four does in each group were adjusted to five (LS5) or to nine (LS9), to manipulate their levels of feed intake. The feeding level strongly affected caecal microbiota in does fed on NAB and BAC diet, whereas the effect of the antibiotic was higher in TIA-supplemented animals, even prevailing over the effect of feeding level. Daily food intake and milk yield (P<0.05) and caecum weight (P<0.10) were higher in feeding of LS9 does. The total volatile fatty acid concentration was lower with BAC (P<0.05). CONCLUSIONS: The feeding level strongly affects caecal biodiversity in lactating does. The extent of the antibiotic effect depends on its nature, being significant with TIA but not with BAC. SIGNIFICANCE AND IMPACT OF THE STUDY: Changes in the feeding level promote different profiles of caecal microbiota. Therapeutic doses of TIA may affect caecal microbiota, whereas BAC would not reduce diversity.

Effect of synthetic matrix metalloproteinase inhibitors on lipopolysaccharide-induced blood-brain barrier opening in rodents: Differences in response based on strains and solvents.

Matrix metalloproteinase inhibitors (MMPIs) reduce blood-brain barrier (BBB) disruption and prevent cell death. Animal models of multiple sclerosis, cerebral ischemia and hemorrhage, and bacterial meningitis respond to treatment with MMPIs. We have used the intracerebral injection of lipopolysaccharide (LPS) in rat, which induces MMP production and results in a delayed opening of the BBB, to screen MMPIs to identify therapeutic agents. We hypothesized that the mouse would respond similarly to LPS and that the mouse/LPS model of BBB damage would be more useful for screening of MMPIs. Therefore, we adapted the rat LPS model to the mouse and compared the response to LPS and treatment with MMPIs. Wistar-Kyoto rats (WKY) and three strains of mice had stereotactic injections of LPS into the caudate. (14)C-sucrose was used to measure permeability of the BBB 24 h after injection. Initially, we tested three broad-spectrum MMPIs in the rat, BB-1101, BB-94, and BB-2293, and a MMP-2 selective inhibitor, IW449; both BB-1101 and BB-94 significantly suppressed LPS-induced BBB damage (p<0.05). In the 3 mouse strains, C57/BL6, C57/BL10, and C57/BL10HIIIR2, LPS significantly opened the BBB in C57/BL6, and it was the only strain that showed a reduction in BBB permeability with BB-94. Treatment with methylprednisolone and several broad-spectrum MMPIs, including BB-1101, was ineffective in the C57/BL6. There was a significant reduction in BBB permeability seen with 10% dimethyl sulfoxide (DMSO) alone, which was used to dissolve the selective MMP-2 and-9 inhibitor, SB-3CT. The tetracycline derivative, minocycline, reduced the BBB injury in mouse by blocking the production of MMP-9. Our results show variability in rats and mice to LPS and MMPIs, which most likely is based on genetic make-up. Understanding these differences may provide important clues that could guide selection of MMPIs in treatment of neurological diseases.

Significant variations in differentiation properties between independent mouse ES cell lines cultured under defined conditions.

Mouse embryonic stem (ES) cells are isolated from the inner cell mass (ICM)/epiblast of preimplantation embryos and are widely used in cell differentiation studies. We have previously observed differences in transcript and antigen expression following differentiation of ES cells lines in vitro. We have investigated this further by comparing the differentiation characteristics of five independently derived ES cell lines cultured and differentiated under defined conditions. Undifferentiated ES cell lines exhibited similar morphology and antigen/transcript marker expression. However, upon differentiation in monolayer culture by LIF withdrawal, only two of the lines expressed similar germ layer transcript profiles, and these were significantly altered compared to differentiation in serum-supplemented media. Neurofilament-68k was the only transcript marker common to all cell lines, however, induction of neuroectoderm lineages using 1 microM all-trans retinoic acid (RA) resulted in significant variations in cell number and morphology between the lines. Furthermore, neurons were only formed from clones of the two cell lines that exhibited similar transcript profiles, although the morphology was different between the two. We conclude that the independent ES cell lines in this study differ in their response to alterations in culture conditions in vitro, and the use of an appropriate cell line enables relatively homogeneous neuronal populations to be achieved in monolayer culture under defined conditions.

A human oral capsaicin pain model to assess topical anesthetic-analgesic drugs.

Repeated application of capsaicin on the tongue has been used as a human oral pain model to assess topical anesthetic-analgesic drugs. The reliability of the model was evaluated by observing the variability of the response to repeated applications of capsaicin after three successive sessions at 1 day intervals. No session effect was observed for the time course of the visual analogue scale (VAS) scores and the area under the curve, but a significant decrease of VAS peak scores was noted from the first to the third session. The sensitivity of the model was assessed by mouth rinses with three doses of lidocaine (0.25, 0.5 and 1%). Lidocaine significantly reduced the burning pain. This effect was rapid, reversible and dose dependent. It is concluded that the oral capsaicin pain model displays good reliability and sensitivity and allows safe evaluation of candidate topical analgesic and anesthetic drugs.

[A comparative analysis of plant hereditary variability during mutagenic treatment of the generative cells and seeds of corn]. / Sravnitel'nyi analiz nasledstvennoi izmenchivosti rastenii pri mutagennoi obrabotke generativnykh kletok i semian kukuruzy.

The effect of mutagenic factors on maize generative cells during different gametogenesis stages, as well as on mature pollen and gametes causes an essential raise in frequency, widening in visible mutation spectra and seems to be more efficient than on dry seeds. Original mutations on qualitative and quantitative characters have been obtained.

Genetic variation in the susceptibility to mercury and other metal compounds in Drosophila melanogaster.

The tolerance of Drosophila melanogaster to heavy metal compounds was investigated with special emphasis on methylmercury. A pronounced variation in tolerance to CH3HgOH, HgCl2, (C2H5)3PbCl, (CH3)3SnCl, and CdCl2 was recorded between 12 wild-type strains. After ranking the tolerance of the strains with respect to the five compounds rank correlations for experiments within and between compounds were calculated. The results showed a high degree of correlation within compounds but no unequivocal indication of a correlation between compounds, indicating that different mechanisms of genetic control for tolerance were operating for the five compounds. Rank correlations for experiments with 12 different mercury, lead, tin, and cadmium compounds and the same 12 wild-type strains only indicated one significant correlated response, between tripropyltin and tributyltin. A selection experiment for tolerance to methylmercury was performed with a foundation population, synthesized from four wild-type strains, showing a high initial tolerance. One control and two levels of treatment doses were used. A distinct selection response was obtained and a high tolerance was reached particularly for the high-dose selection line after 12 generations, when the experiment ended. Genetic analysis of the tolerance indicated a dominant and polygenic inheritance. Investigation of the uptake and excretion of CH3Hg203OH showed that the level of tolerance to methylmercury was correlated with the uptake of the mercury but apparently not with the rate of excretion. Cystein increased the susceptibility to methylmercury. Inorganic mercury and trimethyl lead exhibited a synergistic toxic effect, evidently as the result of an in vitro transmethylation of mercury. A high somatic susceptibility to methylmercury also applied to the induction of nondisjunction and sex-linked recessive lethals.

[Polymorphism of a tumor ce-l population and selection processes. IV. The effect of dibunol and nitrosourea on the variability of Ehrlich-I. Ch. Ph. ascitic strain tumor cells]. / Polimorfizm populiatsii opukholevykh kletok i selektivnye protsessy. IV. Vliianie dibunola i nitrozomocheviny na izmenchivost' opukholevykh kletok astsitnogo shtamma Erlikha-IKhF.

A study was made of the effect of dibunol and methyl-N-nitrosourea (MNU) on two tumor cell subpopulations of the Ehrlich-I. Ch. Ph. ascites strain, one of which is characterized with A + B + 2C and A + D + 2C--markers and the other one--with A1 + A2 + 2B + D + C markers. Dibunol that belongs to the class of inhibitors of free-radical processes was shown to bring about changes in cell subpopulations, the mode of changes depending on the dose and regime of treatment. The effect of MNU on the population resulted predominantly in the accumulation of cells with various chromosome aberrations. At early stages of tumor progression, aberrations were more pronounced in cells with marker chromosome "A" than in the cells with 44 chromosomes and markers A1 + A2 + 2B + D + C.