Exploring the genetic diversity and population structure of upland cotton germplasm by iPBS-retrotransposons markers

BACKGROUND

Upland cotton is one of the utmost significant strategic fiber crops, and play a vital role in the global textile industry.

METHODS AND RESULTS

A total of 128 genotypes comprised Gossypium hirsutum L, Gossypium barbadense L., and pure lines were used to examine genetic diversity using iPBS-retrotransposon markers system. Eleven highly polymorphic primers yielded 287 bands and 99.65% polymorphism was recorded. The mean polymorphism information content was estimated at 0.297 and the average diversity indices for the effective number of alleles, Shannon's information index, and overall gene diversity were 1.481, 0.443, and 0.265, respectively. The analysis of molecular variance (AMOVA) revealed that 69% of the genetic variation was within the population. A model-based STRUCTURE algorithm divided the entire germplasm into four populations and one un-classified population, the genotypes G42 (originating in Egypt) and G128 (originating in the United States), showed the highest genetic distance (0.996) so these genotypes could be suggested for breeding programs as parental lines.

CONCLUSIONS

This is the first investigation using an iPBS-retrotransposon marker system to examine the genetic diversity and population structure of upland cotton germplasm. The rich diversity found in upland cotton germplasm could be exploited as a genetic resource when developing breeding programs and could also help with efforts to breed cotton around the world. These findings also show the applicability and effectiveness of iPBS-retrotransposons for the molecular characterization of cotton germplasm.

Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes

The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.

Transcriptional cascades in the regulation of 2-AP biosynthesis under Zn supply in fragrant rice

Transcription factors (TFs) regulate gene expression to control certain genetic programs, such as growth and development, phytohormone regulation, and environmental stresses. 2-acetyl-1-pyrroline (2-AP) is the key element involved in aroma biosynthesis pathway, and the application of micronutrients can increase the 2-AP levels. However, little is known about the micronutrient-induced TFs involved in 2-AP biosynthesis. Here, we identify a number of TF families in two fragrant rice varieties, "Meixiangzhan-2" (M) and "Xiangyaxiangzhan" (X), in response to Zinc (Zn) application through transcriptomic analysis. A total of ~678 TFs were identified and grouped into 26 TF families, each of which was found to be involved in numerous signaling pathways. The WRKY TF family was found to be the most abundant, followed by bHLH and MYB. Furthermore, members of the WRKY, bHLH, MYB, ERF, HSF, MADS-box, NFY, and AP2 TF families were significantly upregulated and may be involved in the transcriptional regulation of aroma biosynthesis. In brief, this study enhances our understanding of the molecular mechanism of 2-AP biosynthesis and highlights the key TFs potentially involved in the production of aroma in fragrant rice.

Individual and joint toxicity of the herbicide S-metolachlor and a metabolite, deethylatrazine on aquatic crustaceans: Difference between ecological groups

We studied the individual and joint acute toxicity of S-metolachlor (SMOC) and deethylatrazine (DEA - a metabolite of atrazine) on different non-target freshwater crustaceans. We used animals from different ecological groups: two amphipods from surface running water (Gammarus pulex and Gammarus cf. orinos), an isopod from surface stagnant water (Asellus aquaticus) and an amphipod living in groundwater (Niphargus rhenorhodanensis). Organisms were exposed to different levels of SMOC and DEA, alone or in binary mixture. Temperature effect on SMOC toxicity was assessed by exposing G. pulex and N. rhenorhodanensis to SMOC at 11 °C and 15 °C. Studying mortality as the biological endpoint, N. rhenorhodanensis was more resistant than surface water species towards SMOC and DEA. Among surface water species, G. pulex was the most sensitive while Gammarus cf. orinos and A. aquaticus showed similar responses to both compounds. Temperature increase did not change SMOC toxicity but modify the shape and steepness of the dose-response curve. We used a Model Deviation Ratio (MDR) approach to evaluate the predictability of Concentration Addition (CA) and Independent Action (IA) models to mixture toxicity. Results indicated either an additive or an antagonistic or a synergistic interaction depending on the concentrations combination and the test species. Our finding conclusively show the suitability of CA and IA in predicting mixture toxicities but results should be interpreted with caution according to ecological group of exposed species in risk assessment procedures.

Persistent and emerging micro-organic contaminants in Chalk groundwater of England and France

The Chalk aquifer of Northern Europe is an internationally important source of drinking water and sustains baseflow for surface water ecosystems. The areal distribution of microorganic (MO) contaminants, particularly non-regulated emerging MOs, in this aquifer is poorly understood. This study presents results from a reconnaissance survey of MOs in Chalk groundwater, including pharmaceuticals, personal care products and pesticides and their transformation products, conducted across the major Chalk aquifers of England and France. Data from a total of 345 sites collected during 2011 were included in this study to provide a representative baseline assessment of MO occurrence in groundwater. A suite of 42 MOs were analysed for at each site including industrial compounds (n=16), pesticides (n=14) and pharmaceuticals, personal care and lifestyle products (n=12). Occurrence data is evaluated in relation to land use, aquifer exposure, well depth and depth to groundwater to provide an understanding of vulnerable groundwater settings.

Impact Strength of β-Nucleated Polypropylene

Structural transformations of semicrystalline polymers form an important field of current scientific research. The preparation of controlled supermolecular structure may lead to significant improvements in mechanical, thermal and optical properties. As for isotactic polypropylene (iPP), its properties essentially depend on its crystalline phase composition, which is due to polymorphism of iPP. Thus, the aim of this work is to analyze the influence of the β-phase content in polypropylene and of its spatial arrangement on mechanical properties, in particular on its impact strength. Commercially available isotactic polypropylene (iPP) was modified by various amounts of a specific β-nucleating agent (N, N'-dicyclohexylnaphtalene-2,6-dicarboxamide). From the prepared mixtures standard impact testing bars were injection molded. The structure of the specimens was studied by X-ray diffractometry, and impact properties were determined using Charpy impact tester. It was found that addition of the nucleator led to β-phase content increase, especially in the core region of the injection molded samples. The skin (surface layer of the samples) contained lower amount of β-phase. Furthermore, notch impact strength dramatically increased with increasing concentrations of the β-nucleating agent. The concentration of 0.03 wt.% of the nucleator can be considered a “boundary value” due to the fact that the maximum notch impact strength value was reached. With further addition of the nucleating agent the impact strength slowly decreased. Therefore it should be noted that the improvement of impact properties is not only due to the presence of β-phase, but also there are some synergy-applied factors – such as the structural heterogeneity and spatial arrangement of the β-phase in injection molded samples.

Emerging organic contaminants in groundwater: A review of sources, fate and occurrence

Emerging organic contaminants (EOCs) detected in groundwater may have adverse effects on human health and aquatic ecosystems. This paper reviews the existing occurrence data in groundwater for a range of EOCs including pharmaceutical, personal care, 'life-style' and selected industrial compounds. The main sources and pathways for organic EOCs in groundwater are reviewed, with occurrence data for EOCs in groundwater included from both targeted studies and broad reconnaissance surveys. Nanogram-microgram per litre concentrations are present in groundwater for a large range of EOCs as well as metabolites and transformation products and under certain conditions may pose a threat to freshwater bodies for decades due to relatively long groundwater residence times. In the coming decades, more of these EOCs are likely to have drinking water standards, environmental quality standards and/or groundwater threshold values defined, and therefore a better understanding of the spatial and temporal variation remains a priority.

Hydrodynamic and geochemical constraints on pesticide concentrations in the groundwater of an agricultural catchment (Brévilles, France)

The monitoring of a spring and seven piezometers in the 3km(2) Brévilles agricultural catchment (France) over five and a half years revealed considerable spatial and temporal variability in the concentrations of atrazine and its metabolite deethylatrazine (both systematically quantified at the outlet spring): maximum 0.97 and 2.72microgL(-1), mean 0.19 and 0.59microgL(-1), respectively. Isoproturon, the pesticide applied in the greatest amount, was detected in only 10 of the 133 samples. These observations can only partly be explained by land use and intrinsic pesticide properties. Geochemical measurements and tritium dating showed the importance of the stratification of the sandy saturated zone and the buffer function of the unsaturated limestone. Principal component analysis on 39 monthly data series of atrazine, deethylatrazine, nitrate, chloride and piezometric levels revealed a temporal structuring of the data possibly reflecting the existence within the aquifer of two different reservoirs with time-variable contributions.

Pesticides in the groundwater of a spring draining a sandy aquifer: temporal variability of concentrations and fluxes

A 250 ha agricultural catchment has been characterized with respect to its hydrogeology and groundwater contamination by pesticides from October 1999 to August 2004. Five years after the ending of atrazine (At) application, used since the sixties, At and deethylatrazine (DEA) are still systematically quantified at the outlet of the watershed with concentrations from 0.07 to 0.43 microg l(-1) for At, and between 0.14 and 1.16 microg l(-1) for DEA. Isoproturon and chlortoluron are detected in only one (0.3 microg l(-1)) and two (0.7 and 2.0 microg l(-1)) of the 124 semi-monthly samples, respectively. DEA concentrations can be very different between two samples with a 15-day time step. The annual mean exported fluxes of cumulated At and DEA are stable, which indicates a long time transfer in the unsaturated or saturated zone with a progressive leaching of the stock of At and DEA probably accumulated in the soil and the vadose zone. These fluxes, between 0.90% and 2.82% of the annual mean dose of At applied before 1999, similar to those calculated in several studies at the bottom of the root zone, could be explained by low adsorption and degradation properties of At and DEA in the unsaturated and saturated zone.

The persisting analgesic effect of low-dose intravenous ketamine after spinal anaesthesia for Caesarean section

BACKGROUND AND OBJECTIVES

To compare the analgesic effects of intrathecal fentanyl and low-dose intravenous ketamine as adjuvants to intrathecal bupivacaine for Caesarean section.

METHODS

Ninety elective Caesarean section patients were randomized into three groups. Spinal anaesthesia was performed with 15 mg hyperbaric bupivacaine in all groups. Ketamine (0.15 mg kg(-1)) or an equal volume of normal saline was given intravenously immediately after initiating spinal anaesthesia in the ketamine and control group, respectively. In the fentanyl group, 10 microg fentanyl was added to the intrathecal bupivacaine. Arterial pressures, heart rate values, adverse effects, the time of first request for postoperative analgesia, visual analogue pain scores, total analgesic consumptions at 24 and 48 h were recorded in all patients.

RESULTS

The time to first request for analgesia was significantly longer in the ketamine (197 min) and fentanyl (165 min) groups compared to the control group (144 min). Postoperative pain scores were significantly lower in the ketamine group than in both other groups. Although the analgesic requirements during first 24 h were significantly lower in the ketamine group, there was no significant difference between the groups during the following 24 h.

CONCLUSION

Intravenous low-dose ketamine combined with intrathecal bupivacaine for Caesarean section provides longer postoperative analgesia and lower postoperative analgesic consumption than bupivacaine alone suggesting a pre-emptive effect.

Determination of chloroacetanilides, triazines and phenylureas and some of their metabolites in soils by pressurised liquid extraction, GC–MS/MS, LC–MS and LC–MS/MS

Pressurised liquid extraction (PLE) technique was used for the simultaneous extraction of phenylureas, triazines and chloroacetanilides and some of their metabolites from soils. Extractions were performed by mixing 15 g of dried soil with 30 mL of acetone under 100 atm at 50 degrees C, during 3 min and with three PLE cycles. Prior to the analysis of naturally contaminated soils, each of the five representative soil matrices used as blanks (of different depths) was spiked in triplicate with standards of each parent and degradation compound at about 10, 30 and 120 microg/kg. For each experiment, isoproturon-D6 and atrazine-D5 were used as surrogates. Analysis of phenylureas and metabolites of triazines and phenylureas was carried out by reversed phase liquid chromatography/mass spectrometry (LC-MS) and LC-MS/MS in the positive mode. Gas chromatography (GC)/ion trap mass spectrometry was used in the MS/MS mode for the parent triazines and chloroacetanilides. The average extraction recoveries were above 85%, except for didesmethyl-isoproturon, and quantification limits were between 0.5 and 5 microg/kg. The optimised multi-residue method was applied to soils and solids below the root zone, sampled from agricultural plots of a small French hydrogeological basin.

Determination of oxanilic and sulfonic acid metabolites of acetochlor in soils by liquid chromatography-electrospray ionisation mass spectrometry

An analytical method is presented that describes the extraction and quantification of oxanilic and sulfonic acid metabolites of the herbicide acetochlor in soil samples. Experiments were performed on 50 g of soil using a solvent extraction technique with an acetonitrile-water (60:40) mixture in an acidic medium. Analysis was carried out by reversed-phase liquid chromatography and detection by electrospray ionisation mass spectrometry in single ion monitoring and negative modes. Four different soil matrices were spiked in triplicate with standards of each degradation compound at three concentration levels between 2 and 80 microg/kg. The average recoveries range from 90 to 120% for both the metabolites, with relative standard deviations lower than 15%. The limits of quantification are about 1 and 2 microg/kg for the ethanesulfonic acid and the oxanilic acid metabolites, respectively. The method has been applied to soils and solids recovered from the deeper unsaturated zone of a small French catchment closely monitored as part of the European project "Pesticides in European Groundwaters: detailed study of Aquifers and Simulation of possible Evolution scenarios (PEGASE)".

Rescue of preimplantatory egg development and embryo implantation in prolactin receptor-deficient mice after progesterone administration

PRL, a hormone secreted essentially by the pituitary and other extrapituitary sources such as decidua, has been attributed regulatory roles in reproduction and cell growth in mammals. These effects are mediated by a membrane PRL receptor belonging to the cytokine receptor superfamily. Null mutation of the PRL receptor gene leads to female sterility due to a severely compromised preimplantation development and a complete failure of the implantation of the few embryos reaching the blastocyst stage, strongly implicating PRL in the maternal control of implantation. We measured the hormonal status of -/- mice, which confirmed that the corpus luteum is unable to produce progesterone. Progesterone administration to -/- mice completely rescued the development of preimplantatory eggs and embryo implantation. Pregnancy could be maintained to 19.5 days postcoitum, with about 22% of resulting embryos reaching adulthood. Although progesterone and perhaps PRL appear to facilitate mouse preembryo development throughout the preimplantation stages, other factors as well as a possible direct effect of PRL on the uterus are probably necessary to fully maintain pregnancy. Finally, reduced ductal side-branching in the mammary gland can be rescued by progesterone treatment, but females exhibit reduced alveolar formation. Our model establishes the PRL receptor as a key regulator of reproduction and provides novel insights into the function of lactogenic hormones and their receptor.

Interference footprinting analysis of telomerase elongation complexes

Telomerase is a reverse transcriptase that adds single-stranded telomeric repeats to the ends of linear eukaryotic chromosomes. It consists of an RNA molecule including a template sequence, a protein subunit containing reverse transcriptase motifs, and auxiliary proteins. We have carried out an interference footprinting analysis of the Tetrahymena telomerase elongation complexes. In this study, single-stranded oligonucleotide primers containing telomeric sequences were modified with base-specific chemical reagents and extended with the telomerase by a single (32)P-labeled dGMP or dTMP. Base modifications that interfered with the primer extension reactions were mapped by footprinting. Major functional interactions were detected between the telomerase and the six or seven 3'-terminal residues of the primers. These interactions occurred not only with the RNA template region, but also with another region in the enzyme ribonucleoprotein complex designated the telomerase DNA interacting surface (TDIS). This was indicated by footprints generated with dimethyl sulfate (that did not affect Watson-Crick hydrogen bonding) and by footprinting assays performed with mutant primers. In primers aligned at a distance of 2 nucleotides along the RNA template region, the footprints of the six or seven 3'-terminal residues were shifted by 2 nucleotides. This shift indicated that during the elongation reaction, TDIS moved in concert with the 3' ends of the primers relative to the template region. Weak interactions occurred between the telomerase and residues located upstream of the seventh nucleotide. These interactions were stronger in primers that were impaired in the ability to align with the template.

From the molecular biology of prolactin and its receptor to the lessons learned from knockout mice models

Prolactin (PRL), a polypeptide hormone secreted mainly by the pituitary and, to a lesser extent, by peripheral tissues, affects more physiological processes than all other pituitary hormones combined since it is involved in > 300 separate functions in vertebrates. Its main actions are related to lactation and reproduction. The initial step of PRL action is the binding to a specific membrane receptor, the PRLR, which belongs to the class 1 cytokine receptor superfamily. PRL-binding sites have been identified in a number of tissues and cell types in adult animals. Signal transduction by this receptor is mediated, at least in part, by two families of signaling molecules: Janus tyrosine kinases and signal transducers and activators of transcription (STATs). Disruption of the PRLR gene has provided a new mouse model with which to identify actions directly associated with PRL or any other PRLR ligands, such as placental lactogens. To date, several different phenotypes have been analyzed and are briefly described in this review. Coupled with the SAGE technique, this PRLR knockout model is being used to qualitatively and quantitatively evaluate the expression pattern of hepatic genes in two physiological situations: transcriptomes corresponding to livers from both wild type and PRLR KO mice are being compared, and following statistical analyses, candidate genes presenting a differential profile will be further characterized. Such a new approach will undoubtedly open future avenues of research for PRL targets. To date, no pathology linked to any mutation in the genes encoding PRL or its receptor have been identified. The development of genetic models provides new opportunities to understand how PRL can participate to the development of pathologies throughout life, as for example the initiation and progression of breast cancer.

DNA molecules can drive the assembly of other DNA molecules into specific four-stranded structures

Single-stranded DNA molecules containing clustered G-repeats can be assembled into various four-stranded structures linked by G-quartets. Here, we report that such molecules can also drive the assembly of other DNA molecules containing G-repeats into specific four-stranded structures. In these assays, the oligonucleotides 5'-CAGGCTGAGCAGGTACGGGGGAGCTGGGGTAGATTGGAATGTAG-3' (oligo D) and 5'-CGGGGGAGCTGGGGT-3' (oligo B), consisting of sequences found in immunoglobulin switch regions, were annealed in a buffer containing K+ and the annealing products were analyzed by polyacrylamide gel electrophoresis. This analysis revealed that whereas annealing of each oligo alone produced four-stranded structures designated D2 and B2, annealing of mixtures containing both oligos produced additional complexes designated D2* and B2*. D2* and B2* were found to contain only D molecules and only B molecules, respectively. The yield of D2* increased and the yield of B2* decreased, as the concentration ratio oligo B/oligo D was increased. These results indicated that B can drive the assembly of D into D2* and D can drive the assembly of B into B2*. Further studies revealed that while the assembly of D2 followed a second order kinetics, the B-driven assembly of D2* followed a first order kinetics. Dimethyl sulfate footprinting indicated that both D2 and D2* are four-stranded structures containing two parallel and two antiparallel chains. In addition, annealing of D mixed with various B mutants showed that only mutants containing two G-clusters can drive the assembly of D2*. Based on these data, we propose that in the process of D2* assembly, a four-stranded intermediate containing B and D is formed and then dissociates into D2* and B in a rate-limiting first order reaction. Driver mechanisms of this type may cause formation of specific four-stranded structures at G-rich chromosomal sites, thereby regulating processes such as recombination and telomere synthesis.

Leukemia inhibitory factor-dependent transcriptional activation in embryonic stem cells

STAT transcription factors are induced by a number of growth factors and cytokines. Within minutes of induction, the STAT proteins are phosphorylated on tyrosine and serine residues and translocated to the nucleus, where they bind to their DNA targets. The leukemia inhibitory factor (LIF) mediates pleiotropic and sometimes opposite effects both in vivo and in cultured cells. It is known, for example, to prevent differentiation of embryonic stem (ES) cells in vitro. To get insights into LIF-regulated signaling in ES cells, we have analyzed protein-binding and transcriptional properties of STAT recognition sites in ES cells cultivated in the presence and in the absence of LIF. We have detected a specific LIF-regulated DNA-binding activity implicating the STAT3 protein. We show that STAT3 phosphorylation is essential for this LIF-dependent DNA-binding activity. The possibility that ERK2 or a closely related protein kinase, whose activity is modulated in a LIF-dependent manner, contributes to this phosphorylation is discussed. Finally, we show that the multimerized STAT3-binding DNA element confers LIF responsiveness to a minimal thymidine kinase promoter. This, together with our observation that overexpression of STAT3 dominant-negative mutants abrogates this LIF responsiveness, clearly indicates that STAT3 is involved in LIF-regulated transcriptional events in ES cells. Finally, stable expression of such a dominant negative mutant of STAT3 induces morphological differentiation of ES cells despite continuous LIF supply. Our results suggest that STAT3 is a critical target of the LIF signaling pathway, which maintains pluripotent cell proliferation.

Evaluation of ELISA microtiter plate-based assays for the direct determination of isoproturon in water samples and soil extracts

Trials were carried out on the commercially available Millipore isoproturon ELISA microtiter plate tests and on laboratory assays developed by Hirst as part of a Joint European Union research project (BIOPTICAS). The lowest detectable dose (LDD) was determined as three times the standard deviation of the blanks. Depending on the calibration curves obtained on different days with different plates, the LDD varied from 0.020 to 0.064 microgram/L for the Millipore test and from 0.080 to 0.329 microgram/L for the Hirst test. The mean coefficients of variation within a single plate for triplicate determinations of standard solutions in the 0.05 to 0.5 microgram/L range were 5.5 and 3.6% for Millipore and Hirst respectively. Cross-reactivity was studied for mono- and di-demethylated isoproturon, chlortoluron, diuron and linuron. The highest cross-reactivity with both tests was that of mono-demethylated isoproturon (22% for Millipore, 4% for Hirst). This molecule was the only one to show significant cross-reactivity in the Hirst test, whereas in the Millipore test, the di-demethylated isoproturon also cross-reacted (4%). Natural water samples, 19 ground-, 53 lysimetric plate and 47 suction cup water samples, and 32 soil samples were also analysed with the ELISA tests. HPLC with a diode array detector was used as a validated control technique for the natural samples. For each water type, ELISA concentrations of both tests were significantly correlated with the HPLC values (r > or = 0.937; p < 0.001). For the soil extracts, the correlations were also significant (p < 0.001), but the scatter in the data was greater. Overall, the Millipore correlation coefficients were higher than those of Hirst.

The SV40 large T-antigen helicase can unwind four stranded DNA structures linked by G-quartets

We describe a novel activity of the SV40 large T-ag helicase, the unwinding of four stranded DNA structures linked by stacked G-quartets, namely stacked groups of four guanine bases bound by Hoogsteen hydrogen bonds. The structures unwound by the helicase were of two types: (i) quadruplexes comprising four parallel strands that were generated by annealing oligonucleotides including clustered G residues in a buffer containing Na+ions. Each parallel quadruplex consisted of four oligonucleotide molecules. (ii) Complexes comprising two parallel and two antiparallel strands that were generated by annealing the above oligonucleotides in a buffer containing K+ions. Each antiparallel complex consisted of two folded oligonucleotide molecules. Unwinding of these unusual DNA structures by the T-ag was monitored by gel electrophoresis. The unwinding process required ATP and at least one single stranded 3'-tail extending beyond the four stranded region. These data indicated that the T-ag first binds the 3'-tail and moves in a 3'-->5'direction, using energy provided by ATP hydrolysis; then it unwinds the four stranded DNA into single strands. This helicase activity may affect processes such as recombination and telomere extension, in which four stranded DNA could play a role.

The first international intercomparison of EPR-dosimetry with teeth: first results

Intercomparison of EPR-dosimetric techniques using tooth enamel had been performed in order to check whether the results produced by different laboratories are consistent and accurate. Participants were supposed to evaluate doses applied to pulverized enamel samples, using routine techniques from their laboratories. The intercomparison has demonstrated a great variety of methods used for dose reconstruction. Peculiarities of experimental approaches are discussed systematically in terms of procedure for recording the EPR-spectra, determination of the amplitude of the radiation induced signal, determination of the dose, and error propagation.

Unwinding of the third strand of a DNA triple helix, a novel activity of the SV40 large T-antigen helicase

We present experiments indicating that the SV40 large T-antigen (T-ag) helicase is capable of unwinding the third strand of DNA triple helices. Intermolecular d(TC)(20)d(GA)(20)d(TC)(20) triplexes were generated by annealing, at pH 5.5, a linearized double-stranded plasmid containing a d(TC)(27).d(GA)27 tract with a (32)P-labeled oligonucleotide consisting of a d(TC)(20) tract flanked by a sequence of 15 nt at the 3'-end. The triplexes remained stable at pH 7.2, as determined by agarose gel electrophoresis and dimethyl sulfate footprinting. Incubation with the T-ag helicase caused unwinding of the d(TC)(20) tract and consequent release of the oligonucleotide, while the plasmid molecules remained double-stranded. ATP was required for this reaction and could not be replaced by the non-hydrolyzable ATP analog AMP-PNP. T-ag did not unwind similar triplexes formed with oligonucleotides containing a d(TC)(20) tract and a 5' flanking sequence or no flanking sequence. These data indicate that unwinding of DNA triplexes by the T-ag helicase must be preceded by binding of the helicase to a single-stranded 3' flanking sequence, then the enzyme migrates in a 3'--> 5' direction, using energy provided by ATP hydrolysis, and causes release of the third strand. Unwinding of DNA triplexes by helicases may be required for processes such as DNA replication, transcription, recombination and repair.

The effect of tubular penetration of root canal sealers on dye microleakage

An in vitro study of a possible correlation between penetration of dentinal tubules by four root canal sealers and microleakage of external fluids into the canal was done using a dye leakage method and scanning electron microscopy. The root canals of 45 teeth were instrumented and the smear layer removed prior to obturation of root canals with gutta-percha and one of four sealers: Diaket, Endomethasone, CRCS or Ketac-Endo. The extent of leakage was scored after immersion in India ink for 72 h. The same specimens were also used for scanning electron microscopic evaluation. There was a statistical difference in leakage patterns between the groups (P < 0.05). Diaket had lower microleakage scores than the other sealers (P < 0.05). When the scores for penetration of sealers into the tubules were analysed, Ketac-Endo demonstrated the least penetration (P < 0.01). There appeared to be a converse relation between tubular penetration and dye leakage, but the correlation was not statistically significant (P > 0.05).

Characterization of a multisubunit human protein which selectively binds single stranded d(GA)n and d(GT)n sequence repeats in DNA

A protein which selectively binds d(GA)n and d(GT)n sequence repeats in single stranded DNA has been identified in human fibroblasts. This protein, designated PGB, has been purified at least 500-fold by ammonium sulfate precipitation followed by DEAE-Sepharose column chromatography and affinity chromatography in a column of d(GA)-Sepharose. Electrophoretic mobility shift assays revealed that the PGB protein bound most avidly d(GA)n and d(GT)n tracts of n > 5. It also bound other G-rich DNA sequence repeats, including dGn tracts, with lower affinities. It did not manifest significant binding affinities to single stranded M13 DNA, or to the homopolynucleotides poly dA, poly dC and poly dT, or to various DNA sequence repeats which do not contain G residues, such as d(A-C)n and d(TC)n. It did not bind double stranded d(T-C)n.d(GA)n tracts or other double stranded DNA sequences. In glycerol gradient centrifugation assays the d(GA)n- and the d(GT)n-binding activities cosedimented as a homogeneous protein species having an S20,w = 9.4 +/- 0.7 and an estimated native molecular weight of 190,000 +/- 7,000. UV crosslinking assays revealed that the protein contains 33.6 +/- 2.1 kd subunits which bind d(GA)n and d(GT)n sequences. However, SDS-polyacrylamide gel electrophoresis of the purified protein followed by silver staining indicated that it may also contain other subunits that do not contact the DNA. It is proposed that binding of the PGB protein to single stranded d(GA)n or d(GT)n tracts in double stranded topologically restricted DNA may stimulate strand separation and formation of triple helices or other unusual DNA structures.

(dT-dC)n and (dG-dA)n tracts arrest single stranded DNA replication in vitro

Previous in vivo studies have indicated that (dT-dC)n.(dG-dA)n tracts (referred to here as (TC)n.(GA)n), which are widely dispersed in vertebrate genomes, may serve as pause or arrest signals for DNA replication and amplification. To determine whether these repeat elements act as stop signals for DNA replication in vitro, single stranded DNAs including (TC)n or (GA)n tracts of various lengths, were prepared by cloning such tracts into phage M13 vectors, and were replicated with the Klenow fragment of the E. coli DNA polymerase I, or with the calf thymus DNA polymerase alpha, by extension of an M13 primer. Gel electrophoresis of the reaction products revealed that the replication was specifically arrested around the middle of both (TC)n and (GA)n tracts of n greater than or equal to 16. However, whereas in the (TC)n tracts the arrests were less prominent at pH = 8.0 than at pH = 6.5-7.5, and were completely eliminated at pH = 8.5, the arrests in the (GA)n tracts were stronger at the higher pH values. These results, and previous data, suggest that the arrests were caused by formation of unusual DNA structures, possibly triple helices between partially replicated (TC)n or (GA)n tracts, and unreplicated portions of these sequences.

Unusual sequence element found at the end of an amplicon

In a polyomavirus-transformed rat cell line, designated LPT, the polyomavirus DNA is integrated into a single chromosomal site. Treatment of LPT cells with carcinogens induces amplification of the integrated virus DNA and flanking cellular sequences. We show that the amplification is arrested within a specific cell DNA segment that maps 1.3 to 1.85 kilobases beyond one virus-cell DNA junction, defined as the left junction. We also present the sequence of an 897-base-pair fragment spanning the arrest site. This fragment contains an unusual sequence element, which consists of two contiguous components, a potential cruciform with stems of 6 base pairs and a d(G-A)27 X d(T-C)27 tract, and maps 1,497 to 1,564 nucleotides beyond the left junction. The possibility that this unusual sequence plays a role in the arrest of the amplification process is discussed.

'Illegitimate' recombination events in polyoma-transformed rat cells

In the LPT line of polyoma (Py)-transformed rat cells, amplification of the integrated viral DNA and of cell nucleotide sequences flanking the viral integration site, can be induced either spontaneously or by treatment with carcinogens. We show here that the amplified DNA includes interspersed viral and cellular sequences generated by 'illegitimate' recombination events. Genomic libraries have been prepared in phage lambda vectors from LPT cells treated with the inducing agent mitomycin C and from untreated LPT cells. Four phages, including viral-cell DNA recombinants, have been isolated from these libraries. Sequencing through the recombination sites revealed the following characteristics: (i) The crossover points map at four different positions in the viral DNA and at four different positions in the flanking cell DNA. (ii) There are very short homologous sequences of 1, 2, or 4 bp, at the recombination sites. (iii) Aside from the exchanges between the viral and the cellular DNA, no further rearrangements occurred around the new viral-cellular DNA junctions. (iv) Next to the recombination sites, there are blocks of homopurine-homopyrimidine sequences, which may assume a structure that differs from the Watson-Crick double helix. (v) Clustered homologous sequence blocks of up to 10 bp are present less than 200 bp away from the recombination sites. These homologies are not in register. Based on these results, we propose a model that may account for these recombination events and, more generally, for recombination events that occur during gene amplification in mammalian cells.

"Onion skin" replication of integrated polyoma virus DNA and flanking sequences in polyoma-transformed rat cells: termination within a specific cellular DNA segment

Replication of integrated polyoma virus DNA and flanking cellular sequences was studied in an inducible line of polyoma-transformed rat cells, designated the LPT line, that contains a single viral integration site. Chromosomal DNAs were purified from LPT cells treated with the virus-inducing agent mitomycin C and from untreated cells and were digested with restriction enzymes. The digests were analyzed by the Southern blotting technique. The virus DNA and a recombinant plasmid containing flanking cell DNA were used as hybridization probes. The analysis showed that mitomycin C treatment caused a more than 10-fold amplification of restriction fragments extending up to about 2.0 kilobase pairs into the cellular DNA flanking one end of the viral insertions, defined as the left joint. Fragments extending beyond this region were not amplified. These results showed that (i) integrated polyoma virus DNA undergoes multiple rounds of replication in mitomycin C-treated LPT cells and (ii) the replication extends into the flanking sequences and is arrested within a 0.40-kilobase-pair cellular DNA segment located about 2.0 kilobase pairs beyond the left joint. This segment may include a terminator of a normal cellular replicon.

Integration of polyoma virus DNA into chromosomal DNA in transformed rat cells causes deletion of flanking cell sequences

In order to find out whether polyoma virus (Py) integration into chromosomes causes rearrangements in the cell DNA flanking the integration site, we have mapped the flanking sequences in the inducible LPT line of Py-transformed rat cells and the corresponding sequences in normal rat fibroblasts, and then compared the two maps. To carry out this study we have cloned a segment including Py DNA and flanking sequences in the bacteriophage vector lambda gt WES and subcloned the flanking cell DNA in a bacterial plasmid. We performed a Southern blot analysis of LPT and rat fibroblast DNA digested with various restriction enzymes and used the cloned flanking cell DNA and Py DNA as hybridization probes. Autoradiography of the LPT DNA blots revealed two sets of fragments. One set includes fragments containing both Py and cell DNA sequences; the second set consists of fragments which contain no virus DNA sequences, and are identical to the fragments observed in the corresponding normal rat DNA digests. These data indicate that LPT cells are heterozygous with respect to the Py inserts. The same data were used to map the flanking sequences in the two types of cells. A comparison between the two maps revealed that a 3.0 kb cell DNA segment, which is located next to the unoccupied integration site in the normal rat chromosomes, has been deleted from the LPT chromosome which carries Py DNA, but not from the LPT chromosome which does not carry the virus DNA. The implications for papovavirus integration are discussed.

Integration site of polyoma virus DNA in the inducible LPT line of polyoma-transformed rat cells

The structure of the polyoma virus (Py) integration site in the inducible LPT line of Py-transformed rat cells was determined by biochemical methods of gene mapping. LPT cell DNA was digested with various restriction enzymes. The digestion products were electrophoresed in agarose gels and transferred onto nitrocellulose sheets by Southern blotting. Fragments containing viral or cell DNA sequences, or both, were identified by hybridization with Py DNA or with a cloned flanking cell DNA probe. Cleavage of LPT DNA with enzymes that restrict the Py genome once generated linear Py DNA molecules and two fragments containing both cell and viral DNA sequences. Cleavage of LPT DNA with enzymes which do not restrict Py DNA generated series of fragments whose lengths were found to differ by increments of a whole Py genome; the smallest fragment in each series was found to be longer than the viral genome. These data indicate that LPT cultures contain Py insertions of various lengths integrated into the same chromosomal site in all the cells. The length heterogeneity of the viral insertions is due to the presence of 0, 1, 2, 3. . . Py genomes arranged in a direct tandem repeat within invariable sequences of viral DNA. Double-digestion experiments were also carried out with the above enzymes and with enzymes that cleave the Py genome at multiple sites. The data obtained in these experiments were used to construct a physical map of the integration site. This map showed that the early region of the virus remained intact even in the smallest insertion (which contains no whole duplicated genomes), whereas the late region was partially duplicated and split during integration. The smallest insertion is colinear with the Py physical map over a region including the entire Py genome and at least a part of the duplicated segment. This structure could give rise to nondefective circular viral DNA molecules by single homologous recombination events. Similar recombination events may occur at a higher frequency in the longer insertions, which include longer regions of homology, and may yield many more free viral genomes. The presence of these insertions in LPT cells could thus be one of the factors which account for the high inducibility of the LPT line.

Electron microscopic mapping of RNA transcribed from the late region of polyoma virus DNA

The polyoma virus (Py) RNA species transcribed from the L DNA strand of the "late" region of the Py genome in Py-infected mouse cells have been mapped by hybridization with specific fragments of Py DNA followed by electron microscopic visualization of the hybrids. Total cellular polyadenylated Py-specific RNA molecules having an S value in the range of 16S to 20S were purified by oligodeoxythymidylic acidcellulose column chromatography, preparative hybridization with Py DNA, and sucrose gradient centrifugation. Cytoplasmic Py-specific RNA was similarily purified, except that it was not fractionated by sucrose gradient centrifugation. Hybrids of these RNA molecules and Py DNA fragments were spread for electron microscopy by either the cytochrome c technique or the bacteriophage T4 gene 32 protein method. The polyadenylic acid at the 3'-end of the RNA in the hybrids was identified by labeling with simian virus 40 DNA circles to which polybromodeoxyuridylic acid tails had been covalently attached. These experiments revealed the presence of three L DNA strand transcripts in both RNA preparations. Two of these RNA molecules were found to be spliced from chains transcribed from two noncontiguous parts of the late region. The third molecule either is a continuous transcript of the entire late region or contains a splicing feature which is too small to be reliably observed by the electron microscope methods used. The 5'-ends of the three RNA species map within a region extending from 68 to 70 map units on the Py restriction endonuclease map. Each of the two spliced molecules contains a 5'-terminal leader sequence transcribed from a DNA segment with an estimated length of 60 to 110 nuvleotides. The 3'-ends of the leaders map at 66.7 +/- 1.0 and 66.4 +/- 0.50 map units. In these molecules the 5'-ends of the other part (the main body) map at 59.4 +/- 0.90 and 49.4 +/- 2.0 map units, respectively. The 3'-termini of all three RNA species map at 24 to 25 map units.

Circular dimers of a lambda DNA in infected, nonlysogenic Escherichia coli

Covalently closed circular dimers of phage lambda DNA have been found in Escherichia coli infected with lambda. These dimers can be formed by either the lambda Red or Int systems, by a nonrecombinational replicative mechanism requiring the activity of the lambda O and P genes or by joining of the cohesive ends. Dimers mediated by the E. coli Rec system have not been observed. Those formed by the Int system often result from recombination between different DNA molecules; however, the Red-mediated dimers may be a result of replicative extension of a single DNA molecule. Trimers have also been observed but studied only briefly.