Multicopy single-stranded DNA of Escherichia coli enhances mutation and recombination frequencies by titrating MutS protein

Multicopy single-stranded DNA (msDNA) molecules consist of single-stranded DNA covalently linked to RNA. In Escherichia coli, such molecules are encoded by genetic elements called retrons. The DNA moieties of msDNAs have characteristic stem-loop structures, and most of these structures contain mismatched base pairs. Previously, we showed that retrons encoding msDNAs with mismatched base pairs are mutagenic when present in multicopy plasmids. In this study we show that such msDNAs, in a similar manner to genetic defects in mismatch repair, increase the frequency of interspecies recombination in matings between Salmonella typhimurium and E. coli. To demonstrate interference with mismatch repair by msDNA, we show that the addition of a plasmid containing the gene for MutS protein suppresses the mutagenic and recombinogenic effects of msDNAs. We also show that in mutS mutants, msDNA does not increase the frequency of either mutations or interspecies recombination. We conclude from these findings that the mutagenic and recombinogenic effects of msDNAs are due to titrating out MutS protein.

Multicopy single-stranded DNAs with mismatched base pairs are mutagenic in Escherichia coli

Retrons are genetic elements that encode multicopy single-stranded DNAs called msDNAs. They are clonally distributed in Escherichia coli and retrons in different clones produce DNAs with different nucleotide sequences. msDNAs consist of an RNA molecule covalently linked to a single-stranded DNA molecule. The latter contains an inverted repeat, resulting in a stem-loop structure. In two retrons, Ec83 and Ec78, the DNA is cleaved off from the RNA. All known retrons except Ec78, have one or more mismatched base pairs in the stem-loop structure. We found that two retrons, Ec86 and Ec83, when present in high copy numbers are mutagenic. The ratios of mutation frequencies observed in Lac- indicator strains were similar to the ratios observed for a mutant defective in mismatch repair. It is known that some proteins required for mismatch repair bind to mismatched base pairs prior to carrying out repair. The similarity in the mutation frequency ratios suggested that the mutagenesis caused by msDNAs of retrons Ec86 and Ec83 might be due to sequestration of a mismatch repair protein by msDNA. Strong support for this interpretation was obtained from the finding that the msDNA produced by retron Ec78 is not mutagenic.

Human papillomavirus testing as an optional screening tool in low-resource settings of Latin America: experience from the Latin American Screening study

Hybrid capture II (HC II) test for oncogenic human papillomaviruses (HPV) was carried out in a cohort of 4284 women at their first clinical visit. Overall prevalence of HPV was 17.1%, decreasing with age from 33.9% among women below 20 years to only 11.0% among those older than 41 years. HPV prevalence was significantly higher among current smokers (odds ratio [OR] = 1.31; 95% CI 1.1-1.6), in women with two or more lifetime sexual partners (OR = 1.9; 95% CI 1.6-2.4), and those women with two or more sexual partners during the past 12 months prior to examination (OR = 1.6; 95% CI 1.2-2.2). HPV detection increased in parallel with increasing cytologic abnormality, being highest in women with high-grade squamous intraepithelial lesion (P= 0.001). Specificity of the HPV test in detecting histologically confirmed cervical disease was 85% (95% CI 83.9-86.1). Sensitivity of the HPV test in detecting histologic abnormalities increased in parallel with disease severity, ranging from 51.5% for cervical intraepithelial neoplasia (CIN) 1 to 96.5% for CIN 3 and 100.0% for cancer, with respective decline of positive predictive value. These data suggest that HPV testing with HC II assay might be a viable screening tool among this population with relatively high prevalence of cervical disease.

Evidence for an interaction between alpha-MSH and opioids in the regulation of gonadotropin secretion in man

Gonadotropin secretion is inhibited by the endogenous opioids and stimulated by their antagonist naloxone. LH secretion is stimulated by alpha-MSH, a tridecapeptide derived from the post-translational processing of POMC. The possibility that alpha-MSH interacts with the opioids, as suggested by the experimental evidence, was investigated in 7 normal males aged 24-29 through the performance of seven tests: naloxone (0.8 mg i.v. bolus, followed by infusion of 1.6 mg/h for 120'); alpha-MSH (2.5 mg i.v. bolus); naloxone + alpha-MSH (2.5 mg i.v. 15' after commencement of the naloxone infusion); naloxone + GnRH (100 micrograms i.v. 15' after commencement of the naloxone infusion); alpha-MSH + GnRH (respectively 2.5 mg and 100 micrograms at time 0), GnRH alone (100 micrograms at time 0), placebo (150 nmol/l NaCl solution). The LH AUCs during both naloxone (30.3 +/- 2.7 mIU/ml.min-1) and alpha-MSH test (32.9 +/- 4.6 mIU/ml.min-1) were significantly greater (p < 0.005) than that observed during placebo (16.9 +/- 3.6 mIU/ml.min-1). The LH AUC during alpha-MSH + naloxone (37.6 +/- 2.6 mIU/ml.min-1) was not significantly different from that recorded during their separate administration. GnRH injected alone, during the naloxone infusion and with alpha-MSH produced similar increases in LH, that were significantly higher than that observed during the other tests (AUCs: GnRH 89.4 +/- 10.6, GnRH + naloxone 100.5 +/- 9.1, GnRH + alpha-MSH 94.6 +/- 7.9 mIU/ml.min-1, p < 0.001). Significant increase in FSH (p < 0.001) was only observed during GnRH, GnRH + naloxone and GnRH + aMSH tests (AUCs: placebo 13.3 +/- 1.7; naloxone 14.7 +/- 2.5; alpha-MSH 15.5 +/- 2.3; alpha-MSH + naloxone 16.9 +/- 1.9; GnRH 19.1 +/- 1.1; GnRH + alpha-MSH 20.7 +/- 1.3; GnRH + naloxone 21.2 +/- 1.8 mIU/ml.min-1). These results are in line with the possibility of an interaction between alpha-MSH and the opioids in the regulation of gonadotropin secretion, perhaps with opposing effects on a final common pathway.

Distribution of human immunodeficiency virus type 1 subtypes in the State of Amazonas, Brazil, and subtype C identification

Few studies have reported the molecular epidemiological characterization of HIV-1 in the Northern region of Brazil. The present study reports the molecular and epidemiological characterization of 31 HIV-1 isolates from blood donors from the State of Amazonas who donated blood between April 2006 and March 2007. Serum/plasma samples from all donors were screened for HIV antibodies by ELISA and the results confirmed by Western blot analysis. Genomic DNA was extracted from the buffy coat using the Super Quik-Gene-DNA Isolation kit. Nested PCR was performed on the env, gag, and pol regions of HIV-1 using the Gene Amp PCR System 9700. Sequencing reactions were performed using the inner PCR primers and the DYEnamic™ ET Dye Terminator Kit, and phylogenetic analysis was performed using the gag, pol, and env gene sequences. We collected samples from 31 blood donors who tested positive for HIV-1 in confirmatory experiments. The male:female ratio of blood donors was 3.4:1, and the mean age was 32.4 years (range: 19 to 61 years). Phylogenetic analysis showed that subtype B is the most prevalent among Northern Brazilian HIV-1-seropositive blood donors. One HIV-1 subtype C and one circulating recombinant form (CRF_BF) of HIV-1 were identified in the State of Amazonas. This is the first study showing the occurrence of a possible “homogenous” subtype C in this region of Brazil. This finding could contribute to a better characterization of the HIV-1 strains that circulate in the country. Key words: HIV-1; Subtypes; Phylogenetic analysis; Blood donors; Molecular and epidemiological characterization

Communication: Glass transition and melting lines of an ionic liquid

The phase diagram of the ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesufonyl)imide, [Pyrr_1,4][NTf₂], was explored by synchroton X-ray diffraction and Raman scattering measurements as a function of temperature and pressure. Glass transition T_g(p) and melting T_m(p) temperatures were obtained from atmospheric pressure up to ca. 2.0 GPa. We found that both the T_g(p) and T_m(p) curves follow essentially the same pressure dependence. The similarity of pressure coefficients, dT_g/dp ≈ dT_m/dp, is explained within the non-equilibrium thermodynamics approach for the glass transition by assuming that one of the Ehrenfest equations is appropriated for T_g(p), whereas T_m(p) follows the Clausius-Clapeyron equation valid for the first-order transitions. The results highlight that ionic liquids are excellent model systems to address fundamental questions related to the glass transition.

Valsalva manoeuvre effect on distribution of lung damage in heroin inhalation

This article reports the case of a patient demonstrating acute bilateral pneumonitis almost completely confined to the upper lobes as a result of inhaling heroin. We attribute this distribution to the patient performing the Valsalva manoeuvre immediately after inhaling heroin. This pattern has not been reported before and we believe it may be seen more frequently owing to a switch amongst drug users from intravenous to inhaled heroin.

Influence of central sidechain on self-assembly of glycine-x-glycine peptides

Low molecular weight gelators (LMWGs) are the subject of intense research for a range of biomedical and engineering applications. Peptides are a special class of LMWG, which offer infinite sequence possibilities and, therefore, engineered properties. This work examines the propensity of the GxG peptide family, where x denotes a guest residue, to self-assemble into fibril networks via changes in pH and ethanol concentration. These triggers for gelation are motivated by recent work on GHG and GAG, which unexpectedly self-assemble into centimeter long fibril networks with unique rheological properties. The propensity of GxG peptides to self-assemble, and the physical and chemical properties of the self-assembled structures are characterized by microscopy, spectroscopy, rheology, and X-ray diffraction. Interestingly, we show that the number, length, size, and morphology of the crystalline self-assembled aggregates depend significantly on the x-residue chemistry and the solution conditions, i.e. pH, temperature, peptide concentration, etc. The different x-residues allow us to probe the importance of different peptide interactions, e.g. π-π stacking, hydrogen bonding, and hydrophobicity, on the formation of fibrils. We conclude that fibril formation requires π-π stacking interactions in pure water, while hydrogen bonding can form fibrils in the presence of ethanol-water solutions. These results validate and support theoretical arguments on the propensity for self-assembly and leads to a better understanding of the relationship between peptide chemistry and fibril self-assembly. Overall, GxG peptides constitute a unique family of peptides, whose characterization will aid in advancing our understanding of self-assembly driving forces for fibril formation in peptide systems.

Forbidden Secondary Structures Found in Gel-Forming Fibrils of Glycylphenylalanylglycine

The zwitterionic l-tripeptide glycylphenylalanylglycine self-assembles into very long crystalline fibrils in an aqueous solution, which causes the formation of an exceptionally strong gel phase (G' ∼ 5 × 10⁶ Pa). The Rietveld refinement analysis of its powder X-ray diffraction (PXRD) pattern reveals a unit cell with four peptides forming a P2₁2₁2₁ space group and adopting an inverse polyproline II conformation, that is, a right-handed helical structure that occupies the "forbidden" region of the Ramachandran plot. This unusual structure is stabilized by a plethora of intermolecular interactions facilitated by the large number of different functional groups of the unblocked tripeptide. Comparisons of simulated and experimental Fourier transform infrared and vibrational circular dichroism (VCD) amide I' profiles corroborate the PXRD structure. Our experimental setup reduces the sample to a quasi-two-dimensional network of fibrils. We exploited the influence of this reduced dimensionality on the amide I VCD to identify the main fibril axis. We demonstrate that PXRD, vibrational spectroscopy, and amide I simulations provide a powerful toolset for secondary structure and fibril axis determination.

Local Order-Disorder Transition Driving by Structural Heterogeneity in a Benzyl Functionalized Ionic Liquid

A local order-disorder transition has been disclosed in the thermophysical behavior of the ionic liquid 1-benzyl-3-methylimidazolium dicyanamide, [Bzmim][N(CN)₂], and its microscopic nature revealed by spectroscopic techniques. Differential scanning calorimetry and specific heat measurements show a thermal event of small enthalpy variation taking place in the range 250-260 K, which is not due to crystallization or melting. Molecular dynamic simulations and X-ray diffraction measurements have been used to discuss the segregation of domains in the liquid structure of [Bzmim][N(CN)₂]. Raman and NMR spectroscopy measurements as a function of temperature indicate that the microscopic origin of the event observed in the calorimetric measurements comes from structural rearrangement involving the benzyl group. The results indicate that the characteristic structural heterogeneity allow for rearrangements within local domains implying the good glass-forming ability for the low viscosity ionic liquid [Bzmim][N(CN)₂]. This work sheds light on our understanding of the microscopic origin behind complex thermal behavior of ionic liquids.

An inelastic neutron scattering, Raman, far-infrared, and molecular dynamics study of the intermolecular dynamics of two ionic liquids

The intermolecular dynamics in the THz frequency range of the ionic liquids n-butyl-trimethylammonium bis(trifluoromethanesulfonyl)imide, [N1114][NTf2], and methyl-tributylammonium bis(trifluoromethanesulfonyl)imide, [N1444][NTf2], were investigated by a combined usage of inelastic neutron scattering (INS), Raman, and far-infrared (FIR) spectroscopies and the power spectrum calculated by molecular dynamics (MD) simulations. The collective dynamics of the simulated systems is also discussed by the calculation of time correlation functions of charge and mass currents that are projected onto acoustic- and optic-like motions. The INS and Raman measurements have been performed as a function of temperature in the glassy, crystalline, and liquid phases. The excess in the vibrational density of states over the expectation of the Debye theory, the so-called boson peak, is found in the INS and Raman spectra as a peak at ∼2 meV (∼16 cm-1) and also in the direct measurement of heat capacity at very low temperatures (4-20 K). This low-frequency vibration is incorporated into the curve fits of Raman, FIR, and MD data at room temperature. Fits of spectra from these different sources in the range below 100 cm-1 are consistently achieved with three components at ca. 25, 50, and 80 cm-1, but with distinct relative intensities among the different techniques. It is proposed as the collective nature of the lowest-frequency component and the anion-cation intermolecular vibration nature of the highest-frequency component. The MD results indicate that there is no clear distinction between acoustic and optic vibrations in the spectral range investigated in this work for the ionic liquids [N1114][NTf2] and [N1444][NTf2]. The analysis carried out here agrees in part, but not entirely, with other propositions in the literature, mainly from optical Kerr effect (OKE) and FIR spectroscopies, concerning the intermolecular dynamics of ionic liquids.

Low-frequency Raman spectra of a glass-forming ionic liquid at low temperature and high pressure

The frequency range below ∼100 cm^-1 of the Raman spectrum of a glass-forming liquid exhibits two features that characterize the short-time (THz) dynamics: the quasi-elastic scattering (QES) tail and the boson peak (BP). In this work, we follow temperature and pressure effects on the intermolecular dynamics of a typical ionic liquid, 1-butyl-1-methylpiperidinium bis(trifluoromethanesulfonyl)imide, [Pip₁₄][[NTf₂]. The glass transition temperature of [Pip₁₄][[NTf₂] at atmospheric pressure is T_g = 198 K, and the pressure of glass transition at room temperature is P_g = 1.1 GPa. Raman spectra obtained while cooling the liquid or heating the glass exhibit hysteresis in QES and BP intensities, I_QES and I_BP. The dependence of I_QES, I_BP, and the BP frequency, ω_BP, with pressure up to the glass transition is steeper than the temperature dependence due to the stronger pressure effect on density within the GPa range. The temperature and pressure behaviors of the parameters I_QES, I_BP, and ω_BP obtained here for [Pip₁₄][[NTf₂] are discussed in light of known results for other glass-formers.

Anharmonic transitions in nearly dry L-cysteine I

Two special dynamical transitions of universal character have recently been observed in macromolecules (lysozyme, myoglobin, bacteriorhodopsin, DNA and RNA) at T* ~100-150 K and T(D) ~180-220 K. The underlying mechanisms governing these transitions have been the subject of debate. In the present work, a survey is reported on the temperature dependence of structural, vibrational and thermodynamical properties of a nearly anhydrous amino acid (orthorhombic polymorph of the amino acid l-cysteine at a hydration level of 3.5%). The temperature dependence of x-ray powder diffraction patterns, Raman spectra and specific heat revealed these two transitions at T* = 70 K and T(D) = 230 K for this sample. The data were analyzed considering amino acid-amino acid, amino acid-water, water-water phonon-phonon interactions and molecular rotor activation. Our results indicated that the two referred temperatures define the triggering of very simple and particular events that govern all the interactions of the biomolecular: activation of CH(2) rigid rotors (T < T* ), phonon-phonon interactions between specific amino acid and water dimer vibrational modes (T* < T < T(D)), and water rotational barriers surpassing (T > T(D)).

Determining the nanostructure and main axis of gly-his-gly fibrils using the amide I' bands in FTIR, VCD, and Raman spectra

The zwitterionic tripeptide glycyl-histidine-glycine (GHG) has been shown to self-assemble into visible crystalline fibrils that form a gel-supporting network with a very high storage modulus. Here we elaborate on the theory and experimental setup behind our novel approach employed to determining the main fibril axis for these gel-forming fibrils by simulating the amide I band profile for infrared absorption (IR), vibrational circular dichroism (VCD), and visible Raman scattering. We also highlight that combining these three vibrational spectroscopies can help in validating structures that are solved using powder x-ray diffraction analysis (PXRD). The PXRD analysis yielded a GHG fibril unit cell with P21 symmetry containing two peptide monomers and two water molecules. The monomers adopt a conformation reminiscent of the distorted polyproline II conformation obtained for tri-lysine in aqueous solution. Stabilization occurs primarily through peptide-peptide intermolecular hydrogen bond interactions, while the role of water in peptide hydration is minimal. The comparison of simulated and experimental amide I' band profiles suggests that the xz plane of the crystal unit cell is being predominantly probed in the experimental IR and VCD spectra, with the x axis of the unit cell pointing in the direction of the main fibril axis. The monomer peptide in the unit cell interacts with six adjacent peptides forming hydrophobic channels by edge-to-face and parallel-displaced ππstacking in the y direction. These cores are further stabilized by a plethora of intermolecular interactions in the x and z directions. Our result suggests that the hydrophobic xz-surfaces would be a good target for the adsorption of hydrophobic drugs.

Osler-Weber-Rendu syndrome during pregnancy

Osler-Weber-Rendu syndrome is a very rare systemic fibrovascular dysplasia. Rupture of angiomas can cause haemorrhages, which sometimes can be severe with difficult bleeding control. The main manifestation is recurrent epistaxis. Treatment of this disorder is symptomatic. During pregnancy, there may be an increased risk of complications. We describe a case of a pregnant woman with Osler-Weber-Rendu syndrome. Besides frequent epistaxis and microcytic hypochromic anaemia that resolved with oral iron treatment, she had a normal pregnancy, vaginal delivery and puerperium without complications.

Spatial and thermal signatures of α and β relaxations in glassy and glacial aliphatic ionic liquids

The competition between Coulomb and van der Waals interactions brings forth unique dynamic features and broad applications to ionic liquids. Herein, we present a combined calorimetric, X-ray diffraction, incoherent elastic, and quasi-elastic neutron scattering study, over a wide temperature range (180-340 K), of the relaxational dynamics of the liquid, supercooled liquid, crystalline, glassy, and glacial states of two model ionic liquids: tributylmethylammonium (a good glass-former) and butyltrimethylammonium (a good crystal-former) cations and the bis(trifluoromethanesulfonyl)imide anion. In both systems, we observed two distinct relaxation processes. The Q-dependence of the respective relaxation time shows that the α-process is diffusive, while the β-process is modulated by the structure of the liquids.

Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae) Oviposition Behavior in Previous Oviposition Situation

Blowflies use their sense of smell to locate oviposition substrates and their vision to direct and assist in landing decision. Blowflies' ovipositions are usually aggregated. Chrysomya megacephala (Fabricius) females, for example, prefer to lay eggs on substrates containing fresh eggs of the same species. However, it is possible that females would be capable of evaluating the substrate, reducing the size of egg cluster in sites with a high amount of eggs or larvae, or finding another site for laying their eggs, preventing the progeny from facing high competition for space and food. The present study aimed to investigate whether females of C. megacephala could distinguish and preferentially select previously infested substrates and whether females would lay their eggs attached or separate from eggs previously laid on the substrate. Behavioral measures were conducted inside cages under laboratory conditions in free-choice tests. Data analysis confirmed that C. megacephala females are able to distinguish the presence of cospecific eggs in the substrate and preferentially select previously infested substrates for egg laying, depositing their eggs separate from pre-existing large egg masses.

Correlations between radiometric analysis of Quaternary deposits and the chronology of prehistoric settlements from the southeastern Brazilian coast

Natural gamma radiation measurements of sand deposits were carried out in order to study the chronology of prehistoric colonization of the Brazilian coast during the Holocene. The method employs thorium, uranium and potassium as tracers of the geological provenance of Quaternary deposits, where artificial shellmounds are found. The so-called sambaquis are archaeological settlements, characteristic of fisher-gatherers, specialized in the exploitation of shellfish. Our results show a considerable positive correlation between the formation of coastal deposits, based on cross plots of eTh/eU and eTh/K, and the antiquity of its prehistoric human occupation.