Metal-ion catalyzed polymerization in the eutectic phase in water-ice: a possible approach to template-directed RNA polymerization

The emergence of an RNA world requires among other processes the non-enzymatic, template-directed replication of genetic polymers such as RNA or related nucleic acids, possibly catalyzed by metal-ions. The absence of uridilate derivative polymerization on adenine containing templates has been the main issue preventing an efficient template-directed RNA polymerization. We report here the investigation of template-directed RNA polymerization in the eutectic phase in water–ice. In particular, it was found that activated uridilate monomers in the presence of metal-ion catalysts could efficiently elongate RNA hairpins whose 5′-overhangs served as the templating sequence. The same applies for every other pyrimidine and purine nucleobase. Moreover, the initial elongation rates were always higher in the presence of a template complementary to the nucleotide than in systems without proper base-pairing opportunities. These results suggest that a template-directed RNA polymerization catalyzed by metal-ions could be carried out under eutectic phase in water–ice conditions.     

Linear polyethylenimine as a tool for comparative studies of antisense and short double-stranded RNA oligonucleotides

Despite the recently enlarged field of available RNA knock-down technologies, e.g., antisense oligonucleotides (ASOs) and duplexes of synthetic 21 nucleotides RNAs (siRNAs), no versatile transfection reagent has been reported to deliver different nucleic acids formats at high rates of efficiency. We have evaluated the versatility and efficacy of linear PEI in transfecting and properly delivering a broad panel of nucleic acids such as short oligonucleotides and double-stranded RNA into cells in culture.     

Eutectic phase in water-ice: a self-assembled environment conducive to metal-catalyzed non-enzymatic RNA polymerization

Information and catalytic polymers play an essential role in contemporary cellular life, and their emergence must have been crucial during the complex processes that led to the assembly of the first living systems. Polymerization reactions producing these molecules would have had to occur in aqueous medium, which is known to disfavor such reactions. Thus, it was proposed early on that these polymerizations had to be supported by particular environments, such as mineral surfaces and eutectic phases in water-ice, which would have led to the concentration of the monomers out of the bulk aqueous medium and their condensation. This review presents the work conducted to understand how the eutectic phases in water-ice might have promoted RNA polymerization, thereby presumably contributing to the emergence of the ancient information and catalytic system envisioned by the 'RNA-World' hypothesis.     

A method for the rapid and precise determination of acclimated phytoplankton reproduction rates

A rapid method for measuring, simultaneously, the asexual reproductionrates of hundreds of phytoplankton cultures is described. Thismethod is based on the dairy measurement of in vivo chlorophyllfluorescence read directly in the culture tubes. Hundreds ofthese culture tubes, containing specially prepared culture medium,can be maintained in identical environments in specially designedconstant environment devices. The method is capable of measuringthe acclimated reproduction rates of phytoplankton cultureswith an error of 3–4% (coefficient of variation). Completeacclimation, crucial to the detection of small genetic differencesbetween clones, takes one to three weeks, thus necessitatinglong-term experiments. Studies using the methods described indicatethat, in a constant environment, coccolithophores and dinoflagellatesreproduce at constant rates, but diatoms do not.     

Fast atom bombardment mass spectrometry as a tool for the rapid determination of enantioselective binding of methylated cyclodextrins

The first FABMS study of the enantioselectivity shown during complex formation between per-methylated cyclodextrins and pairs of enantiomeric guest molecules is described. The 1:1 mixtures of the cyclodextrins, both α- and β-, with the guests, the methyl esters of the amino acids tryptophan and phenylalanine, were studied in a 100:50:1 glycerol-thioglycerol-trifluoro-acetic acid matrix. The uncomplexed cyclodextrin peaks were then used as internal standards to determine the preference of the cavity for one or other of the enantiomers. A clear trend for the preferential binding, greater than 5:1 in each case, of the d-enantiomers of the amino acid esters was observed in agreement with literature ¹H NMR experiments. This methodology provides a rapid route to assessing the enantioselectivity shown by the widely used cyclodextrins towards pairs of enantiomeric guests.     

Stem-loop oligonucleotides: a robust tool for molecular biology and biotechnology

The specific structural features of stem-loop (hairpin) DNA constructs provide increased specificity of target recognition. Recently, several robust assays have been developed that exploit the potential of structurally constrained oligonucleotides to hybridize with their cognate targets. Here, I review new diagnostic approaches based on the formation of stem-loop DNA oligonucleotides: molecular beacon methodology, suppression PCR approaches and the use of hairpin probes in DNA microarrays. The advantages of these techniques over existing ones for sequence-specific DNA detection, amplification and manipulation are discussed.     

Riboprints as a tool for rapid preliminary identification of sphingomonads

Fourtythree strains of the genus Sphingomonas and close relatives were subjected to riboprint analyses generated after digestion of genomic DNA with the restriction enzyme EcoRI and hybridization with E. coli rrnB operon. The majority of strains were characterized by a complex banding pattern in the riboprints. High degrees of similarities in the riboprints were only observed among strains of the same species such as S. yanoikuyae, S. aromaticivorans, S. subarctica and S. chlorophenolica. Strains of different species including close phylogenetic relatives such as S. asaccharolytica, S. mali and S. pruni were easily distinguished by the differences in the riboprints even after visual evaluation. Thus, our data demonstrate that riboprint analysis is useful for preliminary identification of new sphingomonad isolates at the species level.     

A rapid technique for the determination of RNA and DNA in marine phytoplankton

An adaptation of the ethidium bromide technique for the analysisof nucleic acids is presented for marine phytoplankton. Themethod involves an initial homogenization of cells in phosphatebuffered saline, followed by incubation of subsamples of thecell homogenate in the presence and absence of ribonudease.Quantities of DNA and DNA + RNA in the respective sub-samplesare then determined by reaction with ethidium bromide. An evaluationis made of appropriate levels of bentonite required in the assayto inhibit endogenous cellular ribonucleases. Two nucleoproteindissociating agents, pronase and heparin, are also investigatedfor their capacities to enhance nucleic add fluorescence yield.The final recommended method resulted in maximum measured levelsof RNA and DNA in phytoplankton samples tested. The method canbe rapidly performed, involves a minimum amount of sample manipulation,and yields numbers having a high degree of precision. ¹Current address: School of Fisheries, University of Washington,WH-l0, Seattle, WA 98195, USA. ²Current address: Bigelow Laboratory for Ocean Sciences, WestBoothbay Harbor, ME 04575, USA.     

Loopstructures in synthetic oligonucleotides. Hairpin stability and structure studied as a function of loop elongation

The formation of hairpin structures in the homologous, (partly) self-complementary DNA fragments d(ATCCTAT_nTAGGAT), n = 0–7, was studied by means of nuclear magnetic resonance, T-jump and ultra-violet techniques. It is shown that all compounds in the series may adopt hairpin-like conformations, albeit for n < 3 this only occurs to a significant amount at relatively low concentrations (∼ 10μM). For the present series of oligonucleotides, hairpin formation is accompanied by an apparent loop enthalpy significantly different from zero. The stability of the DNA hairpins turns out to be at its maximum for loop lengths of four or five residues, whereas earlier experiments (Tinocoet al., 1973) indicated that loop lengths of six to seven residues are most favourable for RNA hairpins. This is explained by considering the difference in geometry of A-RNA and B-DNA helices.     

Identification of an EcoRI restriction site for a rapid and precise determination of beta-asarone-free Acorus calamus cytotypes

Calamus (Acorus calamus L., Araceae) is an aromatic herb, indigenous to Central Asia and Eastern Europe. The fragrant oils obtained by alcoholic extraction of the rhizome are mainly used in the pharmaceutical and oenological industries. Nevertheless, the occurrence of beta-asarone [(Z)-1,2,4-trimethoxy-5-prop-1-enyl-benzene] limits the possibility of its use due to the carcinogenic properties of this compound. The aim of this work was to identify a diploid beta-asarone-free A. calamus by using chemical and molecular approaches. For these purposes alcoholic extracts of both diploid and triploid A. calamus were analyzed by gas chromatography-mass spectrometry (GC-MS) and comparison of the 700 bp sequence of the non-transcribed spacer (NTS) in the 5S-rRNA gene was also performed. Alcoholic extracts of the triploid A. calamus were characterized by a higher percentage of beta-asarone (11%), which was the main compound, followed by higher percentages of camphene (2.27%), E-beta-ocimene (3.28%), camphor (1.54%), calarene (1.42%), alpha-selinene (5.02%) and tau-cadinol (2.00%), when compared to the diploid A. calamus. The latter had higher percentages of iso-shyobunone (8.62%), beta-sesquiphellandrene (3.28%), preiso calamendiol (22.81%) and acorone (26.33%), and completely lacked of beta-asarone. The 5S-rRNA spacer region of both diploid and triploid A. calamus were amplified by PCR using a pair of primers located at the 3' and 5' ends of the coding sequence of 5S-rRNA gene. The resulting PCR products (about 700 bp) were gel purified, subcloned into pGEM-T Easy vector and sequenced. By aligning the isolated nucleotide sequences of the two varieties and the sequences from different A. calamus chemotypes present in Genbank, sequence diversities were found in the spacer region. Furthermore, the PCR products were digested by using EcoRI. The restriction profile of the spacer domain resulted different for the two cytotypes. Along with chemical analysis of alcoholic extracts, sequence analysis coupled to restriction mapping was demonstrated to represent a powerful tool to distinguish the A. calamus diploid cytotype from the others. The security and effective usage of the diploid beta-asarone-free A. calamus was also discussed.     

A photochemical method for rapid and precise determination of carbon monoxide levels in blood.

A simple and inexpensive flash photolysis apparatus for determination of the level of carbon monoxide saturation of blood samples is described. Saturation with CO is determined by observing the change in light transmission at 432 nm produced on photolysis of bound CO with a light flash. The procedure is highly specific for carbon monoxide, requires less than 5 μl of blood (obtainable from a finger prick), and has a resolution better than 0.1% in saturation. In addition the apparatus does not require frequent calibration.     

Turbidity as a probe of tubulin polymerization kinetics: a theoretical and experimental re-examination

We report here an examination of the validity of the experimental practice of using solution turbidity to study the polymerization kinetics of microtubule formation. The investigative approach proceeds via numerical solution of model rate equations to yield the time dependence of each microtubule species, followed by the calculation of the time- and wavelength-dependent turbidity generated by the calculated distribution of rod lengths. The wavelength dependence of the turbidity along the time course is analyzed to search for generalized kinetic regimes that satisfy a constant proportionality relationship between the observed turbidity and the weight concentration of polymerized tubulin. An empirical analysis, which permits valid interpretation of turbidity data for distributions of microtubules that are not long relative to the wavelength of incident light, is proposed. The basic correctness of the simulation work is shown by the analysis of the experimental time dependence of the turbidity wavelength exponent for microtubule formation in taxol-supplemented 0.1 M Pipes buffer (1 mM GTP, 1 mM EGTA, 1 mM MgSO4, pH 6.4). We believe that the general findings and principles outlined here are applicable to studies of other fibril-forming systems that use turbidity as a marker of polymerization progress.     

H-Y antigen as a tool for the determination of the heterogametic sex in Amphibia

H-Y antigen was investigated in three amphibian species with different degrees of sex-chromosome differentiation: Bufo bufo, Triturus vulgaris, and Pyxicephalus adspersus. No heteromorphic sex chromosomes were found in B. bufo, but an examination of the progeny of hermaphrodites (Ponse, 1942) indicated that the female of this species was heterogametic (ZW). Sex chromosomes differing only by a very small heterochromatic region at their telomeres were found in the male of T. vulgaris (XY). Pyxicephalus adspersus revealed high differentiated ZW sex chromosomes. The results of the H-Y antigen studies on these three species indicate that H-Y antigen is expressed only in the heterogametic sex, irrespective of differences in morphological differentiation of the sex chromosomes. Therefore, H-Y antigen could be a valuable tool in determining the heterogametic sex, not only in Amphibia but possibly also in other vertebrate species that have either evolved no heteromorphic sex chromosomes or where sex-reversal experiments are not possible.