Thomas Buhse

Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs

Making ribose in interstellar ices Astrobiologists have long speculated on the origin of prebiotic molecules such as amino acids and sugars. Meinert et al. demonstrated that numerous prebiotic molecules can be formed in an interstellar-analog sample containing a mixture of simple ices of water, methanol, and ammonia. They irradiated the sample with ultraviolet light under conditions similar to those expected during the formation of the solar system. This yielded a wide variety of sugars, including ribose—a major constituent of ribonucleic acid (RNA). Science, this issue p. 208 Prebiotic sugars, including ribose, can be made by irradiating simple ices under interstellar conditions. Ribose is the central molecular subunit in RNA, but the prebiotic origin of ribose remains unknown. We observed the formation of substantial quantities of ribose and a diversity of structurally related sugar molecules such as arabinose, xylose, and lyxose in the room-temperature organic residues of photo-processed interstellar ice analogs initially composed of H2O, CH3OH, and NH3. Our results suggest that the generation of numerous sugar molecules, including the aldopentose ribose, may be possible from photochemical and thermal treatment of cosmic ices in the late stages of the solar nebula. Our detection of ribose provides plausible insights into the chemical processes that could lead to formation of biologically relevant molecules in suitable planetary environments.

A tentative kinetic model for chiral amplification in autocatalytic alkylzinc additions

A simplified kinetic model is proposed to describe stereoselective autocatalysis in specific alkylzinc additions. The model is based on current experimental knowledge and by the use of exclusively mono- or bimolecular processes attempting a chemically and kinetically realistic description. The underlying dynamics were expressed in terms of a template-directed self-replication in which a zinc alkoxide dimer acts as the active autocatalytic species. The model was shown to reproduce previously obtained kinetic data well, to address to the phenomenon of chiral amplification in a semi-quantitative manner, and to enlighten the cause of the effect of the initial enantiomeric excess on the globally observed kinetics. Amplification of enantiomeric excess occurs by considering a homogeneous and entirely symmetric reaction network.

Aldehydes and sugars from evolved precometary ice analogs: Importance of ices in astrochemical and prebiotic evolution

Significance In molecular clouds out of which stars and planetary systems form, simple solid-state molecules made in large part of H2O, CO, CO2, CH3OH, and NH3 are abundantly present. In these environments, energetic and thermal processes on these ices, which can be simulated in the laboratory, lead to complex organic matter. Possibly at the origin of the organic matter in our Solar System and incorporated into planetesimals, this material may be considered as a potential source for prebiotic chemistry on telluric planets, following a process that may be quite universal. The composition of these laboratory-evolved ices includes potentially prebiotic species such as amino acids and, as presented in this paper, aldehydes and sugars. Evolved interstellar ices observed in dense protostellar molecular clouds may arguably be considered as part of precometary materials that will later fall on primitive telluric planets, bringing a wealth of complex organic compounds. In our laboratory, experiments reproducing the photo/thermochemical evolution of these ices are routinely performed. Following previous amino acid identifications in the resulting room temperature organic residues, we have searched for a different family of molecules of potential prebiotic interest. Using multidimensional gas chromatography coupled to time-of-flight mass spectrometry, we have detected 10 aldehydes, including the sugar-related glycolaldehyde and glyceraldehyde—two species considered as key prebiotic intermediates in the first steps toward the synthesis of ribonucleotides in a planetary environment. The presence of ammonia in water and methanol ice mixtures appears essential for the recovery of these aldehydes in the refractory organic residue at room temperature, although these products are free of nitrogen. We finally point out the importance of detecting aldehydes and sugars in extraterrestrial environments, in the gas phase of hot molecular clouds, and, more importantly, in comets and in primitive meteorites that have most probably seeded the Earth with organic material as early as 4.2 billion years ago.

Kinetic Insight into Specific Features of the Autocatalytic Soai Reaction

The addition of diisopropylzinc to prochiral pyrimidine carbaldehydes (Soai reaction) is the onlyknown example of spontaneous asymmetric synthesis in organic chemistry. It serves as a model systemfor the spontaneous occurrence of chiral asymmetry from achiral initial conditions. This review describesthe possible kinetic origin of specific experimental features of this reaction. It is shown that generickinetic models, including enantioselective autocatalysis and mutual inhibition between the enantiomers,are adequate to describe a variety of the astonishing properties of the Soai reaction. Namely, theseare the unprecedented strong chiral amplification, extreme sensitivity to the presence of very small amountsof chiral initiator, mirror-symmetry breaking when starting from achiral conditions, and the reversal ofenantioselectivity of chiral catalysts by addition of achiral additives. The described kinetic approachallows a closer insight into the nonlinear dynamics of the Soai reaction. It also reveals that a numberof open questions concerning the detailed reaction mechanism are still to be solved and that further experimentalstudies are required.

Expression of Cholera Toxin under Non-AKI Conditions in Vibrio cholerae El Tor Induced by Increasing the Exposed Surface of Cultures

The regulatory systems controlling expression of the ctxAB genes encoding cholera toxin (CT) in the classical and El Tor biotypes of pathogenic Vibrio cholerae have been characterized and found to be almost identical. Notwithstanding this, special in vitro conditions, called AKI conditions, are required for El Tor bacteria to produce CT. The AKI conditions involve biphasic cultures. In phase 1 the organism is grown in a still tube for 4 h. In phase 2 the medium is poured into a flask to continue growth with shaking. Virtually no expression of CT occurs if this protocol is not followed. Here we demonstrated that CT expression takes place in single-phase still cultures if the volume-to-surface-area ratio is decreased, both under air and under an inert atmosphere. The expression of key genes involved in the regulation of CT production was analyzed, and we found that the expression pattern closely resembles the in vivo expression pattern.

Characterization of Selective Antibacterial Peptides by Polarity Index

In the recent decades, antibacterial peptides have occupied a strategic position for pharmaceutical drug applications and became subject of intense research activities since they are used to strengthen the immune system of all living organisms by protecting them from pathogenic bacteria. This work proposes a simple and easy statistical/computational method through a peptide polarity index measure by which an antibacterial peptide subgroup can be efficiently identified, that is, characterized by a high toxicity to bacterial membranes but presents a low toxicity to mammal cells. These peptides also have the feature not to adopt to an alpha-helicoidal structure in aqueous solution. The double-blind test carried out to the whole Antimicrobial Peptide Database (November 2011) showed an accuracy of 90% applying the polarity index method for the identification of such antibacterial peptide groups.

Noise-Induced Enantioselection in Chiral Autocatalysis

Noise added to a chirally autocatalytic model system is usually known to cause mirror-symmetry breaking with statistically equal distributions for the two product enantiomers. We show that if such a system is asymmetrically perturbed by means of a very small undetectable bias in the racemization equilibrium between the two enantiomers, adding Gaussian white noise can lead to an efficient enantioselection. Consequently, within a certain range of the noise amplitude, symmetry breaking gives rise to an entirely biased statistical distribution in favor of one of the enantiomers. In contrast, racemic results will be obtained for the corresponding deterministic case (in the absence of noise). Thus, added noise plays a constructive role by directing the chiral system into a specific enantiomeric direction while being influenced only by a subthreshold asymmetric input. This effect could be of conceptual interest for the impact of weak asymmetric fields on nonlinear chemical reactions.

Anomalous behaviour of the quartz crystal microbalance in the presence of electrolytes

Quartz crystal microbalance (QCM) impedance analysis was used as a microgravimetric tool for thiol adsorptions in a flow injection system. The presence of electrolyte was found to interfere with the proper measurement of the deposited mass and resulted in an error of more than 70%. Aqueous solutions of 1∶1 electrolytes, of up to 6 mM can cause mass errors as high as 60 ng cm−2, that is the equivalent of a monolayer of medium sized molecules. 1∶2, 1∶3, and 2∶2 electrolytes yield even higher errors. The interference is mainly due to the mechanical elasticity of the Gouy Chapman diffuse double layer and cannot be excluded even by using sophisticated QCM impedance methods.

Detection of Severe Respiratory Disease Epidemic Outbreaks by CUSUM-Based Overcrowd-Severe-Respiratory-Disease-Index Model

A severe respiratory disease epidemic outbreak correlates with a high demand of specific supplies and specialized personnel to hold it back in a wide region or set of regions; these supplies would be beds, storage areas, hemodynamic monitors, and mechanical ventilators, as well as physicians, respiratory technicians, and specialized nurses. We describe an online cumulative sum based model named Overcrowd-Severe-Respiratory-Disease-Index based on the Modified Overcrowd Index that simultaneously monitors and informs the demand of those supplies and personnel in a healthcare network generating early warnings of severe respiratory disease epidemic outbreaks through the interpretation of such variables. A post hoc historical archive is generated, helping physicians in charge to improve the transit and future allocation of supplies in the entire hospital network during the outbreak. The model was thoroughly verified in a virtual scenario, generating multiple epidemic outbreaks in a 6-year span for a 13-hospital network. When it was superimposed over the H1N1 influenza outbreak census (2008–2010) taken by the National Institute of Medical Sciences and Nutrition Salvador Zubiran in Mexico City, it showed that it is an effective algorithm to notify early warnings of severe respiratory disease epidemic outbreaks with a minimal rate of false alerts.

The Origin of Biomolecular Chirality

Life is characterized by broken mirror symmetry (Palyi et al., 1999). On the molecular level, proteins are composed almost exclusively of L-amino acids while nucleic acids only contain D-sugars. Without this chiral asymmetry, prebiotic molecular complexity leading to the formation of biologically active polymers could probably not have evolved (Joyce et al., 1984; Avetisov and Goldanskii, 1991). Nevertheless, more than 1½ century after Pasteur’s discovery, the origin of biomolecular chiral asymmetry is still a mystery. Meanwhile, it is accepted that homochirality has already appeared early during chemical evolution and that a homochiral molecular environment was rather a pre-condition than a consequence of life (Keszthelyi, 1995; Avalos et al., 2000). Parity violation (MacDermott, 1993) and other chiral factors such as circularly polarized light are omnipresent and can lead under favorable conditions to enantio-meric enrichment. However, this enhancement usually remains tiny and can be annihilated by long-term racemization processes.