Organic synthesis by quench reactions.

The effects of chemical quench reactions on the formation of organic compounds at a water surface under simulated primordial earth conditions were investigated for the study of chemical evolution. A mixture of gaseous methane and ammonia over a water surface was exposed to an arc discharge between an electrode and the water surface. This discharge served as a source of dissociated, ionized and excited atomic and molecular species. Various organic molecules were formed in the gaseous, aqueous, and solid states by a subsequent quenching of these reactive species on the water surface. The effects of these water-surface quench reactions were assessed by comparing the amounts of synthesized molecules to the amounts which formed during the discharge of an arc above the water level. The results showed that: (1) the water-surface quench reaction permitted faster rates of formation of an insoluble solid and (2) the quench discharge yielded twice as much amino acids and 17 times more insoluble solids by weight than the other discharge. The highest yield of amino acids with the quench reaction was 9 x 10-7 molecules per erg of input energy. These observations indicate that quench reactions on the oceans, rain, and clouds that would have followed excitation by lightning and shock waves may have played an important role in the prebiotic milieu. Furthermore, the possibility exists that quench reactions can be exploited for the synthesis of organic compounds on a larger scale from simple starting materials.     

Origin of terrestrial polypeptides: A theory based on data from discharge-tube experiments

Polymeric materials derived from HCN have been synthesized from reactants containing only carbon, hydrogen and nitrogen, as the solid product formed at high temperature on the walls of a discharge tube, and at room temperature from the gaseous products of that discharge condensed in a cold trap and allowed to warm up in the dark. These compounds were hydrolyzed with acid, and when possible with alkali. Amphoteric molecules were separated from the hydrolysate and examined for amino acids by GLC, after preparation of the TAB derivative. In all cases where nitrogenous solids were hydrolyzed, many natural and a few synthetic amino acids were formed, while blank runs indicated no trace of amino acids under the same treatment. These results have been used to show that many previous experiments in which amino acids have been synthesized from supposed ‘prebiological’ atmospheres have probably all involved the same general reaction steps.

1. Formation of HCN from high-energy reaction of C?H?N(?O) systems.
2. Radical or ionic polymerization or oligomerization of HCN.
3. Hydrolysis of the product.

A new theory for the origin of proteins on the primitive earth has been described in the light of these experimental results. It is suggested that high molecular weight aliphatic and aromatic hydro carbons and polymers derived from HCN are formed in the methane-ammonia atmosphere, and settle on the Earth's surface before the formation of oceans. Rainstorms wash the materials into alkaline pools, where the polymer is hydrolyzed in the presence of other materials necessary for the formation of replicating polypeptides (aromatic hydrocarbons, purines and pyrimidines and possibly phosphate ion). The close similarity between the products of discharge experiments and organic materials found in carbonaceous chondrites has also been discussed.     

Soil and water and its relationship to the origin of life

Soils of the terrestrial planets form at the boundaries between lithosphere, atmosphere and hydrosphere. Biogenesis occurred in these zones; thus, it is axiomatic that some, perhaps many, stages of biogenesis occurred in intimate association with the mineral constituents of soils. Because of a high surface to mass ratio and, consequently, a high surface reactivity, the layer lattice clay minerals are the most important of these. according to the geological record, clay minerals appeared very early on the primordial Earth. Recent investigations have confirmed their presence in carbonaceous meteorites and have indicated their occurrence on Mars. In this paper we collect pertinent physico-chemical data and summarize the organic reactions and interactions that are induced or catalyzed by clays. Many clay-organic reactions that do not occur readily at high water contents proceed rapidly at adsorbed water contents corresponding to surface coverages of one or two molecular layers. One or two monolayers of adsorbed water correspond to extremely dry on cold planetary environments. Some consequences of these factsvis à vis biogenesis on Mars are considered.     

Bacterial diversity assessment in soil of an active Brazilian copper mine using high-throughput sequencing of 16S rDNA amplicons

Mining activities pose severe environmental risks worldwide, generating extreme pH conditions and high concentrations of heavy metals, which can have major impacts on the survival of organisms. In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. For the analysis, soil samples were collected from the slopes (geotechnical structures) and the surrounding drainage of the Sossego mine (comprising the Sossego and Sequeirinho deposits). The results revealed complex bacterial diversity, and there was no influence of deposit geographic location on the composition of the communities. However, the environment type played an important role in bacterial community divergence; the composition and frequency of OTUs in the slope samples were different from those of the surrounding drainage samples, and Acidobacteria, Chloroflexi, Firmicutes, and Gammaproteobacteria were responsible for the observed difference. Chemical analysis indicated that both types of sample presented a high metal content, while the amounts of organic matter and water were higher in the surrounding drainage samples. Non-metric multidimensional scaling (N-MDS) analysis identified organic matter and water as important distinguishing factors between the bacterial communities from the two types of mine environment. Although habitat-specific OTUs were found in both environments, they were more abundant in the surrounding drainage samples (around 50 %), and contributed to the higher bacterial diversity found in this habitat. The slope samples were dominated by a smaller number of phyla, especially Firmicutes. The bacterial communities from the slope and surrounding drainage samples were different in structure and composition, and the organic matter and water present in these environments contributed to the observed differences.     

Dissolved organic carbon and UV-absorption in a polluted lowland brook-pond system

A natural water (brook-pond system), polluted with organic waste, was aerated by the Phallus technique. The evolution of the organic carbon concentration and the UV-absorption was followed. Aeration resulted in an abrupt decrease of the organic carbon concentration in the immediate vicinity of the experimental station, while in the downstream sampling sites a slower decrease occurred. A relationship between UV-absorption and total organic carbon was demonstrated. The use of UV-absorption measurements as a measure of organic matter content is discussed.     

Removal of sulfur-containing organic molecules adsorbed on inorganic supports by <Emphasis Type="Italic">Rhodococcus Rhodochrous</Emphasis> spp.

Objective

To remove dibenzothiophene (DBT) and 4,6-dimethyl-dibenzothiophene (4,6-DMDBT) adsorbed on alumina, silica and sepiolite through biodesulfurization (BDS) using Rhodococcus Rhodochrous spp., that selectively reduce sulfur molecules without generating of gaseous pollutants.

Results

The adsorption of DBT and 4,6-DMDBT was affected by the properties of the supports, including particle size and the presence of surface acidic groups. The highest adsorption of both sulfur-containing organic molecules used particle sizes of 0.43–0.063 mm. The highest percentage removal was with sepiolite (80 % for DBT and 56 % for 4,6-DMDBT) and silica (71 % for DBT and 37 % for 4,6-DMDBT). This is attributed to the close interaction between these supports and the bacteria.

Conclusions

Biodesulfurization is effective for removing the sulfur-containing organic molecules adsorbed on inorganic materials and avoids the generation of gaseous pollutants.

     

Pinocytotic uptake of protein from the reservoir inEuglena

Alveolate vesicles in the anterior regions ofEuglena gracilis are shown to function in pinocytosis, being capable of incorporating exogenous horseradish peroxidase through the reservoir wall. It is thought that this represents a mechanism for recovering large molecules otherwise lost during contractile vacuole discharge.     

Planetary Organic Chemistry and the Origins of Biomolecules

Organic chemistry on a planetary scale is likely to have transformed carbon dioxide and reduced carbon species delivered to an accreting Earth. According to various models for the origin of life on Earth, biological molecules that jump-started Darwinian evolution arose via this planetary chemistry. The grandest of these models assumes that ribonucleic acid (RNA) arose prebiotically, together with components for compartments that held it and a primitive metabolism that nourished it. Unfortunately, it has been challenging to identify possible prebiotic chemistry that might have created RNA. Organic molecules, given energy, have a well-known propensity to form multiple products, sometimes referred to collectively as “tar” or “tholin.” These mixtures appear to be unsuited to support Darwinian processes, and certainly have never been observed to spontaneously yield a homochiral genetic polymer. To date, proposed solutions to this challenge either involve too much direct human intervention to satisfy many in the community, or generate molecules that are unreactive “dead ends” under standard conditions of temperature and pressure. Carbohydrates, organic species having carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1 and an aldehyde or ketone group, conspicuously embody this challenge. They are components of RNA and their reactivity can support both interesting spontaneous chemistry as part of a “carbohydrate world,” but they also easily form mixtures, polymers and tars. We describe here the latest thoughts on how on this challenge, focusing on how it might be resolved using minerals containing borate, silicate, and molybdate, inter alia.Interesting organic chemistry occurs throughout the cosmos, including in presolar nebulae (see the article in this collection by Pascale Erhrenfreund), asteroidal bodies (see the article in this collection by Sandra Pizzarello) and icy bodies near the outer boundary of our solar system (Bernstein et al. 2002). Although organic molecules made in off-Earth locales almost certainly contributed to the reduced carbon inventory on Earth before life emerged, planetary processing on Earth undoubtedly also contributed to the inventory of prebiotic molecules that were available to life as it originated (assuming that Earth was the site of life''s origin). Indeed, in the RNA first model for the origin of life on Earth (Joyce and Orgel 1999)(Benner 2009), it is often proposed that terran-based chemistry produced RNA in oligomeric form to initiate Darwinian evolution.How are we to constrain models for planetary processing to converge on a model for what actually happened on Earth four billion years ago? Today, atmospheric dioxygen (O₂) readily converts organic materials to carbon dioxide, making it essentially impossible to observe such processing on the surface of Earth. Furthermore, the ubiquity of life on modern Earth means that any organic processing is more likely to reflect biology than prebiology. The closest we may come today to observe organic transformations absent biology on a planetary scale might be on Titan, a moon of Saturn whose atmosphere and surface is rich in reduced carbon.Nevertheless, it is possible to apply a general understanding of organic chemical reactivity to suggest chemical reactions that might have occurred on early Earth and the products that they might have produced. These suggestions are constrained by models for the atmosphere and mineralogy of early Earth, although these constraints might change as models improve.In this article, we assume that the atmosphere of early Earth was less oxidizing than today''s atmosphere, although not as rich in methane as the simulated atmosphere used in the classic experiments of Stanley Miller (Miller 1955). Further, we assume that the atmosphere on early Earth had access to many sources of energy. These include electrical discharge, ultraviolet and visible light (although the Sun was almost certainly dimmer then than now, a Titan-like haze may have prevented high energy photons from reacting the Earth''s surface), volcanism (providing not only heat but also reactive species and mixtures not at thermodynamic equilibrium), ionizing radiation, and impacts. (See Pizzarello and Shock 2010 for a discussion of such energy sources.)We also assume that life emerged after the planet underwent a geological fractionation in which heavier minerals and elemental iron sank towards the core, leaving lighter rocks to form the crust. Open questions concern the inventory of water relative to the surface of early Earth, an inventory that determined whether planetary organic transformations might have occurred on dry land or below water on a planetary surface that was totally submerged.     

Microbiological examination of Lake Erie and Lake Ontario sediments

Diver collected cores from three sites in Lake Erie, west of Cleveland, Eastern basin and near Buffalo, and one from Lake Ontario near the mouth of the Niagara River, were sectioned to 20 cm and examined for sulfur cycle and nitrogen cycle bacteria, heterotrophic bacteria, insoluble organic and inorganic phosphate solubilizing bacteria and manganese oxidizing bacteria. Eh, pH, nitrogen, organic carbon and percentage moisture determinations were also made. Data from this study support and confirm other microbiological data collected from Lower Great Lakes sediment and also support the hypothesis that microbial flora of similar type sediments are numerically similar irrespective of the sediments source within the Lower Great Lakes.     

Contribution to the hydrographical structure of the eastern German Bight

Temperature, salinity, micronutrients, seston components and mesozooplankton were measured on a cruise in the eastern German Bight during November 1976. Three different water bodies and a mixing area which is divided into two subareas could be identified. The water masses differed significantly in regard to temperature, salinity, micronutrients and seston components. In some cases differences in the amounts of mesozooplankton could be found. Temperature and salinity of the water of the Elbe estuary and of the Wadden Sea were relatively low, but amounts of micronutrients and seston were high, whereas the water of the North Sea water body was of higher temperature and salinity with lower amounts of micronutrients and seston. The North Frisian coastal water and a southern mixing area can be regarded as mixing areas between these water bodies.     

Influence of long-term CO2 storage on δ13C in vials capped with butyl and butyl/PTFE caps and the relevance for ecological samples

Background

The carbon (C) isotope signature of solid materials such as plants and soil, or gaseous samples (atmospheric or soil air), can be used as a useful tool for investigations of the C cycle. In gaseous samples, stability of δ¹³C of carbon dioxide (CO₂) in air during storage represents a problem.

Methods

We tested the long-term storage effect of δ¹³C originated from CO₂ in vials both capped with butyl or butyl coated with polytetrafluoroethylene (PTFE) on the internal surface. Therefore, pure CO₂, depleted in ¹³C, was stored for up to 736 days. In addition, the relevance of long-term storage for ecological soil air data collected from a free-air CO₂ enrichment (FACE) experiment located in Stuttgart (Germany) during one growing period with a maximum storage period of 210 days was judged.

Results

With increasing storage time, a change in isotopic composition towards less depleted δ¹³C was observed. The changes in δ¹³C were highest at the beginning of the storage period and decreased over time, which could be described with an asymptotic model. The maximum change in δ¹³C was less than 2?‰ and lower for vials capped with butyl/PTFE septa. In the FACE experiment, the comparison between corrected and uncorrected data showed that δ¹³C originated from soil air changed within this data set by up to 1?‰. The calculation of the fraction of plant derived C resulted in an underestimation of up to 10 %.

Conclusion

The storage effect should be taken into consideration when interpreting δ¹³C values in order to avoid miscalculations.     

Modulation of aquaporin 2 expression in the kidney of young goats by changes in nitrogen intake

In ruminants, a decrease of dietary nitrogen (N) is an appropriate feeding concept to reduce environmental pollution and costs. In our previous study, when goats were kept on an N-reduced diet, a decrease of plasma urea concentration and an increase of renal urea transporters were demonstrated. Renal urea absorption plays a crucial role for renal water absorption and urine concentration. Renal collecting duct water absorption is mainly mediated by the water channel aquaporin 1 and 2 (AQP1 and AQP2). Therefore, the aim of the present study was to investigate the effects of a dietary N reduction on expression of renal AQP1 and AQP2 in young goats. Twenty male White Saanen goats, 3 months old, were divided equally into two feeding groups, receiving either a diet with an adequate or a reduced-N supply. Goats fed a reduced-N diet showed significantly higher amounts of AQP1 mRNA in cortical tissue, and the expression of AQP2 mRNA and protein were highly elevated in renal outer medulla. An increase of vasopressin concentrations in plasma were detected for the N-reduced fed goats. Therefore, a stimulation of renal water absorption can be assumed. This might be an advantage for ruminants in times of N reduction due to higher urea concentrations in the tubular fluid and which might result in higher absorption of urea by renal urea transporters. Therefore, interplay of aquaporin water channels and urea transporters in the kidney may occur to maintain urea metabolism in times of N scarcity in young goats.     

Chemical Analysis of a “Miller-Type” Complex Prebiotic Broth

We have analyzed the chemical variety obtained by Miller-Urey-type experiments using nuclear magnetic resonance (NMR) spectroscopy and coherent anti-Stokes Raman scattering (CARS) spectroscopy, gas chromatography followed by mass spectrometry (GC/MS) and two-dimensional gas chromatography followed by mass spectrometry (GCxGC/MS). In the course of a running Miller-Urey-type experiment, a hydrophobic organic layer emerged besides the hydrophilic aqueous phase and the gaseous phase that were initially present. The gas phase mainly consisted of aromatic compounds and molecules containing C≡C?or?C≡N triple bonds. The hydrophilic phase contained at least a few thousands of different molecules, primarily distributed in a range of 50 and 500 Da. The hydrophobic phase is characterized by carbon-rich, oil-like compounds and their amphiphilic derivatives containing oxygen with tensioactive properties. The presence of a wide range of oxidized molecules hints to the availability of oxygen radicals. We suggest that they intervene in the formation of alkylated polyethylene glycol (PEG) in the oil/water interface. CARS spectroscopy revealed distinct vibrational molecular signatures. In particular, characteristic spectral bands for cyanide compounds were observed if the broth was prepared with electric discharges in the gaseous phase. The characteristic spectral bands were absent if discharges were released onto the water surface. NMR spectroscopy on the same set of samples independently confirmed the observation. In addition, NMR spectroscopy revealed overall high chemical variability that suggests strong non-linearities due to interdependent, sequential reaction steps.     

Structure of aggregates of water and Li+, Na+, or K+ counterions with nucleic acid in solution

The position and orientation of water molecules hydrating fragments of DNA in the B and Z conformations are analyzed with the help of computer simulations. Monte Carlo studies are carried out at room temperature, high relative humidity (500 water molecules per pitch) and in the presence of counterions such as Li⁺, Na⁺, and K⁺. Differences in hydration patterns and in the counterionic structures were found by compairing B-DNA with Z-DNA double helices and B-DNA helices with different base-pair distributions. The present extension of our similations to Z-DNA and to Li⁺ and K⁺ counterions permits some general conclusions concerning nucleic acids in solution.     

Clusters of nonsolvent water in partially destroyed Saccharomyces cerevisiae yeast cells

The state of water in partially destroyed dry yeast cells has been studied using low-temperature ¹H NMR spectroscopy. It has been shown that the residual water is in the form of clusters of strongly and weakly associated water (SAW and WAW, respectively). Three or more types of SAW different in the chemical shift values have been found. It has been established that the interfacial water poorly dissolves hydrochloric and trifluoroacetic acids as well as DMSO and CD₃CN. Hydrochloric acid on a surface of biomaterials can be separated into HCl and water. This process is stabilized by polar co-solvents (DMSO and CD₃CN) added to the CDCl₃ dispersion medium.     

Could life have evolved in cometary nuclei?

Hoyle and Wickramasinghe have recently suggested that life may have originated in cometary nuclei rather than directly on Earth. Even though comets are known to contain substantial amounts of organic compounds which may have contributed to the formation of biochemical molecules on the primitive Earth, it is doubtful that the process of chemical evolution has proceeded in comets beyond the stage that has occurred in carbonaceous chondrites. Some of the arguments which do not favor the occurrence of biopoesis in comets are:

1. A large layer of cometary ices is ablated from the nucleus' surface each time the comet passes through perihelion, so that essentially most of the organic products on the surface would be sublimed, blown off or polymerized.
2. Because of the low temperatures of the cometary ices, polymers formed on one perihelion passage would not migrate deep enough into the nucleus to be preserved before they would be ablated away by the next perihelion passage.
3. In the absence of atmosphere, and discrete liquid and solid surfaces, it is difficult to visualize the synthesis of key life molecules, such as oligopeptides, oligonucleotides and phospholipids by condensation and dehydration reactions as is presumed to have occurred in the evaporating ponds of the primitive Earth.
4. Observations suggest that cometary nuclei have a rather weak structure. Hence, the low central pressures in comets combined with the high vapor pressures of cometary ices at the melting point of water ice, suggest that a liquid core is not a tenable structure. Yet, even if a cometary nucleus is compact enough to hold a liquid core and a transient liquid water environment was provided by the decay of²⁶Al, the continuous irradiation in water of most of the biologically relevant polymers would have hydrolyzed and degraded them.
5. Needless to say that the effects of radiation on self-replicating systems would also have caused the demise of any life forms which may have appeared under any circumstances.
6. Concerning viruses, the high specificity of host-parasite relationships and their coevolutionary lines of descent, rule out a cometary origin for them.

In summary, the view that life originated in comets is untenable in the light of all the available evidence.     

Influence of physical and chemical properties of HTSXT-FTIR samples on the quality of prediction models developed to determine absolute concentrations of total proteins,carbohydrates and triglycerides: a preliminary study on the determination of their absolute concentrations in fresh microalgal biomass

Absolute concentrations of total macromolecules (triglycerides, proteins and carbohydrates) in microorganisms can be rapidly measured by FTIR spectroscopy, but caution is needed to avoid non-specific experimental bias. Here, we assess the limits within which this approach can be used on model solutions of macromolecules of interest. We used the Bruker HTSXT-FTIR system. Our results show that the solid deposits obtained after the sampling procedure present physical and chemical properties that influence the quality of the absolute concentration prediction models (univariate and multivariate). The accuracy of the models was degraded by a factor of 2 or 3 outside the recommended concentration interval of 0.5–35 µg spot^?1. Change occurred notably in the sample hydrogen bond network, which could, however, be controlled using an internal probe (pseudohalide anion). We also demonstrate that for aqueous solutions, accurate prediction of total carbohydrate quantities (in glucose equivalent) could not be made unless a constant amount of protein was added to the model solution (BSA). The results of the prediction model for more complex solutions, here with two components: glucose and BSA, were very encouraging, suggesting that this FTIR approach could be used as a rapid quantification method for mixtures of molecules of interest, provided the limits of use of the HTSXT-FTIR method are precisely known and respected. This last finding opens the way to direct quantification of total molecules of interest in more complex matrices.     

Field observations on the influence of low water velocities on drifting of Bulinus globosus

The influence of water velocities of less than 30 cm/s on drifting of Bulinus globosus in a natural stream was investigated. It is shown that although a low water velocity does not sweep away adhering snails, it carries away snails releasing their hold and crawling along the water surface in search of new food sources. A low water velocity therefore assists considerably to the spreading of a snail species. Vegetation was found to have a decisive impact on local water velocity conditions by reducing the current and creating protected pockets. Upstream migration was found not to be common among Bulinus globosus. In addition, evidence for snail drifting under natural conditions within well established Schistosoma haematobium transmission sites is presented.     

A new model for the calcification of the green macro-alga Halimeda opuntia (Lamouroux)

Halimeda opuntia is a cosmopolitan marine calcifying green alga in shallow tropical marine environments. Besides Halimeda’s contribution to a diverse habitat, the alga is an important sediment producer. Fallen calcareous segments of Halimeda spp. are a major component of carbonate sediments in many tropical settings and play an important role in reef framework development and carbonate platform buildup. Consequently the calcification of H. opuntia accounts for large portions of the carbonate budget in tropical shallow marine ecosystems. Earlier studies investigating the calcification processes of Halimeda spp. have tended to focus on the microstructure or the physiology of the alga, thus overlooking the interaction of physiological and abiotic processes behind the formation of the skeleton. By analyzing microstructural skeletal features of Halimeda segments with the aid of scanning electron microscopy and relating their occurrence to known physiological processes, we have been able to identify the initiation of calcification within an organic matrix and demonstrate that biologically induced cementation is an important process in calcification. For the first time, we propose a model for the calcification of Halimeda spp. that considers both the alga’s physiology and the carbon chemistry of the seawater with respect to the development of different skeletal features. The presence of an organic matrix and earlier detected external carbonic anhydrase activity suggest that Halimeda spp. exhibit biotic precipitation of calcium carbonate, as many other species of marine organisms do. On the other hand, it is the formation of micro-anhedral carbonate through the alga’s metabolism that leads to a cementation of living segments. Precisely, this process allows H. opuntia to contribute substantial amounts of carbonate sediments to tropical shallow seas.