Selecting representative model micro-organisms

Background  

Micro-biological research relies on the use of model organisms that act as representatives of their species or subspecies, these are frequently well-characterized laboratory strains. However, it has often become apparent that the model strain initially chosen does not represent important features of the species. For micro-organisms, the diversity of their genomes is such that even the best possible choice of initial strain for sequencing may not assure that the genome obtained adequately represents the species. To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species.     

Evidence for organic synthesis in high temperature aqueous media — Facts and prognosis

Hydrothermal systems are common along the active tectonic areas of the earth. Potential sites being studied for organic matter alteration and possible organic synthesis are spreading ridges, off-axis systems, back-arc activity, hot spots, volcanism, and subduction. Organic matter alteration, primarily reductive and generally from immature organic detritus, occurs in these high temperature and rapid fluid flow hydrothermal regimes. Hot circulating water (temperature range — warm to >400 °C) is responsible for these molecular alterations, expuslion and migration. Compounds that are obviously synthesized are minor components because they are generally masked by the pyrolysis products formed from contemporary natural organic precursors. Heterocyclic sulfur compounds have been identified in high temperature zones and hydrothermal petroleums of the Guaymas Basin vent systems. They can be interpreted as being synthesized from formaldehyde and sulfur or HS _x ^– in the hydrothermal fluids.Other products from potential synthesis reactions have not yet been found in the natural systems but are expected based on known industrial processes and inferences from experimental simulation data. Various industrial processes have been reviewed and are of relevance to hydrothermal synthesis of organic compounds. The reactivity of organic compounds in hot water (200–350 °C) has been studied in autoclaves, and supercritical water as a medium for chemistry has also been evaluated. This high temperature aqueous organic chemistry and the strong reducing conditions of the natural systems suggest this as an important route to produce organic compounds on the primitive earth. Thus a better understanding of the potential syntheses of organic compounds in hydrothermal systems will require investigations of the chemistry of condensation, autocatalysis, catalysis and hydrolysis reactions in aqueous mineral buffered systems over a range of temperatures from warm to >400 °C.Presented in part at the International Society for the Study of the Origin of Life Meeting, Barcelona, Spain, July 1993.     

Alkanetriols in psilotophyte cutins

The covalently bonded components of the stem cutin of Psilotum include 16-hydroxyhexadecanoic acid and substantial amounts of hexadecane-1,8,16-triol. While of generally similar composition, leaf cutin of Tmesipteris contains a mixture of hexadecanetriol isomers. The findings suggest that psilotophyte cutins evolved in a different manner from those of other land plants.     

Modelling expected trout ranges under current and future water temperature regimes in the Eastern Cape,South Africa

Different values have resulted in conflicts between anglers and conservation lobbies in the management of trout in South Africa. Key to the conflict is the demarcation of boundaries to areas in which brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss currently occur, or are likely to establish following stocking for angling. To provide a longer-term perspective on these areas, we developed models to link salmonid biological thermal thresholds to elevation. These, when applied spatially using a digital elevation model with a probability of occurrence model, provided the basis for estimating potentially available thermal habitat for these two cold water species. Here, we acknowledge that other variables (stocking history; river connectivity) also play a role in understanding trout distributions. Using a simple scenario of an increase in mean daily water temperatures of 2 °C, we demonstrated that both brown and rainbow trout are likely to exhibit considerable range reductions in the future. Because it is possible that these range restrictions will result in an increasing desire to introduce trout into areas above their current distribution limits for the maintenance of angling opportunities, conservation managers should prioritise these areas, with management interventions seeking to understand what will help to limit introductions.     

Organic Tracers from Asphalt in Propolis Produced by Urban Honey Bees,Apis mellifera Linn.

Propolis is a gummy material produced by honey bees to protect their hives and currently has drawn the attention of researchers due to its broad clinical use. It has been reported, based only on observations, that honey bees also collect other non-vegetation substances such as paint or asphalt/tar to make propolis. Therefore, propolis samples were collected from bee hives in Riyadh and Al-Bahah, a natural area, Saudi Arabia to determine their compositional characteristics and possible sources of the neutral organic compounds. The samples were extracted with hexane and analyzed by gas chromatography-mass spectrometry. The results showed that the major compounds were n-alkanes, n-alkenes, methyl n-alkanoates, long chain wax esters, triterpenoids and hopanes. The n-alkanes (ranging from C₁₇ to C₄₀) were significant with relative concentrations varying from 23.8 to 56.8% (mean = 44.9+9.4%) of the total extracts. Their odd carbon preference index (CPI) ranged from 3.6 to 7.7, with a maximum concentration at heptacosane indicating inputs from higher plant vegetation wax. The relative concentrations of the n-alkenes varied from 23.8 to 41.19% (mean = 35.6+5.1%), with CPI = 12.4-31.4, range from C₂₅ to C₃₅ and maximum at tritriacontane. Methyl n-alkanoates, ranged from C₁₂ to C₂₆ as acids, with concentrations from 3.11 to 33.2% (mean = 9.6+9.5%). Long chain wax esters and triterpenoids were minor. The main triterpenoids were α- and β-amyrins, amyrones and amyryl acetates. The presence of hopanes in some total extracts (up to 12.5%) indicated that the bees also collected petroleum derivatives from vicinal asphalt and used that as an additional ingredient to make propolis. Therefore, caution should be taken when considering the chemical compositions of propolis as potential sources of natural products for biological and pharmacological applications. Moreover, beekeepers should be aware of the proper source of propolis in the flight range of their bee colonies.     

The extent and significance of petroleum hydrocarbon contamination in Crater Lake,Oregon

In order to evaluate hydrocarbon inputs to Crater Lake from anthropogenic and natural sources, samples of water, aerosol, surface slick and sediment were collected and analyzed by gas chromatography-mass spectrometry (GC-MS) for determination of their aliphatic and aromatic hydrocarbon concentrations and compositions. Results show that hydrocarbons originate from both natural (terrestrial plant waxes and algae) and anthropogenic (petroleum use) sources and are entering the lake through direct input and atmospheric transport. The concentrations of petroleum hydrocarbons range from low to undetectable. The distributions and abundances of n-alkanes, polycyclic aromatic hydrocarbons (PAH) and unresolved complex mixture (UCM) from petroleum are similar for all surface slick sampling sites. The estimated levels of PAH in surface slicks range from 7–9 ng/m² which are low. Transport of petroleum-derived hydrocarbons from the lake surface has resulted in their presence in some sediments, particularly near the boat operations mooring (total petroleum HC = 1440 μg/kg, dry wt. compared to naturally derived n-alkanes, 240 μg/kg, dry wt.). The presence of biomarkers such as the tricyclic terpanes, hopanes and steranes in shallow sediments further confirms petroleum input from boat traffic. In the deep lake sediments, petroleum hydrocarbon concentrations were very low (16 μg/kg, dry wt.). Very low concentrations of PAH were detected in shallow sediments (17–40 μg/kg at 5 m depth near the boat operations) and deep sediments (3–15 μg/kg at 580 m depth). The individual PAH concentrations in sediments (μg/kg or ppb range) are at least three orders of magnitude less than reported threshold effects levels (mg/kg or ppm range, test amphipod Hyalella azteca). Therefore, no adverse effects are expected to occur in benthic biota exposed to these sediments. Boating activities are leaving a detectable level of petroleum in surface waters and lake sediments but these concentrations are very low.     

Bronchoabsorption; a novel bronchoscopic technique to improve biomarker sampling of the airway

Background

Current techniques used to obtain lung samples have significant limitations and do not provide reproducible biomarkers of inflammation. We have developed a novel technique that allows multiple sampling methods from the same area (or multiple areas) of the lung under direct bronchoscopic vision. It allows collection of mucosal lining fluid and bronchial brushing from the same site; biopsy samples may also be taken. The novel technique takes the same time as standard procedures and can be conducted safely.

Methods

Eight healthy smokers aged 40–65 years were included in this study. An absorptive filter paper was applied to the bronchial mucosa under direct vision using standard bronchoscopic techniques. Further samples were obtained from the same site using bronchial brushings. Bronchoalveolar lavage (BAL) was obtained using standard techniques. Chemokine (C-C Motif) Ligand 20 (CCL20), CCL4, CCL5, Chemokine (C-X-C Motif) Ligand 1 (CXCL1), CXCL8, CXCL9, CXCL10, CXCL11, Interleukin 1 beta (IL-1β), IL-6, Vascular endothelial growth factor (VEGF), Matrix metalloproteinase 8 (MMP-8) and MMP-9 were measured in exudate and BAL. mRNA was collected from the bronchial brushings for gene expression analysis.

Results

A greater than 10 fold concentration of all the biomarkers was detected in lung exudate in comparison to BAL. High yield of good quality RNA with RNA integrity numbers (RIN) between 7.6 and 9.3 were extracted from the bronchial brushings. The subset of genes measured were reproducible across the samples and corresponded to the inflammatory markers measured in exudate and BAL.

Conclusions

The bronchoabsorption technique as described offers the ability to sample lung fluid direct from the site of interest without the dilution effects caused by BAL. Using this method we were able to successfully measure the concentrations of biomarkers present in the lungs as well as collect high yield mRNA samples for gene expression analysis from the same site. This technique demonstrates superior sensitivity to standard BAL for the measurement of biomarkers of inflammation. It could replace BAL as the method of choice for these measurements. This method provides a systems biology approach to studying the inflammatory markers of respiratory disease progression.

Trial registration

NHS Health Research Authority (13/LO/0256).     

Predicted warming and browning affect timing and magnitude of plankton phenological events in lakes: a mesocosm study

1. Aquatic ecosystems in Northern Europe are expected to face increases in temperature and water colour (TB) in future. While effects of these factors have been studied separately, it is unknown whether and how a combination of them might affect phenological events and trophic interactions. 2. In a mesocosm study, we combined both factors to create conditions expected to arise during the coming century. We focused on quantifying effects on timing and magnitude of plankton spring phenological events and identifying possible mismatches between resources (phytoplankton) and consumers (zooplankton). 3. We found that the increases in TB had important effects on timing and abundance of different plankton groups. While increased temperature led to an earlier peak in phytoplankton and zooplankton and a change in the relative timing of different zooplankton groups, increased water colour reduced chlorophyll‐a concentrations. 4. Increased TB together benefitted cladocerans and calanoid copepods and led to stronger top‐down control of algae by zooplankton. There was no sign of a mismatch between primary producers and grazers as reported from other studies. 5. Our results point towards an earlier onset of plankton spring growth in shallow lakes in future with a stronger top‐down control of phytoplankton by zooplankton grazers.     

Effects of brown and turbid water on piscivore–prey fish interactions along a visibility gradient

1. Environmental changes such as eutrophication and increasing inputs of humic matter (brownification) may have strong effects on predator–prey interactions in lakes through a reduction in the visual conditions affecting foraging behaviour of visually oriented predators. 2. In this experiment, we studied the effects of visual range (25–200 cm) in combination with optically deteriorating treatments (algae, clay or brown humic water) on predator–prey interactions between pike (Esox lucius) and roach (Rutilus rutilus). We measured effects on reaction distance and strike distance for pike and escape distance for roach, when pike individuals were exposed to free‐swimming roach as well as to roach held in a glass cylinder. 3. We found that reaction distance decreased with decreasing visual range caused by increasing levels of algae, clay or humic matter. The effect of reaction distance was stronger in turbid water (clay, algae) than in the brown water treatment. 4. Strike distance was neither affected by visual range nor by optical treatment, but we found shorter strike distances when pike attacked roach using visual cues only (roach held in a cylinder) compared to when pike could use multiple senses (free‐swimming roach). Escape distance for roach was longer in turbid than in brown water treatments. 5. Changes in environmental drivers, such as eutrophication and brownification, affecting the optical climate should thus have consequences for the strength of predator–prey interactions through changes in piscivore foraging efficiency and prey escape behaviour. This in turn may affect lake ecosystems through higher‐order interactions.     

Lipid Formation by Aqueous Fischer-Tropsch-Type Synthesis over a Temperature Range of 100 to 400 °C

The formation of lipid compounds during anaqueous Fischer-Tropsch-type reaction was studied withsolutions of oxalic acid as the carbon and hydrogensource. The reactions were conducted in stainlesssteel vessels by heating the oxalic acid solution atdiscrete temperatures from 100 to 400 °C, atintervals of 50 °C for two days each. Themaximum lipid yield, especially for oxygenatedcompounds, is in the window of 150–250 °C. At atemperature of 100 °C only a trace amount oflipids was detected. At temperatures above150 °C the lipid components ranged from C₁₂to >C₃₃ and included n-alkanols, n-alkanoic acids, n-alkyl formates, n-alkanals, n-alkanones, n-alkanes, andn-alkenes, all with essentially no carbon numberpreference. The n-alkanes increased inconcentration over the oxygenated compounds attemperatures of 200 °C and above, with a slightreduction in their carbon number ranges due tocracking. It was also noted that the n-alkanoicacids increased while n-alkanols decreased withincreasing temperature above 200 °C. Attemperatures above 300 °C synthesis competeswith cracking and reforming reactions. At 400 °Csignificant cracking was observed and polynucleararomatic hydrocarbons and their alkylated homologswere detected. The results of this work suggest thatthe formation of lipid compounds by aqueous FTTreactions proceeds by insertion of a CO group at theterminal end of a carboxylic acid functionality toform n-oxoalkanoic acids, followed by reductionto n-alkanoic acids, to n-alkanals, thento n-alkanols. The n-alkenes areintermediate homologs for n-alkan-2-ones andn-alkanes. This proposed mechanism for aqueousFTT synthesis differs from the surface-catalyzedstepwise FT process (i.e., gaseous) of polymerization of methylene reported in the literature.