Mining genomic databases to identify novel hydrogen producers

The realization that fossil fuel reserves are limited and their adverse effect on the environment has forced us to look into alternative sources of energy. Hydrogen is a strong contender as a future fuel. Biological hydrogen production ranges from 0.37 to 3.3 moles H(2) per mole of glucose and, considering the high theoretical values of production (4.0 moles H(2) per mole of glucose), it is worth exploring approaches to increase hydrogen yields. Screening the untapped microbial population is a promising possibility. Sequence analysis and pathway alignment of hydrogen metabolism in complete and incomplete genomes has led to the identification of potential hydrogen producers.     

Development of the system for protoplast generation in Streptomyces aureofaciens strains--chlortetracycline producers

Conditions for preparation and regeneration of protoplasts in a commercial strain of the culture producing chlortetracycline and its derivatives were determined. The protoplasting level depended on the conditions of the mycelium cultivation and composition of a regeneration medium. Under the optimal conditions it amounted up to 10(6) protoplasts/ml. A mutant able to form regenerating protoplasts at a rate of 10(9) protoplasts/ml was isolated. An autoinhibition effect in regenerating protoplasts was observed. As a result ofprotoplast generationing, the morphological variation increased and the protoplast antibiotic activity changed within wide ranges. Variants with higher productivity in comparison to that of the initial strain were isolated. Stability of the inherited property of antibiotic production in the variants is being studied.     

SEAS: a system for SEED-based pathway enrichment analysis

Pathway enrichment analysis represents a key technique for analyzing high-throughput omic data, and it can help to link individual genes or proteins found to be differentially expressed under specific conditions to well-understood biological pathways. We present here a computational tool, SEAS, for pathway enrichment analysis over a given set of genes in a specified organism against the pathways (or subsystems) in the SEED database, a popular pathway database for bacteria. SEAS maps a given set of genes of a bacterium to pathway genes covered by SEED through gene ID and/or orthology mapping, and then calculates the statistical significance of the enrichment of each relevant SEED pathway by the mapped genes. Our evaluation of SEAS indicates that the program provides highly reliable pathway mapping results and identifies more organism-specific pathways than similar existing programs. SEAS is publicly released under the GPL license agreement and freely available at http://csbl.bmb.uga.edu/~xizeng/research/seas/.     

A stereo music system as environmental enrichment for captive chimpanzees

Music has been shown to have beneficial effects on humans but little is known about the effects of music on nonhuman primates in biomedical research settings. The authors monitored the effects of music on the behavior of captive chimpanzees and found that music had significant positive effects, including a reduction in agitated and aggressive behaviors.     

Bacterial stress enrichment enhances anaerobic hydrogen production in cattle manure sludge

Methodology was evaluated to selectively enrich hydrogen-producing species present in biological sludge produced during organic wastewater treatment. The influence of bacterial stress enrichment on anaerobic hydrogen-producing microorganisms was investigated in batch tests using serum bottles. Enrichment conditions investigated included application of acute physical and chemical stresses: wet heat, dry heat and desiccation, use of a methanogen inhibitor, freezing and thawing, and chemical acidification with and without preacidification of the sludge at pH 3. For each enrichment sample, cultivation pH value was set at an initial value of 7. After application of selective enrichment (by bacterial stress), hydrogen production was significantly higher than that of untreated original sludge. Hydrogen production from the inocula with bacterial stress enrichment was 1.9–9.8 times greater when compared with control sludge. Chemical acidification using perchloric acid showed the best hydrogen production potential, irrespective of preacidification. Enhancement is due to the selective capture of hydrogen-producing sporeformers, which induces altered anaerobic fermentative metabolism.     

Effects of increased temperature and nutrient enrichment on the stoichiometry of primary producers and consumers in temperate shallow lakes

1. We studied the effects of increased water temperatures (0–4.5 °C) and nutrient enrichment on the stoichiometric composition of different primary producers (macrophytes, epiphytes, seston and sediment biofilm) and invertebrate consumers in 24 mesocosm ecosystems created to mimic shallow pond environments. The nutrient ratios of primary producers were used as indicative of relative nitrogen (N) or phosphorus (P) limitation. We further used carbon stable isotopic composition (δ¹³C) of the different primary producers to elucidate differences in the degree of CO₂ limitation. 2. Epiphytes were the only primary producer with significantly higher δ¹³C in the enriched mesocosms. No temperature effects were observed in δ¹³C composition of any primary producer. Independently of the treatment effects, the four primary producers had different δ¹³C signatures indicative of differences in CO₂ limitation. Seston had signatures indicating negligible or low CO₂ limitation, followed by epiphytes and sediment biofilm, with moderate CO₂ limitation, while macrophytes showed the strongest CO₂ limitation. CO₂ together with biomass of epiphytes were the key variables explaining between 50 and 70% of the variability in δ¹³C of the different primary producers, suggesting that epiphytes play an important role in carbon flow of temperate shallow lakes. 3. The ratio of carbon to chlorophyll a decreased with increasing temperature and enrichment in both epiphytes and seston. The effects of temperature were mainly attributed to changes in algal Chl a content, while the decrease with enrichment was probably a result of a higher proportion of algae in the seston and epiphytes. 4. Macrophytes, epiphytes and seston decreased their C : N with enrichment, probably as an adaptation to the different N availability levels. The C : N of epiphytes and Elodea canadensis decreased with increasing temperature in the control mesocosms. Sediment biofilm was the only primary producer with lower C : P and N : P with enrichment, probably as a result of higher P accumulation in the sediment. 5. Independently of nutrient level and increased temperature effects the four primary producers had significantly different stoichiometric compositions. Macrophytes had higher C : N and C : P and, together with epiphytes, also the highest N : P. Seston had no N or P limitation, while macrophytes and epiphytes may have been P limited in a few mesocosms. Sediment biofilm indicated strong N deficiency. 6. Consumers had strongly homeostatic stoichiometric compositions in comparison to primary producers, with weak or no significant treatment effects in any of the groups (insects, leeches, molluscs and crustaceans). Among consumers, predators had significantly higher N content and lower C : N than grazers.     

Search for methanotrophic producers of exopolysaccharides]

Bacteria that produce exopolysaccharides (EPS) and use methane as the only source of carbon were selected by studying a collection of methanotroph strains: Methylococcus capsulatus E 494, 874, and 3009; M. thermophilus 111p, 112p, and 119p; Methylobacter ucrainicus 159 and 161; M. luteus 57v and 12b; Methylobacter sp. 100; Methylomonas rubra 15 sh and SK-32; Methylosinus trichosporium OV3b, OV5b and 4e; M. sporium 5, 12, A20d, and 90v; and Methylocystis parvus OVVP. Mesophilic methanotroph strains with the ribulose monophosphate way of C1-compound assimilation synthesized EPS more actively than bacteria operating the serine cycle. The dynamics of EPS synthesis by methanotrophs during chemostat cultivation was studied.     

Simple miniaturized gel system for DNA sequence analysis.

A simple miniaturized gel system suitable for DNA sequencing is described. Small ultrathin polyacrylamide gels are cast, eight or more at a time, using standard microscope slides. Gels, ready to use, can be stored for approximately 2 weeks. Gels are run horizontally in a standard mini-agarose gel apparatus. Typical run times are 6-8 min. A novel sample loading system permits volumes of standard sequencing reactions as small as 0.1 microl to be analyzed. Sequencing ladders were visualized using 35S-labeled DNA by autoradiography and by colorimetric detection. Band resolution compares favorably with that of large gels. The methods introduced here serve as a step toward the miniaturization of DNA sequencing and are amenable to automated sample loading and detection.     

Modeling alginate encapsulation system for biological hydrogen production

Wastewater treatment using encapsulated biomass is a promising approach for high-rate resource recovery. Encapsulation matrices can be customized to achieve desired biomass retention and mass transport performance. This, in turn, facilitates treatment of different waste streams. In this study, a model was developed to describe calcium-alginate beads encapsulating hydrogen-producing biomass, with the goal of enabling appropriate a priori customization of the system. The model was based on a classic diffusion-reaction model, but also included the growth of encapsulated biomass and product inhibition. Experimental data were used to verify the model, which accurately described the effect of hydraulic retention time, bead size, and feed concentration on resource (hydrogen) recovery from brewery wastewater. Sensitivity analyses revealed that the hydrogen production rate was insensitive to substrate diffusivity and bead size, but sensitive to the substrate partition coefficient, initial encapsulated biomass concentration, and the total volume of beads in the reactor, demonstrating that this system was growth-limited rather than diffusion-limited under the tested conditions. Because the model quantifies the relationship between the hydrogen production rate and various input and operating parameters, it should be possible to extend the model to determine the most cost-effective system for optimal performance with a given waste stream.     

Immunoenzyme method for detecting microbial producers of palytoxin

A competitive ELISA using the intact toxin as a coating antigen for detecting palytoxin was developed. This immunoassay allows palytoxin (PTX) to be determined in the range of 6-250 ng/ml. In sensitivity, this determination is comparable with RIA but is three times inferior to ELISA using monoclonal antibodies. Inhibition experiments using some toxins of marine invertebrates proved the serological specificity of the palytoxin binding to antibodies. Both the indirect and competitive ELISA were used to find PTX-producing bacteria among 420 isolates of sea bacteria. It was found that gram-negative bacteria Aeromonas sp. and Vibrio sp. associated with toxic samples of the soft coral Palythoa sp. produced compounds antigenically related to PTX.     

Simple life-history omnivory: responses to enrichment and harvesting in systems with intraguild predation

This article analyzes the nature of top-down and bottom-up effects and alternative states in systems characterized by life-history omnivory. The analysis is based on a three-species food web with intraguild predation (IGP). The top predator population has juvenile and adult stages, which consume the basal resource and the intermediate prey, respectively; the prey consumes only the resource. The per capita reproduction of the adult predators depends on their consumption rate of prey, while the maturation rate of the juvenile predators depends on their resource consumption rate. Enriching the resource can increase or decrease the abundances of one or both of the two consumer species; an increased density is more likely in the intermediate species than in the systems where IGP is not based on stage differences. Alternative states that have or lack the predator occur frequently, particularly when the prey population is capable of reducing the resource to very low densities. These results differ from those of several other recent models of life-history omnivory. They suggest that life-history omnivory may be one of the primary reasons why exploited populations undergo sudden collapses and why collapsed populations fail to recover in spite of large reductions in the exploitation rate.     

Microbial producers of butanol

This review is written due to an increased interest in the production of energy carriers and basic substrates of the chemical industry from renewable natural resources. In this review, the microbiological aspects of biobutanol production are reflected and the microbial producers of butanol (both natural, i.e., members of the Clostridium genus, and recombinant), obtained by genetic modification of Clostridia and other microorganisms, are characterised.     

Simple system for controlling dissolved oxygen concentration in laboratory fermentors

A simple system for the control of oxygen transfer in laboratory fermentation units has been devised. This system employs pure oxygen to elevate the driving force for oxygen transfer. In addition, the aeration is controlled in a closed loop manner in order to minimize total exit flow of the gas from the fermentor. Fermentation study using Bacillus stearothermophilus grown on n-dodecane at 55°C illustrates excellent carbon recovery as well as the ease of controlling oxygen transfer.     

CoOOH nanosheet electrodes: Simple fabrication for sensitive electrochemical sensing of hydrogen peroxide and hydrazine

Cobalt oxyhydroxide, CoOOH, nanosheets were prepared via a surface alkaline treatment of cobalt foil at room temperature without using templates and catalysts. The morphology, chemical composition and structures of the nanosheets were characterized by XRD, FTIR and Raman spectroscopy, FESEM and TEM. These oriented and nanostructured arrays can be used directly as electrodes, thus simplifying the electrode fabrication process, as well as offering advantages such as enhanced electrode-electrolyte contact area, minimum diffusion resistance and direct active material-current collector connection for fast electron transport. The electrode was used as an electrochemical sensor towards non-enzymatic detection of hydrogen peroxide and hydrazine in alkaline solution. The amperometric detection of H(2)O(2) and N(2)H(4) was carried out at low potential (0V and 0.1V). At 0.1V, the amperometric signals are linearly proportional to H(2)O(2) concentration up to 1.6mM (R(2)=0.995), showing a detection limit (S/N=3) of 40μM and a high sensitivity of 99μAmM(-1)cm(-2). For N(2)H(4), the amperometric signals are linearly proportional to concentration up to 1.2mM (R(2)=0.99), showing a detection limit (S/N=3) of 20μM and a high sensitivity of 155μAmM(-1)cm(-2) at 0.1V.