Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater

The phylogenetic diversity of the bacterial communities supported by a seven-stage, full-scale biological wastewater treatment plant was studied. These reactors were operated at both mesophilic (28 to 32 degrees C) and thermophilic (50 to 58 degrees C) temperatures. Community fingerprint analysis by denaturing gradient gel electrophoresis (DGGE) of the PCR-amplified V3 region of the 16S rRNA gene from the domain Bacteria revealed that these seven reactors supported three distinct microbial communities. A band-counting analysis of the PCR-DGGE results suggested that elevated reactor temperatures corresponded with reduced species richness. Cloning of nearly complete 16S rRNA genes also suggested a reduced species richness in the thermophilic reactors by comparing the number of clones with different nucleotide inserts versus the total number of clones screened. While these results imply that elevated temperature can reduce species richness, other factors also could have impacted the number of populations that were detected. Nearly complete 16S rDNA sequence analysis showed that the thermophilic reactors were dominated by members from the beta subdivision of the division Proteobacteria (beta-proteobacteria) in addition to anaerobic phylotypes from the low-G+C gram-positive and Synergistes divisions. The mesophilic reactors, however, included at least six bacterial divisions, including Cytophaga-Flavobacterium-Bacteroides, Synergistes, Planctomycetes, low-G+C gram-positives, Holophaga-Acidobacterium, and Proteobacteria (alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria and delta-proteobacteria subdivisions). The two PCR-based techniques detected the presence of similar bacterial populations but failed to coincide on the relative distribution of these phylotypes. This suggested that at least one of these methods is insufficiently quantitative to determine total community biodiversity-a function of both the total number of species present (richness) and their relative distribution (evenness).     

Genomic imprinting in plants: observations and evolutionary implications

The epigenetic phenomenon of genomic imprinting occurs among both plants and animals. In species where imprinting is observed, there are parent-of-origin effects on the expression of imprinted genes in offspring. This review focuses on imprinting in plants with examples from maize, where gene imprinting was first described, and Arabidopsis. Our current understanding of imprinting in plants is presented in the context of cytosine methylation and imprinting in mammals, where developmentally essential genes are imprinted. Important considerations include the structure and organization of imprinted genes and the role of regional, differential methylation. Imprinting in plants may be related to other epigenetic phenomena including paramutation and transgene silencing. Finally, we discuss the role of gene structure and evolutionary implications of imprinting in plants.     

A limited survey of aflatoxins and fumonisins in retail maizebased products in the UK using immunoassay detection

A total of 27 maize-based products destined for human consumption were collected from retail outlets within the city of Glasgow in the UK and were analysed for the presence of aflatoxins using immunoaftinity column chromatography with fluorescence detection and for fumonisins by competitive ELISA. Aflatoxins were detected at a trace level below 4 in eight (30%) of the 27 samples tested, no sample contained aflatoxins at a high level although one sample of sweetcorn did contain aflatoxins at a level of 5-10 Fumonisins were detected in eight (30%) of the samples at levels from 1 to 8mgkg^-1 and a further eight samples contained fumonisin at a level below 1 mgkg^-1 but above the detectable level. The highest concentration of fumonisins was found in a sample of fine corn meal at 8-12mgkg^-1.     

Refinement of the fundamental niche of black mangrove (<Emphasis Type="Italic">Avicennia germinans</Emphasis>) seedlings in Louisiana: Applications for restoration

Black mangrove (Avicennia germinans) occurs at the northern boundary of its North American range in the coastal salt marshes and barrier islands of Louisiana. This species provides important habitat and sustainability to Louisiana’s coastal salt marshes via its woody structure and extensive root system. Refinement of the physiological tolerances of A. germinans seedlings to salinity, sand burial and hydrologic regime provides valuable insight into the fundamental niche of A. germinans and thereby the potential for increased restoration success in coastal and back-barrier salt marshes. We subjected two age classes of A. germinans seedlings used in restoration (young seedlings of 6 or 12 months of age, and older seedlings of either 18 or 24 months of age) to abiotic stressors frequently encountered at coastal restoration sites: (1) elevated salinity levels, from 0 to 96 ppt, (2) sediment burial, from 0 to +20 cm, and (3) varying water levels, ranging from 0 cm to −60 cm. A. germinans seedlings displayed a non-linear response to each environmental factor, with greatest biomass occurring between low and moderate levels of stress or disturbance (i.e., between 24 and 48 ppt salinity, 0 to +10 cm burial, and −15 to −30 cm water level). The two age classes displayed similar physiological tolerances; however, older seedlings may confer an advantage due to greater total biomass and reserves, most notably in response to burial. We suggest that this refinement of the fundamental niche be utilized as a guideline for improved restoration success in micro-tidal environments within black mangrove’s range.     

Partial protein domains: evolutionary insights and bioinformatics challenges

Protein domains are generally thought to correspond to units of evolution. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable.With the rapid expansion in the number of determined protein sequences - over 92 million in UniProt in March 2015 - an ever-increasing number of biologists are using bioinformatics tools for annotation of these sequences. One widely used strategy is to identify occurrences of Pfam families within the sequence of interest [1]. A Pfam family is a multiple sequence alignment of the occurrences of a particular domain both in different species and in different regions of the same protein. The concept underpinning Pfam is that proteins typically comprise one or more domains (regions), each of which is an evolutionary unit that generally has a well-defined biological function. A significant sequence similarity between a query protein and a Pfam family provides the basis for annotations. Two recent articles [2,3] in Genome Biology evaluate the implications of having the query sequence only matching part of a Pfam family, which is an intriguing finding, given that a Pfam family is considered to be an evolutionary unit.     

The evolutionary emergence of stochastic phenotype switching in bacteria

Stochastic phenotype switching - or bet hedging - is a pervasive feature of living systems and common in bacteria that experience fluctuating (unpredictable) environmental conditions. Under such conditions, the capacity to generate variable offspring spreads the risk of being maladapted in the present environment, against offspring likely to have some chance of survival in the future. While a rich subject for theoretical studies, little is known about the selective causes responsible for the evolutionary emergence of stochastic phenotype switching. Here we review recent work - both theoretical and experimental - that sheds light on ecological factors that favour switching types over non-switching types. Of particular relevance is an experiment that provided evidence for an adaptive origin of stochastic phenotype switching by subjecting bacterial populations to a selective regime that mimicked essential features of the host immune response. Central to the emergence of switching types was frequent imposition of 'exclusion rules' and 'population bottlenecks' - two complementary faces of frequency dependent selection. While features of the immune response, exclusion rules and bottlenecks are likely to operate in many natural environments. Together these factors define a set of selective conditions relevant to the evolution of stochastic switching, including antigenic variation and bacterial persistence.     

Scats and den contents as indicators of the diet of stoats (Mustela erminea) in the Tasman Valley,South Canterbury,New Zealand

Stoats are significant predators of native fauna in New Zealand. They occur in many habitat types and consume a wide range of prey. The diet of stoats in the Tasman River, South Canterbury, was studied by analysis of scats and den contents. Analysis of 206 scats showed that stoats ate mainly lagomorphs, birds and invertebrates. Minor components included mice, lizards, fish and hedgehogs. Stoats ate more birds in spring than in autumn, and female stoats ate more invertebrates than did males. The contents of 219 dens collected in the same area at the same time provided further information. Birds and lagomorphs occurred at high frequency in dens, and other components were minor. Remains in dens were larger than in scats and allowed identification of many more prey items to species level. Den contents revealed a potentially substantial impact of stoats on threatened shorebirds locally; this impact was not detected by analysis of scats.     

Effects of 2-nitrooxy ethyl 2-amino 3-methylbutanoate gel on resistance exercise performance and blood nitrate/nitrite in resistance trained men

Nitric oxide dietary supplements are popular within the sport community. Our recent work involving the oral intake of 2-nitrooxy ethyl 2-amino 3-methylbutanoate demonstrated an approximately 6.7% increase in circulating nitrate/nitrite. However, no measures of exercise performance were obtained. The present study used a topical form of this molecule to determine the impact on exercise performance and blood nitrate/nitrite. Fourteen resistance trained men (24 ± 1 years old) reported to the laboratory on 2 occasions to undergo exercise testing, which consisted of arm curl isometric force and muscular endurance (3 sets to fatigue using 80, 65, and 50% of 1 repetition maximum [1RM]: total of 9 sets). The gel (2-nitrooxy ethyl 2-amino 3-methylbutanoate; mixed in tea tree oil) or placebo (tea tree oil) was applied topically by the subjects for 7 days before each test day, with 7-10 days separating the randomly ordered conditions. Blood samples, arm circumference, and perceived "muscle pump" were taken before and immediately after exercise on both test days. The heart rate and perceived exertion were measured after each set. No statistically significant differences were noted between conditions for performance variables (p > 0.05). However, when using a load of 50% of 1RM, 6.2% more repetitions were performed when using the gel as compared with when using the placebo; 19.9% more repetitions were performed by 8 subjects noted to be "responders" to gel treatment. Blood lactate and muscle pump significantly increased with exercise (p < 0.0001) but were not different between conditions (p > 0.05). Minimal change was noted in nitrate/nitrite, and the heart rate and perceived exertion were nearly identical between conditions (p > 0.05). These findings indicate that 2-nitrooxy ethyl 2-amino 3-methylbutanoate gel has a modest (6.2%), nonstatistically significant effect on exercise performance, in particular when using a load of 50% 1RM-with greater benefit noted in selected individuals. Studies inclusive of a larger sample size are needed to extend these initial findings.