Epigenetic modifications of brain and behavior: Theory and practice

Evolutionary change is a product of selection. Selection operates on the phenotype, and its consequences are manifest in representation of the genotype in successive generations. Of particular interest to both evolutionary and behavioral biologists is the newly emerging field of epigenetics and behavior. Two broad categories of epigenetic modifications must be distinguished. Context-dependent epigenetic change can be observed if the environmental factors that bring about the epigenetic modification persists (e.g., the frequency and quality of maternal care modifying the brain and future behavior of the offspring each generation). Because the environment induces epiallelic change, removing the causative factor can reverse a context-dependent epigenetic state. Germline-dependent epigenetic change occurs when the epigenetic imprint is mediated through the germline. Such effects are independent of the causative agent and there is no evidence at present that a germline-dependent epigenetic state can be reversed. Finally, only germline-dependent epigenetic modifications can be truly transgenerational. Although an individual's life history is progressive and continuous, it might usefully be viewed as the cumulation of divisions: each period emerging from what has gone before and, at the same time, setting the stage for what follows. These life history stages are somewhat arbitrary, with many traits spanning conventional divisions, but each period tends to have its own characteristic ethologies and particular contribution to neural and behavioral phenotypes. To understand how these episodes ‘fit’ together, it is necessary to deconstruct early life events and study each period both in its’ own right and how it interacts with the preceding and subsequent stages. Lastly, it seems intuitive that germline- and context-dependent epigenetic modifications interact, resulting in the individual variation observed in behaviors, but until now this hypothesis has never been tested experimentally.     

Analysis of the bacterial community developing in the course of <Emphasis Type="Italic">Sphagnum</Emphasis> moss decomposition

Slow degradation of organic matter in acidic Sphagnum peat bogs suggests a limited activity of organotrophic microorganisms. Monitoring of the Sphagnum debris decomposition in a laboratory simulation experiment showed that this process was accompanied by a shift in the water color to brownish due to accumulation of humic substances and by the development of a specific bacterial community with a density of 2.4 × 10⁷ cells ml^?1. About half of these organisms are metabolically active and detectable with rRNA-specific oligonucleotide probes. Molecular identification of the components of this microbial community showed the numerical dominance of bacteria affiliated with the phyla Alphaproteobacteria, Actinobacteria, and Planctomycetes. The population sizes of the Firmicutes and Bacteroidetes, which are believed to be the main agents of bacterially-mediated decomposition in eutrophic wetlands, were low. The numbers of planctomycetes increased at the final stage of Sphagnum decomposition. The representative isolates of the Alphaproteobacteria were able to utilize galacturonic acid, the only low-molecular-weight organic compound detected in the water samples; the representatives of the Planctomycetes were able to decompose some heteropolysaccharides, which points to the possible functional role of these groups of microorganisms in the community under study. Thus, the composition of the bacterial community responsible for Sphagnum decomposition in acidic and low-mineral oligotrophic conditions seems to be fundamentally different from that of the bacterial community which decomposes plant debris in eutrophic ecosystems at neutral pH.     

Evidence for polyproline II helical structure in short polyglutamine tracts

Nine neurodegenerative diseases, including Huntington's disease, are associated with the aggregation of proteins containing expanded polyglutamine sequences. The end result of polyglutamine aggregation is a beta-sheet-rich deposit. There exists evidence that an important intermediate in the aggregation process involves intramolecular beta-hairpin structures. However, little is known about the starting state, monomeric polyglutamine. Most experimental studies of monomeric polyglutamine have concluded that the backbone is completely disordered. However, such studies are hampered by the inherent tendency for polyglutamine to aggregate. A recent computational study suggested that the glutamine residues in polyglutamine tracts have a significant propensity to adopt the left-handed polyproline II (P(II)) helical conformation. In this work, we use NMR spectroscopy to demonstrate that glutamine residues possess a high propensity to adopt the P(II) conformation. We present circular dichroism spectra that indicate the presence of significant amounts of P(II) helical structure in short glutamine tracts. These data demonstrate that the propensity to adopt the P(II) structure is retained for glutamine repeats of up to at least 15 residues. Although other structures, such as alpha-helices and beta-sheets, become possible at greater lengths, our data indicate that glutamine residues in monomeric polyglutamine have a significant propensity to adopt the P(II) structure, although not necessarily in long contiguous helical stretches. We note that we have no evidence to suggest that the observed P(II) helical structure is a precursor to polyglutamine aggregation. Nonetheless, increased understanding of monomeric polyglutamine structures will aid our understanding of the aggregation process.     

An experimental assessment of biodiversity and species turnover in terrestrial vs canopy leaf litter

Forest canopies support diverse assemblages of free-living mites. Recent studies suggest mite species complementarity between canopy and terrestrial soils is as high as 80–90%. However, confounding variation in habitat quality and resource patchiness between ground and canopy has not been controlled in previous comparative studies. We used experimental litter bags with standardized microhabitat structure and resource quality to contrast the colonization dynamics of 129 mite species utilizing needle accumulations on the ground vs in the canopy of Abies amabilis trees in a temperate montane forest in Canada. Mite abundance and species richness per litter bag were five to eight times greater on the ground than in the canopy, and composition differed markedly at family-, genus-, and species-level. Seventy-seven species (57%) were restricted to either ground or canopy litter bags, but many of these species were rare (n<5 individuals). Of 49 ‘common’ species, 30.6% were entirely restricted to one habitat, which is considerably lower than most published estimates. In total, 87.5% of canopy specialists had rare vagrants on the ground, whereas only 51.9% of ground specialists had rare vagrants in the canopy. Canonical correspondence analysis of mite community structure showed high species turnover through time and a high degree of specialization for early-, mid-, and late-successional stages of litter decomposition, in both ground and canopy mites. In addition, distinct assemblages of ground-specialist mites dominated each elevation (800, 1000, and 1200 m), whereas few canopy-specialist mites had defined elevational preferences. This suggests that canopy mites may have greater tolerance for wide variation in environmental conditions than soil mites. The degree of species turnover between adjacent mountains also differed markedly, with 46.5% turnover of ground species, but 63.4% turnover of canopy species between the two montane areas. While ground and canopy assemblages are similar in total biodiversity, it appears that local mite richness (alpha diversity) is higher on the ground, whereas species turnover between sites (beta diversity) is higher in the canopy. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

A method for studying dead bole dynamics in Pinus contorta var. latifolia - Picea engelmannii forests

Rates of decomposition were determined for the boles of Pinus contorta var. latifolia Engelm. and Picea engelmannii Parry ex. Engelm. in five lower subalpine forest stands in the Southern Canadian Rocky Mountains. Stands ranged in age from 58 to 222 yr since last fire. The date of death of standing dead and fallen boles was determined by cross-dating their ring-width patterns to stand master ring- width chronologies. Boles could be dated which had been dead for up to 35 years in a 58-yr old stand and 100 yr in a 222-yr old stand. An empirical relationship between mass density and diameter of live trees was used to predict the mass density at death for trees already dead. The falling rate of dead standing boles was estimated from the dead bole's time of death and whether it was standing or on the ground at the time of observation. The falling rates for both Pinus contorta and Picea engelmannii ranged from 0.020 to 0.064/yr falling with most stands in the 0.050 range. No effect of size was found on the falling rate probably as a result of the small size of the boles (< 20 cm). Because of their dry condition standing dead boles do not decompose. An equation was developed which estimates the time a dead bole has been on the ground, given that it would have stood for some time before falling over and been subject to little decomposition during this time. Decomposition rates, using a negative exponential model, gave only marginally better r² than linear models. Pinus contorta had exponential decay rates from 0.0299 and 0.0171 mass density loss/yr for the most recent 15 and 25 yr in stands 58 yr old, to 0.0045 and 0.0035 mass loss/yr for the most recent 65 and 80 yr in stands 215 and 222 yr old. Picea engelmannii had exponential decay rates of 0.0054 and 0.0025 mass loss/yr for the most recent 20 and 65 yr in stands 99 and 215 yr old.     

Alkaliphilic sulfidogenesis on cellulose by combined cultures

Soda lakes are characterized by an intense sulfur cycle that begins with sulfidogenesis. Model laboratory experiments that involved combining of pure cultures showed that, during anaerobic decomposition of cellulose by Clostridium alkalicellulosi, the sulfate-reducing bacteria (SRB) of the species Desulfonatronovibrio hydrogenovorans, Desulfonatronum lacustre, and Desulfonatronum cooperativum, different in their nutritional requirements, may directly use the cellulose fermentation products for sulfidogenesis without mediatory microorganisms. In binary cocultures with SRB, the amount of the H₂S formed constituted from one-third to two-thirds of the cellulose [H] equivalents; acetate was among the products formed. When the syntrophic Contubernalis alkalaceticum, capable of acetate oxidation, was incorporated into the trophic chain along with hydrogenotrophic SRB, the amount of the H₂S formed exceeded by 33–42% the amount of the [H] equivalents in the utilized cellulose, water being the source of additional hydrogen. Thus, the trophic pathway from plant residues to sulfide, previously considered to be the longest in the alkaliphilic microbial community, may involve a minimal number of stages and do without intermediate participation of dissipotrophic fermenting organisms.     

A fungal growth model fitted to carbon-limited dynamics of Rhizoctonia solani

Here, a quasi-steady-state approximation was used to simplify a mathematical model for fungal growth in carbon-limiting systems, and this was fitted to growth dynamics of the soil-borne plant pathogen and saprotroph Rhizoctonia solani. The model identified a criterion for invasion into carbon-limited environments with two characteristics driving fungal growth, namely the carbon decomposition rate and a measure of carbon use efficiency. The dynamics of fungal spread through a population of sites with either low (0.0074 mg) or high (0.016 mg) carbon content were well described by the simplified model with faster colonization for the carbon-rich environment. Rhizoctonia solani responded to a lower carbon availability by increasing the carbon use efficiency and the carbon decomposition rate following colonization. The results are discussed in relation to fungal invasion thresholds in terms of carbon nutrition.     

Earthworms,Collembola and residue management change wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis>) and herbivore pest performance (Aphidina: <Emphasis Type="Italic">Rhophalosiphum padi</Emphasis>)

Management practices of arable systems determine the distribution of soil organic matter thereby changing decomposer animal activity and their impact on nutrient mineralization, plant growth and plant-herbivore interactions. Decomposer-mediated changes in plant growth and insect pest performance were investigated in wheat-aphid model systems in the greenhouse. Three types of litter distribution were established: litter patch at the soil surface (simulating mulching), litter patch deeper in soil (simulating ploughing) and litter homogeneously mixed into soil (simulating disk cultivation). The litter was labelled with (15)N to follow the mineralization and uptake of nutrients by the plants. Earthworms (Aporrectodea caliginosa) and Collembola (Protaphorura armata) were included as representatives of major functional groups of decomposers. Wheat (Triticum aestivum) was planted and aphids (Rhophalosiphum padi) were introduced to leaves as one of the most important pests. Earthworms, Collembola and litter distribution affected plant growth, N acquisition and aphid development in an interactive way. Earthworms and Collembola increased biomass of seeds, shoots and roots of wheat. Increased plant growth by earthworms and Collembola was mainly due to increased transfer of N from soil (rather than litter) into plants. Despite increasing plant growth, earthworms reduced aphid reproduction. Aphid reproduction was not correlated closely with plant N concentrations, but rather with the concentration of litter N in wheat. Unexpectedly, both Collembola and earthworms predominantly affected the mobilization of N from soil organic matter, and by altering the distribution of litter earthworms reduced infestation of crops by aphids via reducing plant capture of litter N, in particular if the litter was concentrated deeper in soil. The results suggest that management practices stimulating a continuous moderate increase in nutrient mobilization from soil organic matter rather than nutrient flushes from decomposing fresh organic matter result in maximum plant growth with minimum plant pest infestation.     

Litter pool sizes,decomposition, and nitrogen dynamics in <Emphasis Type="Italic">Spartina alterniflora</Emphasis>-invaded and native coastal marshlands of the Yangtze Estuary

Past studies have focused primarily on the effects of invasive plants on litter decomposition at soil surfaces. In natural ecosystems, however, considerable amounts of litter may be at aerial and belowground positions. This study was designed to examine the effects of Spartina alterniflora invasion on the pool sizes and decomposition of aerial, surficial, and belowground litter in coastal marshlands, the Yangtze Estuary, which were originally occupied by two native species, Scirpus mariqueter and Phragmites australis. We collected aerial and surficial litter of the three species once a month and belowground litter once every 2 months. We used the litterbag method to quantify litter decomposition at the aerial, surficial and belowground positions for the three species. Yearly averaged litter mass in the Spartina stands was 1.99 kg m⁻²; this was 250 and 22.8% higher than that in the Scirpus (0.57 kg m⁻²) and Phragmites (1.62 kg m⁻²) stands, respectively. The litter in the Spartina stands was primarily distributed in the air (45%) and belowground (48%), while Scirpus and Phragmites litter was mainly allocated to belowground positions (85 and 59%, respectively). The averaged decomposition rates of aerial, surficial, and belowground litter were 0.82, 1.83, and 1.27 year⁻¹ for Spartina, respectively; these were 52, 62 and 69% of those for Scirpus litter at corresponding positions and 158, 144 and 78% of those for Phragmites litter, respectively. The differences in decomposition rates between Spartina and the two native species were largely due to differences in litter quality among the three species, particularly for the belowground litter. The absolute amount of nitrogen increased during the decomposition of Spartina stem, sheath and root litter, while the amount of nitrogen in Scirpus and Phragmites litter declined during decomposition for all tissue types. Our results suggest that Spartina invasion altered the carbon and nitrogen cycling in the coastal marshlands of China.