Genome-wide Epigenetic Data Facilitate Understanding of Disease Susceptibility Association Studies

Complex traits such as susceptibility to diseases are determined in part by variants at multiple genetic loci. Genome-wide association studies can identify these loci, but most phenotype-associated variants lie distal to protein-coding regions and are likely involved in regulating gene expression. Understanding how these genetic variants affect complex traits depends on the ability to predict and test the function of the genomic elements harboring them. Community efforts such as the ENCODE Project provide a wealth of data about epigenetic features associated with gene regulation. These data enable the prediction of testable functions for many phenotype-associated variants.     

Phenology constrains opportunistic growth response in <Emphasis Type="Italic">Bromus tectorum</Emphasis> L.

Seasonal resource availability may act as a constraint on plant phenology and thereby influence the range of growth responses observed among populations of annual species, especially those occupying a wide range of environments. We compared a mesic and a xeric population of the non-native, annual grass, Bromus tectorum, to examine phenology in response to interspecific competition and water availability. Using a target-neighborhood approach, we assessed how phenological patterns of the two populations affected morphological and growth responses to enhanced resource availability represented by late-season soil moisture. The xeric population exhibited a highly constrained phenology and was unable to extend the growing season despite available soil resources. Because of the low phenotypic variation, allocation to reproduction was similar across resource conditions. In contrast, the mesic population flowered later and showed a more opportunistic phenology in response to late-season water availability. The mesic population was not able to maintain consistent reproductive allocation at low resource levels. The responses of the two populations to late-season water availability were not affected by the density of neighboring plants. We suggest that post-introduction selection pressure on B. tectorum in the xeric habitat has resulted in a more fixed phenology which limits opportunistic response to unpredictable, particularly late-season resource availability. Opportunistic and fixed responses represent contrasting strategies for optimizing fitness in temporally varying environments and, while both play important roles for ensuring reproductive success, these results suggest that local adaptation to temporal resource variation may reflect a balance between flexible and inflexible phenology.     

A closed artificial stream for conducting experiments requiring a controlled species pool

Experimental testing of ecological theory in the field is often difficult because of the number of factors influencing the test system. Adequate control of relevant variables may require the use of laboratory microcosms for the performance of proper experimental tests. Our efforts to study the effects of species invasion sequence on community structure and ecosystem properties of the developing system, requires that the experimental systems be closed. To meet our demanding experimental requirements, we have designed a closed artificial stream that permits careful control over algal species introductions while minimizing the risks of contamination by unwanted species. In assessing the performance of these streams, we examined the variability among experimental replicates in water chemistry parameters and biomass accumulation. Those water chemistry parameters that were not greatly influenced by biological processes in the streams (Ca, Mg, bicarbonate, and sulfate) had average coefficients of variation less than 10%. Those parameters that were clearly influenced by biological processes (P, N, Fe, and Si) had average coefficients of variation ranging from 13.5%–40.4%. Ash free dry mass had an average coefficient of variation of 23.3%, but chlorophyll a was much more variable at 183%. This pattern of variation indicates that the artificial streams performed well in terms of replicability, but some experimental goals may require carefully conceived designs that adequately partition sources of variation in biologically mediated variables to obtain satisfactory results.     

Phospholipid, cholesterol, polypeptide and glycoprotein composition of hepatic endosome subfractions.

The composition of hepatic endosome subfractions was compared directly with that of plasma membranes and Golgi-apparatus fractions. The neutral lipid and phospholipid composition of two endosome subfractions separated on Nycodenz gradients from a parent endosome fraction was similar to that of plasma membranes. The phospholipid/cholesterol ratios and the sphingomyelin contents were high, as in plasma membranes. However, the phosphatidylserine content was low. Endosomal subfractions contained a simpler polypeptide profile than did plasma membranes. However, a large number of glycoproteins were common to both fractions. Two endosome-specific glycoproteins, of Mr 59 000 and 38 000, were identified. Sialic acid was present at concentrations higher than in plasma membranes. The results indicate that endosomal membranes have a similar composition to plasma membranes that probably reflects their functional interaction during endocytosis and receptor recycling.     

Short interspersed repeats in rabbit DNA can provide functional polyadenylation signals

Analysis of 37 short repetitive elements (SINEs) in rabbit DNA that are known as C repeats has revealed three that contribute functional polyadenylation signals to genes into which they have been inserted. Similar roles have been attributed to particular individual SINEs in rodents and primates before, suggesting that these roles may be common to SINEs in all mammalian orders. Although most SINEs appear to have little influence on the genome individually, the observation that three of 36 rabbit C repeats provide functional sequences suggests a mechanism for the maintenance of SINEs within mammalian genomes.     

An approach to histone nearest neighbours in extended chromatin.

The primary sequence organization of histones upon the DNA molecule in chromatin has been analyzed by extension of the nucleoprotein at very low ionic strength and crosslinking with a reversible crosslinking reagent, methyl-4-mercaptobutyrimidate. Histones extracted after limited reaction were fractionated into different classes and the composition of the oligomers analyzed after reduction of the crosslinked material. We have found that the following dimers occur at a high frequency: (F3-F2b), (F3-F2a2), and (F2b-F2a2), whereas (F2b-F2al), (F3-F2al) and (F3-F3) occur with a lower frequency. F1 appears to polymerize rapidly to largely homogeneous polymers of high molecular weight. These results are analyzed in terms of several models proposed for chromatin structure.