Increased chromosomal instability in lymphocytes from elderly humans

Lymphocytes from young and old donors were incubated with PHA for 96 h and exposed to [3H]Tdr during the last 24 h of culture. Comparable amounts of [3H]Tdr were incorporated into chromosomes of old and young lymphocytes as measured by autoradiography of metaphase chromosomes. However, chromosomal damage and cell-cycle arrest were far greater in lymphocytes from old as compared to young humans. The frequency of chromosome breaks, fragments, exchange figures and dicentric chromosomes induced by [3H]Tdr was greater in cultures from old than in cultures from young humans. Lymphocytes from old donors exposed to 20 microM BrdU during the last 24 h of culture showed significantly more sister-chromatid exchanges than did lymphocytes from young donors. These data suggest that chromosomes in lymphocytes from old donors express more damage after exposure to [3H]Tdr or BrdU than do chromosomes in lymphocytes from young donors.     

Regression modelling of HLA haplotype sharing in affected siblings

A link between the HLA system and disease susceptibility can be assessed through the observation of families containing two or more affected siblings. Departures from Mendelian inheritance of the parental haplotypes among the affected siblings are an indication of such a relationship. Other variables, such as environmental factors, may also be related to disease susceptibility. An approach to examining the degree of haplotype sharing and the effect of other variables of interest on observed sharing is presented and two examples analyzed.     

Assessing habitat quality of farm-dwelling house sparrows in different agricultural landscapes

Having historically been abundant throughout Europe, the house sparrow (Passer domesticus) has in recent decades suffered severe population declines in many urban and rural areas. The decline in rural environments is believed to be caused by agricultural intensification, which has resulted in landscape simplification. We used giving-up densities (GUDs) of house sparrows feeding in artificial food patches placed in farmlands of southern Sweden to determine habitat quality during the breeding season at two different spatial scales: the landscape and the patch scale. At the landscape scale, GUDs were lower on farms in homogeneous landscapes dominated by crop production compared to more heterogeneous landscapes with mixed farming or animal husbandry. At the patch level, feeding patches with a higher predation risk (caused by fitting a wall to the patch to obstruct vigilance) had higher GUDs. In addition, GUDs were positively related to population size, which strongly implies that GUDs reflect habitat quality. However, the increase followed different patterns in homogeneous and heterogeneous landscapes, indicating differing population limiting mechanisms in these two environments. We found no effect of the interaction between patch type and landscape type, suggesting that predation risk was similar in both landscape types. Thus, our study suggests that simplified landscapes constitute a poorer feeding environment for house sparrows during breeding, that the population-regulating mechanisms in the landscapes differ, but that predation risk is the same across the landscape types.     

Identifying the genome of wood barley Hordelymus europaeus (Poaceae: Triticeae)

Wood barley, Hordelymus europaeus, was compared with other Triticeae species by Southern and fluorescence in situ hybridisation using total genomic DNA and repetitive sequences as probes. On Southern blots, the total genomic probe from H. europaeus hybridised strongly to DNA of its own species and to Leymus and Psathyrostachys, indicating the presence of Ns genome in H. europaeus. Furthermore, the total genomic probe from P. fragilis hybridised to DNA of H. europaeus as much as to all of the Psathyrostachys and Leymus species examined. Ns genome-specific DNA sequences isolated from L. mollis (pLmIs1, pLmIs44 and pLmIs53) hybridised essentially to H. europaeus and all of the species of Leymus and Psathyrostachys. Chromosomal localization of these clones on H. europaeus confirmed the presence of Ns genome-specific DNA on all chromosomes, indiscriminately. Under moderate hybridisation stringency the Ns genome-specific probes, together with repetitive sequences pTa71 and pAesKB7, produced species-specific RFLP banding profiles on Southern blots. A phenetic tree based on these profiles revealed a distinct Ns species cluster within the Triticeae, represented by Leymus and Psathyrostachys species. Hordelymus europaeus belonged to this Ns cluster. Chromosomal mapping of the 18S-25S and the 5S ribosomal genes, together with the repetitive sequence pLrTaiI, corroborated that H. europaeus was most probably related to Leymus, especially the European/Eurasian members of sect. Leymus. In an attempt to identify the genome of H. europaeus, different approaches were employed; the results clearly showed that wood barley had the Ns basic genome and nothing else.     

On the precision of experimentally determined protein folding rates and phi-values

Phi-values, a relatively direct probe of transition-state structure, are an important benchmark in both experimental and theoretical studies of protein folding. Recently, however, significant controversy has emerged regarding the reliability with which phi-values can be determined experimentally: Because phi is a ratio of differences between experimental observables it is extremely sensitive to errors in those observations when the differences are small. Here we address this issue directly by performing blind, replicate measurements in three laboratories. By monitoring within- and between-laboratory variability, we have determined the precision with which folding rates and phi-values are measured using generally accepted laboratory practices and under conditions typical of our laboratories. We find that, unless the change in free energy associated with the probing mutation is quite large, the precision of phi-values is relatively poor when determined using rates extrapolated to the absence of denaturant. In contrast, when we employ rates estimated at nonzero denaturant concentrations or assume that the slopes of the chevron arms (mf and mu) are invariant upon mutation, the precision of our estimates of phi is significantly improved. Nevertheless, the reproducibility we thus obtain still compares poorly with the confidence intervals typically reported in the literature. This discrepancy appears to arise due to differences in how precision is calculated, the dependence of precision on the number of data points employed in defining a chevron, and interlaboratory sources of variability that may have been largely ignored in the prior literature.