Eukaryotic topoisomerase I-DNA interaction is stabilized by helix curvature.

The influence of DNA structure on topoisomerase I-DNA interaction has been investigated using a high affinity binding site and mutant derivatives thereof. Parallel determinations of complex formation and helix structure in the absence of superhelical stress suggest that the interaction is intensified by stable helix curvature. Previous work showed that a topoisomerase I binding site consists of two functionally distinct subdomains. A region located 5' to the topoisomerase I cleavage site is essential for binding. The region 3' to the cleavage site is covered by the enzyme, but not essential. We report here that the helix conformation of the latter region is an important modulator of complex formation. Thus, complex formation is markedly stimulated, when an intrinsically bent DNA segment is installed in this region. A unique pattern of phosphate ethylation interferences in the 3'-part of the binding site indicates that sensing of curvature involves backbone contacts. Since dynamic curvature in supercoiled DNA may substitute for stable curvature, our findings suggest that topoisomerase I is able to probe DNA topology by assessment of writhe, rather than twist.     

Interrogating accessibility of telomeric sequences with FRET-PAINT: evidence for length-dependent telomere compaction

Single-stranded telomeric overhangs are ∼200 nucleotides long and can form tandem G-quadruplex (GQ) structures, which reduce their accessibility to nucleases and proteins that activate DNA damage response. Whether these tandem GQs further stack to form compact superstructures, which may provide better protection for longer telomeres, is not known. We report single-molecule measurements where the accessibility of 24–144 nucleotide long human telomeric DNA molecules is interrogated by a short PNA molecule that is complementary to a single GGGTTA repeat, as implemented in the FRET-PAINT method. Binding of the PNA strand to available GGGTTA sequences results in discrete FRET bursts which were analyzed in terms of their dwell times, binding frequencies, and topographic distributions. The binding frequencies were greater for binding to intermediate regions of telomeric DNA compared to 3′- or 5′-ends, suggesting these regions are more accessible. Significantly, the binding frequency per telomeric repeat monotonically decreased with increasing telomere length. These results are consistent with telomeres forming more compact structures at longer lengths, reducing accessibility of these critical genomic sites.     

The diversity and function of soil microbial communities exposed to different disturbances

To improve understanding of the relationship between the diversity and function of the soil ecosystem, we investigated the effect of two different disturbances on soil bacterial communities—long-term exposure to the heavy metal mercury and transient exposure to the antibiotic tylosin. In the mercury-contaminated soil the diversity (Shannon index) was reduced as assessed from denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA sequences from the soil community DNA and from colony morphology typing of the culturable bacterial population. However, analysis of the substrate utilization profiles did not reveal any differences in diversity. In the tylosin-treated soil, DGGE revealed a small difference in the diversity of 16S rDNA compared to the control soil, whereas analysis of the colony morphology typing or substrate utilization results did not reveal any differences in diversity. Soil function was also affected by mercury contamination. The lag time before soil respiration increased following addition of glucose or alfalfa substrate was longer in the mercury-contaminated soil than in the control soil. Moreover, it was markedly prolonged in mercury-contaminated soil subjected to heat treatment prior to substrate addition, thus indicating reduced resistance to a new disturbance in the mercury-contaminated soil as compared to the control soil. Tylosin treatment did not have any significant effect on any of the respiration parameters measured, either with or without prior heat treatment of the soil.     

Throwing behavior and mass distribution of stone selection in tufted capuchin monkeys (Cebus apella)

Cannell [Journal of Archaeological Science 29:335-339, 2002] argued that sex-based differences among humans in terms of the mass of chosen throwing stones could be used to infer body mass and patterns of sexual dimorphism in early hominids from Olduvai and Koobi Fora by examining the mass distributions of unaltered stone tools at those sites. We examined this hypothesis in tufted capuchin monkeys using a comparative approach, by investigating the relationships among body mass, sex, stone weight preference, and accuracy in a throwing task. The subject sample consisted of nine monkeys trained to perform an aimed-throwing task in which a food reward could be obtained by throwing a stone into a bucket. We found that 1) the subjects showed a strong mean stone mass preference; 2) the females chose heavier stones than the males, in terms of absolute mean selected stone mass and selected stone mass relative to body mass; 3) subjects threw more accurately when they used stones of preferred mass vs. stones of nonpreferred mass; and 4) overall, the males were more accurate in the throwing task than the females. We conclude that capuchins are highly selective when choosing throwing stones, and that this confers an advantage for throwing accuracy. Our results indicate that the sexually dimorphic pattern in stone mass preference observed among humans does not generalize to Cebus apella. We suggest that researchers examining this pattern in humans in an attempt to explain early hominid patterns of dimorphism and behavior should take into account not only stone weight preference, but also its adaptive advantage.     

Pestle use and modification by tufted capuchins (Cebus apella)

We examined the use and modification of pestles by tufted capuchins (Cebus apella). In each of two experiments we presented 18 subjects with an apparatus that held sugarcane along with materials that the animals could use as tools. In Experiment 1 we presented the subjects with sticks, and in Experiment 2 we presented them with sticks, stones, paper towels, and food biscuits. Seven subjects used sticks as pestles to break down fiber to and squeeze sap from sugarcane in Experiment 1. Five of them modified sticks for this purpose. In Experiment 2, 10 animals used pestles and sponges, combined tools, and used pestles to mix together different kinds of food. These results provide further evidence of functional convergence for the use and modification of tools byCebus andPan and are consistent with the view that extractive foraging is associated with the tool-using and toolmaking behavior of primates.     

Transfer of tools and food between groups of tufted capuchins (Cebus apella)

This research examined tool and food transfer between two groups of tufted capcuhin monkeys (Cebus apella). Subjects in one group transferred stones to subjects in a second group who in turn used the stones as cutting tools and then transferred food to subjects in the first group. Aspects of the capuchins' behavior are similar to those described for food-sharing in Cebus, cooperative tool use in Papio, and tool and food exchange in Pan. We propose that tool use and food-sharing facilitate tool and food transfer between captive groups of Cebus apella. Am. J. Primatol. 43:33–41, 1997. © 1997 Wiley-Liss, Inc.     

Rhesus macaque (Macaca mulatta) group formation and housing: wounding and reproduction in a specific pathogen free (SPF) colony.

In the present report, we examined the effects of group formation strategy and corral design on wounding and reproduction rates in rhesus macaques. Specifically, we examined group formation using a staged strategy, in which small groups of animals were introduced incrementally over a period of weeks, and a rapid formation strategy, in which all animals were introduced in 1 day. We also examined group formation using a divided corral design that facilitated visual and social separation of individuals, and an undivided corral design that did not facilitate visual or social separation. Dependent measures were wounding and reproductive rates over each of the 2 years that followed group formation. Results indicate that incrementally releasing subgroups of animals, and using a corral design that provides for visual and social separation of individuals, are effective strategies for reducing rates of traumatic wounding when forming multimale-multifemale rhesus macaque breeding groups. However, it must be noted that differences in formation strategy and corral design did not lead to higher reproductive rates. We conclude that incrementally releasing animals in hierarchical subgroups, and using a divided vs. undivided housing design, reduced intra-group wounding and associated demands on veterinary and animal management resources following formation of rhesus macaque breeding groups.