An experimental analysis of cache recovery in Clark's nutcracker

Five hypotheses of cache recovery behaviour in Clark's nutcracker (Nucifraga columbiana) were examined experimentally. Most caches were made in soil within 5 cm of conspicuous large objects. Both seed-caching and non-seed-caching nutcrackers were able to locate caches. Seed-caching nutcrackers relocated caches using large objects as remembered visual cues. Soil microtopography and small (<2 cm diameter) objects may be used as cues to facilitate cache recovery but are not essential. Non-seed-caching nutcrackers located caches by using soil disturbances at cache sites as visual cues and by searching preferentially near objects where caches were concentrated. Success rates of seed-caching nutcrackers ranged from 52 to 78% and those of non-seed-caching nutcrackers ranged from 8 to 12%. Nutcrackers do not use random search or olfactory cues to locate caches.     

A MONTE CARLO SIMULATION OF CLONE GROWTH

A Monte Carlo simulation of clone growth is discussed from the point of view of clonal volume. It is shown that clone volume is a good representation of the number of cells per clone for a wide range of single cell growth equations. However, the rate at which the coefficient of variation in clonal volume approaches that of cell number per clone is strongly dependent upon the particular growth equation.     

In Pursuit of Safety: One-Hundred Years of Toxicological Risk Assessment

The publication in 1962 of Rachel Carson's Silent Spring marks the mid-point in a century that saw, in its first half, the emergence of public health concerns related to human exposures to chemicals, and, in its second half, the emergence of public policies to deal with those concerns. Those policies made it imperative that the scientific community come to grips with the problem of identifying exposure levels not likely to cause harm. This problem was not significantly discussed within the scientific community until the 1950s, and well-described methods for practical solutions to it did not appear until the 1970s. An important report from the National Academy of Sciences, published in 1983 (Risk Assessment in the Federal Government), provided an analysis of these emerging methods, and recommended a useful framework for the assessment and management of risk. This framework remains central to public health and regulatory decision-making. A high-level perspective is offered on events leading to and following the 1983 report. The article describes early thinking about chemical toxicity and the scientific path that thinking followed through the 20th century, and to the present.     

Diversification of Hawaiian Cyrtandra (Gesneriaceae) under the influence of incomplete lineage sorting and hybridization

Cyrtandra (Gesneriaceae) is a genus of flowering plants with over 800 species distributed throughout Southeast Asia and the Pacific Islands. On the Hawaiian Islands, 60 named species and over 89 putative hybrids exist, most of which are identified on the basis of morphology. Despite many previous studies on the Hawaiian Cyrtandra lineage, questions regarding the reconciliation of morphology and genetics remain, many of which can be attributed to the relatively young age and evidence of hybridization between species. We utilized targeted enrichment, high‐throughput sequencing, and modern phylogenomics tools to test 31 Hawaiian Cyrtandra samples (22 species, two putative hybrids, four species with two samples each, one species with four samples) and two outgroups for species relationships and hybridization in the presence of incomplete lineage sorting (ILS). Both concatenated and species‐tree methods were used to reconstruct species relationships, and network analyses were conducted to test for hybridization. We expected to see high levels of ILS and putative hybrids intermediate to their parent species. Phylogenies reconstructed from the concatenated and species‐tree methods were highly incongruent, most likely due to high levels of incomplete lineage sorting. Network analyses inferred gene flow within this lineage, but not always between taxa that we expected. Multiple hybridizations were inferred, but many were on deeper branches of the island lineages suggesting a long history of hybridization. We demonstrated the utility of high‐throughput sequencing and a phylogenomic approach using 569 loci to understanding species relationships and gene flow in the presence of ILS.     

Calculation of effective diffusivities for biofilms and tissues.

In this study we describe a scheme for numerically calculating the effective diffusivity of cellular systems such as biofilms and tissues. This work extends previous studies in which we developed the macroscale representations of the transport equations for cellular systems based on the subcellular-scale transport and reaction processes. A finite-difference model is used to predict the effective diffusivity of a cellular system on the basis of the subcellular-scale geometry and transport parameters. The effective diffusivity is predicted for a complex three-dimensional structure that is based on laboratory observations of a biofilm, and these numerical predictions are compared with predictions from a simple analytical solution and with experimental data. Our results indicate that, under many practical circumstances, the simple analytical solution can be used to provide reasonable estimates of the effective diffusivity.     

Role of methyl groups in dynamics and evolution of biomolecules

Recent studies have discovered strong differences between the dynamics of nucleic acids (RNA and DNA) and proteins, especially at low hydration and low temperatures. This difference is caused primarily by dynamics of methyl groups that are abundant in proteins, but are absent or very rare in RNA and DNA. In this paper, we present a hypothesis regarding the role of methyl groups as intrinsic plasticizers in proteins and their evolutionary selection to facilitate protein dynamics and activity. We demonstrate the profound effect methyl groups have on protein dynamics relative to nucleic acid dynamics, and note the apparent correlation of methyl group content in protein classes and their need for molecular flexibility. Moreover, we note the fastest methyl groups of some enzymes appear around dynamical centers such as hinges or active sites. Methyl groups are also of tremendous importance from a hydrophobicity/folding/entropy perspective. These significant roles, however, complement our hypothesis rather than preclude the recognition of methyl groups in the dynamics and evolution of biomolecules.     

Retinal Changes Precede Visual Dysfunction in the Complement Factor H Knockout Mouse

We previously reported that aged mice lacking complement factor H (CFH) exhibit visual defects and structural changes in the retina. However, it is not known whether this phenotype is age-related or is the consequence of disturbed development. To address this question we investigated the effect of Cfh gene deletion on the retinal phenotype of young and mid-age mice. Cfh ^−/− mouse eyes exhibited thickening of the retina and reduced nuclear density, but relatively normal scotopic and photopic electroretinograms. At 12 months there was evidence of subtle astroglial activation in the Cfh ^−/− eyes, and significant elevation of the complement regulator, decay-accelerating factor (DAF) in Müller cells. In the retinal pigment epithelium (RPE) of young control and Cfh ^−/− animals mitochondria and melanosomes were oriented basally and apically respectively, whereas the apical positioning of melanosomes was significantly perturbed in the mid-age Cfh ^−/− RPE. We conclude that deletion of Cfh in the mouse leads to defects in the retina that precede any marked loss of visual function, but which become progressively more marked as the animals age. These observations are consistent with a lifelong role for CFH in retinal homeostasis.