Harry Potter and the structural biologist's (Key)stone

A report on the first European Keystone symposium 'Multi-protein complexes involved in cell regulation', Cambridge, UK, 18-23 August 2006.     

A structural biologist's view of the oestrogen receptor

Here we review the results that have emerged from our structural studies on the oestrogen receptor ligand-binding domain (ER-LBD). The effects of agonists and antagonists on the structure of ER- and ERβ-LBDs are examined. In addition, the findings from structural studies of ER-LBD in complex with peptide fragments corresponding to the NR-box II and III modules of the p160 coactivator TIF2 are discussed in the context of the assembly of ER:coactivator complexes. Together these studies have broadened our understanding of ER function by providing a unique insight into ER's ligand specificity, it's ability to interact with coactivators and the structural changes that underlie receptor agonism and antagonism.     

Muggles,Wizards, and Witches Using Harry Potter Characters to Teach Human Pedigrees

These activities allow students to investigate behavioral responses of the large Milkweed bug, Oncopeltus fasciatus, and the mealworm, Tenebrio molitor or Tenebrio obscurus, to external stimuli of light, color, and temperature. During the activities, students formulate hypotheses to research questions presented. They also observe insects for a period of time, record observations, analyze the data, and draw conclusions. Important outcomes include experience with critical and analytical thinking and appreciation for the process of science as well as the biology of living things. The activities described herein are appropriate for upper elementary grades, middle school, and high school biology classes.     

Phylogeography of the Southeast Asian stone oaks (Lithocarpus)

Abstract Aim To describe current geographical patterns of genetic diversity and infer the historical population dynamics of the stone oaks (Lithocarpus) in Southeast Asia. Location We sampled three populations in Indochina: (1) Yunnan province, China; (2) Pyin Oo Lwin area, Myanmar and (3) north‐western Vietnam; two in western Borneo: (1) South‐western Sarawak and (2) West Kalimantan, Indonesia; two in central Borneo: (1) north coastal Sarawak and (2) north‐eastern Sarawak, Malaysia; and two in northern Borneo: (1) Central Sabah and (2) Northern Sabah, Malaysia. Methods A phylogenetic reconstruction of chloroplast DNA sequence variation from numerous individuals of multiple species was used to determine geographical distribution of genetic diversity. A resampling scheme was used to determine the significance of these patterns at different hierarchical levels of the phylogeny. Results were compared with a previously published set of nuclear DNA sequence data. Results A high level of chloroplast sequence variation was found, which was divided equally between two major clades separated by four non‐homoplasious changes. One clade was confined to the island of Borneo, while the other was widespread. Strong geographical structure was observed in the chloroplast sequence variation. The Indo‐chinese populations were much more closely related than expected, comparable with the highly endemic and isolated population on the western coast of Borneo. Conversely, individuals from the Kelabit Highlands were found to be more distantly related than expected. The highest levels of genetic endemism were observed in western Borneo. More geographical structure was observed in the Bornean clade than in the Widespread clade, because of limited genetic diversity in the Widespread clade. Relatively weak geographical structure was found in the nuclear sequence variation: only populations in southern China and central Sabah were significantly related. Conclusions The high levels of chloroplast genetic diversity and the persistence of an ancestral haplotype that is a single step away from a haplotype found in Castanopsis indicates the continuous presence of tropical rain forest in Southeast Asia throughout the evolutionary history of the genus (c. 40 Myr). This conclusion is supported by the high frequency of numerous endemic types observed in every population and the relatively few number of ‘missing’ haplotypes. This situation suggests both limited migration and limited extinction. In contrast, the nuclear genetic diversity contained less geographical structure, indicating that our taxonomic sampling among populations was unbiased and that gene flow mediated through pollen is less geographically restricted and contains less geographical structure than purely seed‐mediated (chloroplast) gene flow. The most likely scenario suggested by the evidence involves four major patterns: (1) the widespread presence of an ancestral haplotype; (2) the large degree of separation (four non‐homoplasious base pairs) between the types found in the two major clades; (3) the concentration of derived types from both major clades found in central and northern Borneo; and (4) the molecular endemism found in each location. These patterns suggest four primary things about the population dynamics of Lithocarpus since the late Eocene: (1) populations have either spanned the entire region throughout much of the evolutionary history of the genus or substantial populations have persisted in both Indochina and Borneo with limited migration between them; (2) significant fragmentation has occurred subsequently between the Asian mainland and the Melasian island archipelago, leading to independent genetic diversification in both regions; (3) several locations possessing significant independent histories, have experienced little migration and have never gone completely extinct; and (4) that the central highlands of Borneo have been re‐invaded from the north and the west. The timing of these events is difficult to ascertain but probably predate the Quaternary Period, suggesting that although the recent ice ages might have affected the overall distribution of rain forest in Southeast Asia, it managed to persist in most regions even through the most dramatic drying events.     

The Magical Activation of Left Amygdala when Reading Harry Potter: An fMRI Study on How Descriptions of Supra-Natural Events Entertain and Enchant

Literature containing supra-natural, or magical events has enchanted generations of readers. When reading narratives describing such events, readers mentally simulate a text world different from the real one. The corresponding violation of world-knowledge during this simulation likely increases cognitive processing demands for ongoing discourse integration, catches readers’ attention, and might thus contribute to the pleasure and deep emotional experience associated with ludic immersive reading. In the present study, we presented participants in an MR scanner with passages selected from the Harry Potter book series, half of which described magical events, while the other half served as control condition. Passages in both conditions were closely matched for relevant psycholinguistic variables including, e.g., emotional valence and arousal, passage-wise mean word imageability and frequency, and syntactic complexity. Post-hoc ratings showed that readers considered supra-natural contents more surprising and more strongly associated with reading pleasure than control passages. In the fMRI data, we found stronger neural activation for the supra-natural than the control condition in bilateral inferior frontal gyri, bilateral inferior parietal lobules, left fusiform gyrus, and left amygdala. The increased activation in the amygdala (part of the salience and emotion processing network) appears to be associated with feelings of surprise and the reading pleasure, which supra-natural events, full of novelty and unexpectedness, brought about. The involvement of bilateral inferior frontal gyri likely reflects higher cognitive processing demand due to world knowledge violations, whereas increased attention to supra-natural events is reflected in inferior frontal gyri and inferior parietal lobules that are part of the fronto-parietal attention network.     

Totipotency, somatic embryogenesis, and Harry Waris (1893–1973)

F. C. Steward and Jakob Reinert in the late 1950s, independently and with different degrees of scientific exactness, demonstrated that somatic cells of cultivated carrot can produce embryo-like structures in aseptic culture. Growth substances in the nutrient medium were viewed as central to the process. The now classic papers of Steward and Reinert have found a special and enduring place in the literature of plant development. But Harry Waris also deserves credit for his observation that vegetative cells sloughed off from aseptically germinated seedlings reared in liquid nutrient medium can produce 'embryos'. In his studies, seedlings of Oenanthe aquatica (Umbelliferae) were maintained in culture for protracted periods under nutrient conditions designed to foster imbalance in protein metabolism, but without exogenous growth hormones. Seedlings placed in media with high concentrations of glycine grew normally for 3–4 months; after this a "period of morbidity" occurred, followed by production of new plants from the root tips. These new plants, later called "neomorphs", in turn reproduced by colorless outgrowths of leaf epidermis. Such outgrowths, and "nodules" formed in a callus produced by the original seedlings, passed through stages described as "nodule", "fusiform", and a stage with two or more "lobes". Transfer of the neomorphs to a medium lacking glycine resulted in the development of normal plants. We show that Waris was among the first, if not the first, to observe and recognize somatic embryo production in aseptic culture, and indeed to call them "embryos". We also discuss his investigations in the context of understanding development at the cellular level, then and now.     

Nest maintenance and stone theft in the Chinstrap penguin (Pygoscelis antarctica)

The intensity of stone collection and stone theft by breeding Chinstrap penguins was measured, and estimations made of the number of stones per nest in large (> 400 nests) and small subcolonies (< 50 nests) in the large Vapour Col colony on Deception Island, South Shetland Islands. Stone availability was significantly higher both inside and outside small subcolonies. Penguins carried stones to the nest at the same rate in large and small subcolonies, but stole more intensively in large subcolonies. Stones obtained by theft were significantly larger than those collected elsewhere. When stone availability was increased experimentally, individuals of large subcolonies collected more intensively than control individuals in large and small subcolonies, and stole significantly less than control individuals in large subcolonies, and as much as individuals in small subcolonies. The greater theft pressure in large subcolonies was accompanied by more aggressive defence by nest owners and by reduced succession stealing. However, the reduced availability of stones on the ground near large subcolonies led to a significantly lower number of stones per nest than in small subcolonies. These results are interpreted in the light of the geometric effects of breeding group size (perimeter to surface ratio) on stone accessibility.     

On the competitive balance of macroalgae at Potter Cove (King George Island,South Shetlands)

The sublittoral zonation of macroalgae and abundant animals in Potter Cove, King George Island, is described in relation to substrate, exposure to turbulence and impact of grounding icebergs. Implications on the ecological niches of the most prominent phaeophytes are discussed. It is concluded that Desmarestia anceps and D. menziesii exclude Himantothallus grandifolius under favourable conditions. However, Himantothallus, by its potential to inhabit unstable substrates, may be better adapted to withstand the ice impact. The replacement of Desmarestia by Himantothallus at greater depth can be explained only partially at present.     

The stone tools of capuchins (Cebus apella)

We examined the production of stone took by capuchins (Cebus apella). Eleven subjects used five reduction techniques to produce 346 stone tools (48 cores and 298 flakes). They produced a sharp edge on 83% of the cores and largest flakes. Three monkeys later used a sample of these objects as cutting tools. These results demonstrate that monkeys produce lithic tools analogous to those produced by Oldowan hominids.     

Biodeterioration of ancient stone materials from the Persepolis monuments (Iran)

The problem of deterioration of art works is particularly relevant in countries like Iran that are rich in cultural heritage. According to UNESCO data, Iran holds the tenth rank in a list of countries possessing the highest number of monuments belonging to the world cultural heritage. Archaeological areas, buildings, mosques, statues, museums and objects are all exposed to different biogenic and abiogenic stresses under generally aggressive climatic conditions. Lichens and fungi are known to actively decompose stone surfaces. This process is both physical and chemical in nature and often reaches deep below the stone surfaces. This is caused by chemical and physical interactions of the microbiota with the fluctuating and often drastically changing environmental conditions. Here, we describe and analyze the mainly physical degradation by invading fungal hyphae between stone crystals and a generally destabilizing stone texture. In addition to physical deterioration, organic acids produced by lichens enhance the chemical decomposing processes. In this work, penetration of hyphal bundles as well as individual fungi was studied, and the biodeteriorating patterns were documented and compared to general physical–chemical weathering phenomena. Several strains of aggressive black yeast-like fungi and bacteria were isolated and cultivated and will be described in a taxonomical context with many other isolates from different localities using physiological, morphological and molecular data.     

Optical properties of developing pip and stone fruit reveal underlying structural changes

Analyzing the optical properties of fruits represents a powerful approach for non‐destructive observations of fruit development. With classical spectroscopy in the visible and near‐infrared wavelength ranges, the apparent attenuation of light results from its absorption or scattering. In horticultural applications, frequently, the normalized difference vegetation index (NDVI) is employed to reduce the effects of varying scattering properties on the apparent signal. However, this simple approach appears to be limited. In the laboratory, with time‐resolved reflectance spectroscopy, the absorption coefficient, μ_a, and the reduced scattering coefficient, μ_s′, can be analyzed separately. In this study, these differentiated optical properties were recorded (540–940 nm), probing fruit tissue from the skin up to 2 cm depth in apple (Malus × domestica ‘Elstar’) and plum (Prunus domestica ‘Tophit plus’) harvested four times (65–145 days after full bloom). The μ_a spectra showed typical peak at 670 nm of the chlorophyll absorption. The μ_s′ at 670 nm in apple changed by 14.7% (18.2–15.5 cm^?1), while in plum differences of 41.5% (8.5–5.0 cm^?1) were found. The scattering power, the relative change of μ_s′, was zero in apple, but enhanced in plum over the fruit development period. This mirrors more isotropic and constant structures in apple compared with plum. For horticultural applications, the larger variability in scattering properties of plum explains the discrepancy between commercially assessed NDVI values or similar indices and the absolute μ_a values in plum (R < 0.05), while the NDVI approach appeared reasonable in apple (R ≥ 0.80).     

Phylogenetic and structural studies in the thelebolaceae (Ascomycota)

Several minute dung-inhabiting discomycetes have been classified in the family Thelebolaceae, which has traditionally been included in the order Pezizales. The non-operculate type-genusThelebolus has recently been excluded from the Pezizales. The phylogenetic distribution of other genera associated with Thelebolaceae is still obscure. We have analysed ca. 580 bp from a variable part of the nuclear SSU rRNA gene fromAscozonus, Caccobius, Lasiobolus andThecotheus, and compared these with ca. 1700 bp sequences fromThelebolus, Pleospora, Pezizales, leotiales and Leotiales-related taxa. In the resulting tree,Ascozonus andCaccobius group withThelebolus and the inoperculate discomycetes;Lasiobolus groups withAscodesmis, andThecotheus withAscobolus within Pezizales. SEM pictures of fruit-bodies and ascus apices ofAscozonus, and ascospores fromThecotheus are presented to illustrate characteristic features of these taxa. Submitting author: FAX: +47-22 85 46 64, TEL: +47-22 85 46 61.     

Sequestration of environmental cadmium by metallothionein in the roach (Rutilus rutilus) and the stone loach (Noemacheilus barbatulus)

Two species of coarse fish that are relatively resistant to cadmium poisoning were exposed to sub-lethal concentrations of the metal in their aquarium water. Thus, roach were exposed to cadmium concentrations between 30 and 500 micrograms/l for periods of 14-70 days whereas stone loach were exposed to 1250 micrograms Cd/l for 21-77 days. Under all conditions of exposure, it was found upon analysis of the major organs of accumulation of cadmium in the two species that the toxic metal was sequestered by a single isoform of metallothionein. The amino acid compositions of roach and stone loach metallothionein were determined and found to be similar to those reported for other piscine metallothioneins. The two proteins were found to contain Cd:Zn:Cu in approximate ratios of 4:1:2 per mole of protein. The sequestration of Cd by metallothionein in the two resistant species of fish is contrasted with the situation observed previously in a cadmium-sensitive species, the rainbow trout.     

Phytoplankton structure and dynamics in a turbid Antarctic lake (Potter Peninsula, King George Island)

Qualitative and quantitative changes in the freshwater phytoplankton from one of the largest lakes in Potter Peninsula were studied during the summer period of 1995/1996. The main limnological features were analysed. This research constitutes the first study dealing with the phytoplankton structure and dynamics from lakes in Potter Peninsula. Due to the mixing of the water column by the constant wind action during the ice-free period, neither physical, chemical nor biological parameters showed differences between depths. Soluble reactive phosphorus remained low (26 μg l⁻¹) while total phosphorus concentrations were up to 232 μg l⁻¹. Suspended solids and total phosphorus differed significantly between the two basins in which the lake is divided. Sixty-five taxa were identified. The Bacillariophyceae was the dominant class followed by Chrysophyceae. Achnanthes lanceolata var. haynaldii and Hydrurus foetidus (cysts) were the dominant species. Tychoplanktonic species were the best represented in terms of abundance and species richness. The principal component analysis carried out with abiotic variables showed a temporal gradient characterised by the augmentation of suspended solids, total phosphorus, conductivity, pH and NH₄-N to the end of the summer period. The Principal Component Analysis performed with biotic variables also showed a temporal trend related to a decline in phytoplankton density and an enhancement of chlorophyll-a despite a slight increase of light limitation during the study period. This inverse relation may be due to the presence of picoplankton in chlorophyll-a samples. The potential effect of grazing on the phytoplankton structure is a subject to be tested in future studies. Accepted: 7 February 1999