Prospects and pitfalls in whole genome association studies

Recent large-scale studies of common genetic variation throughout the human genome are making it feasible to conduct whole genome studies of genotype-phenotype associations. Such studies have the potential to uncover novel contributors to common complex traits and thus lead to insights into the aetiology of multifactorial phenotypes. Despite this promise, it is important to recognize that the availability of genetic markers and the ability to assay them at realistic cost does not guarantee success of this approach. There are a number of practical issues that require close attention, some forms of allelic architecture are not readily amenable to the association approach with even the most rigorous design, and doubtless new hurdles will emerge as the studies begin. Here we discuss the promise and current challenges of the whole genome approach, and raise some issues to consider in interpreting the results of the first whole genome studies.     

Binocular contributions to the responsiveness and integrative capacity of the circadian rhythm system to light

The retinohypothalamic tract (RHT), a monosynaptic retinal projection to the SCN, is the major path by which light entrains the circadian system to the external photoperiod. The circadian system of rodents effectively integrates or counts photons, and the magnitude of the rhythm phase response is proportional to the total energy of the photic stimulus. In the present studies, responsiveness to light and integrative capacity of the circadian system were tested in hamsters after reduction of retinal photoreceptor input by 50%. At CT 19, animals in constant darkness with or without unilateral retinal occlusion were exposed to 1 of 6 irradiances of 5-min white-light pulses ranging from 0.0011 to 70 microW/cm(2) or 5 white-light pulses of 0.6 microW/cm(2) with durations ranging from 0.25 to 150.0 min. Assessment of light-induced circadian rhythm phase response and Fos expression in the SCN by these animals revealed that a 50% reduction in input from photoreceptors stimulated directly with light caused a decrease in responsiveness to the longest duration and highest irradiance pulses presented. Despite this effect, both the magnitude of Fos induction in the SCN and phase-shift response remained directly proportional to the total energy in the photic stimuli. The results support the view that a reciprocal relationship between stimulus irradiance and duration persists despite the 50% reduction in retinal photoreceptor input. The mechanism of integration neither resides in the retina nor in the RHT.     

Adaptive plasticity of floral display size in animal-pollinated plants

Plants need not participate passively in their own mating, despite their immobility and reliance on pollen vectors. Instead, plants may respond to their recent pollination experience by adjusting the number of flowers that they display simultaneously. Such responsiveness could arise from the dependence of floral display size on the longevity of individual flowers, which varies with pollination rate in many plant species. By hand-pollinating some inflorescences, but not others, we demonstrate plasticity in display size of the orchid Satyrium longicauda. Pollination induced flower wilting, but did not affect the opening of new flowers, so that within a few days pollinated inflorescences displayed fewer flowers than unpollinated inflorescences. During subsequent exposure to intensive natural pollination, pollen removal and receipt increased proportionally with increasing display size, whereas pollen-removal failure and self-pollination accelerated. Such benefit-cost relations allow plants that adjust display size in response to the prevailing pollination rate to increase their attractiveness when pollinators are rare (large displays), or to limit mating costs when pollinators are abundant (small displays). Seen from this perspective, pollination-induced flower wilting serves the entire plant by allowing it to display the number of flowers that is appropriate for the current pollination environment.     

Phytoplankton production,biomass and community structure following a summer nutrient pulse in Chesapeake Bay

Unusually high concentrations of NH₄⁺ (up to 10 μM) were observed in the surface waters of polyhaline Chesapeake Bay during July 2000, supporting elevated rates of simulated in situ integrated primary production (4.6 g C m⁻² day⁻¹) and chlorophyll-a (chl-a) specific integrated primary production (56 mg C mg chl-a⁻¹ day⁻¹). These rates were the highest measured in the polyhaline Bay during a 5-year sampling program. Chl-a and the percent contribution of phytoplankton >20 μm to the total phytoplankton increased after the ammonium pulse. We hypothesize that increased wind-driven mixing and a tilting of the pycnocline caused by northeast winds combined to increase the transport of NH₄⁺ from below the pycnocline to the surface water. Summer wind and chl-a data collected in the southern Bay between 1984 and 2000 revealed that chl-a was significantly higher 2 weeks after northeast winds than in years when no northeast wind occurred. Episodic peaks in NH₄⁺ and primary productivity resulting from wind events lasting only a few days are poorly captured by traditional shipboard surveys, but may be detected if sampling is focused on periods when wind forcing favors enhanced NH₄⁺ transport to the surface waters. This process of introduction of NH₄⁺ to the surface water from sediments followed by enhanced primary productivity may help explain some of the phytoplankton blooms that are observed in the polyhaline Bay and other estuaries during summer months.     

In vitro analysis of the chain termination reaction in the synthesis of poly-(R)-beta-hydroxybutyrate by the class III synthase from Allochromatium vinosum

Allochromatium vinosum polyhydroxyalkanoate synthase catalyzes formation of poly-(R)-3-hydroxybutyrate (PHB) from (R)-3-hydroxybutyryl-coenzyme A (HB-CoA). (R)-3-Hydroxybutyryl-N-acetylcysteamine (HB-NAC) is an alternative substrate for this synthase in vitro, with a turnover 1% that of HB-CoA. With HB-NAC, the molecular weight (M(w)) of PHB produced at substrate-to-enzyme ratios of 1500-15 000 is approximately 75 kDa. (1)H NMR shows that PHB produced has hydroxybutyrate at the alcohol end and N-acetylcysteamine (NAC) at the carboxylate end of the polymer. Exogenous NAC has no effect on the M(w) of PHB produced with HB-CoA or HB-NAC in vitro, whereas PHB from a polymerization reaction with both HB-CoA and HB-NAC has intermediate M(w). These results can be accommodated by two models. In the first, NAC liberated at the active site during polymerization acts as a chain transfer agent. In the second, there is a noncovalent polymer intermediate covalently linked to NAC, which can dissociate from the active site.     

Age-related diffuse chronic telogen effluvium- type alopecia in female squirrel monkeys (Saimiri boliviensis boliviensis)

We investigated the diffuse alopecia affecting some female squirrel monkeys (Saimiri boliviensis boliviensis) housed in a breeding facility. We randomly selected 100 female and 10 male animals and performed a complete physical exam and a hair assessment on all animals; blood tests, trichograms, hair density; and skin biopsies in representative cases; and a dominance behavioral assessment of 50 animals. Hair coat was normal in 35 female monkeys and all 10 male animals. Of the 65 females with diffuse alopecia, 17 had mild, 22 moderate, and 26 severe hair loss. The alopecia group had a mean age of 9.6 +/- 0.6 years, whereas that of the normal group was 4.7 +/- 0.6 years (P < 0.05). The parity in the alopecia group was 4.2 +/- 0.6 but 2.0 +/- 0.6 (P < 0.05) in the normal group. There were no statistically significant differences in body weight, hemoglobin, blood urea nitrogen, serum glucose, liver aspartate aminotransaminase, or free thyroxine. The trichogram demonstrated 20.8% +/- 1.6% (mean +/- standard error) of telogen hairs in the alopecia group compared with 9.5% +/- 2.8% of the control group (P < 0.05). The hair density in the alopecia group was 52.8 +/- 4.1/cm2 and 79.6 +/- 14.3/cm2 in the control group. Skin biopsies in affected monkeys demonstrated increased telogen follicles, with no fibrosis or inflammation. There were no statistically significant differences in the dominance behavioral analysis. The findings are consistent with chronic telogen effluvium (CTE). A number of organic, behavioral, and dominance-related stress causes of CTE were excluded. CTE appears to be predominantly age-related in this population. CTE in female squirrel monkeys may serve as an animal model for human diffuse alopecia.