Promiscuous binding of ligands by beta-lactoglobulin involves hydrophobic interactions and plasticity

Bovine beta-lactoglobulin (betaLG) binds a variety of hydrophobic ligands, though precisely how is not clear. To understand the structural basis of this promiscuous binding, we studied the interaction of betaLG with palmitic acid (PA) using heteronuclear NMR spectroscopy. The titration was monitored using tryptophan fluorescence and a HSQC spectrum confirmed a 1:1 stoichiometry for the PA-betaLG complex. Upon the binding of PA, signal disappearances and large changes in chemical shifts were observed for the residues located at the entrance and bottom of the cavity, respectively. This observation indicates that the lower region makes a rigid connection with PA whereas the entrance is more flexible. The result is in contrast to the binding of PA to intestinal fatty acid-binding protein, another member of the calycin superfamily, in which structural consolidation occurs upon ligand binding. On the other hand, the ability of betaLG to accommodate various hydrophobic ligands resembles that of GroEL, in which a large hydrophobic cavity and flexible binding site confer the ability to bind various hydrophobic substrates. Considering these observations, it is suggested that, in addition to the presence of the hydrophobic cavity, the plasticity of the entrance region makes possible the binding of hydrophobic ligands of various shapes. Thus, in contrast to the specific binding seen for many enzymes, betaLG provides an example of binding with low specificity but high affinity, which may play an important role in protein-ligand and protein-protein networks.     

Organic and inorganic nutrient effects on growth rate–irradiance relationships in the Texas brown‐tide alga Aureoumbra lagunensis (Pelagophyceae)1

Pelagophyte species in the genera Aureococcus and Auroumbra form brown tides in coastal bays that cause food‐web disruption and extensive shading of benthic primary producers. Organic nutrients have been suggested as key factors in the origination and persistence of the East Coast (USA) brown‐tide alga Aureococcus anophagefferens Hargraves et Sieburth. To evaluate this finding for the Texas brown‐tide alga Aureoumbra lagunensis D. A. Stockw., DeYoe, Hargraves et P. W. Johnson, we grew strain TBA‐2 with dissolved inorganic nitrogen (DIN; or ) or dissolved organic nitrogen (DON; urea or glutamate) as the nitrogen (N) source under eight light intensities. Maximum growth rates decreased with N source from (1.0 div · d^?1) to (0.48 div · d^?1). Neither growth rate efficiency (α) nor I_k varied significantly between N treatments. Both inorganic phosphorus (P) and β‐glycerophosphate supported growth. Aureoumbra lagunensis can utilize at least some forms of organic N and P and can use them to persist or grow when inorganic forms become limiting. We found no evidence to support the hypothesis that organic utilization enhances or supplements growth at low light levels.     

Measuring bidirectional mutation

The estimation of mutation rates is usually based on a model in which mutations are rare independent Poisson events. Back-mutation of mutants, an even rarer event, is ignored. In the hypermutating B cells of the immune system, mutation between phenotypes exhibiting, vs. not exhibiting, surface immunoglobulin is common in both directions. We develop three strategies for the estimation of mutation rates under circumstances such as these, where mutation rates in both directions are estimated simultaneously. Our model for the growth of a cell culture departs from the classical assumption of cell division as a memoryless (Poisson) event; we model cell division as giving rise to sequential generations of cells. On this basis, a Monte-Carlo simulation is developed. We develop also a numerical approach to calculating the probability distribution for the proportion of mutants in each culture as a function of forward- and backward-mutation rates. Although both approaches are too computationally intensive for routine laboratory use, they provide the insight necessary to develop and evaluate a third, 'hand-calculator' approach to extracting mutation rate estimators from experiments of this type.     

Uncertainty in allometric exponent estimation: a case study in scaling metabolic rate with body mass

Many factors could influence the allometric scaling exponent β estimation, but have not been explored systematically. We investigated the influences of three factors on the estimate of β based on a data set of 626 species of basal metabolic rate and mass in mammals. The influence of sampling error was tested by re-sampling with different sample sizes using a Monte Carlo method. Small random errors were introduced to measured data to examine their influence on parameter estimations. The influence of analysis method was also evaluated by applying nonlinear and linear regressions to the original data. Results showed that a relative large sample size was required to lower statistical inference errors. When sample size n was 10% of the base population size (n=63), 35% of the samples supported β=2/3, 39% supported β=3/4, and 15% rejected β=0.711, even though the base population had a β=0.711. The controversy surrounding the estimation of β in the literature could be partially attributable to such small sample sizes in many studies. Measurement errors in body mass and base metabolic rate, especially in body mass, could largely increase alpha and beta errors. Analysis methods also affected parameter estimations. Nonlinear regressions provided better estimates of the scaling exponent that were significantly higher than these commonly estimated by linear regressions. This study demonstrated the importance of the quantity and quality of data as well as analysis method in power law analysis, raising caution in interpreting power law results. Meta-data synthesis using data from independent studies seems to be a proper approach in the future, but caution should be taken to make sure that such measurements are made using similar protocols.     

Salinities, not diets, affect strontium/calcium ratios in otoliths of Anguilla japonica

Although otolith Strontium (Sr)/calcium (Ca) ratios have been widely used to reconstruct the past salinity environmental history of anguillid eels, factors affecting the Sr/Ca ratios in otoliths are incompletely understood. Japanese Eel (Anguilla japonica) elvers (mean length 54.7 ± 2.1 mm) were collected in the estuary during their upstream migration and reared at 5 different salinities (0, 5, 15, 25, and 35 psu) and 3 types of feeding conditions (formulated feed, tubifex, and starvation) for 30 days to evaluate the effects of salinity and diets on otolith Sr/Ca ratios. Ca and Sr concentrations in the ambient water significantly increased with salinity (SAL) as [Ca] _water = 15.50SAL − 5.56, and [Sr] _water = 0.21SAL + 0.03, respectively. Sr/Ca ratios in otoliths increased with salinity (SAL) of the rearing water as [(Sr/Ca) × 1000] _otolith = 0.091SAL + 3.790. In diets, Sr/Ca ratios were 4 times higher in tubifex than in formulated feed. However, in otoliths, ANOVA indicated that Sr/Ca ratios did not differ significantly between groups fed on tubifex or formulated feed (p = 0.118). Otolith Sr/Ca ratios were negatively correlated with fish growth rates while the growth rates differed significantly among rearing conditions with different salinities and diets. Partition coefficients of the Sr/Ca ratios from ambient water to fish tissues and otoliths significantly increased with salinity. The Sr/Ca ratios of Japanese Eel otoliths thus were positively correlated with the ambient salinity and decreased with increasing fish growth rate, but was not affected by fish diet.     

Effects of Joint Space Use and Group Membership on Contact Rates Among White-Tailed Deer

Abstract: Establishment and spread of infectious diseases are controlled by the frequency of contacts among hosts. Although managers can estimate transmission coefficients from the relationship between disease prevalence and age or time, they may wish to quantify or compare contact rates before a disease is established or while it is at very low prevalence. Our objectives were to quantify direct and indirect contacts rates among white-tailed deer (Odocoileus virginianus) and to compare these measures of contact rate with simpler measures of joint space use. We deployed Global Positioning System (GPS) collars on 23 deer near Carbondale, Illinois, USA, from 2002 to 2005. We used location data from the GPS collars to measure pairwise rates of direct and indirect contact, based on a range of proximity criteria and time lags, as well as volume of intersection (VI) of kernel utilization distributions. We analyzed contact rates at a given distance criterion and time lag using mixed-model logistic regression. Direct contact rates increased with increasing VI and were higher in autumn—spring than in summer. After accounting for VI, the estimated odds of direct contact during autumn—spring periods were 5.0–22.1-fold greater (depending on the proximity criterion) for pairs of deer in the same social group than for between-group pairs, but for direct contacts during summer the within:between-group odds ratio did not differ significantly from 1. Indirect contact rates also increased with VI, but the effects of both season and pair-type were much smaller than for direct contacts and differed little as the time lag increased from 1–30 days. These results indicate that simple measures of joint space use are insufficient indices of direct contact because group membership can substantially increase contacts at a given level of joint space use. With indirect transmission, however, group membership had a much smaller influence after accounting for VI. Relationships between contact rates and season, VI, and pair-type were generally robust to changes in the proximity criterion defining a contact, and patterns of indirect contacts were affected little by the choice of time lag from 1–30 days. The use of GPS collars provides a framework for testing hypotheses about the form of contact networks among large mammals and comparing potential direct and indirect contact rates across gradients of ecological factors, such as population density or landscape configuration.     

Wolf Movement Patterns: a Key to Estimation of Kill Rate?

Abstract: To estimate wolf (Canis lupus) kill rates from fine-scale movement patterns, we followed adult wolves in 3 territories of the Scandinavian wolf population using Global Positioning Systems (GPS) during the winters of 2001–2003. The resulting 6 datasets of 62–84 study days gave a total of 8,747 hourly GPS positions. We visited clusters of positions in the field on average 8.8 days after positioning and found moose (Alces alces) killed by wolves during the study period on 74 (8%) of the 953 clusters. The number of positions and visits to a cluster, their interaction, and the proportion of afternoon positions were significant fixed effects in mixed logistic-regression models predicting the probability of a cluster containing a wolf-killed moose. The models, however, displayed a poor goodness-of-fit and were not a suitable tool for estimating kill rates from positioning data alone. They might be used to reduce fieldwork by excluding unlikely clusters, although the reduction was not substantial. We discuss proximate factors (i.e., human disturbance and access to prey) as well as ultimate factors (i.e., social organization, intra-guild dominance, and litter size) as potential causes of the observed high temporal and spatial variation in prey-handling. For similar future kill-rate studies, we recommend increasing field efforts and shortening positioning intervals.     

Predation on Moose Calves by European Brown Bears

Abstract: In North America, brown bears (Ursus arctos) can be a significant predator on moose (Alces alces) calves. Our study in Sweden is the first in which brown bears are the only predator on moose calves. Bears and moose occurred at densities of about 30/1,000 km² and 920/1,000 km², respectively, and bears killed about 26% of the calves. Ninety-two percent of the predation took place when calves were <1 month old. Bear predation was probably additive to other natural mortality, which was about 10% in areas both with and without bears. Females that lost their calves in spring produced more calves the following year (1.54 calves/F) than females that kept their calves (1.11 calves/F), which reduced the net loss of calves due to predation to about 22%.     

Hair Sampling Techniques for River Otters

ABSTRACT River otter (Lontra canadensis) populations have been difficult to monitor and information on densities is lacking throughout their range. To obtain DNA-based population estimates of river otters we developed 2 traps to capture hair; a modified body-snare and a modified foot-hold trap. Of 82 traps activated 77 captured hairs (94%). Traps snagged 3–20 guard hairs per capture. Our capture rates of otter hair ranged from one capture per 3.6 trap nights to one capture per 156.6 trap-nights. Our traps provide an effective, noninvasive technique for obtaining hair DNA from individual river otters.     

褐藻寡糖抗环磷酰胺诱导蚕豆根尖的细胞遗传毒性

采用蚕豆根尖细胞的微核试验和染色体畸变试验方法,测定不同浓度的褐藻寡糖对环磷酰胺(cyclophosphamide,CP)诱导的蚕豆根尖细胞的微核率、有丝分裂指数和染色体畸变率的影响。结果表明:褐藻寡糖能有效抑制环磷酰胺诱导的蚕豆根尖细胞微核的产生,即在一定浓度范围内,微核率随褐藻寡糖处理浓度的降低而减少,但低于一定浓度后反而呈上升趋势;不同浓度的褐藻寡糖均可使蚕豆根尖细胞有丝分裂指数增大;褐藻寡糖还能有效降低蚕豆根尖细胞染色体畸变率。因此,褐藻寡糖对蚕豆根尖细胞具有明显的诱抗活性和调节细胞分裂生长的效应。