Analysis of Clostridium botulinum serotype E strains by using multilocus sequence typing, amplified fragment length polymorphism, variable-number tandem-repeat analysis, and botulinum neurotoxin gene sequencing

A total of 41 Clostridium botulinum serotype E strains from different geographic regions, including Canada, Denmark, Finland, France, Greenland, Japan, and the United States, were compared by multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) analysis, variable-number tandem-repeat (VNTR) analysis, and botulinum neurotoxin (bont) E gene sequencing. The strains, representing environmental, food-borne, and infant botulism samples collected from 1932 to 2007, were analyzed to compare serotype E strains from different geographic regions and types of botulism and to determine whether each of the strains contained the transposon-associated recombinase rarA, involved with bont/E insertion. MLST examination using 15 genes clustered the strains into several clades, with most members within a cluster sharing the same BoNT/E subtype (BoNT/E1, E2, E3, or E6). Sequencing of the bont/E gene identified two new variants (E7, E8) that showed regions of recombination with other E subtypes. The AFLP dendrogram clustered the 41 strains similarly to the MLST dendrogram. Strains that could not be differentiated by AFLP, MLST, or bont gene sequencing were further examined using three VNTR regions. Both intact and split rarA genes were amplified by PCR in each of the strains, and their identities were confirmed in 11 strains by amplicon sequencing. The findings suggest that (i) the C. botulinum serotype E strains result from the targeted insertion of the bont/E gene into genetically conserved bacteria and (ii) recombination events (not random mutations) within bont/E result in toxin variants or subtypes within strains.     

Factors affecting nest choice by Pekin ducks

To encourage nest use in breeder poultry flocks, it is important that nest boxes are attractive. Few studies have evaluated factors affecting nest attractiveness to ducks. We assessed the effects of nest box experience (Experiments 1 and 2) and features of nests, including degree of enclosure (Experiments 1 and 2) and the presence of an egg (Experiment 3), on nest site selection by sexually mature Pekin ducks. The hens were tested individually in pens containing different nest box choices. Nest preferences were determined based on the locations of 14 successively laid eggs. Ducks in Experiment 1 were provided with nest box access prior to the onset of lay (20 weeks of age, EXP group, N = 12) or at the time of preference testing (35 weeks of age, DELAYED-EXP group, N = 12). Delaying nest box access by 15 weeks did not significantly affect the proportion of eggs laid in nest boxes rather than on the floor (P = 0.40). Regardless of experience ducks laid more than 66% of their eggs in nest boxes offering a higher degree of enclosure. Ducks in Experiment 2 were reared with either open-top (OP, N = 12) or closed-top (CL, N = 12) boxes. Regardless of rearing condition, ducks preferred boxes with the highest level of enclosure offered. Ducks laid twice the expected proportion (25%) of eggs in CL boxes with curtains (P = 0.0004). CL boxes without curtains were used as predicted by chance, 25% (P = 0.746), while OP boxes with (P = 0.009) and without (P = 0.015) curtains each contained only half the expected number of eggs. Ducks in Experiment 3 were provided with two nest boxes, one of which contained the egg laid the previous day. Each day, the newly laid egg was marked and either placed back in the nest box where it was found (HANDLED, N = 12) or moved into the adjacent nest box (MOVED, N = 12). Ducks in HANDLED and MOVED laid 97.6% and 79.8%, respectively, of their eggs in boxes containing the previous day's egg. While ducks in HANDLED were consistent in their choice throughout the test, those in MOVED developed the preference over time (P = 0.039), suggesting that the preference for laying in a nest containing an egg may be influenced by experience. These results indicate that nest box enclosure and the presence of an egg are important in determining the nesting choices of Pekin ducks. Incorporating these features into nest boxes may be useful for increasing consistency of nest use in breeder duck flocks.     

Metallic copper corrosion rates, moisture content, and growth medium influence survival of copper ion-resistant bacteria

The rapid killing of various bacteria in contact with metallic copper is thought to be influenced by the influx of copper ions into the cells, but the exact mechanism is not fully understood. This study showed that the kinetics of contact killing of copper surfaces depended greatly on the amount of moisture present, copper content of alloys, type of medium used, and type of bacteria. We examined antibiotic- and copper ion-resistant strains of Escherichia coli and Enterococcus faecium isolated from pig farms following the use of copper sulfate as feed supplement. The results showed rapid killing of both copper ion-resistant E. coli and E. faecium strains when samples in rich medium were spread in a thin, moist layer on copper alloys with 85% or greater copper content. E. coli strains were rapidly killed under dry conditions, while E. faecium strains were less affected. Electroplated copper surface corrosion rates were determined from electrochemical polarization tests using the Stern–Geary method and revealed decreased corrosion rates with benzotriazole and thermal oxide coating. Copper ion-resistant E. coli and E. faecium cells suspended in 0.8% NaCl showed prolonged survival rates on electroplated copper surfaces with benzotriazole coating and thermal oxide coating compared to surfaces without anti-corrosion treatment. Control of surface corrosion affected the level of copper ion influx into bacterial cells, which contributed directly to bacterial killing.     

Mathematical and computational modeling in biology at multiple scales

A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms. The use of maximum entropy as an inference tool in the fields of biology and drug discovery is discussed. Mathematical and computational methods and models in the areas of epidemiology, cell physiology and cancer are surveyed. The technique of molecular dynamics is covered, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. The utility of quantum mechanical methods in biophysical and biochemical modeling is explored. The field of computational enzymology is examined.     

Cost-Effective Mapping of Benthic Habitats in Inland Reservoirs through Split-Beam Sonar,Indicator Kriging,and Historical Geologic Data

Because bottom substrate composition is an important control on the temporal and spatial location of the aquatic community, accurate maps of benthic habitats of inland lakes and reservoirs provide valuable information to managers, recreational users, and scientists. Therefore, we collected vertical, split-beam sonar data (roughness [E1], hardness [E2], and bathymetry) and sediment samples to make such maps. Statistical calibration between sonar parameters and sediment classes was problematic because the E1:E2 ratios for soft (muck and clay) sediments overlapped a lower and narrower range for hard (gravel) substrates. Thus, we used indicator kriging (IK) to map the probability that unsampled locations did not contain coarse sediments. To overcome the calibration issue we tested proxies for the natural processes and anthropogenic history of the reservoir as potential predictive variables. Of these, a geologic map proved to be the most useful. The central alluvial valley and mudflats contained mainly muck and organic-rich clays. The surrounding glacial till and shale bedrock uplands contained mainly poorly sorted gravels. Anomalies in the sonar data suggested that the organic-rich sediments also contained trapped gases, presenting additional interpretive issues for the mapping. We extended the capability of inexpensive split-beam sonar units through the incorporation of historic geologic maps and other records as well as validation with dredge samples. Through the integration of information from multiple data sets, were able to objectively identify bottom substrate and provide reservoir users with an accurate map of available benthic habitat.     

Synchronous biological feedbacks in parrotfishes associated with pantropical coral bleaching

Biological feedbacks generated through patterns of disturbance are vital for sustaining ecosystem states. Recent ocean warming and thermal anomalies have caused pantropical episodes of coral bleaching, which has led to widespread coral mortality and a range of subsequent effects on coral reef communities. Although the response of many reef‐associated fishes to major disturbance events on coral reefs is negative (e.g., reduced abundance and condition), parrotfishes show strong feedbacks after disturbance to living reef structure manifesting as increases in abundance. However, the mechanisms underlying this response are poorly understood. Using biochronological reconstructions of annual otolith (ear stone) growth from two ocean basins, we tested whether parrotfish growth was enhanced following bleaching‐related coral mortality, thus providing an organismal mechanism for demographic changes in populations. Both major feeding guilds of parrotfishes (scrapers and excavators) exhibited enhanced growth of individuals after bleaching that was decoupled from expected thermal performance, a pattern that was not evident in other reef fish taxa from the same environment. These results provide evidence for a more nuanced ecological feedback system—one where disturbance plays a key role in mediating parrotfish–benthos interactions. By influencing the biology of assemblages, disturbance can thereby stimulate change in parrotfish grazing intensity and ultimately reef geomorphology over time. This feedback cycle operated historically at within‐reef scales; however, our results demonstrate that the scale, magnitude, and severity of recent thermal events are entraining the biological responses of disparate communities to respond in synchrony. This may fundamentally alter feedbacks in the relationships between parrotfishes and reef systems.     

Carry‐over effects provide linkages across the annual cycle of a Neotropical migratory bird,the Louisiana Waterthrush Parkesia motacilla

Population limitation models of migratory birds have sought to include impacts from events across the full annual cycle. Previous work has shown that events occurring in winter result in some individuals transitioning to the breeding grounds earlier or in better physical condition than others, thereby affecting reproductive success (carry‐over effects). However, evidence for carry‐over effects from breeding to wintering grounds has been shown less often. We used feather corticosterone (CORT_f) levels of the migratory Louisiana Waterthrush Parkesia motacilla as a measure of the physiological state of birds at the time of moult on the breeding territory to investigate whether carry‐over effects provide linkages across the annual cycle of this stream‐obligate bird. We show that birds arriving on wintering grounds with lower CORT_f scores, indicating reduced energetic challenges or stressors at the time of moult, occupied higher quality territories, and that these birds then achieved a better body condition during the overwinter period. Body condition, in turn, was important in determining whether adult birds returned the following winter, with birds in better condition returning at higher rates. Together these data suggest a carry‐over effect from the breeding grounds to the wintering grounds that is further extended with respect to annual return rates. Very few other studies have linked conditions during the previous breeding season with latent effects during the subsequent overwintering period or with annual survival. This study shows that the effects of variation in energetic challenges or stressors can potentially carry over from the natal stream and accumulate over more than one life‐history period before being manifested in reduced survival. This is of particular relevance to models of population limitation in migratory birds.