Hydrodynamic entrapment of bacteria swimming near a solid surface.

The near-surface motility of bacteria is important in the initial formation of biofilms and in many biomedical applications. The swimming motion of Escherichia coli near a solid surface is investigated both numerically and experimentally. A boundary element method is used to predict the hydrodynamic entrapment of E. coli bacteria, their trajectories, and the minimum separation of the cell from the surface. The numerical results show the existence of a stable swimming distance from the boundary that depends only on the shape of the cell body and the flagellum. The experimental validation of the numerical approach allows one to use the numerical method as a predictive tool to estimate with reasonable accuracy the near-wall motility of swimming bacteria of known geometry. The analysis of the numerical database demonstrated the existence of a correlation between the radius of curvature of the near-wall circular trajectory and the separation gap. Such correlation allows an indirect estimation of either of the two quantities by a direct measure of the other without prior knowledge of the cell geometry. This result may prove extremely important in those biomedical and technical applications in which the near-wall behavior of bacteria is of fundamental importance.

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.

Swimming crab Callinectes amnicola (Decapoda-Portunidae) capture analysis of a lagoon with high continental influence (Aby Lagoon, Cote d'Ivoire, West Africa)

The study describes the main causes of captures and productions decreasing of swimming crab Callinectes amnicola (Decapoda Portunidae) in Aby lagoon complex. For that, docks of two Sub Prefectures of Adiaké and Assini-Mafia respectively including the villages of Adiaké, Anga, Assomlan, Epleman, Aby and Man-Man, M'Bratty, Assini-Ngouankro and Assini-Mafia were studied from 2006 to 2009 and completed with previous results obtained from 1988 to 2005. Field investigators were identified by site/village and they recorded daily activities of fishermen (number of effective fishermen, number of gears and area of fishing, duration of fishing, types and quantity of bait) and landing of swimming crabs. During recent period of the study, total production decreased from 3742 tons in 2006 to 1500 tons in 2009. Matrix correlations and correlation analysis indicated that this downward trend was due to the increase of the number of fishermen, number of fishing gear, the decrease in female crabs capture and degradation of the environment related to gradual closure of the Assini-Mafia channel. Despite this decline, total production in Aby lagoon remained high compared to the productions of some lagoons of the country and the region. Given the importance of fishing swimming crabs in Aby lagoon, since it concerns many young people and it is a source of income, stringent measures for sustainable and responsible management must be taken and implemented as part of a co-management plan involving all stakeholders to sustainably manage the resource

Swimming depth, ambient water temperature preference, and feeding frequency of young Pacific bluefin tuna (Thunnus orientalis) determined with archival tags

We investigated the migration and behavior of young Pacific Bluefin tuna (Thunnus orientalis) using archival tags. The archival tag measures environmental variables, records them in its memory, and estimates daily geographical locations based on measured light levels. Of 166 archival tags implanted in Pacific bluefin tuna that were released at the northeastern end of the East China Sea from 1995 to 1997, 30 tags were recovered, including one from a fish that migrated across the Pacific. This article describes swimming depth, ambient water temperature, and feeding frequency of young Pacific bluefin tuna based on retrieved data. Tag performance, effect of the tag on the fish, and horizontal movements of the species are described in another paper. Young Pacific bluefin tuna swim mainly in the mixed layer, usually near the sea surface, and swim in deeper water in daytime than at nighttime. They also exhibit a pattern of depth changes, corresponding to sunrise and sunset, apparently to avoid a specific low light level. The archival tags recorded temperature changes in viscera that appear to be caused by feeding, and those changes indicate that young Pacific bluefin tuna commonly feed at dawn and in the daytime, but rarely at dusk or at night. Water temperature restricts their distribution, as indicated by changes in their vertical distribution with the seasonal change in depth of the thermocline and by the fact that their horizontal distribution is in most cases confined to water in the temperature range of 14−20°C.

The physiological effects of multiple forced submergences in loggerhead sea turtles (Caretta caretta)

Sea turtles are subjected to involuntary submergence and potential mortality due to incidental capture by the commercial shrimp fishing industry. Despite implementation of turtle excluder devices (TEDs) to reduce at-sea mortality, dead stranded turtles continue to be found in near-record numbers along the coasts of the western Atlantic Ocean and northern Gulf of Mexico. Although this mortality may be due to an increase in the number of turtles available to strand, one alternative explanation is that sea turtles are repetitively submerged (as one fishing vessel follows the path of another) in legal TEDs. In the present study, laboratory and field investigations were undertaken to examine the physiological effects of multiple submergence of loggerhead sea turtles (Caretta caretta). Turtles in the laboratory study were confined during the submersion episodes, whereas under field conditions, turtles were released directly into TED-equipped commercial fishing nets. Under laboratory and field conditions, pre- and postsubmergence blood samples were collected from turtles submerged three times at 7.5 min per episode with an in-water rest interval of 10, 42, or 180 min between submergences. Analyses of pre- and postsubmergence blood samples revealed that the initial submergence produced a severe and pronounced metabolic and respiratory acidosis in all turtles. Successive submergences produced significant changes in blood pH, Pco2, and lactate, although the magnitude of the acid-base imbalance was substantially reduced as the number of submergences increased. In addition, increasing the interval between successive submergences permitted greater recovery of blood homeostasis. No turtles died during these studies. Taken together, these data suggest that repetitive sub-mergence of sea turtles in TEDs would not significantly affect their survival potential provided that the animal has an adequate rest interval at the surface between successive submergences.

Local distribution and abundance of swimming crabs (Callinectes spp. and Arenaeus cribrarius) on a tropical arid beach

Distribution, abundance, and several population features were studied in Ensenada de La Vela (Venezuela) between 1993 and 1998 as a first step in the assessment of local fisheries of swimming crabs. Arenaeus cribrarius was the most abundant species at the marine foreshore. Callinectes danae prevailed at the estuarine location. Callinectes bocourti was the most abundant species at the offshore. Abundances of A. cribrarius and C. danae fluctuated widely and randomly. Ovigerous females were almost absent. Adults of several species were smaller than previously reported. This study suggests that fisheries based on these swimming crabs probably will be restricted to an artisanal level because abundances appear too low to support industrial exploitation.