Making water flow: a comparison of the hydrodynamic characteristics of 12 different benthic biological flumes

Flume tanks are becoming increasingly important research tools in aquatic ecology, to link biological to hydrodynamical processes. There is no such thing as a “standard flume tank”, and no flume tank is suitable for every type of research question. A series of experiments has been carried out to characterise and compare the hydrodynamic characteristics of 12 different flume tanks that are designed specifically for biological research. These facilities are part of the EU network BioFlow. The flumes could be divided into four basic design types: straight, racetrack, annular and field flumes. In each facility, two vertical velocity profiles were measured: one at 0.05 m s⁻¹ and one at 0.25 m s⁻¹. In those flumes equipped with Acoustic Doppler Velocimeters (ADV), time series were also recorded for each velocity at two heights above the bottom: 0.05 m and 20% of the water depth. From these measurements turbulence characteristics, such as TKE and Reynolds stress, were derived, and autocorrelation spectra of the horizontal along-stream velocity component were plotted. The flume measurements were compared to two sets of velocity profiles measured in the field.Despite the fact that some flumes were relatively small, turbulence was fully developed in all channels. Straight and racetrack flumes generally produced boundary layers with a clearly definable logarithmic layer, similar to measurements in the field taken under steady flow conditions. The two annular flumes produced relatively thin boundary layers, presumably due to secondary flows developing in the curved channels. The profiles in the field flumes also differed considerably from the expected log profile. This may either have been due the construction of the flume, or due to unsteady conditions during measurement. Constraints imposed by the different flume designs on the suitability for different types of boundary layer research, as well as scaling issues are discussed.     

A homologue of the breast cancer-associated gene BARD1 is involved in DNA repair in plants

hBRCA1 and hBARD1 are tumor suppressor proteins that are involved as heterodimer via ubiquitinylation in many cellular processes, such as DNA repair. Loss of BRCA1 or BARD1 results in early embryonic lethality and chromosomal instability. The Arabidopsis genome carries a BRCA1 homologue, and we were able to identify a BARD1 homologue. AtBRCA1 and the putative AtBARD1 protein are able to interact with each other as indicated by in vitro and in planta experiments. We have identified T-DNA insertion mutants for both genes, which show no visible phenotype under standard growth conditions and are fully fertile. Thus, in contrast to animals, both genes have no indispensable role during development and meiosis in plants. The two single as well as the double mutant are to a similar extent sensitive to mitomycin C, indicating an epistatic interaction in DNA crosslink repair. We could further demonstrate that in Arabidopsis BARD1 plays a prominent role in the regulation of homologous DNA repair in somatic cells.     

Prostate-specific membrane antigen regulates angiogenesis by modulating integrin signal transduction

The transmembrane peptidase prostate-specific membrane antigen (PSMA) is universally upregulated in the vasculature of solid tumors, but its functional role in tumor angiogenesis has not been investigated. Here we show that angiogenesis is severely impaired in PSMA-null animals and that this angiogenic defect occurs at the level of endothelial cell invasion through the extracellular matrix barrier. Because proteolytic degradation of the extracellular matrix is a critical component of endothelial invasion in angiogenesis, it is logical to assume that PSMA participates in matrix degradation. However, we demonstrate a novel and more complex role for PSMA in angiogenesis, where it is a principal component of a regulatory loop that is tightly modulating laminin-specific integrin signaling and GTPase-dependent, p21-activated kinase 1 (PAK-1) activity. We show that PSMA inhibition, knockdown, or deficiency decreases endothelial cell invasion in vitro via integrin and PAK, thus abrogating angiogenesis. Interestingly, the neutralization of beta(1) or the inactivation of PAK increases PSMA activity, suggesting that they negatively regulate PSMA. This negative regulation is mediated by the cytoskeleton as the disruption of interactions between the PSMA cytoplasmic tail and the anchor protein filamin A decreases PSMA activity, integrin function, and PAK activation. Finally, the inhibition of PAK activation enhances the PSMA/filamin A interaction and, thus, boosts PSMA activity. These data imply that PSMA participates in an autoregulatory loop, wherein active PSMA facilitates integrin signaling and PAK activation, leading to both productive invasion and downregulation of integrin beta(1) signaling via reduced PSMA activity. Therefore, we have identified a novel role for PSMA as a true molecular interface, integrating both extracellular and intracellular signals during angiogenesis.     

Modelling multivariate outcomes in hierarchical data, with application to cluster randomised trials

In the cluster randomised study design, the data collected have a hierarchical structure and often include multivariate outcomes. We present a flexible modelling strategy that permits several normally distributed outcomes to be analysed simultaneously, in which intervention effects as well as individual-level and cluster-level between-outcome correlations are estimated. This is implemented in a Bayesian framework which has several advantages over a classical approach, for example in providing credible intervals for functions of model parameters and in allowing informative priors for the intracluster correlation coefficients. In order to declare such informative prior distributions, and fit models in which the between-outcome covariance matrices are constrained, priors on parameters within the covariance matrices are required. Careful specification is necessary however, in order to maintain non-negative definiteness and symmetry between the different outcomes. We propose a novel solution in the case of three multivariate outcomes, and present a modified existing approach and novel alternative for four or more outcomes. The methods are applied to an example of a cluster randomised trial in the prevention of coronary heart disease. The modelling strategy presented would also be useful in other situations involving hierarchical multivariate outcomes.     

Relative efficiency of fecal versus regurgitated samples for assessing diet and the deleterious effects of a tartar emetic on migratory birds

ABSTRACT We describe the deleterious effects of using an antimony potassium tartrate emetic to obtain diet samples from birds, and compare information obtained from regurgitated samples versus fecal samples in describing diets of autumn migrants. We also examined dose effectiveness in captive Dark‐eyed Juncos (Junco hyemalis) subjected to the same emetic technique used in the field. Over 70% of migrants given an emetic at a study site in Idaho regurgitated useful samples. For 5 of 7 species analyzed, regurgitated samples produced significantly more arthropods per sample than fecal samples, and one species, Warbling Vireo, showed higher numbers of distinct arthropod taxa per sample. In most species, regurgitated samples accumulated arthropod taxa more quickly than fecal samples. However, increasing the number of fecal samples by 5–17 produced a similar number of taxa. Diet composition based on fecal versus regurgitated samples was generally similar, but there were significant differences. Two of 130 treated migrants died soon after treatment. Recapture frequency for treated birds was less than half that for untreated birds, but it is not clear whether this difference was due to treatment‐related mortality or emigration. Each treated bird that we recaptured had lost mass and this suggests a deleterious effect because untreated migrants tended to gain mass. In captivity, 18 Dark‐eyed Juncos were treated with emetic: 6 with the full mass‐specific recommended dose, 6 with half the recommended dose, and the final 6 with one quarter the recommended dose. All were alive 15–20 min posttreatment (recommended release time), but 17 of 18 died within 30 min after receiving the emetic. Together, our data suggest that although the emetic technique may be slightly more information‐rich in assessing diet, it is more harmful than previously reported especially in certain species and should be used only after adequate consideration of the immediate mortality and short‐term physiological effects on birds to be studied.     

Scent marking in sifaka: no one function explains it all

Various hypotheses to explain possible functions of scent-marking have been put forth and basically fall into five categories: territorial demarcation, ownership of resources, mate attraction, noncombative fighting, and self-advertisement. Verreaux's sifaka (Propithecus verreauxi verreauxi), like many prosimians, use scent-marking as one form of communication. The goal of this study was to determine the function of scent-marking in sifaka. All-occurrence of scent-marks, scent-mark context, and scent-mark style were collected on 23 sifaka in the Kirindy Forest of western Madagascar for 7 months (September 2001-March 2002). Scent-mark rates were collected using continuous focal animal sampling from November 2000-March 2002. Home range data were collected using monthly censuses and instantaneous focal sampling throughout the 17 months. Scent-marking behavior was exhibited almost exclusively by adults. Scent-mark rates were not related to the number of resident adult males, number of resident adult females, rank, or group size. The majority of scent-marks occurred in the perimeter of the home range; however, less than a quarter of the home range was used by only a single group. Sifaka did not preferentially mark food trees, mark during the mating season, or mark during intergroup encounters. The results from this study indicate that none of the five hypothesized functions best explains all scent-marking in Verreaux's sifaka. Rather, scent-marking may serve different functions for different individuals.     

Characterization of the γδ T cell response to acute leukemia

Background: Previous work from our center has suggested a correlation between increased donor-derived Vδ1+ γδ T cells and long-term relapse-free survival following bone marrow transplantation for leukemia. Questions remain, however, as to whether this observation can be explained by a γδ T cell-based immune response against primary leukemia. Methods: We examined γδ T cell receptor (TCR) phenotype, cell proliferation, and cytolytic activity following culture with irradiated primary leukemia blasts from a haploidentical first-degree relative. Subsequently, we also studied the γδ TCR phenotype and complimentarity determining region 3 (CDR3) cDNA sequences from 17 newly diagnosed leukemia patients. Results: In 17/28 (61%) of in vitro cultures, γδ T cells proliferated in culture with primary blasts. Vδ1+ T cells were proportionally increased in all cultures and were the predominant cell population in 6/17. In the 7 cultures where cytotoxicity could be assessed, 6 (86%) showed some degree of cytotoxicity to the primary leukemia. Vδ1+ T cells were also the predominant γδ T cell subtype in pre-treatment leukemia patients principally due to loss of Vδ2+ T cells rather than expansion of Vδ1+ cells. The Vδ1 CDR3-region cDNA sequence from these patients revealed exclusive use of the Jδ1 constant region and sequence conservation in 4/11 patients. Conclusions: γδ T cells exhibit an in vitro response to primary leukemia blasts that is manifested by proliferation, an increased proportion of Vδ1+ T cells, and cytotoxicity to the primary leukemia blasts. The Vδ1+ T cell population is also predominant in newly diagnosed leukemia patients likely due to a loss of circulating Vδ2+ T cells. A small proportion of newly diagnosed patients showed Vδ1 CDR3 region similarity. These findings suggest a role for γδ T cells in the immune response to leukemia.Paul F. Meeh and Michelle King are contributed equally to this work.     

Use of isotope ratio mass spectrometry to detect doping with oral testosterone undecanoate: inter-individual variability of 13C/12C ratio

The metabolic effect of multiple oral testosterone undecanoate (TU) doses over 4 weeks was assessed in seven voluntary men. The protocol was designed to detect accumulation of the substance by choosing the appropriate spot urines collections time and to study the urinary clearance of the substance after weeks of treatment. Urines were analysed by a new GC/C/isotope ratio mass spectrometry (IRMS) method to establish the delta(13)C-values of testosterone metabolites (androsterone and etiocholanolone) together with an endogenous reference compound (16(5alpha)-androsten-3alpha-ol). The significant differences in inter-individual metabolism following TU intake was illustrated by large variations in delta(13)C-values of both T metabolites (maximum Deltadelta(13)C-values = 5.5 per thousand), as well as by very stable longitudinal T/E profiles and carbon isotopic ratios in the first hours following administration. According to T/E ratios and delta(13)C-values, the washout period after 80 mg TU intake was less than 48 h for all subjects and no accumulation phenomenon was observed upon chronic oral administration.