Comparing survival among species with imperfect detection using multilevel analysis of mark—recapture data: a case study on bats

For comparative demography studies, 2 prerequisites are usually needed: 1) using typical parameter values for species, 2) correctly accounting for the uncertainty in the species specific estimates. However, although within‐species variability may be essential, it is typically not considered in analytical procedures, resulting in parameter estimates that may not be representative of the species. Further, data are analysed in 2 steps, first separately for each species, then estimates are compared among species. Accounting for the uncertainty in the species specific estimates is then difficult. Here we propose the application of multilevel Bayesian models on mark—recapture (MR) data for comparative studies on survival probabilities that solves these problems. Our models account for within‐species variability in space and time in the form of random effects. Models reflecting different biological predictions related to the species’ ecology and life‐history traits may further be contrasted. To illustrate our approach, we used long‐term data from 5 temperate tree‐roosting bat species and compared their survival probabilities. Results suggest that species foraging in open space, high reproductive output and short longevity records have lower survival than species foraging at short distances, with low reproductive output and high longevity records. Multilevel models provided relatively precise estimates, away from the edges of the parameter space, even for species with low encounter rates and short study duration. This is particularly valuable for less studied taxa such as bats for which available data are often more sparse. Our approach can be easily extended to include additional groups or levels of interest and effects at the individual level (e.g. sex or age). Different hypotheses regarding differences or similarities in parameters among species can be tested through the application of different models. Overall, it offers a flexible tool to ecologists, and population and evolutionary biologists for comparative studies, explicitly accounting for multilevel structures often encountered in MR data.     

Purification and properties of phenolic acid decarboxylase from Candida guilliermondii

A heat-labile phenolic acid decarboxylase from Candida guilliermondii (an anamorph of Pichia guilliermondii) was purified to homogeneity by simple successive column chromatography within 3 days. The molecular mass was 20 kDa by sodium dodecyl sulfate–polyacrylamide gel electrophoresis and 36 kDa by gel-filtration chromatography, suggesting that the purified enzyme is a homodimer. The optimal pH and temperature were approximately 6.0 and 25°C. Characteristically, more than 50% of the optimal activity was observed at 0°C, suggesting that this enzyme is cold-adapted. The enzyme converted p-coumaric acid, ferulic acid, and caffeic acid to corresponding products with high specific activities of approximately 600, 530, and 46 U/mg, respectively. The activity was stimulated by Mg²⁺ ions, whereas it was completely inhibited by Fe²⁺, Ni²⁺, Cu²⁺, Hg²⁺, 4-chloromericuribenzoate, N-bromosuccinimide, and diethyl pyrocarbonate. The enzyme was inducible and expressed inside the cells moderately by ferulic acid and p-coumaric acid and significantly by non-metabolizable 6-hydroxy-2-naphthoic acid.     

Brucella Cyclic β-1,2-Glucan Plays a Critical Role in the Induction of Splenomegaly in Mice

Brucella, the etiological agent of animal and human brucellosis, is a bacterium with the capacity to modulate the inflammatory response. Cyclic β-1,2-glucan (CβG) is a virulence factor key for the pathogenesis of Brucella as it is involved in the intracellular life cycle of the bacteria. Using comparative studies with different CβG mutants of Brucella, cgs (CβG synthase), cgt (CβG transporter) and cgm (CβG modifier), we have identified different roles for this polysaccharide in Brucella. While anionic CβG is required for bacterial growth in low osmolarity conditions, the sole requirement for a successful Brucella interaction with mammalian host is its transport to periplasmic space. Our results uncover a new role for CβG in promoting splenomegaly in mice. We showed that CβG-dependent spleen inflammation is the consequence of massive cell recruitment (monocytes, dendritics cells and neutrophils) due to the induction of pro-inflammatory cytokines such as IL-12 and TNF-α and also that the reduced splenomegaly response observed with the cgs mutant is not the consequence of changes in expression levels of the characterized Brucella PAMPs LPS, flagellin or OMP16/19. Complementation of cgs mutant with purified CβG increased significantly spleen inflammation response suggesting a direct role for this polysaccharide.     

Hybridization and polyploidization effects on LTR-retrotransposon activation in potato genome

Hybridization and polyploidization are major forces in plant evolution and potatoes are not an exception. It is proposed that the proliferation of Long Terminal Repeat-retrotransposons (LTR-RT) is related to genome reorganization caused by hybridization and/or polyploidization. The main purpose of the present work was to evaluate the effect of interspecific hybridization and polyploidization on the activation of LTR-RT. We evaluated the proliferation of putative active LTR-RT in a diploid hybrid between the cultivated potato Solanum tuberosum and the wild diploid potato species S. kurtzianum, allotetraploid lines derived from this interspecific hybrid and S. kurtzianum autotetraploid lines (ktz-autotetraploid) using the S-SAP (sequence-specific amplified polymorphism) technique and normalized copy number determination by qPCR. Twenty-nine LTR-RT copies were activated in the hybrid and present in the allotetraploid lines. Major LTR-RT activity was detected in Copia-27, Copia-12, Copia-14 and, Gypsy-22. According to our results, LTR-RT copies were activated principally in the hybrid, there was no activation in allotetraploid lines and only one copy was activated in the autotetraploid.

     

PERMANENT GENETIC RESOURCES: Isolation and characterization of polymorphic trinucleotide and dinucleotide microsatellite loci for the ice goby, Leucopsarison petersii

Eleven microsatellite markers were isolated and characterized for the ice goby, Leucopsarion petersii, from genomic libraries enriched for (ATG)(9) and (CA)(16) . Twenty individuals from a single population were used to screen polymorphism in these loci. The number of alleles per locus and observed heterozygosity ranged from four to 22 and from 0.35 to 1.00, respectively. All loci did not significantly deviated from Hardy-Weinberg equilibrium, and there was no evidence of linkage disequilibrium between all loci-pairs. These loci showed Mendelian inheritance in a full-sib family. The high level of polymorphism of these loci will be useful for studies of population genetics.     

A rational use of glucocorticoids in patients with early arthritis has a minimal impact on bone mass

Introduction  

Glucocorticoid (GC)-induced osteoporosis is a frequent complication in patients with rheumatoid arthritis. However, little information exists about the consequences of GC use in patients with early arthritis. Here we describe the variables underlying the use of GC in early arthritis, as well as its effect on bone-mineral density.     

Associative learning and discrimination of motion cues in the harnessed honeybee Apis mellifera L.

We previously studied a conditioning paradigm to associate the proboscis extension reflex (PER) with monochromatic light (conditioned stimulus; CS) in harnessed honeybees. Here, we established a novel conditioning paradigm to associate the PER with a motion cue generated using graphics interchange format (GIF) animations with a speed of 12 mm/s speed and a frame rate of 25 Hz as the CS, which were projected onto a screen consisting of a translucent circular cone that largely covered the visual field of the harnessed bee using two liquid crystal projectors. The acquisition rate reached a plateau at approximately 40% after seven trials, indicating that the bees were successfully conditioned with the motion cue. We demonstrated four properties of the conditioning paradigm. First, the acquisition rate was enhanced by antennae deprivation, suggesting that sensory input from the antennae interferes with the visual associative learning. Second, bees conditioned with a backward-direction motion cue did not respond to the forward-direction, suggesting that bees can discriminate the two directions in this paradigm. Third, the bees can retain memory for motion cue direction for 48 h. Finally, the acquisition rate did not differ significantly between foragers and nurse bees. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Homeobox B3, FoxA1 and FoxA2 interactions in epithelial lung cell differentiation of the multipotent M3E3/C3 cell line

HOM/C homeobox (Hox) and forkhead box (Fox) factors are reported to be expressed in the foregut endoderm and are subsequently detected in a spatio-temporal pattern during lung development. Some of these factors were reported to influence the expression of lung marker proteins or to modulate lung development. To clarify the molecular mechanisms for generating functional lung cells from progenitor cell populations, we introduced the forkhead box factors, FoxA1 and FoxA2, and the homeobox factor, HoxB3, into the differentiation process in a multipotent hamster lung epithelial M3E3/C3 cell line. Ectopic expression of FoxA2 promoted differentiation to Clara-like cells with up-regulation of the expression of the lung marker proteins, Clara cell-specific 10-kDa protein and surfactant protein-B. In contrast, FoxA1 repressed the differentiation. HoxB3 transfection induced FoxA2 expression transiently at the pre-differentiation stage. The endogenous HoxB3 expression level decreased at later stages of Clara-like cell differentiation, and the attenuation was enhanced by FoxA2 transfection. HoxB3 is a putative upstream regulator that enhances FoxA2 expression at the pre-differentiation stage. In addition, we found that the expression of HoxA4, HoxA5, and HoxC9 increased differentially during Clara-like cell differentiation. These results suggest that HoxB3 may be a putative positive regulator of FoxA2 expression at the pre-differentiation stage, and those interactions of Fox factors and Hox factors could participate in Clara cell differentiation.     

Nodal cilia dynamics and the specification of the left/right axis in early vertebrate embryo development

Nodal cilia dynamics is a key factor for left/right axis determination in mouse embryos through the induction of a leftward fluid flow. So far it has not been clearly established how such dynamics is able to induce the asymmetric leftward flow within the node. Herein we propose that an asymmetric two-phase nonplanar beating cilia dynamics that involves the bending of the ciliar axoneme is responsible for the leftward fluid flow. We support our proposal with a host of hydrodynamic arguments, in silico experiments and in vivo video microscopy data in wild-type embryos and inv mutants. Our phenomenological modeling approach underscores how the asymmetry and speed of the flow depends on different relevant parameters. In addition, we discuss how the combination of internal and external mechanisms might cause the two-phase beating cilia dynamics.