Night-time roosting in laying hens and the effect of thwarting access to perches

Free-living hens roost on branches in trees at night, and laying hens in aviary systems or cages provided with perches also make extensive use of these for night-time roosting. It is therefore suggested that roosting on perches is important to the hens and that domestic hens should be provided with perches in order to promote welfare. However, no study has addressed the question of motivation for roosting. In the present experiment, we studied undisturbed roosting behaviour and the reaction of commercial laying hens when roosting on perches was thwarted. Fifty-two adult hens (Lohmann Selected Leghorn, LSL) were kept in two groups of 26 hens in litter pens with perches at heights of 23, 43 and 63 cm. Behaviour was observed for 60 min starting at lights-off, registering the number of hens on each perch level. The hens started to get onto the perch immediately and within 10 min after lights-off, more than 90% of the hens were on the perch. All hens roosted close together on the top perch. In a second experiment, 24 hens were kept in eight groups of three birds each in experimental pens equipped with perches. Birds were tested in four different situations: (1) the pen unchanged (Base), (2) the perch covered with plexiglass (PCov), (3) the perch removed (PRem) and (4) the unchanged pen (Post). The order of PCov and PRem alternated between groups in a balanced manner and all groups of birds experienced all four treatments. The hens were observed for 60 min from lights-off using focal sampling. For comparisons, the Post treatment served as the control. In the treatments where perching was not possible, the hens spent less time sitting (p=0.042), and also tended to spend more time standing (p=0.06), than in the control. Furthermore, the hens moved more (p=0.042) when the perch was inaccessible, and when the perch was visible but inaccessible they also showed more attempts to take off (p=0.042). These findings can be interpreted as increased frustration and/or exploration, probably to find an alternative roosting site. Together with the high use of perches for night-time roosting under undisturbed conditions, these results indicate that laying hens are motivated to perch and imply that hens kept under conditions where perching is not possible may experience reduced welfare.     

Are snakes right-handed ? Asymmetry in hemipenis size and usage in gartersnakes (Thamnophis sirtalis)

Male snakes possess paired reproductive systems (testes, efferentducts, hemipenes and associated components of the kidneys),with an independent set on either side of the body. Our studieson gartersnakes (Thamnophis sirtalis parietalis) reveal significantmorphological asymmetry in this system : testes, kidneys, andhemipenes on the right-hand-side of the body are larger thanthose on the left. Data from matings in the field, and in outdoor enclosures, suggest that this asymmetry has implications forreproductive behavior and, possibly, reproductive success.Copulations using the right hemipenis produced a larger gelatinous"mating plug," and may thus more effectively delay rematingby the female. Although the overall usage of the two hemipenesin field matings averaged close to 50/50, hemipenis usage wasnot random. Males tended to alternate hemipenis use in successivematings, perhaps because of depletion of plug material. Also,male gartersnakes preferentially used their larger (right)hemipenis when mating at high body temperatures, perhaps becausethey are more able to make subtle postural adjustments (andthus, select the better system) under these conditions.     

A new species of Asparagus (Asparagaceae) from Somalia

Asparagus brachiatus , a new unarmed species from limestone rocks in north-eastern Somalia, is described, illustrated, and compared with A. leptocladodius and A. africanus.     

PieceMaker: selection of DNA fragments for selector-guided multiplex amplification

We describe PieceMaker, a software tool for the design of applications of selector probes–oligonucleotide probes that direct circularization of target nucleic acid molecules. Such probes can be combined in parallel to circularize a selection of fragments from restriction digested total genomic DNA. These fragments can then be amplified in a single PCR using a common primer pair, yielding substrates for subsequent analyses, such as parallel genotyping or sequencing. However, designing multiplex selector assays is a laborious task. The PieceMaker program alleviates this problem by selecting restriction enzymes to generate suitable fragments for selection, and generating the output data required to design the selector probes.     

On the impossibility of coexistence of infinitely many strategies

We investigate the possibility of coexistence of pure, inherited strategies belonging to a large set of potential strategies. We prove that under biologically relevant conditions every model allowing for coexistence of infinitely many strategies is structurally unstable. In particular, this is the case when the "interaction operator" which determines how the growth rate of a strategy depends on the strategy distribution of the population is compact. The interaction operator is not assumed to be linear. We investigate a Lotka-Volterra competition model with a linear interaction operator of convolution type separately because the convolution operator is not compact. For this model, we exclude the possibility of robust coexistence supported on the whole real line, or even on a set containing a limit point. Moreover, we exclude coexistence of an infinite set of equidistant strategies when the total population size is finite. On the other hand, for infinite populations it is possible to have robust coexistence in this case. These results are in line with the ecological concept of "limiting similarity" of coexisting species. We conclude that the mathematical structure of the ecological coexistence problem itself dictates the discreteness of the species.     

Multiple displacement amplification of DNA from human colon and rectum biopsies: bacterial profiling and identification of Helicobacter pylori-DNA by means of 16S rDNA-based TTGE and pyrosequencing analysis

Amplifying bacterial DNA by PCR from human biopsy specimens has sometimes proved to be difficult, mainly due to the low amount of bacterial DNA present. Therefore, nested or semi-nested 16S rDNA PCR amplification has been the method of choice. In this study, we evaluate the potential use of whole genome amplification of total DNA isolated from human colon and rectum biopsy specimens, followed by 16S rDNA PCR amplification of multiple displacement amplified (MDA)-DNA. Subsequently, a H. pylori-specific 16S rDNA variable V3 region PCR assay was applied directly on MDA-DNA and, combined with pyrosequencing analysis; the presence of H. pylori in some biopsies from colon in patients with microscopic colitis was confirmed. Furthermore, temporal temperature gradient gel electrophoresis (TTGE) of 16S rDNA amplicons using primers flanking variable regions V3, V4, and V9, was used to establish bacterial profiles from individual biopsies. A variation of the bacterial profiles in the colonic mucosa in microscopic colitis and in normal rectal mucosa was observed. In conclusion we find the MDA technique to be a useful method to overcome the problem of insufficient bacterial DNA in human biopsy specimens.     

13C incorporation into signature fatty acids as an assay for carbon allocation in arbuscular mycorrhiza

The ubiquitous arbuscular mycorrhizal fungi consume significant amounts of plant assimilated C, but this C flow has been difficult to quantify. The neutral lipid fatty acid 16:1omega5 is a quantitative signature for most arbuscular mycorrhizal fungi in roots and soil. We measured carbon transfer from four plant species to the arbuscular mycorrhizal fungus Glomus intraradices by estimating (13)C enrichment of 16:1omega5 and compared it with (13)C enrichment of total root and mycelial C. Carbon allocation to mycelia was detected within 1 day in monoxenic arbuscular mycorrhizal root cultures labeled with [(13)C]glucose. The (13)C enrichment of neutral lipid fatty acid 16:1omega5 extracted from roots increased from 0.14% 1 day after labeling to 2.2% 7 days after labeling. The colonized roots usually were more enriched for (13)C in the arbuscular mycorrhizal fungal neutral lipid fatty acid 16:1omega5 than for the root specific neutral lipid fatty acid 18:2omega6,9. We labeled plant assimilates by using (13)CO(2) in whole-plant experiments. The extraradical mycelium often was more enriched for (13)C than was the intraradical mycelium, suggesting rapid translocation of carbon to and more active growth by the extraradical mycelium. Since there was a good correlation between (13)C enrichment in neutral lipid fatty acid 16:1omega5 and total (13)C in extraradical mycelia in different systems (r(2) = 0.94), we propose that the total amount of labeled C in intraradical and extraradical mycelium can be calculated from the (13)C enrichment of 16:1omega5. The method described enables evaluation of C flow from plants to arbuscular mycorrhizal fungi to be made without extraction, purification and identification of fungal mycelia.     

Alpha-dioxygenases

Alpha-dioxygenases constitute a family of fatty acid-metabolizing enzymes recently discovered in plants. The present paper gives a brief overview of the literature dealing with these enzymes and additionally reports the new finding of an alpha-dioxygenase in the moss, Physcomitrella patens, and some properties of this enzyme.     

Simulating redox coupled proton transfer in cytochrome c oxidase: looking for the proton bottleneck

Gaining a detailed understanding of the molecular nature of the redox coupled proton transfer in cytochrome c oxidase (COX) is one of the challenges of modern biophysics. The present work addresses this by integrating approaches for simulations of proton transport (PTR) and electron transfer (ET). The resulting method converts the electrostatic energies of different charge configurations and reorganization energies to free-energy profiles for different PTR and ET pathways. This approach provides for the first time a tool to study the actual activation barriers and kinetics of different feasible PTR processes in the cycle of COX. Using this tool, we explore the PTR through the bottleneck water molecules. It is found that a stepwise PTR along this commonly assumed path leads to far too high barriers and is, thus, inconsistent with the observed kinetics. Furthermore, the simulated free-energy profile does not provide a simple gating mechanism. Fortunately, we obtain reasonable kinetics when we consider a PTR that involves a concerted transfer of protons to and from E286. Finally, semi-qualitative considerations of the forward and backward barriers point toward open questions about the actual gating process and offer a feasible pumping mechanism. Although further studies are clearly needed, we believe that our approach offers a general and effective tool for correlating the structure of COX with its function.     

Role of the conserved threonine 309 in mechanism of oxidation by cytochrome P450 2D6

Based on sequence alignments and homology modeling, threonine 309 in cytochrome P450 2D6 (CYP2D6) is proposed to be the conserved I-helix threonine, which is supposed to be involved in dioxygen activation by CYPs. The T309V mutant of CYP2D6 displayed a strong shift from O-dealkylation to N-dealkylation reactions in oxidation of dextromethorphan and 3,4-methylenedioxymethylamphetamine. This may be explained by an elevated ratio of hydroperoxo-iron to oxenoid-iron of the oxygenating species. In consistence, using cumene hydroperoxide, which directly forms the oxenoid-iron, the T309V mutant again selectively catalyzed the O-dealkylation reactions. The changed ratio of oxygenating species can also explain the decreased activity and changed regioselectivity that were observed in 7-methoxy-4-(aminomethyl)-coumarin and bufuralol oxidation, respectively, by the T309V mutant. Interestingly, the T309V mutant always showed a significantly increased, up to 75-fold, higher activity compared to that of the wild-type when using cumene hydroperoxide. These results indicate that T309 in CYP2D6 is involved in maintaining the balance of multiple oxygenating species and thus influences substrate and regioselectivity.