The influence of American mink odour on the spatial distribution and behaviour of water voles

The perception and assessment of predation risk often cause changes in the activities of animals and induce behavioural responses that may in turn affect their movements and distribution. To simulate high predation risk in a midfield pond riparian habitat, we used fresh faeces from ranch American mink Neovison vison and recorded behavioural responses of water voles Arvicola amphibius. In areas where mink odour was deployed, the numbers of captured vole individuals and their trappability were significantly lower than in control areas. Several voles migrated from the zones with deployed mink faeces to the areas without faeces, thus proving that increased predation risk affects the distribution of individuals in a population. The response to mink odour was much more pronounced in females than in males; in areas with deployed mink faeces, not a single female was trapped. We conclude that although American mink is a non‐native, invasive predator, water voles respond to mink odour by reducing their activity and/or by avoiding places with higher predation risk.     

Laboratory study of the susceptibility of hatchery reared Atlantic sturgeon (Acipenser oxyrinchus Mitchill, 1815) larvae to predation

The aim of the study was to determine the susceptibility to predation of Atlantic sturgeon larvae (Acipenser oxyrinchus) reared under traditional hatchery conditions. Experiments were conducted to determine whether predators would prey on Atlantic sturgeon if alternative prey was available and if the presence of substrate on the tank bottom impacted the number of Atlantic sturgeon consumed. European perch (Perca fluviatilis) was used as the predator, and the alternative prey were three‐spined stickleback (Gasterosteus aculeatus) or gudgeon (Gobio gobio). The predators and alternative prey were obtained from the wild. The mortality of sturgeon (n = 10) and alternative prey (n = 10) caused by four predators was recorded during 15 min trials. Trials with three‐spined stickleback and gudgeon as alternative prey were performed separately. Each experimental trial was repeated five times. The predators consumed significantly more Atlantic sturgeon than alternative prey in both the experimental setups when the bottom of the tank was covered with gravel and stone substrate and when there was no substrate. In trials with three‐spined stickleback the mortality of Atlantic sturgeon in both experimental setups was 94 ± 8.94%, while that of three‐spined stickleback in the setup with substrate was 20 ± 19.23%, and without substrate it was 22 ± 10.00%. European perch also consumed more Atlantic sturgeon than they did gudgeon, and the mean Atlantic sturgeon mortality in the experimental setup with substrate was 94 ± 5.48%, while for gudgeon it was 48 ± 8.37%. In the experimental setup without substrate the predators also consumed substantially more Atlantic sturgeon than gudgeon, with a mean Atlantic sturgeon mortality of 94 ± 8.94%, while for gudgeon it was 76 ± 5.48%. The study indicated that hatchery reared Atlantic sturgeon larvae are susceptible to predation by European perch. Predation could impact the survival of juvenile Atlantic sturgeon in the natural environment, and it could be one of the factors that is impeding the restoration of this species in the Baltic Sea basin.     

Long-term Changes in Macrozoobenthos of the Gdańsk Deep

The paper presents an analysis of the bottom fauna occurrence in the central part of the Gdańsk Deep in the past four decades. In 53% of the samples there were not any bottom invertebrates at all and they periodically disappeared in every decade. At the beginning of the study period, Priapuloidea, Bivalvia, Crustacea and Polychaeta were present in the bottom fauna communities, while only the two latter groups occurred towards the end of the period and the hemipelagic polychaete Harmothoe sarsi was often noted as the only species of the macrozoobenthos.     

Low sequence similarity and gene content of symbiotic clusters of Bradyrhizobium sp. WM9 (Lupinus) indicate early divergence of “lupin” lineage in the genus Bradyrhizobium

Two sequenced nodulation regions of lupin Bradyrhizobium sp. WM9 carried the majority of genes involved in the Nod factor production. The nod region I harbored: nolA, nodD, nodA, nodB, nodC, nodS, nodI, nodJ, nolO, nodZ, fixR, nifA, fixA, nodM, nolK and noeL. This gene arrangement resembled that found in the nodulation region of Bradyrhizobium japonicum USDA110, however strain WM9 harbored only one nodD gene copy, while the nodM, nolK and noeL genes had no counterparts in the 410 kb symbiotic region of strain USDA110. Region II harbored nolL and nodW, but lacked an nodV gene. Both regions carried ORFs that lacked similarity to the published USDA110 sequences, though they had homologues in symbiotic regions of Rhizobium etli, Sinorhizobium sp. NGR234 and Mesorhizobium loti. These differences in gene content, as well as a low average sequence identity (70%) of symbiotic genes with respect to B. japonicum USDA110 were in contrast with the phylogenetic relationship of USDA110 and WM9 revealed by the analysis of 16S rDNA and dnaK sequences. This most likely reflected an early divergence of symbiotic loci, and possible co-speciation with distinct legumes. During this process the loss of a noeI gene and the acquisition of a nolL gene could be regarded as an adaptation towards these legumes that responded to Nod factors carrying 4-O-acetylfucose rather than 2-O-methylfucose. This explained various responses of lupins and serradella plants to infection by mutants in nodZ and nolL genes, knowing that serradella is a stringent legume while lupins are more promiscuous legumes. This revised version was published online in August 2006 with corrections to the Cover Date.     

A cross-platform public domain PC image-analysis program for the comet assay

The single-cell gel electrophoresis, also known as the comet assay, has gained wide-spread popularity as a simple and reliable method to measure genotoxic and cytotoxic effects of physical and chemical agents as well as kinetics of DNA repair. Cells are generally stained with fluorescent dyes. The analysis of comets--damaged cells which form a typical comet-shaped pattern--is greatly facilitated by the use of a computer image-analysis program. Although several image-analysis programs are available commercially, they are expensive and their source codes are not provided. For Macintosh computers a cost-free public domain macro is available on the Internet. No ready for use, cost-free program exists for the PC platform. We have, therefore, developed such a public domain program under the GNU license for PC computers. The program is called CASP and can be run on a variety of hardware and software platforms. Its practical merit was tested on human lymphocytes exposed to gamma-rays and found to yield reproducible results. The binaries for Windows 95 and Linux, together with the source code can be obtained from: http://www.casp.of.pl.     

Structures of the alpha L I domain and its complex with ICAM-1 reveal a shape-shifting pathway for integrin regulation

The structure of the I domain of integrin alpha L beta 2 bound to the Ig superfamily ligand ICAM-1 reveals the open ligand binding conformation and the first example of an integrin-IgSF interface. The I domain Mg2+ directly coordinates Glu-34 of ICAM-1, and a dramatic swing of I domain residue Glu-241 enables a critical salt bridge. Liganded and unliganded structures for both high- and intermediate-affinity mutant I domains reveal that ligand binding can induce conformational change in the alpha L I domain and that allosteric signals can convert the closed conformation to intermediate or open conformations without ligand binding. Pulling down on the C-terminal alpha 7 helix with introduced disulfide bonds ratchets the beta 6-alpha 7 loop into three different positions in the closed, intermediate, and open conformations, with a progressive increase in affinity.     

Accounting for nonignorable verification bias in assessment of diagnostic tests

A "gold" standard test, providing definitive verification of disease status, may be quite invasive or expensive. Current technological advances provide less invasive, or less expensive, diagnostic tests. Ideally, a diagnostic test is evaluated by comparing it with a definitive gold standard test. However, the decision to perform the gold standard test to establish the presence or absence of disease is often influenced by the results of the diagnostic test, along with other measured, or not measured, risk factors. If only data from patients who received the gold standard test were used to assess the test performance, the commonly used measures of diagnostic test performance--sensitivity and specificity--are likely to be biased. Sensitivity would often be higher, and specificity would be lower, than the true values. This bias is called verification bias. Without adjustment for verification bias, one may possibly introduce into the medical practice a diagnostic test with apparent, but not truly, high sensitivity. In this article, verification bias is treated as a missing covariate problem. We propose a flexible modeling and computational framework for evaluating the performance of a diagnostic test, with adjustment for nonignorable verification bias. The presented computational method can be utilized with any software that can repetitively use a logistic regression module. The approach is likelihood-based, and allows use of categorical or continuous covariates. An explicit formula for the observed information matrix is presented, so that one can easily compute standard errors of estimated parameters. The methodology is illustrated with a cardiology data example. We perform a sensitivity analysis of the dependency of verification selection process on disease.     

Short and Long Term Investor Synchronization Caused by Decoupling

The dynamics of collective decision making is not yet well understood. Its practical relevance however can be of utmost importance, as experienced by people who lost their fortunes in turbulent moments of financial markets. In this paper we show how spontaneous collective “moods” or “biases” emerge dynamically among human participants playing a trading game in a simple model of the stock market. Applying theory and computer simulations to the experimental data generated by humans, we are able to predict the onset of such moments before they actually happen.