A web server to locate periodicities in a sequence

Summary : FT is a tool written in C++, which implements the Fourier analysis method to locate periodicities in aminoacid or DNA sequences. It is provided for free public use on a WWW server with a Java interface. Availability : The server address is http://o2.db. uoa.gr/FT Contact : shamodr@atlas.uoa.gr      

Revisiting the use of Iprodione and Trichoderma in the integrated management of onion white rot

The biocontrol properties of Trichoderma species are well documented, but their effectiveness in antagonism of the problematic Sclerotium cepivorum, the causal agent of white rot in Allium species, appears limited with reports of significant control only relating to deliberately-mutated strains of Trichoderma. Our previous studies have indicated the possibility of using selected naturally-occurring strains of the antagonist in the suppression of other diseases; now in vitro and controlled environment in vivo studies have indicated that a degree of control of Onion White Rot is possible, and that the selected antagonist strains can be used in integrated treatments with Iprodione to good effect. The possible value of such treatments is considered in light of other approaches to the suppression of this continuing problem.     

Reconstructing the reproductive history of female polar bears using cementum patterns of premolar teeth

Premolar teeth collected from 220 adult female polar bears (Ursus maritimus) from western Hudson Bay, Canada, were examined to determine whether past reproductive events are recorded in cementum. The widths of annular cementum growth layer groups (GLGs) were measured and compared as proportional width index (PWI) values to correct for age and body size bias. Known reproductive states (pregnant, with cubs, or with yearlings) were used to confirm and calibrate cementum annuli. Significant differences in PWI were observed between GLGs formed the year females were pregnant versus when accompanied by cubs or yearlings. The probability of a female having produced a cub in adulthood was determined by fitting a logistic regression model between the ΔPWI of females when pregnant and with their cubs. Logistic regression of ΔPWI (β₀ = −0.229, β₁ = −13.465, G ² = 46.55, df = 1, P < 0.001) correctly classified the presence or absence of cubs in 72% of GLGs. Cementum width did not vary between different litter sizes. Observations of females with early litter loss suggests that longer periods of lactation contributes to decreased cementum width and therefore cementum may record a minimum age of litter survival. Predictions of litter production rate (0.43 litters/female/year) derived from cementum were similar to field observations; however, age at first parturition was underestimated by 1 year. We conclude that patterns of cementum deposition may be useful to determine individual reproductive histories and establish course estimates of reproductive parameters when regular field observations are not feasible. We also conclude that reproductive parameters derived from cementum are not adequate on their own for monitoring populations which are in decline or under stress and field observation should not be replaced under these conditions.     

Ontogeny and sexual dimorphism in a captive population of juvenile striped skunks <Emphasis Type="Italic">Mephitis mephitis</Emphasis>

Three main hypotheses can explain the origin of the sexual size dimorphism: (1) the birth-size hypothesis, which states that birth size of males is larger than that of females; (2) the growth-rate hypothesis, which states that males grow faster than females; (3) the growth-length hypothesis, which states that males grow for a longer period of time than females. We examined the factors that may contribute to sexual size dimorphism with growth data of striped skunks Mephitis mephitis Schreber, 1776 held in captivity in Manitoba (Canada), from 7 to 72 days of age. At seven days of age, the mass of male skunks (mean = 79.7 g ± 13.9 SE, n = 37) was significantly larger than that of females (mean = 71.2 g ± 15.0 SE, n = 35) but the head and body length was not statistically different between males (mean = 110.3 mm ± 8.0 SE, n = 37) and females (mean = 95.3 mm ± 7.4 SE, n = 35). There was no difference in growth rate for mass or for length between sexes. We were not able to test for a difference in growth length between sexes. Our results suggest that mass dimorphism occurs early in life.     

Interacting effects of age,density, and weather on survival and current reproduction for a large mammal

Individual‐based study of natural populations allows for accurate and precise estimation of fitness components and the extent to which they might vary with ecological conditions. By tracking the fates of all 701 horses known to have lived on Sable Island, Canada, from 2009 to 2013 (where there is no predation, human interference, or interspecific competition for food), we present a detailed analysis of structured population dynamics with focus on interacting effects of intraspecific competition and weather on reproduction and survival. Annual survival of adult females (0.866 ± 0.107 [ ± SE]) was lower than that of 3‐year‐olds (0.955 ± 0.051), although annual fecundity (producing a foal in a year that was observed during our census) was higher in adults (0.616 ± 0.023) compared to 3‐year‐olds (0.402 ± 0.054). Milder winters and lower densities during gestation increased fecundity. Density negatively impacted survival for all age and sex categories; however, highest adult female survival was observed during high‐density years coupled with a harsh winter, the result expected if pregnancy loss during winter or loss of foals in spring improved survival. Three‐year‐old females, which reproduced at lower rates, experienced higher survival than adults. Our results contrast with a previous study of feral horses that suggested recently feral ungulates might be artificially selected to reproduce even when costs to survival are high. In part, this may be because of the comparably long history of feralization (250 years; at least 25 generations) for Sable Island horses.     

Utility of the white gene in estimating phylogenetic relationships among mosquitoes (Diptera: Culicidae)

The utility of a nuclear protein-coding gene for reconstructing phylogenetic relationships within the family Culicidae was explored. Relationships among 13 species representing three subfamilies and nine genera of Culicidae were analyzed using a 762-bp fragment of coding sequence from the eye color gene, white. Outgroups for the study were two species from the sister group Chaoboridae. Sequences were determined from clone PCR products amplified from genomic DNA, and aligned following conceptual intron splicing and amino acid translation. Third codon positions were characterized by high levels of divergence and biased nucleotide composition, the intensity and direction of which varied among taxa. Equal weighting of all characters resulted in parsimony and neighboring-joining trees at odds with the generally accepted phylogenetic hypothesis based on morphology and rDNA sequences. The application of differential weighting schemes recovered the traditional hypothesis, in which the subfamily Anophelinae formed the basal clade. The subfamily Toxorhynchitinae occupied an intermediate position, and was a sister group to the subfamily Culicinae. Within Culicinae, the genera Sabethes and Tripteroides formed an ancestral clade, while the Culex-Deinocerites and Aedes- Haemagogus clades occupied increasingly derived positions in the molecular phylogeny. An intron present in the Culicinae- Toxorhynchitinae lineage and one outgroup taxon was absent in the basal Anophelinae lineage and the second outgroup taxon, suggesting that intron insertions or deletions may not always be reliable systematic characters.      

Mannose-binding lectin deficiency is associated with early onset of polyarticular juvenile rheumatoid arthritis: a cohort study

Background  

Mannose-binding lectin (MBL) is an innate immune protein. The aim of our study was to determine whether genetically determined MBL deficiency is associated with susceptibility to juvenile rheumatoid arthritis (JRA) and whether MBL2 genotypes are associated with JRA severity.     

Facultative response to a kleptoparasite by the cooperatively breeding pied babbler

In many cases of interspecific kleptoparasitism, hosts developdefensive behaviors to minimize the impact of kleptoparasites.Because vigilance and defensive behaviors are often costly,selection should favor hosts that adjust the amount of investmentneeded to minimize losses to kleptoparasitism. However, examplesof such facultative responses are rare. Here, we investigatethe response of cooperatively breeding pied babblers (Turdoidesbicolor) to the drongo (Dicrurus adsimilis), an avian kleptoparasitethat regularly follows pied babbler groups, often giving alarmcalls to alert the group to predators but also occasionallygiving false alarm calls in order to steal food items. We showthat pied babbler response to drongos varies markedly accordingto babbler group size. In small groups, where there are fewindividuals available to act as sentinels, babblers sentinelless when a drongo is present and respond strongly to drongoalarm calls. However, in large groups, where there are manyindividuals available to participate in predator vigilance,babblers sentinel more often when a drongo is present, rarelyrespond to drongo alarm calls, and aggressively displace drongos,with a consequent decline in the number of successful kleptoparasitismevents. This behavior represent a facultative response to akleptoparasite according to the costs versus benefits of toleratingtheir presence.     

In situ hybridization at the electron microscope level: hybrid detection by autoradiography and colloidal gold

In situ hybridization has become a standard method for localizing DNA or RNA sequences in cytological preparations. We developed two methods to extend this technique to the transmission electron microscope level using mouse satellite DNA hybridization to whole mount metaphase chromosomes as the test system. The first method devised is a direct extension of standard light microscope level using mouse satellite DNA hybridization to whole mount metaphase chromosomes as the test system. The first method devised is a direct extension of standard light microscope in situ hybridization. Radioactively labeled complementary RNA (cRNA) is hybridized to metaphase chromosomes deposited on electron microscope grids and fixed in 70 percent ethanol vapor; hybridixation site are detected by autoradiography. Specific and intense labeling of chromosomal centromeric regions is observed even after relatively short exposure times. Inerphase nuclei present in some of the metaphase chromosome preparations also show defined paatterms of satellite DNA labeling which suggests that satellite-containing regions are associate with each other during interphase. The sensitivity of this method is estimated to at least as good as that at the light microscope level while the resolution is improved at least threefold. The second method, which circumvents the use of autoradiogrphic detection, uses biotin-labeled polynucleotide probes. After hybridization of these probes, either DNA or RNA, to fixed chromosomes on grids, hybrids are detected via reaction is improved at least threefold. The second method, which circumvents the use of autoradiographic detection, uses biotin-labeled polynucleotide probes. After hybridization of these probes, either DNA or RNA, to fixed chromosomes on grids, hybrids are detected via reaction with an antibody against biotin and secondary antibody adsorbed to the surface of over centromeric heterochromatin and along the associated peripheral fibers. Labeling is on average ten times that of background binding. This method is rapid and possesses the potential to allow precise ultrastructual localization of DNA sequences in chromosomes and chromatin.