Fiber-optic interferometric sensor of magnetic field for structural health monitoring

AbstractIn this paper we report on results of measurement of AC and DC magnetic field by fiber-optic interferometric sensor. Principle of operation is based on change of length of optical path cavity between the magnetostrictive wire and fiber-optic tip. Any change of the outside magnetic field causes elongation or contraction of the sensing wire. Using a fiber-optic sensing configuration based on single-mode 3×3 coupler and low-coherence interferometry we were able to read the instant separation between the wire and fiber ends with accuracy of about 50 nm. This separation corresponds with the intensity of the magnetic field in the range of 50 nT to 800 μT what is measured by using well calibrated magnetometer. The sensor is dedicated for on-line structural health monitoring of composite materials made of carbon reinforced epoxy matrix with integrated magnetic particles. Due to final purpose to be embedded in the structure, the sensor is designed to have small overall size of about 250 μm in outside diameter

Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete Trichoderma/Hypocrea

<p>Abstract</p> <p>Background</p> <p>Hydrophobins are proteins containing eight conserved cysteine residues that occur uniquely in mycelial fungi. Their main function is to confer hydrophobicity to fungal surfaces in contact with air or during attachment of hyphae to hydrophobic surfaces of hosts, symbiotic partners or themselves resulting in morphogenetic signals. Based on their hydropathy patterns and solubility characteristics, hydrophobins are divided into two classes (I and II), the latter being found only in ascomycetes.</p> <p>Results</p> <p>We have investigated the mechanisms driving the evolution of the class II hydrophobins in nine species of the mycoparasitic ascomycetous genus <it>Trichoderma/Hypocrea</it>, using three draft sequenced genomes (<it>H. jecorina = T. reesei, H. atroviridis = T. atroviride; H. virens = T. virens</it>) an additional 14,000 ESTs from six other Trichoderma spp. (<it>T. asperellum, H. lixii = T. harzianum, T. aggressivum </it>var. <it>europeae, T. longibrachiatum</it>, <it>T</it>. cf. <it>viride</it>). The former three contained six, ten and nine members, respectively. Ten is the highest number found in any ascomycete so far. All the hydrophobins we examined had the conserved four beta-strands/one helix structure, which is stabilized by four disulfide bonds. In addition, a small number of these hydrophobins (HFBs)contained an extended N-terminus rich in either proline and aspartate, or glycine-asparagine. Phylogenetic analysis reveals a mosaic of terminal clades containing duplicated genes and shows only three reasonably supported clades. Calculation of the ratio of differences in synonymous vs. non-synonymous nucleotide substitutions provides evidence for strong purifying selection (<it>K</it>_<it>S</it>/<it>K</it>_{<it>a </it>}>> 1). A genome database search for class II HFBs from other ascomycetes retrieved a much smaller number of hydrophobins (2–4) from each species, and most were from Sordariomycetes. A combined phylogeny of these sequences with those of <it>Trichoderma </it>showed that the <it>Trichoderma </it>HFBs mostly formed their own clades, whereas those of other Sordariomycetes occurred in shared clades.</p> <p>Conclusion</p> <p>Our study shows that the genus <it>Trichoderma/Hypocrea </it>has a proliferated arsenal of class II hydrophobins which arose by birth-and-death evolution followed by purifying selection.</p

Synthesizing Robust Systems with RATSY

Specifications for reactive systems often consist of environment assumptions and system guarantees. An implementation should not only be correct, but also robust in the sense that it behaves reasonably even when the assumptions are (temporarily) violated. We present an extension of the requirements analysis and synthesis tool RATSY that is able to synthesize robust systems from GR(1) specifications, i.e., system in which a finite number of safety assumption violations is guaranteed to induce only a finite number of safety guarantee violations. We show how the specification can be turned into a two-pair Streett game, and how a winning strategy corresponding to a correct and robust implementation can be computed. Finally, we provide some experimental results.Comment: In Proceedings SYNT 2012, arXiv:1207.055

The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome

<p>Abstract</p> <p>Background</p> <p>The hypercellulolytic mutant <it>Hypocrea jecorina </it>(anamorph <it>Trichoderma reesei</it>) RUT C30 is the <it>H. jecorina </it>strain most frequently used for cellulase fermentations and has also often been employed for basic research on cellulase regulation. This strain has been reported to contain a truncated carbon catabolite repressor gene <it>cre1 </it>and is consequently carbon catabolite derepressed. To date this and an additional frame-shift mutation in the glycoprotein-processing β-glucosidase II encoding gene are the only known genetic differences in strain RUT C30.</p> <p>Results</p> <p>In the present paper we show that <it>H. jecorina </it>RUT C30 lacks an 85 kb genomic fragment, and consequently misses additional 29 genes comprising transcription factors, enzymes of the primary metabolism and transport proteins. This loss is already present in the ancestor of RUT C30 – NG 14 – and seems to have occurred in a palindromic AT-rich repeat (PATRR) typically inducing chromosomal translocations, and is not linked to the <it>cre1 </it>locus. The mutation of the <it>cre1 </it>locus has specifically occurred in RUT C30. Some of the genes that are lacking in RUT C30 could be correlated with pronounced alterations in its phenotype, such as poor growth on α-linked oligo- and polyglucosides (loss of maltose permease), or disturbance of osmotic homeostasis.</p> <p>Conclusion</p> <p>Our data place a general caveat on the use of <it>H. jecorina </it>RUT C30 for further basic research.</p

Tiny Bird, Huge Mystery - The Possibly Extinct Hooded Seedeater (Sporophila melanops) Is a Capuchino with a Melanistic Cap

Known with certainty solely from a unique male specimen collected in central Brazil in the first quarter of the 19th century, the Critically Endangered (Possibly Extinct) Hooded Seedeater Sporophila melanops has been one of the great enigmas of Neotropical ornithology, arguably the only one of a host of long-lost species from Brazil to remain obstinately undiscovered. We reanalysed the morphology of the type specimen, as well as a female specimen postulated to represent the same taxon, and sequenced mitochondrial DNA (COI and Cyt-b) from both individuals. Furthermore, we visited the type locality, at the border between Goiás and Mato Grosso, and its environs on multiple occasions at different seasons, searching for birds with similar morphology to the type, without success. Novel genetic and morphological evidence clearly demonstrates that the type of S. melanops is not closely related to Yellow-bellied Seedeater S. nigricollis, as has been frequently postulated in the literature, but is in fact a representative of one of the so-called capuchinos, a clade of attractively plumaged seedeaters that breed mostly in the Southern Cone of South America. Our morphological analysis indicates that S. melanops has a hitherto unreported dark-coffee throat and that it is probably a Dark-throated Seedeater S. ruficollis collected within its wintering range, acquiring breeding plumage and showing melanism on the cap feathers. Alternatively, it may be a melanistic-capped individual of a local population of seedeaters known to breed in the Esteros del Iberá, Corrientes, Argentina, to which the name S. ruficollis might be applicable, whilst the name S. plumbeiceps might be available for what is currently known as S. ruficollis. A hybrid origin for S. melanops cannot be ruled out from the available data, but seems unlikely. The purported female specimen of S. melanops pertains either to S. nigricollis or to Double-collared Seedeater S. caerulescens based on genetic and morphological data, and thus cannot be a female of S. melanops. We conclude that Sporophila melanops is not typical of any natural population of seedeaters, appears to have been collected far from its breeding grounds while overwintering in central Brazil, and should not be afforded any conservation status.Fil: Areta, Juan Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Bio y Geociencias del NOA. Universidad Nacional de Salta. Facultad de Ciencias Naturales. Museo de Ciencias Naturales. Instituto de Bio y Geociencias del NOA; ArgentinaFil: Piacentini, Vítor de Q. Universidade de Sao Paulo; BrasilFil: Haring, Elisabeth. Universidad de Viena; AustriaFil: Gamauf, Anita. Universidad de Viena; AustriaFil: Silveira, Luís Fábio. Universidad de Viena; AustriaFil: Machado, Erika. Universidade de Sao Paulo; BrasilFil: Kirwan, Guy M.. The Field Museum; Estados Unido

Reduced ectoparasite load, body mass and blood haemolysis in Eurasian kestrels (Falco tinnunculus) along an urban-rural gradient

Urbanisation is proceeding at an alarming rate which forces wildlife to either retreat from urban areas or cope with novel stressors linked to human presence and activities. For example, urban stressors like anthropogenic noise, artificial light at night and chemical pollution can have severe impacts on the physiology of wildlife (and humans), in particular the immune system and antioxidant defences. These physiological systems are important to combat and reduce the severity of parasitic infections, which are common among wild animals. One question that then arises is whether urban-dwelling animals, whose immune and antioxidant system are already challenged by the urban stressors, are more susceptible to parasitic infections. To assess this, we studied nestlings of Eurasian kestrels (Falco tinnunculus) in Vienna, Austria, during 2015 and 2017. We measured biomarkers of innate immune function, oxidative stress and body mass index and ectoparasite infection intensity in 143 nestlings (from 56 nests) along an urban gradient. Nestlings in more urbanised areas had overall fewer ectoparasites, lower haemolysis (complement activity) and lower body mass index compared to nestlings in less urbanised areas. None of the other immune or oxidative stress markers were associated with the urban gradient. Despite some non-significant results, our data still suggest that kestrel nestlings experience some level of reduced physiological health, perhaps as a consequence of exposure to more urban stressors or altered prey availability in inner-city districts even though they had an overall lower ectoparasite burden in these heavily urbanised areas.</p

Utility of arsenic-treated bird skins for DNA extraction

Background: Natural history museums receive a rapidly growing number of requests for tissue samples from preserved specimens for DNA-based studies. Traditionally, dried vertebrate specimens were treated with arsenic because of its toxicity and insect-repellent effect. Arsenic has negative effects on in vivo DNA repair enzymes and consequently may inhibit PCR performance. In bird collections, foot pad samples are often requested since the feet were not regularly treated with arsenic and because they are assumed to provide substantial amounts of DNA. However, the actual influence of arsenic on DNA analyses has never been tested. Findings: PCR success of both foot pad and body skin samples was significantly lower in arsenic-treated samples. In general, foot pads performed better than body skin samples. Moreover, PCR success depends on collection date in which younger samples yielded better results. While the addition of arsenic solution to the PCR mixture had a clear negative effect on PCR performance after the threshold of 5.4 &#956;g/&#956;l, such high doses of arsenic are highly unlikely to occur in dried zoological specimens. Conclusions: While lower PCR success in older samples might be due to age effects and/or DNA damage through arsenic treatment, our results show no inhibiting effect on DNA polymerase. We assume that DNA degradation proceeds more rapidly in thin tissue layers with low cell numbers that are susceptible to external abiotic influences. In contrast, in thicker parts of a specimen, such as foot pads, the outermost horny skin may act as an additional barrier. Since foot pads often performed better than body skin samples, the intention to preserve morphologically important structures of a specimen still conflicts with the aim to obtain optimal PCR success. Thus, body skin samples from recently collected specimens should be considered as alternative sources of DNA

The Genomic Footprints of the Fall and Recovery of the Crested Ibis

Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of endangered species [1-4]. However, factors such as outbreeding depression [5, 6] and a reduction in available genetic diversity render the success of such approaches uncertain. An improved evaluation of the consequence of genetic restoration requires knowledge of temporal changes to genetic diversity before and after the advent of management programs. To provide such information, a growing number of studies have included small numbers of genomic loci extracted from historic and even ancient specimens [7, 8]. We extend this approach to its natural conclusion, by characterizing the complete genomic sequences of modern and historic population samples of the crested ibis (Nipponia nippon), an endangered bird that is perhaps the most successful example of how conservation effort has brought a species back from the brink of extinction. Though its once tiny population has today recovered to >2,000 individuals [9], this process was accompanied by almost half of ancestral loss of genetic variation and high deleterious mutation load. We furthermore show how genetic drift coupled to inbreeding following the population bottleneck has largely purged the ancient polymorphisms from the current population. In conclusion, we demonstrate the unique promise of exploiting genomic information held within museum samples for conservation and ecological research.© 2018 The Author(s). Published by Elsevier Ltd. This is an open access article available to all published under a Creative Commons Attribution – NonCommercial – NoDerivs (CC BY-NC-ND 4.0). The attached file is the published pdf

Magyar Tanítóképző 5 (1890) 07

A Tanítóképző-intézeti Tanárok Országos Egyesületének közlönye V. évfolyam 1890. július 25. VII. füze