Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus

Background: Flagella have been lost in the vegetative phase of the diatom life cycle, but they are still present in male gametes of centric species, thereby representing a hallmark of sexual reproduction. This process, besides maintaining and creating new genetic diversity, in diatoms is also fundamental to restore the maximum cell size following its reduction during vegetative division. Nevertheless, sexual reproduction has been demonstrated in a limited number of diatom species, while our understanding of its different phases and of their genetic control is scarce. Results: In the transcriptome of Leptocylindrus danicus, a centric diatom widespread in the world's seas, we identified 22 transcripts related to the flagella development and confirmed synchronous overexpression of 6 flagellum-related genes during the male gamete formation process. These transcripts were mostly absent in the closely related species L. aporus, which does not have sexual reproduction. Among the 22 transcripts, L. danicus showed proteins that belong to the Intra Flagellar Transport (IFT) subcomplex B as well as IFT-A proteins, the latter previously thought to be absent in diatoms. The presence of flagellum-related proteins was also traced in the transcriptomes of several other centric species. Finally, phylogenetic reconstruction of the IFT172 and IFT88 proteins showed that their sequences are conserved across protist species and have evolved similarly to other phylogenetic marker genes. Conclusion: Our analysis describes for the first time the diatom flagellar gene set, which appears to be more complete and functional than previously reported based on the genome sequence of the model centric diatom, Thalassiosira pseudonana. This first recognition of the whole set of diatom flagellar genes and of their activation pattern paves the way to a wider recognition of the relevance of sexual reproduction in individual species and in the natural environment

Age estimation by tooth/pulp ratio in canines by peri-apical X-rays: reliability in age determination of Spanish and Italian medieval skeletal remains

Estimation of age at death is an unavoidable step in the process of human identification, both in forensic practice and in the anthropological and palaeopathological study of skeletal remains. In several cases, in which medical or demographic records are completely lacking, a reliable estimation of the age at death becomes very important. Skeletal remains from archaeological contexts suffer from several biasing factors such as post-mortem changes, taphonomy and various burial practices depending on age, sex and social status of the deceased persons. Currently, anthropological methods of age determination reveal several possibilities of inaccuracy. Of all the body parts used in age estimation, teeth are the least affected by any taphonomic process. Although there are many dental methods for age at death estimation, some of them are very complex and/or destructive and they are not normally used in anthropology. However, study of the apposition of secondary dentine by examining peri-apical X-rays of canines is beginning to supply very interesting results. The aim of this work was to test Cameriere\u2019s method on a large sample of historical subjects from several cemeteries in Spain and Italy. The Spanish sample belongs to the Medieval cemetery of La Torrecilla (Arenas del Rey, Granada) and is housed in the Laboratory of Anthropology, Faculty of Medicine, University of Granada. The Italian samples come from the Medieval cemeteries of Comacchio (Ferrara) and Castel S. Pietro (Bologna). In order to test the reliability of Cameriere\u2019s method, age estimations of canines were compared with the mean ranges of age of the most commonly applied anthropological methods such as tooth wear changes in the pubic symphysis or the metamorphosis of the auricular surface of the ilium. Tests on these Middle Ages cemeteries produced satisfactory results, indicating that Cameriere\u2019s method is a reliable tool in determining age at death in skeletal remains of archaeological context

Displacement power spectrum measurement of a macroscopic optomechanical system at thermal equilibrium

The mirror relative motion of a suspended Fabry-Perot cavity is studied in the frequency range 3-10 Hz. The experimental measurements presented in this paper, have been performed at the Low Frequency Facility, a high finesse optical cavity 1 cm long suspended to a mechanical seismic isolation system identical to that one used in the VIRGO experiment. The measured relative displacement power spectrum is compatible with a system at thermal equilibrium within its environmental. In the frequency region above 3 Hz, where seismic noise contamination is negligible, the measurement distribution is stationary and Gaussian, as expected for a system at thermal equilibrium. Through a simple mechanical model it is shown that: applying the fluctuation dissipation theorem the measured power spectrum is reproduced below 90 Hz and noise induced by external sources are below the measurement.Comment: 11 pages, 9 figures, 2 tables, to be submitte

New results on pushdown module checking with imperfect information

Model checking of open pushdown systems (OPD) w.r.t. standard branching temporal logics (pushdown module checking or PMC) has been recently investigated in the literature, both in the context of environments with perfect and imperfect information about the system (in the last case, the environment has only a partial view of the system's control states and stack content). For standard CTL, PMC with imperfect information is known to be undecidable. If the stack content is assumed to be visible, then the problem is decidable and 2EXPTIME-complete (matching the complexity of PMC with perfect information against CTL). The decidability status of PMC with imperfect information against CTL restricted to the case where the depth of the stack content is visible is open. In this paper, we show that with this restriction, PMC with imperfect information against CTL remains undecidable. On the other hand, we individuate an interesting subclass of OPDS with visible stack content depth such that PMC with imperfect information against the existential fragment of CTL is decidable and in 2EXPTIME. Moreover, we show that the program complexity of PMC with imperfect information and visible stack content against CTL is 2EXPTIME-complete (hence, exponentially harder than the program complexity of PMC with perfect information, which is known to be EXPTIME-complete).Comment: In Proceedings GandALF 2011, arXiv:1106.081

Theory of x-ray absorption by laser-dressed atoms

An ab initio theory is devised for the x-ray photoabsorption cross section of atoms in the field of a moderately intense optical laser (800nm, 10^13 W/cm^2). The laser dresses the core-excited atomic states, which introduces a dependence of the cross section on the angle between the polarization vectors of the two linearly polarized radiation sources. We use the Hartree-Fock-Slater approximation to describe the atomic many-particle problem in conjunction with a nonrelativistic quantum-electrodynamic approach to treat the photon-electron interaction. The continuum wave functions of ejected electrons are treated with a complex absorbing potential that is derived from smooth exterior complex scaling. The solution to the two-color (x-ray plus laser) problem is discussed in terms of a direct diagonalization of the complex symmetric matrix representation of the Hamiltonian. Alternative treatments with time-independent and time-dependent non-Hermitian perturbation theories are presented that exploit the weak interaction strength between x rays and atoms. We apply the theory to study the photoabsorption cross section of krypton atoms near the K edge. A pronounced modification of the cross section is found in the presence of the optical laser.Comment: 13 pages, 3 figures, 1 table, RevTeX4, corrected typoe

On the relationships between tectonics and volcanism in the offshore Capo Vaticano, SE Tyrrhenian Sea, during the Plio-Pleistocene

High-resolution bathymetry and a grid of single-channel reflection seismic profiles (Sparker and Chirp) were recently recorded in a sector of the upper slope of Capo Vaticano (CV) promontory (Tyrrhenian coast, W Calabria) where forward and inverse modeling of previously acquired aeromagnetic data highlight the presence of a WNW©\ESE elongated, 20 km long and 3¨C5 km wide, magnetized body extending from sea floor to about 3 km below sea level. Magnetic properties of this body are consistent with those of the medium to highly evolved volcanic rocks of the Aeolian Arc (De Ritis et al., 2010). Forthwith offshore promontory, the bathymetry highlights a complex-shape seamount that develops along a WNW direction, orthogonally interrupted by NE-trending ridges (Loreto et al., 2013), the largest of which shows major- and minor-axes of ca. 11 and 2 km, respectively. Summit elevation is ca. 70 m. Several vented fluids points were imaged on top of the seamount by chirp profiles. The largest of which rises from seafloor up to 6/7 m within water column, assuming the acoustic water velocity of 1500 m/s. Two faults systems associated with extensional faults are mainly observed on seismic profiles. High-angle NW-trending normal faults, SW-dipping, formed along the continental slope connecting the south-west continental shelf of the CV promontory to the Gioia Tauro basin (Pepe et al., 2013). These faults generally have small displacements, up to 40 m, and are sealed by Pleistocene deposits. A NE-trending normal fault, SE-dipping, is also observed on both chirp and sparker profiles. Its length is estimate to be more than 30 km, partially borders the NE-trending ridge intersecting the NW-trending fault. Landward, another NE-trending normal fault affects Pliocene and lower Pleistocene, and is sealed by upper Pleistocene. The described new geophysical data lead to a re-examination of the magnetic anomaly field interpretation. In fact, the revealed NE-trending ridge encounters the CV NW-SE ridge just where the peak value of the Reduced-to-the-Pole magnetic anomaly lies. Therefore, the inherent source body is emplaced where the maximum fracturing occurs. This suggests highly magnetized material crystallized in a vertical conduit that fed a volcanic system, likely fault-controlled, surrounded by the almost not magnetized rocks of the Gioia and the Paola sedimentary basins and of the Arco Calabro Peloritano units

On the Feasibility of Malware Authorship Attribution

There are many occasions in which the security community is interested to discover the authorship of malware binaries, either for digital forensics analysis of malware corpora or for thwarting live threats of malware invasion. Such a discovery of authorship might be possible due to stylistic features inherent to software codes written by human programmers. Existing studies of authorship attribution of general purpose software mainly focus on source code, which is typically based on the style of programs and environment. However, those features critically depend on the availability of the program source code, which is usually not the case when dealing with malware binaries. Such program binaries often do not retain many semantic or stylistic features due to the compilation process. Therefore, authorship attribution in the domain of malware binaries based on features and styles that will survive the compilation process is challenging. This paper provides the state of the art in this literature. Further, we analyze the features involved in those techniques. By using a case study, we identify features that can survive the compilation process. Finally, we analyze existing works on binary authorship attribution and study their applicability to real malware binaries.Comment: FPS 201

Extensive Spectroscopy and Photometry of the Type IIP Supernova 2013ej

We present extensive optical ($UBVRI$, $g'r'i'z'$, and open CCD) and near-infrared ($ZYJH$) photometry for the very nearby Type IIP SN ~2013ej extending from +1 to +461 days after shock breakout, estimated to be MJD $56496.9\pm0.3$. Substantial time series ultraviolet and optical spectroscopy obtained from +8 to +135 days are also presented. Considering well-observed SNe IIP from the literature, we derive $UBVRIJHK$ bolometric calibrations from $UBVRI$ and unfiltered measurements that potentially reach 2\% precision with a $B-V$ color-dependent correction. We observe moderately strong Si II $\lambda6355$ as early as +8 days. The photospheric velocity ($v_{\rm ph}$) is determined by modeling the spectra in the vicinity of Fe II $\lambda5169$ whenever observed, and interpolating at photometric epochs based on a semianalytic method. This gives $v_{\rm ph} = 4500\pm500$ km s$^{-1}$ at +50 days. We also observe spectral homogeneity of ultraviolet spectra at +10--12 days for SNe IIP, while variations are evident a week after explosion. Using the expanding photosphere method, from combined analysis of SN 2013ej and SN 2002ap, we estimate the distance to the host galaxy to be $9.0_{-0.6}^{+0.4}$ Mpc, consistent with distance estimates from other methods. Photometric and spectroscopic analysis during the plateau phase, which we estimated to be $94\pm7$ days long, yields an explosion energy of $0.9\pm0.3\times10^{51}$ ergs, a final pre-explosion progenitor mass of $15.2\pm4.2$~M$_\odot$ and a radius of $250\pm70$~R$_\odot$. We observe a broken exponential profile beyond +120 days, with a break point at +$183\pm16$ days. Measurements beyond this break time yield a $^{56}$Ni mass of $0.013\pm0.001$~M$_\odot$.Comment: 29 pages, 23 figures, 15 tables, Published in The Astrophisical Journa

TURBOGEN: Computer-controlled vertically oscillating grid system for small-scale turbulence studies on plankton

11 pages, 10 figures, 3 tablesIn recent years, there has been a renewed interest in the impact of turbulence on aquatic organisms. In response to this interest, a novel instrument has been constructed, TURBOGEN, that generates turbulence in water volumes up to 13 l. TURBOGEN is fully computer controlled, thus, allowing for a high level of reproducibility and for variations of the intensity and characteristics of turbulence during the experiment. The calibration tests, carried out by particle image velocimetry, showed TURBOGEN to be successful in generating isotropic turbulence at the typical relatively low levels of the marine environment. TURBOGEN and its sizing have been devised with the long-term scope of analyzing in detail the molecular responses of plankton to different mixing regimes, which is of great importance in both environmental and biotechnological processesRachel Macmasters is acknowledged for language check. A.A., M.I.F., D.I., M.R.d’A., and R.W. thank the Flagship project RITMARE—The Italian Research for the Sea Programme (Ricerca ITaliana per il MARE) for partial support. A.A. was funded by the European Union under FP7-People—GA No. 600407Peer Reviewe

Evaluation of the efficiency of a conventional PCR protocol for the diagnosis of bacterial spot disease caused by Xanthomonas arboricola pv. pruni in stone fruits and almond

Xanthomonas arboricola pv. pruni (Xap), the causal agent of bacterial spot disease of stone fruits and almond, has a quarantine status for the European Union and the European and Mediterranean Plant Protection Organization. The symptoms in the diverse hosts show some differences and, although being quite typical, could be confused with those of some fungal diseases or other biotic or abiotic causes. Consequently, an accurate molecular diagnosis method is required for a rapid identification of the pathogen in samples of imported plants, from nurseries, orchards, etc. A protocol for conventional PCR designed by Pagani (2004) has been the only molecular analytic tool available for several years. It has been optimised for improving its specificity and sensitivity, and the results of its evaluation in 316 bacterial spot-like symptomatic samples of almond, apricot, cherry, Japanese plum and peach, compared with those of isolation and real-time PCR, are reported. The optimised PCR protocol showed specificity for a collection of Xap strains tested. Few non-desired reactions were obtained with some other xanthomonads which have not been reported from Prunus species. Sensitivity thresholds ranged from 102 to 105 CFU ml-1, depending on the hosts and type of plant material. This conventional PCR assay proved to be an excellent candidate for a rapid screening and presumptive diagnosis in cases where real-time PCR equipment is not available