Ab initio detection of fuzzy amino acid tandem repeats in protein sequences

Background Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (fuzzy tandem repeats). Results In this paper we present PTRStalker, a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences. In the reported results we show that by feeding PTRStalker with amino acid sequences from the UniProtKB/Swiss-Prot database we detect novel tandemly repeated structures not captured by other state-of-the-art tools. Experiments with membrane proteins indicate that PTRStalker can detect global symmetries in the primary structure which are then reflected in the tertiary structure. Conclusions PTRStalker is able to detect fuzzy tandem repeating structures in protein sequences, with performance beyond the current state-of-the art. Such a tool may be a valuable support to investigating protein structural properties when tertiary X-ray data is not available

Seven exercises planned to stimulate the flow of ideas in creative composition

Thesis (Ed.M.)--Boston Universit

Dissociation between cognitive-behavioral and emotional-psychopgysiological aspects in eating disorders and pre post treatment stability

Objective The present work aims to assess the effectiveness of an integrate treatment in a group of patients with Eating Disorders (EDs). Methods 15 women with an ED, who underwent a multidisciplinary treatment, were subdivided into two groups (Anorexia Nervosa and Bulimia Nervosa). Participants were evaluated by: Symptom Questionnaire (SQ) and Psychophysiological Profile (PPP). Administration was repeated six months after the start of treatment and at treatment termination. Results Elevated levels of anxiety, depression, somatic symptoms and hostility at the diagnostic phase and low levels of physiological reactivity were observed. A significant reduction in patient-reported depressive symptoms was detected within six months following the onset of treatment. Progressive improvement of anxiety and hostility was observed in the medium- long term. At the physiological level, an increase in skin conductance values was observed during the stress phase in the medium-long term. Discussion A partial desynchronization emerged between patients’ physiological and cognitive responses

Chromosome Segregation Is Biased by Kinetochore Size

Chromosome missegregation during mitosis or meiosis is a hallmark of cancer and the main cause of prenatal death in humans. The gain or loss of specific chromosomes is thought to be random, with cell viability being essentially determined by selection. Several established pathways including centrosome amplification, sister-chromatid cohesion defects, or a compromised spindle assembly checkpoint can lead to chromosome missegregation. However, how specific intrinsic features of the kinetochore—the critical chromosomal interface with spindle microtubules—impact chromosome segregation remains poorly understood. Here we used the unique cytological attributes of female Indian muntjac, the mammal with the lowest known chromosome number (2n = 6), to characterize and track individual chromosomes with distinct kinetochore size throughout mitosis. We show that centromere and kinetochore functional layers scale proportionally with centromere size. Measurement of intra-kinetochore distances, serial-section electron microscopy, and RNAi against key kinetochore proteins confirmed a standard structural and functional organization of the Indian muntjac kinetochores and revealed that microtubule binding capacity scales with kinetochore size. Surprisingly, we found that chromosome segregation in this species is not random. Chromosomes with larger kinetochores bi-oriented more efficiently and showed a 2-fold bias to congress to the equator in a motor-independent manner. Despite robust correction mechanisms during unperturbed mitosis, chromosomes with larger kinetochores were also strongly biased to establish erroneous merotelic attachments and missegregate during anaphase. This bias was impervious to the experimental attenuation of polar ejection forces on chromosome arms by RNAi against the chromokinesin Kif4a. Thus, kinetochore size is an important determinant of chromosome segregation fidelity

A Comparison between High-order Temporal Integration Methods Applied to the Discontinuous Galerkin Discretized Euler Equations

Abstract In this work we present a high-order Discontinuous Galerkin (DG) space approximation coupled with two high-order temporal integration methods for the numerical solution of time-dependent compressible flows. The time integration methods analyzed are the explicit Strong-Stability-Preserving Runge-Kutta (SSPRK) and the Two Implicit Advanced Step-point (TIAS) schemes. Their accuracy and efficiency are evaluated by means of an inviscid test case for which an exact solution is available. The study is carried out for several time-steps using different polynomial order approximations and several levels of grid refinement. The effect of mesh irregularities on the accuracy is also investigated by considering randomly perturbed meshes. The analysis of the results has the twofold objective of (i) assessing the performances of the temporal schemes in the context of the high-order DG discretization and(ii) determining if high-order implicit schemes can displace widely used high-order explicit schemes

A kinematically selected, metal-poor stellar halo in the outskirts of M31

We present evidence for a metal-poor, [Fe/H]$\sim-1.4$ $\sigma$=0.2 dex, stellar halo component detectable at radii from 10 kpc to 70 kpc, in our nearest giant spiral neighbor, the Andromeda galaxy. This metal-poor sample underlies the recently-discovered extended rotating component, and has no detected metallicity gradient. This discovery uses a large sample of 9861 radial velocities of Red Giant Branch (RGB) stars obtained with the Keck-II telescope and DEIMOS spectrograph, with 827 stars with robust radial velocity measurements isolated kinematically to lie in the halo component primarily by windowing out the extended rotating component which dominates the photometric profile of Andromeda out to $<$50 kpc (de-projected). The stars lie in 54 spectroscopic fields spread over an 8 square degree region, and are expected to fairly sample the halo to a radius of $\sim$70 kpc. The halo sample shows no significant evidence for rotation. Fitting a simple model in which the velocity dispersion of the component decreases with radius, we find a central velocity dispersion of 152\kms decreasing by -0.90\kms/\kpc. By fitting a cosmologically-motivated NFW halo model to the halo stars we constrain the virial mass of M31 to be greater than 9.0 \times 10^{11} \msun with 99% confidence. The properties of this halo component are very similar to that found in our Milky Way, revealing that these roughly equal mass galaxies may have led similar accretion and evolutionary paths in the early Universe.Comment: 13 pages, 12 figures, accepted in ApJ. substantially revised versio

Mediterranean spreading of the bicolor purse oyster, Isognomon bicolor, and the chicken trigger, Malleus sp., vs. the Lessepsian prejudice

The introduction rate of alien species in the Mediterranean Sea is rapidly growing, and their taxonomical identification is increasingly challenging. This uncertain identification often leads to an incorrect estimation of the number of alien species, their route of introduction, and their potential negative effects. This is particularly true for some bivalves, which are characterized by high variation in their shells, resulting in uncertain morphological identification. This is the case for two alien bivalves, i.e., an Isognomonidae and a Malleidae species, both characterized by confused historical colonization records in the Mediterranean Sea, misidentifications, and controversial and changing nomenclatures that have insofar negatively affected our knowledge on their geographical distributions. In this respect, molecular approaches provide a strategy that is especially useful when traditional taxonomy fails, and DNA barcoding is a powerful and well-known tool to obtain reliable identifications through efficient molecular markers. In this work, we used the 16S rRNA marker to assess the preliminary identification of Isognomon sp. and Malleus sp. specimens from different localities in the Southern Mediterranean Sea. Bayesian inference (BI) and maximum likelihood (ML) methods were applied to test the monophyly of the phylogenetic linages and to clarify their taxonomic positions, allowing a complete overview of the colonization and spreading of these two alien bivalves in the Mediterranean Sea. In particular, the Isognomon sp. specimens were identified as the Atlantic I. bicolor, highlighting that previously suggested invasive migration patterns, (i.e., the Lessepsian migration), must be reconsidered with stronger critical attention in light of currently occurring global changes