Propagation of twist solitons in real DNA chains

We report on numerical investigations concerning the propagation of solitons in a real DNA chain (the Human Adenovirus 2) using a realistic model of DNA torsional dynamics; this takes fully into account the inhomogeneities in the real chain. We find that twist solitons propagate for considerable distances (2-10 times their diameters) before stopping due to phonon emission. Our results show that twist solitons may exist in real DNA chains; and on a more general level that solitonic propagation can take place in highly inhomogeneous media.Comment: 6 pages, 3 figure

An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer

This report describes an integrated study on identification of potential markers for gastric cancer in patients’ cancer tissues and sera based on: (i) genome-scale transcriptomic analyses of 80 paired gastric cancer/reference tissues and (ii) computational prediction of blood-secretory proteins supported by experimental validation. Our findings show that: (i) 715 and 150 genes exhibit significantly differential expressions in all cancers and early-stage cancers versus reference tissues, respectively; and a substantial percentage of the alteration is found to be influenced by age and/or by gender; (ii) 21 co-expressed gene clusters have been identified, some of which are specific to certain subtypes or stages of the cancer; (iii) the top-ranked gene signatures give better than 94% classification accuracy between cancer and the reference tissues, some of which are gender-specific; and (iv) 136 of the differentially expressed genes were predicted to have their proteins secreted into blood, 81 of which were detected experimentally in the sera of 13 validation samples and 29 found to have differential abundances in the sera of cancer patients versus controls. Overall, the novel information obtained in this study has led to identification of promising diagnostic markers for gastric cancer and can benefit further analyses of the key (early) abnormalities during its development

Comprehensive inventory of true flies (Diptera) at a tropical site

Peer reviewe

The structural plasticity of white matter networks following anterior temporal lobe resection

Anterior temporal lobe resection is an effective treatment for refractory temporal lobe epilepsy. The structural consequences of such surgery in the white matter, and how these relate to language function after surgery remain unknown. We carried out a longitudinal study with diffusion tensor imaging in 26 left and 20 right temporal lobe epilepsy patients before and a mean of 4.5 months after anterior temporal lobe resection. The whole-brain analysis technique tract-based spatial statistics was used to compare pre- and postoperative data in the left and right temporal lobe epilepsy groups separately. We observed widespread, significant, mean 7%, decreases in fractional anisotropy in white matter networks connected to the area of resection, following both left and right temporal lobe resections. However, we also observed a widespread, mean 8%, increase in fractional anisotropy after left anterior temporal lobe resection in the ipsilateral external capsule and posterior limb of the internal capsule, and corona radiata. These findings were confirmed on analysis of the native clusters and hand drawn regions of interest. Postoperative tractography seeded from this area suggests that this cluster is part of the ventro-medial language network. The mean pre- and postoperative fractional anisotropy and parallel diffusivity in this cluster were significantly correlated with postoperative verbal fluency and naming test scores. In addition, the percentage change in parallel diffusivity in this cluster was correlated with the percentage change in verbal fluency after anterior temporal lobe resection, such that the bigger the increase in parallel diffusivity, the smaller the fall in language proficiency after surgery. We suggest that the findings of increased fractional anisotropy in this ventro-medial language network represent structural reorganization in response to the anterior temporal lobe resection, which may damage the more susceptible dorso-lateral language pathway. These findings have important implications for our understanding of brain injury and rehabilitation, and may also prove useful in the prediction and minimization of postoperative language deficits

Compressibility systematics of calcite-type borates : An experimental and theoretical structural study on ABO3 (A = Al, Sc, Fe and In)

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C , copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp4124259The structural properties of calcite-type orthoborates ABO(3) (A = Al, Fe, Sc, and In) have been investigated at high pressures up to 32 GPa. They were studied experimentally using synchrotron powder X-ray diffraction and theoretically by means of ab initio total-energy calculations. We found that the calcite-type structure remains stable up to the highest pressure explored in the four studied compounds. Experimental and calculated static geometries (unit-cell parameters and internal coordinates), bulk moduli, and their pressure derivatives are in good agreement. The compressibility along the c axis is roughly three times that along the a axis. Our data clearly indicate that the compressibility of borates is dominated by that of the [AO(6)] octahedral group and depends on the size of the trivalent A cations. An analysis of the relationship between isomorphic borates and carbonates is also presented, which points to the potentiality of considering borates as chemical analogues of the carbonate mineral family.This study was supported by the Spanish government MEC under Grant Nos.: MAT2010-21270-C04-01/03/04 and CTQ2009-14596-C02-01, by MALTA Consolider Ingenio 2010 Project (CSD2007-00045), by Generalitat Valenciana (GVA-ACOMP-2013-1012), and by the Vicerrectorado de Investigacion y Desarrollo of the Universidad Politecnica de Valencia (UPV2011-0914 PAID-05-11 and UPV2011-0966 PAID-06-11). We thank ALBA and Diamond synchrotrons for providing beamtime for the XRD experiments. A.M. and P.R-H. acknowledge computing time provided by Red Espanola de Supercomputacion (RES) and MALTA-Cluster. J.A.S. and B.G.-D. acknowledge Juan de la Cierva fellowship and FPI programs for financial support. We are gratefully indebted to Dr. Capponi and Dr. Diehl for supplying us single crystals of AlBO3 and FeBO3, respectively.Santamaría Pérez, D.; Gomis Hilario, O.; Sans, JÁ.; Ortiz, HM.; Vegas, Á.; Errandonea, D.; Ruiz-Fuertes, J.... (2014). Compressibility systematics of calcite-type borates : An experimental and theoretical structural study on ABO3 (A = Al, Sc, Fe and In). Journal of Physical Chemistry C. 118(8):4354-4361. https://doi.org/10.1021/jp4124259S43544361118

A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci

Genome-wide association studies (GWAS) in European populations have identified genetic risk variants associated with multiple myeloma (MM)

Membrane vesicles, current state-of-the-art: emerging role of extracellular vesicles

Release of membrane vesicles, a process conserved in both prokaryotes and eukaryotes, represents an evolutionary link, and suggests essential functions of a dynamic extracellular vesicular compartment (including exosomes, microparticles or microvesicles and apoptotic bodies). Compelling evidence supports the significance of this compartment in a broad range of physiological and pathological processes. However, classification of membrane vesicles, protocols of their isolation and detection, molecular details of vesicular release, clearance and biological functions are still under intense investigation. Here, we give a comprehensive overview of extracellular vesicles. After discussing the technical pitfalls and potential artifacts of the rapidly emerging field, we compare results from meta-analyses of published proteomic studies on membrane vesicles. We also summarize clinical implications of membrane vesicles. Lessons from this compartment challenge current paradigms concerning the mechanisms of intercellular communication and immune regulation. Furthermore, its clinical implementation may open new perspectives in translational medicine both in diagnostics and therapy