The latch modulates nucleotide and DNA binding to the helicase-like domain of Thermotoga maritima reverse gyrase and is required for positive DNA supercoiling

Reverse gyrase is the only topoisomerase that can introduce positive supercoils into DNA in an ATP-dependent process. It has a modular structure and harnesses a helicase-like domain to support a topoisomerase activity, thereby creating the unique function of positive DNA supercoiling. The isolated topoisomerase domain can relax negatively supercoiled DNA, an activity that is suppressed in reverse gyrase. The isolated helicase-like domain is a nucleotide-dependent switch that is attenuated by the topoisomerase domain. Inter-domain communication thus appears central for the functional cooperation of the two domains. The latch, an insertion into the helicase-like domain, has been suggested as an important element in coordinating their activities. Here, we have dissected the influence of the latch on nucleotide and DNA binding to the helicase-like domain, and on DNA supercoiling by reverse gyrase. We find that the latch is required for positive DNA supercoiling. It is crucial for the cooperativity of DNA and nucleotide binding to the helicase-like domain. The latch contributes to DNA binding, and affects the preference of reverse gyrase for ssDNA. Thus, the latch coordinates the individual domain activities by modulating the helicase-like domain, and by communicating changes in the nucleotide state to the topoisomerase domai

Demystifying Open Access Workshop

Among the avenues for sharing research and scholarship, open access journals offer an increasingly viable and important option. However, it can be challenging not only to identify these journals but also to evaluate their quality and reach, as well as to weigh the benefits of publishing in them. To help demystify this process, Raynor Memorial Libraries offered a workshop on evaluating open access journals. Aimed at faculty, graduate students, and others interested in publishing their academic work, the workshop offered an overview of current open access options for sharing research, criteria to help assess the rigor and reliability of open access journals, and tips for navigating related copyright issues

Sarcopenia and vitamin d deficiency in patients with crohn’s disease: Pathological conditions that should be linked together

Sarcopenia is a prevalent condition in patients with Crohn’s disease (CD), representing an independent predictor factor for the development of major postoperative complications. Thus, a proper assessment of the muscle strength, by using different validated tools, should be deemed an important step of the clinical management of these patients. Patients with CD are frequently malnourished, presenting a high prevalence of different macro-and micro-nutrient deficiencies, including that of vitamin D. The available published studies indicate that vitamin D is involved in the regulation of proliferation, differentiation, and regeneration of muscle cells. The relationship between vitamin D deficiency and sarcopenia has been extensively studied in other populations, with interesting evidence in regards to a potential role of vitamin D supplementation as a means to prevent and treat sarcopenia. The aim of this review was to find studies that linked together these pathological conditions

Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling

Reverse gyrase is an ATP-dependent topoisomerase that is unique to hyperthermophilic archaea and eubacteria. The only reverse gyrase structure determined to date has revealed the arrangement of the N-terminal helicase domain and the C-terminal topoisomerase domain that intimately cooperate to generate the unique function of positive DNA supercoiling. Although the structure has elicited hypotheses as to how supercoiling may be achieved, it lacks structural elements important for supercoiling and the molecular mechanism of positive supercoiling is still not clear. We present five structures of authentic Thermotoga maritima reverse gyrase that reveal a first view of two interacting zinc fingers that are crucial for positive DNA supercoiling. The so-called latch domain, which connects the helicase and the topoisomerase domains is required for their functional cooperation and presents a novel fold. Structural comparison defines mobile regions in parts of the helicase domain, including a helical insert and the latch that are likely important for DNA binding during catalysis. We show that the latch, the helical insert and the zinc fingers contribute to the binding of DNA to reverse gyrase and are uniquely placed within the reverse gyrase structure to bind and guide DNA during strand passage. A possible mechanism for positive supercoiling by reverse gyrases is presente

Effect of glass on the frictional behavior of basalts at seismic slip rates

We performed 31 friction experiments on glassy basalts (GB) and glass-free basalts (GFB) at slip rates up to 6.5 m s−1 and normal stress up to 40 MPa (seismic conditions). Frictional weakening was associated to bulk frictional melting and lubrication. The weakening distance (Dw) was about 3 times shorter in GB than in GFB, but the steady state friction was systematically higher in GB than in GFB. The shorter Dw in GB may be explained by the thermal softening occurring at the glass transition temperature (Tg ~500°C), which is lower than the bulk melting temperature (Tm ~1250°C) of GFB. Postexperiment microanalyses suggest that the larger crystal fraction measured in GB melts results in the higher steady state friction value compared to the GFB melts. The effect of interstitial glass is to facilitate frictional instability and rupture propagation in GB with respect to GFB

Spotlight Your Research: Making your Research Visible on the Internet

Confused by the host of online services available to gather and promote your scholarly work, such as Google Scholar Citations, ResearchGate, Academia.edu, ORCID, Researcher ID, BioSketch, MyBibliography, etc., etc., etc.? This workshop by the librarians of Raynor Memorial Libraries and Office of Research and Programs staff allowed faculty to learn how to manage their online presence then put it to work to promote their research, track their impact and leverage funding applications. They learned: How to create and connect author profiles in popular platforms such as Google Scholar Citations, ResearchGate and ORCID How to set up their MyNCBI MyBibliography for NIH grant submissions Do’s and don’ts of online sharin

Frictional melting of peridotite and seismic slip

The evolution of the frictional strength along a fault at seismic slip rates (about 1 m/s) is a key factor controlling earthquake mechanics. At mantle depths, friction-induced melting and melt lubrication may influence earthquake slip and seismological data. We report on laboratory experiments designed to investigate dynamic fault strength and frictional melting processes in mantle rocks. We performed 20 experiments with Balmuccia peridotite in a high-velocity rotary shear apparatus and cylindrical samples (21.8 mm in diameter) over a wide range of normal stresses (5.4–16.1 MPa), slip rates (0.23–1.14 m/s), and displacements (1.5–71 m). During the experiments, shear stress evolved with cumulative displacement in five main stages (stages 1–5). In stage 1 (first strengthening), the coefficient of friction m increased up to 0.4–0.7 (first peak in friction). In stage 2 (abrupt firstweakening), m decreased to about 0.25–0.40. In stage 3 (gradual second strengthening), shear stress increased toward a second peak in friction (m = 0.30–0.40). In stage 4 (gradual second weakening), the shear stress decreased toward a steady state value (stage 5) with m = 0.15. Stages 1 and 2 are of too short duration to be investigated in detail with the current experimental configuration. By interrupting the experiments during stages 3, 4, and 5, microstructural (Field Emission Scanning Electron Microscope) and geochemical (Electron Probe Micro-Analyzer and Energy Dispersive X-Ray Spectroscopy) analysis of the slipping zone suggest that second strengthening (stage 3) is associated with the production of a grain-supported melt-poor layer, while second weakening (stage 4) and steady state (stage 5) are associated with the formation of a continuous melt-rich layer with an estimated temperature up to 1780 C. Microstructures formed during the experiments were very similar to those found in natural ultramafic pseudotachylytes. By performing experiments at different normal stresses and slip rates, (1) the ‘‘thermal’’ (as it includes the thermally activated first and second weakening) slip distance to achieve steady state from the first peak in strength decreased with increasing normal stress and slip rate and (2) the steady state shear stress slightly increased with increasing normal stress and, for a given normal stress, decreased with increasing slip rate. The ratio of shear stress versus normal stress was about 0.15, well below the typical friction coefficient of rocks (0.6–0.8). The dependence of steady state shear stress with normal stress was described by means of a constitutive equation for melt lubrication. The presence of microstructures similar to those found in natural pseudotachylytes and the determination of a constitutive equation that describes the experimental data allows extrapolation of the experimental observations to natural conditions and to the study of rupture dynamics in mantle rocks

PTTG2 silencing results in induction of epithelial-to-mesenchymal transition and apoptosis

Human securin, also known as human pituitary tumor-transforming gene 1 (pttg1), plays a key role in cell-cycle regulation. Two homologous genes, pttg2 and pttg3, have been identified although very little is known about their physiological function. In this study, we aimed at the characterization of these two pttg1 homologs. Real-time PCR analysis using specific probes demonstrated that Pttg2 is expressed at very low levels in various cell lines and tissues whereas Pttg3 was largely undetectable. We focused on the study of Pttg2 and found that, unlike PTTG1, PTTG2 lacks transactivation activity and does not bind to separase, making improbable a role in the control of sister chromatids separation. To further investigate the biological role of pttg2, we used short hairpin RNA inhibition of Pttg2 and found that cells with reduced Pttg2 levels assumed a rounded morphology compatible with a defect in cell adhesion and died by apoptosis in a p53- and p21-dependent manner. Using microarray technology, we generated a gene expression profile of Pttg2-depleted cells versus wild-type cells and found that knockdown of PTTG2 results in concomitant downregulation of E-cadherin and elevated vimentin levels, consistent with EMT induction. The observation of aberrant cellular behaviors in Pttg2-silenced cells reveals functions for pttg2 in cell adhesion and provides insights into a potential role in cell invasion. © 2013 Macmillan Publishers Limited.JAP-T was supported by grants from the Ministerio de Educación y Cultura of Spain and the Dirección General de Universidades e Investigación of Junta de Andalucía. CM-V and MAM-M were recipients of a postdoctoral contract from the Spanish National Research Council (JAE-DOC) and Junta de Andalucía, respectivelyPeer Reviewe

PTTG2 silencing results in induction of epithelial-to-mesenchymal transition and apoptosis

Human securin, also known as human pituitary tumor-transforming gene 1 (pttg1), plays a key role in cell-cycle regulation. Two homologous genes, pttg2 and pttg3, have been identified although very little is known about their physiological function. In this study, we aimed at the characterization of these two pttg1 homologs. Real-time PCR analysis using specific probes demonstrated that Pttg2 is expressed at very low levels in various cell lines and tissues whereas Pttg3 was largely undetectable. We focused on the study of Pttg2 and found that, unlike PTTG1, PTTG2 lacks transactivation activity and does not bind to separase, making improbable a role in the control of sister chromatids separation. To further investigate the biological role of pttg2, we used short hairpin RNA inhibition of Pttg2 and found that cells with reduced Pttg2 levels assumed a rounded morphology compatible with a defect in cell adhesion and died by apoptosis in a p53- and p21-dependent manner. Using microarray technology, we generated a gene expression profile of Pttg2-depleted cells versus wild-type cells and found that knockdown of PTTG2 results in concomitant downregulation of E-cadherin and elevated vimentin levels, consistent with EMT induction. The observation of aberrant cellular behaviors in Pttg2-silenced cells reveals functions for pttg2 in cell adhesion and provides insights into a potential role in cell invasion. © 2013 Macmillan Publishers Limited