A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system

BACKGROUND: Restriction/modification systems provide the dual function of protecting host DNA against restriction by methylation of appropriate bases within their recognition sequences, and restriction of foreign invading un-methylated DNA, such as promiscuous plasmids or infecting bacteriphage. The plasmid-encoded LlaJI restriction/modification system from Lactococcus lactis recognizes an asymmetric, complementary DNA sequence, consisting of 5'GACGC'3 in one strand and 5'GCGTC'3 in the other and provides a prodigious barrier to bacteriophage infection. LlaJI is comprised of four similarly oriented genes, encoding two 5mC-MTases (M1.LlaJI and M2.LlaJI) and two subunits responsible for restriction activity (R1.LlaJI and R2.LlaJI). Here we employ a detailed genetic analysis of the LlaJI restriction determinants in an attempt to characterize mechanistic features of this unusual hetero-oligomeric endonuclease. RESULTS: Detailed bioinformatics analysis confirmed the presence of a conserved GTP binding and hydrolysis domain within the C-terminal half of the R1.LlaJI amino acid sequence whilst the N-terminal half appeared to be entirely unique. This domain architecture was homologous with that of the "B" subunit of the GTP-dependent, methyl-specific McrBC endonuclease from E.coli K-12. R1.LlaJI did not appear to contain a catalytic centre, whereas this conserved motif; PD....D/EXK, was clearly identified within the amino acid sequence for R2.LlaJI. Both R1.LlaJI and R2.LlaJI were found to be absolutely required for detectable LlaJI activity in vivo. The LlaJI restriction subunits were purified and examined in vitro, which allowed the assignment of R1.LlaJI as the sole specificity determining subunit, whilst R2.LlaJI is believed to mediate DNA cleavage. CONCLUSION: The hetero-subunit structure of LlaJI, wherein one subunit mediates DNA binding whilst the other subunit is predicted to catalyze strand hydrolysis distinguishes LlaJI from previously characterized restriction-modification systems. Furthermore, this distinction is accentuated by the fact that whilst LlaJI behaves as a conventional Type IIA system in vivo, in that it restricts un-methylated DNA, it resembles the Type IV McrBC endonuclease, an enzyme specific for methylated DNA. A number of similar restriction determinants were identified in the database and it is likely LlaJI together with these homologous systems, comprise a new subtype of the Type II class incorporating features of Type II and Type IV systems

The Ursinus Weekly, June 5, 1961

198 diplomas sum up 4 Ursinus years: Prizes bestowed on outstanding Ursinus students • Sandberg \u2761 valedictorian; Graduates summa cum laude • Four honorary degrees awarded this morning: Robert N. Hilkert delivers address to Ursinus\u27 198 senior graduates • Roadside billboard inspiration for Hilkert\u27s speech • Cash prize given four cited for teaching merit • Barbara Pine wins scholarship; Her blindness no obstacle • Biology instructor leaves to tie up loose ends • Amigo to retire; Students\u27 friend for eleven years • Dr. Paisley\u27s death saddens commencement; Board President served Ursinus for 51 years • Newspaperman elected new trustee board head • September may bring 280 freshmen; U.C. Admissions Department reports • New Weekly ad manager wins Wayne Brown prize • Editorial: Sharpened incisors; Good luck • Ursinus in the past • Art of understanding • Seniors submit post-graduation plans; Many teach, work for further degrees • Lacrosse players undefeated again; Trample Drexel • Snell softballers post 3-2 log; Ask more games • Intramural corner • Wait\u27ll next year when nine starters return to diamond • Lynne Crosley lacrosse all-American first team • Netmen competent despite 3-5 log; Famous is MVP • Sport page outlet for creativity, magazine writes • Track team tallies 5-5 \u2761 record; Wise made captain • Morgan finally defeated; Moran wins in AAU run • Mrs. Shryock to retire; Mrs. Bugelholl plans move • Ursinus professor to attend nuclear session • Organizations list late election results • Ursinus College gets $92,000 in Lehigh estate • Late track news: Morgan runs 4:04.2 in Boardwalk Mile • Dr. Creager reported doing well; Needs rest • Ursinus awarded$12,000 F. J. Clamer memorial fundhttps://digitalcommons.ursinus.edu/weekly/1344/thumbnail.jp

The performance of differential point positioning using low-cost GNSS in comparison to DInSAR for monitoring coseismic displacement of the Provenzana–Pernicana fault system (Mt. Etna, 2018 December eruptive phase)

Mt. Etna is a perfect laboratory for testing new approaches and new technologies in a very active geodynamic environment. It offers, in fact, the opportunity for measuring active crustal deformation, related to volcanic activity as well as to seismic faulting on its flanks. In this work, a network of low-cost/low-power Global Navigation Satellite System stations has been installed and tested on Mt. Etna, across a very active fault, the Provenzana–Pernicana system, cutting its north-eastern flank. During the test period, a lateral eruption occurred (starting on 2018 December 24), with a forceful dyke intrusion that stressed all the flanks of the volcano, soliciting all the main faults dissecting the edifice. Also the Provenzana–Pernicana fault system, where this network was recording, was activated during the dyke intrusion, producing a significant seismic swarm. The low-cost/low-power network data analysis allowed the fault slip during the intrusion to be clearly traced in time and space at all the stations lying on the hangingwall mobile block of the fault. All the stations lying south of the fault trace showed an eastward displacement, in very good agreement with the usual kinematics of the fault and the temporal duration of the M3.5 December 24 earthquake, related to the seaward dislocation of the eastern mobile flank of the volcano, promoted and accelerated by dyke emplacement on the upper part of the edifice

Fault2SHA Central Apennines database and structuring active fault data for seismic hazard assessment

We present a database of field data for active faults in the central Apennines, Italy, including trace, fault and main fault locations with activity and location certainties, and slip-rate, slip-vector and surface geometry data. As advances occur in our capability to create more detailed fault-based hazard models, depending on the availability of primary data and observations, it is desirable that such data can be organized in a way that is easily understood and incorporated into present and future models. The database structure presented herein aims to assist this process. We recommend stating what observations have led to different location and activity certainty and presenting slip-rate data with point location coordinates of where the data were collected with the time periods over which they were calculated. Such data reporting allows more complete uncertainty analyses in hazard and risk modelling. The data and maps are available as kmz, kml, and geopackage files with the data presented in spreadsheet files and the map coordinates as txt files. The files are available at: https://doi. org/10.1594/PANGAEA.922582

Which fault threatens me most? Bridging the gap between geologic data-providers and seismic risk practitioners

The aim of the Fault2SHA European Seismological Commission Working Group Central Apennines laboratory is to enhance the use of geological data in fault-based seismic hazard and risk assessment and to promote synergies between data providers (earthquake geologists), end users and decision-makers. Here we use the Fault2SHA Central Apennines Database where geologic data are provided in the form of characterized fault traces, grouped into faults and master faults, with individual slip rate estimates. The proposed methodology first derives slip rate profiles for each master fault. Master faults are then divided into distinct sections of length comparable to the seismogenic depth to allow consideration of variable slip rates along master faults and the exploration of multi-fault ruptures in the computations. The methodology further allows exploration of epistemic uncertainties documented in the database (e.g. master fault definition, slip rates) as well as additional parameters required to characterize the seismogenic potential of fault sources (e.g. 3D fault geometries). To illustrate the power of the methodology, in this paper we consider only one branch of the uncertainties affecting each step of the computation procedure. The resulting hazard and typological risk maps allow both data providers and end-users (1) to visualize the faults that threaten specific localities the most, (2) to appreciate the density of observations used for the computation of slip rate profiles, and (3) interrogate the degree of confidence on the fault parameters documented in the database (activity and location certainty). Finally, closing the loop, the methodology highlights priorities for future geological investigations in terms of where improvements in the density of data within the database would lead to the greatest decreases in epistemic uncertainties in the hazard and risk calculations. Key to this new generation of fault-based seismic hazard and risk methodology are the user-friendly open source codes provided with this publication, documenting, step-by-step, the link between the geological database and the relative contribution of each section to seismic hazard and risk at specific localities

Revealing Nuclear Pions Using Electron Scattering

A model for the pionic components of nuclear wave functions is obtained from light front dynamical calculations of binding energies and densities. The pionic effects are small enough to be consistent with measured nuclear di-muon production data and with the nucleon sea. But the pion effects are large enough to predict substantial nuclear enhancement of the cross section for longitudinally polarized virtual photons for the kinematics accessible at Jefferson Laboratory.Comment: 9 pages, 4 figure

International Coercion, Emulation and Policy Diffusion: Market-Oriented Infrastructure Reforms, 1977-1999

Why do some countries adopt market-oriented reforms such as deregulation, privatization and liberalization of competition in their infrastructure industries while others do not? Why did the pace of adoption accelerate in the 1990s? Building on neo-institutional theory in sociology, we argue that the domestic adoption of market-oriented reforms is strongly influenced by international pressures of coercion and emulation. We find robust support for these arguments with an event-history analysis of the determinants of reform in the telecommunications and electricity sectors of as many as 205 countries and territories between 1977 and 1999. Our results also suggest that the coercive effect of multilateral lending from the IMF, the World Bank or Regional Development Banks is increasing over time, a finding that is consistent with anecdotal evidence that multilateral organizations have broadened the scope of the “conditionality” terms specifying market-oriented reforms imposed on borrowing countries. We discuss the possibility that, by pressuring countries into policy reform, cross-national coercion and emulation may not produce ideal outcomes.http://deepblue.lib.umich.edu/bitstream/2027.42/40099/3/wp713.pd

Regional deformation and offshore crustal local faulting as combined processes to explain uplift through time constrained by investigating differentially-uplifted Late Quaternary palaeoshorelines: the foreland Hyblean Plateau, SE Sicily

Quaternary uplift is well documented in SE Sicily, a region prone to damaging seismic events, such as the 1693 “Val di Noto” Earthquake (Mw 7.4), the largest seismic event reported within the Italian Earthquake Catalogue, whose seismogenic source is still debated and, consequently, the long-term seismic hazard is poorly-understood. However, the spatial variation in the timing and rates of uplift are still debated, so it is difficult to link the dominant tectonic process(es) responsible for the uplift and the location of seismogenic sources. To better constrain the uplift rate, we have refined the dating of Late Quaternary marine terraces, using a synchronous correlation approach, driven by both published and newly obtained numerical age controls (234U/230Th dating on corals). This has allowed re-calculation of uplift rates along a N-S oriented transect within the Hyblean Plateau (HP) foreland region. Consequently, we have mapped the geometry of palaeoshorelines along a coastline-parallel transect, and hence the rates of uplift. The results suggest increasing uplift rate from south to north across the HP, and that uplift rates have remained constant through the late Quaternary. This spatially-changing but temporally constant uplift places constraints on the proportion of uplift produced by regional geodynamic processes versus produced by local faults, such as an offshore E-dipping active normal fault. We discuss these new findings in terms of the long-term seismic hazard for one of the most seismically-active regions in the Mediterranean Basin