On the use of sensitivity tests in seismic tomography

ACKNOWLEDGEMENTS This work was partly supported by ARC Discovery Project DP120103673 and by the Research Council of Norway through its Centres of Excellence funding scheme, project number 223272. We thank Maximilliano Bezada and an anonymous referee for constructive comments which improved the original version of the manuscript. We also thank the Editor, A. Morelli, for providing additional helpful comments.Peer reviewedPublisher PD

Generating Negatively Supercoiled DNA Using Dual-Trap Optical Tweezers

Many genomic processes lead to the formation of underwound (negatively supercoiled) or overwound (positively supercoiled) DNA. These DNA topological changes regulate the interactions of DNA-binding proteins, including transcription factors, architectural proteins and topoisomerases. In order to advance our understanding of the structure and interactions of supercoiled DNA, we recently developed a single-molecule approach called Optical DNA Supercoiling (ODS). This method enables rapid generation of negatively supercoiled DNA (with between <5% and 70% lower helical twist than nonsupercoiled DNA) using a standard dual-trap optical tweezers instrument. ODS is advantageous as it allows for combined force spectroscopy, fluorescence imaging, and spatial control of the supercoiled substrate, which is difficult to achieve with most other approaches. Here, we describe how to generate negatively supercoiled DNA using dual-trap optical tweezers. To this end, we provide detailed instructions on the design and preparation of suitable DNA substrates, as well as a step-by-step guide for how to control and calibrate the supercoiling density produced

Конкурентоспроможність машинобудівних підприємств на ринку залізничного рухомого складу

Охарактеризовано распределение производственных мощностей и потребителей вагоно-строительной продукции на экономических рынках СНГ. Дана оценка конкурентной среды в подотрасли машиностроения железнодорожного подвижного состава на макро и микроуровне, выявлены факторы риска и обоснованы мероприятия, ориентированные на укрепление конкурентоспособности исследуемых предприятий. Ключевые слова: машиностроительное предприятие, конкурентоспособность, рынок, железнодорожный подвижной состав.Охарактеризовано розподіл виробничих потужностей і споживачів вагонобудівної продукції на економічних ринках СНД. Наведено оцінку конкурентного середовища в підгалузі маши-нобудування залізничного рухомого складу на макро і мікрорівні, виявлено фактори ризику й обґрунтовано заходи, орієнтовані на зміцнення конкурентоспроможності досліджуваних підприємств. Ключові слова: машинобудівне підприємство, конкурентоспроможність, ринок, залізничний рухомий склад.The paper characterizes production capacities and consumers of wagon products on the economic markets of CIS countries. The competition environment in the sector of railway rolling stock building on macro and micro-level was assessed, the factors of risk were identified, and measures oriented to streng-thening the competitiveness of the enterprises under investigation are well-grounded. Keywords: machine-building enterprise, competitiveness, market, railway rolling stock

Constructing arrays of nucleosome positioning sequences using Gibson Assembly for single-molecule studies

As the basic building blocks of chromatin, nucleosomes play a key role in dictating the accessibility of the eukaryotic genome. Consequently, nucleosomes are involved in essential genomic transactions such as DNA transcription, replication and repair. In order to unravel the mechanisms by which nucleosomes can influence, or be altered by, DNA-binding proteins, single-molecule techniques are increasingly employed. To this end, DNA molecules containing a defined series of nucleosome positioning sequences are often used to reconstitute arrays of nucleosomes in vitro. Here, we describe a novel method to prepare DNA molecules containing defined arrays of the ‘601’ nucleosome positioning sequence by exploiting Gibson Assembly cloning. The approaches presented here provide a more accessible and efficient means to generate arrays of nucleosome positioning motifs, and facilitate a high degree of control over the linker sequences between these motifs. Nucleosomes reconstituted on such arrays are ideal for interrogation with single-molecule techniques. To demonstrate this, we use dual-trap optical tweezers, in combination with fluorescence microscopy, to monitor nucleosome unwrapping and histone localisation as a function of tension. We reveal that, although nucleosomes unwrap at ~20 pN, histones (at least histone H3) remain bound to the DNA, even at tensions beyond 60 pN

Основні напрямки маркетингу і менеджменту в архівній справі

Gondwana breakup since the Jurassic and the northward motion of India toward Eurasia were associated with formation of ocean basins and ophiolite obduction between and onto the Indian and Arabian margins. Here we reconcile marine geophysical data from preserved oceanic basins with the age and location of ophiolites in NW India and SE Arabia and seismic tomography of the mantle below the NW Indian Ocean. The North Somali and proto-Owen basins formed due to 160-133-Ma N-S extension between India and Somalia. Subsequent convergence destroyed part of this crust, simultaneous with the uplift of the Masirah ophiolites. Most of the preserved crust in the Owen Basin may have formed between 84 and 74-Ma, whereas the Mascarene and the Amirante basins accommodated motion between India and Madagascar/East Africa between 85 and circa 60-Ma and 75 and circa 66-Ma, respectively. Between circa 84 and 45-Ma, oblique Arabia-India convergence culminated in ophiolite obduction onto SE Arabia and NW India and formed the Carlsberg slab in the lower mantle below the NW Indian Ocean. The NNE-SSW oriented slab may explain the anomalous bathymetry in the NW Indian Ocean and may be considered a paleolongitudinal constraint for absolute plate motion. NW India-Asia collision occurred at circa 20-Ma deforming the Sulaiman ranges or at 30-Ma if the Hindu Kush slab north of the Afghan block reflects intra-Asian subduction. Our study highlights that the NW India ophiolites have no relationship with India-Asia motion or collision but result from relative India-Africa/Arabia motions instead. Key Points We present a new tectonic model for the evolution of NW Indian Ocean Subducted slab under the Carlsberg Ridge resulted from Arabia-India convergenc

Neogene evolution of the Aegean arc: paleomagnetic and geodetic evidence for a rapid and young rotation phase

New paleomagnetic data of the entire Aegean outer-arc are presented. The results indicate a young Pleistocene and rapid clockwise rotation phase in the western Aegean arc, covering at least Zakynthos and the Peloponessos. The eastern Aegean arc, incorporating Kassos, Karpathos and Rhodos, also experienced Pleistocene anticlockwise rotations. The anisotropies of the magnetic susceptibility (AMS) data are in agreement with arc-parallel extension in the south and south-eastern Aegean arc and arc-normal compression in the north-west, in agreement with structural and geodetic observations. We compare the paleomagnetic results with the present-day pattern of rotation as computed from geodetic data, and we find good agreement. The onset of the Pleistocene rotations coincides with the beginning of uplift and a change in the stress pattern of extension. We compare our findings with existing models for the Aegean area

Travel-time tomography of the European-Mediterranean mantle down to 1400 km

The 3-D P-wave velocity structure of the mantle below Europe, the Mediterranean region and a part of Asia Minor is investigated. This study is a considerable extension of an earlier tomographic experiment that was limited to imaging upper-mantle structure only. Here, the Earth’s volume under study encompasses the mantle to a depth of 1400 km, and we increase the number of International Seismological Centre (ISC) data for inversion by a factor of four by taking more years of observation, and by including data from teleseismic events. The most important departure from the earlier study is that we do not use the Jeffreys—Bullen model as a reference model, but an improved radially symmetricvelocity model, the PM2 model, which is appropriate for the European—Mediterranean mantle. Our inversion procedure consists of two steps. First, the radial model PM2 is determined from the ISC delay times by a nonlinear trial-and-error inversion of the data. As opposed to the Jeffreys—Bullen model, the new reference model has a high-velocity lithosphere, a low-velocity zone, and seismic discontinuities at depths of 400 and 670 km. Next, the ISC data are corrected for effects related to the change in reference model and inverted for 3-D heterogeneity relative to the PM2 model. We follow this two-step approach to attain a better linearizable tomographic problem in which ray paths computed in the PM2 model provide a better approximation of the actual ray paths than those computed from the Jeffreys—Bullen model. Hence, the two-step scheme leads to a more credible application of Fermat’s Principle in linearizing the tomographic equations. Inversion results for the 3-D heterogeneity are computed for both the uncorrected ISC data and for the PM2 data. The data fit obtained in the two-step approach is slightly better than in the inversion of ISC data (using the Jeffreys—Bullen reference model). A comparison of the tomographic results demonstrates that the PM2 data inversion is to be preferred. To assess the spatial resolution an analysis is given of hit count patterns (sampling of the mantle by ray paths) and results of sensitivity tests with 3-D synthetic velocity models. The spatial resolution obtained varies with position in the mantle and is studied both in map view and in cross-section. In the well-sampled regions of the mantle the spatial resolution for larger-scale structure can (qualitatively) be denoted as reasonable to good, and at least sufficient to allow interpretation of larger-scale anomalies. A comparison is made of the results of this study with independent models of S-velocity heterogeneity obtained in a number of investigations, and with a prediction of the seismic velocity structure of the mantle computed from tectonic reconstructions of the Mediterranean region. In the context of this comparison, interpretations of large-scale positive anomalies found in the Mediterranean upper mantle in terms of subducted lithosphere are given. Specifically addressed are subduction below southern Spain, below the Western Mediterranean and Italy, and below the Aegean. In the last region a slab anomaly is mapped down to depths of 80

A new absolute arrival time data set for Europe

The main aim of this study is to create a data set of accurate absolute arrival times for stations in Europe which do not report to the International Seismological Centre (ISC). Waveforms were obtained from data centres and temporary experiments and a semi-automatic picking method was applied to determine absolute arrival times for P and S phases. 85 000 arrival times were picked whose distribution of residuals shows generally low standard deviations on the order of 0.5-0.7 s. Furthermore, mean teleseismic station residuals reflect the properties of the underlying crust and uppermost mantle. Comparison to ISC data for matching event-station-phase combinations also confirms the good quality of the new absolute arrival time picks. Most importantly, this data set complements the ISC data as it fills regional data coverage gaps in Europ

A map-view restoration of the Alpine-Carpathian-Dinaridic system for the Early Miocene

A map-view palinspastic restoration of tectonic units in the Alps, Carpathians and Dinarides reveals the plate tectonic configuration before the onset of Miocene to recent deformations. Estimates of shortening and extension from the entire orogenic system allow for a semi-quantitative restoration of translations and rotations of tectonic units during the last 20Ma. Our restoration yielded the following results: (1) The Balaton Fault and its eastern extension along the northern margin of the Mid-Hungarian Fault Zone align with the Periadriatic Fault, a geometry that allows for the eastward lateral extrusion of the Alpine-Carpathian-Pannonian (ALCAPA) Mega-Unit. The Mid-Hungarian Fault Zone accommodated simultaneous strike-perpendicular shortening and strike-slip movements, concomitant with strike-parallel extension. (2) The Mid-Hungarian Fault Zone is also the locus of a former plate boundary transforming opposed subduction polarities between Alps (including Western Carpathians) and Dinarides. (3) The ALCAPA Mega-Unit was affected by 290km extension and fits into an area W of present-day Budapest in its restored position, while the Tisza-Dacia Mega-Unit was affected by up to 180km extension during its emplacement into the Carpathian embayment. (4) The external Dinarides experienced Neogene shortening of over 200km in the south, contemporaneous with dextral wrench movements in the internal Dinarides and the easterly adjacent Carpatho-Balkan orogen. (5) N-S convergence between the European and Adriatic plates amounts to some 200km at a longitude of 14° E, in line with post-20Ma subduction of Adriatic lithosphere underneath the Eastern Alps, corroborating the discussion of results based on high-resolution teleseismic tomography. The displacement of the Adriatic Plate indenter led to a change in subduction polarity along a transect through the easternmost Alps and to substantial Neogene shortening in the eastern Southern Alps and external Dinarides. While we confirm that slab-pull and rollback of oceanic lithosphere subducted beneath the Carpathians triggered back-arc extension in the Pannonian Basin and much of the concomitant folding and thrusting in the Carpathians, we propose that the rotational displacement of this indenter provided a second important driving force for the severe Neogene modifications of the Alpine-Carpathian-Dinaridic orogenic syste

Unravelling the mechanisms of Type 1A topoisomerases using single-molecule approaches

Topoisomerases are essential enzymes that regulate DNA topology. Type 1A family topoisomerases are found in nearly all living organisms and are unique in that they require single-stranded (ss)DNA for activity. These enzymes are vital for maintaining supercoiling homeostasis and resolving DNA entanglements generated during DNA replication and repair. While the catalytic cycle of Type 1A topoisomerases has been long-known to involve an enzyme-bridged ssDNA gate that allows strand passage, a deeper mechanistic understanding of these enzymes has only recently begun to emerge. This knowledge has been greatly enhanced through the combination of biochemical studies and increasingly sophisticated single-molecule assays based on magnetic tweezers, optical tweezers, atomic force microscopy and Förster resonance energy transfer. In this review, we discuss how single-molecule assays have advanced our understanding of the gate opening dynamics and strand-passage mechanisms of Type 1A topoisomerases, as well as the interplay of Type 1A topoisomerases with partner proteins, such as RecQ-family helicases. We also highlight how these assays have shed new light on the likely functional roles of Type 1A topoisomerases in vivo and discuss recent developments in single-molecule technologies that could be applied to further enhance our understanding of these essential enzymes