OriCiro® Cell-Free Cloning System/PASS V4.1.2 v1

OriCiro® Cell-Free Cloning System is a rapid and powerful tool replacing cumbersome DNA cloning (plasmid construction) process relying on E. coli. The system consists of two kits. OriCiro Assembly Kit allows seamless assembly of multiple overlapping DNA fragments. The assembly product can be added directly to OriCiro Amp Kit to get selective amplification of your target circular DNA (Figure 1). The amplified product is supercoiled DNA topologically identical to plasmid DNA isolated from E. coli. 1. OriCiro Assembly Kit: Multiple DNA fragments are assembled seamlessly at 42 ̊C for 30 minutes via ~40 bp overlapping ends (Figure 2). DNA fragments generated by PCR or restriction enzyme digestion are available. Our unique enzyme-based annealing mechanism allows powerful assembly up to 50 fragments simultaneously. 2. OriCiro Amp Kit: The reaction consists of 26 purified enzymes involved in chromosome replication of E. coli. The chromosome replication cycle repeats autonomously at around 30 ̊C, enabling exponential amplification of circular DNA having oriC with extremely high fidelity (10-8 error/base/cycle) (Figure 3). The kit yields up to 1 μg circular DNA per 10 μL reaction at 33 ̊C for 6 hr. The maximum amplification size is 50 kb in the current version of the kit. n.b. OriCiro Amp NEEDS oriC Cassette (0.4 kb) which can be inserted into circular DNA using OriCiro assembly kit. References: 1. T. Mukai, T. Yoneji, K. Yamada, H. Fujita, S. Nara, M. Su'etsugu, Overcoming the Challenges of Megabase-Sized Plasmid Construction in Escherichia coli, ACS Synthetic Biology, 2020, 9 (6), 1315- 1327 2. T. Hasebe, K. Narita, S. Hidaka, M. Su'etsugu, Efficient Arrangement of the Replication Fork Trap for In Vitro Propagation of Monomeric Circular DNA in the Chromosome-Replication Cycle Reaction. Life, 2018, 8 (43) 3. M. Su’etsugu, H. Takada, T. Katayama, H. Tsujimoto, Exponential propagation of large circular DNA by reconstitution of a chromosome-replication cycle, Nucleic Acids Research, 2017, 45 (20), 11525– 11534

Seismic Vulnerability Index Calculation for Mitigation Purposes at Cilacap District

Seismic vulnerability index is one of the key factors in mitigation that shows the vulnerability of the soil layer beneath when passed through with a wave, the more vulnerable the soil layer, the more damage it done when an earthquake happens. Seismic vulnerability is calculated using two variables, that is dominant frequencies and amplification that are obtained by analyzing HVSR curve. HVSR are used to determine the dominant frequency by determining the maximum amplification in that area. HVSR curve is obtained by measuring microbemor data in 163 spots with 30 minutes-minimum duration in Cilacap with a portable seismograph. Mierotremor is a natural vibration that is caused by continuous vibration that come from beneath the surface, sometimes mixed up by the vibrabon that is caused by human activities such as pipe-flow, vehicles, etc. Thus, the purposes of this research are to determine which area is more vulnerable than others, based on the seismic vulnerability index, so it could be a reference for regional development to classified is it safe or unsafe to build in that area, remembering Cilacap is one of the most developed Districts in Central Java.

A Study on the Influence of Different Constraint Modes and Number of Disc Springs on the Dynamics of Disc Spring System

In this work, the influences of constraint modes and the number of disc springs on the dynamic characteristics of the disc spring system are studied by simulation and experiment. The amplitudes and amplification factors of the disc spring system under different constraint modes and different numbers of disc springs are obtained. The results show that the maximum amplitude and amplification factor both appear at the constraint modes of locking and no preloading, which indicates that the locking and no preloading is the best constraint mode among the four different constraint modes. Moreover, the amplitude of the disc spring system first increases and then decreases with the number of disc springs increasing, while the amplification factor increases with the number of disc springs increasing. The maximum amplification factor (10.21 in experiment) of the disc spring system appears at 10 disc springs. By studying the relationship between the number of disc springs and amplification factor and damping, we find that the damping of the disc spring system can be reduced by increasing the disc spring numbers, and thus, the corresponding amplification factor can be improved. Furthermore, as the number of disc spring increases, the height differences of disc springs before and after locking are all close to 3 mm, which indicates that the amount of locking compression in the assembly process has a good consistency when the number of disc springs changes. The aforementioned works can provide guidance for the industrial production in screen vibration.

Tidal-charge effects on the superradiance of rotating black holes

The changes a (negative) tidal charge causes at the phenomenon of superradiance which occurs around rotating black holes are investigated. This is made by computing the amplification factors of massless scalar waves being scattered by the black hole. It is shown that the increase of the tidal-charge intensity leads to a considerable enhancement of energy extraction from near-extreme black holes. Such improvement results from the fact that extreme black holes with more negative tidal charges spin faster. Maximum amplification decreases with the increase of the tidal charge intensity if the angular momentum of the black hole per unit mass is fixed. The tidal charge may also change crucially the superradiance phenomenon of massless scalar waves causing maximum amplification to occur for $$m > 1$$ m > 1 differently from the case of Kerr black holes.

A Numerical Study on the Seismic Site Response of Rocky Valleys with Irregular Topographic Conditions

This paper investigates topographic effects of rocky valleys with irregular topographic conditions subjected to vertically propagating SV waves of Ricker type using a boundary element code. Valleys with two intersecting slopes, [Formula: see text] and [Formula: see text], are modelled in order to study their combined effects on ground motion. Presented in the form of pseudo-acceleration response spectra, results of this work can be extended to similar topographies. The main findings are: (i) [Formula: see text] (the first slope angle) and [Formula: see text] (L is the half width of the valley and [Formula: see text] is its corresponding height) have amplifying effects, and [Formula: see text] (the second slope angle) has de-amplifying effects on the site response. (ii) [Formula: see text] has a straight effect on intensifying the effects of both [Formula: see text] and [Formula: see text]. (iii) The combined effects of slope angles have been found to be important in modifying the response so more than a single slope should be considered for seismic analysis. (iv) Engineers should use the maximum amplification of 2.4 in case of valleys with the first and second slope angles below [Formula: see text].

Recent Strengthening of Greenland Blocking Drives Summertime Surface Warming over Northern Canada and Eastern Siberia

In the last three decades, rapid surface warming is observed in the land areas of northern high latitudes during boreal summer months. Although the warming trend is thought to be driven by early snowmelt, the exact causes, especially its relationship with atmospheric circulation changes, remain a subject of debate. By analyzing ERA-Interim data, this study examines the possible factors for rapid subarctic warming. It is found that more than half of the warming trend over the entire subarctic and 80% over northern Canada and eastern Siberia (regions with maximum amplification) can be explained by enhanced downward infrared radiation (IR). Downward IR is largely driven by horizontal atmospheric moisture flux convergence and warm-air advection. The positive trend in geopotential height over the Greenland region is key for moisture flux convergence over northern Canada and eastern Siberia through changes in the storm tracks. An enhanced summertime blocking activity in the Greenland region seems responsible for the positive trend in geopotential heights.

PAIRWISE INTERACTIONS OF COHERENT STRUCTURES ON THE SURFACE OF DEEP WATER

The interactions of coherent structures (different types of solitary wave groups) on the surface of deep water is an important nonlinear wave process, which has been studied both theoretically and experimentally (Dyachenko et al., 2013a, b; Slunyaev et al., 2017). At the moment, a complete theoretical description of such interactions is known only for the simplest model – the nonlinear Schrödinger equation (NSE) where exact multi-soliton solutions are found. In the work (Kachulin, Gelash, 2018), the dynamics of pairwise interactions of coherent structures (breathers) on the surface of deep water were numerically investigated in the framework of the Dyachenko-Zakharov model. Significant differences were found in the collision dynamics of breathers of the compact Dyachenko-Zakharov equation when compared to the behavior of the NLSE solitons. It was found that in a more precise model of gravitational surface waves, in contrast to the NLSE, the maximum amplification of the wave field amplitude during the collision process of coherent structures can exceed the sum of the initial amplitudes of the breathers. In addition, the maximum amplification of the wave field amplitude increases with increasing steepness of the interacting breathers and exceeds unity by 20% at the value of the wave steepness m ≈ 0.2. It was revealed that an important parameter determining the dynamics of pairwise collisions of breathers is the relative phase of these objects at the moment of interaction. The interaction of breathers in the non-integrable Dyachenko-Zakharov model leads to the appearance of small radiation, which was discovered earlier in 2013 (Dyachenko et al., 2013a, b). In the work (Kachulin, Gelash, 2018) we demonstrate that the magnitude of the energy losses of the colliding solitons to radiation also depends on their relative phase. Maximum of the energy losses is observed at the same relative phase, at which the amplitude amplification maximum is observed. In addition, depending on the value of the relative phase, solitons can both gain and lose the energy, which results in increase or decrease of their amplitude after a collision. It was found that, in contrast to the NSE model, the spatial shifts of solitons in a more precise model can be both positive and negative. We use the exact breather solutions of the Dyachenko-Zakharov model and the canonical transformation to physical variables (the free surface profile and the potential on the liquid surface) to find approximate solutions in the form of breathers within the framework of exact nonlinear equations for potential incompressible fluid flows. The preliminary results of our numerical experiments in the exact model demonstrate similar dynamics of the interaction of breathers, which indicates that the theoretical picture of the interaction of coherent structures presented here is universal and can be observed in laboratory experiments. The study of the dynamics of breather interactions in the exact model performed by D.I. Kachulin was supported by the Russian Science Foundation (Grant No. 18-71-00079). The work of V.E. Zakharov and A.I. Dyachenko on the dynamics of breather interactions in approximate models was supported by the state assignment “Dynamics of the complex materials”.