Dynamics of DNA Supercoils

Science ◽  
2012 ◽  
Vol 338 (6103) ◽  
pp. 94-97 ◽  
Author(s):  
M. T. J. van Loenhout ◽  
M. V. de Grunt ◽  
C. Dekker
Keyword(s):  
Ionic Strength ◽  
Long Range ◽  
Time Scale ◽  
Double Helix ◽  
Long Distance ◽  
Cellular Processes ◽  
Millisecond Time Scale ◽  
In Cells

DNA in cells exhibits a supercoiled state in which the double helix is additionally twisted to form extended intertwined loops called plectonemes. Although supercoiling is vital to many cellular processes, its dynamics remain elusive. In this work, we directly visualize the dynamics of individual plectonemes. We observe that multiple plectonemes can be present and that their number depends on applied stretching force and ionic strength. Plectonemes moved along DNA by diffusion or, unexpectedly, by a fast hopping process that facilitated very rapid (<20 milliseconds) long-range plectoneme displacement by nucleating a new plectoneme at a distant position. These observations directly reveal the dynamics of plectonemes and identify a mode of movement that allows long-distance reorganization of the conformation of the genome on a millisecond time scale.

scholarly journals A Long-Distance Communication Architecture for Medical Devices Based on LoRaWAN Protocol

Electronics ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 940
Author(s):  
Nicoleta Cristina Gaitan
Keyword(s):  
Energy Consumption ◽  
Long Range ◽  
Medical Devices ◽  
Low Energy ◽  
Area Network ◽  
Wide Area Network ◽  
Long Distance ◽  
Communication Architecture ◽  
Low Energy Consumption ◽  
Distance Communication

Recent market studies show that the market for remote monitoring devices of different medical parameters will grow exponentially. Globally, more than 4 million individuals will be monitored remotely from the perspective of different health parameters by 2023. Of particular importance is the way of remote transmission of the information acquired from the medical sensors. At this time, there are several methods such as Bluetooth, WI-FI, or other wireless communication interfaces. Recently, the communication based on LoRa (Long Range) technology has had an explosive development that allows the transmission of information over long distances with low energy consumption. The implementation of the IoT (Internet of Things) applications using LoRa devices based on open Long Range Wide-Area Network (LoRaWAN) protocol for long distances with low energy consumption can also be used in the medical field. Therefore, in this paper, we proposed and developed a long-distance communication architecture for medical devices based on the LoRaWAN protocol that allows data communications over a distance of more than 10 km.

scholarly journals Intracellular Ionic Strength Sensing Using NanoLuc

2021 ◽  
Vol 22 (2) ◽  
pp. 677
Author(s):  
Tausif Altamash ◽  
Wesam Ahmed ◽  
Saad Rasool ◽  
Kabir H. Biswas
Keyword(s):  
Thermal Stability ◽  
Phase Separation ◽  
Drug Discovery ◽  
Ionic Strength ◽  
Cellular Signaling ◽  
Live Cells ◽  
Protein Activity ◽  
Cellular Survival ◽  
Cellular Processes ◽  
Wide Range

Intracellular ionic strength regulates myriad cellular processes that are fundamental to cellular survival and proliferation, including protein activity, aggregation, phase separation, and cell volume. It could be altered by changes in the activity of cellular signaling pathways, such as those that impact the activity of membrane-localized ion channels or by alterations in the microenvironmental osmolarity. Therefore, there is a demand for the development of sensitive tools for real-time monitoring of intracellular ionic strength. Here, we developed a bioluminescence-based intracellular ionic strength sensing strategy using the Nano Luciferase (NanoLuc) protein that has gained tremendous utility due to its high, long-lived bioluminescence output and thermal stability. Biochemical experiments using a recombinantly purified protein showed that NanoLuc bioluminescence is dependent on the ionic strength of the reaction buffer for a wide range of ionic strength conditions. Importantly, the decrease in the NanoLuc activity observed at higher ionic strengths could be reversed by decreasing the ionic strength of the reaction, thus making it suitable for sensing intracellular ionic strength alterations. Finally, we used an mNeonGreen–NanoLuc fusion protein to successfully monitor ionic strength alterations in a ratiometric manner through independent fluorescence and bioluminescence measurements in cell lysates and live cells. We envisage that the biosensing strategy developed here for detecting alterations in intracellular ionic strength will be applicable in a wide range of experiments, including high throughput cellular signaling, ion channel functional genomics, and drug discovery.

Field Study of Low-Energy Long-Distance Wireless Communication for IoT Application in Remote Areas

Mekatronika ◽  
2020 ◽  
Vol 2 (1) ◽  
pp. 52-62
Author(s):  
Kwai Yang Sak ◽  
Ahmad Najmuddin Ibrahim
Keyword(s):  
Radio Frequency ◽  
Long Range ◽  
Essential Element ◽  
Low Energy ◽  
Line Of Sight ◽  
Area Network ◽  
Structural Elements ◽  
Wide Area Network ◽  
Residential Areas ◽  
Long Distance

Long Range (LoRa) is a wireless radio frequency technology under the Low Power Wide Area Network (LPWAN). LoRa is able to communicate long range and low energy consumption. The communication range has become an essential element in the wireless radio frequency technology in the Internet of Things (IoT). The presence of LoRa is able IoT application performs in long communication distances with high noise sensitivity ability. People can operate, monitor, and do a variety of tasks from a remote distance. Therefore, this research aims to evaluate the performance of the LoRa connection between radio transceivers in remote locations. The different environment and structural elements affect the LoRa performance. This thesis will be supported by the experiment that LoRa communication in different environments and tests. This experiment tests in line of sight (LOS) and non-line of sight (NLOS). Two sets of LoRa parameters, including Spreading Factor (SF), Bandwidth, and coding rate, are tested in different environments. The experiment tests the LoRa performance in various aspects: received signal strength indicator (RSSI) and packet received ratio (PPR) at different coverage ranges. In addition, the LoRa performance is evaluated in university, residential areas and vegetation areas under similar temperature, weather, and time. The LoRa coverage distance in the vegetation area and university area is reached 900 meters in the LOS test. Still, the vegetation area's signal is more stable and able to receive weaker RSSI signals. The LoRa coverage distance in the NLOS test is shorter compared to the LOS test. NLOS test has only one-third of the LOS LoRa communication distance. It is due to the signal penetration on structural elements such as buildings and woods cause the signal power loss and only transmitting a shorter distance. The LoRa parameter with SF9, 31.25kHz bandwidth and 4/8 coding rate has a better coverage range and stable connection.

Sensing oxygen at the millisecond time-scale using an ultra-microelectrode array (UMEA)

2017 ◽  
Vol 238 ◽  
pp. 1008-1016 ◽  
Author(s):  
Fleur van Rossem ◽  
Johan G. Bomer ◽  
Hans L. de Boer ◽  
Yawar Abbas ◽  
Eddy de Weerd ◽  
...  
Keyword(s):  
Time Scale ◽  
Microelectrode Array ◽  
Millisecond Time Scale

scholarly journals Media-Media Pembelajaran Efektif dalam Membantu Pembelajaran Matematika Jarak Jauh

2021 ◽  
Vol 2 (2) ◽  
pp. 59-69
Author(s):  
Dewasni Hasiru ◽  
Syamsu Qamar Badu ◽  
Hamzah B. Uno
Keyword(s):  
Long Range ◽  
Qualitative Approach ◽  
Learning System ◽  
Sources Of Information ◽  
Long Distance ◽  
Library Research ◽  
Effective Media ◽  
The Media ◽  
Study Type ◽  
System 1

The study is done with the goal of providing a glimpse of what media is effectively used in assisting remote math. The method used in the study is a qualitative approach with a library study type (library research). Retrieval with a documentary technique that is, locate appropriate literature sources through books, research journals and other sources of information relating to effective long-range learning media in mathematics. To see the effectiveness of media using media indicators in the long-range learning system: (1) create motivation, (2) increase learning yields, (3) make learners remember old knowledge, (4) learners capable of applying the knowledge learned. Research shows the media that can be used in long-distance math study is google classroom, learning video, Whatsapp, and zoom. However, effective media used in long-distance math study is google classroom and learning videos, Whatsapp and zoom is still less effective in the long-distance mathematical learning process

scholarly journals FcαRI binding at the IgA1 CH2–CH3 interface induces long-range conformational changes that are transmitted to the hinge region

2018 ◽  
Vol 115 (38) ◽  
pp. E8882-E8891 ◽  
Author(s):  
Monica T. Posgai ◽  
Sam Tonddast-Navaei ◽  
Manori Jayasinghe ◽  
George M. Ibrahim ◽  
George Stan ◽  
...  
Keyword(s):  
Binding Site ◽  
Long Range ◽  
Conformational Changes ◽  
Lectin Binding ◽  
Coarse Grained ◽  
Alanine Scanning Mutagenesis ◽  
Long Distance ◽  
Receptor Binding Site ◽  
Binding Interface ◽  
Functional Dynamics

IgA effector functions include proinflammatory immune responses triggered upon clustering of the IgA-specific receptor, FcαRI, by IgA immune complexes. FcαRI binds to the IgA1–Fc domain (Fcα) at the CH2–CH3 junction and, except for CH2 L257 and L258, all side-chain contacts are contributed by the CH3 domain. In this study, we used experimental and computational approaches to elucidate energetic and conformational aspects of FcαRI binding to IgA. The energetic contribution of each IgA residue in the binding interface was assessed by alanine-scanning mutagenesis and equilibrium surface plasmon resonance (SPR). As expected, hydrophobic residues central to the binding site have strong energetic contributions to the FcαRI:Fcα interaction. Surprisingly, individual mutation of CH2 residues L257 and L258, found at the periphery of the FcαRI binding site, dramatically reduced binding affinity. Comparison of antibody:receptor complexes involving IgA or its precursor IgY revealed a conserved receptor binding site at the CH2–CH3 junction (or its equivalent). Given the importance of residues near the CH2–CH3 junction, we used coarse-grained Langevin dynamics simulations to understand the functional dynamics in Fcα. Our simulations indicate that FcαRI binding, either in an asymmetric (1:1) or symmetric (2:1) complex with Fcα, propagated long-range conformational changes across the Fc domains, potentially impacting the hinge and Fab regions. Subsequent SPR experiments confirmed that FcαRI binding to the Fcα CH2–CH3 junction altered the kinetics of HAA lectin binding at the IgA1 hinge. Receptor-induced long-distance conformational transitions have important implications for the interaction of aberrantly glycosylated IgA1 with anti-glycan autoantibodies in IgA nephropathy.

scholarly journals Correlation Dynamics of Dipolar Bosons in 1D Triple Well Optical Lattice

Symmetry ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 909
Author(s):  
Sangita Bera ◽  
Luca Salasnich ◽  
Barnali Chakrabarti
Keyword(s):  
Time Evolution ◽  
Long Range ◽  
Contact Interaction ◽  
Time Scale ◽  
Optical Lattice ◽  
Sudden Change ◽  
Dipolar Interaction ◽  
Einstein Condensation ◽  
Range Interaction ◽  
Definite Time

The concept of spontaneous symmetry breaking and off-diagonal long-range order (ODLRO) are associated with Bose–Einstein condensation. However, as in the system of reduced dimension the effect of quantum fluctuation is dominating, the concept of ODLRO becomes more interesting, especially for the long-range interaction. In the present manuscript, we study the correlation dynamics triggered by lattice depth quench in a system of three dipolar bosons in a 1D triple-well optical lattice from the first principle using the multiconfigurational time-dependent Hartree method for bosons (MCTDHB). Our main motivation is to explore how ODLRO develops and decays with time when the system is brought out-of-equilibrium by a sudden change in the lattice depth. We compare results of dipolar bosons with contact interaction. For forward quench ( V f > V i ) , the system exhibits the collapse–revival dynamics in the time evolution of normalized first- and second-order Glauber’s correlation function, time evolution of Shannon information entropy both for the contact as well as for the dipolar interaction which is reminiscent of the one observed in Greiner’s experiment [Nature, 415 (2002)]. We define the collapse and revival time ratio as the figure of merit ( τ ) which can uniquely distinguish the timescale of dynamics for dipolar interaction from that of contact interaction. In the reverse quench process ( V i > V f ) , for dipolar interaction, the dynamics is complex and the system does not exhibit any definite time scale of evolution, whereas the system with contact interaction exhibits collapse–revival dynamics with a definite time-scale. The long-range repulsive tail in the dipolar interaction inhibits the spreading of correlation across the lattice sites.

scholarly journals Cetacean movements in coastal waters of the southwestern Atlantic ocean

2019 ◽  
Vol 19 (2) ◽  
Author(s):  
Marcos C. de O. Santos ◽  
José Laílson-Brito ◽  
Leonardo Flach ◽  
Júlia E. F. Oshima ◽  
Giovanna C. Figueiredo ◽  
...  
Keyword(s):  
Atlantic Ocean ◽  
Long Range ◽  
Coastal Waters ◽  
Individual Identification ◽  
Southwestern Atlantic ◽  
Long Distance ◽  
Cetacean Species ◽  
Photo Identification ◽  
Southwestern Atlantic Ocean ◽  
Janeiro State

Abstract: Cetaceans were monitored along ca. 700 km of the southeast coast of Brazil (22°S to 25°S) from 1995 to 2014 using photo-identification. The objective of this study was to identify any presence of long-distance movements for monitored cetacean species and discuss implications. Data on long-range movements of four of the monitored species are presented after the analysis of 321,765 photographs taken for individual identification. Seven individuals from four populations of Guiana dolphins (Sotalia guianensis) considered resident to particular estuaries or bays were reported in dispersal involving movement between pairs of protected areas over long-range distances varying between 86 and 135 km. Three cataloged rough-toothed dolphins (Steno bredanensis), first seen in Guanabara Bay, Rio de Janeiro state (22°46'S) in November 2011, were sighted 240 km southwards as members of the same group in coastal waters of São Paulo state (23°46'S) in July 2014. Water depth for those sightings ranged from 16 to 52.7 m; local sightings of rough-toothed dolphins in Brazil have frequently been in shallow waters, but the species global distribution is usually associated with deeper waters. In a 27-day interval in the spring of 2012, a group of 16 orcas (Orcinus orca) travelled ca. 277 km in shallow coastal waters ranging from 20 to 30 m deep. Orcas are commonly observed between November and February in southeast Brazil, probably in search for prey. In summer months between 2012 and 2014, three Bryde's whales (Balaenoptera edeni) sighted in waters ranging from 14 to 49 m deep, moved between 218 and 327 km. Bryde's whales are usually found in local coastal waters where they spend summer months feeding on sardines. To date, these are the longest estimated movements reported to S. guianensis, S. bredanensis, O. orca and B. edeni in the Southwestern Atlantic Ocean.

scholarly journals Substitutions at Nonconserved Rheostat Positions Modulate Function by Rewiring Long-Range, Dynamic Interactions

2020 ◽  
Vol 38 (1) ◽  
pp. 201-214 ◽  
Author(s):  
Paul Campitelli ◽  
Liskin Swint-Kruse ◽  
S Banu Ozkan
Keyword(s):  
Dna Binding ◽  
Long Range ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Dynamic Coupling ◽  
Long Distance ◽  
Repressor Protein ◽  
Functional Changes ◽  
Lactose Repressor ◽  
Wide Range

Abstract Amino acid substitutions at nonconserved protein positions can have noncanonical and “long-distance” outcomes on protein function. Such outcomes might arise from changes in the internal protein communication network, which is often accompanied by changes in structural flexibility. To test this, we calculated flexibilities and dynamic coupling for positions in the linker region of the lactose repressor protein. This region contains nonconserved positions for which substitutions alter DNA-binding affinity. We first chose to study 11 substitutions at position 52. In computations, substitutions showed long-range effects on flexibilities of DNA-binding positions, and the degree of flexibility change correlated with experimentally measured changes in DNA binding. Substitutions also altered dynamic coupling to DNA-binding positions in a manner that captured other experimentally determined functional changes. Next, we broadened calculations to consider the dynamic coupling between 17 linker positions and the DNA-binding domain. Experimentally, these linker positions exhibited a wide range of substitution outcomes: Four conserved positions tolerated hardly any substitutions (“toggle”), ten nonconserved positions showed progressive changes from a range of substitutions (“rheostat”), and three nonconserved positions tolerated almost all substitutions (“neutral”). In computations with wild-type lactose repressor protein, the dynamic couplings between the DNA-binding domain and these linker positions showed varied degrees of asymmetry that correlated with the observed toggle/rheostat/neutral substitution outcomes. Thus, we propose that long-range and noncanonical substitutions outcomes at nonconserved positions arise from rewiring long-range communication among functionally important positions. Such calculations might enable predictions for substitution outcomes at a range of nonconserved positions.

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