scholarly journals Single-molecule sizing through nano-cavity confinement

2021 ◽  
Author(s):  
Raphael P.B. Jacquat ◽  
Georg Krainer ◽  
Quentin Peter ◽  
Ali Nawaz Babar ◽  
Oliver Vanderpoorten ◽  
...  
Keyword(s):  
Diffusion Coefficient ◽  
Confocal Microscopy ◽  
Residence Time ◽  
Single Molecule ◽  
Potential Application ◽  
Clinical Diagnostics ◽  
Theoretical Modelling ◽  
Residence Times ◽  
Nanoscale Particles ◽  
Dna Oligonucleotides

An approach relying on nano-cavity confinement is developed in this paper for the sizing of nanoscale particles and single biomolecules in solution. The approach, termed nano-cavity diffusional sizing (NDS), measures particle residence times within fluidic nano-cavities to determine their hydrodynamic radii. Using theoretical modelling and simulation, we show that the residence time of particles within nano-cavities above a critical timescale depends on the diffusion coefficient of the particle, which allows estimation of the particle's size. We demonstrate this approach experimentally through measurement of particle residence times within nano-fluidic cavities using single-molecule confocal microscopy. Our data show that the residence times scale linearly with the sizes of nanoscale colloids, protein aggregates and single DNA oligonucleotides. NDS thus constitutes a new single molecule optofluidic approach that allows rapid and quantitative sizing of nanoscale objects for potential application in nanobiotechnology, biophysics, and clinical diagnostics.

scholarly journals Treadmilling FtsZ polymers drive the directional movement of sPG-synthesis enzymes via a Brownian ratchet mechanism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joshua W. McCausland ◽  
Xinxing Yang ◽  
Georgia R. Squyres ◽  
Zhixin Lyu ◽  
Kevin E. Bruce ◽  
...  
Keyword(s):  
Cell Wall ◽  
Single Molecule ◽  
Theoretical Modelling ◽  
Binding Potential ◽  
Central Component ◽  
Macromolecular Complex ◽  
Bacterial Cells ◽  
Brownian Ratchet ◽  
Ratchet Mechanism ◽  
Directional Movement

AbstractThe FtsZ protein is a central component of the bacterial cell division machinery. It polymerizes at mid-cell and recruits more than 30 proteins to assemble into a macromolecular complex to direct cell wall constriction. FtsZ polymers exhibit treadmilling dynamics, driving the processive movement of enzymes that synthesize septal peptidoglycan (sPG). Here, we combine theoretical modelling with single-molecule imaging of live bacterial cells to show that FtsZ’s treadmilling drives the directional movement of sPG enzymes via a Brownian ratchet mechanism. The processivity of the directional movement depends on the binding potential between FtsZ and the sPG enzyme, and on a balance between the enzyme’s diffusion and FtsZ’s treadmilling speed. We propose that this interplay may provide a mechanism to control the spatiotemporal distribution of active sPG enzymes, explaining the distinct roles of FtsZ treadmilling in modulating cell wall constriction rate observed in different bacteria.

scholarly journals Effect of bathymetric changes on residence time in Buenaventura bay (Colombia)

DYNA ◽  
2019 ◽  
Vol 86 (211) ◽  
pp. 241-248
Author(s):  
Francisco Fernando Garcia Renteria ◽  
Mariela Patricia Gonzalez Chirino
Keyword(s):  
Finite Elements ◽  
Residence Time ◽  
Particle Tracking ◽  
Hydrodynamic Model ◽  
Residence Times ◽  
Particle Tracking Model ◽  
Tracking Model ◽  
Bathymetric Changes

In order to study the effects of dredging on the residence time of the water in Buenaventura Bay, a 2D finite elements hydrodynamic model was coupled with a particle tracking model. After calibrating and validating the hydrodynamic model, two scenarios that represented the bathymetric changes generated by the dredging process were simulated. The results of the comparison of the simulated scenarios, showed an important reduction in the velocities fields that allow an increase of the residence time up to 12 days in some areas of the bay. In the scenario without dredging, that is, with original bathymetry, residence times of up to 89 days were found.

scholarly journals Next-Generation Sequencing: From Basic Research to Diagnostics

2009 ◽  
Vol 55 (4) ◽  
pp. 641-658 ◽  
Author(s):  
Karl V Voelkerding ◽  
Shale A Dames ◽  
Jacob D Durtschi
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
Single Molecule ◽  
Basic Research ◽  
Clinical Diagnostics ◽  
Massively Parallel ◽  
Next Generation ◽  
New Paradigm ◽  
The Impact ◽  
Generation Sequencing

Abstract Background: For the past 30 years, the Sanger method has been the dominant approach and gold standard for DNA sequencing. The commercial launch of the first massively parallel pyrosequencing platform in 2005 ushered in the new era of high-throughput genomic analysis now referred to as next-generation sequencing (NGS). Content: This review describes fundamental principles of commercially available NGS platforms. Although the platforms differ in their engineering configurations and sequencing chemistries, they share a technical paradigm in that sequencing of spatially separated, clonally amplified DNA templates or single DNA molecules is performed in a flow cell in a massively parallel manner. Through iterative cycles of polymerase-mediated nucleotide extensions or, in one approach, through successive oligonucleotide ligations, sequence outputs in the range of hundreds of megabases to gigabases are now obtained routinely. Highlighted in this review are the impact of NGS on basic research, bioinformatics considerations, and translation of this technology into clinical diagnostics. Also presented is a view into future technologies, including real-time single-molecule DNA sequencing and nanopore-based sequencing. Summary: In the relatively short time frame since 2005, NGS has fundamentally altered genomics research and allowed investigators to conduct experiments that were previously not technically feasible or affordable. The various technologies that constitute this new paradigm continue to evolve, and further improvements in technology robustness and process streamlining will pave the path for translation into clinical diagnostics.

Flow pattern and residence time of conduit flow and diffuse flow in calcareous sandstones (Bohemian Cretaceous Basin, Czech Republic)

2021 ◽  
Author(s):  
Iva Kůrková ◽  
Jiří Bruthans
Keyword(s):  
Czech Republic ◽  
Groundwater Flow ◽  
Residence Time ◽  
Dispersion Model ◽  
Tracer Tests ◽  
Water Levels ◽  
Northwestern Part ◽  
Residence Times ◽  
Karst Springs ◽  
Bohemian Cretaceous Basin

<p>Localities containing karst features were studied in the northwestern part of Bohemian Cretaceous Basin. Namely Turnov area in facies transition between coarse-delta sandstones and marlstones (Jizera Formation, Turonian) and Miskovice area in limestones and sandy limestones - sandstones (Peruc-Korycany Formation, Cenomanian). Evolution of karst conduits is discussed elsewhere (Kůrková et al. 2019).</p><p>In both localities, disappearing streams, caves and karst springs with maximum discharge up to 100 L/s were documented. Geology and hydrogeology of this area was studied from many points of view to describe formation of karst conduits and characterize groundwater flow. Tracer tests were performed using NaCl and Na-fluoresceine between sinkholes and springs under various flow rates to evaluate residence times of water in conduits and to describe geometry of conduits. Breatkthrough curves of tracer tests were evaluated by means of Qtracer2 program (Field 2002). Groundwater flow velocity in channels starts at 0.6 km/day during low water levels up to 15 km/day during maximum water levels, the velocity increases logarithmically as a function of discharge. Similar karst conduits probably occur in other parts of Bohemian Cretaceous Basin where lot of large springs can be found.</p><p>Mean residence time of difussed flow based on tritium, CFC and SF<sub>6</sub> sampled at karst springs is 20 years for 75% of water and 100 years for remaining 25%, based on binary mixing dispersion model. This shows that most of the water drained by karst conduits is infiltrated through the soil and fractured environment with relatively high residence time. Residence times in different types of wells and springs were also measured in whole north-western part of Bohemian Cretaceous Basin. Results indicate long residence times in semi-stagnant zones represented by monitoring wells and short residence times in preferential zones represented by springs and water-supply wells.</p><p> </p><p>Research was funded by the Czech Science Foundation (GA CR No. 19-14082S), Czech Geological Survey – internal project 310250</p><p> </p><p>Field M. (2002): The QTRACER2 program for Tracer Breakthrough Curve Analysis for Tracer Tests in Karstic Aquifers and Other hydrologic Systems. – U.S. Environmental protection agency hypertext multimedia publication in the Internet at http://cfpub.epa.gov/ncea/cfm/recordisplay.cfm?deid=54930.</p><p>Kůrková I., Bruthans J., Balák F., Slavík M., Schweigstillová J., Bruthansová J., Mikuš P., Grundloch J. (2019): Factors controlling evolution of karst conduits in sandy limestone and calcareous sandstone (Turnov area, Czech Republic). Journal of Hydrology: 574: 1062-1073</p>

scholarly journals Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin

2016 ◽  
Vol 44 (21) ◽  
pp. e160-e160 ◽  
Author(s):  
David A Ball ◽  
Gunjan D Mehta ◽  
Ronit Salomon-Kent ◽  
Davide Mazza ◽  
Tatsuya Morisaki ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Residence Time ◽  
Single Molecule ◽  
Specific Binding ◽  
Underlying Mechanism ◽  
Specific Interactions ◽  
Single Molecule Tracking ◽  
Reliable Performance ◽  
Transient Interactions

Abstract In vivo single molecule tracking has recently developed into a powerful technique for measuring and understanding the transient interactions of transcription factors (TF) with their chromatin response elements. However, this method still lacks a solid foundation for distinguishing between specific and non-specific interactions. To address this issue, we took advantage of the power of molecular genetics of yeast. Yeast TF Ace1p has only five specific sites in the genome and thus serves as a benchmark to distinguish specific from non-specific binding. Here, we show that the estimated residence time of the short-residence molecules is essentially the same for Hht1p, Ace1p and Hsf1p, equaling 0.12–0.32 s. These three DNA-binding proteins are very different in their structure, function and intracellular concentration. This suggests that (i) short-residence molecules are bound to DNA non-specifically, and (ii) that non-specific binding shares common characteristics between vastly different DNA-bound proteins and thus may have a common underlying mechanism. We develop new and robust procedure for evaluation of adverse effects of labeling, and new quantitative analysis procedures that significantly improve residence time measurements by accounting for fluorophore blinking. Our results provide a framework for the reliable performance and analysis of single molecule TF experiments in yeast.

scholarly journals Transcription factor residence time dominates over concentration in transcription activation

2020 ◽  
Author(s):  
Achim P. Popp ◽  
Johannes Hettich ◽  
J. Christof M. Gebhardt
Keyword(s):  
Transcription Factor ◽  
Residence Time ◽  
Single Molecule ◽  
Search Time ◽  
Mrna Synthesis ◽  
Burst Frequency ◽  
Quantitative Measurements ◽  
Rna Fish ◽  
Transition Times ◽  
Basic Course

Transcription is a vital process activated by transcription factor (TF) binding. The active gene releases a burst of transcripts before turning inactive again. While the basic course of transcription is well understood, it is unclear how binding of a TF affects the frequency, duration and size of a transcriptional burst. We systematically varied the residence time and concentration of a synthetic TF and characterized the transcription of a reporter gene by combining single molecule imaging, single molecule RNA-FISH, live transcript visualisation and analysis with a novel algorithm, Burst Inference from mRNA Distributions (BIRD). For this well-defined system, we found that TF binding solely affected burst frequency and variations in TF residence time had a stronger influence than variations in concentration. This enabled us to device a model of gene transcription, in which TF binding triggers multiple successive steps before the gene transits to the active state and actual mRNA synthesis is decoupled from TF presence. We quantified all transition times of the TF and the gene, including the TF search time and the delay between TF binding and the onset of transcription. Our quantitative measurements and analysis revealed detailed kinetic insight, which may serve as basis for a bottom-up understanding of gene regulation.

Rate of advancement of reactions in turbulent flows

1964 ◽  
Vol 17 (8) ◽  
pp. 821 ◽  
Author(s):  
RCL Bosworth ◽  
CM Groden
Keyword(s):  
Laminar Flow ◽  
Turbulent Flow ◽  
Turbulent Flows ◽  
Residence Time ◽  
Time Distribution ◽  
Residence Time Distribution ◽  
Residence Times ◽  
Cylindrical Reactor ◽  
The Times ◽  
Very High

When a reacting substance or mixture is caused to flow in a cylindrical reactor, all portions of the stream will not flow at the same rate and will exhibit different residence times and, accordingly, are subject to different extents of degrees of reaction. The average degrees of reaction following the residence time distribution proper to laminar flow are given in the earlier publication1 and this paper extends the treatment to that of turbulent flow. In the earlier treatment of laminar flow the ratio of average extent of reaction with non-interacting streams to that of complete intermingling, or the C/Cm, is plotted against the ratio of the times of flow with those of reaction (S). The C/Cm versus S curves are all above unity and increase with increasing S, with the exception of very high orders of chemical reaction for which values of C/Cm are all unity. In the case of turbulent flow the values of C/Cm are more nearly unity at all values of S.

Distribution of 226Ra and 210Pb in the mixed layer of the western equatorial Pacific Ocean

1997 ◽  
Vol 48 (5) ◽  
pp. 371 ◽  
Author(s):  
Philip H. Towler ◽  
J. David Smith
Keyword(s):  
Surface Water ◽  
Pacific Ocean ◽  
Residence Time ◽  
Mixed Layer ◽  
Equatorial Pacific ◽  
Nutrient Concentrations ◽  
Residence Times ◽  
Equatorial Pacific Ocean ◽  
Depth Profiles ◽  
Western Equatorial Pacific

The residence time of particulate and dissolved 210Pb in the upper layer of the western equatorial Pacific Ocean is examined. Activities of dissolved 226Ra, dissolved and particulate 210Pb, and particulate 210Po were determined to a depth of 300 m in a series of depth profiles collected along a transect across the equator at 155˚E in November 1993. Total 210Pb in the surface water decreased from 2·7 Bq m-3 at 10˚N to 1·8 Bq m-3 at 10˚S. Dissolved 210Pb generally decreased with depth but showed subsurface (100–150 m) maxima at 10˚N and 5˚N. The nutrient concentrations at 300 m were highest at these stations, suggesting some degree of upwelling. Calculations indicate that the residence times of dissolved (<0·45 µm) and particulate (>0·45 µm) 210Pb in the top 300 m were 4·6–9·6 years and 0·15–0·29 year respectively.

scholarly journals Modelling Study of Transport Time Scales for a Hyper-Tidal Estuary

Water ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2434
Author(s):  
Guanghai Gao ◽  
Junqiang Xia ◽  
Roger A. Falconer ◽  
Yingying Wang
Keyword(s):  
Numerical Model ◽  
Water Level ◽  
Residence Time ◽  
Exposure Time ◽  
Neap Tide ◽  
Spring Tide ◽  
High Water ◽  
Residence Times ◽  
Severn Estuary ◽  
Release Times

This paper presents a study of two transport timescales (TTS), i.e., the residence time and exposure time, of a hyper-tidal estuary using a widely used numerical model. The numerical model was calibrated against field measured data for various tidal conditions. The model simulated current speeds and directions generally agreed well with the field data. The model was then further developed and applied to study the two transport timescales, namely the exposure time and residence time for the hyper-tidal Severn Estuary. The numerical model predictions showed that the inflow from the River Severn under high flow conditions reduced the residence and exposure times by 1.5 to 3.5% for different tidal ranges and tracer release times. For spring tide conditions, releasing a tracer at high water reduced the residence time and exposure time by 49.0% and 11.9%, respectively, compared to releasing the tracer at low water. For neap tide conditions, releasing at high water reduced the residence time and exposure time by 31.6% and 8.0%, respectively, compared to releasing the tracer at low water level. The return coefficient was found to be vary between 0.75 and 0.88 for the different tidal conditions, which indicates that the returning water effects for different tidal ranges and release times are all relatively high. For all flow and tide conditions, the exposure times were significantly greater than the residence times, which demonstrated that there was a high possibility for water and/or pollutants to re-enter the Severn Estuary after leaving it on an ebb tide. The fractions of water and/or pollutants re-entering the estuary for spring and neap tide conditions were found to be very high, giving 0.75–0.81 for neap tides, and 0.79–0.88 for spring tides. For both the spring and neap tides, the residence and exposure times were lower for high water level release. Spring tide conditions gave significantly lower residence and exposure times. The spatial distribution of exposure and residence times showed that the flow from the River Severn only had a local effect on the upstream part of the estuary, for both the residence and exposure time.

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