Wi-Fi Live-Streaming Centrifuge Force Microscope for Benchtop Single-Molecule Experiments

The ability to apply controlled forces to individual molecules has been revolutionary in shaping our understanding of biophysics in areas as diverse as dynamic bond strength, biological motor operation, and DNA replication. However, the methodology to perform single-molecule experiments remains relatively inaccessible because of cost and complexity. In 2010, we introduced the centrifuge force microscope (CFM) as a platform for accessible and high-throughput single-molecule experimentation. The CFM consists of a rotating microscope with which prescribed centrifugal forces can be applied to microsphere-tethered biomolecules. In this work, we develop and demonstrate a next-generation Wi-Fi CFM that offers unprecedented ease of use and flexibility in design. The modular CFM unit fits within a standard benchtop centrifuge and connects by Wi-Fi to an external computer for live control and streaming at near gigabit speeds. The use of commercial wireless hardware allows for flexibility in programming and provides a streamlined upgrade path as Wi-Fi technology advances. To facilitate ease of use, detailed build and setup instructions, as well as LabVIEW-based control software and MATLAB-based analysis software, are provided. We demonstrate the instrument’s performance by analysis of force-dependent dissociation of short DNA duplexes of 7, 8, and 9 bp. We showcase the sensitivity of the approach by resolving distinct dissociation kinetic rates for a 7 bp duplex in which one G-C basepair is mutated to an A-T basepair.     

The separation of affinity flocculated yeast cell debris using a pilot-plant scroll decanter centrifuge

The use of a scroll decanter centrifuge for the removal and dewatering of affinity-flocculated yeast cell debris from a crude homogenate is described. Laboratory shear modulus measurements were used to compare the structure of flocculated and nonflocculated sediments and to indicate the dewatering conditions under which the sediment could be discharged from the centrifuge. The structure of the flocculated sediment was such that a dry beach could be used within the centrifuge while still being able to discharge the solids. The scroll decanter performance for recovery and dewatering of the flocculated homogenate was found to be independent of feed flow rate and differential scroll rate. Eighty-five percent of the solid material was recovered from the flocculated homogenate while the extent of sediment dewatering resulted in the loss of only 7% of the soluble protein in the sediment. The supernatant clarity matched that achieved by low-gravity laboratory centrifugation studies.     

Immobilization of endoplasm flowing contiguous to the actin cables upon electrical stimulus inNitella internodes

Summary Using a stroboscopic centrifuge microscope, we demonstrated that, when actin cables (=bundles of F-actin) had been previously removed locally from the cell cortex ofNitella internodes, the passively flowing endoplasm found there under centrifugal force did not stop at all upon electrical stimulus, while the actively flowing endoplasm contiguous to the actin cables at the normal cell cortex promptly stopped following the stimulus and was immobilized for several seconds. The results present evidence that, upon electrical stimulus, the presence of actin cables is required to immobilize the endoplasm flowing contiguous to the actin cables in a state that resists displacement by centrifugal force.Abbreviations APW artificial pond water - CMS centrifuge microscope     

Aquatic animals and use of centrifuge in space experiments]

There are some experiments which do not need a centrifuge apparatus in space, however, for other space experiments the use of centrifuge is indispensable as the control. The characteristics of these two types of space experiments are explained. Generally, the more quantitatively the phenomenon is analyzed, the greater the need of centrifuge apparatus becomes. The centrifuge in space can realize various gravity values ranging from 0 to 1 G, and this will extend the present biology to a more universal biology.     

Functional comparative histology. 5. Communication: History of histology

The present author gives a survey on the development of microscopy by centuries: 16th Invention of the simple microscope--at the end of the century the compound microscope was invented. 17th HOOKE's microscope was the leading of this century--binocular microscope--introduction of screw fine adjustment. 18th The first microscope in America came to Yale in 1734. CHARLES SPENCER started to manufacture microscopes at the continent in 1847. 19th Establishment of precondition for electron microscopy. ZEISS introduced apochromatic optics. The Royal Microscopical Society was established in 1858. The American Microscopical Society in 1878, The New York Microscopical Society in 1877. 20th 1906 invention of the ultraviolet microscope, 1911 of the fluorescence microscope, 1931 of the electron microscope, the first American in 1938, 1932 the centrifuge microscope, 1932 the phase contrast microscope. The first American phase contrast microscope in 1944, 1942 phosphorescence microscope, in the 1950th the interference and x-ray microscopes.     

Recognition of 5'-YpG-3' sequences by coupled stacking/hydrogen bonding interactions with amino acid residues

The combined biochemical and structural study of hundreds of protein-DNA complexes has indicated that sequence-specific interactions are mediated by two mechanisms termed direct and indirect readout. Direct readout involves direct interactions between the protein and base-specific atoms exposed in the major and minor grooves of DNA. For indirect readout, the protein recognizes DNA by sensing conformational variations in the structure dependent on nucleotide sequence, typically through interactions with the phosphodiester backbone. Based on our recent structure of Ndt80 bound to DNA in conjunction with a search of the existing PDB database, we propose a new method of sequence-specific recognition that utilizes both direct and indirect readout. In this mode, a single amino acid side-chain recognizes two consecutive base-pairs. The 3'-base is recognized by canonical direct readout, while the 5'-base is recognized through a variation of indirect readout, whereby the conformational flexibility of the particular dinucleotide step, namely a 5'-pyrimidine-purine-3' step, facilitates its recognition by the amino acid via cation-pi interactions. In most cases, this mode of DNA recognition helps explain the sequence specificity of the protein for its target DNA.     

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition

Protein-DNA recognition plays an essential role in the regulation of gene expression. Regulatory proteins are known to recognize specific DNA sequences directly through atomic contacts (intermolecular readout) and/or indirectly through the conformational properties of the DNA (intramolecular readout). However, little is known about the respective contributions made by these so-called direct and indirect readout mechanisms. We addressed this question by making use of information extracted from a structural database containing many protein-DNA complexes. We quantified the specificity of intermolecular (direct) readout by statistical analysis of base-amino acid interactions within protein-DNA complexes. The specificity of the intramolecular (indirect) readout due to DNA was quantified by statistical analysis of the sequence-dependent DNA conformation. Systematic comparison of these specificities in a large number of protein-DNA complexes revealed that both intermolecular and intramolecular readouts contribute to the specificity of protein-DNA recognition, and that their relative contributions vary depending upon the protein-DNA complexes. We demonstrated that combination of the intermolecular and intramolecular energies derived from the statistical analyses lead to enhanced specificity, and that the combined energy could explain experimental data on binding affinity changes caused by base mutations. These results provided new insight into the relationship between specificity and structure in the process of protein-DNA recognition, which would lead to prediction of specific protein-DNA binding sites.     

Total containment of a continuous-flow zonal centrifuge

A continuous-flow, high throughput, turbine-driven zonal centrifuge has been contained for use with biologically hazardous materials. The centrifuge and all ancillary equipment are enclosed in three sealed cabinets that are maintained at negative pressure, decontaminated with ethylene oxide, and provide cooling for the process fluids. Sample handling is semiautomated and remotely controlled for ease of operation and includes an automated decontamination system. The centrifuge subsystems can be decontaminated prior to an engineer servicing the machine, and apparatus is provided for absolute filtration of the centrifuge turbine exhaust.     

Visualization of a rapid,red/far-red light-dependent reaction by centrifuge microscopy

Summary Using a centrifuge microscope with stroboscopic illumination, we examined the effects of light irradiation on the passive movement of chloroplasts in dark-adapted mesophyll cells ofVallisneria gigantea. While irradiation with red light accelerates the passive gliding of chloroplasts produced by centrifugal force, irradiation with far-red light negates this effect. Irradiation with blue light does not accelerate the passive gliding, while red light is completely effective even in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea, an inhibitor of photosynthesis. An apparently active movement of chloroplasts can be induced by irradiation with red or blue light only in the presence of the far-red light-absorbing form of phytochrome. The significance of the reaction in the light with respect to the regulation of cytoplasmic streaming is discussed.Abbreviations APW artificial pond water - CMS centrifuge microscope of the stroboscopic type - DCMU 3-(3,4-dichlorophenyl)-1,1-dimethylurea - Pfr phytochrome, far-red light-absorbing form - Pr phytochrome, red light-absorbing form     

Tidy up cryo-EM sample grids with 3D printed tools

Cryo-EM technology has developed to the point of high-throughput structure determination of biological macromolecules embedded in vitreous ice. Nonetheless, challenging targets need extensive sample screening, often of many cryo-EM sample grids prepared under various conditions. We have designed and made tools for manipulating sample grids in storage cases. These tools are made of a plastic fiber using a wide-use 3D printer, a fused deposition modeling type, and polished under acetone gas. A grid case stacker organizes many frozen-hydrated cryo-EM grids and the stackers can be piled up inside a standard 50 mL centrifuge tube. We have also introduced tools that facilitate handling of grid cases under liquid nitrogen and a stocker of the grid retainers contained in a CRYO ARM electron microscope. Blueprints of the tools named CryoGridTools are available from a GitHub site.     

A new method for evaluating the specificity of indirect readout in protein-DNA recognition

Proteins recognize a specific DNA sequence not only through direct contact (direct readout) with base pairs but also through sequence-dependent conformation and/or flexibility of DNA (indirect readout). However, it is difficult to assess the contribution of indirect readout to the sequence specificity. What is needed is a straightforward method for quantifying its contributions to specificity. Using Bayesian statistics, we derived the probability of a particular sequence for a given DNA structure from the trajectories of molecular dynamics (MD) simulations of DNAs containing all possible tetramer sequences. Then, we quantified the specificity of indirect readout based on the information entropy associated with the probability. We tested this method with known structures of protein-DNA complexes. This method enabled us to correctly predict those regions where experiments suggested the involvement of indirect readout. The results also indicated new regions where the indirect readout mechanism makes major contributions to the recognition. The present method can be used to estimate the contribution of indirect readout without approximations to the distributions in the conformational ensembles of DNA, and would serve as a powerful tool to study the mechanism of protein-DNA recognition.     

Evaluation of a single-use disk stack centrifuge for improved efficiency and sustainability at 1000 L GMP manufacturing scale

Direct depth filtration is an established technology for single-use harvest operation. Advantages of direct depth filtration include familiarity with depth filtration in downstream processes and simplicity of the operation. Drawbacks include low capacity, large footprint, labor-intensive set-up, high water use, and high waste in the form of discarded filters. Single-use centrifugation is emerging as an alternative to depth filtration for the single-use harvest step. Within the single-use centrifugation space, disc stack centrifugation represents the newest entrant. In this study, we evaluated the performance of the GEA kytero single-use disc stack centrifuge to clarify two monoclonal antibody-producing cell culture fluids. The separation performance of the GEA kytero centrifuge varied between the two cell culture fluids, with differences in centrate turbidity and centrate filterability measured. A comparison was then performed to determine resource savings, compared to direct two-stage depth filtration, when using a GEA kytero centrifuge to harvest a 1000 L bioreactor. The analysis concluded that replacement of the first stage of depth filters with a GEA kytero centrifuge has the potential to decrease the required second stage depth filtration area by up to 80%. The decrease in depth filter area resulting from the use of the GEA kytero would result in a decrease in the harvest step footprint, a decrease in buffer volume required to prime and rinse depth filters, and a decrease in the volume of plastic waste. An economic comparison of the GEA kytero single-use centrifuge against a direct depth filtration step found that for a 1000 L harvest step, the GEA kytero centrifuge may reduce costs by up to 20% compared with two-stage direct depth filtration.     

Shear stress analysis of mammalian cell suspensions for prediction of industrial centrifugation and its verification

This article describes the use of ultra scale-down studies requiring milliliter quantities of process material to study the clarification of mammalian cell culture broths using industrial-scale continuous centrifuges during the manufacture of a monoclonal antibody for therapeutic use. Samples were pretreated in a small high-speed rotating-disc device in order to mimic the effect on the cells of shear stresses in the feed zone of the industrial scale centrifuges. The use of this feed mimic was shown to predict a reduction of the clarification efficiency by significantly reducing the particle size distribution of the mammalian cells. The combined use of the rotating-disc device and a laboratory-scale test tube centrifuge successfully predicted the separation characteristics of industrial-scale, disc stack centrifuges operating with different feed zones. A 70% reduction in flow rate in the industrial-scale centrifuge was shown to arise from shear effects. A predicted 2.5-fold increase in throughput for the same clarification performance, achieved by the change to a centrifuge using a feed zone designed to give gentler acceleration of the bioprocess fluid, was also verified at large-scale.     

The slow rotating centrifuge microscope NIZEMI--a versatile instrument for terrestrial hypergravity and space microgravity research in biology and materials science

NIZEMI (slow rotating centrifuge microscope) is a tool for optical investigations of small biological and non-biological specimens during variable accelerations. Two laboratory models for ground research designed for accelerations from 1 to 5 x g and 10 x g respectively are used for terrestrial research, especially in gravitational biology. A space facility was developed and built for the Spacelab mission IML-2 during which eight experiments were performed successfully. The specifications and topic design features of the NIZEMI models are presented in this paper.     

The total containment of a batch-type zonal centrifuge.

A batch-type zonal centrifuge has been modified and totally contained for use with biologically hazardous materials. A sealed cabinet encloses the centrifuge and the ancilliary equipment. It is operated with a flow of filtered air when the zonal system is on, decontaminated with ethylene oxide, and maintained at a negative pressure throughout. The centrifuge subsystems can be drained, flushed, and decontaminated with ethylene oxide before an engineer services the machine. The sample handling system within the cabinet is remotely controlled.     

BIOLAB, EPU and EMCS for cell culture experiments on the ISS

Two ESA facilities are under development for biological research on the International Space Station: BIOLAB as part of the European "Columbus" Laboratory and the European Modular Cultivation System (EMCS), foreseen for accommodation in the US Lab "Destiny". Both facilities have an incubator (18-40 degrees C) and use standard Experiment Containers, mounted on two centrifuge rotors providing either microgravity or variable g-levels from 0.001 x g to 2.0 x g. Standard interface plates supply each container with power and data lines, with gas (controlled CO2, O2 and water vapour concentration; trace gas removal), and--for EMCS only--with water. The degree of automation is higher in BIOLAB: it contains a robotic Handling Mechanism for automatic sampling and handling of liquids, which can be stored at cool or cold temperatures or injected for automatic on-board analysis into a microscope or a spectrophotometer. For analyses on the running centrifuge, small automatic microscopes can be installed in the Experiment Containers. Several designs for supporting cell culture experiments have been studied for BIOLAB and EMCS. BIOLAB has in addition a Bio-Glovebox, which can be sterilised and where new cell cultures may be prepared under 1 x g conditions from deep-frozen samples in the Experiment Preparation Unit (EPU): the cryo-protectant will be removed by automatic washing cycles. Both facilities, EMCS and BIOLAB (with EPU), have also provisions for telescience operations through video, data and command lines, either operated by the crew or by the experimenter on ground.     

Biohazards Assessment in Large-Scale Zonal Centrifugation

A study was conducted to determine the biohazards associated with use of the large-scale zonal centrifuge for purification of moderate risk oncogenic viruses. To safely and conveniently assess the hazard, coliphage T₃ was substituted for the virus in a typical processing procedure performed in a National Cancer Institute contract laboratory. Risk of personnel exposure was found to be minimal during optimal operation but definite potential for virus release from a number of centrifuge components during mechanical malfunction was shown by assay of surface, liquid, and air samples collected during the processing. High concentration of phage was detected in the turbine air exhaust and the seal coolant system when faulty seals were employed. The simulant virus was also found on both centrifuge chamber interior and rotor surfaces.     

Cytoplasmic streaming inChara rhizoids

Summary In-vivo videomicroscopy ofChara rhizoids under 10^–4g demonstrated that gravity affected the velocities of cytoplasmic streaming. Both, the acropetal and basipetal streaming velocities increased on the change to microgravity. The endogenous difference in the velocities of the oppositely directed cytoplasmic streams was maintained under microgravity, yet the difference was diminished as the basipetal streaming velocity increased more than the acropetal streaming velocity. Direction and structure of microfilaments labeled by rhodamine-phalloidin had not changed after 6 min of microgravity.Abbreviations g gravitational acceleration - Nizemi slow rotating centrifuge microscope - Texus technological experiments under reduced gravity     

The Mechanical Structure of the Cytoplasm of the Echinoderm Egg Determined by "Gold Particle Method" using a Centrifuge Microscope

A method was developed to investigate the mechanical structure of the cytoplasm based on the movement of an intracellular gold particle subjected to centrifugal acceleration (the gold particle method). The movement of the particle in the cell was observed and recorded with a new centrifuge microscope of stroboscopic type (13). In eggs and oocytes of the echinoderms, Clypeaster japonicus, Asterias amurensis , and Asterina pectinifera , the particle moved in the cytoplasm by an applied centrifugal acceleration in the centrifugal direction, but the course was not exactly straight and the velocity fluctuated during the movement, suggesting the existence of a network structure in the cytoplasm. In fertilized eggs, the movement of the particle by the centrifugal acceleration was impeded by the structures of the sperm aster and the cleavage diaster. The apparent viscosity of the cytoplasm in fertilized eggs changed in parallel to the development of the sperm aster and the mitotic diaster in the cell. These results indicate that the asters are really rigid structures in the cell as previously shown by the magnetic particle method (8).     

On the Number of Neurons and Time Scale of Integration Underlying the Formation of Percepts in the Brain

All of our perceptual experiences arise from the activity of neural populations. Here we study the formation of such percepts under the assumption that they emerge from a linear readout, i.e., a weighted sum of the neurons’ firing rates. We show that this assumption constrains the trial-to-trial covariance structure of neural activities and animal behavior. The predicted covariance structure depends on the readout parameters, and in particular on the temporal integration window w and typical number of neurons K used in the formation of the percept. Using these predictions, we show how to infer the readout parameters from joint measurements of a subject’s behavior and neural activities. We consider three such scenarios: (1) recordings from the complete neural population, (2) recordings of neuronal sub-ensembles whose size exceeds K, and (3) recordings of neuronal sub-ensembles that are smaller than K. Using theoretical arguments and artificially generated data, we show that the first two scenarios allow us to recover the typical spatial and temporal scales of the readout. In the third scenario, we show that the readout parameters can only be recovered by making additional assumptions about the structure of the full population activity. Our work provides the first thorough interpretation of (feed-forward) percept formation from a population of sensory neurons. We discuss applications to experimental recordings in classic sensory decision-making tasks, which will hopefully provide new insights into the nature of perceptual integration.