journal
MENU ▼
Read by QxMD icon Read
search

Biophysical Journal

journal
https://www.readbyqxmd.com/read/28427715/multiplexed-dynamic-imaging-of-genomic-loci-by-combined-crispr-imaging-and-dna-sequential-fish
#1
Yodai Takei, Sheel Shah, Sho Harvey, Lei S Qi, Long Cai
Visualization of chromosome dynamics allows the investigation of spatiotemporal chromatin organization and its role in gene regulation and other cellular processes. However, current approaches to label multiple genomic loci in live cells have a fundamental limitation in the number of loci that can be labeled and uniquely identified. Here we describe an approach we call "track first and identify later" for multiplexed visualization of chromosome dynamics by combining two techniques: CRISPR imaging and DNA sequential fluorescence in situ hybridization...
April 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28410623/impact-of-gm1-on-membrane-mediated-aggregation-oligomerization-of-%C3%AE-amyloid-unifying-view
#2
REVIEW
Marek Cebecauer, Martin Hof, Mariana Amaro
In this perspective we summarize current knowledge of the effect of monosialoganglioside GM1 on the membrane-mediated aggregation of the β-amyloid (Aβ) peptide. GM1 has been suggested to be actively involved in the development of Alzheimer's disease due to its ability to seed the aggregation of Aβ. However, GM1 is known to be neuroprotective against Aβ-induced toxicity. Here we suggest that the two scenarios are not mutually exclusive but rather complementary, and might depend on the organization of GM1 in membranes...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28400045/rapid-snare-mediated-fusion-of-liposomes-and-chromaffin-granules-with-giant-unilamellar-vesicles
#3
Agata Witkowska, Reinhard Jahn
Soluble N-ethylmaleimide-sensitive factor activating protein receptor (SNARE) proteins are the main catalysts for membrane fusion in the secretory pathway of eukaryotic cells. In vitro, SNAREs are sufficient to mediate effective fusion of both native and artificial membranes. Here we have established, to our knowledge, a new platform for monitoring SNARE-mediated docking and fusion between giant unilamellar vesicles (GUVs) and smaller liposomes or purified secretory granules with high temporal and spatial resolution...
April 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28242011/multivalent-molecules-as-modulators-of-rna-granule-size-and-composition
#4
Cibele Vieira Falkenberg, John H Carson, Michael L Blinov
RNA granules are ensembles of specific RNA and protein molecules that mediate localized translation in eukaryotic cells. The mechanisms for formation and selectivity of RNA granules are unknown. Here we present a model for assembly of one type of RNA granule based on experimentally measured binding interactions among three core multivalent molecular components necessary for such assembly: specific RNA molecules that contain a cis-acting sequence called the A2 response element (A2RE), hnRNP A2 proteins that bind specifically (with high affinity) to A2RE sequences or nonspecifically (with lower affinity) to other RNA sequences, and heptavalent protein cytoskeleton-associated protein 5 (CKAP5, an alternative name for TOG protein) that binds both hnRNP A2 molecules and RNA...
February 24, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28214480/nonlinear-actin-deformations-lead-to-network-stiffening-yielding-and-nonuniform-stress-propagation
#5
Bekele Gurmessa, Shea Ricketts, Rae M Robertson-Anderson
We use optical tweezers microrheology and fluorescence microscopy to apply nonlinear microscale strains to entangled and cross-linked actin networks, and measure the resulting stress and actin filament deformations. We couple nonlinear stress response and relaxation to the velocities and displacements of individual fluorescent-labeled actin segments, at varying times throughout the strain and varying distances from the strain path, to determine the underlying molecular dynamics that give rise to the debated nonlinear response and stress propagation of cross-linked and entangled actin networks at the microscale...
February 15, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28162235/opportunities-and-challenges-in-rna-structural-modeling-and-design
#6
REVIEW
Tamar Schlick, Anna Marie Pyle
We describe opportunities and challenges in RNA structural modeling and design, as recently discussed during the second Telluride Science Research Center workshop organized in June 2016. Topics include fundamental processes of RNA, such as structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used for structural prediction and functional inference. We also highlight the software and database issues associated with RNA structures, such as the multiple approaches for motif annotation, the need for frequent database updating, and the importance of quality control of RNA structures...
February 2, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402893/magnetic-resonance-relaxation-anisotropy-physical-principles-and-uses-in-microstructure-imaging
#7
Michael J Knight, Serena Dillon, Lina Jarutyte, Risto A Kauppinen
Magnetic resonance imaging (MRI) provides an excellent means of studying tissue microstructure noninvasively since the microscopic tissue environment is imprinted on the MRI signal even at macroscopic voxel level. Mesoscopic variations in magnetic field, created by microstructure, influence the transverse relaxation time (T2) in an orientation-dependent fashion (T2 is anisotropic). However, predicting the effects of microstructure upon MRI observables is challenging and requires theoretical insight. We provide a formalism for calculating the effects upon T2 of tissue microstructure, using a model of cylindrical magnetic field perturbers...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402892/geometric-asymmetry-induces-upper-limit-of-mitotic-spindle-size
#8
Jingchen Li, Hongyuan Jiang
Proper organelle size is critical for many cell functions. However, how cells sense and control their organelle size remains elusive. Here, we develop a general model to study the size control of mitotic spindles by considering both extrinsic and intrinsic factors, such as the limited number of building blocks of the spindle, the interaction between the spindle and cell boundary, the DNA content, the forces generated by various molecular motors, and the dynamics of microtubules. We show that multiple pairs of chromatids, two centrosomes, and microtubules can self-assemble to form a mitotic spindle robustly...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402891/brownian-ratchet-mechanism-for-faithful-segregation-of-low-copy-number-plasmids
#9
Longhua Hu, Anthony G Vecchiarelli, Kiyoshi Mizuuchi, Keir C Neuman, Jian Liu
Bacterial plasmids are extrachromosomal DNA that provides selective advantages for bacterial survival. Plasmid partitioning can be remarkably robust. For high-copy-number plasmids, diffusion ensures that both daughter cells inherit plasmids after cell division. In contrast, most low-copy-number plasmids need to be actively partitioned by a conserved tripartite ParA-type system. ParA is an ATPase that binds to chromosomal DNA; ParB is the stimulator of the ParA ATPase and specifically binds to the plasmid at a centromere-like site, parS...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402890/cholesterol-regulates-monocyte-rolling-through-cd44-distribution
#10
Amit K Saha, Pawel Osmulski, Shatha F Dallo, Maria Gaczynska, Tim H-M Huang, Anand K Ramasubramanian
Cholesterol is an important risk factor of atherosclerosis, due to its active uptake by monocytes/macrophages. Monocyte recruitment from flowing blood to atherosclerotic foci is the key first step in the development of atherosclerosis. Cholesterol content alters cell membrane stiffness, and lateral lipid and protein diffusion. We hypothesized that cholesterol content will modulate the recruitment of monocytes to inflamed endothelial surface by altering the dynamics of adhesion receptors. We depleted or enriched the cellular cholesterol levels using methyl-β-cyclodextran in freshly isolated human monocytes...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402889/unbiased-high-precision-cell-mechanical-measurements-with-microconstrictions
#11
Janina R Lange, Claus Metzner, Sebastian Richter, Werner Schneider, Monika Spermann, Thorsten Kolb, Graeme Whyte, Ben Fabry
We describe a quantitative, high-precision, high-throughput method for measuring the mechanical properties of cells in suspension with a microfluidic device, and for relating cell mechanical responses to protein expression levels. Using a high-speed (750 fps) charge-coupled device camera, we measure the driving pressure Δp, maximum cell deformation εmax, and entry time tentry of cells in an array of microconstrictions. From these measurements, we estimate population averages of elastic modulus E and fluidity β (the power-law exponent of the cell deformation in response to a step change in pressure)...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402888/influence-of-physical-effects-on-the-swarming-motility-of-pseudomonas-aeruginosa
#12
Alexander Yang, Wai Shing Tang, Tieyan Si, Jay X Tang
Many species of bacteria can spread over a moist surface via a particular form of collective motion known as "surface swarming". This form of motility is typically studied by inoculating bacteria on a gel formed by 0.4-1.5% agar, which contains essential nutrients for their growth and proliferation. Using Pseudomonas aeruginosa and its pili-less mutant, ΔPilA, we investigate physical factors that either facilitate or restrict the swarming motility, measured by the rate of increase in area covered by a spreading bacterial colony, i...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402887/the-closed-state-of-the-thin-filament-is-not-occupied-in-fully-activated-skeletal-muscle
#13
Sergey Y Bershitsky, Natalia A Koubassova, Michael A Ferenczi, Galina V Kopylova, Theyencheri Narayanan, Andrey K Tsaturyan
Muscle contraction is powered by actin-myosin interaction controlled by Ca(2+) via the regulatory proteins troponin (Tn) and tropomyosin (Tpm), which are associated with actin filaments. Tpm forms coiled-coil dimers, which assemble into a helical strand that runs along the whole ∼1 μm length of a thin filament. In the absence of Ca(2+), Tn that is tightly bound to Tpm binds actin and holds the Tpm strand in the blocked, or B, state, where Tpm shields actin from the binding of myosin heads. Ca(2+) binding to Tn releases the Tpm from actin so that it moves azimuthally around the filament axis to a closed, or C, state, where actin is partially available for weak binding of myosin heads...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402886/three-dimensional-super-resolution-in-eukaryotic-cells-using-the-double-helix-point-spread-function
#14
Alexander R Carr, Aleks Ponjavic, Srinjan Basu, James McColl, Ana Mafalda Santos, Simon Davis, Ernest D Laue, David Klenerman, Steven F Lee
Single-molecule localization microscopy, typically based on total internal reflection illumination, has taken our understanding of protein organization and dynamics in cells beyond the diffraction limit. However, biological systems exist in a complicated three-dimensional environment, which has required the development of new techniques, including the double-helix point spread function (DHPSF), to accurately visualize biological processes. The application of the DHPSF approach has so far been limited to the study of relatively small prokaryotic cells...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402885/line-tension-controls-liquid-disordered%C3%A2-liquid-ordered-domain-size-transition-in-lipid-bilayers
#15
Rebecca D Usery, Thais A Enoki, Sanjula P Wickramasinghe, Michael D Weiner, Wen-Chyan Tsai, Mary B Kim, Shu Wang, Thomas L Torng, David G Ackerman, Frederick A Heberle, John Katsaras, Gerald W Feigenson
To better understand animal cell plasma membranes, we studied simplified models, namely four-component lipid bilayer mixtures. Here we describe the domain size transition in the region of coexisting liquid-disordered (Ld) + liquid-ordered (Lo) phases. This transition occurs abruptly in composition space with domains increasing in size by two orders of magnitude, from tens of nanometers to microns. We measured the line tension between coexisting Ld and Lo domains close to the domain size transition for a variety of lipid mixtures, finding that in every case the transition occurs at a line tension of ∼0...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402884/interdigitation-between-triglycerides-and-lipids-modulates-surface-properties-of-lipid-droplets
#16
Amélie Bacle, Romain Gautier, Catherine L Jackson, Patrick F J Fuchs, Stefano Vanni
Intracellular lipid droplets (LDs) are the main cellular site of metabolic energy storage. Their structure is unique inside the cell, with a core of esterified fatty acids and sterols, mainly triglycerides and sterol esters, surrounded by a single monolayer of phospholipids. Numerous peripheral proteins, including several that were previously associated with intracellular compartments surrounded by a lipid bilayer, have been recently shown to target the surface of LDs, but how they are able to selectively target this organelle remains largely unknown...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402883/a-role-of-bk-channel-in-regulation-of-ca-2-channel-in-ventricular-myocytes-by-substrate-stiffness
#17
Hucheng Zhao, Yang Yu, Xiaoan Wu, Sisi Liu, Bailin Liu, Jing Du, Bo Li, Linhua Jiang, Xiqiao Feng
Substrate stiffness is crucial for diverse cell functions, but the mechanisms conferring cells with mechanosensitivity are still elusive. By tailoring substrate stiffness with 10-fold difference, we showed that L-type voltage-gated Ca(2+) channel current density was greater in chick ventricular myocytes cultured on the stiff substrate than on the soft substrate. Blockage of the BK channel increased the Ca(2+) current density on the soft substrate and consequently eliminated substrate stiffness regulation of the Ca(2+) channel...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402882/gating-charge-calculations-by-computational-electrophysiology-simulations
#18
Jan-Philipp Machtens, Rodolfo Briones, Claudia Alleva, Bert L de Groot, Christoph Fahlke
Electrical cell signaling requires adjustment of ion channel, receptor, or transporter function in response to changes in membrane potential. For the majority of such membrane proteins, the molecular details of voltage sensing remain insufficiently understood. Here, we present a molecular dynamics simulation-based method to determine the underlying charge movement across the membrane-the gating charge-by measuring electrical capacitor properties of membrane-embedded proteins. We illustrate the approach by calculating the charge transfer upon membrane insertion of the HIV gp41 fusion peptide, and validate the method on two prototypical voltage-dependent proteins, the Kv1...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402881/stability-and-conformation-of-a-chemoreceptor-hamp-domain-chimera-correlates-with-signaling-properties
#19
Nattakan Sukomon, Joanne Widom, Peter P Borbat, Jack H Freed, Brian R Crane
HAMP domains are dimeric, four-helix bundles that transduce conformational signals in bacterial receptors. Genetic studies of the Escherichia coli serine receptor (Tsr) provide an opportunity to understand HAMP conformational behavior in terms of functional output. To increase its stability, the Tsr HAMP domain was spliced into a poly-HAMP unit from the Pseudomonas aeruginosa Aer2 receptor. Within the chimera, the Tsr HAMP undergoes a thermal melting transition at a temperature much lower than that of the Aer2 HAMP domains...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402880/sedimentation-of-reversibly-interacting-macromolecules-with-changes-in-fluorescence-quantum-yield
#20
Sumit K Chaturvedi, Huaying Zhao, Peter Schuck
Sedimentation velocity analytical ultracentrifugation with fluorescence detection has emerged as a powerful method for the study of interacting systems of macromolecules. It combines picomolar sensitivity with high hydrodynamic resolution, and can be carried out with photoswitchable fluorophores for multicomponent discrimination, to determine the stoichiometry, affinity, and shape of macromolecular complexes with dissociation equilibrium constants from picomolar to micromolar. A popular approach for data interpretation is the determination of the binding affinity by isotherms of weight-average sedimentation coefficients sw...
April 11, 2017: Biophysical Journal
journal
journal
23362
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"