journal

# Physical Biology

journal
#1
David Pincus, Orna Resnekov, Kimberly Reynolds
Allosteric regulation provides a way to control protein activity at the time scale of milliseconds to seconds inside the cell. An ability to engineer synthetic allosteric systems would be of practical utility for the development of novel biosensors, creation of synthetic cell signaling pathways, and design of small molecule pharmaceuticals with regulatory impact. To this end, we outline a general approach - termed Rational Engineering of Allostery at Conserved Hotspots (REACH) - to introduce novel regulation into a protein of interest by exploiting latent allostery that has been hard-wired by evolution into its structure...
March 6, 2017: Physical Biology
#2
Bartolome Sabater, Dolores Marin
Cancer cells consume more glucose by glycolytic fermentation to lactate than by respiration, a characteristic known as the Warburg effect. In contrast with the 34 moles of ATP produced by respiration, fermentation produces two moles of ATP per mole of glucose consumed, which poses a puzzle on the function of the Warburg effect. Productions of free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) per mole linearly vary with the fraction (x) of glucose consumed by fermentation that is frequently estimated around 0...
March 6, 2017: Physical Biology
#3
Robert Noest, Zheng Jane Wang
Tiger beetles pursue prey by adjusting their heading according to a time-delayed proportional control law that minimizes the error angle (1). This control law can be further interpreted in terms of mechanical actuation: to catch a prey, tiger beetles exert a sideways force by biasing their tripod gait in proportion to the error angle measured half a stride earlier. The proportional gain was found to be nearly optimal in the sense that it minimizes the time to point directly toward the prey. For a time-delayed linear proportional controller, the optimal gain, $k$, is inversely proportional to the time delay, $\tau$, and satisfies $k \tau = 1/e$ (2)...
February 24, 2017: Physical Biology
#4
Thomas Blasi, Florian Buettner, Michael Strasser, Carsten Marr, Fabian Theis
MOTIVATION: Accessing gene expression at the single cell level has unraveled often large heterogeneity among seemingly homogeneous cells, which remained obscured in traditional population based approaches. The computational analysis of single-cell transcriptomics data, however, still imposes unresolved challenges with respect to normalization, visualization and modeling the data. One such issue are differences in cell size, which introduce additional variability into the data, for which appropriate normalization techniques are needed...
February 15, 2017: Physical Biology
#5
Alexander Krah, Ulrich Zachariae
Bacteria have developed a variety of different mechanisms to defend themselves from compounds that are toxic to them, such as antibiotics. One of these defence mechanisms is the expulsion of drugs or other noxious compounds by multidrug efflux pumps. Multidrug and toxic compound extrusion (MATE) transporters are efflux pumps that extrude metabolic waste and a variety of antibiotics out of the cell, using an ion gradient as energy source. They function via an alternative-access mechanism. When ions bind in the outward facing conformation, a large conformational change to the inward facing conformation is induced, from which the ion is released and the extruded chemical compound is bound...
February 7, 2017: Physical Biology
#6
Eric Keaveny, Andre Brown
A basic issue in the physics of behaviour is the mechanical relationship between an animal and its surroundings. The model nematode <i>C. elegans</i> provides an excellent platform to explore this relationship due to its anatomical simplicity. Nonetheless, the physics of nematode crawling, in which the worm undulates its body to move on a wet surface, is not completely understood and the mathematical models often used to describe this phenomenon are empirical. We confirm that linear resistive force theory, one such empirical model, is effective at predicting a worm's path from its sequence of body postures for forward crawling, reversing, and turning and for a broad range of different behavioural phenotypes observed in mutant worms...
January 31, 2017: Physical Biology
#7
Eleanor Ory, Lekhana Bhandary, Amanda Boggs, Kristi Chakrabarti, Joshua Parker, Wolfgang Losert, Stuart S Martin
The periphery of epithelial cells is shaped by opposing cytoskeletal physical forces generated predominately by two dynamic force generating systems - growing microtubule ends push against the boundary from the cell center, and the actin cortex contracts the attached plasma membrane. Here we investigate how changes to the structure and dynamics of the actin cortex alter the dynamics of microtubules. Current drugs target actin polymerization and contraction to reduce cell division and invasiveness; however, the impacts on microtubule dynamics remain incompletely understood...
January 16, 2017: Physical Biology
#8
Mathieu Rivière, Julien Derr, Stéphane Douady
The study on aerial plant organs (leaves and stems) motions is reviewed. The history of observations and studies is put in the perspective of the ideas surrounding them, leading to a presentation of the current classification of these motions. After showing the shortcomings of such a classification, we present, following an idea of Darwin's, the various movements in a renewed and observation-based perspective of the plant development. With this perspective, the different movements fit together logically, and in particular we point out that the mature reversible movements, such as the sensitive or circadian movements, are just partial regressions of the developmental ones...
January 13, 2017: Physical Biology
#9
Chronic alcoholism is known to alter the morphology of the hippocampus, an important region of cognitive function in the brain. Therefore, to understand the effect of chronic alcoholism on hippocampal neural cells, we employed a mouse model of chronic alcoholism and quantified intranuclear nanoscale structural alterations in these cells. Transmission electron microscopy (TEM) images of hippocampal neurons were obtained, and the degree of structural alteration in terms of mass density fluctuation was determined using the light-localization properties of optical media generated from TEM imaging...
March 1, 2017: Physical Biology
#10
M Schenkelberger, S Shanak, M Finkler, E G Worst, V Noireaux, V Helms, A Ott
Cytosine methylation plays an important role in the epigenetic regulation of eukaryotic gene expression. The methyl-CpG binding domain (MBD) is common to a family of eukaryotic transcriptional regulators. How MBD, a stretch of about 80 amino acids, recognizes CpGs in a methylation dependent manner, and as a function of sequence, is only partly understood. Here we show, using an Escherichia coli cell-free expression system, that MBD from the human transcriptional regulator MeCP2 performs as a specific, methylation-dependent repressor in conjunction with the BDNF (brain-derived neurotrophic factor) promoter sequence...
March 1, 2017: Physical Biology
#11
Michal Wlodarski, Bianca Raciti, Jurij Kotar, Marco Cosentino Lagomarsino, Gillian M Fraser, Pietro Cicuta
While the action of many antimicrobial drugs is well understood at the molecular level, a systems-level physiological response to antibiotics remains largely unexplored. This work considers fluctuation dynamics of both the chromosome and cytosol in Escherichia coli, and their response to sublethal treatments of a clinically important antibiotic, rifampicin. We precisely quantify the changes in dynamics of chromosomal loci and cytosolic aggregates (a rheovirus nonstructural protein known as μNS-GFP), measuring short time-scale displacements across several hours of drug exposure...
February 16, 2017: Physical Biology
#12
Ugne Klibaite, Gordon J Berman, Jessica Cande, David L Stern, Joshua W Shaevitz
Behaviors involving the interaction of multiple individuals are complex and frequently crucial for an animal's survival. These interactions, ranging across sensory modalities, length scales, and time scales, are often subtle and difficult to characterize. Contextual effects on the frequency of behaviors become even more difficult to quantify when physical interaction between animals interferes with conventional data analysis, e.g. due to visual occlusion. We introduce a method for quantifying behavior in fruit fly interaction that combines high-throughput video acquisition and tracking of individuals with recent unsupervised methods for capturing an animal's entire behavioral repertoire...
February 16, 2017: Physical Biology
#13
M S Zamil, A Geitmann
In plant tissues, cells are glued to each other by a pectic polysaccharide rich material known as middle lamella (ML). Along with many biological functions, the ML plays a crucial role in maintaining the structural integrity of plant tissues and organs, as it prevents the cells from separating or sliding against each other. The macromolecular organization and the material properties of the ML are different from those of the adjacent primary cell walls that envelop all plant cells and provide them with a stiff casing...
February 16, 2017: Physical Biology
#14
Xiaona Fang, Jin Wang
Cellular networks have been the focus of studies in modern systems biology. They are crucial in understanding cell functions and related diseases. We review some past progress in both the theory and experiments, and we also provide several future perspectives for the field.
February 16, 2017: Physical Biology
#15
L Shahriyari, A Mahdipour-Shirayeh
Studying the stem cell (SC) niche architecture is a crucial step for investigating the process of oncogenesis and obtaining an effective stem cell therapy for various cancers. Recently, it has been observed that there are two groups of SCs in the SC niche collaborating with each other to maintain tissue homeostasis: border stem cells (BSCs), which are responsible in controlling the number of non-stem cells as well as stem cells, and central stem cells (CeSCs), which regulate the SC niche. Here, we develop a bi-compartmental stochastic model for the SC niche to study the spread of mutants within the niche...
February 16, 2017: Physical Biology
#16
T Yu Starkova, A M Polyanichko, T O Artamonova, M A Khodorkovskii, E I Kostyleva, E V Chikhirzhina, A N Tomilin
The covalent modifications of the linker histone H1 and the core histones are thought to play an important role in the control of chromatin functioning. Histone H1 variants from K562 cell line (hH1), mouse (mH1) and calf (cH1) thymi were studied by matrix-activated laser desorption/ionization fourier transform ion cyclotron resonance mass-spectroscopy (MALDI-FT-ICR-MS). The proteomics analysis revealed novel post-translational modifications of the histone H1, such as meK34-mH1.4, meK35-cH1.1, meK35-mH1.1, meK75-hH1...
February 16, 2017: Physical Biology
#17
Gabriella Mosca, Aleksandra Sapala, Soeren Strauss, Anne-Lise Routier-Kierzkowska, Richard S Smith
The effect of geometry on cell stiffness measured with micro-indentation techniques has been explored in single cells, however it is unclear if results on single cells can be readily transferred to indentation experiments performed on a tissue in vivo. Here we explored this question by using simulation models of osmotic treatments and micro-indentation experiments on 3D multicellular tissues with the finite element method. We found that the cellular context does affect measured cell stiffness, and that several cells of context in each direction are required for optimal results...
February 9, 2017: Physical Biology
#18
D Thirumalai
February 8, 2017: Physical Biology
#19
Hans Frauenfelder
February 8, 2017: Physical Biology
#20
Jaemin Chin, Devkumar Mustafi, Michael J Poellmann, Raphael C Lee
Certain amphiphilic block copolymers are known to prevent aggregation of unfolded proteins. To better understand the mechanism of this effect, the optical properties of heat-denatured and dithiothreitol reduced lysozyme were evaluated with respect to controls using UV-Vis spectroscopy, transmission electron microscopy (TEM) and circular dichroism (CD) measurements. Then, the effects of adding Polyethylene Glycol (8000 Da), the triblock surfactant Poloxamer 188 (P188), and the tetrablock copolymer Tetronic 1107 (T1107) to the lysozyme solution were compared...
February 8, 2017: Physical Biology
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