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Physical Biology

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https://www.readbyqxmd.com/read/28198357/cgcorrect-a-method-to-correct-for-confounding-cell-cell-variation-due-to-cell-growth-in-single-cell-transcriptomics
#1
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
https://www.readbyqxmd.com/read/28169223/insights-into-the-ion-coupling-mechanism-in-the-mate-transporter-norm-vc
#2
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
https://www.readbyqxmd.com/read/28140372/expression-regulation-by-a-methyl-cpg-binding-domain-in-an-i-e-coli-i-based-cell-free-tx-tl-system
#3
Marc Schenkelberger, Siba Shanak, Marc Finkler, Emanuel Worst, Vincent Noireaux, Volkhard Helms, Albrecht 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<i> E. coli</i> 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...
January 31, 2017: Physical Biology
https://www.readbyqxmd.com/read/28140351/predicting-path-from-undulations-for-i-c-elegans-i-using-linear-and-nonlinear-resistive-force-theory
#4
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
https://www.readbyqxmd.com/read/28092269/analysis-of-microtubule-growth-dynamics-arising-from-altered-actin-network-structure-and-contractility-in-breast-tumor-cells
#5
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
https://www.readbyqxmd.com/read/28084220/motions-of-leaves-and-stems-from-growth-to-potential-use
#6
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
https://www.readbyqxmd.com/read/28207419/both-genome-and-cytosol-dynamics-change-in-e-coli-challenged-with-sublethal-rifampicin
#7
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
https://www.readbyqxmd.com/read/28140374/an-unsupervised-method-for-quantifying-the-behavior-of-paired-animals
#8
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
https://www.readbyqxmd.com/read/28140367/the-middle-lamella-more-than-a-glue
#9
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
https://www.readbyqxmd.com/read/28140350/from-molecules-to-cellular-networks-past-and-future-outlook
#10
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
https://www.readbyqxmd.com/read/28102174/modeling-dynamics-of-mutants-in-heterogeneous-stem-cell-niche
#11
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
https://www.readbyqxmd.com/read/28000612/post-translational-modifications-of-linker-histone-h1-variants-in-mammals
#12
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
https://www.readbyqxmd.com/read/28181475/on-the-micro-indentation-of-plant-cells-in-a-tissue-context
#13
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
https://www.readbyqxmd.com/read/28177933/theory-and-computations-in-biology-kamal-s-legacy
#14
D Thirumalai
No abstract text is available yet for this article.
February 8, 2017: Physical Biology
https://www.readbyqxmd.com/read/28177932/physical-concepts-in-biology-past-and-future
#15
Hans Frauenfelder
No abstract text is available yet for this article.
February 8, 2017: Physical Biology
https://www.readbyqxmd.com/read/28061483/amphiphilic-copolymers-reduce-aggregation-of-unfolded-lysozyme-more-effectively-than-polyethylene-glycol
#16
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
https://www.readbyqxmd.com/read/28054512/the-effect-of-reactions-on-the-formation-and-readout-of-the-gradient-of-bicoid
#17
Emiliano Perez Ipiña, Silvina Ponce Dawson
During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in Drosophila melanogaster embryos is well documented and studied. There are still controversies as to whether SDD models in which Bcd is Synthesized at one end, then Diffuses and is Degraded can explain the gradient formation within the timescale observed experimentally. The Bcd gradient is observed in embryos that express a Bicoid-eGFP fusion protein (Bcd-GFP) which cannot differentiate if Bcd is freely diffusing or bound to immobile sites...
February 8, 2017: Physical Biology
https://www.readbyqxmd.com/read/28169227/the-design-features-cells-use-to-build-their-transmembrane-proton-gradient
#18
M R Gunner, Ronald Koder
Organisms store energy from food and sunlight as an electrochemical gradient across the membranes of mitochondria, chloroplasts and bacteria. The gradient arises from differences in the concentration of protons and ions on the negative (N) and positive (P) sides of these membranes. This perspective describes how the proton gradient is formed. One strategy is the movement of electrons but not protons across a membrane-embedded protein from a site of proton-releasing oxidative chemistry on the P-side of the protein to a site of proton-binding reductive chemistry on the N-side...
February 7, 2017: Physical Biology
https://www.readbyqxmd.com/read/28169222/linking-computation-and-experiments-to-study-the-role-of-charge-charge-interactions-in-protein-folding-and-stability
#19
George I Makhatadze
Over the past two decades there has been an increase in appreciation for the role of surface charge-charge interactions in protein folding and stability. The perception shifted from the belief that charge-charge interactions are not important for protein folding and stability to the near quantitative understanding of how these interactions shape the folding energy landscape. This led to the ability of computational approaches to rationally redesign surface charge-charge interactions to modulate thermodynamic properties of proteins...
February 7, 2017: Physical Biology
https://www.readbyqxmd.com/read/28166059/systematic-exploration-of-unsupervised-methods-for-mapping-behavior
#20
Jeremy G Todd, Jamey S Kain, Benjamin L de Bivort
To fully understand the mechanisms giving rise to behavior, we need to be able to precisely measure it. When coupled with large behavioral data sets, unsupervised clustering methods offer the potential of unbiased mapping of behavioral spaces. However, unsupervised techniques to map behavioral spaces are in their infancy, and there have been few systematic considerations of all the methodological options. We compared the performance of seven distinct mapping methods in clustering a wavelet-transformed data set consisting of the x- and y-positions of the six legs of individual flies...
February 6, 2017: Physical Biology
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