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Physical Biology

Benjamin Croop, Kyu Young Han
The single-molecule pull-down (SiMPull) assay analyzes molecular complexes in physiological conditions from cell or tissue lysates. Currently the approach requires a lengthy sample preparation process, which has largely prevented the widespread adoption of this technique in bioanalysis. Here, we present a simplified SiMPull assay based upon dichlorodimethylsilane - Tween-20 passivation and F(ab) fragment labeling. Our passivation is a much shorter process than the standard polyethylene glycol passivation used in most single-molecule studies...
February 15, 2019: Physical Biology
Daniel Worroll, Giuseppe Galletti, Ada Gjyrezi, David Nanus, Scott T Tagawa, Paraskevi Giannakakou
Androgen receptor (AR) signaling drives prostate cancer (PC) progression and remains active upon transition to castration resistant prostate cancer (CRPC). Active AR signaling is achieved through the nuclear accumulation of AR following ligand binding and through expression of ligand-independent, constitutively active AR splice variants, such as AR-V7, which is the most commonly expressed variant in metastatic CRPC patients. Most currently approved PC therapies aim to abrogate AR signaling and activity by inhibiting this ligand-mediated nuclear translocation...
February 14, 2019: Physical Biology
Shaohua Chen, Wenxiang Xu, Jihan Kim, Hanqing Nan, Yu Zheng, Bo Sun, Yang Jiao
Accurately resolving the traction forces on active cells in 3D extra-cellular matrix (ECM) is crucial to understanding stress homeostasis in cellularized ECM systems and the resulting collective cellular behavior. The majority of 3D traction force microscopy techniques, which compute the stress distribution in ECM as well as cellular traction forces from experimentally measured deformation field in the ECM using dispersed tracing particles or fluorescently-tagged matrix proteins, have assumed a spatially homogeneous ECM with constant material properties at every location in the system...
February 5, 2019: Physical Biology
Sam P B van Beljouw, Simon van der Els, Koen J A Martens, Michiel Kleerebezem, Peter A Bron, Johannes Hohlbein
Lactic acid bacteria (LAB) are frequently used in food fermentation and are invaluable for the taste and nutritional value of the fermentation end-product. To gain a better understanding of underlying biochemical and microbiological mechanisms and cell-to-cell variability in LABs, single-molecule techniques such as single-particle tracking photo-activation localization microscopy (sptPALM) hold great promises but are not yet employed due to the lack of detailed protocols and suitable assays.
 Here, we qualitatively test various fluorescent proteins including variants that are photoactivatable and therefore suitable for sptPALM measurements in Lactococcus lactis, a key LAB for the dairy industry...
January 23, 2019: Physical Biology
Xiaokan Guo, Kalinga Pavan Thushara Silva, James Boedicker
Cell-cell interaction networks have been examined in many high diversity microbial communities using macroscale approaches. Microscale studies of multispecies communities are lacking and it remains unclear how macroscale trends scale down to small groups of cells. Experimental approaches using microfluidic devices have revealed heterogeneity in the behavior of single cells, however this analysis has not been extended towards the variability of cell-cell interactions. Using a microwell device, we analyzed cell growth within hundreds of replicate microbial communities consisting of two species and small population sizes...
January 21, 2019: Physical Biology
Jianhua Xing, Xiaojun Tian
The transition between epithelial and mesenchymal (EMT) is a fundamental cellular process that plays critical roles in development, cancer metastasis, and tissue wound healing. EMT is not a binary process but involves multiple partial EMT states that give rise to a high degree of cell state plasticity. Here, we first reviewed several studies on theoretical predictions and experimental verification of these intermediate states, the role of partial EMT on kidney fibrosis development, and how quantitative signaling information controls cell commitment to partial or full EMT upon transient signals...
January 21, 2019: Physical Biology
Jorge Gómez Tejeda Zañudo, M Tyler Guinn, Kevin Scott Farquhar, Mariola Szenk, Steven Nathaniel Steinway, Gabor Balazsi, Réka Albert
We present the epithelial-to-mesenchymal transition (EMT) from two perspectives: experimental/technological and theoretical. We review the state of the current understanding of the regulatory networks that underlie EMT in three physiological contexts: embryonic development, wound healing, and metastasis. We describe the existing experimental systems and manipulations used to better understand the molecular participants and factors that influence EMT and metastasis. We review the mathematical models of the regulatory networks involved in EMT, with a particular emphasis on the network motifs (such as coupled feedback loops) that can generate hybrid states that are intermediate between the epithelial and mesenchymal states...
January 17, 2019: Physical Biology
Nicholas Peter van der Munnik, Melissa Ann Moss, Mark Jacob Uline
Nanoparticles (NPs) constitute a powerful therapeutic platform with exciting prospects as potential inhibitors of amyloid-β (Aβ) aggregation, a process associated with Alzheimer's disease (AD). Researchers have synthesized and tested a large collection of NPs with disparate sizes, shapes, electrostatic properties and surface ligands that evoke a variety of responses on Aβ aggregation. In spite of a decade of research on the NP-Aβ system and many promising experimental results, NPs have failed to progress to any level of clinical trials for AD...
January 8, 2019: Physical Biology
Niraj Kumar, Rahul V Kulkarni
Post-transcriptional regulation of gene expression is often a critical component of cellular processes involved in cell-fate decisions. Correspondingly, considerable efforts have focused on modeling post-transcriptional regulation of stochastic gene expression and on quantifying its impact on the mean and variance of protein levels. However, the impact of post-transcriptional regulation on rare events corresponding to large deviations in gene expression is less well understood. Here, we study a simple model involving post-transcriptional control of gene expression and characterize the impact of regulation on large deviations in activity fluctuations...
January 4, 2019: Physical Biology
Chen-Yi Gao, Fabio Cecconi, Angelo Vulpiani, Haijun Zhou, Erik Aurell
Direct Coupling Analysis (DCA)is a now widely used method to leverage statistical information from many similar biological systems to draw meaningful conclusions on each system separately. DCA has been applied with great success to sequences of homologous proteins, and also more recently to whole-genome population-wide sequencing data. We here argue that the use of DCA on the genome scale is contingent on fundamental issues of population genetics. DCA can be expected to yield meaningful results when a population is in the Quasi-Linkage Equilibrium (QLE) phase studied by Kimura and others, but not, for instance, in a phase of Clonal Competition...
January 3, 2019: Physical Biology
Juan Raphael Diaz Simões, Denis Grebenkov, Paul Bourgine, Nadine Peyrieras
We investigate cell trajectories during zebrafish early embryogenesis based on 3D+time 2-photon microscopy imaging data. To remove the collective flow motion and focus on fluctuations, we analyze the deviations of pairs of neighboring cells. These deviations resemble Brownian motion and reveal different behaviors between pairs containing daughter cells generated by cell division and other pairs of neighboring cells. This observation justifies a common practice of using white noise fluctuations in modeling cell movement...
December 18, 2018: Physical Biology
Yutong Sha, Daniel Haensel, Guadalupe Gutierrez, Huijing Du, Xing Dai, Qing Nie
The transition of epithelial cells into a mesenchymal state (epithelial-to-mesenchymal transition or EMT) is a highly dynamic process implicated in various biological processes. During EMT, cells do not necessarily exist in "pure" epithelial or mesenchymal states. There are cells with mixed (or hybrid) features of the two, which are termed as the intermediate cell states (ICSs). While the exact functions of ICS remain elusive, together with EMT it appears to play important roles in embryogenesis, tissue development, and pathological processes such as cancer metastasis...
December 18, 2018: Physical Biology
Dongya Jia, Jason George, Satyendra Tripathi, Deepali Kundnani, Mingyang Lu, Samir Hanash, Jose Onuchic, Mohit Kumar Jolly, Herbert Levine
The epithelial-mesenchymal transition (EMT) plays a central role in cancer metastasis and drug resistance - two persistent clinical challenges. Epithelial cells can undergo a partial or full EMT, attaining either a hybrid epithelial/mesenchymal (E/M) or mesenchymal phenotype, respectively. Recent studies have emphasized that hybrid E/M cells may be more aggressive than their mesenchymal counterparts. However, mechanisms driving hybrid E/M phenotypes remain largely elusive. Here, to better characterize the hybrid E/M phenotype(s) and tumor aggressiveness, we integrate two computational methods - (a) RACIPE - to identify the robust gene expression patterns emerging from the dynamics of a given gene regulatory network, and (b) EMT scoring metric - to calculate the probability that a given gene expression profile displays a hybrid E/M phenotype...
December 17, 2018: Physical Biology
Kuheli Biswas, Mohit Kumar Jolly, Anandamohan Ghosh
Cancer metastasis and drug resistance remain unsolved clinical challenges. A phenotypic transition
 that is often implicated in both these processes is Epithelial-Mesenchymal Transition (EMT) during
 which epithelial cells weaken their cell-cell adhesion and gain traits of migration and invasion, typical
 of mesenchymal cells. However, recent studies indicate that apart from these two states, cells can also
 exist in one or more hybrid E/M state(s) which plays an aggressive role in progression of the disease...
December 11, 2018: Physical Biology
Yusuke Himeoka, Namiko Mitarai
In type-I toxin-antitoxin (TA) systems, the action of growth-inhibiting toxin proteins
 is counteracted by the antitoxin small RNAs (sRNAs) that prevent the translation of toxin
 messenger RNAs (mRNAs). When a TA module is encoded on a plasmid, the short lifetime
 of antitoxin sRNA compared to toxin mRNAs mediates post-segregational killing (PSK) that
 contribute the plasmid maintenance, while some of the chromosomal encoded TA loci have been
 reported to contribute to persister formation in response to a specific upstream signal...
November 26, 2018: Physical Biology
Anne Doerr, Elise de Reus, Pauline van Nies, Mischa van der Haar, Katy Wei, Johannes Kattan, Aljoscha Wahl, Christophe Danelon
DNA-guided cell-free protein synthesis using a minimal set of purified components has emerged as a versatile platform in constructive biology. The E. coli-based PURE (protein synthesis using recombinant elements) system offers the basic protein synthesis factory in a prospective minimal cell relying on extant molecules. However, there is an urgent need to improve the system's performance and to build a mechanistic computational model that can help interpret and predict gene expression dynamics. Herein, we utilized all three commercially available PURE system variants: PURExpress, PUREfrex and PUREfrex2...
January 9, 2019: Physical Biology
Balaramamahanti Srinivas, Manoj Gopalakrishnan
The microtubule-bound motors kinesin and dynein differ in many respects, a striking difference being that while kinesin is known to function mostly alone, dynein operates in large groups, much like myosinV in actin. Optical tweezer experiments in vitro have shown that the mean detachment time of a bead attached to [Formula: see text] kinesins under stall conditions is a slowly decreasing function of [Formula: see text], while for dyneins, the time increases almost linearly with [Formula: see text]. This makes dynein a team worker, capable of producing and sustaining a large collective force without detaching...
December 7, 2018: Physical Biology
M Akiyama, M Nonomura, A Tero, R Kobayashi
A method of numerical simulation of cell division using phase fields is presented. The cell division plane is obtained as a result of the spindle position and orientation considered with the spatial distribution of the activated cortical force generators and the dividing cell shape. To exemplify the application of the proposed method, numerical simulations of the development of cysts and early embryos are performed. The numerical results demonstrate that the activated cortical force generators that are localized at the lateral cortices of the epithelial cells lead to the formation of a single central lumen...
November 28, 2018: Physical Biology
Gregory R Hart, Andrew L Ferguson
Hepatitis C virus (HCV) afflicts 170 million people and kills 700 000 annually. Vaccination offers the most realistic and cost effective hope of controlling this epidemic, but despite 25 years of research, no vaccine is available. A major obstacle is HCV's extreme genetic variability and rapid mutational escape from immune pressure. Coupling maximum entropy inference with population dynamics simulations, we have employed a computational approach to translate HCV sequence databases into empirical landscapes of viral fitness and simulate the intrahost evolution of the viral quasispecies over these landscapes...
November 28, 2018: Physical Biology
Mario D'Acunto, Luisa Trombi, Delfo D'Alessandro, Serena Danti
Osteosarcoma is the most common primary malignant bone tumor. In the last years, several studies have demonstrated that the increase of Hydroxyapatite (HA) and Interleukin-6 (IL-6) syntheses compared to those expressed by normal osteoblasts could be used to detect the degree of malignancy of osteosarcoma cells. Conventional biochemical methods widely employed to evaluate bone cell differentiation, including normal and cancerous phenotypes, are time consuming and may require a large amount of cells. HA is a mineral form of calcium phosphate whose presence increases with maturation of osteosarcoma cells...
November 9, 2018: Physical Biology
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