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Integrative Biology: Quantitative Biosciences From Nano to Macro

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https://www.readbyqxmd.com/read/27868126/new-insights-into-mammalian-signaling-pathways-using-microfluidic-pulsatile-inputs-and-mathematical-modeling
#1
REVIEW
M Sumit, S Takayama, J J Linderman
Temporally modulated input mimics physiology. This chemical communication strategy filters the biochemical noise through entrainment and phase-locking. Under laboratory conditions, it also expands the observability space for downstream responses. A combined approach involving microfluidic pulsatile stimulation and mathematical modeling has led to deciphering of hidden/unknown temporal motifs in several mammalian signaling pathways and has provided mechanistic insights, including how these motifs combine to form distinct band-pass filters and govern fate regulation under dynamic microenvironment...
November 21, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27841423/improving-selective-targeting-to-macrophage-subpopulations-through-modifying-liposomes-with-arginine-based-materials
#2
Lilusi Ma, Hannah C Bygd, Kaitlin M Bratlie
The effects of surface modifications on liposomes using a library of arginine derivatives for improved drug delivery were examined. Both unmodified and modified liposomes were tested for their drug delivery properties and propensity for internalization by macrophages. All materials were characterized by dynamic light scattering (DLS) and zeta potential. The resulting liposomes were able to encapsulate doxorubicin with a loading efficiency greater than 90% and cumulative releases of less than 15% after 144 h...
November 14, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27747338/robust-regulation-of-hepatic-pericentral-amination-by-glutamate-dehydrogenase-kinetics
#3
Soumen Bera, Sanjay Lamba, Mubasher Rashid, Anuj K Sharma, Alexander B Medvinsky, Claudia Acquisti, Amit Chakraborty, Bai-Lian Li
Impaired glutamate dehydrogenase (GDH) sensitivity to its inhibitors causes excessive insulin secretion by pancreatic beta-cells and defective ammonia metabolism in the liver. These symptoms are commonly associated with hyperinsulinism/hyperammonemia syndrome (HI/HA), which causes recurrent hypoglycaemia in early infancy. Hepatic localization of GDH amination and deamination activities linked with the urea cycle is known to be involved in ammonia metabolism and detoxification. Although deamination activities of hepatic GDH in the periportal zones of liver lobules and its connection to the urea cycle have been exhaustively investigated, physiological roles of GDH amination activity observed at pericentral zones have often been overlooked...
October 17, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27738682/modulation-of-collective-cell-behaviour-by-geometrical-constraints
#4
Mariia Lunova, Vitalii Zablotskii, Nora M Dempsey, Thibaut Devillers, Milan Jirsa, Eva Syková, Šárka Kubinová, Oleg Lunov, Alexandr Dejneka
Intracellular and extracellular mechanical forces play a crucial role during tissue growth, modulating nuclear shape and function and resulting in complex collective cell behaviour. However, the mechanistic understanding of how the orientation, shape, symmetry and homogeneity of cells are affected by environmental geometry is still lacking. Here we investigate cooperative cell behaviour and patterns under geometric constraints created by topographically patterned substrates. We show how cells cooperatively adopt their geometry, shape, positioning of the nucleus and subsequent proliferation activity...
October 14, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27735002/measuring-systematic-changes-in-invasive-cancer-cell-shape-using-zernike-moments
#5
Elaheh Alizadeh, Samanthe Merrick Lyons, Jordan Marie Castle, Ashok Prasad
We study the shape characteristics of osteosarcoma cancer cell lines on surfaces of differing hydrophobicity using Zernike moments to represent cell shape. We compare the shape characteristics of four invasive cell lines with a corresponding less-invasive parental line on three substrates. Cell shapes of each pair of cell lines are quite close and display overlapping characteristics. To quantitatively study shape changes in high-dimensional parameter space we project down to principal component space and define a vector that summarizes average shape differences...
October 13, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27731447/allosteric-effects-of-atp-binding-on-the-nucleotide-binding-domain-of-a-heterodimeric-atp-binding-cassette-transporter
#6
Xianchao Pan, Qiaoxia Zhang, Sujun Qu, Shuheng Huang, Huicong Wang, Hu Mei
ATP-binding cassette (ABC) exporters mediate vital transport of a variety of molecules across the lipid bilayer in all organisms. To explore the allosteric effect of ATP binding at the asymmetric ATPase sites, molecular dynamics simulations were performed on the nucleotide-binding domains (NBDs) of a heterodimeric exporter TM287/288 in 4 different ATP-bound states. The results showed that ATP bound at the degenerate site can maintain a semi-open conformation of NBD1-NBD2, which may be defective in ATP hydrolysis...
October 12, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27723847/a-multiphysics-model-of-the-pacinian-corpuscle
#7
Julia C Quindlen, Henryk K Stolarski, Matthew D Johnson, Victor H Barocas
The Pacinian corpuscle (PC) is a dermal mechanoreceptor that responds to high-frequency (20-1000 Hz) vibrations. The PC's structure allows transmission of vibrations through its layers (lamellae) to the centrally-located nerve fiber (neurite). This work combines mechanical models of the PC with an electrochemical model of peripheral nerves to simulate the tactile response of the entire system. A three-stage model of response to a vibratory input was developed, consisting of (1) outer core mechanics, (2) inner core mechanics, and (3) neurite electrochemistry...
October 10, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27722366/differential-regulation-of-nsc-phenotype-and-genotype-by-chronically-activated-microglia-within-cocultures
#8
Kurt Farrell, Ali Borazjani, Margot Damaser, Chandrasekhar R Kothapalli
Under disease or injury conditions in the central nervous system (CNS), activated microglia release cytokines and chemokines to modulate the microenvironment and influence tissue remodeling. To exploit the full potential of neural stem cell (NSC) transplantation approaches, a permissive microenvironment needs to be created for their survival, homing and differentiation. To investigate the role of chronically activated microglia in the fate of NSCs, spontaneously immortalized murine microglial cells (SIM-A9) were cocultured with embryonic murine cortical NSCs on 2D substrates or within 3D gels...
October 10, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27918606/contents-list
#9
(no author information available yet)
No abstract text is available yet for this article.
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27918605/front-cover
#10
(no author information available yet)
No abstract text is available yet for this article.
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27918603/back-cover
#11
(no author information available yet)
No abstract text is available yet for this article.
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27853786/identification-and-isolation-of-antigen-specific-cytotoxic-t-lymphocytes-with-an-automated-microraft-sorting-system
#12
Peter J Attayek, Sally A Hunsucker, Christopher E Sims, Nancy L Allbritton, Paul M Armistead
The simultaneous measurement of T cell function with recovery of individual T cells would greatly facilitate characterizing antigen-specific responses both in vivo and in model systems. We have developed a microraft array methodology that automatically measures the ability of individual T cells to kill a population of target cells and viably sorts specific cells into a 96-well plate for expansion. A human T cell culture was generated against the influenza M1p antigen. Individual microrafts on a 70 × 70 array were loaded with on average 1 CD8(+) cell from the culture and a population of M1p presenting target cells...
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27845457/gotta-catch-em-all-the-microscale-quest-to-understand-cancer-biology
#13
Zhenwei Ma, Christopher Moraes
Developing an improved understanding of the processes that drive cancer initiation and progression has been the focus of intense research in recent years. Here, we highlight recent advances in the innovative use of microscale engineered technologies to gain new insight into the integrative biophysical mechanisms that drive these processes.
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27801472/accurate-prediction-of-the-age-incidence-of-chronic-myeloid-leukemia-with-an-improved-two-mutation-mathematical-model
#14
Paola Lecca, Claudio Sorio
Chronic myeloid leukemia (CML) is a malignant clonal disorder whose hallmark is a reciprocal translocation between chromosomes 9 and 22 occurring in 95% of affected patients. This translocation causes the expression of a deregulated BCR/ABL fusion oncogene and, interestingly, is detectable in healthy individuals. Based on this information we assumed that the sole presence of the BCR/ABL transcript represents a necessary but not sufficient event for the clonal expansion of CML precursors. We developed a mathematical model introducing a probability that any normal cell undergoes a first aberration, and a probability that a cell that experienced a first mutation undergoes a second mutation as well...
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27796394/mapping-lung-tumor-cell-drug-responses-as-a-function-of-matrix-context-and-genotype-using-cell-microarrays
#15
Kerim B Kaylan, Stefan D Gentile, Lauren E Milling, Kaustubh N Bhinge, Farhad Kosari, Gregory H Underhill
Carcinoma progression is influenced by interactions between epithelial tumor cells and components of their microenvironment. In particular, cell-extracellular matrix (ECM) interactions are known to drive tumor growth, metastatic potential, and sensitivity or resistance to therapy. Yet the intrinsic complexity of ECM composition within the tumor microenvironment remains a barrier to comprehensive investigation of these interactions. We present here a high-throughput cell microarray-based approach to study the impact of defined combinations of ECM proteins on tumor cell drug responses...
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27787529/self-assembly-of-vascularized-tissue-to-support-tumor-explants-in-vitro
#16
Despina Bazou, Nir Maimon, Gabriel Gruionu, Lance L Munn
Testing the efficacy of cancer drugs requires functional assays that recapitulate the cell populations, anatomy and biological responses of human tumors. Although current animal models and in vitro cell culture platforms are informative, they have significant shortcomings. Mouse models can reproduce tissue-level and systemic responses to tumor growth and treatments observed in humans, but xenografts from patients often do not grow, or require months to develop. On the other hand, current in vitro assays are useful for studying the molecular bases of tumorigenesis or drug activity, but often lack the appropriate in vivo cell heterogeneity and natural microenvironment...
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27785513/modulating-the-microtubule-tau-interactions-in-biomotility-systems-by-altering-the-chemical-environment
#17
S Bhattacharyya, K Kim, H Nakazawa, M Umetsu, W Teizer
Obstacles in microtubule mediated neuronal transport can trigger dementia. We use bio-motility assays, that simulate the neuron chemistry in axonopathy, to screen chemicals, that retain the microtubule dynamics in healthy neuronal activity. Tau protein inhibits microtubule activity and leads to oligomerization. Iron(iii) untangles, whereas mono-sodium-glutamate destabilizes the microtubule oligomer.
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27785511/investigation-of-the-adhesive-characteristics-of-polymer-protein-systems-through-molecular-dynamics-simulation-and-their-relation-to-cell-adhesion-and-proliferation
#18
Amir Shamloo, Morteza Sarmadi
Protein adhesion is a prevalent, however, intricate phenomenon that occurs immediately after exposure of a biomaterial to the biological system. A study on the adhesive characteristics of biomaterial-protein systems has encountered serious hurdles as experimental methods cannot properly capture the initial stages of protein adhesion, taking place within nano/picoseconds. This propels research studies toward utilizing computational approaches to gain an understanding of the interactions between different proteins and biomaterial surfaces...
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27775742/interstitial-flow-differentially-increases-patient-derived-glioblastoma-stem-cell-invasion-via-cxcr4-cxcl12-and-cd44-mediated-mechanisms
#19
Kathryn M Kingsmore, Daniel K Logsdon, Desiree H Floyd, Shayn M Peirce, Benjamin W Purow, Jennifer M Munson
Glioblastoma (GBM) prognosis remains dismal due in part to the invasiveness of GBM cells. Interstitial fluid flow (IFF) has been shown to increase invasion of glioma cells in vitro through the CXCR4 receptor interacting with autologous, pericellular gradients of CXCL12 (autologous chemotaxis) or through the CD44 receptor interactions with the extracellular matrix (hyaluronan-mediated mechanotransduction). These mechanisms have not been examined together and thus we hypothesized that both mechanisms contribute to invasion in populations of cancer cells...
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27761545/stiffness-of-pancreatic-cancer-cells-is-associated-with-increased-invasive-potential
#20
Angelyn V Nguyen, Kendra D Nyberg, Michael B Scott, Alia M Welsh, Andrew H Nguyen, Nanping Wu, Sophia V Hohlbauch, Nicholas A Geisse, Ewan A Gibb, A Gordon Robertson, Timothy R Donahue, Amy C Rowat
Metastasis is a fundamentally physical process in which cells are required to deform through narrow gaps as they invade surrounding tissues and transit to distant sites. In many cancers, more invasive cells are more deformable than less invasive cells, but the extent to which mechanical phenotype, or mechanotype, can predict disease aggressiveness in pancreatic ductal adenocarcinoma (PDAC) remains unclear. Here we investigate the invasive potential and mechanical properties of immortalized PDAC cell lines derived from primary tumors and a secondary metastatic site, as well as noncancerous pancreatic ductal cells...
December 5, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
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