Mechanobiology
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3D Printer Uses Microscopic Water Droplets That May Be Used For Tissue Engineering and Wound Healing

3D Printer Uses Microscopic Water Droplets That May Be Used For Tissue Engineering and Wound Healing | Mechanobiology | Scoop.it
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PAzQuvFPQL

#FDA draft guidance “Reporting of Computational Modeling Studies in Medical Device Submissions.” Read Here: http://t.co/PAzQuvFPQL
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Tiny swimming bio-bots boldly go where no bot has swum before - ScienceBlog.com (blog)

Tiny swimming bio-bots boldly go where no bot has swum before - ScienceBlog.com (blog) | Mechanobiology | Scoop.it
Tiny swimming bio-bots boldly go where no bot has swum before ScienceBlog.com (blog) “The most intriguing aspect of this work is that it demonstrates the capability to use computational modeling in conjunction with biological design to optimize...
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Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems (Computational Neuroscience) by Peter Dayan, Laurence F. Abbott - EbookNetworking.net

Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems (Computational Neuroscience) by Peter Dayan, Laurence F. Abbott - EbookNetworking.net | Mechanobiology | Scoop.it
Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems (Computational Neuroscience), a book by Peter Dayan, Laurence F.
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Computational Modeling of 3D Tumor Growth and Angiogenesis for Chemotherapy Evaluation

Computational Modeling of 3D Tumor Growth and Angiogenesis for Chemotherapy Evaluation | Mechanobiology | Scoop.it
Lei Tang, Anne L. van de Ven, Dongmin Guo, Vivi Andasari, Vittorio Cristini, King C. Li, Xiaobo Zhou Published: January 03, 2014 DOI: 10.1371/journal.pone.0083962 Solid tumors develop abnormally at spatial and temporal scales, giving rise to biophysical barriers that impact anti-tumor chemotherapy. This may increase the expenditure and time for conventional drug pharmacokinetic and pharmacodynamic studies. In order to facilitate drug discovery, we propose a mathematical model that couples three-dimensional tumor growth and angiogenesis to simulate tumor progression for chemotherapy evaluation. This application-oriented model incorporates complex dynamical processes including cell- and vascular-mediated interstitial pressure, mass transport, angiogenesis, cell proliferation, and vessel maturation to model tumor progression through multiple stages including tumor initiation, avascular growth, and transition from avascular to vascular growth. Compared to pure mechanistic models, the proposed empirical methods are not only easy to conduct but can provide realistic predictions and calculations. A series of computational simulations were conducted to demonstrate the advantages of the proposed comprehensive model. The computational simulation results suggest that solid tumor geometry is related to the interstitial pressure, such that tumors with high interstitial pressure are more likely to develop dendritic structures than those with low interstitial pressure.
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Biological transistor (transcriptor) enables computing within living cells

Biological transistor (transcriptor) enables computing within living cells | Mechanobiology | Scoop.it

ENIAC, the first modern computer developed in the 1940s, used vacuum tubes and electricity. Today, computers use transistors made from highly engineered semiconducting materials to carry out their logical operations. And now a team of Stanford University bioengineers has taken computing beyond mechanics and electronics into the living realm of biology. In a paper to be published March 28 in Science, the team details a biological transistor made from genetic material — DNA and RNA — in place of gears or electrons. The team calls its biological transistor the “transcriptor.”

 

“Transcriptors are the key component behind amplifying genetic logic — akin to the transistor and electronics,” said Jerome Bonnet, PhD, a postdoctoral scholar in bioengineering and the paper’s lead author. The creation of the transcriptor allows engineers to compute inside living cells to record, for instance, when cells have been exposed to certain external stimuli or environmental factors, or even to turn on and off cell reproduction as needed. “Biological computers can be used to study and reprogram living systems, monitor environments and improve cellular therapeutics,” said Drew Endy, PhD, assistant professor of bioengineering and the paper’s senior author.

In electronics, a transistor controls the flow of electrons along a circuit. Similarly, in biologics, a transcriptor controls the flow of a specific protein, RNA polymerase, as it travels along a strand of DNA.

 

“We have repurposed a group of natural proteins, called integrases, to realize digital control over the flow of RNA polymerase along DNA, which in turn allowed us to engineer amplifying genetic logic,” said Endy. Using transcriptors, the team has created what are known in electrical engineering as logic gates that can derive true-false answers to virtually any biochemical question that might be posed within a cell. They refer to their transcriptor-based logic gates as “Boolean Integrase Logic,” or “BIL gates” for short. Transcriptor-based gates alone do not constitute a computer, but they are the third and final component of a biological computer that could operate within individual living cells.

 

Despite their outward differences, all modern computers, from ENIAC to Apple, share three basic functions: storing, transmitting and performing logical operations on information.

 

Last year, Endy and his team made news in delivering the other two core components of a fully functional genetic computer. The first was a type of rewritable digital data storage within DNA. They also developed a mechanism for transmitting genetic information from cell to cell, a sort of biological Internet.

 

“The potential applications are limited only by the imagination of the researcher,” said co-author Monica Ortiz, a PhD candidate in bioengineering who demonstrated autonomous cell-to-cell communication of DNA encoding various BIL gates.

 

To create transcriptors and logic gates, the team used carefully calibrated combinations of enzymes — the integrases mentioned earlier — that control the flow of RNA polymerase along strands of DNA. If this were electronics, DNA is the wire and RNA polymerase is the electron.

 

“The choice of enzymes is important,” Bonnet said. “We have been careful to select enzymes that function in bacteria, fungi, plants and animals, so that bio-computers can be engineered within a variety of organisms.”

 

On the technical side, the transcriptor achieves a key similarity between the biological transistor and its semiconducting cousin: signal amplification. 

With transcriptors, a very small change in the expression of an integrase can create a very large change in the expression of any two other genes.

 

To understand the importance of amplification, consider that the transistor was first conceived as a way to replace expensive, inefficient and unreliable vacuum tubes in the amplification of telephone signals for transcontinental phone calls. Electrical signals traveling along wires get weaker the farther they travel, but if you put an amplifier every so often along the way, you can relay the signal across a great distance. The same would hold in biological systems as signals get transmitted among a group of cells.

 

“It is a concept similar to transistor radios,” said Pakpoom Subsoontorn, a PhD candidate in bioengineering and co-author of the study who developed theoretical models to predict the behavior of BIL gates. “Relatively weak radio waves traveling through the air can get amplified into sound.”


Via Dr. Stefan Gruenwald
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Synthetic two-way communication between mammalian cells

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Bacchus W, Lang M, El-Baba MD, Weber W, Stelling J, Fussenegger M.

"The design of synthetic biology-inspired control devices enabling entire mammalian cells to receive, process and transfer metabolic information and so communicate with each other via synthetic multichannel networks may provide new insight into the organization of multicellular organisms and future clinical interventions. Here we describe communication networks that orchestrate behavior in individual mammalian cells in response to cell-to-cell metabolic signals. We engineered sender, processor and receiver cells that interact with each other in ways that resemble natural intercellular communication networks such as multistep information processing cascades, feed-forward-based signaling loops, and two-way communication. The engineered two-way communication devices mimicking natural control systems in the development of vertebrate extremities and vasculature was used to program temporal permeability in vascular endothelial cell layers. These synthetic multicellular communication systems may inspire future therapies or tissue engineering strategies."
http://1.usa.gov/T00Sns


Via Gerd Moe-Behrens
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Vascular tissue engineering: the next generation.

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Cleary MA, Geiger E, Grady C, Best C, Naito Y, Breuer C.

"It is the ultimate goal of tissue engineering: an autologous tissue engineered vascular graft (TEVG) that is immunologically compatible, nonthrombogenic, and can grow and remodel. Currently, native vessels are the preferred vascular conduit for procedures such as coronary artery bypass (CABG) or peripheral bypass surgery. However, in many cases these are damaged, have already been harvested, or are simply unusable. The use of synthetic conduits is severely limited in smaller diameter vessels due to increased incidence of thrombosis, infection, and graft failure. Current research has therefore energetically pursued the development of a TEVG that can incorporate into a patient's circulatory system, mimic the vasoreactivity and biomechanics of the native vasculature, and maintain long-term patency."

 

 

http://1.usa.gov/TpZGrx


Via Gerd Moe-Behrens
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Computational Modeling of Synthetic Microbial Biofilm

Computational Modeling of Synthetic Microbial Biofilm | Mechanobiology | Scoop.it

Via Gerd Moe-Behrens
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Gerd Moe-Behrens's curator insight, March 17, 2013 1:12 PM

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Timothy J. Rudge, Paul J. Steiner, Andrew Phillips, and Jim Haseloff 

"Microbial biofilms are complex, self-organized communities of bacteria, which employ physiological cooperation and spatial organization to increase both their metabolic efficiency and their resistance to changes in their local environment. These properties make biofilms an attractive target for engineering, particularly for the production of chemicals such as pharmaceutical ingredients or biofuels, with the potential to significantly improve yields and lower maintenance costs. Biofilms are also a major cause of persistent infection, and a better understanding of their organization could lead to new strategies for their disruption. Despite this potential, the design of synthetic biofilms remains a major challenge, due to the complex interplay between transcriptional regulation, intercellular signaling, and cell biophysics. Computational modeling could help to address this challenge by predicting the behavior of synthetic biofilms prior to their construction; however, multiscale modeling has so far not been achieved for realistic cell numbers. This paper presents a computational method for modeling synthetic microbial biofilms, which combines three-dimensional biophysical models of individual cells with models of genetic regulation and intercellular signaling. The method is implemented as a software tool (CellModeller), which uses parallel Graphics Processing Unit architectures to scale to more than 30,000 cells, typical of a 100 μm diameter colony, in 30 min of computation ti..."

http://bit.ly/144Xnko

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Three-dimensional graphene foam as a biocompatible and conductive scaffold for neural stem cells

Three-dimensional graphene foam as a biocompatible and conductive scaffold for neural stem cells | Mechanobiology | Scoop.it

Neural stem cell (NSC) based therapy provides a promising approach for neural regeneration. For the success of NSC clinical application, a scaffold is required to provide three-dimensional (3D) cell growth microenvironments and appropriate synergistic cell guidance cues. A team of scientists reports now the first utilization of graphene foam, a 3D porous structure, as a novel scaffold for NSCs in vitro. It was found that three-dimensional graphene foams (3D-GFs) can not only support NSC growth, but also keep cell at an active proliferation state with upregulation of Ki67 expression than that of two-dimensional graphene films. Meanwhile, phenotypic analysis indicated that 3D-GFs can enhance the NSC differentiation towards astrocytes and especially neurons. Furthermore, a good electrical coupling of 3D-GFs with differentiated NSCs for efficient electrical stimulation was observed. These findings implicate 3D-GFs could offer a powerful platform for NSC research, neural tissue engineering and neural prostheses.


Via Dr. Stefan Gruenwald
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Organic Social Media's curator insight, May 2, 2014 1:30 PM

Three-dimensional #graphene foam as a biocompatible and conductive scaffold for neural stem cells

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A catalyst with a million uses - R & D Magazine

A catalyst with a million uses - R & D Magazine | Mechanobiology | Scoop.it
A catalyst with a million uses R & D Magazine Recent advances in surface studies of metals and computational modeling have given chemists new insights into how to promote more efficient catalytic transformations.
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'Bio-Bot' That Swims Like Sperm (VIDEO) - Headlines & Global News

'Bio-Bot' That Swims Like Sperm (VIDEO) - Headlines & Global News | Mechanobiology | Scoop.it
Headlines & Global News 'Bio-Bot' That Swims Like Sperm (VIDEO) Headlines & Global News "The most intriguing aspect of this work is that it demonstrates the capability to use computational modeling in conjunction with biological design to optimize...
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Pluripotent stem cells in regenerative medicine: challenges and recent progress : Nature Reviews Genetics

Pluripotent stem cells in regenerative medicine: challenges and recent progress : Nature Reviews Genetics | Mechanobiology | Scoop.it
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Organovo – The Company Behind The First Commercial Bioprinter - 3D Printing Industry

Organovo – The Company Behind The First Commercial Bioprinter - 3D Printing Industry | Mechanobiology | Scoop.it
Organovo is a company that specialises in bioprinting – the laboratory engineering of tissue. Bioengineering is also the focus of several other universities and research instates.

Via Gerd Moe-Behrens
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Outlines on nanotechnologies applied to bladder tissue engineering

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Alberti C.

"Tissue engineering technologies are more and more expanding as consequence of recent developments in the field of biomaterial science and nanotechnology research. An important issue in designing scaffold materials is that of recreating the ECM (extra-cellular matrix) functional features - particularly ECM-derived complex molecule signalling - to mimic its capability of directing cell-growth and neotissue morphogenesis. In this way the nanotechnology may offer intriguing chances, biomaterial nanoscale-based scaffold geometry behaving as nanomechanotransducer complex interacting with different cell nanosize proteins, especially with those of cell surface mechanoreceptors. To fabricate 3D-scaffold complex architectures, endowed with controlled geometry and functional properties, bottom-up approaches, based on molecular self-assembling of small building polymer units, are used, sometimes functionalizing them by incorporation of bioactive peptide sequences such as RDG (arginine - glycine - aspartic acid, a cell-integrin binding domain of fibronectin), whereas the top-down approaches are useful to fabricate micro/nanoscale structures, such as a microvasculature within an existing complex bioarchitecture. Synthetic polymer-based nanofibers, produced by electrospinning process, may be used to create fibrous scaffolds that can facilitate, given their nanostructured geometry and surface roughness, cell adhesion and growth. Also bladder tissue engineering may benefit by nanotechnology advances to achieve a better reliability of the bladder engineered tissue. Particularly, bladder smooth muscle cell adhesion to nanostructured polymeric surfaces is significantly enhanced in comparison with that to conventional biomaterials. Moreover nanostructured surfaces of bladder engineered tissue show a decreased calcium stone production. In a bladder tumor animal model, the dispersion of carbon nanofibers in a polymeric scaffold-based tissue engineered replacement neobladder, appears to inhibit a carcinogenic relapse in bladder prosthetic material. Facing the future, a full success of bladder tissue engineering will mainly depend on the progress of both biomaterial nanotechnologies and stem cell biology research..."
http://1.usa.gov/QLINT9


Via Gerd Moe-Behrens
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Robust Action Recognition Using Multi-Scale Spatial-Temporal Concatenations of Local Features as Natural Action Structures

Robust Action Recognition Using Multi-Scale Spatial-Temporal Concatenations of Local Features as Natural Action Structures | Mechanobiology | Scoop.it

Human and many other animals can detect, recognize, and classify natural actions in a very short time. How this is achieved by the visual system and how to make machines understand natural actions have been the focus of neurobiological studies and computational modeling in the last several decades. A key issue is what spatial-temporal features should be encoded and what the characteristics of their occurrences are in natural actions. Current global encoding schemes depend heavily on segmenting while local encoding schemes lack descriptive power. Here, we propose natural action structures, i.e., multi-size, multi-scale, spatial-temporal concatenations of local features, as the basic features for representing natural actions. In this concept, any action is a spatial-temporal concatenation of a set of natural action structures, which convey a full range of information about natural actions.

 

We took several steps to extract these structures. First, we sampled a large number of sequences of patches at multiple spatial-temporal scales. Second, we performed independent component analysis on the patch sequences and classified the independent components into clusters. Finally, we compiled a large set of natural action structures, with each corresponding to a unique combination of the clusters at the selected spatial-temporal scales. To classify human actions, we used a set of informative natural action structures as inputs to two widely used models. We found that the natural action structures obtained here achieved a significantly better recognition performance than low-level features and that the performance was better than or comparable to the best current models. We also found that the classification performance with natural action structures as features was slightly affected by changes of scale and artificially added noise. We concluded that the natural action structures proposed here can be used as the basic encoding units of actions and may hold the key to natural action understanding.


Via Ashish Umre
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*Supramolecular chemical biology; bioactive synthetic self-assemblies*

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Petkau-Milroy K, Brunsveld L.

"The regulation of recognition events in nature via dynamic and reversible self-assembly of building blocks has inspired the emergence of supramolecular architectures with similar biological activity. Synthetic molecules of diverse geometries self-assemble in water to target biological systems for applications ranging from imaging and diagnostics, through to drug delivery and tissue engineering. Many of these applications require the ability of the supramolecular system to actively recognize specific cell surface receptors. This molecular recognition is typically achieved with ligands, such as small molecules, peptides, and proteins, which are introduced either prior to or post self-assembly. Advantages of the non-covalent organization of ligands include the responsive nature of the self-assembled structures, the ease of supramolecular synthesis and the possibility to incorporate a multiple array of different ligands through pre-mixing of the building blocks. This review aims to highlight the diversity of self-assembled nanostructures constructed from mono-disperse synthetic building blocks; with a particular focus on their design, self-assembly, functionalization with bioactive ligands and effects thereof on the self-assembly, and possible applications."

http://1.usa.gov/WhXGjg


Via Gerd Moe-Behrens
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Segregation mechanisms of tissue cells: from experimental data to models

Considerable advance has been made in recent years in the research field of pattern formation by segregation of tissue cells. Research has become more quantitative partly due to more in-depth analysis of experimental data and the emergence modeling approaches. In this review we present experimental observations, including some of our new results, on various aspects of two and three dimensional segregation events and then summarize the computational modeling approaches.

 

Segregation mechanisms of tissue cells: from experimental data to models
Előd Méhes and Tamás Vicsek

Complex Adaptive Systems Modeling 2013, 1:4 http://dx.doi.org/10.1186/2194-3206-1-4


Via Complexity Digest
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Chemistry World : 3D Printing of a Soft Network ~ The *Official AndreasCY*

Chemistry World : 3D Printing of a Soft Network ~ The *Official AndreasCY* | Mechanobiology | Scoop.it

3D Printing technology could find it's way into tissue engineering applications, helping to support cells that are being grown into healthy new organs.


Via THE OFFICIAL ANDREASCY
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