Mammalian skin cell biology: at the interface between laboratory and clinic.

PubMed

Watt, Fiona M

2014-11-21

Mammalian skin research represents the convergence of three complementary disciplines: cell biology, mouse genetics, and dermatology. The skin provides a paradigm for current research in cell adhesion, inflammation, and tissue stem cells. Here, I discuss recent insights into the cell biology of skin. Single-cell analysis has revealed that human epidermal stem cells are heterogeneous and differentiate in response to multiple extrinsic signals. Live-cell imaging, optogenetics, and cell ablation experiments show skin cells to be remarkably dynamic. High-throughput, genome-wide approaches have yielded unprecedented insights into the circuitry that controls epidermal stem cell fate. Last, integrative biological analysis of human skin disorders has revealed unexpected functions for elements of the skin that were previously considered purely structural. Copyright © 2014, American Association for the Advancement of Science.

Cell Migration Analysis: A Low-Cost Laboratory Experiment for Cell and Developmental Biology Courses Using Keratocytes from Fish Scales

ERIC Educational Resources Information Center

Prieto, Daniel; Aparicio, Gonzalo; Sotelo-Silveira, Jose R.

2017-01-01

Cell and developmental processes are complex, and profoundly dependent on spatial relationships that change over time. Innovative educational or teaching strategies are always needed to foster deep comprehension of these processes and their dynamic features. However, laboratory exercises in cell and developmental biology at the undergraduate level…

A reverse engineering approach to optimize experiments for the construction of biological regulatory networks.

PubMed

Zhang, Xiaomeng; Shao, Bin; Wu, Yangle; Qi, Ouyang

2013-01-01

One of the major objectives in systems biology is to understand the relation between the topological structures and the dynamics of biological regulatory networks. In this context, various mathematical tools have been developed to deduct structures of regulatory networks from microarray expression data. In general, from a single data set, one cannot deduct the whole network structure; additional expression data are usually needed. Thus how to design a microarray expression experiment in order to get the most information is a practical problem in systems biology. Here we propose three methods, namely, maximum distance method, trajectory entropy method, and sampling method, to derive the optimal initial conditions for experiments. The performance of these methods is tested and evaluated in three well-known regulatory networks (budding yeast cell cycle, fission yeast cell cycle, and E. coli. SOS network). Based on the evaluation, we propose an efficient strategy for the design of microarray expression experiments.

Dynamic cell culture system: a new cell cultivation instrument for biological experiments in space

NASA Technical Reports Server (NTRS)

Gmunder, F. K.; Nordau, C. G.; Tschopp, A.; Huber, B.; Cogoli, A.

1988-01-01

The prototype of a miniaturized cell cultivation instrument for animal cell culture experiments aboard Spacelab is presented (Dynamic cell culture system: DCCS). The cell chamber is completely filled and has a working volume of 200 microliters. Medium exchange is achieved with a self-powered osmotic pump (flowrate 1 microliter h-1). The reservoir volume of culture medium is 230 microliters. The system is neither mechanically stirred nor equipped with sensors. Hamster kidney (Hak) cells growing on Cytodex 3 microcarriers were used to test the biological performance of the DCCS. Growth characteristics in the DCCS, as judged by maximal cell density, glucose consumption, lactic acid secretion and pH, were similar to those in cell culture tubes.

Cellular changes in microgravity and the design of space radiation experiments

NASA Technical Reports Server (NTRS)

Morrison, D. R.

1994-01-01

Cell metabolism, secretion and cell-cell interactions can be altered during space flight. Early radiobiology experiments have demonstrated synergistic effects of radiation and microgravity as indicated by increased mutagenesis, increased chromosome aberrations, inhibited development, and retarded growth. Microgravity-induced changes in immune cell functions include reduced blastogenesis and cell-mediated, delayed-type hypersensitivity responses, increased cytokine secretions, but inhibited cytotoxic effects an macrophage differentiation. These effects are important because of the high radiosensitivity of immune cells. It is difficult to compare ground studies with space radiation biology experiments because of the complexity of the space radiation environment, types of radiation damage and repair mechanisms. Altered intracellular functions and molecular mechanisms must be considered in the design and interpretation of space radiation experiments. Critical steps in radiocarcinogenesis could be affected. New cell systems and hardware are needed to determine the biological effectiveness of the low dose rate, isotropic, multispectral space radiation and the potential usefulness of radioprotectants during space flight.

Multiweek Cell Culture Project for Use in Upper-Level Biology Laboratories

ERIC Educational Resources Information Center

Marion, Rebecca E.; Gardner, Grant E.; Parks, Lisa D.

2012-01-01

This article describes a laboratory protocol for a multiweek project piloted in a new upper-level biology laboratory (BIO 426) using cell culture techniques. Human embryonic kidney-293 cells were used, and several culture media and supplements were identified for students to design their own experiments. Treatments included amino acids, EGF,…

Glucose Transport in Cultured Animal Cells: An Exercise for the Undergraduate Cell Biology Laboratory

ERIC Educational Resources Information Center

Ledbetter, Mary Lee S.; Lippert, Malcolm J.

2002-01-01

Membrane transport is a fundamental concept that undergraduate students of cell biology understand better with laboratory experience. Formal teaching exercises commonly used to illustrate this concept are unbiological, qualitative, or intricate and time consuming to prepare. We have developed an exercise that uses uptake of radiolabeled nutrient…

Biology Notes.

ERIC Educational Resources Information Center

School Science Review, 1979

1979-01-01

Organized by topic is a reading list for A- and S-level biology. Described are experiments for measuring rate of water uptake in a shoot; questions to aid students in designing experiments; rise of overhead projection to demonstrate osmosis and blood cell counting; and microbial manufacture of vinegar. (CS)

Serotonin (5-HT) released by activated white blood cells in a biological fuel cell provide a potential energy source for electricity generation.

PubMed

Justin, Gusphyl A; Sun, Mingui; Zhang, Yingze; Cui, X Tracy; Sclabassi, Robert

2006-01-01

Previous studies by our group have demonstrated the ability of white blood cells to generate small electrical currents, on the order of 1-3 microA/cm(2), when placed at the anode compartment of a proton exchange membrane (PEM) biological fuel cell. In this research study, an electrochemical technique is used to further investigate the electron transfer ability of activated white blood cells at interfacing electrodes in an attempt to elucidate the mechanism of electron transfer in the original biological fuel cell experiments. Cyclic voltammograms were obtained for human white blood cells using a three-electrode system. The working and counter electrodes were made from carbon felt and platinum, respectively, while the reference was a saturated calomel electrode (SCE). Oxidation peaks were observed at an average potential of 363 mV vs. SCE for the PMA/ionomycin activated white blood cells in glucose solution. However a corresponding reduction peak was not observed, suggesting irreversibility of the redox reaction. The cyclic voltammograms recorded for the white blood cells bear very close similarities to those of the neurotransmitter serotonin (5-HT). Serotonin released by white blood cells into the extracellular environment may be irreversibly oxidized at the working electrode in the cyclic voltammetry experiments and at the PEM biological fuel cell anode in our earlier electrochemical cell studies.

“Sickle cell anemia: tracking down a mutation”: an interactive learning laboratory that communicates basic principles of genetics and cellular biology

PubMed Central

Jarrett, Kevin; Williams, Mary; Horn, Spencer; Radford, David

2016-01-01

“Sickle cell anemia: tracking down a mutation” is a full-day, inquiry-based, biology experience for high school students enrolled in genetics or advanced biology courses. In the experience, students use restriction endonuclease digestion, cellulose acetate gel electrophoresis, and microscopy to discover which of three putative patients have the sickle cell genotype/phenotype using DNA and blood samples from wild-type and transgenic mice that carry a sickle cell mutation. The inquiry-based, problem-solving approach facilitates the students' understanding of the basic concepts of genetics and cellular and molecular biology and provides experience with contemporary tools of biotechnology. It also leads to students' appreciation of the causes and consequences of this genetic disease, which is relatively common in individuals of African descent, and increases their understanding of the first principles of genetics. This protocol provides optimal learning when led by well-trained facilitators (including the classroom teacher) and carried out in small groups (6:1 student-to-teacher ratio). This high-quality experience can be offered to a large number of students at a relatively low cost, and it is especially effective in collaboration with a local science museum and/or university. Over the past 15 yr, >12,000 students have completed this inquiry-based learning experience and demonstrated a consistent, substantial increase in their understanding of the disease and genetics in general. PMID:26873898

"Sickle cell anemia: tracking down a mutation": an interactive learning laboratory that communicates basic principles of genetics and cellular biology.

PubMed

Jarrett, Kevin; Williams, Mary; Horn, Spencer; Radford, David; Wyss, J Michael

2016-03-01

"Sickle cell anemia: tracking down a mutation" is a full-day, inquiry-based, biology experience for high school students enrolled in genetics or advanced biology courses. In the experience, students use restriction endonuclease digestion, cellulose acetate gel electrophoresis, and microscopy to discover which of three putative patients have the sickle cell genotype/phenotype using DNA and blood samples from wild-type and transgenic mice that carry a sickle cell mutation. The inquiry-based, problem-solving approach facilitates the students' understanding of the basic concepts of genetics and cellular and molecular biology and provides experience with contemporary tools of biotechnology. It also leads to students' appreciation of the causes and consequences of this genetic disease, which is relatively common in individuals of African descent, and increases their understanding of the first principles of genetics. This protocol provides optimal learning when led by well-trained facilitators (including the classroom teacher) and carried out in small groups (6:1 student-to-teacher ratio). This high-quality experience can be offered to a large number of students at a relatively low cost, and it is especially effective in collaboration with a local science museum and/or university. Over the past 15 yr, >12,000 students have completed this inquiry-based learning experience and demonstrated a consistent, substantial increase in their understanding of the disease and genetics in general. Copyright © 2016 The American Physiological Society.

Full load of ESA experiments on Maxus-2 sounding rocket

NASA Astrophysics Data System (ADS)

1995-11-01

Maxus sounding rockets are built and commercialised by an industrial joint venture, a team comprising of the Swedish Space Corporation (SSC) and DASA of Germany. ESA is fully funding the scientific payload for this mission. The payload comprises 8 experiments spanning the fields of fluid physics, electrophoresis and cell biology. Scientists from Belgium, France, Germany and Switzerland designed these experiments and the hardware was built by Swedish, German and Italian firms. The experiments are accommodated in 5 autonomous experiment modules and account for an overall mass of about 500 kg out of a total payload of about 800 kg. The first module contains an experiment which aims to check the static and dynamic behaviour of liquids at corners and edges. The second contains a biological experiment on two unicellular organisms (loxodes and paramecium). In their natural habitat (lakes), these organisms make use of the gravity vector for their orientation. Their swimming behaviour in microgravity will be observed on Earth in real time. The third module houses two other biology experiments. One examines the effect of microgravity on particle ingestion of gold beads by human macrophage cells (a type of white blood cell). Macrophage cells digest foreign particles, such as bacteria and viruses, thereby performing an important function in our immune system. The other experiment investigates the influence of weightlessness on the structure of lymphocytes (white blood cells). The fourth module accommodates three different experiments all dealing with convection phenomena due to surface-tension instabilities (Marangoni convection). Surface tension is that property of liquids which makes raindrops nearly spherical and allows insects to move on water surfaces. These phenomena, which are masked by the effect of gravity on Earth, can be easily studied in microgravity conditions. The fifth module contains an experiment that deals with electrophoresis, i.e. a process which is used to separate biological products in solution by application of a strong electric field. A highly concentrated solution with two proteins will be separated into its fractions and collected in a set of 59 syringes.

Droplet microfluidics for synthetic biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gach, Philip Charles; Iwai, Kosuke; Kim, Peter Wonhee

Here, synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility. Liquid handling robotics may reduce labor and improve reproducibility, but are themselves expensive and thus inaccessible to mostmore » researchers. Microfluidic platforms offer a lower entry price point alternative to robotics, and maintain high throughput and reproducibility while further reducing operating costs through diminished reagent volume requirements. Droplet microfluidics have shown exceptional promise for synthetic biology experiments, including DNA assembly, transformation/transfection, culturing, cell sorting, phenotypic assays, artificial cells and genetic circuits.« less

Droplet microfluidics for synthetic biology

DOE PAGES

Gach, Philip Charles; Iwai, Kosuke; Kim, Peter Wonhee; ...

2017-08-10

Here, synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility. Liquid handling robotics may reduce labor and improve reproducibility, but are themselves expensive and thus inaccessible to mostmore » researchers. Microfluidic platforms offer a lower entry price point alternative to robotics, and maintain high throughput and reproducibility while further reducing operating costs through diminished reagent volume requirements. Droplet microfluidics have shown exceptional promise for synthetic biology experiments, including DNA assembly, transformation/transfection, culturing, cell sorting, phenotypic assays, artificial cells and genetic circuits.« less

A Constructivist Approach to Inquiry-Based Learning: A TUNEL Assay for the Detection of Apoptosis in Cheek Cells

ERIC Educational Resources Information Center

Correiro, Elizabeth E.; Griffin, Leanne R.; Hart, Peter E.

2008-01-01

A laboratory exercise is presented that incorporates constructivist principles into a learning experience designed for upper-level university biology courses. The specific objectives for this exercise are as follows: (1) To introduce students to cancer biology and to the regulation of programmed cell death as part of the cell cycle; (2) To engage…

[Cell biology researches aboard the robotic space vehicles: preparation and performance].

PubMed

Tairbekov, M G

2006-01-01

The article reviews the unique aspects of preparation and performance of cell biology experiments flown on robotic space vehicles Bion and Foton, and gives an overview of key findings in researches made under the author's leadership over the past decades. Described are the criteria of selecting test objects, and the conditions required for preparation and implementation of space and control (synchronous) experiments. The present-day status and issues of researches into cell responsivity to space microgravity and other factors are discussed. Also, potentialities of equipment designed to conduct experiments with cell cultures in vitro and populations of single-celled organisms are presented, as well as some ideas for new devices and systems. Unveiled are some circumstances inherent to the development and performance of space experiments, setting up laboratory facilities at the launch and landing site, and methods of safe transportation and storage of biosamples. In conclusion, the author puts forward his view on biospecies, equipment and areas of research aboard future space vehicles.

Experiences of Judeo-Christian Students in Undergraduate Biology.

PubMed

Barnes, M Elizabeth; Truong, Jasmine M; Brownell, Sara E

2017-01-01

A major research thrust in science, technology, engineering, and mathematics (STEM) education is focused on how to retain students as STEM majors. The accumulation of seemingly insignificant negative experiences in STEM classes can, over time, lead STEM students to have a low sense of belonging in their disciplines, and this can lead to lower retention. In this paper, we explore how Judeo-Christian students in biology have experiences related to their religious identities that could impact their retention in biology. In 28 interviews with Judeo-Christian students taking undergraduate biology classes, students reported a religious identity that can conflict with the secular culture and content of biology. Some students felt that, because they are religious, they fall within a minority in their classes and would not be seen as credible within the biology community. Students reported adverse experiences when instructors had negative dispositions toward religion and when instructors were rigid in their instructional practices when teaching evolution. These data suggest that this may be a population susceptible to experiences of cultural conflict between their religious identities and their STEM identities, which could have implications for retention. We argue that more research should explore how Judeo-Christian students' experiences in biology classes influence their sense of belonging and retention. © 2017 M. E. Barnes et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Generation of monodisperse cell-sized microdroplets using a centrifuge-based axisymmetric co-flowing microfluidic device.

PubMed

Yamashita, Hitoyoshi; Morita, Masamune; Sugiura, Haruka; Fujiwara, Kei; Onoe, Hiroaki; Takinoue, Masahiro

2015-04-01

We report an easy-to-use generation method of biologically compatible monodisperse water-in-oil microdroplets using a glass-capillary-based microfluidic device in a tabletop mini-centrifuge. This device does not require complicated microfabrication; furthermore, only a small sample volume is required in experiments. Therefore, we believe that this method will assist biochemical and cell-biological experiments. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Calculations of the Acceleration of Centrifugal Loading on Adherent Cells

NASA Astrophysics Data System (ADS)

Chen, Kang; Song, Yang; Liu, Qing; Zhang, Chunqiu

2017-07-01

Studies have shown that the morphology and function of living cells are greatly affected by the state of different high acceleration. Based on the centrifuge, we designed a centrifugal cell loading machine for the mechanical biology of cells under high acceleration loading. For the machine, the feasibility of the experiment was studied by means of constant acceleration or variable acceleration loading in the Petri dish fixture and/or culture flask. Here we analyzed the distribution of the acceleration of the cells with the change of position and size of the culturing device quantitatively. It is obtained that Petri dish fixture and/or culture flask can be used for constant acceleration loading by experiments; the centripetal acceleration of the adherent cells increases with the increase of the distance between the rotor center of the centrifuge and the fixture of the Petri dish and the size of the fixture. It achieves the idea that the general biology laboratory can conduct the study of mechanical biology at high acceleration. It also provides a basis for more accurate study of the law of high acceleration on mechanobiology of cells.

The Next Frontier: Quantitative Biochemistry in Living Cells.

PubMed

Honigmann, Alf; Nadler, André

2018-01-09

Researchers striving to convert biology into an exact science foremost rely on structural biology and biochemical reconstitution approaches to obtain quantitative data. However, cell biological research is moving at an ever-accelerating speed into areas where these approaches lose much of their edge. Intrinsically unstructured proteins and biochemical interaction networks composed of interchangeable, multivalent, and unspecific interactions pose unique challenges to quantitative biology, as do processes that occur in discrete cellular microenvironments. Here we argue that a conceptual change in our way of conducting biochemical experiments is required to take on these new challenges. We propose that reconstitution of cellular processes in vitro should be much more focused on mimicking the cellular environment in vivo, an approach that requires detailed knowledge of the material properties of cellular compartments, essentially requiring a material science of the cell. In a similar vein, we suggest that quantitative biochemical experiments in vitro should be accompanied by corresponding experiments in vivo, as many newly relevant cellular processes are highly context-dependent. In essence, this constitutes a call for chemical biologists to convert their discipline from a proof-of-principle science to an area that could rightfully be called quantitative biochemistry in living cells. In this essay, we discuss novel techniques and experimental strategies with regard to their potential to fulfill such ambitious aims.

Vision-guided micromanipulation system for biomedical application

NASA Astrophysics Data System (ADS)

Shim, Jae-Hong; Cho, Sung-Yong; Cha, Dong-Hyuk

2004-10-01

In these days, various researches for biomedical application of robots have been carried out. Particularly, robotic manipulation of the biological cells has been studied by many researchers. Usually, most of the biological cell's shape is sphere. Commercial biological manipulation systems have been utilized the 2-Dimensional images through the optical microscopes only. Moreover, manipulation of the biological cells mainly depends on the subjective viewpoint of an operator. Due to these reasons, there exist lots of problems such as slippery and destruction of the cell membrane and damage of the pipette tip etc. In order to overcome the problems, we have proposed a vision-guided biological cell manipulation system. The newly proposed manipulation system makes use of vision and graphic techniques. Through the proposed procedures, an operator can inject the biological cell scientifically and objectively. Also, the proposed manipulation system can measure the contact force occurred at injection of a biological cell. It can be transmitted a measured force to the operator by the proposed haptic device. Consequently, the proposed manipulation system could safely handle the biological cells without any damage. This paper presents the introduction of our vision-guided manipulation techniques and the concept of the contact force sensing. Through a series of experiments the proposed vision-guided manipulation system shows the possibility of application for precision manipulation of the biological cell such as DNA.

Tissue aging: the integration of collective and variant responses of cells to entropic forces over time.

PubMed

Todhunter, Michael E; Sayaman, Rosalyn W; Miyano, Masaru; LaBarge, Mark A

2018-06-13

Aging is driven by unavoidable entropic forces, physicochemical in nature, that damage the raw materials that constitute biological systems. Single cells experience and respond to stochastic physicochemical insults that occur either to the cells themselves or to their microenvironment, in a dynamic and reciprocal manner, leading to increased age-related cell-to-cell variation. We will discuss the biological mechanisms that integrate cell-to-cell variation across tissues resulting in stereotypical phenotypes of age. Copyright © 2018 Elsevier Ltd. All rights reserved.

Extracting Cell Stiffness from Real-Time Deformability Cytometry: Theory and Experiment.

PubMed

Mietke, Alexander; Otto, Oliver; Girardo, Salvatore; Rosendahl, Philipp; Taubenberger, Anna; Golfier, Stefan; Ulbricht, Elke; Aland, Sebastian; Guck, Jochen; Fischer-Friedrich, Elisabeth

2015-11-17

Cell stiffness is a sensitive indicator of physiological and pathological changes in cells, with many potential applications in biology and medicine. A new method, real-time deformability cytometry, probes cell stiffness at high throughput by exposing cells to a shear flow in a microfluidic channel, allowing for mechanical phenotyping based on single-cell deformability. However, observed deformations of cells in the channel not only are determined by cell stiffness, but also depend on cell size relative to channel size. Here, we disentangle mutual contributions of cell size and cell stiffness to cell deformation by a theoretical analysis in terms of hydrodynamics and linear elasticity theory. Performing real-time deformability cytometry experiments on both model spheres of known elasticity and biological cells, we demonstrate that our analytical model not only predicts deformed shapes inside the channel but also allows for quantification of cell mechanical parameters. Thereby, fast and quantitative mechanical sampling of large cell populations becomes feasible. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Extracting Cell Stiffness from Real-Time Deformability Cytometry: Theory and Experiment

PubMed Central

Mietke, Alexander; Otto, Oliver; Girardo, Salvatore; Rosendahl, Philipp; Taubenberger, Anna; Golfier, Stefan; Ulbricht, Elke; Aland, Sebastian; Guck, Jochen; Fischer-Friedrich, Elisabeth

2015-01-01

Cell stiffness is a sensitive indicator of physiological and pathological changes in cells, with many potential applications in biology and medicine. A new method, real-time deformability cytometry, probes cell stiffness at high throughput by exposing cells to a shear flow in a microfluidic channel, allowing for mechanical phenotyping based on single-cell deformability. However, observed deformations of cells in the channel not only are determined by cell stiffness, but also depend on cell size relative to channel size. Here, we disentangle mutual contributions of cell size and cell stiffness to cell deformation by a theoretical analysis in terms of hydrodynamics and linear elasticity theory. Performing real-time deformability cytometry experiments on both model spheres of known elasticity and biological cells, we demonstrate that our analytical model not only predicts deformed shapes inside the channel but also allows for quantification of cell mechanical parameters. Thereby, fast and quantitative mechanical sampling of large cell populations becomes feasible. PMID:26588562

Collective Behavior of Brain Tumor Cells: the Role of Hypoxia

NASA Astrophysics Data System (ADS)

Khain, Evgeniy; Katakowski, Mark; Hopkins, Scott; Szalad, Alexandra; Zheng, Xuguang; Jiang, Feng; Chopp, Michael

2013-03-01

We consider emergent collective behavior of a multicellular biological system. Specifically we investigate the role of hypoxia (lack of oxygen) in migration of brain tumor cells. We performed two series of cell migration experiments. The first set of experiments was performed in a typical wound healing geometry: cells were placed on a substrate, and a scratch was done. In the second set of experiments, cell migration away from a tumor spheroid was investigated. Experiments show a controversy: cells under normal and hypoxic conditions have migrated the same distance in the ``spheroid'' experiment, while in the ``scratch'' experiment cells under normal conditions migrated much faster than under hypoxic conditions. To explain this paradox, we formulate a discrete stochastic model for cell dynamics. The theoretical model explains our experimental observations and suggests that hypoxia decreases both the motility of cells and the strength of cell-cell adhesion. The theoretical predictions were further verified in independent experiments.

Evaluation of the health impact of aerosols emitted from different combustion sources: Comprehensive characterization of the aerosol physicochemical properties as well as the molecular biological and toxicological effects of the aerosols on human lung cells and macrophages.

NASA Astrophysics Data System (ADS)

Zimmermann, R.; Dittmar, G.; Kanashova, T.; Buters, J.; Öder, S.; Paur, H. R.; Mülhopt, S.; Dilger, M.; Weiss, C.; Harndorf, H.; Stengel, B.; Hirvonen, M. R.; Jokiniemi, J.; Hiller, K.; Sapcariu, S.; Sippula, O.; Streibel, T.; Karg, E.; Weggler, B.; Schnelle-Kreis, J.; Lintelmann, J.; Sklorz, M.; Orasche, J.; Müller, L.; Passig, J.; Gröger, T.; Jalava, P. I.; Happo, M.; Uski, O.

2016-12-01

A novel approach to evaluate the health effects of anthropogenic combustion emissions is the detailed comparison of comprehensive physicochemical data on the combustion aerosol properties with the biological response of aerosol-exposed lung cells. In this context the "HICE-Aerosol and Health" project consortium studies the properties as well as the biological and toxicological effects on lung cells induced by different combustion aerosol emissions (e.g. ship diesel exhaust, wood combustion effluents or automobile aerosol). Human alveolar epithelial cells (e.g. A549 cells) as well as murine macrophages were exposed to diluted emissions, using field deployable ALI-exposition systems in a mobile S2-biological laboratory. This allows a realistic lung-cell exposure by simulation of the lung situation. The cellular effects were then comprehensively characterized (cytotoxicology, transcriptomics, proteomics etc.) effects monitoring and put in context with the chemical and physical aerosol data. Emissions of wood combustion, a ship engine as well as diesel and gasoline engines were investigated. Furthermore for some experiments the atmospheric aging of the emission was simulated in a flow tube reactor using UV-light and ozone. Briefly the following order of cellular response-strength was observed: A relatively mild cellular effect is observed for the diluted wood combustion emissions, regardless if log-wood and pellet burner emissions are investigated. Similarly mild biological effects are observed for gasoline car emissions. The ship diesel engine emissions and construction machine diesel engine induced much more intense biological responses. A surprising result in this context is, that heavy fuel oil (HFO)-emissions show lower biological effect strengths than the supposedly cleaner diesel fuel emissions (DF). The HFO-emissions contain high concentrations of known toxicants (metals, polycyclic aromatics). This result was confirmed by experiments with murine macrophages. Detailed analyses suggest a large difference in relative toxicity for different combustion sources. Recently the cell experiments were successively evaluated and verified by animal exposure tests. This is important to develop a reliable animal-test free-monitoring method for aerosol-induced health effects.

Evaluation of the health impact of aerosols emitted from different combustion sources: Comprehensive characterization of the aerosol physicochemical properties as well as the molecular biological and toxicological effects of the aerosols on human lung cells and macrophages.

NASA Astrophysics Data System (ADS)

Zimmermann, R.; Dittmar, G.; Kanashova, T.; Buters, J.; Öder, S.; Paur, H. R.; Mülhopt, S.; Dilger, M.; Weiss, C.; Harndorf, H.; Stengel, B.; Hirvonen, M. R.; Jokiniemi, J.; Hiller, K.; Sapcariu, S.; Sippula, O.; Streibel, T.; Karg, E.; Weggler, B.; Schnelle-Kreis, J.; Lintelmann, J.; Sklorz, M.; Orasche, J.; Müller, L.; Passig, J.; Gröger, T.; Jalava, P. I.; Happo, M.; Uski, O.

2017-12-01

A novel approach to evaluate the health effects of anthropogenic combustion emissions is the detailed comparison of comprehensive physicochemical data on the combustion aerosol properties with the biological response of aerosol-exposed lung cells. In this context the "HICE-Aerosol and Health" project consortium studies the properties as well as the biological and toxicological effects on lung cells induced by different combustion aerosol emissions (e.g. ship diesel exhaust, wood combustion effluents or automobile aerosol). Human alveolar epithelial cells (e.g. A549 cells) as well as murine macrophages were exposed to diluted emissions, using field deployable ALI-exposition systems in a mobile S2-biological laboratory. This allows a realistic lung-cell exposure by simulation of the lung situation. The cellular effects were then comprehensively characterized (cytotoxicology, transcriptomics, proteomics etc.) effects monitoring and put in context with the chemical and physical aerosol data. Emissions of wood combustion, a ship engine as well as diesel and gasoline engines were investigated. Furthermore for some experiments the atmospheric aging of the emission was simulated in a flow tube reactor using UV-light and ozone. Briefly the following order of cellular response-strength was observed: A relatively mild cellular effect is observed for the diluted wood combustion emissions, regardless if log-wood and pellet burner emissions are investigated. Similarly mild biological effects are observed for gasoline car emissions. The ship diesel engine emissions and construction machine diesel engine induced much more intense biological responses. A surprising result in this context is, that heavy fuel oil (HFO)-emissions show lower biological effect strengths than the supposedly cleaner diesel fuel emissions (DF). The HFO-emissions contain high concentrations of known toxicants (metals, polycyclic aromatics). This result was confirmed by experiments with murine macrophages. Detailed analyses suggest a large difference in relative toxicity for different combustion sources. Recently the cell experiments were successively evaluated and verified by animal exposure tests. This is important to develop a reliable animal-test free-monitoring method for aerosol-induced health effects.

Life science experiments performed in space in the ISS/Kibo facility and future research plans

PubMed Central

Ohnishi, Takeo

2016-01-01

Over the past several years, current techniques in molecular biology have been used to perform experiments in space, focusing on the nature and effects of space radiation. In the Japanese ‘Kibo’ facility in the International Space Station (ISS), the Japan Aerospace Exploration Agency (JAXA) has performed five life science experiments since 2009, and two additional experiments are currently in progress. The first life science experiment in space was the ‘Rad Gene’ project, which utilized two human cultured lymphoblastoid cell lines containing a mutated p53 gene (mp53) and a parental wild-type p53 gene (wtp53) respectively. Four parameters were examined: (i) detecting space radiation–induced DSBs by observing γH2AX foci; (ii) observing p53-dependent gene expression during space flight; (iii) observing p53-dependent gene expression after space flight; and (iv) observing the adaptive response in the two cell lines containing the mutated and wild type p53 genes after exposure to space radiation. These observations were completed and have been reported, and this paper is a review of these experiments. In addition, recent new information from space-based experiments involving radiation biology is presented here. These experiments involve human cultured cells, silkworm eggs, mouse embryonic stem cells and mouse eggs in various experiments designed by other principal investigators in the ISS/Kibo. The progress of Japanese science groups involved in these space experiments together with JAXA are also discussed here. The Japanese Society for Biological Sciences in Space (JSBSS), the Utilization Committee of Space Environment Science (UCSES) and the Science Council of Japan (ACJ) have supported these new projects and new experimental facilities in ISS/Kibo. Currently, these organizations are proposing new experiments for the ISS through 2024. PMID:27130692

Live cell imaging at the Munich ion microbeam SNAKE - a status report.

PubMed

Drexler, Guido A; Siebenwirth, Christian; Drexler, Sophie E; Girst, Stefanie; Greubel, Christoph; Dollinger, Günther; Friedl, Anna A

2015-02-18

Ion microbeams are important tools in radiobiological research. Still, the worldwide number of ion microbeam facilities where biological experiments can be performed is limited. Even fewer facilities combine ion microirradiation with live-cell imaging to allow microscopic observation of cellular response reactions starting very fast after irradiation and continuing for many hours. At SNAKE, the ion microbeam facility at the Munich 14 MV tandem accelerator, a large variety of biological experiments are performed on a regular basis. Here, recent developments and ongoing research projects at the ion microbeam SNAKE are presented with specific emphasis on live-cell imaging experiments. An overview of the technical details of the setup is given, including examples of suitable biological samples. By ion beam focusing to submicrometer beam spot size and single ion detection it is possible to target subcellular structures with defined numbers of ions. Focusing of high numbers of ions to single spots allows studying the influence of high local damage density on recruitment of damage response proteins.

Probing the biology of cell boundary conditions through confinement of Xenopus cell-free cytoplasmic extracts.

PubMed

Bermudez, Jessica G; Chen, Hui; Einstein, Lily C; Good, Matthew C

2017-01-01

Cell-free cytoplasmic extracts prepared from Xenopus eggs and embryos have for decades provided a biochemical system with which to interrogate complex cell biological processes in vitro. Recently, the application of microfabrication and microfluidic strategies in biology has narrowed the gap between in vitro and in vivo studies by enabling formation of cell-size compartments containing functional cytoplasm. These approaches provide numerous advantages over traditional biochemical experiments performed in a test tube. Most notably, the cell-free cytoplasm is confined using a two- or three-dimensional boundary, which mimics the natural configuration of a cell. This strategy enables characterization of the spatial organization of a cell, and the role that boundaries play in regulating intracellular assembly and function. In this review, we describe the marriage of Xenopus cell-free cytoplasm and confinement technologies to generate synthetic cell-like systems, the recent biological insights they have enabled, and the promise they hold for future scientific discovery. © 2017 Wiley Periodicals, Inc.

Bioprocessing in Space

NASA Technical Reports Server (NTRS)

Morrison, D. R. (Compiler)

1977-01-01

Proceedings are presented of the 1976 NASA Colloquium on bioprocessing in space. The program included general sessions and formal presentations on the following topics: NASA's Space Shuttle, Spacelab, and space-processing programs; the known unusual behavior of materials in space; space-processing experiment results; cell biology, gravity sensors in cells, space electrophoresis of living cells, new approaches to biosynthesis of biologicals from cell culture in space, and zero-g fermentation concepts; and upcoming flight opportunities and industrial application planning studies already underway.

A review of the theory, methods and recent applications of high-throughput single-cell droplet microfluidics

NASA Astrophysics Data System (ADS)

Lagus, Todd P.; Edd, Jon F.

2013-03-01

Most cell biology experiments are performed in bulk cell suspensions where cell secretions become diluted and mixed in a contiguous sample. Confinement of single cells to small, picoliter-sized droplets within a continuous phase of oil provides chemical isolation of each cell, creating individual microreactors where rare cell qualities are highlighted and otherwise undetectable signals can be concentrated to measurable levels. Recent work in microfluidics has yielded methods for the encapsulation of cells in aqueous droplets and hydrogels at kilohertz rates, creating the potential for millions of parallel single-cell experiments. However, commercial applications of high-throughput microdroplet generation and downstream sensing and actuation methods are still emerging for cells. Using fluorescence-activated cell sorting (FACS) as a benchmark for commercially available high-throughput screening, this focused review discusses the fluid physics of droplet formation, methods for cell encapsulation in liquids and hydrogels, sensors and actuators and notable biological applications of high-throughput single-cell droplet microfluidics.

Choosing an Appropriate Modelling Framework for Analysing Multispecies Co-culture Cell Biology Experiments.

PubMed

Markham, Deborah C; Simpson, Matthew J; Baker, Ruth E

2015-04-01

In vitro cell biology assays play a crucial role in informing our understanding of the migratory, proliferative and invasive properties of many cell types in different biological contexts. While mono-culture assays involve the study of a population of cells composed of a single cell type, co-culture assays study a population of cells composed of multiple cell types (or subpopulations of cells). Such co-culture assays can provide more realistic insights into many biological processes including tissue repair, tissue regeneration and malignant spreading. Typically, system parameters, such as motility and proliferation rates, are estimated by calibrating a mathematical or computational model to the observed experimental data. However, parameter estimates can be highly sensitive to the choice of model and modelling framework. This observation motivates us to consider the fundamental question of how we can best choose a model to facilitate accurate parameter estimation for a particular assay. In this work we describe three mathematical models of mono-culture and co-culture assays that include different levels of spatial detail. We study various spatial summary statistics to explore if they can be used to distinguish between the suitability of each model over a range of parameter space. Our results for mono-culture experiments are promising, in that we suggest two spatial statistics that can be used to direct model choice. However, co-culture experiments are far more challenging: we show that these same spatial statistics which provide useful insight into mono-culture systems are insufficient for co-culture systems. Therefore, we conclude that great care ought to be exercised when estimating the parameters of co-culture assays.

Droplet microfluidics for synthetic biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gach, PC; Iwai, K; Kim, PW

2017-01-01

© 2017 The Royal Society of Chemistry. Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility. Liquid handling robotics may reduce labor and improve reproducibility, but are themselvesmore » expensive and thus inaccessible to most researchers. Microfluidic platforms offer a lower entry price point alternative to robotics, and maintain high throughput and reproducibility while further reducing operating costs through diminished reagent volume requirements. Droplet microfluidics have shown exceptional promise for synthetic biology experiments, including DNA assembly, transformation/transfection, culturing, cell sorting, phenotypic assays, artificial cells and genetic circuits.« less

Cellular fluid mechanics.

PubMed

Kamm, Roger D

2002-01-01

The coupling of fluid dynamics and biology at the level of the cell is an intensive area of investigation because of its critical role in normal physiology and disease. Microcirculatory flow has been a focus for years, owing to the complexity of cell-cell or cell-glycocalyx interactions. Noncirculating cells, particularly those that comprise the walls of the circulatory system, experience and respond biologically to fluid dynamic stresses. In this article, we review the more recent studies of circulating cells, with an emphasis on the role of the glycocalyx on red-cell motion in small capillaries and on the deformation of leukocytes passing through the microcirculation. We also discuss flows in the vicinity of noncirculating cells, the influence of fluid dynamic shear stress on cell biology, and diffusion in the lipid bi-layer, all in the context of the important fluid-dynamic phenomena.

Induced Pluripotent Stem Cells from Nonhuman Primates.

PubMed

Mishra, Anuja; Qiu, Zhifang; Farnsworth, Steven L; Hemmi, Jacob J; Li, Miao; Pickering, Alexander V; Hornsby, Peter J

2016-01-01

Induced pluripotent stem cells from nonhuman primates (NHPs) have unique roles in cell biology and regenerative medicine. Because of the relatedness of NHPs to humans, NHP iPS cells can serve as a source of differentiated derivatives that can be used to address important questions in the comparative biology of primates. Additionally, when used as a source of cells for regenerative medicine, NHP iPS cells serve an invaluable role in translational experiments in cell therapy. Reprogramming of NHP somatic cells requires the same conditions as previously established for human cells. However, throughout the process, a variety of modifications to the human cell protocols must be made to accommodate significant species differences.

Genomewide effects of peroxisome proliferator-activated receptor gamma in macrophages and dendritic cells--revealing complexity through systems biology.

PubMed

Cuaranta-Monroy, Ixchelt; Kiss, Mate; Simandi, Zoltan; Nagy, Laszlo

2015-09-01

Systems biology approaches have become indispensable tools in biomedical and basic research. These data integrating bioinformatic methods gained prominence after high-throughput technologies became available to investigate complex cellular processes, such as transcriptional regulation and protein-protein interactions, on a scale that had not been studied before. Immunology is one of the medical fields that systems biology impacted profoundly due to the plasticity of cell types involved and the accessibility of a wide range of experimental models. In this review, we summarize the most important recent genomewide studies exploring the function of peroxisome proliferator-activated receptor γ in macrophages and dendritic cells. PPARγ ChIP-seq experiments were performed in adipocytes derived from embryonic stem cells to complement the existing data sets and to provide comparators to macrophage data. Finally, lists of regulated genes generated from such experiments were analysed with bioinformatics and system biology approaches. We show that genomewide studies utilizing high-throughput data acquisition methods made it possible to gain deeper insights into the role of PPARγ in these immune cell types. We also demonstrate that analysis and visualization of data using network-based approaches can be used to identify novel genes and functions regulated by the receptor. The example of PPARγ in macrophages and dendritic cells highlights the crucial importance of systems biology approaches in establishing novel cellular functions for long-known signaling pathways. © 2015 Stichting European Society for Clinical Investigation Journal Foundation.

Collective behavior of brain tumor cells: The role of hypoxia

NASA Astrophysics Data System (ADS)

Khain, Evgeniy; Katakowski, Mark; Hopkins, Scott; Szalad, Alexandra; Zheng, Xuguang; Jiang, Feng; Chopp, Michael

2011-03-01

We consider emergent collective behavior of a multicellular biological system. Specifically, we investigate the role of hypoxia (lack of oxygen) in migration of brain tumor cells. We performed two series of cell migration experiments. In the first set of experiments, cell migration away from a tumor spheroid was investigated. The second set of experiments was performed in a typical wound-healing geometry: Cells were placed on a substrate, a scratch was made, and cell migration into the gap was investigated. Experiments show a surprising result: Cells under normal and hypoxic conditions have migrated the same distance in the “spheroid” experiment, while in the “scratch” experiment cells under normal conditions migrated much faster than under hypoxic conditions. To explain this paradox, we formulate a discrete stochastic model for cell dynamics. The theoretical model explains our experimental observations and suggests that hypoxia decreases both the motility of cells and the strength of cell-cell adhesion. The theoretical predictions were further verified in independent experiments.

Review on thin-film transistor technology, its applications, and possible new applications to biological cells

NASA Astrophysics Data System (ADS)

Tixier-Mita, Agnès; Ihida, Satoshi; Ségard, Bertrand-David; Cathcart, Grant A.; Takahashi, Takuya; Fujita, Hiroyuki; Toshiyoshi, Hiroshi

2016-04-01

This paper presents a review on state-of-the-art of thin-film transistor (TFT) technology and its wide range of applications, not only in liquid crystal displays (TFT-LCDs), but also in sensing devices. The history of the evolution of the technology is first given. Then the standard applications of TFT-LCDs, and X-ray detectors, followed by state-of-the-art applications in the field of chemical and biochemical sensing are presented. TFT technology allows the fabrication of dense arrays of independent and transparent microelectrodes on large glass substrates. The potential of these devices as electrical substrates for biological cell applications is then described. The possibility of using TFT array substrates as new tools for electrical experiments on biological cells has been investigated for the first time by our group. Dielectrophoresis experiments and impedance measurements on yeast cells are presented here. Their promising results open the door towards new applications of TFT technology.

A novel cell culture model as a tool for forensic biology experiments and validations.

PubMed

Feine, Ilan; Shpitzen, Moshe; Roth, Jonathan; Gafny, Ron

2016-09-01

To improve and advance DNA forensic casework investigation outcomes, extensive field and laboratory experiments are carried out in a broad range of relevant branches, such as touch and trace DNA, secondary DNA transfer and contamination confinement. Moreover, the development of new forensic tools, for example new sampling appliances, by commercial companies requires ongoing validation and assessment by forensic scientists. A frequent challenge in these kinds of experiments and validations is the lack of a stable, reproducible and flexible biological reference material. As a possible solution, we present here a cell culture model based on skin-derived human dermal fibroblasts. Cultured cells were harvested, quantified and dried on glass slides. These slides were used in adhesive tape-lifting experiments and tests of DNA crossover confinement by UV irradiation. The use of this model enabled a simple and concise comparison between four adhesive tapes, as well as a straightforward demonstration of the effect of UV irradiation intensities on DNA quantity and degradation. In conclusion, we believe this model has great potential to serve as an efficient research tool in forensic biology. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A universal fluid cell for the imaging of biological specimens in the atomic force microscope.

PubMed

Kasas, Sandor; Radotic, Ksenja; Longo, Giovanni; Saha, Bashkar; Alonso-Sarduy, Livan; Dietler, Giovanni; Roduit, Charles

2013-04-01

Recently, atomic force microscope (AFM) manufacturers have begun producing instruments specifically designed to image biological specimens. In most instances, they are integrated with an inverted optical microscope, which permits concurrent optical and AFM imaging. An important component of the set-up is the imaging chamber, whose design determines the nature of the experiments that can be conducted. Many different imaging chamber designs are available, usually designed to optimize a single parameter, such as the dimensions of the substrate or the volume of fluid that can be used throughout the experiment. In this report, we present a universal fluid cell, which simultaneously optimizes all of the parameters that are important for the imaging of biological specimens in the AFM. This novel imaging chamber has been successfully tested using mammalian, plant, and microbial cells. Copyright © 2013 Wiley Periodicals, Inc.

Effects of geophysical extra-terrestrial and terrestrial physical stimuli on living organisms - Effects of gravity fields on living organisms

NASA Technical Reports Server (NTRS)

Saunders, R. J. F.

1972-01-01

The biologic effects of greatly reduced gravity resulting from space flight are examined. Aspects of U.S. space biology during the period from 1960 to 1972 are discussed, giving attention to the Discoverer satellites, the Gemini series, the OV1-4 satellite, the biosatellite project, the orbiting frog otolith experiment, and the Apollo program. Other studies considered are related to the effects of galactic particles on nonproliferating cells, a recoverable tissue culture experiment, cell cycle maintenance in human lung cells, and effects of space flight on circadian rhythms. Viking will land on the planet Mars in 1975 in search for life forms.

Action Biology. Advanced Placement for the Second Year. First Edition.

ERIC Educational Resources Information Center

Davis, Mary Pitt

This document provides biology experiments designed for students who have completed a first year biology course. This self contained laboratory booklet contains four sections. In section 1, "Instrumentation in the Study of Cells," discussion sections and suggestions for teacher demonstrations are provided. It also includes some basic materials…

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Štys, Dalibor; Urban, Jan; Vaněk, Jan; Císař, Petr

2011-06-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space. This space is reflected as colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them.

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Stys, Dalibor; Urban, Jan; Vanek, Jan; Císar, Petr

2010-07-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space reflected in space an colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them. Copyright 2010 Elsevier Ltd. All rights reserved.

Actin Immobilization on Chitin for Purifying Myosin II: A Laboratory Exercise That Integrates Concepts of Molecular Cell Biology and Protein Chemistry

ERIC Educational Resources Information Center

de Souza, Marcelle Gomes; Grossi, Andre Luiz; Pereira, Elisangela Lima Bastos; da Cruz, Carolina Oliveira; Mendes, Fernanda Machado; Cameron, Luiz Claudio; Paiva, Carmen Lucia Antao

2008-01-01

This article presents our experience on teaching biochemical sciences through an innovative approach that integrates concepts of molecular cell biology and protein chemistry. This original laboratory exercise is based on the preparation of an affinity chromatography column containing F-actin molecules immobilized on chitin particles for purifying…

Constitutive expression of tdTomato protein as a cytotoxicity and proliferation marker for space radiation biology

NASA Astrophysics Data System (ADS)

Chishti, Arif A.; Hellweg, Christine E.; Berger, Thomas; Baumstark-Khan, Christa; Feles, Sebastian; Kätzel, Thorben; Reitz, Günther

2015-01-01

The radiation risk assessment for long-term space missions requires knowledge on the biological effectiveness of different space radiation components, e.g. heavy ions, on the interaction of radiation and other space environmental factors such as microgravity, and on the physical and biological dose distribution in the human body. Space experiments and ground-based experiments at heavy ion accelerators require fast and reliable test systems with an easy readout for different endpoints. In order to determine the effect of different radiation qualities on cellular proliferation and the biological depth dose distribution after heavy ion exposure, a stable human cell line expressing a novel fluorescent protein was established and characterized. tdTomato, a red fluorescent protein of the new generation with fast maturation and high fluorescence intensity, was selected as reporter of cell proliferation. Human embryonic kidney (HEK/293) cells were stably transfected with a plasmid encoding tdTomato under the control of the constitutively active cytomegalovirus (CMV) promoter (ptdTomato-N1). The stably transfected cell line was named HEK-ptdTomato-N1 8. This cytotoxicity biosensor was tested by ionizing radiation (X-rays and accelerated heavy ions) exposure. As biological endpoints, the proliferation kinetics and the cell density reached 100 h after irradiation reflected by constitutive expression of the tdTomato were investigated. Both were reduced dose-dependently after radiation exposure. Finally, the cell line was used for biological weighting of heavy ions of different linear energy transfer (LET) as space-relevant radiation quality. The relative biological effectiveness of accelerated heavy ions in reducing cellular proliferation peaked at an LET of 91 keV/μm. The results of this study demonstrate that the HEK-ptdTomato-N1 reporter cell line can be used as a fast and reliable biosensor system for detection of cytotoxic damage caused by ionizing radiation.

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa

PubMed Central

Petegrosso, Raphael; Tolar, Jakub

2018-01-01

Single-cell RNA sequencing (scRNA-seq) has been widely applied to discover new cell types by detecting sub-populations in a heterogeneous group of cells. Since scRNA-seq experiments have lower read coverage/tag counts and introduce more technical biases compared to bulk RNA-seq experiments, the limited number of sampled cells combined with the experimental biases and other dataset specific variations presents a challenge to cross-dataset analysis and discovery of relevant biological variations across multiple cell populations. In this paper, we introduce a method of variance-driven multitask clustering of single-cell RNA-seq data (scVDMC) that utilizes multiple single-cell populations from biological replicates or different samples. scVDMC clusters single cells in multiple scRNA-seq experiments of similar cell types and markers but varying expression patterns such that the scRNA-seq data are better integrated than typical pooled analyses which only increase the sample size. By controlling the variance among the cell clusters within each dataset and across all the datasets, scVDMC detects cell sub-populations in each individual experiment with shared cell-type markers but varying cluster centers among all the experiments. Applied to two real scRNA-seq datasets with several replicates and one large-scale droplet-based dataset on three patient samples, scVDMC more accurately detected cell populations and known cell markers than pooled clustering and other recently proposed scRNA-seq clustering methods. In the case study applied to in-house Recessive Dystrophic Epidermolysis Bullosa (RDEB) scRNA-seq data, scVDMC revealed several new cell types and unknown markers validated by flow cytometry. MATLAB/Octave code available at https://github.com/kuanglab/scVDMC. PMID:29630593

Cell biology and biotechnology research for exploration of the Moon and Mars

NASA Astrophysics Data System (ADS)

Pellis, N.; North, R.

Health risks generated by human long exposure to radiation, microgravity, and unknown factors in the planetary environment are the major unresolved issues for human space exploration. A complete characterization of human and other biological systems adaptation processes to long-duration space missions is necessary for the development of countermeasures. The utilization of cell and engineered tissue cultures in space research and exploration complements research in human, animal, and plant subjects. We can bring a small number of humans, animals, or plants to the ISS, Moon, and Mars. However, we can investigate millions of their cells during these missions. Furthermore, many experiments can not be performed on humans, e.g. radiation exposure, cardiac muscle. Cells from critical tissues and tissue constructs per se are excellent subjects for experiments that address underlying mechanisms important to countermeasures. The development of cell tissue engineered for replacement, implantation of biomaterial to induce tissue regeneration (e.g. absorbable collagen matrix for guiding tissue regeneration in periodontal surgery), and immunoisolation (e.g. biopolymer coating on transplanted tissues to ward off immunological rejection) are good examples of cell research and biotechnology applications. NASA Cell Biology and Biotechnology research include Bone/Muscle and Cardiovascular cell culture and tissue engineering; Environmental Health and Life Support Systems; Immune System; Radiation; Gravity Thresholds ; and Advanced Biotechnology Development to increase the understanding of animal and plant cell adaptive behavior when exposed to space, and to advance technologies that facilitates exploration. Cell systems can be used to investigate processes related to food, microbial proliferation, waste management, biofilms and biomaterials. The NASA Cell Science Program has the advantage of conducting research in microgravity based on significantly small resources, and the ability to conduct experiments in the early phase of the development of requirements for exploration. Supporting the NASA concept of stepping stones, we believe that ground based, International Space Station, robotic and satellite missions offer the ideal environment to perform experiments and secure answers necessary for human exploration.

Cell-Selective Biological Activity of Rhodium Metalloinsertors Correlates with Subcellular Localization

PubMed Central

Komor, Alexis C.; Schneider, Curtis J.; Weidmann, Alyson G.; Barton, Jacqueline K.

2013-01-01

Deficiencies in the mismatch repair (MMR) pathway are associated with several types of cancers, as well as resistance to commonly used chemotherapeutics. Rhodium metalloinsertors have been found to bind DNA mismatches with high affinity and specificity in vitro, and also exhibit cell-selective cytotoxicity, targeting MMR-deficient cells over MMR-proficient cells. Ten distinct metalloinsertors with varying lipophilicities have been synthesized and their mismatch binding affinities and biological activities determined. Although DNA photocleavage experiments demonstrate that their binding affinities are quite similar, their cell-selective antiproliferative and cytotoxic activities vary significantly. Inductively coupled plasma mass spectrometry (ICP-MS) experiments have uncovered a relationship between the subcellular distribution of these metalloinsertors and their biological activities. Specifically, we find that all of our metalloinsertors localize in the nucleus at sufficient concentrations for binding to DNA mismatches. However, the metalloinsertors with high rhodium localization in the mitochondria show toxicity that is not selective for MMR-deficient cells, whereas metalloinsertors with less mitochondrial rhodium show activity that is highly selective for MMR-deficient versus proficient cells. This work supports the notion that specific targeting of the metalloinsertors to nuclear DNA gives rise to their cell-selective cytotoxic and antiproliferative activities. The selectivity in cellular targeting depends upon binding to mismatches in genomic DNA. PMID:23137296

Determination of morphological parameters of biological cells by analysis of scattered-light distributions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burger, D.E.

1979-11-01

The extraction of morphological parameters from biological cells by analysis of light-scatter patterns is described. A light-scattering measurement system has been designed and constructed that allows one to visually examine and photographically record biological cells or cell models and measure the light-scatter pattern of an individual cell or cell model. Using a laser or conventional illumination, the imaging system consists of a modified microscope with a 35 mm camera attached to record the cell image or light-scatter pattern. Models of biological cells were fabricated. The dynamic range and angular distributions of light scattered from these models was compared to calculatedmore » distributions. Spectrum analysis techniques applied on the light-scatter data give the sought after morphological cell parameters. These results compared favorably to shape parameters of the fabricated cell models confirming the mathematical model procedure. For nucleated biological material, correct nuclear and cell eccentricity as well as the nuclear and cytoplasmic diameters were determined. A method for comparing the flow equivalent of nuclear and cytoplasmic size to the actual dimensions is shown. This light-scattering experiment provides baseline information for automated cytology. In its present application, it involves correlating average size as measured in flow cytology to the actual dimensions determined from this technique. (ERB)« less

Mechanics of biological networks: from the cell cytoskeleton to connective tissue.

PubMed

Pritchard, Robyn H; Huang, Yan Yan Shery; Terentjev, Eugene M

2014-03-28

From the cell cytoskeleton to connective tissues, fibrous networks are ubiquitous in metazoan life as the key promoters of mechanical strength, support and integrity. In recent decades, the application of physics to biological systems has made substantial strides in elucidating the striking mechanical phenomena observed in such networks, explaining strain stiffening, power law rheology and cytoskeletal fluidisation - all key to the biological function of individual cells and tissues. In this review we focus on the current progress in the field, with a primer into the basic physics of individual filaments and the networks they form. This is followed by a discussion of biological networks in the context of a broad spread of recent in vitro and in vivo experiments.

Life science experiments performed in space in the ISS/Kibo facility and future research plans.

PubMed

Ohnishi, Takeo

2016-08-01

Over the past several years, current techniques in molecular biology have been used to perform experiments in space, focusing on the nature and effects of space radiation. In the Japanese 'Kibo' facility in the International Space Station (ISS), the Japan Aerospace Exploration Agency (JAXA) has performed five life science experiments since 2009, and two additional experiments are currently in progress. The first life science experiment in space was the 'Rad Gene' project, which utilized two human cultured lymphoblastoid cell lines containing a mutated P53 : gene (m P53 : ) and a parental wild-type P53 : gene (wt P53 : ) respectively. Four parameters were examined: (i) detecting space radiation-induced DSBs by observing γH2AX foci; (ii) observing P53 : -dependent gene expression during space flight; (iii) observing P53 : -dependent gene expression after space flight; and (iv) observing the adaptive response in the two cell lines containing the mutated and wild type P53 : genes after exposure to space radiation. These observations were completed and have been reported, and this paper is a review of these experiments. In addition, recent new information from space-based experiments involving radiation biology is presented here. These experiments involve human cultured cells, silkworm eggs, mouse embryonic stem cells and mouse eggs in various experiments designed by other principal investigators in the ISS/Kibo. The progress of Japanese science groups involved in these space experiments together with JAXA are also discussed here. The Japanese Society for Biological Sciences in Space (JSBSS), the Utilization Committee of Space Environment Science (UCSES) and the Science Council of Japan (ACJ) have supported these new projects and new experimental facilities in ISS/Kibo. Currently, these organizations are proposing new experiments for the ISS through 2024. © The Author 2016. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

Effects of space flight exposure on cell growth, tumorigenicity and gene expression in cancer cells

NASA Astrophysics Data System (ADS)

Yang, Cheng; Li, Yuehui; Zhang, Zhijie; Luo, Chen; Tong, Yongqing; Zhou, Guohua; Xie, Pingli; Hu, Jinyue; Li, Guancheng

2008-12-01

It is well recognized that harsh outer space environment, consisting of microgravity and radiation, poses significant health risks for human cells. To investigate potential effects of the space environment exposure on cancer cells we examined the biological changes in Caski cells carried by the "Shen Zhou IV" spaceship. After exposure for 7 days in spaceflight, 1440 survival subclonal cell lines were established and 4 cell lines were screened. 44F10 and 17E3 were selected because of their increased cell proliferation and tumorigenesis, while 48A9 and 31F2 had slower cytological events. Experiments with cell proliferation assay, flow cytometry, soft agar assay, tumorigenesis assay and DNA microarray analysis have shown that selected cell lines presented multiple biological changes in cell morphology, cell growth, tumorigenicity and gene expression. These results suggest that space environment exposure can make significant biological impact on cancer cells and provide an entry point to find the immunological target of tumorigenesis.

FE-2 Nicole Stott works on the CBEF Space Seed Experiment

NASA Image and Video Library

2009-10-13

ISS021-E-006261 (13 Oct. 2009) --- NASA astronaut Nicole Stott, Expedition 21 flight engineer, works with the Cell Biology Experiment Facility (CBEF) SPACE SEED experiment in the Kibo laboratory of the International Space Station.

FE-2 Nicole Stott works on the CBEF Space Seed Experiment

NASA Image and Video Library

2009-10-13

ISS021-E-006267 (13 Oct. 2009) --- NASA astronaut Nicole Stott, Expedition 21 flight engineer, works with the Cell Biology Experiment Facility (CBEF) SPACE SEED experiment in the Kibo laboratory of the International Space Station.

Design and interpretation of cell trajectory assays

PubMed Central

Bowden, Lucie G.; Simpson, Matthew J.; Baker, Ruth E.

2013-01-01

Cell trajectory data are often reported in the experimental cell biology literature to distinguish between different types of cell migration. Unfortunately, there is no accepted protocol for designing or interpreting such experiments and this makes it difficult to quantitatively compare different published datasets and to understand how changes in experimental design influence our ability to interpret different experiments. Here, we use an individual-based mathematical model to simulate the key features of a cell trajectory experiment. This shows that our ability to correctly interpret trajectory data is extremely sensitive to the geometry and timing of the experiment, the degree of motility bias and the number of experimental replicates. We show that cell trajectory experiments produce data that are most reliable when the experiment is performed in a quasi-one-dimensional geometry with a large number of identically prepared experiments conducted over a relatively short time-interval rather than a few trajectories recorded over particularly long time-intervals. PMID:23985736

BIOLAB experiment development status 2005

NASA Astrophysics Data System (ADS)

Brinckmann, Enno; Manieri, Pierfilippo

2005-08-01

BIOLAB, ESA's major facility for biological Space research on the International Space Station (ISS), will accommodate the first two batches of experiments after its launch with the "Columbus" Laboratory (spring 2007). Seven experiments have been selected for development: three of the first batch have concluded Phase A/B with the testing of the breadboards, in which the main functions of the scientific studies can be simulated and defined for further inputs to the final design of the experiment hardware. The biological specimens of the first batch are scorpions, plant seedlings, bacteria suspensions and cell cultures of mammalian and invertebrate origin. The experiment protocols request demanding resources ranging from life support for the entire mission (90 days) to skilled crew operations and transport/storage in deep freezers. Even more sophisticated experiments are in preparation for the second batch, dealing with various cell culture systems. This presentation gives an overview about the experiment development status, whilst the science background and breadboard test results will be presented by the respective experiment teams.

Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)

PubMed Central

George, Ansel; Dorval, Alan D.; Christini, David J.

2017-01-01

The ability to experimentally perturb biological systems has traditionally been limited to static pre-programmed or operator-controlled protocols. In contrast, real-time control allows dynamic probing of biological systems with perturbations that are computed on-the-fly during experimentation. Real-time control applications for biological research are available; however, these systems are costly and often restrict the flexibility and customization of experimental protocols. The Real-Time eXperiment Interface (RTXI) is an open source software platform for achieving hard real-time data acquisition and closed-loop control in biological experiments while retaining the flexibility needed for experimental settings. RTXI has enabled users to implement complex custom closed-loop protocols in single cell, cell network, animal, and human electrophysiology studies. RTXI is also used as a free and open source, customizable electrophysiology platform in open-loop studies requiring online data acquisition, processing, and visualization. RTXI is easy to install, can be used with an extensive range of external experimentation and data acquisition hardware, and includes standard modules for implementing common electrophysiology protocols. PMID:28557998

Biological filter capable of simultaneous nitrification and denitrification for Aquatic Habitat in International Space Station

NASA Astrophysics Data System (ADS)

Uemoto, H.; Shoji, T.; Uchida, S.

2014-04-01

The biological filter capable of simultaneous nitrification and denitrification was constructed for aquatic animal experiments in the International Space Station (ISS). The biological filter will be used to remove harmful ammonia excreted from aquatic animals in a closed water circulation system (Aquatic Habitat). The biological filter is a cylindrical tank packed with porous glass beads for nitrification and dual plastic bags for denitrification. The porous beads are supporting media for Nitrosomonas europaea and Nitrobacter winogradskyi. The N. europaea cells and N. winogradskyi cells on the porous beads, oxidize the excreted ammonia to nitrate via nitrite. On the other hand, the dual bag is composed of an outer non-woven fabric bag and an inner non-porous polyethylene film bag. The outer bag is supporting media for Paracoccus pantotrophus. The inner bag, in which 99.5% ethanol is packed, releases the ethanol slowly, since ethanol can permeate through the non-porous polyethylene film. The P. pantotrophus cells on the outer bag reduce the produced nitrate to nitrogen gas by using the released ethanol as an electron donor for denitrification. The biological filter constructed in this study consequently removed the ammonia without accumulating nitrate. Most of the excess ethanol was consumed and did not affect the nitrification activity of the N. europaea cells and N. winogradskyi cells severely. In accordance with the aquatic animal experiments in the ISS, small freshwater fish had been bred in the closed water circulation system equipped with the biological filter for 90 days. Ammonia concentration daily excreted from fish is assumed to be 1.7 mg-N/L in the recirculation water. Under such conditions, the harmful ammonia and nitrite concentrations were kept below 0.1 mg-N/L in the recirculation water. Nitrate and total organic carbon concentrations in the recirculation water were kept below 5 mg-N/L and 3 mg-C/L, respectively. All breeding fish were alive and ate the feed well. The results show that the nitrification and denitrification abilities of the biological filter sufficed to keep water quality for aquatic animal experiments in the ISS. This simple and effective system is certainly applicable to aquarium systems and aquaculture systems.

Preparing High School Students for the Interdisciplinary Nature of Modern Biology

ERIC Educational Resources Information Center

Nagle, Barbara

2013-01-01

Fostering interdisciplinary learning in biology will require significant changes in the way one teaches science to K-12 students. The perspective on interdisciplinary biology teaching and learning in this essay is based on the author's experiences as a former research cell biologist, high school science teacher, and developer of secondary science…

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

The Neural Development Section (NDS) headed by Dr. Lino Tessarollo has an open postdoctoral fellow position. The candidate should have a background in neurobiology and basic expertise in molecular biology, cell biology, immunoistochemistry and biochemistry.  Experience in confocal analysis is desired. The NDS study the biology of neurotrophin and Trk receptors function by

Compact, Automated, Frequency-Agile Microspectrofluorimeter

NASA Technical Reports Server (NTRS)

Fernandez, Salvador M.; Guignon, Ernest F.

1995-01-01

Compact, reliable, rugged, automated cell-culture and frequency-agile microspectrofluorimetric apparatus developed to perform experiments involving photometric imaging observations of single live cells. In original application, apparatus operates mostly unattended aboard spacecraft; potential terrestrial applications include automated or semiautomated diagnosis of pathological tissues in clinical laboratories, biomedical instrumentation, monitoring of biological process streams, and portable instrumentation for testing biological conditions in various environments. Offers obvious advantages over present laboratory instrumentation.

Integrated, multi-scale, spatial-temporal cell biology--A next step in the post genomic era.

PubMed

Horwitz, Rick

2016-03-01

New microscopic approaches, high-throughput imaging, and gene editing promise major new insights into cellular behaviors. When coupled with genomic and other 'omic information and "mined" for correlations and associations, a new breed of powerful and useful cellular models should emerge. These top down, coarse-grained, and statistical models, in turn, can be used to form hypotheses merging with fine-grained, bottom up mechanistic studies and models that are the back bone of cell biology. The goal of the Allen Institute for Cell Science is to develop the top down approach by developing a high throughput microscopy pipeline that is integrated with modeling, using gene edited hiPS cell lines in various physiological and pathological contexts. The output of these experiments and models will be an "animated" cell, capable of integrating and analyzing image data generated from experiments and models. Copyright © 2015 Elsevier Inc. All rights reserved.

Importance of dose-rate and cell proliferation in the evaluation of biological experimental results

NASA Technical Reports Server (NTRS)

Curtis, S. B.

1994-01-01

The nuclei of cells within the bodies of astronauts traveling on extended missions outside the geomagnetosphere will experience single traversals of particles with high Linear Energy Transfer (LET) (e.g., one iron ion per one hundred years, on average) superimposed on a background of tracks with low LET (approximately one proton every two to three days, and one helium ion per month). In addition, some cell populations within the body will be proliferating, thus possibly providing increasing numbers of cells with 'initiated' targets for subsequent radiation hits. These temporal characteristics are not generally reproduced in laboratory experimental protocols. Implications of the differences in the temporal patterns of radiation delivery between conventionally designed radiation biology experiments and the pattern to be experienced in space are examined and the importance of dose-rate and cell proliferation are pointed out in the context of radiation risk assessment on long mission in space.

Genome annotation in a community college cell biology lab.

PubMed

Beagley, C Timothy

2013-01-01

The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning skills. Additionally, the project strengthens student understanding of the scientific method and contributes to student learning gains in curricular objectives centered around basic molecular biology, specifically, the Central Dogma. Importantly, inclusion of this project in the laboratory course provides students with a positive learning environment and allows for the use of cooperative learning strategies to increase overall student success. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

Seeking the Light: Gravity Without the Influence of Gravity

NASA Technical Reports Server (NTRS)

Sack, Fred; Kern, Volker; Reed, Dave; Etheridge, Guy (Technical Monitor)

2002-01-01

All living things sense gravity like humans might sense light or sound. The Biological Research In Canisters (BRIC-14) experiment, explores how moss cells sense and respond to gravity and light. This experiment studies how gravity influences the internal structure of moss cells and seeks to understand the influences of the spaceflight environment on cell growth. This knowledge will help researchers understand the role of gravity in the evolution of cells and life on earth.

Teaching resources. Movement of macromolecules in plant cells through plasmodesmata.

PubMed

Jorgensen, Richard A; Lucas, William J

2006-02-21

Plasmodesmata are intercellular organelles in plants that allow the passage of molecules between plant cells. Movement through plasmodesmata may allow transcription factors expressed in one cell to move into adjacent cells, thereby regulating gene expression non-cell autonomously. The two animations illustrate (i) movement of a protein through an individual plasmodesma and (ii) an experiment to detect the movement of the transcription factor through plasmodesmata from the L1 layer of a plant meristem into the L2 and L3 layers. These two animations would be useful in teaching plant biology or plant development or a cell biology class discussing mechanisms of intercellular transport.

View of CBEF Space Seed Experiment Hardware

NASA Image and Video Library

2009-10-13

ISS021-E-006274 (13 Oct. 2009) --- A close-up view of the Cell Biology Experiment Facility (CBEF) SPACE SEED experiment is featured in this image photographed by an Expedition 21 crew member in the Kibo laboratory on the International Space Station.

View of CBEF Space Seed Experiment Hardware

NASA Image and Video Library

2009-10-13

ISS021-E-006256 (13 Oct. 2009) --- A close-up view of the Cell Biology Experiment Facility (CBEF) SPACE SEED experiment is featured in this image photographed by an Expedition 21 crew member in the Kibo laboratory on the International Space Station.

Tested Studies for Laboratory Teaching. Proceedings of the Workshop/Conference of the Association for Biology Laboratory Education (ABLE) (16th, Atlanta, Georgia, June 7-11, 1994). Volume 16.

ERIC Educational Resources Information Center

Goldman, Corey A., Ed.

The focus of the Association for Biology Laboratory Education (ABLE) is to improve the undergraduate biology laboratory experience by promoting the development and dissemination of interesting, innovative, and reliable laboratory exercises. This proceedings volume contains 17 papers on the topics of cell and molecular biology, genetics, and…

Moles of a Substance per Cell Is a Highly Informative Dosing Metric in Cell Culture

PubMed Central

Wagner, Brett A.; Buettner, Garry R.

2015-01-01

Background The biological consequences upon exposure of cells in culture to a dose of xenobiotic are not only dependent on biological variables, but also the physical aspects of experiments e.g. cell number and media volume. Dependence on physical aspects is often overlooked due to the unrecognized ambiguity in the dominant metric used to express exposure, i.e. initial concentration of xenobiotic delivered to the culture medium over the cells. We hypothesize that for many xenobiotics, specifying dose as moles per cell will reduce this ambiguity. Dose as moles per cell can also provide additional information not easily obtainable with traditional dosing metrics. Methods Here, 1,4-benzoquinone and oligomycin A are used as model compounds to investigate moles per cell as an informative dosing metric. Mechanistic insight into reactions with intracellular molecules, differences between sequential and bolus addition of xenobiotic and the influence of cell volume and protein content on toxicity are also investigated. Results When the dose of 1,4-benzoquinone or oligomycin A was specified as moles per cell, toxicity was independent of the physical conditions used (number of cells, volume of medium). When using moles per cell as a dose-metric, direct quantitative comparisons can be made between biochemical or biological endpoints and the dose of xenobiotic applied. For example, the toxicity of 1,4-benzoquinone correlated inversely with intracellular volume for all five cell lines exposed (C6, MDA-MB231, A549, MIA PaCa-2, and HepG2). Conclusions Moles per cell is a useful and informative dosing metric in cell culture. This dosing metric is a scalable parameter that: can reduce ambiguity between experiments having different physical conditions; provides additional mechanistic information; allows direct comparison between different cells; affords a more uniform platform for experimental design; addresses the important issue of repeatability of experimental results, and could increase the translatability of information gained from in vitro experiments. PMID:26172833

Explanatory chapter: introducing exogenous DNA into cells.

PubMed

Koontz, Laura

2013-01-01

The ability to efficiently introduce DNA into cells is essential for many experiments in biology. This is an explanatory chapter providing an overview of the various methods for introducing DNA into bacteria, yeast, and mammalian cells. Copyright © 2013 Elsevier Inc. All rights reserved.

Electrophoretic separation of cells and particles from rat pituitary and rat spleen

NASA Technical Reports Server (NTRS)

Hymer, Wesley C.

1993-01-01

There are 3 parts to the IML-2 TX-101 experiment. Part 1 is a pituitary cell culture experiment. Part 2 is a pituitary cell separation experiment using the Japanese free flow electrophoresis unit (FFEU). Part 3 is a pituitary secretory granule separation experiment using the FFEU. The objectives of this three part experiment are: (1) to determine the kinetics of production of biologically active growth hormone (GH) and prolactin (PRL) in rat pituitary GH and PRL cells in microgravity (micro-g); (2) to investigate three mechanisms by which a micro-g-induced lesion in hormone production may occur; and (3) to determine the quality of separations of pituitary cells and organelles by continuous flow electrophoresis (CFE) in micro-g under conditions where buoyancy-induced convection is eliminated.

Extremely Low-Frequency Electromagnetic Fields Cause G1 Phase Arrest through the Activation of the ATM-Chk2-p21 Pathway

PubMed Central

Huang, Chao-Ying; Chang, Cheng-Wei; Chen, Chaang-Ray; Chuang, Chun-Yu; Chiang, Chi-Shiun; Shu, Wun-Yi; Fan, Tai-Ching; Hsu, Ian C.

2014-01-01

In daily life, humans are exposed to the extremely low-frequency electromagnetic fields (ELF-EMFs) generated by electric appliances, and public concern is increasing regarding the biological effects of such exposure. Numerous studies have yielded inconsistent results regarding the biological effects of ELF-EMF exposure. Here we show that ELF-EMFs activate the ATM-Chk2-p21 pathway in HaCaT cells, inhibiting cell proliferation. To present well-founded results, we comprehensively evaluated the biological effects of ELF-EMFs at the transcriptional, protein, and cellular levels. Human HaCaT cells from an immortalized epidermal keratinocyte cell line were exposed to a 1.5 mT, 60 Hz ELF-EMF for 144 h. The ELF-EMF could cause G1 arrest and decrease colony formation. Protein expression experiments revealed that ELF-EMFs induced the activation of the ATM/Chk2 signaling cascades. In addition, the p21 protein, a regulator of cell cycle progression at G1 and G2/M, exhibited a higher level of expression in exposed HaCaT cells compared with the expression of sham-exposed cells. The ELF-EMF-induced G1 arrest was diminished when the CHK2 gene expression (which encodes checkpoint kinase 2; Chk2) was suppressed by specific small interfering RNA (siRNA). These findings indicate that ELF-EMFs activate the ATM-Chk2-p21 pathway in HaCaT cells, resulting in cell cycle arrest at the G1 phase. Based on the precise control of the ELF-EMF exposure and rigorous sham-exposure experiments, all transcriptional, protein, and cellular level experiments consistently supported the conclusion. This is the first study to confirm that a specific pathway is triggered by ELF-EMF exposure. PMID:25111195

``Physical Concepts in Cell Biology,'' an upper level interdisciplinary course in cell biophysics/mathematical biology

NASA Astrophysics Data System (ADS)

Vavylonis, Dimitrios

2009-03-01

I will describe my experience in developing an interdisciplinary biophysics course addressed to students at the upper undergraduate and graduate level, in collaboration with colleagues in physics and biology. The students had a background in physics, biology and engineering, and for many the course was their first exposure to interdisciplinary topics. The course did not depend on a formal knowledge of equilibrium statistical mechanics. Instead, the approach was based on dynamics. I used diffusion as a universal ``long time'' law to illustrate scaling concepts. The importance of statistics and proper counting of states/paths was introduced by calculating the maximum accuracy with which bacteria can measure the concentration of diffuse chemicals. The use of quantitative concepts and methods was introduced through specific biological examples, focusing on model organisms and extremes at the cell level. Examples included microtubule dynamic instability, the search and capture model, molecular motor cooperativity in muscle cells, mitotic spindle oscillations in C. elegans, polymerization forces and propulsion of pathogenic bacteria, Brownian ratchets, bacterial cell division and MinD oscillations.

FE-2 Nicole Stott works on the CBEF Space Seed Experiment

NASA Image and Video Library

2009-10-14

ISS021-E-006292 (14 Oct. 2009) --- NASA astronaut Nicole Stott, Expedition 21 flight engineer, using a watering syringe, supplies water to the Cell Biology Experiment Facility (CBEF) SPACE SEED experiment in the Kibo laboratory on the International Space Station.

DomeGene Sample Removal from Cell Biology Experiment Facility (CBEF)

NASA Image and Video Library

2009-03-28

ISS018-E-044235 (28 March 2009) --- Japan Aerospace Exploration Agency (JAXA) astronaut Koichi Wakata, Expedition 18/19 flight engineer, works on an experiment at the Ryutai fluid science experiment rack in the Kibo laboratory of the International Space Station.

Biology Labs That Work: The Best of How-To-Do-Its. Volume II.

ERIC Educational Resources Information Center

Black, Suzanne, Ed.; Moore, Randy, Ed.; Haugen, Heidi, Ed.

This selected collection of How-To-Do-It articles published in the American Biology Teacher during the past six years presents experiments that can be conducted safely under properly trained and responsible teacher supervision. Contents include: (1) "General Biology and the Nature of Science"; (2) "Cells and Molecules"; (3) "Microbes and Fungi";…

Co-culture systems and technologies: taking synthetic biology to the next level.

PubMed

Goers, Lisa; Freemont, Paul; Polizzi, Karen M

2014-07-06

Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Common stock solutions, buffers, and media.

PubMed

2001-05-01

This section describes the preparation of buffers and reagents used in this manual for cell culture, manipulation of tissue, and cell biological methods. Also discussed are special considerations for PCR experiments and for working with RNA.

Lessons learned about spaceflight and cell biology experiments

NASA Technical Reports Server (NTRS)

Hughes-Fulford, Millie

2004-01-01

Conducting cell biology experiments in microgravity can be among the most technically challenging events in a biologist's life. Conflicting events of spaceflight include waiting to get manifested, delays in manifest schedules, training astronauts to not shake your cultures and to add reagents slowly, as shaking or quick injection can activate signaling cascades and give you erroneous results. It is important to select good hardware that is reliable. Possible conflicting environments in flight include g-force and vibration of launch, exposure of cells to microgravity for extended periods until hardware is turned on, changes in cabin gases and cosmic radiation. One should have an on-board 1-g control centrifuge in order to eliminate environmental differences. Other obstacles include getting your funding in a timely manner (it is not uncommon for two to three years to pass between notification of grant approval for funding and actually getting funded). That said, it is important to note that microgravity research is worthwhile since all terrestrial life evolved in a gravity field and secrets of biological function may only be answered by removing the constant of gravity. Finally, spaceflight experiments are rewarding and worth your effort and patience.

Feasibility of a Short-Arm Centrifuge for Mouse Hypergravity Experiments.

PubMed

Morita, Hironobu; Obata, Koji; Abe, Chikara; Shiba, Dai; Shirakawa, Masaki; Kudo, Takashi; Takahashi, Satoru

2015-01-01

To elucidate the pure impact of microgravity on small mammals despite uncontrolled factors that exist in the International Space Station, it is necessary to construct a 1 g environment in space. The Japan Aerospace Exploration Agency has developed a novel mouse habitat cage unit that can be installed in the Cell Biology Experiment Facility in the Kibo module of the International Space Station. The Cell Biology Experiment Facility has a short-arm centrifuge to produce artificial 1 g gravity in space for mouse experiments. However, the gravitational gradient formed inside the rearing cage is larger when the radius of gyration is shorter; this may have some impact on mice. Accordingly, biological responses to hypergravity induced by a short-arm centrifuge were examined and compared with those induced by a long-arm centrifuge. Hypergravity induced a significant Fos expression in the central nervous system, a suppression of body mass growth, an acute and transient reduction in food intake, and impaired vestibulomotor coordination. There was no difference in these responses between mice raised in a short-arm centrifuge and those in a long-arm centrifuge. These results demonstrate the feasibility of using a short-arm centrifuge for mouse experiments.

Feasibility of a Short-Arm Centrifuge for Mouse Hypergravity Experiments

PubMed Central

Morita, Hironobu; Obata, Koji; Abe, Chikara; Shiba, Dai; Shirakawa, Masaki; Kudo, Takashi; Takahashi, Satoru

2015-01-01

To elucidate the pure impact of microgravity on small mammals despite uncontrolled factors that exist in the International Space Station, it is necessary to construct a 1 g environment in space. The Japan Aerospace Exploration Agency has developed a novel mouse habitat cage unit that can be installed in the Cell Biology Experiment Facility in the Kibo module of the International Space Station. The Cell Biology Experiment Facility has a short-arm centrifuge to produce artificial 1 g gravity in space for mouse experiments. However, the gravitational gradient formed inside the rearing cage is larger when the radius of gyration is shorter; this may have some impact on mice. Accordingly, biological responses to hypergravity induced by a short-arm centrifuge were examined and compared with those induced by a long-arm centrifuge. Hypergravity induced a significant Fos expression in the central nervous system, a suppression of body mass growth, an acute and transient reduction in food intake, and impaired vestibulomotor coordination. There was no difference in these responses between mice raised in a short-arm centrifuge and those in a long-arm centrifuge. These results demonstrate the feasibility of using a short-arm centrifuge for mouse experiments. PMID:26221724

[Bio-objects and biological methods of space radiation effects evaluation].

PubMed

Kaminskaia, E V; Nevzgodina, L V; Platova, N G

2009-01-01

The unique conditions of space experiments place austere requirements to bio-objects and biological methods of radiation effects evaluation. The paper discusses suitability of a number of bio-objects varying in stage of evolution and metabolism for space researches aimed to state common patterns of the radiation damage caused by heavy ions (HI), and character of HI-cell interaction. Physical detectors in space experiments of the BIOBLOCK series make it possible to identify bio-objects hit by space HI and to set correlation between HI track topography and biological effect. The paper provides an all-round description of the bio-objects chosen for two BIOBLOCK experiments (population of hydrophyte Wolffia arrhiza (fam. duckweed) and Lactuca sativa seeds) and the method of evaluating effects from single space radiation HI. Direct effects of heavy ions on cells can be determined by the criteria of chromosomal aberrations and delayed morphologic abnormalities. The evaluation results are compared with the data about human blood lymphocytes. Consideration is being given to the procedures of test-objects' treatment and investigation.

Infrared microspectroscopy of live cells in microfluidic devices (MD-IRMS): toward a powerful label-free cell-based assay.

PubMed

Vaccari, L; Birarda, G; Businaro, L; Pacor, S; Grenci, G

2012-06-05

Until nowadays most infrared microspectroscopy (IRMS) experiments on biological specimens (i.e., tissues or cells) have been routinely carried out on fixed or dried samples in order to circumvent water absorption problems. In this paper, we demonstrate the possibility to widen the range of in-vitro IRMS experiments to vibrational analysis of live cellular samples, thanks to the development of novel biocompatible IR-visible transparent microfluidic devices (MD). In order to highlight the biological relevance of IRMS in MD (MD-IRMS), we performed a systematic exploration of the biochemical alterations induced by different fixation protocols, ethanol 70% and formaldehyde solution 4%, as well as air-drying on U937 leukemic monocytes by comparing their IR vibrational features with the live U937 counterpart. Both fixation and air-drying procedures affected lipid composition and order as well as protein structure at a different extent while they both induced structural alterations in nucleic acids. Therefore, only IRMS of live cells can provide reliable information on both DNA and RNA structure and on their cellular dynamic. In summary, we show that MD-IRMS of live cells is feasible, reliable, and biologically relevant to be recognized as a label-free cell-based assay.

Space experiment "Rad Gene"-report 1; p53-Dependent gene expression in human cultured cells exposed to space environment

NASA Astrophysics Data System (ADS)

Takahashi, Akihisa; Ohnishi, Takeo; Suzuki, Hiromi; Omori, Katsunori; Seki, Masaya; Hashizume, Toko; Shimazu, Toru; Ishioka, Noriaki

The space environment contains two major biologically significant influences: space radiations and microgravity. A p53 tumor suppressor protein plays a role as a guardian of the genome through the activity of p53-centered signal transduction pathways. The aim of this study was to clarify the biological effects of space radiations, microgravity and a space environment on the gene and protein expression of p53-dependent regulated genes. Space experiments were performed with two human cultured lymphoblastoid cell lines: one cells line (TSCE5) bears a wild-type p53 gene status, and another cells line (WTK1) bears a mutated p53 gene status. Un-der one gravity or microgravity condition, the cells were grown in the cell biology experimental facility (CBEF) of the International Space Station (ISS) for 8 days without experiencing the stress during launching and landing because the cells were frozen during these periods. Ground control samples also were cultured for 8 days in the CBEF on the ground during the same periods as space flight. Gene and protein expression was analyzed by using DNA chip (a 44k whole human genome microarray, Agilent Technologies Inc.) and protein chip (PanoramaTM Ab MicroArray, Sigma-Aldrich Co.), respectively. In addition, we analyzed the gene expression in cultured cells after space flight during 133 days with frozen condition. We report the results and discussion from the viewpoint of the functions of the up-regulated and down-regulated genes after an exposure to space radiations and/or microgravity. The initial goal of this space experiment was completely achieved. It is expected that data from this type of work will be helpful in designing physical protection from the deleterious effects of space radiations during long term stays in space.

Fluid flows and forces in development: functions, features and biophysical principles

PubMed Central

Freund, Jonathan B.; Goetz, Jacky G.; Hill, Kent L.; Vermot, Julien

2012-01-01

Throughout morphogenesis, cells experience intracellular tensile and contractile forces on microscopic scales. Cells also experience extracellular forces, such as static forces mediated by the extracellular matrix and forces resulting from microscopic fluid flow. Although the biological ramifications of static forces have received much attention, little is known about the roles of fluid flows and forces during embryogenesis. Here, we focus on the microfluidic forces generated by cilia-driven fluid flow and heart-driven hemodynamics, as well as on the signaling pathways involved in flow sensing. We discuss recent studies that describe the functions and the biomechanical features of these fluid flows. These insights suggest that biological flow determines many aspects of cell behavior and identity through a specific set of physical stimuli and signaling pathways. PMID:22395739

Co-culture systems and technologies: taking synthetic biology to the next level

PubMed Central

Goers, Lisa; Freemont, Paul; Polizzi, Karen M.

2014-01-01

Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell–cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions. PMID:24829281

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images.

PubMed

Christiansen, Eric M; Yang, Samuel J; Ando, D Michael; Javaherian, Ashkan; Skibinski, Gaia; Lipnick, Scott; Mount, Elliot; O'Neil, Alison; Shah, Kevan; Lee, Alicia K; Goyal, Piyush; Fedus, William; Poplin, Ryan; Esteva, Andre; Berndl, Marc; Rubin, Lee L; Nelson, Philip; Finkbeiner, Steven

2018-04-19

Microscopy is a central method in life sciences. Many popular methods, such as antibody labeling, are used to add physical fluorescent labels to specific cellular constituents. However, these approaches have significant drawbacks, including inconsistency; limitations in the number of simultaneous labels because of spectral overlap; and necessary perturbations of the experiment, such as fixing the cells, to generate the measurement. Here, we show that a computational machine-learning approach, which we call "in silico labeling" (ISL), reliably predicts some fluorescent labels from transmitted-light images of unlabeled fixed or live biological samples. ISL predicts a range of labels, such as those for nuclei, cell type (e.g., neural), and cell state (e.g., cell death). Because prediction happens in silico, the method is consistent, is not limited by spectral overlap, and does not disturb the experiment. ISL generates biological measurements that would otherwise be problematic or impossible to acquire. Copyright © 2018 Elsevier Inc. All rights reserved.

Detailed results of ASTP experiment MA-011. [biological processing facility in space

NASA Technical Reports Server (NTRS)

Seaman, G. V. F.; Allen, R. E.; Barlow, G. H.; Bier, M.

1976-01-01

This experiment was developed in order to conduct engineering and operational tests of electrokinetic equipment in a micro-gravity environment. The experimental hardware in general functioned as planned and electrophoretic separations were obtained in space. The results indicated the development of satisfactory sample collection, return, and preservation techniques. The application of a near-zero zeta potential interior wall coating to the experimental columns, confirmation of biocompatibility of all appropriate hardware components, and use of a sterile operating environment provided a significant step forward in the development of a biological processing facility in space. A separation of a test of aldehyde-fixed rabbit, human, and horse red blood cells was obtained. Human kidney cells were separated into several components and viable cells returned to earth. The isotachophoretic separation of red cells was also demonstrated. Problems associated with the hardware led to a lack of success in the attempt to separate subpopulations of human lymphocytes.

Theory and Practice of Lineage Tracing.

PubMed

Hsu, Ya-Chieh

2015-11-01

Lineage tracing is a method that delineates all progeny produced by a single cell or a group of cells. The possibility of performing lineage tracing initiated the field of Developmental Biology and continues to revolutionize Stem Cell Biology. Here, I introduce the principles behind a successful lineage-tracing experiment. In addition, I summarize and compare different methods for conducting lineage tracing and provide examples of how these strategies can be implemented to answer fundamental questions in development and regeneration. The advantages and limitations of each method are also discussed. © 2015 AlphaMed Press.

Validation and Application of the Survey of Teaching Beliefs and Practices for Undergraduates (STEP-U): Identifying Factors Associated with Valuing Important Workplace Skills among Biology Students.

PubMed

Marbach-Ad, Gili; Rietschel, Carly; Thompson, Katerina V

2016-01-01

We present a novel assessment tool for measuring biology students' values and experiences across their undergraduate degree program. Our Survey of Teaching Beliefs and Practices for Undergraduates (STEP-U) assesses the extent to which students value skills needed for the workplace (e.g., ability to work in groups) and their experiences with teaching practices purported to promote such skills (e.g., group work). The survey was validated through factor analyses in a large sample of biology seniors (n = 1389) and through response process analyses (five interviewees). The STEP-U skills items were characterized by two underlying factors: retention (e.g., memorization) and transfer (e.g., knowledge application). Multiple linear regression models were used to examine relationships between classroom experiences, values, and student characteristics (e.g., gender, cumulative grade point average [GPA], and research experience). Student demographic and experiential factors predicted the extent to which students valued particular skills. Students with lower GPAs valued retention skills more than those with higher GPAs. Students with research experience placed greater value on scientific writing and interdisciplinary understanding. Greater experience with specific teaching practices was associated with valuing the corresponding skills more highly. The STEP-U can provide feedback vital for designing curricula that better prepare students for their intended postgraduate careers. © 2016 G. Marbach-Ad et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Scaling Up: Adapting a Phage-Hunting Course to Increase Participation of First-Year Students in Research.

PubMed

Staub, Nancy L; Poxleitner, Marianne; Braley, Amanda; Smith-Flores, Helen; Pribbenow, Christine M; Jaworski, Leslie; Lopatto, David; Anders, Kirk R

2016-01-01

Authentic research experiences are valuable components of effective undergraduate education. Research experiences during the first years of college are especially critical to increase persistence in science, technology, engineering, and mathematics fields. The Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) model provides a high-impact research experience to first-year students but is usually available to a limited number of students, and its implementation is costly in faculty time and laboratory space. To offer a research experience to all students taking introductory biology at Gonzaga University (n = 350/yr), we modified the traditional two-semester SEA-PHAGES course by streamlining the first-semester Phage Discovery lab and integrating the second SEA-PHAGES semester into other courses in the biology curriculum. Because most students in the introductory course are not biology majors, the Phage Discovery semester may be their only encounter with research. To discover whether students benefit from the first semester alone, we assessed the effects of the one-semester Phage Discovery course on students' understanding of course content. Specifically, students showed improvement in knowledge of bacteriophages, lab math skills, and understanding experimental design and interpretation. They also reported learning gains and benefits comparable with other course-based research experiences. Responses to open-ended questions suggest that students experienced this course as a true undergraduate research experience. © 2016 N. L. Staub et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Multidisciplinary Graduate Curriculum on Integrative Biointerfacial Engineering

ERIC Educational Resources Information Center

Moghe, Prabhas V.; Roth, Charles M.

2006-01-01

A wide range of biotechnological and biomedical processes and products involves the design, synthesis, and analysis of biological interfaces. Such biointerfaces mediate interactions between living cells or intracellular species and designed materials or biologics. Incorporating the experiences of a NSF-­sponsored IGERT (Integrative Graduate…

Using Phylogenetic Analysis to Detect Market Substitution of Atlantic Salmon for Pacific Salmon: An Introductory Biology Laboratory Experiment

ERIC Educational Resources Information Center

Cline, Erica; Gogarten, Jennifer

2012-01-01

We describe a laboratory exercise developed for the cell and molecular biology quarter of a year-long majors' undergraduate introductory biology sequence. In an analysis of salmon samples collected by students in their local stores and restaurants, DNA sequencing and phylogenetic analysis were used to detect market substitution of Atlantic salmon…

Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using the X-ray free-electron laser at SACLA

PubMed Central

Kobayashi, Amane; Sekiguchi, Yuki; Oroguchi, Tomotaka; Okajima, Koji; Fukuda, Asahi; Oide, Mao; Yamamoto, Masaki; Nakasako, Masayoshi

2016-01-01

Coherent X-ray diffraction imaging (CXDI) allows internal structures of biological cells and cellular organelles to be analyzed. CXDI experiments have been conducted at 66 K for frozen-hydrated biological specimens at the SPring-8 Angstrom Compact Free-Electron Laser facility (SACLA). In these cryogenic CXDI experiments using X-ray free-electron laser (XFEL) pulses, specimen particles dispersed on thin membranes of specimen disks are transferred into the vacuum chamber of a diffraction apparatus. Because focused single XFEL pulses destroy specimen particles at the atomic level, diffraction patterns are collected through raster scanning the specimen disks to provide fresh specimen particles in the irradiation area. The efficiency of diffraction data collection in cryogenic experiments depends on the quality of the prepared specimens. Here, detailed procedures for preparing frozen-hydrated biological specimens, particularly thin membranes and devices developed in our laboratory, are reported. In addition, the quality of the frozen-hydrated specimens are evaluated by analyzing the characteristics of the collected diffraction patterns. Based on the experimental results, the internal structures of the frozen-hydrated specimens and the future development for efficient diffraction data collection are discussed. PMID:27359147

Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using the X-ray free-electron laser at SACLA.

PubMed

Kobayashi, Amane; Sekiguchi, Yuki; Oroguchi, Tomotaka; Okajima, Koji; Fukuda, Asahi; Oide, Mao; Yamamoto, Masaki; Nakasako, Masayoshi

2016-07-01

Coherent X-ray diffraction imaging (CXDI) allows internal structures of biological cells and cellular organelles to be analyzed. CXDI experiments have been conducted at 66 K for frozen-hydrated biological specimens at the SPring-8 Angstrom Compact Free-Electron Laser facility (SACLA). In these cryogenic CXDI experiments using X-ray free-electron laser (XFEL) pulses, specimen particles dispersed on thin membranes of specimen disks are transferred into the vacuum chamber of a diffraction apparatus. Because focused single XFEL pulses destroy specimen particles at the atomic level, diffraction patterns are collected through raster scanning the specimen disks to provide fresh specimen particles in the irradiation area. The efficiency of diffraction data collection in cryogenic experiments depends on the quality of the prepared specimens. Here, detailed procedures for preparing frozen-hydrated biological specimens, particularly thin membranes and devices developed in our laboratory, are reported. In addition, the quality of the frozen-hydrated specimens are evaluated by analyzing the characteristics of the collected diffraction patterns. Based on the experimental results, the internal structures of the frozen-hydrated specimens and the future development for efficient diffraction data collection are discussed.

Pharmaceutical experiment aboard STS-67 mission

NASA Technical Reports Server (NTRS)

1995-01-01

Astronaut William G. Gregory, pilot, works with a pharmaceutical experiment on the middeck of the Earth-orbiting Space Shuttle Endeavour during the STS-67 mission. Commercial Materials Dispersion Apparatus Instruments Technology Associates Experiments (CMIX-03) includes not only pharmaceutical, but also biotechnology, cell biology, fluids, and crystal growth investigation

Astronaut William Gregory works with pharmaceutical experiments on middeck

NASA Technical Reports Server (NTRS)

1995-01-01

Astronaut William G. Gregory, STS-67 pilot, works with a pharmaceutical experiment on the middeck of the Earth-orbiting Space Shuttle Endeavour. Commercial Materials Dispersion Apparatus Instruments Technology Associates Experiments (CMIX-03) includes not only pharmaceutical but also biotechnology, cell biology, fluids and crystal growth investigations.

Protein Delivery into Plant Cells: Toward In vivo Structural Biology

PubMed Central

Cedeño, Cesyen; Pauwels, Kris; Tompa, Peter

2017-01-01

Understanding the biologically relevant structural and functional behavior of proteins inside living plant cells is only possible through the combination of structural biology and cell biology. The state-of-the-art structural biology techniques are typically applied to molecules that are isolated from their native context. Although most experimental conditions can be easily controlled while dealing with an isolated, purified protein, a serious shortcoming of such in vitro work is that we cannot mimic the extremely complex intracellular environment in which the protein exists and functions. Therefore, it is highly desirable to investigate proteins in their natural habitat, i.e., within live cells. This is the major ambition of in-cell NMR, which aims to approach structure-function relationship under true in vivo conditions following delivery of labeled proteins into cells under physiological conditions. With a multidisciplinary approach that includes recombinant protein production, confocal fluorescence microscopy, nuclear magnetic resonance (NMR) spectroscopy and different intracellular protein delivery strategies, we explore the possibility to develop in-cell NMR studies in living plant cells. While we provide a comprehensive framework to set-up in-cell NMR, we identified the efficient intracellular introduction of isotope-labeled proteins as the major bottleneck. Based on experiments with the paradigmatic intrinsically disordered proteins (IDPs) Early Response to Dehydration protein 10 and 14, we also established the subcellular localization of ERD14 under abiotic stress. PMID:28469623

NASA-Ames Life Sciences Flight Experiments program - 1980 status report

NASA Technical Reports Server (NTRS)

Berry, W. E.; Dant, C. C.; Macleod, G.; Williams, B. A.

1980-01-01

The paper deals with the ESA's Spacelab LSFE (Life Sciences Flight Experiments) program which, once operational, will provide new and unique opportunities to conduct research into the effects of spaceflight and weightlessness on living organisms under conditions approximating ground-based laboratories. Spacelab missions, launched at 18-month intervals, will enable scientists to test hypotheses from such disciplines as vestibular physiology, developmental biology, biochemistry, cell biology, plant physiology, and similar life sciences.

STS-42 Phase Partitioning Experiment (PPE) closeup taken onboard OV-103

NASA Technical Reports Server (NTRS)

1992-01-01

STS-42 Phase Partitioning Experiment (PPE), an International Microgravity Laboratory 1 (IML-1) experiment, is documented in a closeup taken onboard Discovery, Orbiter Vehicle (OV) 103. Phase partitioning is a very effective technique used by biochemists and cell biologists to obtain fairly pure cells. Cells are separated and collected in a mixture of two immiscible liquids (fluids that tend not to mix) by their surface characteristics. In the PPE, investigators feel they will be able to separate closely related cells because cell density and convection flows are not factors in the phase partitioning process in space. They also hope to study other factors that influence the process. Phase partitioning is used to separate biological materials such as bone marrow cells for cancer treatment.

Bioinformatics.

PubMed

Moore, Jason H

2007-11-01

Bioinformatics is an interdisciplinary field that blends computer science and biostatistics with biological and biomedical sciences such as biochemistry, cell biology, developmental biology, genetics, genomics, and physiology. An important goal of bioinformatics is to facilitate the management, analysis, and interpretation of data from biological experiments and observational studies. The goal of this review is to introduce some of the important concepts in bioinformatics that must be considered when planning and executing a modern biological research study. We review database resources as well as data mining software tools.

Autoradiography and the Cell Cycle.

ERIC Educational Resources Information Center

Jones, C. Weldon

1992-01-01

Outlines the stages of a cell biology "pulse-chase" experiment in which the students apply autoradiography techniques to learn about the concept of the cell cycle. Includes (1) seed germination and plant growth; (2) radioactive labeling and fixation of root tips; (3) feulgen staining of root tips; (4) preparation of autoradiograms; and…

The Biotechnology Facility for International Space Station

NASA Technical Reports Server (NTRS)

Goodwin, Thomas; Lundquist, Charles; Hurlbert, Katy; Tuxhorn, Jennifer

2004-01-01

The primary mission of the Cellular Biotechnology Program is to advance microgravity as a tool in basic and applied cell biology. The microgravity environment can be used to study fundamental principles of cell biology and to achieve specific applications such as tissue engineering. The Biotechnology Facility (BTF) will provide a state-of-the-art facility to perform cellular biotechnology research onboard the International Space Station (ISS). The BTF will support continuous operation, which will allow performance of long-duration experiments and will significantly increase the on-orbit science throughput. With the BTF, dedicated ground support, and a community of investigators, the goals of the Cellular Biotechnology Program at Johnson Space Center are to: Support approximately 400 typical investigator experiments during the nominal design life of BTF (10 years). Support a steady increase in investigations per year, starting with stationary bioreactor experiments and adding rotating bioreactor experiments at a later date. Support at least 80% of all new cellular biotechnology investigations selected through the NASA Research Announcement (NRA) process. Modular components - to allow sequential and continuous experiment operations without cross-contamination Increased cold storage capability (+4 C, -80 C, -180 C). Storage of frozen cell culture inoculum - to allow sequential investigations. Storage of post-experiment samples - for return of high quality samples. Increased number of cell cultures per investigation, with replicates - to provide sufficient number of samples for data analysis and publication of results in peer-reviewed scientific journals.

[Effects of stable ANO1 overexpression on biological behaviors of human laryngeal squamous cell carcinoma Hep-2 cells in vitro].

PubMed

Li, Yadong; Zhang, Jinsong; Yang, Kai; Zhang, Fujun; Chen, Rui; Chen, Dan

2014-02-01

To detect the effects of ANO1 overexpression on the biological behaviors of human laryngeal squamous cell carcinoma Hep-2 cells. A Hep-2 cell line stably overexpressing ANO1 were examined with flow cytometry, soft agar assay, wound healing assay, siRNA experiments, and chloride channel block with DIDS to observe the effect of ANO1 overexpression on the growth, migration and invasion of the cells. Flow cytometry revealed a comparable cell percentage in G0/G1 phase between ANO1-overexpressing cells and the control cells (P>0.05). The two cells showed no significant difference in soft agar assay (P>0.05), but in wound healing experiments, ANO1-overexpressing cells showed significantly accelerated migration (P<0.05), whereas siRNA-mediated silencing of ANO1 significantly inhibited the cell migration (P<0.05). Treatment with DIDS resulted in an effective block of the ANO1 chloride channel activity and obviously decreased the migration speed of Hep-2 cells. ANO1 overexpression does not significantly affect the proliferation of cancer cells, but can enhance the migration ability of head and neck squamous cell carcinoma, suggesting the value of ANO1 as a new gene therapy target for head and neck squamous cell carcinoma.

Quantitative cell biology: the essential role of theory.

PubMed

Howard, Jonathon

2014-11-05

Quantitative biology is a hot area, as evidenced by the recent establishment of institutes, graduate programs, and conferences with that name. But what is quantitative biology? What should it be? And how can it contribute to solving the big questions in biology? The past decade has seen very rapid development of quantitative experimental techniques, especially at the single-molecule and single-cell levels. In this essay, I argue that quantitative biology is much more than just the quantitation of these experimental results. Instead, it should be the application of the scientific method by which measurement is directed toward testing theories. In this view, quantitative biology is the recognition that theory and models play critical roles in biology, as they do in physics and engineering. By tying together experiment and theory, quantitative biology promises a deeper understanding of underlying mechanisms, when the theory works, or to new discoveries, when it does not. © 2014 Howard. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Three-dimensional manipulation of single cells using surface acoustic waves.

PubMed

Guo, Feng; Mao, Zhangming; Chen, Yuchao; Xie, Zhiwei; Lata, James P; Li, Peng; Ren, Liqiang; Liu, Jiayang; Yang, Jian; Dao, Ming; Suresh, Subra; Huang, Tony Jun

2016-02-09

The ability of surface acoustic waves to trap and manipulate micrometer-scale particles and biological cells has led to many applications involving "acoustic tweezers" in biology, chemistry, engineering, and medicine. Here, we present 3D acoustic tweezers, which use surface acoustic waves to create 3D trapping nodes for the capture and manipulation of microparticles and cells along three mutually orthogonal axes. In this method, we use standing-wave phase shifts to move particles or cells in-plane, whereas the amplitude of acoustic vibrations is used to control particle motion along an orthogonal plane. We demonstrate, through controlled experiments guided by simulations, how acoustic vibrations result in micromanipulations in a microfluidic chamber by invoking physical principles that underlie the formation and regulation of complex, volumetric trapping nodes of particles and biological cells. We further show how 3D acoustic tweezers can be used to pick up, translate, and print single cells and cell assemblies to create 2D and 3D structures in a precise, noninvasive, label-free, and contact-free manner.

Chrondrogenesis in micromass cultures of embryonic mouse limb mesenchymal cells exposed to microgravity (7-IML-1)

NASA Technical Reports Server (NTRS)

Duke, Jackie

1992-01-01

A basic question of space biology is whether changes in gravity are perceived at the cellular level. Previous studies with a variety of cells have shown that this is the case, but to date the response of skeletal cells has not been examined, even though the skeleton is sensitive to gravitational changes. The objective of the CELLS Experiment is to examine the effect of microgravity in vitro on a skeletal cell known to be sensitive to gravitational changes both in vivo and in vitro - the mammalian chondrocyte. Various aspects of the experiment are discussed.

Spacelab

NASA Image and Video Library

1992-09-01

Japanese astronaut, Mamoru Mohri, talks to Japanese students from the aft flight deck of the Space Shuttle Orbiter Endeavour during the Spacelab-J (SL-J) mission. The SL-J mission was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a marned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Spacelab-J was launched aboard the Space Shuttle Orbiter Endeavour on September 12, 1992.

Around Marshall

NASA Image and Video Library

1992-09-12

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Pictured in the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC) of Marshall Space Flight Center (MSFC) are NASDA alternate payload specialists Dr. Doi and Dr. Mukai.

Scattering matrix elements of biological particles measured in a flow through system: theory and practice.

PubMed

Sloot, P M; Hoekstra, A G; van der Liet, H; Figdor, C G

1989-05-15

Light scattering techniques (including depolarization experiments) applied to biological cells provide a fast nondestructive probe that is very sensitive to small morphological differences. Until now quantitative measurement of these scatter phenomena were only described for particles in suspension. In this paper we discuss the symmetry conditions applicable to the scattering matrices of monodisperse biological cells in a flow cytometer and provide evidence that quantitative measurement of the elements of these scattering matrices is possible in flow through systems. Two fundamental extensions to the theoretical description of conventional scattering experiments are introduced: large cone integration of scattering signals and simultaneous implementation of the localization principle to account for scattering by a sharply focused laser beam. In addition, a specific calibration technique is proposed to account for depolarization effects of the highly specialized optics applied in flow through equipment.

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.

PubMed

Bleda, Marta; Tarraga, Joaquin; de Maria, Alejandro; Salavert, Francisco; Garcia-Alonso, Luz; Celma, Matilde; Martin, Ainoha; Dopazo, Joaquin; Medina, Ignacio

2012-07-01

During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.

Gateway BioBox: A Compact, Multi-Purpose Biological Hardware Suite for In Situ Experiments and Analyses in Deep Space

NASA Astrophysics Data System (ADS)

Smith, D. J.; Parra, M.; Lane, M.; Almeida, E. A.; Space Biosciences Research Branch

2018-02-01

A compilation of NASA's smallest biological hardware systems (plus 1-g gravity controls and ancillary sensors) that will allow for a wide range of specimen cultivation and analysis, from molecular measurements to broader cell and tissue assays.

Biochemical and Molecular Biological Analyses of space-flown nematodes in Japan, the First International Caenorhabditis elegans Experiment (ICE-First)

PubMed Central

Higashibata, Akira; Higashitani, Atsushi; Adachi, Ryota; Kagawa, Hiroaki; Honda, Shuji; Honda, Yoko; Higashitani, Nahoko; Sasagawa, Yohei; Miyazawa, Yutaka; Szewczyk, Nathaniel J.; Conley, Catharine A.; Fujimoto, Nobuyoshi; Fukui, Keiji; Shimazu, Toru; Kuriyama, Kana; Ishioka, Noriaki

2008-01-01

The first International Caenorhabditis elegans Experiment (ICE-First) was carried out using a Russian Soyuz spacecraft from April 19-30, 2004. This experiment was a part of the program of the DELTA (Dutch Expedition for Life science Technology and Atmospheric research) mission, and the space agencies that participate in the International Space Station (ISS) program formed international research teams. A Japanese research team that conducted by Japan aerospace Exploration Agency (JAXA) investigated the following aspects of the organism: (1) whether meiotic chromosomal dynamics and apoptosis in the germ cells were normal under microgravity conditions, (2) the effect of the space flight on muscle cell development, and (3) the effect of the space flight on protein aggregation. In this article, we summarize the results of these biochemical and molecular biological analyses. PMID:19513185

Optical methods for measuring DNA folding

NASA Astrophysics Data System (ADS)

Smith, Adam D.; Ukogu, Obinna A.; Devenica, Luka M.; White, Elizabeth D.; Carter, Ashley R.

2017-03-01

One of the most important biological processes is the dynamic folding and unfolding of deoxyribonucleic acid (DNA). The folding process is crucial for DNA to fit within the boundaries of the cell, while the unfolding process is essential for DNA replication and transcription. To accommodate both processes, the cell employs a highly active folding mechanism that has been the subject of intense study over the last few decades. Still, many open questions remain. What are the pathways for folding or unfolding? How does the folding equilibrium shift? And, what is the energy landscape for a particular process? Here, we review these emerging questions and the in vitro, optical methods that have provided answers, introducing the topic for those physicists seeking to step into biology. Specifically, we discuss two iconic experiments for DNA folding, the tethered particle motion (TPM) experiment and the optical tweezers experiment.

Material Science

NASA Image and Video Library

2002-08-06

Khalid Alshibli of Louisiana State University, project scientist for the Mechanics of Granular Materials (MGM-III) experiment, explains the MGM experiment to Kristen Erickson, acting deputy associate administrator in NASA's Office of Biological and Physical Research. A training model of the test cell is at right. The activity was part of the Space Research and You education event held by NASA's Office of Biological and Physical Research on June 25, 2002, in Arlington, VA, to highlight the research that will be conducted on STS-107.

Probing eukaryotic cell mechanics via mesoscopic simulations

PubMed Central

Shang, Menglin; Lim, Chwee Teck

2017-01-01

Cell mechanics has proven to be important in many biological processes. Although there is a number of experimental techniques which allow us to study mechanical properties of cell, there is still a lack of understanding of the role each sub-cellular component plays during cell deformations. We present a new mesoscopic particle-based eukaryotic cell model which explicitly describes cell membrane, nucleus and cytoskeleton. We employ Dissipative Particle Dynamics (DPD) method that provides us with the unified framework for modeling of a cell and its interactions in the flow. Data from micropipette aspiration experiments were used to define model parameters. The model was validated using data from microfluidic experiments. The validated model was then applied to study the impact of the sub-cellular components on the cell viscoelastic response in micropipette aspiration and microfluidic experiments. PMID:28922399

Ontology based molecular signatures for immune cell types via gene expression analysis

PubMed Central

2013-01-01

Background New technologies are focusing on characterizing cell types to better understand their heterogeneity. With large volumes of cellular data being generated, innovative methods are needed to structure the resulting data analyses. Here, we describe an ‘Ontologically BAsed Molecular Signature’ (OBAMS) method that identifies novel cellular biomarkers and infers biological functions as characteristics of particular cell types. This method finds molecular signatures for immune cell types based on mapping biological samples to the Cell Ontology (CL) and navigating the space of all possible pairwise comparisons between cell types to find genes whose expression is core to a particular cell type’s identity. Results We illustrate this ontological approach by evaluating expression data available from the Immunological Genome project (IGP) to identify unique biomarkers of mature B cell subtypes. We find that using OBAMS, candidate biomarkers can be identified at every strata of cellular identity from broad classifications to very granular. Furthermore, we show that Gene Ontology can be used to cluster cell types by shared biological processes in order to find candidate genes responsible for somatic hypermutation in germinal center B cells. Moreover, through in silico experiments based on this approach, we have identified genes sets that represent genes overexpressed in germinal center B cells and identify genes uniquely expressed in these B cells compared to other B cell types. Conclusions This work demonstrates the utility of incorporating structured ontological knowledge into biological data analysis – providing a new method for defining novel biomarkers and providing an opportunity for new biological insights. PMID:24004649

Cell migration analysis: A low-cost laboratory experiment for cell and developmental biology courses using keratocytes from fish scales.

PubMed

Prieto, Daniel; Aparicio, Gonzalo; Sotelo-Silveira, Jose R

2017-11-01

Cell and developmental processes are complex, and profoundly dependent on spatial relationships that change over time. Innovative educational or teaching strategies are always needed to foster deep comprehension of these processes and their dynamic features. However, laboratory exercises in cell and developmental biology at the undergraduate level do not often take into account the time dimension. In this article, we provide a laboratory exercise focused in cell migration, aiming to stimulate thinking in time and space dimensions through a simplification of more complex processes occurring in cell or developmental biology. The use of open-source tools for the analysis, as well as the whole package of raw results (available at http://github.com/danielprieto/keratocyte) make it suitable for its implementation in courses with very diverse budgets. Aiming to facilitate the student's transition from science-students to science-practitioners we propose an exercise of scientific thinking, and an evaluation method. This in turn is communicated here to facilitate the finding of common caveats and weaknesses in the process of producing simple scientific communications describing the results achieved. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):475-482, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy.

PubMed

Sun, Shiyu; Zhao, Guangxu; Huang, Yibing; Cai, Mingjun; Shan, Yuping; Wang, Hongda; Chen, Yuxin

2016-07-01

In this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers.

Introducing Undergraduate Students to Real-Time PCR

ERIC Educational Resources Information Center

Hancock, Dale; Funnell, Alister; Jack, Briony; Johnston, Jill

2010-01-01

An experiment is conducted, which in four 3 h laboratory sessions, introduces third year undergraduate Biochemistry students to the technique of real-time PCR in a biological context. The model used is a murine erythroleukemia cell line (MEL cells). These continuously cycling, immature red blood cells, arrested at an early stage in erythropoiesis,…

How and why does the immunological synapse form? Physical chemistry meets cell biology.

PubMed

Chakraborty, Arup K

2002-03-05

During T lymphocyte (T cell) recognition of an antigen, a highly organized and specific pattern of membrane proteins forms in the junction between the T cell and the antigen-presenting cell (APC). This specialized cell-cell junction is called the immunological synapse. It is several micrometers large and forms over many minutes. A plethora of experiments are being performed to study the mechanisms that underlie synapse formation and the way in which information transfer occurs across the synapse. The wealth of experimental data that is beginning to emerge must be understood within a mechanistic framework if it is to prove useful in developing modalities to control the immune response. Quantitative models can complement experiments in the quest for such a mechanistic understanding by suggesting experimentally testable hypotheses. Here, a quantitative synapse assembly model is described. The model uses concepts developed in physical chemistry and cell biology and is able to predict the spatiotemporal evolution of cell shape and receptor protein patterns observed during synapse formation. Attention is directed to how the juxtaposition of model predictions and experimental data has led to intriguing hypotheses regarding the role of null and self peptides during synapse assembly, as well as correlations between T cell effector functions and the robustness of synapse assembly. We remark on some ways in which synergistic experiments and modeling studies can improve current models, and we take steps toward a better understanding of information transfer across the T cell-APC junction.

Cryogenic coherent X-ray diffraction imaging of biological samples at SACLA: a correlative approach with cryo-electron and light microscopy.

PubMed

Takayama, Yuki; Yonekura, Koji

2016-03-01

Coherent X-ray diffraction imaging at cryogenic temperature (cryo-CXDI) allows the analysis of internal structures of unstained, non-crystalline, whole biological samples in micrometre to sub-micrometre dimensions. Targets include cells and cell organelles. This approach involves preparing frozen-hydrated samples under controlled humidity, transferring the samples to a cryo-stage inside a vacuum chamber of a diffractometer, and then exposing the samples to coherent X-rays. Since 2012, cryo-coherent diffraction imaging (CDI) experiments have been carried out with the X-ray free-electron laser (XFEL) at the SPring-8 Ångstrom Compact free-electron LAser (SACLA) facility in Japan. Complementary use of cryo-electron microscopy and/or light microscopy is highly beneficial for both pre-checking samples and studying the integrity or nature of the sample. This article reports the authors' experience in cryo-XFEL-CDI of biological cells and organelles at SACLA, and describes an attempt towards reliable and higher-resolution reconstructions, including signal enhancement with strong scatterers and Patterson-search phasing.

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data.

PubMed

Bray, Mark-Anthony; Carpenter, Anne E

2015-11-04

Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been missing is a single open-source software package to visualize standard tracking output (from software like CellProfiler) in a way that allows convenient assessment of track quality, especially for researchers tuning tracking parameters for high-content time-lapse experiments. This makes quality assessment and algorithm adjustment a substantial challenge, particularly when dealing with hundreds of time-lapse movies collected in a high-throughput manner. We present CellProfiler Tracer, a free and open-source tool that complements the object tracking functionality of the CellProfiler biological image analysis package. Tracer allows multi-parametric morphological data to be visualized on object tracks, providing visualizations that have already been validated within the scientific community for time-lapse experiments, and combining them with simple graph-based measures for highlighting possible tracking artifacts. CellProfiler Tracer is a useful, free tool for inspection and quality control of object tracking data, available from http://www.cellprofiler.org/tracer/.

Cellular track model of biological damage to mammalian cell cultures from galactic cosmic rays

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Katz, Robert; Wilson, John W.; Townsend, Lawrence W.; Nealy, John E.; Shinn, Judy L.

1991-01-01

The assessment of biological damage from the galactic cosmic rays (GCR) is a current interest for exploratory class space missions where the highly ionizing, high-energy, high-charge ions (HZE) particles are the major concern. The relative biological effectiveness (RBE) values determined by ground-based experiments with HZE particles are well described by a parametric track theory of cell inactivation. Using the track model and a deterministic GCR transport code, the biological damage to mammalian cell cultures is considered for 1 year in free space at solar minimum for typical spacecraft shielding. Included are the effects of projectile and target fragmentation. The RBE values for the GCR spectrum which are fluence-dependent in the track model are found to be more severe than the quality factors identified by the International Commission on Radiological Protection publication 26 and seem to obey a simple scaling law with the duration period in free space.

Computational modeling of in vitro biological responses on polymethacrylate surfaces

PubMed Central

Ghosh, Jayeeta; Lewitus, Dan Y; Chandra, Prafulla; Joy, Abraham; Bushman, Jared; Knight, Doyle; Kohn, Joachim

2011-01-01

The objective of this research was to examine the capabilities of QSPR (Quantitative Structure Property Relationship) modeling to predict specific biological responses (fibrinogen adsorption, cell attachment and cell proliferation index) on thin films of different polymethacrylates. Using 33 commercially available monomers it is theoretically possible to construct a library of over 40,000 distinct polymer compositions. A subset of these polymers were synthesized and solvent cast surfaces were prepared in 96 well plates for the measurement of fibrinogen adsorption. NIH 3T3 cell attachment and proliferation index were measured on spin coated thin films of these polymers. Based on the experimental results of these polymers, separate models were built for homo-, co-, and terpolymers in the library with good correlation between experiment and predicted values. The ability to predict biological responses by simple QSPR models for large numbers of polymers has important implications in designing biomaterials for specific biological or medical applications. PMID:21779132

Activation and proliferation of lymphocytes and other mammalian cells in microgravity

NASA Technical Reports Server (NTRS)

Cogoli, A.; Cogoli-Greuter, M.

1997-01-01

The experimental findings reviewed in this chapter support the following conclusions: Proliferation. Human T-lymphocytes, associated with monocytes as accessory cells, show dramatic changes in the centrifuge, in the clinostat and in space. In free-floating cells the mitogenic response is depressed by 90% in microgravity, whereas in cells attached to a substratum activation is enhanced by 100% compared to 1-G ground and inflight controls. The duration of phase G1 of the mitotic cycle of HeLa cells is reduced in hypergravity, resulting in an increased proliferation rate. Other systems like Friend cells and WI38 human embryonic lung cells do not show significant changes. Genetic expression and signal transduction. T-lymphocytes and monocytes show important changes in the expression of cytokines like interleukin-1, interleukin-2, interferon-gamma and tumor necrosis factor. The data from space experiments in Spacelab, Space Shuttle mid-deck, and Biokosmos have helped to clarify certain aspects of the mechanism of T-cell activation. Epidermoid A431 cells show changes in the genetic expression of the proto-oncogenes c-fos and c-jun in the clinostat and in sounding rockets. Membrane function, in particular the binding of ligates as first messengers of a signal, is not changed in most of the cell systems in microgravity. Morphology and Mortility. Free cells, lymphocytes in particular, are able to move and form aggregates in microgravity, indicating that cell-cell contacts and cell communications do take place in microgravity. Dramatic morphological and ultrastructural changes are not detected in cells cultured in microgravity. Important experiments with single mammalian cells, including immune cells, were carried out recently in three Spacelab flights, (SL-J, D-2, and IML-2 in 1992, 1993, and 1994, respectively). The results of the D-2 mission have been published in ref. 75; those of the IML-2 mission in ref. 76. Finally, many cell biology experiments in space have suffered in the past from a lack of adequate controls (like 1-G centrifuges) and of proper experimental conditions (like well-controlled temperature). In this respect the availability of Biorack, outfitted with proper incubators with 1-G control centrifuge as well as a glovebox with a microscope, is a great advantage. It is also desirable that cell biology experiments in space are accompanied or even preceded by a program of ground-based investigations in the fast rotating clinostat and in the centrifuge, and that preparatory experiments be done in parabolic flights and sounding rockets, whenever possible. Proper publication of the results of space experiments is another important need. A great number of data have been published in proceedings and reports that are not available to the broad scientific community. To guarantee the credibility and the international recognition of space biology it is important that the results be published in international, peer reviewed journals.

The Role of Epithelial-Mesenchymal Transition in the Formation of Normal and Neoplastic Mammary Epithelial Stem Cells

DTIC Science & Technology

2011-09-01

separating stem cell and non- stem cell populations of normal and breast cancer cells and identified EMT transcription factors most likely involved in... stem cell biology. Preliminary results directly demonstrate that transient induction of EMT increases the number of mammary epithelial stem cells...EMT and entrance into a stem - cell state. The outcome of these experiments holds important implications for the mechanisms controlling the formation of

Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering.

PubMed

Menolascina, Filippo; Bellomo, Domenico; Maiwald, Thomas; Bevilacqua, Vitoantonio; Ciminelli, Caterina; Paradiso, Angelo; Tommasi, Stefania

2009-10-15

Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics of complex pathologies like cancer: acquiring information for a system understanding of complex reaction networks is time consuming and expensive. Stimulus response experiments (SRE) have been used to gain a deeper insight into the details of biochemical mechanisms underlying cell life and functioning. Optimisation of the input time-profile, however, still remains a major area of research due to the complexity of the problem and its relevance for the task of information retrieval in systems biology-related experiments. We have addressed the problem of quantifying the information associated to an experiment using the Fisher Information Matrix and we have proposed an optimal experimental design strategy based on evolutionary algorithm to cope with the problem of information gathering in Systems Biology. On the basis of the theoretical results obtained in the field of control systems theory, we have studied the dynamical properties of the signals to be used in cell stimulation. The results of this study have been used to develop a microfluidic device for the automation of the process of cell stimulation for system identification. We have applied the proposed approach to the Epidermal Growth Factor Receptor pathway and we observed that it minimises the amount of parametric uncertainty associated to the identified model. A statistical framework based on Monte-Carlo estimations of the uncertainty ellipsoid confirmed the superiority of optimally designed experiments over canonical inputs. The proposed approach can be easily extended to multiobjective formulations that can also take advantage of identifiability analysis. Moreover, the availability of fully automated microfluidic platforms explicitly developed for the task of biochemical model identification will hopefully reduce the effects of the 'data rich--data poor' paradox in Systems Biology.

Quantitative proteomics in biological research.

PubMed

Wilm, Matthias

2009-10-01

Proteomics has enabled the direct investigation of biological material, at first through the analysis of individual proteins, then of lysates from cell cultures, and finally of extracts from tissues and biopsies from entire organisms. Its latest manifestation - quantitative proteomics - allows deeper insight into biological systems. This article reviews the different methods used to extract quantitative information from mass spectra. It follows the technical developments aimed toward global proteomics, the attempt to characterize every expressed protein in a cell by at least one peptide. When applications of the technology are discussed, the focus is placed on yeast biology. In particular, differential quantitative proteomics, the comparison between an experiment and its control, is very discriminating for proteins involved in the process being studied. When trying to understand biological processes on a molecular level, differential quantitative proteomics tends to give a clearer picture than global transcription analyses. As a result, MS has become an even more indispensable tool for biochemically motivated biological research.

A Microcosm of the Biomedical Research Experience for Upper-level Undergraduates

PubMed Central

2008-01-01

The skill set required of biomedical researchers continues to grow and evolve as biology matures as a natural science. Science necessitates creative yet critical thinking, persuasive communication skills, purposeful use of time, and adeptness at the laboratory bench. Teaching these skills can be effectively accomplished in an inquiry-based, active-learning environment at a primarily undergraduate institution. Cell Biology Techniques, an upper-level cell biology laboratory course at St. John Fisher College, features two independent projects that take advantage of the biology of the nematode Caenorhabditis elegans, a premier yet simple model organism. First, students perform a miniature epigenetic screen for novel phenotypes using RNA interference. The results of this screen combined with literature research direct students toward a singe gene that they attempt to subclone in the second project. The biology of the chosen gene/protein also becomes an individualized focal point with respect to the content of the laboratory. Progress toward course goals is evaluated using written, oral, and group-produced assignments, including a concept map. Pre- and postassessment indicates a significant increase in the understanding of broad concepts in cell biological research. PMID:18519612

Emerson Enhancement Effect: A New Student Experiment.

ERIC Educational Resources Information Center

Orr, Alan R.; Knudtson, Dan L.

1977-01-01

Discusses the potential use, by students in cell biology and plant physiology, of isolated chloroplasts for determining the Emerson enhancement effect. The experiment designed to measure spectrophotometrically the photoreduction of a dye by illuminating chloroplasts with short- and long-wavelength light is presented. (HM)

Interplay of migratory and division forces as a generic mechanism for stem cell patterns

NASA Astrophysics Data System (ADS)

Hannezo, Edouard; Coucke, Alice; Joanny, Jean-François

2016-02-01

In many adult tissues, stem cells and differentiated cells are not homogeneously distributed: stem cells are arranged in periodic "niches," and differentiated cells are constantly produced and migrate out of these niches. In this article, we provide a general theoretical framework to study mixtures of dividing and actively migrating particles, which we apply to biological tissues. We show in particular that the interplay between the stresses arising from active cell migration and stem cell division give rise to robust stem cell patterns. The instability of the tissue leads to spatial patterns which are either steady or oscillating in time. The wavelength of the instability has an order of magnitude consistent with the biological observations. We also discuss the implications of these results for future in vitro and in vivo experiments.

Preparation and biological properties of a novel composite scaffold of nano-hydroxyapatite/chitosan/carboxymethyl cellulose for bone tissue engineering

PubMed Central

Liuyun, Jiang; Yubao, Li; Chengdong, Xiong

2009-01-01

In this study, we report the physico-chemical and biological properties of a novel biodegradable composite scaffold made of nano-hydroxyapatite and natural derived polymers of chitosan and carboxymethyl cellulose, namely, n-HA/CS/CMC, which was prepared by freeze-drying method. The physico-chemical properties of n-HA/CS/CMC scaffold were tested by infrared absorption spectra (IR), transmission electron microscope(TEM), scanning electron microscope(SEM), universal material testing machine and phosphate buffer solution (PBS) soaking experiment. Besides, the biological properties were evaluated by MG63 cells and Mesenchymal stem cells (MSCs) culture experiment in vitro and a short period implantation study in vivo. The results show that the composite scaffold is mainly formed through the ionic crossing-linking of the two polyions between CS and CMC, and n-HA is incorporated into the polyelectrolyte matrix of CS-CMC without agglomeration, which endows the scaffold with good physico-chemical properties such as highly interconnected porous structure, high compressive strength and good structural stability and degradation. More important, the results of cells attached, proliferated on the scaffold indicate that the scaffold is non-toxic and has good cell biocompatibility, and the results of implantation experiment in vivo further confirm that the scaffold has good tissue biocompatibility. All the above results suggest that the novel degradable n-HA/CS/CMC composite scaffold has a great potential to be used as bone tissue engineering material. PMID:19594953

Variation in Hydraulic Conductivity with Decreasing pH in a Biologically-Clogged Porous Medium

NASA Astrophysics Data System (ADS)

Kirk, M. F.; Santillan, E.; McGrath, L. K.; Altman, S. J.

2011-12-01

Biological clogging can significantly lower the hydraulic conductivity of porous media, potentially helping to limit CO2 transport from geological carbon storage reservoirs. How clogging is affected by CO2 injection, however, is unclear. We used column experiments to examine how decreasing pH, a geochemical change associated with CO2 injection, will affect the hydraulic conductivity (K) of biologically clogged porous medium. Four biologically-active experiments and two control experiments were performed. Columns consisted of 1 mm2 capillary tubes filled with 105-150 μm diameter glass beads. Artificial groundwater medium containing 1 mM glucose was pumped through the columns at a rate of 0.015 mL/min (q = 21.6 m/day; Re = 0.045). Each column was inoculated with 10^8 CFU of Pseudomonas fluorescens tagged with a green fluorescent protein; cells introduced to control columns were heat sterilized. Biomass distribution and transport was monitored using scanning laser confocal microscopy and effluent plating. Growth was allowed to occur for 5 days in medium with pH 7 in the biologically active columns. During that time, K decreased to values ranging from 10 to 27% of the average control K and effluent cell levels increased to about 10^8 CFU/mL. Next, the pH of the inflowing medium was lowered to 4 in three experiments and 5.5 in one experiment. After pH 4 medium was introduced, K increased to values ranging from 21 to 64% of the average control K and culturable cell levels in the effluent fell by about 4 log units. Confocal images show that clogging persisted in the columns at pH 4 because most of the microbial biomass remained attached to bead surfaces. In the experiment where pH was lowered to 5.5, K changed little because biological clogging remained entirely intact. The concentration of culturable cells in the effluent was also invariant. These results suggest that biomass in porous medium will largely remain in place following exposure to acidic water in a CO2 storage reservoir, particularly where buffering is able to limit the extent of acidification. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Missing data and technical variability in single-cell RNA-sequencing experiments.

PubMed

Hicks, Stephanie C; Townes, F William; Teng, Mingxiang; Irizarry, Rafael A

2017-11-06

Until recently, high-throughput gene expression technology, such as RNA-Sequencing (RNA-seq) required hundreds of thousands of cells to produce reliable measurements. Recent technical advances permit genome-wide gene expression measurement at the single-cell level. Single-cell RNA-Seq (scRNA-seq) is the most widely used and numerous publications are based on data produced with this technology. However, RNA-seq and scRNA-seq data are markedly different. In particular, unlike RNA-seq, the majority of reported expression levels in scRNA-seq are zeros, which could be either biologically-driven, genes not expressing RNA at the time of measurement, or technically-driven, genes expressing RNA, but not at a sufficient level to be detected by sequencing technology. Another difference is that the proportion of genes reporting the expression level to be zero varies substantially across single cells compared to RNA-seq samples. However, it remains unclear to what extent this cell-to-cell variation is being driven by technical rather than biological variation. Furthermore, while systematic errors, including batch effects, have been widely reported as a major challenge in high-throughput technologies, these issues have received minimal attention in published studies based on scRNA-seq technology. Here, we use an assessment experiment to examine data from published studies and demonstrate that systematic errors can explain a substantial percentage of observed cell-to-cell expression variability. Specifically, we present evidence that some of these reported zeros are driven by technical variation by demonstrating that scRNA-seq produces more zeros than expected and that this bias is greater for lower expressed genes. In addition, this missing data problem is exacerbated by the fact that this technical variation varies cell-to-cell. Then, we show how this technical cell-to-cell variability can be confused with novel biological results. Finally, we demonstrate and discuss how batch-effects and confounded experiments can intensify the problem. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

We are looking for a candidate with a strong interest in identifying small molecules that interact with cis-acting regulatory viral and cellular RNAs as a novel therapeutic strategy and exceptional motivation for academic research. Applicants with expertise in molecular biology/biochemistry/cell biology and less than 1 year postdoctoral experience will be considered for this

Using cell deformation and motion to predict forces and collective behavior in morphogenesis.

PubMed

Merkel, Matthias; Manning, M Lisa

2017-07-01

In multi-cellular organisms, morphogenesis translates processes at the cellular scale into tissue deformation at the scale of organs and organisms. To understand how biochemical signaling regulates tissue form and function, we must understand the mechanical forces that shape cells and tissues. Recent progress in developing mechanical models for tissues has led to quantitative predictions for how cell shape changes and polarized cell motility generate forces and collective behavior on the tissue scale. In particular, much insight has been gained by thinking about biological tissues as physical materials composed of cells. Here we review these advances and discuss how they might help shape future experiments in developmental biology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Electrophoresis tests on STS-3 and ground control experiments - A basis for future biological sample selections

NASA Technical Reports Server (NTRS)

Morrison, D. R.; Lewis, M. L.

1982-01-01

Static zone electrophoresis is an electrokinetic method of separating macromolecules and small particles. However, its application for the isolation of biological cells and concentrated protein solutions is limited by sedimentation and convection. Microgravity eliminates or reduces sedimentation, floatation, and density-driven convection arising from either Joule heating or concentration differences. The advantages of such an environment were first demonstrated in space during the Apollo 14 and 16 missions. In 1975 the Electrophoresis Technology Experiment (MA-011) was conducted during the Apollo-Soyuz Test Project flight. In 1979 a project was initiated to repeat the separations of human kidney cells. One of the major objectives of the Electrophoresis Equipment Verification Tests (EEVT) on STS-3 was to repeat and thereby validate the first successful electrophoretic separation of human kidney cells. Attention is given to the EEVT apparatus, the preflight electrophoresis, and inflight operational results.

The AMERE project: Enabling real-time detection of radiation effects in individual cells in deep space

NASA Astrophysics Data System (ADS)

De Vos, Winnok H.; Meesen, Geert; Szpirer, Cedric; Scohy, Sophie; Cherukuri, Chaitanya; Evrard, Olivier; Hutsebaut, Xavier; Beghuin, Didier

2012-12-01

A major concern for long-term deep space missions is the detrimental impact of cosmic radiation on human health. Especially the presence of high-energy particles of high atomic mass (HZE) represents a serious threat. To contribute to a fundamental understanding of space radiation effects and to help improving risk assessment for humans on the Moon, the ESA Lunar Lander mission model payload includes a package dedicated to cell-based radiobiology experiments in the form of an Autonomous Microscope for Examination of Radiation Effects (AMERE). The purpose of this setup is to enable real-time visualization of DNA damage repair in living cells after traversal of HZE particles on the Moon. To assess the feasibility of this challenging experiment, we have analysed the biological and technological demands. In this article, we discuss the experimental concept, the biological considerations and describe the implications for system design.

Induced pluripotent stem cells meet genome editing

PubMed Central

Hockemeyer, Dirk; Jaenisch, Rudolf

2016-01-01

It is extremely rare for a single experiment to be so impactful and timely that it shapes and forecasts the experiments of the next decade. Here, we review how two such experiments --the generation of human induced pluripotent stem cells (iPSCs) and the development of CRISPR/Cas9 technology-- have fundamentally reshaped our approach to biomedical research, stem cell biology and human genetics. We will also highlight the previous knowledge that iPSC and CRISPR/Cas9 technologies were built on as this groundwork demonstrated the need for solutions and the benefits that these technologies provided, and have set the stage for their success. PMID:27152442

Induced Pluripotent Stem Cells Meet Genome Editing.

PubMed

Hockemeyer, Dirk; Jaenisch, Rudolf

2016-05-05

It is extremely rare for a single experiment to be so impactful and timely that it shapes and forecasts the experiments of the next decade. Here, we review how two such experiments-the generation of human induced pluripotent stem cells (iPSCs) and the development of CRISPR/Cas9 technology-have fundamentally reshaped our approach to biomedical research, stem cell biology, and human genetics. We will also highlight the previous knowledge that iPSC and CRISPR/Cas9 technologies were built on as this groundwork demonstrated the need for solutions and the benefits that these technologies provided and set the stage for their success. Copyright © 2016 Elsevier Inc. All rights reserved.

Questioning the utility of pooling samples in microarray experiments with cell lines.

PubMed

Lusa, L; Cappelletti, V; Gariboldi, M; Ferrario, C; De Cecco, L; Reid, J F; Toffanin, S; Gallus, G; McShane, L M; Daidone, M G; Pierotti, M A

2006-01-01

We describe a microarray experiment using the MCF-7 breast cancer cell line in two different experimental conditions for which the same number of independent pools as the number of individual samples was hybridized on Affymetrix GeneChips. Unexpectedly, when using individual samples, the number of probe sets found to be differentially expressed between treated and untreated cells was about three times greater than that found using pools. These findings indicate that pooling samples in microarray experiments where the biological variability is expected to be small might not be helpful and could even decrease one's ability to identify differentially expressed genes.

Discovery of Possible Gene Relationships through the Application of Self-Organizing Maps to DNA Microarray Databases

PubMed Central

Chavez-Alvarez, Rocio; Chavoya, Arturo; Mendez-Vazquez, Andres

2014-01-01

DNA microarrays and cell cycle synchronization experiments have made possible the study of the mechanisms of cell cycle regulation of Saccharomyces cerevisiae by simultaneously monitoring the expression levels of thousands of genes at specific time points. On the other hand, pattern recognition techniques can contribute to the analysis of such massive measurements, providing a model of gene expression level evolution through the cell cycle process. In this paper, we propose the use of one of such techniques –an unsupervised artificial neural network called a Self-Organizing Map (SOM)–which has been successfully applied to processes involving very noisy signals, classifying and organizing them, and assisting in the discovery of behavior patterns without requiring prior knowledge about the process under analysis. As a test bed for the use of SOMs in finding possible relationships among genes and their possible contribution in some biological processes, we selected 282 S. cerevisiae genes that have been shown through biological experiments to have an activity during the cell cycle. The expression level of these genes was analyzed in five of the most cited time series DNA microarray databases used in the study of the cell cycle of this organism. With the use of SOM, it was possible to find clusters of genes with similar behavior in the five databases along two cell cycles. This result suggested that some of these genes might be biologically related or might have a regulatory relationship, as was corroborated by comparing some of the clusters obtained with SOMs against a previously reported regulatory network that was generated using biological knowledge, such as protein-protein interactions, gene expression levels, metabolism dynamics, promoter binding, and modification, regulation and transport of proteins. The methodology described in this paper could be applied to the study of gene relationships of other biological processes in different organisms. PMID:24699245

Creeping, drinking, dying: the cinematic portal and the microscopic world of the twentieth-century cell.

PubMed

Landecker, Hannah

2011-09-01

Film scholars have long posed the question of the specificity of the film medium and the apparatus of cinema, asking what is unique to cinema, how it constrains and enables filmmakers and audiences in particular ways that other media do not. This question has rarely been considered in relation to scientific film, and here it is posed within the specific context of cell biology: What does the use oftime-based media such as film coupled with the microscope allow scientists to experience that other visualization practices do not? Examining three episodes in the twentieth-century study of the cell, this article argues that the apparatus ofmicrocinematography constitutes what might be thought of as a technical portal to another world, a door that determines the experience of the world that lies on the other side of it. In this case, the design of apparatuses to capture time-lapsed images enabled the acceleration of cellular time, bringing it into the realm of human perception and experience. Further, the experience of the cellular temporal world was part of a distinct kind of cell biology, one that was focused on behavior rather than structure, focused on the relation between cells, and between the cell and its milieu rather than on cell-intrinsic features such as chromosomes or organelles. As such, the instruments and technical design of the microcinematographic apparatus may be understood as a kind of materialized epistemology, the history of which can elucidate how cinema was and is used to produce scientific knowledge.

Considering Student Voices: Examining the Experiences of Underrepresented Students in Intervention Programs.

PubMed

Gibau, Gina Sanchez

2015-01-01

Qualitative studies that examine the experiences of underrepresented minority students in science, technology, engineering, and mathematics fields are comparatively few. This study explores the self-reported experiences of underrepresented graduate students in the biomedical sciences of a large, midwestern, urban university. Document analysis of interview transcripts from program evaluations capture firsthand accounts of student experiences and reveal the need for a critical examination of current intervention programs designed to reverse the trend of underrepresentation in the biomedical sciences. Findings point to themes aligned around the benefits and challenges of program components, issues of social adjustment, the utility of supportive relationships, and environmental impacts. © 2015 G. S. Gibau. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Cell and molecular biology of the spiny dogfish Squalus acanthias and little skate Leucoraja erinacea: insights from in vitro cultured cells.

PubMed

Barnes, D W

2012-04-01

Two of the most commonly used elasmobranch experimental model species are the spiny dogfish Squalus acanthias and the little skate Leucoraja erinacea. Comparative biology and genomics with these species have provided useful information in physiology, pharmacology, toxicology, immunology, evolutionary developmental biology and genetics. A wealth of information has been obtained using in vitro approaches to study isolated cells and tissues from these organisms under circumstances in which the extracellular environment can be controlled. In addition to classical work with primary cell cultures, continuously proliferating cell lines have been derived recently, representing the first cell lines from cartilaginous fishes. These lines have proved to be valuable tools with which to explore functional genomic and biological questions and to test hypotheses at the molecular level. In genomic experiments, complementary (c)DNA libraries have been constructed, and c. 8000 unique transcripts identified, with over 3000 representing previously unknown gene sequences. A sub-set of messenger (m)RNAs has been detected for which the 3' untranslated regions show elements that are remarkably well conserved evolutionarily, representing novel, potentially regulatory gene sequences. The cell culture systems provide physiologically valid tools to study functional roles of these sequences and other aspects of elasmobranch molecular cell biology and physiology. Information derived from the use of in vitro cell cultures is valuable in revealing gene diversity and information for genomic sequence assembly, as well as for identification of new genes and molecular markers, construction of gene-array probes and acquisition of full-length cDNA sequences. © 2012 The Author. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

In vitro investigation of anodization and CaP deposited titanium surface using MG63 osteoblast-like cells

NASA Astrophysics Data System (ADS)

Lee, J. M.; Lee, J. I.; Lim, Y. J.

2010-03-01

The aim of the present study was to investigate surface characteristics in four different titanium surfaces (AN: anodized at 270 V; AN-CaP: anodic oxidation and CaP deposited; SLA: sandblasted and acid etched; MA: machined) and to evaluate biological behaviors such as cell adhesion, cell proliferation, cytoskeletal organization, and osteogenic protein expression of MG63 osteoblast-like cells at the early stage. Surface analysis was performed using scanning electron microscopy, thin-film X-ray diffractometry, and a confocal laser scanning microscope. In order to evaluate cellular responses, MG63 osteoblast-like cells were used. The cell viability was evaluated by MTT assay. Immunofluorescent analyses of actin, type I collagen, osteonectin and osteocalcin were performed. The anodized and CaP deposited specimen showed homogeneously distributed CaP particles around micropores and exhibited anatase type oxides, titanium, and HA crystalline structures. This experiment suggests that CaP particles on the anodic oxidation surface affect cellular attachment and spreading. When designing an in vitro biological study for CaP coated titanium, it must be taken into account that preincubation in medium prior to cell seeding and the cell culture medium may affect the CaP coatings. All these observations illustrate the importance of the experimental conditions and the physicochemical parameters of the CaP coating. It is considered that further evaluations such as long-term in vitro cellular assays and in vivo experiments should be necessary to figure out the effect of CaP deposition to biological responses.

Three-dimensional manipulation of single cells using surface acoustic waves

PubMed Central

Guo, Feng; Mao, Zhangming; Chen, Yuchao; Xie, Zhiwei; Lata, James P.; Li, Peng; Ren, Liqiang; Liu, Jiayang; Yang, Jian; Dao, Ming; Suresh, Subra; Huang, Tony Jun

2016-01-01

The ability of surface acoustic waves to trap and manipulate micrometer-scale particles and biological cells has led to many applications involving “acoustic tweezers” in biology, chemistry, engineering, and medicine. Here, we present 3D acoustic tweezers, which use surface acoustic waves to create 3D trapping nodes for the capture and manipulation of microparticles and cells along three mutually orthogonal axes. In this method, we use standing-wave phase shifts to move particles or cells in-plane, whereas the amplitude of acoustic vibrations is used to control particle motion along an orthogonal plane. We demonstrate, through controlled experiments guided by simulations, how acoustic vibrations result in micromanipulations in a microfluidic chamber by invoking physical principles that underlie the formation and regulation of complex, volumetric trapping nodes of particles and biological cells. We further show how 3D acoustic tweezers can be used to pick up, translate, and print single cells and cell assemblies to create 2D and 3D structures in a precise, noninvasive, label-free, and contact-free manner. PMID:26811444

ARC Cell Science Validation (CS-V) Payload Overview

NASA Technical Reports Server (NTRS)

Gilkerson, Nikita

2017-01-01

Automated cell biology system for laboratory and International Space Station (ISS) National Laboratory research. Enhanced cell culture platform that provides undisturbed culture maintenance, including feedback temperature control, medical grade gas supply, perfusion nutrient delivery and removal of waste, and automated experiment manipulations. Programmable manipulations include: media feeds change out, injections, fraction collections, fixation, flow rate, and temperature modification within a one-piece sterile barrier flow path. Cassette provides 3 levels of containment and allows Crew access to the bioculture chamber and flow path assembly for experiment initiation, refurbishment, or sample retrieval and preservation.

Coming Out in Class: Challenges and Benefits of Active Learning in a Biology Classroom for LGBTQIA Students.

PubMed

Cooper, Katelyn M; Brownell, Sara E

As we transition our undergraduate biology classrooms from traditional lectures to active learning, the dynamics among students become more important. These dynamics can be influenced by student social identities. One social identity that has been unexamined in the context of undergraduate biology is the spectrum of lesbian, gay, bisexual, transgender, queer, intersex, and asexual (LGBTQIA) identities. In this exploratory interview study, we probed the experiences and perceptions of seven students who identify as part of the LGBTQIA community. We found that students do not always experience the undergraduate biology classroom to be a welcoming or accepting place for their identities. In contrast to traditional lectures, active-learning classes increase the relevance of their LGBTQIA identities due to the increased interactions among students during group work. Finally, working with other students in active-learning classrooms can present challenges and opportunities for students considering their LGBTQIA identity. These findings indicate that these students' LGBTQIA identities are affecting their experience in the classroom and that there may be specific instructional practices that can mitigate some of the possible obstacles. We hope that this work can stimulate discussions about how to broadly make our active-learning biology classes more inclusive of this specific population of students. © 2016 K. M. Cooper and S. E. Brownell. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Yeast pheromone pathway modeling using Petri nets

PubMed Central

2014-01-01

Background Our environment is composed of biological components of varying magnitude. The relationships between the different biological elements can be represented as a biological network. The process of mating in S. cerevisiae is initiated by secretion of pheromone by one of the cells. Our interest lies in one particular question: how does a cell dynamically adapt the pathway to continue mating under severe environmental changes or under mutation (which might result in the loss of functionality of some proteins known to participate in the pheromone pathway). Our work attempts to answer this question. To achieve this, we first propose a model to simulate the pheromone pathway using Petri nets. Petri nets are directed graphs that can be used for describing and modeling systems characterized as concurrent, asynchronous, distributed, parallel, non-deterministic, and/or stochastic. We then analyze our Petri net-based model of the pathway to investigate the following: 1) Given the model of the pheromone response pathway, under what conditions does the cell respond positively, i.e., mate? 2) What kinds of perturbations in the cell would result in changing a negative response to a positive one? Method In our model, we classify proteins into two categories: core component proteins (set ψ) and additional proteins (set λ). We randomly generate our model's parameters in repeated simulations. To simulate the pathway, we carry out three different experiments. In the experiments, we simply change the concentration of the additional proteins (λ) available to the cell. The concentration of proteins in ψ is varied consistently from 300 to 400. In Experiment 1, the range of values for λ is set to be 100 to 150. In Experiment 2, it is set to be 151 to 200. In Experiment 3, the set λ is further split into σ and ς, with the idea that proteins in σ are more important than those in ς. The range of values for σ is set to be between 151 to 200 while that of ς is 100 to 150. Decision trees were derived from each of the first two experiments to allow us to more easily analyze the conditions under which the pheromone is expressed. Conclusion The simulation results reveal that a cell can overcome the detrimental effects of the conditions by using more concentration of additional proteins in λ. The first two experiments provide evidence that employing more concentration of proteins might be one of the ways that the cell uses to adapt itself in inhibiting conditions to facilitate mating. The results of the third experiment reveal that in some case the protein set σ is sufficient in regulating the response of the cell. Results of Experiments 4 and 5 reveal that there are certain conditions (parameters) in the model that are more important in determining whether a cell will respond positively or not. PMID:25080237

Yeast pheromone pathway modeling using Petri nets.

PubMed

Majumdar, Abhishek; Scott, Stephen D; Deogun, Jitender S; Harris, Steven

2014-01-01

Our environment is composed of biological components of varying magnitude. The relationships between the different biological elements can be represented as a biological network. The process of mating in S. cerevisiae is initiated by secretion of pheromone by one of the cells. Our interest lies in one particular question: how does a cell dynamically adapt the pathway to continue mating under severe environmental changes or under mutation (which might result in the loss of functionality of some proteins known to participate in the pheromone pathway). Our work attempts to answer this question. To achieve this, we first propose a model to simulate the pheromone pathway using Petri nets. Petri nets are directed graphs that can be used for describing and modeling systems characterized as concurrent, asynchronous, distributed, parallel, non-deterministic, and/or stochastic. We then analyze our Petri net-based model of the pathway to investigate the following: 1) Given the model of the pheromone response pathway, under what conditions does the cell respond positively, i.e., mate? 2) What kinds of perturbations in the cell would result in changing a negative response to a positive one? In our model, we classify proteins into two categories: core component proteins (set ψ) and additional proteins (set λ). We randomly generate our model's parameters in repeated simulations. To simulate the pathway, we carry out three different experiments. In the experiments, we simply change the concentration of the additional proteins (λ) available to the cell. The concentration of proteins in ψ is varied consistently from 300 to 400. In Experiment 1, the range of values for λ is set to be 100 to 150. In Experiment 2, it is set to be 151 to 200. In Experiment 3, the set λ is further split into σ and ς, with the idea that proteins in σ are more important than those in ς. The range of values for σ is set to be between 151 to 200 while that of ς is 100 to 150. Decision trees were derived from each of the first two experiments to allow us to more easily analyze the conditions under which the pheromone is expressed. The simulation results reveal that a cell can overcome the detrimental effects of the conditions by using more concentration of additional proteins in λ. The first two experiments provide evidence that employing more concentration of proteins might be one of the ways that the cell uses to adapt itself in inhibiting conditions to facilitate mating. The results of the third experiment reveal that in some case the protein set σ is sufficient in regulating the response of the cell. Results of Experiments 4 and 5 reveal that there are certain conditions (parameters) in the model that are more important in determining whether a cell will respond positively or not.

A microfluidic microprocessor: controlling biomimetic containers and cells using hybrid integrated circuit/microfluidic chips.

PubMed

Issadore, David; Franke, Thomas; Brown, Keith A; Westervelt, Robert M

2010-11-07

We present an integrated platform for performing biological and chemical experiments on a chip based on standard CMOS technology. We have developed a hybrid integrated circuit (IC)/microfluidic chip that can simultaneously control thousands of living cells and pL volumes of fluid, enabling a wide variety of chemical and biological tasks. Taking inspiration from cellular biology, phospholipid bilayer vesicles are used as robust picolitre containers for reagents on the chip. The hybrid chip can be programmed to trap, move, and porate individual living cells and vesicles and fuse and deform vesicles using electric fields. The IC spatially patterns electric fields in a microfluidic chamber using 128 × 256 (32,768) 11 × 11 μm(2) metal pixels, each of which can be individually driven with a radio frequency (RF) voltage. The chip's basic functions can be combined in series to perform complex biological and chemical tasks and can be performed in parallel on the chip's many pixels for high-throughput operations. The hybrid chip operates in two distinct modes, defined by the frequency of the RF voltage applied to the pixels: Voltages at MHz frequencies are used to trap, move, and deform objects using dielectrophoresis and voltages at frequencies below 1 kHz are used for electroporation and electrofusion. This work represents an important step towards miniaturizing the complex chemical and biological experiments used for diagnostics and research onto automated and inexpensive chips.

Clinostats and centrifuges: Their use, value, and limitations in gravitational biological research; Symposium, Washington, Oct. 19, 1991, Report

NASA Technical Reports Server (NTRS)

Halstead, Thora W. (Editor); Todd, Paul (Editor); Powers, Janet V. (Editor)

1992-01-01

The present volume addresses physical phenomena and effects associated with clinostat and centrifuge operations as well as their physiological effects. Particular attention is given to the simulation of the gravity conditions on the ground, the internal dynamics of slowly rotating biological systems, and qualitative and quantitative aspects of the fast-rotating clinostat as a research tool. Also discussed are the development and use of centrifuges in gravitational biology, the use of centrifuges in plant gravitational biology and a comparison of ground-based and flight experiment results, the ability of clinostat to mimic the effect of microgravity on plant cells and organs, and the impact of altered gravity conditions on early EGF-induced signal transduction in human epidermal A431 cells.

Mastracchio assembles the Experiment Container in the Columbus Module

NASA Image and Video Library

2013-11-25

ISS038-E-008037 (25 Nov. 2013) --- NASA astronaut Rick Mastracchio, Expedition 38 flight engineer, works with Biolab hardware in the Columbus laboratory of the International Space Station. Biolab is used to perform space biology experiments on microorganisms, cells, tissue cultures, plants and small invertebrates.

Mastracchio assembles the Experiment Container in the Columbus Module

NASA Image and Video Library

2013-11-25

ISS038-E-008033 (25 Nov. 2013) --- NASA astronaut Rick Mastracchio, Expedition 38 flight engineer, works with Biolab hardware in the Columbus laboratory of the International Space Station. Biolab is used to perform space biology experiments on microorganisms, cells, tissue cultures, plants and small invertebrates.

Using space-based investigations to inform cancer research on Earth.

PubMed

Becker, Jeanne L; Souza, Glauco R

2013-05-01

Experiments conducted in the microgravity environment of space are not typically at the forefront of the mind of a cancer biologist. However, space provides physical conditions that are not achievable on Earth, as well as conditions that can be exploited to study mechanisms and pathways that control cell growth and function. Over the past four decades, studies have shown how exposure to microgravity alters biological processes that may be relevant to cancer. In this Review, we explore the influence of microgravity on cell biology, focusing on tumour cells grown in space together with work carried out using models in ground-based investigations.

Application of Microfluidics in Experimental Ecology: The Importance of Being Spatial.

PubMed

Nagy, Krisztina; Ábrahám, Ágnes; Keymer, Juan E; Galajda, Péter

2018-01-01

Microfluidics is an emerging technology that is used more and more in biology experiments. Its capabilities of creating precisely controlled conditions in cellular dimensions make it ideal to explore cell-cell and cell-environment interactions. Thus, a wide spectrum of problems in microbial ecology can be studied using engineered microbial habitats. Moreover, artificial microfluidic ecosystems can serve as model systems to test ecology theories and principles that apply on a higher level in the hierarchy of biological organization. In this mini review we aim to demonstrate the versatility of microfluidics and the diversity of its applications that help the advance of microbiology, and in more general, experimental ecology.

Blueprints for green biotech: development and application of standards for plant synthetic biology.

PubMed

Patron, Nicola J

2016-06-15

Synthetic biology aims to apply engineering principles to the design and modification of biological systems and to the construction of biological parts and devices. The ability to programme cells by providing new instructions written in DNA is a foundational technology of the field. Large-scale de novo DNA synthesis has accelerated synthetic biology by offering custom-made molecules at ever decreasing costs. However, for large fragments and for experiments in which libraries of DNA sequences are assembled in different combinations, assembly in the laboratory is still desirable. Biological assembly standards allow DNA parts, even those from multiple laboratories and experiments, to be assembled together using the same reagents and protocols. The adoption of such standards for plant synthetic biology has been cohesive for the plant science community, facilitating the application of genome editing technologies to plant systems and streamlining progress in large-scale, multi-laboratory bioengineering projects. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Preparing Fresh Retinal Slices from Adult Zebrafish for Ex Vivo Imaging Experiments.

PubMed

Giarmarco, Michelle M; Cleghorn, Whitney M; Hurley, James B; Brockerhoff, Susan E

2018-05-09

The retina is a complex tissue that initiates and integrates the first steps of vision. Dysfunction of retinal cells is a hallmark of many blinding diseases, and future therapies hinge on fundamental understandings about how different retinal cells function normally. Gaining such information with biochemical methods has proven difficult because contributions of particular cell types are diminished in the retinal cell milieu. Live retinal imaging can provide a view of numerous biological processes on a subcellular level, thanks to a growing number of genetically encoded fluorescent biosensors. However, this technique has thus far been limited to tadpoles and zebrafish larvae, the outermost retinal layers of isolated retinas, or lower resolution imaging of retinas in live animals. Here we present a method for generating live ex vivo retinal slices from adult zebrafish for live imaging via confocal microscopy. This preparation yields transverse slices with all retinal layers and most cell types visible for performing confocal imaging experiments using perfusion. Transgenic zebrafish expressing fluorescent proteins or biosensors in specific retinal cell types or organelles are used to extract single-cell information from an intact retina. Additionally, retinal slices can be loaded with fluorescent indicator dyes, adding to the method's versatility. This protocol was developed for imaging Ca 2+ within zebrafish cone photoreceptors, but with proper markers it could be adapted to measure Ca 2+ or metabolites in Müller cells, bipolar and horizontal cells, microglia, amacrine cells, or retinal ganglion cells. The retinal pigment epithelium is removed from slices so this method is not suitable for studying that cell type. With practice, it is possible to generate serial slices from one animal for multiple experiments. This adaptable technique provides a powerful tool for answering many questions about retinal cell biology, Ca 2+ , and energy homeostasis.

Implementation of a Service-learning Module in Medical Microbiology and Cell Biology Classes at an Undergraduate Liberal Arts University.

PubMed

Larios-Sanz, Maia; Simmons, Alexandra D; Bagnall, Ruth Ann; Rosell, Rosemarie C

2011-01-01

Here we discuss the implementation of a service-learning module in two upper-division biology classes, Medical Microbiology and Cell Biology. This exciting hands-on learning experience provided our students with an opportunity to extend their learning of in-class topics to a real-life scenario. Students were required to volunteer their time (a minimum of 10 hours in a semester) at an under-served clinic in Houston, Texas. As they interacted with the personnel at the clinic, they were asked to identify the most prevalent disease (infectious for Medical Microbiology, and cellular-based for Cell) seen at the clinic and, working in groups, come up with educational material in the form of a display or brochure to be distributed to patients. The material was meant to educate patients about the disease in general terms, as well as how to recognize (symptoms), prevent and treat it. Students were required to keep a reflective journal in the form of a blog throughout the semester, and present their final materials to the class orally. Students were surveyed about their opinion of the experience at the end of the semester. The vast majority of student participants felt that the project was a positive experience and that it helped them develop additional skills beyond what they learn in the classroom and understand how lecture topics relate to every day life.

Space Station Biological Research Project: Reference Experiment Book

NASA Technical Reports Server (NTRS)

Johnson, Catherine (Editor); Wade, Charles (Editor)

1996-01-01

The Space Station Biological Research Project (SSBRP), which is the combined efforts of the Centrifuge Facility (CF) and the Gravitational Biology Facility (GBF), is responsible for the development of life sciences hardware to be used on the International Space Station to support cell, developmental, and plant biology research. The SSBRP Reference Experiment Book was developed to use as a tool for guiding this development effort. The reference experiments characterize the research interests of the international scientific community and serve to identify the hardware capabilities and support equipment needed to support such research. The reference experiments also serve as a tool for understanding the operational aspects of conducting research on board the Space Station. This material was generated by the science community by way of their responses to reference experiment solicitation packages sent to them by SSBRP scientists. The solicitation process was executed in two phases. The first phase was completed in February of 1992 and the second phase completed in November of 1995. Representing these phases, the document is subdivided into a Section 1 and a Section 2. The reference experiments contained in this document are only representative microgravity experiments. They are not intended to define actual flight experiments. Ground and flight experiments will be selected through the formal NASA Research Announcement (NRA) and Announcement of Opportunity (AO) experiment solicitation, review, and selection process.

Transplantation of embryonic stem cell-derived dopaminergic neurons in MPTP-treated monkeys.

PubMed

Takahashi, Jun; Takagi, Yasushi; Saiki, Hidemoto

2009-01-01

One of the target diseases of cell-replacement therapy is Parkinson's disease. Clinical experiences with fetal dopaminergic cell graft have shown that the therapy is effective, but limited and accompanied by side effects, such as dyskinesia. So, the therapy needs to be further improved and sophisticated. Embryonic stem (ES) cells are expected to be another donor cell for the treatment, because of its proliferative and differentiation capacities. For clinical application, experiments using non-human primates are important, because size, anatomy, and biological characteristics of the brain are different between rodents and primates. Here, we would like to discuss induction of dopaminergic neurons from monkey ES cells and cell transplantation into the brain of monkey Parkinson's disease model.

Apoptosis: a four-week laboratory investigation for advanced molecular and cellular biology students.

PubMed

DiBartolomeis, Susan M; Moné, James P

2003-01-01

Over the past decade, apoptosis has emerged as an important field of study central to ongoing research in many diverse fields, from developmental biology to cancer research. Apoptosis proceeds by a highly coordinated series of events that includes enzyme activation, DNA fragmentation, and alterations in plasma membrane permeability. The detection of each of these phenotypic changes is accessible to advanced undergraduate cell and molecular biology students. We describe a 4-week laboratory sequence that integrates cell culture, fluorescence microscopy, DNA isolation and analysis, and western blotting (immunoblotting) to follow apoptosis in cultured human cells. Students working in teams chemically induce apoptosis, and harvest, process, and analyze cells, using their data to determine the order of events during apoptosis. We, as instructors, expose the students to an environment closely simulating what they would encounter in an active cell or molecular biology research laboratory by having students coordinate and perform multiple tasks simultaneously and by having them experience experimental design using current literature, data interpretation, and analysis to answer a single question. Students are assessed by examination of laboratory notebooks for completeness of experimental protocols and analysis of results and for completion of an assignment that includes questions pertaining to data interpretation and apoptosis.

Single Cell Force Spectroscopy for Quantification of Cellular Adhesion on Surfaces

NASA Astrophysics Data System (ADS)

Christenson, Wayne B.

Cell adhesion is an important aspect of many biological processes. The atomic force microscope (AFM) has made it possible to quantify the forces involved in cellular adhesion using a technique called single cell force spectroscopy (SCFS). AFM based SCFS offers versatile control over experimental conditions for probing directly the interaction between specific cell types and specific proteins, surfaces, or other cells. Transmembrane integrins are the primary proteins involved in cellular adhesion to the extra cellular matix (ECM). One of the chief integrins involved in the adhesion of leukocyte cells is alpha Mbeta2 (Mac-1). The experiments in this dissertation quantify the adhesion of Mac-1 expressing human embryonic kidney (HEK Mac-1), platelets, and neutrophils cells on substrates with different concentrations of fibrinogen and on fibrin gels and multi-layered fibrinogen coated fibrin gels. It was shown that multi-layered fibrinogen reduces the adhesion force of these cells considerably. A novel method was developed as part of this research combining total internal reflection microscopy (TIRFM) with SCFS allowing for optical microscopy of HEK Mac-1 cells interacting with bovine serum albumin (BSA) coated glass after interacting with multi-layered fibrinogen. HEK Mac-1 cells are able to remove fibrinogen molecules from the multi-layered fibrinogen matrix. An analysis methodology for quantifying the kinetic parameters of integrin-ligand interactions from SCFS experiments is proposed, and the kinetic parameters of the Mac-1 fibrinogen bond are quantified. Additional SCFS experiments quantify the adhesion of macrophages and HEK Mac-1 cells on functionalized glass surfaces and normal glass surfaces. Both cell types show highest adhesion on a novel functionalized glass surface that was prepared to induce macrophage fusion. These experiments demonstrate the versatility of AFM based SCFS, and how it can be applied to address many questions in cellular biology offering quantitative insights.

Around Marshall

NASA Image and Video Library

1999-09-12

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Featured together in joint ground activities during the SL-J mission are NASA/NASDA personnel at the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC) at Marshall Space Flight Center (MSFC).

Around Marshall

NASA Image and Video Library

1992-09-18

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. From the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC), NASDA President, Mr. Yamano, speaks to Payload Specialist Mamoru Mohri, a Japanese crew member aboard the STS-47 Spacelab J mission.

Around Marshall

NASA Image and Video Library

1992-09-12

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Featured together in the Science Operation Area (SOA) are payload specialists’ first Materials Processing Test during NASA/NASDA joint ground activities at the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC) at Marshall Space Flight Center (MSFC).

Around Marshall

NASA Image and Video Library

1992-09-12

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Pictured along with George Norris in the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC) at Marshall Space Flight Center (MSFC) are NASDA alternate payload specialists Dr. Doi and Dr. Mukai.

Around Marshall

NASA Image and Video Library

1992-09-12

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Featured together in the Science Operation Area (SOA) are payload specialists’ first Materials Processing Test during NASA/NASDA joint ground activities at the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC) at Marshall Space Fight Center (MSFC).

Alternate NASDA Payload Specialists in the Huntsville Operations Support Center (HOSC) Spacelab

NASA Technical Reports Server (NTRS)

1992-01-01

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Pictured along with George Norris in the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC) at Marshall Space Flight Center (MSFC) are NASDA alternate payload specialists Dr. Doi and Dr. Mukai.

Alternate NASDA Payload Specialists in the Huntsville Operations Support Center (HOSC) Spacelab

NASA Technical Reports Server (NTRS)

1992-01-01

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Pictured in the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC) of Marshall Space Flight Center (MSFC) are NASDA alternate payload specialists Dr. Doi and Dr. Mukai.

STS-47 Spacelab-J, Onboard Photograph

NASA Technical Reports Server (NTRS)

1992-01-01

Japanese astronaut, Mamoru Mohri, talks to Japanese students from the aft flight deck of the Space Shuttle Orbiter Endeavour during the Spacelab-J (SL-J) mission. The SL-J mission was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a marned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Spacelab-J was launched aboard the Space Shuttle Orbiter Endeavour on September 12, 1992.

Joint Spacelab-J (SL-J) Activities at the Huntsville Operations Support Center (HOSC) Spacelab

NASA Technical Reports Server (NTRS)

1999-01-01

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Featured together in joint ground activities during the SL-J mission are NASA/NASDA personnel at the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC) at Marshall Space Flight Center (MSFC).

NASDA President Communicates With Japanese Crew Member Aboard the STS-47 Spacelab-J Mission

NASA Technical Reports Server (NTRS)

1992-01-01

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. From the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC), NASDA President, Mr. Yamano, speaks to Payload Specialist Mamoru Mohri, a Japanese crew member aboard the STS-47 Spacelab J mission.

Registered Report: COT drives resistance to RAF inhibition through MAP kinase pathway reactivation.

PubMed

Sharma, Vidhu; Young, Lisa; Cavadas, Miguel; Owen, Kate

2016-03-21

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered Report describes the proposed replication plan of key experiments from "COT drives resistance to RAF inhibition through MAPK pathway reactivation" by Johannessen and colleagues, published in Nature in 2010 (Johannessen et al., 2010). The key experiments to be replicated are those reported in Figures 3B, 3D-E, 3I, and 4E-F. In Figures 3B, D-E, RPMI-7951 and OUMS023 cells were reported to exhibit robust ERK/MEK activity concomitant with reduced growth sensitivity in the presence of the BRAF inhibitor PLX4720. MAP3K8 (COT/TPL2) directly regulated MEK/ERK phosphorylation, as the treatment of RPMI-7951 cells with a MAP3K8 kinase inhibitor resulted in a dose-dependent suppression of MEK/ERK activity (Figure 3I). In contrast, MAP3K8-deficient A375 cells remained sensitive to BRAF inhibition, exhibiting reduced growth and MEK/ERK activity during inhibitor treatment. To determine if RAF and MEK inhibitors together can overcome single-agent resistance, MAP3K8-expressing A375 cells treated with PLX4720 along with MEK inhibitors significantly inhibited both cell viability and ERK activation compared to treatment with PLX4720 alone, as reported in Figures 4E-F. The Reproducibility Project: Cancer Biology is collaboration between the Center for Open Science and Science Exchange and the results of the replications will be published in eLife.

Fluorescent coumarin-based probe for cysteine and homocysteine with live cell application

NASA Astrophysics Data System (ADS)

Wei, Ling-Fang; Thirumalaivasan, Natesan; Liao, Yu-Cheng; Wu, Shu-Pao

2017-08-01

Cysteine (Cys) and homocysteine (Hcy) are two of important biological thiols and function as important roles in several biological processes. The development of Cys and Hcy probes will help to explore the functions of biothiols in biological systems. In this work, a new coumarin-based probe AC, containing an acryloyl moiety, was developed for Cys and Hcy detection in cells. Cys and Hcy undergo a nucleophilic addition and subsequent cyclization reaction to remove to the acryloyl group and yield a fluorescent product, 7-hydroxylcomuarin. The probe AC showed good selectivity for cysteine and homocysteine over glutathione and other amino acids and had low detection limits of 65 nM for Cys and 79 nM for Hcy, respectively. Additionally, confocal imaging experiments demonstrated that the probe AC can be applied to visualize Cys and Hcy in living cells.

Recommendations for the design, optimization, and qualification of cell-based assays used for the detection of neutralizing antibody responses elicited to biological therapeutics.

PubMed

Gupta, Shalini; Indelicato, Stephen R; Jethwa, Vijay; Kawabata, Thomas; Kelley, Marian; Mire-Sluis, Anthony R; Richards, Susan M; Rup, Bonita; Shores, Elizabeth; Swanson, Steven J; Wakshull, Eric

2007-04-10

The administration of biological therapeutics can evoke some level of immune response to the drug product in the receiving subjects. An immune response comprised of neutralizing antibodies can lead to loss of efficacy or potentially more serious clinical sequelae. Therefore, it is important to monitor the immunogenicity of biological therapeutics throughout the drug product development cycle. Immunoassays are typically used to screen for the presence and development of anti-drug product antibodies. However, in-vitro cell-based assays prove extremely useful for the characterization of immunoassay-positive samples to determine if the detected antibodies have neutralizing properties. This document provides scientific recommendations based on the experience of the authors for the development of cell-based assays for the detection of neutralizing antibodies in non-clinical and clinical studies.

Optical micromanipulation of active cells with minimal perturbations: direct and indirect pushing.

PubMed

Wang, Chenlu; Chowdhury, Sagar; Gupta, Satyandra K; Losert, Wolfgang

2013-04-01

The challenge to wide application of optical tweezers in biological micromanipulation is the photodamage caused by high-intensity laser exposure to the manipulated living systems. While direct exposure to infrared lasers is less likely to kill cells, it can affect cell behavior and signaling. Pushing cells with optically trapped objects has been introduced as a less invasive alternative, but the technique includes some exposure of the biological object to parts of the optical tweezer beam. To keep the cells farther away from the laser, we introduce an indirect pushing-based technique for noninvasive manipulation of sensitive cells. We compare how cells respond to three manipulation approaches: direct manipulation, pushing, and indirect pushing. We find that indirect manipulation techniques lessen the impact of manipulation on cell behavior. Cell survival increases, as does the ability of cells to maintain shape and wiggle. Our experiments also demonstrate that indirect pushing allows cell-cell contacts to be formed in a controllable way, while retaining the ability of cells to change shape and move.

Using yeast to determine the functional consequences of mutations in the human p53 tumor suppressor gene: An introductory course-based undergraduate research experience in molecular and cell biology.

PubMed

Hekmat-Scafe, Daria S; Brownell, Sara E; Seawell, Patricia Chandler; Malladi, Shyamala; Imam, Jamie F Conklin; Singla, Veena; Bradon, Nicole; Cyert, Martha S; Stearns, Tim

2017-03-04

The opportunity to engage in scientific research is an important, but often neglected, component of undergraduate training in biology. We describe the curriculum for an innovative, course-based undergraduate research experience (CURE) appropriate for a large, introductory cell and molecular biology laboratory class that leverages students' high level of interest in cancer. The course is highly collaborative and emphasizes the analysis and interpretation of original scientific data. During the course, students work in teams to characterize a collection of mutations in the human p53 tumor suppressor gene via expression and analysis in yeast. Initially, student pairs use both qualitative and quantitative assays to assess the ability of their p53 mutant to activate expression of reporter genes, and they localize their mutation within the p53 structure. Through facilitated discussion, students suggest possible molecular explanations for the transactivation defects displayed by their p53 mutants and propose experiments to test these hypotheses that they execute during the second part of the course. They use a western blot to determine whether mutant p53 levels are reduced, a DNA-binding assay to test whether recognition of any of three p53 target sequences is compromised, and fluorescence microscopy to assay nuclear localization. Students studying the same p53 mutant periodically convene to discuss and interpret their combined data. The course culminates in a poster session during which students present their findings to peers, instructors, and the greater biosciences community. Based on our experience, we provide recommendations for the development of similar large introductory lab courses. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(2):161-178, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

The Biotechnology Facility for International Space Station.

PubMed

Goodwin, Thomas; Lundquist, Charles; Tuxhorn, Jennifer; Hurlbert, Katy

2004-03-01

The primary mission of the Cellular Biotechnology Program is to advance microgravity as a tool in basic and applied cell biology. The microgravity environment can be used to study fundamental principles of cell biology and to achieve specific applications such as tissue engineering. The Biotechnology Facility (BTF) will provide a state-of-the-art facility to perform cellular biotechnology research onboard the International Space Station (ISS). The BTF will support continuous operation, which will allow performance of long-duration experiments and will significantly increase the on-orbit science throughput.

The Biotechnology Facility for International Space Station

NASA Technical Reports Server (NTRS)

Goodwin, Thomas; Lundquist, Charles; Tuxhorn, Jennifer; Hurlbert, Katy

2004-01-01

The primary mission of the Cellular Biotechnology Program is to advance microgravity as a tool in basic and applied cell biology. The microgravity environment can be used to study fundamental principles of cell biology and to achieve specific applications such as tissue engineering. The Biotechnology Facility (BTF) will provide a state-of-the-art facility to perform cellular biotechnology research onboard the International Space Station (ISS). The BTF will support continuous operation, which will allow performance of long-duration experiments and will significantly increase the on-orbit science throughput.

Systems biology approach to transplant tolerance: proof of concept experiments using RNA interference (RNAi) to knock down hub genes in Jurkat and HeLa cells in vitro.

PubMed

Lwin, Wint Wah; Park, Ken; Wauson, Matthew; Gao, Qin; Finn, Patricia W; Perkins, David; Khanna, Ajai

2012-07-01

Systems biology is gaining importance in studying complex systems such as the functional interconnections of human genes [1]. To investigate the molecular interactions involved in T cell immune responses, we used databases of physical gene-gene interactions to constructed molecular interaction networks (interconnections) with R language algorithms. This helped to identify highly interconnected "hub" genes AT(1)P5C1, IL6ST, PRKCZ, MYC, FOS, JUN, and MAPK1. We hypothesized that suppression of these hub genes in the gene network would result in significant phenotypic effects on T cells and examined this in vitro. The molecular interaction networks were then analyzed and visualized with Cytoscape. Jurkat and HeLa cells were transfected with siRNA for the selected hub genes. Cell proliferation was measured using ATP luminescence and BrdU labeling, which were measured 36, 72, and 96 h after activation. Following T cell stimulation, we found a significant decrease in ATP production (P < 0.05) when the hub genes ATP5C1 and PRKCZ were knocked down using siRNA transfection, whereas no difference in ATP production was observed in siRNA transfected HeLa cells. However, HeLa cells showed a significant (P < 0.05) decrease in cell proliferation when the genes MAPK1, IL6ST, ATP5C1, JUN, and FOS were knocked down. In both Jurkat and HeLa cells, targeted gene knockdown using siRNA showed decreased cell proliferation and ATP production in both Jurkat and HeLa cells. However, Jurkat T cells and HELA cells use different hub genes to regulate activation responses. This experiment provides proof of principle of applying siRNA knockdown of T cell hub genes to evaluate their proliferative capacity and ATP production. This novel concept outlines a systems biology approach to identify hub genes for targeted therapeutics. Published by Elsevier Inc.

Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension.

PubMed

Li, Chen; Nagasaki, Masao; Ueno, Kazuko; Miyano, Satoru

2009-04-27

Model checking approaches were applied to biological pathway validations around 2003. Recently, Fisher et al. have proved the importance of model checking approach by inferring new regulation of signaling crosstalk in C. elegans and confirming the regulation with biological experiments. They took a discrete and state-based approach to explore all possible states of the system underlying vulval precursor cell (VPC) fate specification for desired properties. However, since both discrete and continuous features appear to be an indispensable part of biological processes, it is more appropriate to use quantitative models to capture the dynamics of biological systems. Our key motivation of this paper is to establish a quantitative methodology to model and analyze in silico models incorporating the use of model checking approach. A novel method of modeling and simulating biological systems with the use of model checking approach is proposed based on hybrid functional Petri net with extension (HFPNe) as the framework dealing with both discrete and continuous events. Firstly, we construct a quantitative VPC fate model with 1761 components by using HFPNe. Secondly, we employ two major biological fate determination rules - Rule I and Rule II - to VPC fate model. We then conduct 10,000 simulations for each of 48 sets of different genotypes, investigate variations of cell fate patterns under each genotype, and validate the two rules by comparing three simulation targets consisting of fate patterns obtained from in silico and in vivo experiments. In particular, an evaluation was successfully done by using our VPC fate model to investigate one target derived from biological experiments involving hybrid lineage observations. However, the understandings of hybrid lineages are hard to make on a discrete model because the hybrid lineage occurs when the system comes close to certain thresholds as discussed by Sternberg and Horvitz in 1986. Our simulation results suggest that: Rule I that cannot be applied with qualitative based model checking, is more reasonable than Rule II owing to the high coverage of predicted fate patterns (except for the genotype of lin-15ko; lin-12ko double mutants). More insights are also suggested. The quantitative simulation-based model checking approach is a useful means to provide us valuable biological insights and better understandings of biological systems and observation data that may be hard to capture with the qualitative one.

Correlating measured transient temperature rises with damage rate processes in cultured cells

NASA Astrophysics Data System (ADS)

Denton, Michael L.; Tijerina, Amanda J.; Gonzalez, Cherry C.; Gamboa, B. Giovana; Noojin, Gary D.; Ahmed, Elharith M.; Rickman, John M.; Dyer, Phillip H.; Rockwell, Benjamin A.

2017-02-01

Thermal damage rate processes in biological tissues are usually characterized by a kinetics approach. This stems from experimental data that show how the transformation of a specified biological property of cells or biomolecule (plating efficiency for viability, change in birefringence, tensile strength, etc.) is dependent upon both time and temperature. Here, two disparate approaches were used to study thermal damage rate processes in cultured retinal pigment epithelial cells. Laser exposure (photothermal) parameters included 2-μm laser exposure of non-pigmented cells and 532-nm exposures of cells possessing a variety of melanosome particle densities. Photothermal experiments used a mid-IR camera to record temperature histories with spatial resolution of about 8 μm, while fluorescence microscopy of the cell monolayers identified threshold damage at the boundary between live and dead cells. Photothermal exposure durations ranged from 0.05-20 s, and the effects of varying ambient temperature were investigated. Temperature during heat transfer using a water-jacketed cuvette was recorded with a fast microthermister, while damage and viability of the suspended cells were determined as percentages. Exposure durations for the heat transfer experiments ranged from 50- 60 s. Empirically-determined kinetic parameters for the two heating methods were compared with each other, and with values found in the literature.

Sea urchin egg fertilization and development

NASA Technical Reports Server (NTRS)

Young, R. S.

1971-01-01

The effects of subgravity (much less than unit gravity) on fertilization, cell division, differentiation, and growth of a relatively simple biological system (eggs of the sea urchin Arbacia punctulata) were considered. The experiment was flown on Gemini 3 and recovered as scheduled. However, the experiment objectives were not achieved, primarily for mechanical reasons.

Revealing Student Thinking about Experimental Design and the Roles of Control Experiments

ERIC Educational Resources Information Center

Shi, Jia; Power, Joy M.; Klymkowsky, Michael W.

2011-01-01

Well-designed "controls" distinguish experimental from non-experimental studies. Surprisingly, we found that a high percentage of students had difficulty identifying control experiments even after completing three university-level laboratory courses. To address this issue, we designed and ran a revised cell biology lab course in which…

Space Station Biological Research Project (SSBRP) Cell Culture Unit (CCU) and incubator for International Space Station (ISS) cell culture experiments

NASA Technical Reports Server (NTRS)

Vandendriesche, Donald; Parrish, Joseph; Kirven-Brooks, Melissa; Fahlen, Thomas; Larenas, Patricia; Havens, Cindy; Nakamura, Gail; Sun, Liping; Krebs, Chris; de Luis, Javier;

Pressure pulse induced-damage in live biological samples

NASA Astrophysics Data System (ADS)

Bo, C.; Balzer, J.; Godfrey, S.; Francois, M.; Saffell, J. L.; Rankin, S. M.; Proud, W. G.; Brown, K. A.

2012-08-01

Developing a cellular and molecular understanding of the nature of traumatic and post-traumatic effects of blast on live biological samples is critical for improving clinical outcomes. To analyze the effects of blast waves upon the cellular structures and the underlying physiological and biochemical changes, we have constructed an experimental platform capable of delivering compression waves, of amplitudes relevant to blast, to cell suspensions in a contained environment. Initial characterization of the system shows that cell cultures can be subjected to high-intensity compression waves up to 15 MPa in pressure and duration of 80 ± 10μs. Studies of mouse mesenchymal stem cells subjected to two different pressure impulses were analysed by cell counting, cell viability assays and microscopic evaluation: the experiments present evidence suggestive of increased levels of damage and loss of cellular integrity compared to uncompressed cell cultures.

Single cell systems biology by super-resolution imaging and combinatorial labeling

PubMed Central

Lubeck, Eric; Cai, Long

2012-01-01

Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral separability of fluorophores. Here we demonstrate a simple but general strategy to drastically increase the capacity for multiplex detection of molecules in single cells by using optical super-resolution microscopy (SRM) and combinatorial labeling. As a proof of principle, we labeled mRNAs with unique combinations of fluorophores using Fluorescence in situ Hybridization (FISH), and resolved the sequences and combinations of fluorophores with SRM. We measured the mRNA levels of 32 genes simultaneously in single S. cerevisiae cells. These experiments demonstrate that combinatorial labeling and super-resolution imaging of single cells provides a natural approach to bring systems biology into single cells. PMID:22660740

Walker in the JPM

NASA Image and Video Library

2010-10-21

ISS025-E-008414 (21 Oct. 2010) --- NASA astronaut Shannon Walker, Expedition 25 flight engineer, works at the Cell Biology Experiment Facility (CBEF) in the Kibo laboratory of the International Space Station.

Evolution of early embryogenesis in rhabditid nematodes

PubMed Central

Brauchle, Michael; Kiontke, Karin; MacMenamin, Philip; Fitch, David H. A.; Piano, Fabio

2009-01-01

The cell biological events that guide early embryonic development occur with great precision within species but can be quite diverse across species. How these cellular processes evolve and which molecular components underlie evolutionary changes is poorly understood. To begin to address these questions, we systematically investigated early embryogenesis, from the one- to the four-cell embryo, in 34 nematode species related to C. elegans. We found 40 cell-biological characters that captured the phenotypic differences between these species. By tracing the evolutionary changes on a molecular phylogeny, we found that these characters evolved multiple times and independently of one another. Strikingly, all these phenotypes are mimicked by single-gene RNAi experiments in C. elegans. We use these comparisons to hypothesize the molecular mechanisms underlying the evolutionary changes. For example, we predict that a cell polarity module was altered during the evolution of the Protorhabditis group and show that PAR-1, a kinase localized asymmetrically in C. elegans early embryos, is symmetrically localized in the one-cell stage of Protorhabditis group species. Our genome-wide approach identifies candidate molecules—and thereby modules—associated with evolutionary changes in cell-biological phenotypes. PMID:19643102

Mining meiosis and gametogenesis with DNA microarrays.

PubMed

Schlecht, Ulrich; Primig, Michael

2003-04-01

Gametogenesis is a key developmental process that involves complex transcriptional regulation of numerous genes including many that are conserved between unicellular eukaryotes and mammals. Recent expression-profiling experiments using microarrays have provided insight into the co-ordinated transcription of several hundred genes during mitotic growth and meiotic development in budding and fission yeast. Furthermore, microarray-based studies have identified numerous loci that are regulated during the cell cycle or expressed in a germ-cell specific manner in eukaryotic model systems like Caenorhabditis elegans, Mus musculus as well as Homo sapiens. The unprecedented amount of information produced by post-genome biology has spawned novel approaches to organizing biological knowledge using currently available information technology. This review outlines experiments that contribute to an emerging comprehensive picture of the molecular machinery governing sexual reproduction in eukaryotes.

Biological effects due to weak magnetic field on plants

NASA Astrophysics Data System (ADS)

Belyavskaya, N. A.

2004-01-01

Throughout the evolution process, Earth's magnetic field (MF, about 50 μT) was a natural component of the environment for living organisms. Biological objects, flying on planned long-term interplanetary missions, would experience much weaker magnetic fields, since galactic MF is known to be 0.1-1 nT. However, the role of weak magnetic fields and their influence on functioning of biological organisms are still insufficiently understood, and is actively studied. Numerous experiments with seedlings of different plant species placed in weak magnetic field have shown that the growth of their primary roots is inhibited during early germination stages in comparison with control. The proliferative activity and cell reproduction in meristem of plant roots are reduced in weak magnetic field. Cell reproductive cycle slows down due to the expansion of G 1 phase in many plant species (and of G 2 phase in flax and lentil roots), while other phases of cell cycle remain relatively stabile. In plant cells exposed to weak magnetic field, the functional activity of genome at early pre-replicate period is shown to decrease. Weak magnetic field causes intensification of protein synthesis and disintegration in plant roots. At ultrastructural level, changes in distribution of condensed chromatin and nucleolus compactization in nuclei, noticeable accumulation of lipid bodies, development of a lytic compartment (vacuoles, cytosegresomes and paramural bodies), and reduction of phytoferritin in plastids in meristem cells were observed in pea roots exposed to weak magnetic field. Mitochondria were found to be very sensitive to weak magnetic field: their size and relative volume in cells increase, matrix becomes electron-transparent, and cristae reduce. Cytochemical studies indicate that cells of plant roots exposed to weak magnetic field show Ca 2+ over-saturation in all organelles and in cytoplasm unlike the control ones. The data presented suggest that prolonged exposures of plants to weak magnetic field may cause different biological effects at the cellular, tissue and organ levels. They may be functionally related to systems that regulate plant metabolism including the intracellular Ca 2+ homeostasis. However, our understanding of very complex fundamental mechanisms and sites of interactions between weak magnetic fields and biological systems is still incomplete and still deserve strong research efforts.

Islet in weightlessness: Biological experiments on board COSMOS 1129 satellite

NASA Technical Reports Server (NTRS)

Zhuk, Y.

1980-01-01

Biological experiments planned as an international venture for COSMOS 1129 satellite include tests of: (1) adaptation of rats to conditions of weightlessness, and readaption to Earth's gravity; (2) possibility of fertilization and embryonic development in weightlessness; (3) heat exchange processes; (4) amount of gravity force preferred by fruit flies for laying eggs (given a choice of three centrifugal zones); (5) growth of higher plants from seeds; (6) effects of weightlessness on cells in culture and (7) radiation danger from heavy nuclei, and electrostatic protection from charged particles.

Guided by curvature: shaping cells by coupling curved membrane proteins and cytoskeletal forces.

PubMed

Gov, N S

2018-05-26

Eukaryote cells have flexible membranes that allow them to have a variety of dynamical shapes. The shapes of the cells serve important biological functions, both for cells within an intact tissue, and during embryogenesis and cellular motility. How cells control their shapes and the structures that they form on their surface has been a subject of intensive biological research, exposing the building blocks that cells use to deform their membranes. These processes have also drawn the interest of theoretical physicists, aiming to develop models based on physics, chemistry and nonlinear dynamics. Such models explore quantitatively different possible mechanisms that the cells can employ to initiate the spontaneous formation of shapes and patterns on their membranes. We review here theoretical work where one such class of mechanisms was investigated: the coupling between curved membrane proteins, and the cytoskeletal forces that they recruit. Theory indicates that this coupling gives rise to a rich variety of membrane shapes and dynamics, while experiments indicate that this mechanism appears to drive many cellular shape changes.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

A high-enrollment course-based undergraduate research experience improves student conceptions of scientific thinking and ability to interpret data.

PubMed

Brownell, Sara E; Hekmat-Scafe, Daria S; Singla, Veena; Chandler Seawell, Patricia; Conklin Imam, Jamie F; Eddy, Sarah L; Stearns, Tim; Cyert, Martha S

2015-01-01

We present an innovative course-based undergraduate research experience curriculum focused on the characterization of single point mutations in p53, a tumor suppressor gene that is mutated in more than 50% of human cancers. This course is required of all introductory biology students, so all biology majors engage in a research project as part of their training. Using a set of open-ended written prompts, we found that the course shifts student conceptions of what it means to think like a scientist from novice to more expert-like. Students at the end of the course identified experimental repetition, data analysis, and collaboration as important elements of thinking like a scientist. Course exams revealed that students showed gains in their ability to analyze and interpret data. These data indicate that this course-embedded research experience has a positive impact on the development of students' conceptions and practice of scientific thinking. © 2015 S. E. Brownell et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

The retinoblastoma tumor suppressor and stem cell biology.

PubMed

Sage, Julien

2012-07-01

Stem cells play a critical role during embryonic development and in the maintenance of homeostasis in adult individuals. A better understanding of stem cell biology, including embryonic and adult stem cells, will allow the scientific community to better comprehend a number of pathologies and possibly design novel approaches to treat patients with a variety of diseases. The retinoblastoma tumor suppressor RB controls the proliferation, differentiation, and survival of cells, and accumulating evidence points to a central role for RB activity in the biology of stem and progenitor cells. In some contexts, loss of RB function in stem or progenitor cells is a key event in the initiation of cancer and determines the subtype of cancer arising from these pluripotent cells by altering their fate. In other cases, RB inactivation is often not sufficient to initiate cancer but may still lead to some stem cell expansion, raising the possibility that strategies aimed at transiently inactivating RB might provide a novel way to expand functional stem cell populations. Future experiments dedicated to better understanding how RB and the RB pathway control a stem cell's decisions to divide, self-renew, or give rise to differentiated progeny may eventually increase our capacity to control these decisions to enhance regeneration or help prevent cancer development.

Evolving Strategies for the Incorporation of Bioinformatics Within the Undergraduate Cell Biology Curriculum

PubMed Central

Honts, Jerry E.

2003-01-01

Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in three courses, beginning with an introductory course in cell biology. The exercises and projects that were used to help students develop literacy in bioinformatics are described. In a recently offered course in bioinformatics, students developed their own simple sequence analysis tool using the Perl programming language. These experiences are described from the point of view of the instructor as well as the students. A preliminary assessment has been made of the degree to which students had developed a working knowledge of bioinformatics concepts and methods. Finally, some conclusions have been drawn from these courses that may be helpful to instructors wishing to introduce bioinformatics within the undergraduate biology curriculum. PMID:14673489

Three-dimensional printing of human skeletal muscle cells: An interdisciplinary approach for studying biological systems.

PubMed

Bagley, James R; Galpin, Andrew J

2015-01-01

Interdisciplinary exploration is vital to education in the 21st century. This manuscript outlines an innovative laboratory-based teaching method that combines elements of biochemistry/molecular biology, kinesiology/health science, computer science, and manufacturing engineering to give students the ability to better conceptualize complex biological systems. Here, we utilize technology available at most universities to print three-dimensional (3D) scale models of actual human muscle cells (myofibers) out of bioplastic materials. The same methodological approach could be applied to nearly any cell type or molecular structure. This advancement is significant because historically, two-dimensional (2D) myocellular images have proven insufficient for detailed analysis of organelle organization and morphology. 3D imaging fills this void by providing accurate and quantifiable myofiber structural data. Manipulating tangible 3D models combats 2D limitation and gives students new perspectives and alternative learning experiences that may assist their understanding. This approach also exposes learners to 1) human muscle cell extraction and isolation, 2) targeted fluorescence labeling, 3) confocal microscopy, 4) image processing (via open-source software), and 5) 3D printing bioplastic scale-models (×500 larger than the actual cells). Creating these physical models may further student's interest in the invisible world of molecular and cellular biology. Furthermore, this interdisciplinary laboratory project gives instructors of all biological disciplines a new teaching tool to foster integrative thinking. © 2015 The International Union of Biochemistry and Molecular Biology.

Williams installs CBEF Cell Mechanosensing Humidifier

NASA Image and Video Library

2016-04-01

ISS047e032018 (04/01/2016) --- NASA astronaut Jeff Williams works to install the Cell Biology Experiment Facility (CBEF) Cell Mechanosensing Humidifier. Cell Mechanosensing is a Japan Aerospace Exploration Agency (JAXA) investigation that identifies gravity sensors in skeletal muscle cells to develop countermeasures to muscle atrophy, a key space health issue. Scientists believe that the lack of mechanical stress from gravity causes tension fluctuations in the plasma membrane of skeletal muscle cells which changes the expression of key proteins and genes, and allows muscles to atrophy.

Research on equipment of micro-pressure measure and control in loading experiment of plant cell mechanics

NASA Astrophysics Data System (ADS)

Zhang, Lian; Yu, Chengbo; Tao, Hongyan; Chen, Xuejun; Zhai, Feng

2005-12-01

The equipment is developed to measure and control micro-pressure in loading experiment of plant cell mechanics. The motivation for the development of this equipment was to maintain a stationary micro-pressure on the agar of culturing cells to keep cytoactive in biology experiments. A singlechip controls the stepping motor of this equipment to drive loading equipment in the system, in order to load between 50mN and 250mN under a constant voltage. The accuracy is estimated to be +/-0.4 mN. The structure and control system of this equipment is introduced and described in detail. The experimental results show that the equipment is capable of maintaining a constant, stationary micropressure in cell culturing application and is worth of extending and applying.

Multi-scale modelling of the dynamics of cell colonies: insights into cell-adhesion forces and cancer invasion from in silico simulations.

PubMed

Schlüter, Daniela K; Ramis-Conde, Ignacio; Chaplain, Mark A J

2015-02-06

Studying the biophysical interactions between cells is crucial to understanding how normal tissue develops, how it is structured and also when malfunctions occur. Traditional experiments try to infer events at the tissue level after observing the behaviour of and interactions between individual cells. This approach assumes that cells behave in the same biophysical manner in isolated experiments as they do within colonies and tissues. In this paper, we develop a multi-scale multi-compartment mathematical model that accounts for the principal biophysical interactions and adhesion pathways not only at a cell-cell level but also at the level of cell colonies (in contrast to the traditional approach). Our results suggest that adhesion/separation forces between cells may be lower in cell colonies than traditional isolated single-cell experiments infer. As a consequence, isolated single-cell experiments may be insufficient to deduce important biological processes such as single-cell invasion after detachment from a solid tumour. The simulations further show that kinetic rates and cell biophysical characteristics such as pressure-related cell-cycle arrest have a major influence on cell colony patterns and can allow for the development of protrusive cellular structures as seen in invasive cancer cell lines independent of expression levels of pro-invasion molecules.

The Production of Biologically Active Substances by Plant Cell Cultures in Space

NASA Astrophysics Data System (ADS)

Strogov, S. E.; Zaitseva, G. V.; Konstantinova, N. A.; Fetisova, E. M.; Mikhailova, O. M.; Belousova, I. M.; Turkin, V. V.; Ukraintsev, A. D.

2001-07-01

The impact of the conditions of space flight on the productivity of cultures of the plant cells with respect to the biomass and the metabolites is investigated. The experiments were performed with the callus cultures of the cells of ginseng ( Panax ginseng), red root puccoon ( Lithospermum arythrorhizon), and macrotomia coloring ( Macrotomia euchroma) onboard the orbital station Mirand American Space Shuttle. A more pronounced variation of the output of the metabolites is noted with respect to the ground control. This output depends upon the properties of the strain and conditions of the experiment.

A drug-compatible and temperature-controlled microfluidic device for live-cell imaging.

PubMed

Chen, Tong; Gomez-Escoda, Blanca; Munoz-Garcia, Javier; Babic, Julien; Griscom, Laurent; Wu, Pei-Yun Jenny; Coudreuse, Damien

2016-08-01

Monitoring cellular responses to changes in growth conditions and perturbation of targeted pathways is integral to the investigation of biological processes. However, manipulating cells and their environment during live-cell-imaging experiments still represents a major challenge. While the coupling of microfluidics with microscopy has emerged as a powerful solution to this problem, this approach remains severely underexploited. Indeed, most microdevices rely on the polymer polydimethylsiloxane (PDMS), which strongly absorbs a variety of molecules commonly used in cell biology. This effect of the microsystems on the cellular environment hampers our capacity to accurately modulate the composition of the medium and the concentration of specific compounds within the microchips, with implications for the reliability of these experiments. To overcome this critical issue, we developed new PDMS-free microdevices dedicated to live-cell imaging that show no interference with small molecules. They also integrate a module for maintaining precise sample temperature both above and below ambient as well as for rapid temperature shifts. Importantly, changes in medium composition and temperature can be efficiently achieved within the chips while recording cell behaviour by microscopy. Compatible with different model systems, our platforms provide a versatile solution for the dynamic regulation of the cellular environment during live-cell imaging. © 2016 The Authors.

A drug-compatible and temperature-controlled microfluidic device for live-cell imaging

PubMed Central

Chen, Tong; Gomez-Escoda, Blanca; Munoz-Garcia, Javier; Babic, Julien; Griscom, Laurent; Wu, Pei-Yun Jenny

2016-01-01

Monitoring cellular responses to changes in growth conditions and perturbation of targeted pathways is integral to the investigation of biological processes. However, manipulating cells and their environment during live-cell-imaging experiments still represents a major challenge. While the coupling of microfluidics with microscopy has emerged as a powerful solution to this problem, this approach remains severely underexploited. Indeed, most microdevices rely on the polymer polydimethylsiloxane (PDMS), which strongly absorbs a variety of molecules commonly used in cell biology. This effect of the microsystems on the cellular environment hampers our capacity to accurately modulate the composition of the medium and the concentration of specific compounds within the microchips, with implications for the reliability of these experiments. To overcome this critical issue, we developed new PDMS-free microdevices dedicated to live-cell imaging that show no interference with small molecules. They also integrate a module for maintaining precise sample temperature both above and below ambient as well as for rapid temperature shifts. Importantly, changes in medium composition and temperature can be efficiently achieved within the chips while recording cell behaviour by microscopy. Compatible with different model systems, our platforms provide a versatile solution for the dynamic regulation of the cellular environment during live-cell imaging. PMID:27512142

BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models

PubMed Central

Bilgin, Cemal Cagatay; Fontenay, Gerald; Cheng, Qingsu; Chang, Hang; Han, Ju; Parvin, Bahram

2016-01-01

BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation. PMID:26978075

A microfluidic device for continuous manipulation of biological cells using dielectrophoresis.

PubMed

Das, Debanjan; Biswas, Karabi; Das, Soumen

2014-06-01

The present study demonstrates the design, simulation, fabrication and testing of a label-free continuous manipulation and separation micro-device of particles/biological cells suspended on medium based on conventional dielectrophoresis. The current dielectrophoretic device uses three planner electrodes to generate non-uniform electric field and induces both p-DEP and n-DEP force simultaneously depending on the dielectric properties of the particles and thus influencing at least two types of particles at a time. Numerical simulations were performed to predict the distribution of non-uniform electric field, DEP force and particle trajectories. The device is fabricated utilizing the advantage of bonding between PDMS and SU8 polymer. The p-DEP particles move away from the center of the streamline, while the n-DEP particles will follow the central streamline along the channel length. Dielectrophoretic effects were initially tested using polystyrene beads followed by manipulation of HeLa cells. In the experiment, it was observed that polystyrene beads in DI water always response as n-DEP up to 1MHz frequency, whereas HeLa cells in PBS medium response as n-DEP up to 400kHz frequency and then it experiences p-DEP up to 1MHz. Further, the microscopic observations of DEP responses of HeLa cells were verified by performing trapping experiment at static condition. Copyright © 2013 IPEM. Published by Elsevier Ltd. All rights reserved.

The German ISS-Experiment Cellular Responses to Radiation in Space (CERASP): The Effects of Single and Combined Space Flight Conditions on Mammalian Cells

NASA Astrophysics Data System (ADS)

Baumstark-Khan, C.; Hellweg, C. E.; Arenz, A.

The combined action of ionizing radiation and microgravity will continue to influence future space missions with special risks for astronauts on the Moon surface or for long duration missions to Mars Previous space flight experiments have reported additive neither sensitization nor protection as well as synergistic increased radiation effect under microgravity interactions of radiation and microgravity in different cell systems Although a direct effect of microgravity on enzymatic mechanisms can be excluded on thermo dynamical reasons modifications of cellular repair can not be excluded as such processes are under the control of cellular signal transduction systems which are controlled by environmental parameters presumably also by gravity DNA repair studies in space on bacteria yeast cells and human fibroblasts which were irradiated before flight gave contradictory results from inhibition of repair by microgravity to enhancement whereas others did not detect any influence of microgravity on repair At the Radiation Biology Department of the German Aerospace Center DLR recombinant bacterial and mammalian cell systems were developed as reporters for cellular signal transduction modulation by genotoxic environmental conditions The space experiment CERASP Cellular Responses to Radiation in Space to be performed at the International Space Station ISS will make use of such reporter cell lines thereby supplying basic information on the cellular response to radiation applied in microgravity One of the biological endpoints will be survival

Multi-scale modelling of the dynamics of cell colonies: insights into cell-adhesion forces and cancer invasion from in silico simulations

PubMed Central

Schlüter, Daniela K.; Ramis-Conde, Ignacio; Chaplain, Mark A. J.

2015-01-01

Studying the biophysical interactions between cells is crucial to understanding how normal tissue develops, how it is structured and also when malfunctions occur. Traditional experiments try to infer events at the tissue level after observing the behaviour of and interactions between individual cells. This approach assumes that cells behave in the same biophysical manner in isolated experiments as they do within colonies and tissues. In this paper, we develop a multi-scale multi-compartment mathematical model that accounts for the principal biophysical interactions and adhesion pathways not only at a cell–cell level but also at the level of cell colonies (in contrast to the traditional approach). Our results suggest that adhesion/separation forces between cells may be lower in cell colonies than traditional isolated single-cell experiments infer. As a consequence, isolated single-cell experiments may be insufficient to deduce important biological processes such as single-cell invasion after detachment from a solid tumour. The simulations further show that kinetic rates and cell biophysical characteristics such as pressure-related cell-cycle arrest have a major influence on cell colony patterns and can allow for the development of protrusive cellular structures as seen in invasive cancer cell lines independent of expression levels of pro-invasion molecules. PMID:25519994

Development and Evaluation of the Tigriopus Course-Based Undergraduate Research Experience: Impacts on Students' Content Knowledge, Attitudes, and Motivation in a Majors Introductory Biology Course.

PubMed

Olimpo, Jeffrey T; Fisher, Ginger R; DeChenne-Peters, Sue Ellen

2016-01-01

Within the past decade, course-based undergraduate research experiences (CUREs) have emerged as a viable mechanism to enhance novices' development of scientific reasoning and process skills in the science, technology, engineering, and mathematics disciplines. Recent evidence within the bioeducation literature suggests that student engagement in such experiences not only increases their appreciation for and interest in scientific research but also enhances their ability to "think like a scientist." Despite these critical outcomes, few studies have objectively explored CURE versus non-CURE students' development of content knowledge, attitudes, and motivation in the discipline, particularly among nonvolunteer samples. To address these concerns, we adopted a mixed-methods approach to evaluate the aforementioned outcomes following implementation of a novel CURE in an introductory cell/molecular biology course. Results indicate that CURE participants exhibited more expert-like outcomes on these constructs relative to their non-CURE counterparts, including in those areas related to self-efficacy, self-determination, and problem-solving strategies. Furthermore, analysis of end-of-term survey data suggests that select features of the CURE, such as increased student autonomy and collaboration, mediate student learning and enjoyment. Collectively, this research provides novel insights into the benefits achieved as a result of CURE participation and can be used to guide future development and evaluation of authentic research opportunities. © 2016 J. T. Olimpo et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Vitamin C for stabilising biological lasers (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kar, Ajoy K.; Mackenzie, Mark D.; Cialowicz, Katarzyna I.; Saleeb, Rebecca S.; Duncan, Rory R.

2016-04-01

We report on efforts to improve the lifetime of biological lasers through the use of ascorbic acid (also commonly known as vitamin C). Fluorescent proteins and dyes, used in biological lasers, suffer from photobleaching due to the build-up of reactive oxygen species (ROS) which causes damage leading to a decrease in emission over time. This is an issue both for laser lifetime and cell health. It has previously been shown that ascorbic acid can be effective in reducing ROS levels in a variety of applications. For our experiments human embryonic kidney cells (HEK293), containing the fluorescent dye Calcein AM, were placed between two dielectric plane mirrors to form a laser cavity. The cells were pumped using the output of a Ti:Sapphire femtosecond OPO system, frequency doubled twice in BBO crystals, giving an output of 474 nm. Initial results have shown an increase in laser lifetime when ascorbic acid is added to cells indicating a reduction in the build-up of ROS.

GROWTH AND METABOLISM OF INDIVIDUAL BACTERIAL CELLS UTILIZING NANOSIMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

NEALSON, H. K.

This work involved the use of the Nano-SIMS Instrument at Lawrence Livermore Laboratory, in an effort to utilize this unique tool for experiments in Biology. The work consisted primarily of experiments to measure in real time, C and N fixation in cyanobacteria. The work revealed a number of the difficulties in using the nano-SIMS approach with biological material, but with collaboration from a number of individuals at USC and LLNL, major progress was made. The collaborators from LLNL were from the Chemistry Group (Dr. Peter Weber), and the Biology Group (Dr. Jennifer Pett-Ridge). In addition, there were a number ofmore » other scientists involved from LLNL. The USC group consisted of Dr. K.H. Nealson, the PI on the grant, Dr. R. Popa, a postdoctoral fellow and research associate at USC, Professor Douglas Capone, and Juliet Finze, a graduate student in biology. Two major experiments were done, both of which yielded new and exciting data. (1) We studied nitrogen and carbon fixation in Anabaena, demonstrating that fixation ofN occurred rapidly in the heterocysts, and that the fixed N was transported rapidly and completely to the vegetative cells. C fixation occurred in the vegetative cells, with labeled C remaining in these cells in support of their growth and metabolism. This work was accepted in the ISME Journal (Nature Publication), and published last month. (2) We studied nitrogen and carbon fixation in Trichodesmium, a non-heterocystous cyanobacterium that also fixes nitrogen. Interestingly, the nitrogen fixation was confined to regions within the filaments that seem to be identical to the so-called cyanophycaen granules. The fixed N is then transported to other parts of the cyanobacterium, as judged by movement of the heavy N throughout the filaments. On the basis of these very exciting results, we have applied for funding from the NSF to continue the collaboration with LLNL. The results of both studies were presented in the summer of 2007 at the Gordon Research Conference (Applied Environmental Microbiol.).« less

Biological and Mechanical Effects of Micro-Nanostructured Titanium Surface on an Osteoblastic Cell Line In vitro and Osteointegration In vivo.

PubMed

Hao, Jingzu; Li, Ying; Li, Baoe; Wang, Xiaolin; Li, Haipeng; Liu, Shimin; Liang, Chunyong; Wang, Hongshui

2017-09-01

Hybrid micro-nanostructure implant surface was produced on titanium (Ti) surface by acid etching and anodic oxidation to improve the biological and mechanical properties. The biological properties of the micro-nanostructure were investigated by simulated body fluid (SBF) soaking test and MC3T3-E1 cell co-culture experiment. The cell proliferation, spreading, and bone sialoprotein (BSP) gene expression were examined by MTT, SEM, and reverse transcription-polymerase chain reaction (RT-PCR), respectively. In addition, the mechanical properties were evaluated by instrumented nanoindentation test and friction-wear test. Furthermore, the effect of the micro-nanostructure surface on implant osteointegration was examined by in vivo experiment. The results showed that the formation of bone-like apatite was accelerated on the micro-nanostructured Ti surface after immersion in simulated body fluid, and the proliferation, spreading, and BSP gene expression of the MC3T3-E1 cells were also upregulated on the modified surface. The micro-nanostructured Ti surface displayed decreased friction coefficient, stiffness value, and Young's modulus which were much closer to those of the cortical bone, compared to the polished Ti surface. This suggested much better mechanical match to the surrounding bone tissue of the micro-nanostructured Ti surface. Furthermore, the in vivo animal experiment showed that after implantation in the rat femora, the micro-nanostructure surface displayed higher bonding strength between bone tissues and implant; hematoxylin and eosin (H&E) staining suggested that much compact osteoid tissue was observed at the interface of Micro-nano-Ti-bone than polished Ti-bone interface after implantation. Based on these results mentioned above, it was concluded that the improved biological and mechanical properties of the micro-nanostructure endowed Ti surface with good biocompatibility and better osteointegration, implying the enlarged application of the micro-nanostructure surface Ti implants in future.

Biological characterization of metanephric mesenchymal stem cells from the Beijing duck.

PubMed

Chen, Jia; Pu, Yabin; Sun, Yujiao; Zhang, Ping; Li, Qian; Wang, Kunfu; Wang, Wenjie; Ma, Yuehui; Guan, Weijun

2016-02-01

Mesenchymal stem cells (MSCs) possess self-proliferation and multi-directional differentiation abilities. Previous studies on MSCs have mostly focused on the bone marrow, lungs, pancreas and umbilical cord blood, with few studies on metanephric tissues in ducks. For the present study, the Beijing duck was selected as an experimental animal. Duck embryo metanephric mesenchymal stem cells (MMSCs) were studied. MMSC isolation culture, analysis of biological characteristics, induced differentiation and identification were performed in preliminary experiments. In the current study, surface antigens and gene expression patterns were detected using immunofluorescence, reverse transcription-polymerase chain reaction (RT-PCR) and flow cytometry. The induced cells, adipocytes, hepatocytes, epithelial cells and islet cells were identified by oil red O staining, periodic acid-Schiff staining, immunofluorescence and dithizone staining, respectively. RT-PCR was performed for detection of specific marker genes. The results suggested that the biological characteristics of MMSCs were similar to those of the MSCs previously analyzed. Primary MMSCs were sub-cultured to passage 21. The induced cells exhibit typical staining and immunofluorescence indicating the expression of specific genes. This demonstrates that MMSCs may be a novel alternative source of MSCs for experimental and clinical applications.

NASDA life science experiment facilities for ISS

NASA Astrophysics Data System (ADS)

Tanigaki, F.; Masuda, D.; Yano, S.; Fujimoto, N.; Kamigaichi, S.

National Space Development Agency of Japan (NASDA) has been developing various experiment facilities to conduct space biology researches in KIBO (JEM). The Cell Biology Experiment Facility (CBEF) and the Clean Bench (CB) are installed into JEM Life Science Rack. The Biological Experiment Units (BEU) are operated in the CBEF and the CB for many kinds of experiments on cells, tissues, plants, microorganisms, or small animals. It is possible for all researchers to use these facilities under the system of the International Announcement of Opportunity. The CBEF is a CO2 incubator to provide a controlled environment (temperature, humidity, and CO2 concentration), in which a rotating table is equipped to make variable gravity (0-2g) for reference experiments. The containers called "Canisters" can be used to install the BEU in the CBEF. The CBEF supplies power, command, sensor, and video interfaces for the BEU through the utility connectors of Canisters. The BEU is a multiuser system consisting of chambers and control segments. It is operated by pre-set programs and by commands from the ground. NASDA is currently developing three types of the BEU: the Plant Experiment Unit (PEU) for plant life cycle observations and the Cell Experiment Unit (CEU1&2) for cell culture experiments. The PEU has an automated watering system with a water sensor, an LED matrix as a light source, and a CCD camera to observe the plant growth. The CEUs have culture chambers and an automated cultural medium exchange system. Engineering models of the PEU and CEU1 have been accomplished. The preliminary design of CEU2 is in progress. The design of the BEU will be modified to meet science requirements of each experiment. The CB provides a closed aseptic work-space (Operation Chamber) with gloves for experiment operations. Samples and the BEU can be manually handled in the CB. The CB has an air lock (Disinfection Chamber) to prevent contamination, and HEPA filters to make class-100-equivalent clean air inside the Operation Chamber. Alcohol swabs and built-in ultraviolet lamps are used to sterilize instruments and insides of the CB. The phase contrast / fluorescent microscope is equipped in the Operation Chamber to support experiments. The observed image is monitored either on the CB LCD display or on the ground through a video downlink channel. Researchers on the ground can also operate the microscope with its remote control function. Flight models of the CBEF and the CB are scheduled for completion in 2002.

Agent-based modeling: case study in cleavage furrow models.

PubMed

Mogilner, Alex; Manhart, Angelika

2016-11-07

The number of studies in cell biology in which quantitative models accompany experiments has been growing steadily. Roughly, mathematical and computational techniques of these models can be classified as "differential equation based" (DE) or "agent based" (AB). Recently AB models have started to outnumber DE models, but understanding of AB philosophy and methodology is much less widespread than familiarity with DE techniques. Here we use the history of modeling a fundamental biological problem-positioning of the cleavage furrow in dividing cells-to explain how and why DE and AB models are used. We discuss differences, advantages, and shortcomings of these two approaches. © 2016 Mogilner and Manhart. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Antitumor immune activity by chemokine CX3CL1 in an orthotopic implantation of lung cancer model in vivo.

PubMed

Kee, Ji-Ye; Arita, Yoshihisa; Shinohara, Kanna; Ohashi, Yasukata; Sakurai, Hiroaki; Saiki, Ikuo; Koizumi, Keiichi

2013-01-01

Due to their chemoattractant properties stimulating the accumulation of infiltrating immune cells in tumors, chemokines are known to have antitumor effects. Fractalkine, a unique CX3C chemokine, is expressed in activated endothelial cells, while its receptor, CX3CR1, is expressed in cytolytic immune cells, such as natural killer cells, monocytes and some CD8 + T cells. The biological properties of cancer cells are affected by the implantation organ and differences in immune systems, requiring cancer implantation in orthotopic organs in an in vivo experiment. To develop new therapy strategies for lung cancer, an animal model reflecting the clinical features of lung cancer was previously established. This study aimed to determine whether CX3CL1-induced biological functions should be used for immune cell-based gene therapy of lung cancer in the orthotopic implantation model. An orthotopic intrapulmonary implantation of CX3CL1-stable expression in mouse lung cancer (LLC-CX3CL1) was performed to analyze growth. Results showed a significant decrease in tumor growth in the lung compared to the control cells (LLC-mock). Furthermore, the antitumor effects of CX3CL1 were derived from natural killer cell activities in the depletion experiment in vivo . Therefore, CX3CL1 has the potential of a useful therapeutic target in lung cancer.

The Biostack Experiments I and II aboard Apollo 16 and 17.

PubMed

Bucker, H

1974-01-01

The concept of the Biostack experiment has become practicable through European scientific collaboration and with help of NASA. The objectives of this experiment flown aboard Apollo 16 and 17 are to study the biological effects of individual heavy cosmic particles of high-energy loss (HZE) not available on earth; to study the influence of additional spaceflight factors; to get some knowledge on the mechanism by which HZE particles damage biological materials; to get information on the spectrum of charge and energy of the cosmic ions in the spacecraft; to estimate the radiation hazards for man in space. For this purpose the Biostack experiment comprises a widespread spectrum of biological objects, and various radiobiological end-points are under investigation. Bacterial spores, protozoa cysts, plant seeds, shrimp eggs, and insect eggs were included in the Biostack experiment packages together with different physical radiation detectors (nuclear emulsions, plastics, AgCl crystals, and LiF thermoluminescence dosimeters). By using special arrangements of biological objects and physical track detectors, individual evaluation of tracks was obtained allowing the identification of each penetrating particle in relation to the possible biological effects on its path. The response of the different biological objects to space flight and HZE ions bombardment was of different degree, presumably depending on the ability of the organism to replace the cells damaged by a hit. The results help to estimate the radiation hazard for astronauts during space missions of long duration.

No question about exciting questions in cell biology.

PubMed

Pollard, Thomas D

2013-12-01

Although we have a good grasp of many important processes in cell biology, including knowledge of many molecules involved and how they interact with each other, we still do not understand most of the dynamical features that are the essence of living systems. Fortunately, we now have the ability to dissect biological systems in enough detail to understand their dynamics, including the use of mathematical models to account for past observations and predict future experiments. This deep level of mechanistic understanding should be our goal—not simply to satisfy our scientific curiosity, but also to understand the causes of disease well enough to predict risks, make early diagnoses, and treat effectively. Many big questions remain to be answered before we reach this goal of understanding cellular dynamics.

DomeGene Experiment at Cell Biology Experiment Facility (CBEF) in JPM

NASA Image and Video Library

2009-03-18

ISS018-E-040985 (18 March 2009) --- Japan Aerospace Exploration Agency (JAXA) astronaut Koichi Wakata, Expedition 18 flight engineer, uses a computer at the Japanese Remote Manipulator System (JEM-RMS) work station in the Kibo laboratory of the International Space Station while Space Shuttle Discovery (STS-119) remains docked with the station.

DomeGene Experiment at Cell Biology Experiment Facility (CBEF) in JPM

NASA Image and Video Library

2009-03-18

ISS018-E-040986 (18 March 2009) --- Japan Aerospace Exploration Agency (JAXA) astronaut Koichi Wakata, Expedition 18 flight engineer, uses a computer at the Japanese Remote Manipulator System (JEM-RMS) work station in the Kibo laboratory of the International Space Station while Space Shuttle Discovery (STS-119) remains docked with the station.

The effect of cosmic rays on biological systems - an investigation during GLE events

NASA Astrophysics Data System (ADS)

Belisheva, N. K.; Lammer, H.; Biernat, H. K.; Vashenuyk, E. V.

2012-01-01

In this study, first direct and circumstantial evidences of the effects of cosmic rays (CR) on biological systems are presented. A direct evidence of biological effects of CR is demonstrated in experiments with three cellular lines growing in culture during three events of Ground Level Enhancement (GLEs) in the neutron count rate detected by ground-based neutron monitor in October 1989. Various phenomena associated with DNA lesion on the cellular level demonstrate coherent dynamics of radiation effects in all cellular lines coincident with the time of arrival of high-energy solar particles to the near-Earth space and with the main peak in GLE. These results were obtained in the course of six separate experiments, with partial overlapping of the time of previous and subsequent experiments, which started and finished in the quiet period of solar activity (SA). A significant difference between the values of multinuclear cells in all cellular lines in the quiet period and during GLE events indicates that the cause of radiation effects in the cell cultures is an exposure of cells to the secondary solar CR near the Earth's surface. The circumstantial evidence was obtained by statistical analysis of cases of congenital malformations (CM) at two sites in the Murmansk region. The number of cases of all classes of CM reveals a significant correlation with the number of GLE events. The number of cases of CM with pronounced chromosomal abnormalities clearly correlates with the GLE events that occurred a year before the birth of a child. We have found a significant correlation between modulations of the water properties and daily background variations of CR intensity. We believe that the effects of CR on biological systems can be also mediated by fluctuations in water properties, considered as one of possible mechanisms controlling the effects of CRs on biological systems.

Enhanced expression of PKM2 associates with the biological properties of cancer stem cells from A549 human lung cancer cells.

PubMed

Guo, Chang-Ying; Yan, Chen; Luo, Lan; Goto, Shinji; Urata, Yoshishige; Xu, Jian-Jun; Wen, Xiao-Ming; Kuang, Yu-Kang; Tou, Fang-Fang; Li, Tao-Sheng

2017-04-01

Cancer cells express the M2 isoform of glycolytic enzyme pyruvate kinase (PKM2) for favoring the survival under a hypoxic condition. Considering the relative low oxygen microenvironment in stem cell niche, we hypothesized that an enhanced PKM2 expression associates with the biological properties of cancer stem cells. We used A549 human lung cancer cell line and surgical resected lung cancer tissue samples from patients for experiments. We confirmed the co-localization of PKM2 and CD44, a popular marker for cancer stem cells in lung cancer tissue samples from patients. The expression of PKM2 was clearly observed in approximately 80% of the A549 human lung cancer cells. Remarkably, enhanced expression of PKM2 was specially observed in these cells that also positively expressed CD44. Downregulation of PKM2 in CD44+ cancer stem cells by siRNA significantly impaired the potency for spheroid formation, decreased the cell survival under fetal bovine serum deprivation and hypoxic conditions, but increased their sensitivity to anti-cancer drug of cisplatin and γ-ray. The enhanced expression of PKM2 seems to associate with the biological properties of cancer stem cells from A549 human lung cancer cells. Selective targeting of PKM2 may provide a new strategy for cancer therapy, especially for patients with therapeutic resistance.

Phase partitioning, crystal growth, electrodeposition and cosmic ray experiments in microgravity

NASA Technical Reports Server (NTRS)

Wessling, Francis C.

1987-01-01

Five experiments are contained in one Get Away Special Canister (5 cu ft). The first utilizes microgravity to separate biological cells and to study the mechanism of phase partitioning in 12 separate cuvettes. Two experiments are designed to grow organic crystals by physical vapor transport. One experiment consists of eight electroplating cells with various chemicals to produce surfaces electroplated in microgravity. Some of the surfaces have micron sized particles of hard materials co-deposited during electrodeposition. The fifth experiment intercepts cosmic ray particles and records their paths on photographic emulsions. The first four experiments are controlled by an on-board C-MOS controller. The fifth experiment is totally passive. These are the first in Space. Their purpose is to create new commercial products with microgravity processing.

Three-body system metaphor for the two-slit experiment and Escherichia coli lactose-glucose metabolism.

PubMed

Asano, Masanari; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

2016-05-28

We compare the contextual probabilistic structures of the seminal two-slit experiment (quantum interference experiment), the system of three interacting bodies andEscherichia colilactose-glucose metabolism. We show that they have the same non-Kolmogorov probabilistic structure resulting from multi-contextuality. There are plenty of statistical data with non-Kolmogorov features; in particular, the probabilistic behaviour of neither quantum nor biological systems can be described classically. Biological systems (even cells and proteins) are macroscopic systems and one may try to present a more detailed model of interactions in such systems that lead to quantum-like probabilistic behaviour. The system of interactions between three bodies is one of the simplest metaphoric examples for such interactions. By proceeding further in this way (by playing withn-body systems) we shall be able to find metaphoric mechanical models for complex bio-interactions, e.g. signalling between cells, leading to non-Kolmogorov probabilistic data. © 2016 The Author(s).

The Intersection of Theory and Application in Elucidating Pattern Formation in Developmental Biology

PubMed Central

Othmer, Hans G.; Painter, Kevin; Umulis, David; Xue, Chuan

2009-01-01

We discuss theoretical and experimental approaches to three distinct developmental systems that illustrate how theory can influence experimental work and vice-versa. The chosen systems – Drosophila melanogaster, bacterial pattern formation, and pigmentation patterns – illustrate the fundamental physical processes of signaling, growth and cell division, and cell movement involved in pattern formation and development. These systems exemplify the current state of theoretical and experimental understanding of how these processes produce the observed patterns, and illustrate how theoretical and experimental approaches can interact to lead to a better understanding of development. As John Bonner said long ago ‘We have arrived at the stage where models are useful to suggest experiments, and the facts of the experiments in turn lead to new and improved models that suggest new experiments. By this rocking back and forth between the reality of experimental facts and the dream world of hypotheses, we can move slowly toward a satisfactory solution of the major problems of developmental biology.’ PMID:19844610

Three-body system metaphor for the two-slit experiment and Escherichia coli lactose–glucose metabolism

PubMed Central

Asano, Masanari; Ohya, Masanori; Yamato, Ichiro

2016-01-01

We compare the contextual probabilistic structures of the seminal two-slit experiment (quantum interference experiment), the system of three interacting bodies and Escherichia coli lactose–glucose metabolism. We show that they have the same non-Kolmogorov probabilistic structure resulting from multi-contextuality. There are plenty of statistical data with non-Kolmogorov features; in particular, the probabilistic behaviour of neither quantum nor biological systems can be described classically. Biological systems (even cells and proteins) are macroscopic systems and one may try to present a more detailed model of interactions in such systems that lead to quantum-like probabilistic behaviour. The system of interactions between three bodies is one of the simplest metaphoric examples for such interactions. By proceeding further in this way (by playing with n-body systems) we shall be able to find metaphoric mechanical models for complex bio-interactions, e.g. signalling between cells, leading to non-Kolmogorov probabilistic data. PMID:27091163

Hands-on-Entropy, Energy Balance with Biological Relevance

NASA Astrophysics Data System (ADS)

Reeves, Mark

2015-03-01

Entropy changes underlie the physics that dominates biological interactions. Indeed, introductory biology courses often begin with an exploration of the qualities of water that are important to living systems. However, one idea that is not explicitly addressed in most introductory physics or biology textbooks is important contribution of the entropy in driving fundamental biological processes towards equilibrium. From diffusion to cell-membrane formation, to electrostatic binding in protein folding, to the functioning of nerve cells, entropic effects often act to counterbalance deterministic forces such as electrostatic attraction and in so doing, allow for effective molecular signaling. A small group of biology, biophysics and computer science faculty have worked together for the past five years to develop curricular modules (based on SCALEUP pedagogy). This has enabled students to create models of stochastic and deterministic processes. Our students are first-year engineering and science students in the calculus-based physics course and they are not expected to know biology beyond the high-school level. In our class, they learn to reduce complex biological processes and structures in order model them mathematically to account for both deterministic and probabilistic processes. The students test these models in simulations and in laboratory experiments that are biologically relevant such as diffusion, ionic transport, and ligand-receptor binding. Moreover, the students confront random forces and traditional forces in problems, simulations, and in laboratory exploration throughout the year-long course as they move from traditional kinematics through thermodynamics to electrostatic interactions. This talk will present a number of these exercises, with particular focus on the hands-on experiments done by the students, and will give examples of the tangible material that our students work with throughout the two-semester sequence of their course on introductory physics with a bio focus. Supported by NSF DUE.

De Winne with CBEF in Kibo

NASA Image and Video Library

2009-07-10

ISS020-E-019027 (10 July 2009) --- European Space Agency astronaut Frank De Winne, Expedition 20 flight engineer, works at the Cell Biology Experiment Facility (CBEF) in the Kibo laboratory of the International Space Station.

Walker in the JPM

NASA Image and Video Library

2010-10-21

ISS025-E-008416 (21 Oct. 2010) --- NASA astronaut Shannon Walker, Expedition 25 flight engineer, uses a computer while working at the Cell Biology Experiment Facility (CBEF) in the Kibo laboratory of the International Space Station.

Wakata in JPM with CBEF

NASA Image and Video Library

2009-07-09

ISS020-E-020276 (9 July 2009) --- Japan Aerospace Exploration Agency (JAXA) astronaut Koichi Wakata, Expedition 20 flight engineer, works at the Cell Biology Experiment Facility (CBEF) in the Kibo laboratory of the International Space Station.

Real-time Experiment Interface for Biological Control Applications

PubMed Central

Lin, Risa J.; Bettencourt, Jonathan; White, John A.; Christini, David J.; Butera, Robert J.

2013-01-01

The Real-time Experiment Interface (RTXI) is a fast and versatile real-time biological experimentation system based on Real-Time Linux. RTXI is open source and free, can be used with an extensive range of experimentation hardware, and can be run on Linux or Windows computers (when using the Live CD). RTXI is currently used extensively for two experiment types: dynamic patch clamp and closed-loop stimulation pattern control in neural and cardiac single cell electrophysiology. RTXI includes standard plug-ins for implementing commonly used electrophysiology protocols with synchronized stimulation, event detection, and online analysis. These and other user-contributed plug-ins can be found on the website (http://www.rtxi.org). PMID:21096883

Biologische Wirkungen der Bestrahlung mit schweren Ionen

NASA Astrophysics Data System (ADS)

Kiefer, Jürgen

1982-06-01

Experiments with accelerated heavy ions may contribute to the understanding of biological radiation action. After outlining the theoretical background experiments are described which were carried out at the UNILAC-machine (Gesellschaft für Schwerionenforschung, Darmstadt, Germany) where ions up to uranium can be accelerated to maximal specific energies of 10 MeV/u. Yeast cells served as biological test systems with the synthesis of ribosomal RNA (r-RNA), colony-forming ability and mutation induction as experimental endpoints. A relationship between action and energy deposition by individual particles can be demonstrated for the inhibition of r-RNA synthesis, in other cases the ion energy plays also an important role indicating that the interaction of δ-electrons from different particles contributes significantly to the biological effect.

Comparative transcriptomics indicate changes in cell wall organization and stress response in seedlings during spaceflight.

PubMed

Johnson, Christina M; Subramanian, Aswati; Pattathil, Sivakumar; Correll, Melanie J; Kiss, John Z

2017-08-21

Plants will play an important role in the future of space exploration as part of bioregenerative life support. Thus, it is important to understand the effects of microgravity and spaceflight on gene expression in plant development. We analyzed the transcriptome of Arabidopsis thaliana using the Biological Research in Canisters (BRIC) hardware during Space Shuttle mission STS-131. The bioinformatics methods used included RMA (robust multi-array average), MAS5 (Microarray Suite 5.0), and PLIER (probe logarithmic intensity error estimation). Glycome profiling was used to analyze cell wall composition in the samples. In addition, our results were compared to those of two other groups using the same hardware on the same mission (BRIC-16). In our BRIC-16 experiments, we noted expression changes in genes involved in hypoxia and heat shock responses, DNA repair, and cell wall structure between spaceflight samples compared to the ground controls. In addition, glycome profiling supported our expression analyses in that there was a difference in cell wall components between ground control and spaceflight-grown plants. Comparing our studies to those of the other BRIC-16 experiments demonstrated that, even with the same hardware and similar biological materials, differences in results in gene expression were found among these spaceflight experiments. A common theme from our BRIC-16 space experiments and those of the other two groups was the downregulation of water stress response genes in spaceflight. In addition, all three studies found differential regulation of genes associated with cell wall remodeling and stress responses between spaceflight-grown and ground control plants. © 2017 Botanical Society of America.

Establishing laboratory standards for biological flight experiments

NASA Technical Reports Server (NTRS)

Young, Ronald B.; Moriarity, Debra M.

1989-01-01

The general objective of this research was to assess the effects of exposure to simulated microgravity on ultrastructural aspects of the contractile system in chicken skeletal muscle cells. This general objective had two specific experimental components: (1) the progression of changes in cell morphology, fusion, and patterns of contractile filament organization in muscle cell cultures grown in hollow fibers in the Clinostat were evaluated, with appropriate controls; (2) to initiate experiments in which muscle cells were grown on the surface of microcarrier beads. The ultimate objective of this second portion of the work is to determine if these beads can be rotated in a bioreactor and thereby obtain a more accurate approximation of the effects of simulated microgravity on differentiated muscle cells.

Spot Surface Labeling of Magnetic Microbeads and Application in Biological Force Measurements

NASA Astrophysics Data System (ADS)

Estes, Ashley; O'Brien, E. Tim; Hill, David; Superfine, Richard

2006-11-01

Biological force measurements on single molecules and macromolecular structures often use microbeads for the application of force. These techniques are often complicated by multiple attachments and nonspecific binding. In one set of experiments, we are applying a magnetic force microscope that allows us to pull on magnetic beads attached to ciliated human bronchial epithelial cells. These experiments provide a means to measure the stall force of cilia and understand how cilia propel fluids. However, because we are using beads with diameters of one and 2.8 microns, and the diameter of human airway cilia is approximately 200 nm, we cannot be assured that the bead is bound to a single cilium. To address this, we have developed a sputter coating technique to block the biotin binding capability of the streptavidin labeled bead over its entire surface except for a small spot. These beads may also have applications in other biological experiments such as DNA force experiments in which binding of a single target to an individual bead is critical.

[Combined internal-external radiotherapy (CIERT) in a cell model].

PubMed

Oehme, Liane; Bartzsch, Thomas; Maucksch, Ute; Freudenberg, Robert; Wunderlich, Gerd; Kotzerke, Jörg

2018-06-01

Combined internal-external radiotherapy (CIERT) requires a unified assessment of biologic radiation effects in addition to the total dose. The concept of biological effective dose (BED) was evaluated in a cell model. The thyroid NIS-positive cell line FRTL-5 was irradiated with X-ray and the radiotracer Tc-99m pertechnetate either alone or in combination. The cellular uptake of the radionuclide during the incubation time of 24 h was controlled by the presence or absence of perchlorate. Dose calculation was performed based on measured uptake values. Cell specific radiobiologic parameters were derived from dose effect curves using the colony forming assay as biological endpoint. For the combination of the radiation qualities the sequence and time difference were varied. Cell survival was compared with the prediction of the BED model. The radiobiologic parameters from X-ray dose response were α = (0.22 ± 0.02) Gy -1 and β = (0.021 ± 0.001) Gy -2 . The half life for repair was (1.51 ± 0.21) h. These values could also explain the dose response curves for Tc-99m-irradiation with exponential decreasing dose rate. CIERT experiments showed no significant differences in cell survival regarding sequence and irradiation break. When the radionuclide uptake was not prevented the cell survival for the combination of X-ray and Tc-99m was lower than the prediction by BED calculations. The validity of the BED formalism for different dose rates and radiation qualities was verified. Supraaddive effects measured in the combination of X-ray and intracellular Tc-99m might be caused by Auger and conversion electrons, however further experiments are necessary. Schattauer GmbH.

An apolipoprotein-enriched biomolecular corona switches the cellular uptake mechanism and trafficking pathway of lipid nanoparticles.

PubMed

Digiacomo, L; Cardarelli, F; Pozzi, D; Palchetti, S; Digman, M A; Gratton, E; Capriotti, A L; Mahmoudi, M; Caracciolo, G

2017-11-16

Following exposure to biological milieus (e.g. after systemic administration), nanoparticles (NPs) get covered by an outer biomolecular corona (BC) that defines many of their biological outcomes, such as the elicited immune response, biodistribution, and targeting abilities. In spite of this, the role of BC in regulating the cellular uptake and the subcellular trafficking properties of NPs has remained elusive. Here, we tackle this issue by employing multicomponent (MC) lipid NPs, human plasma (HP) and HeLa cells as models for nanoformulations, biological fluids, and target cells, respectively. By conducting confocal fluorescence microscopy experiments and image correlation analyses, we quantitatively demonstrate that the BC promotes a neat switch of the cell entry mechanism and subsequent intracellular trafficking, from macropinocytosis to clathrin-dependent endocytosis. Nano-liquid chromatography tandem mass spectrometry identifies apolipoproteins as the most abundant components of the BC tested here. Interestingly, this class of proteins target the LDL receptors, which are overexpressed in clathrin-enriched membrane domains. Our results highlight the crucial role of BC as an intrinsic trigger of specific NP-cell interactions and biological responses and set the basis for a rational exploitation of the BC for targeted delivery.

In vitro cell irradiation systems based on 210Po alpha source: construction and characterisation

NASA Technical Reports Server (NTRS)

Szabo, J.; Feher, I.; Palfalvi, J.; Balashazy, I.; Dam, A. M.; Polonyi, I.; Bogdandi, E. N.

2002-01-01

One way of studying the risk to human health of low-level radiation exposure is to make biological experiments on living cell cultures. Two 210Po alpha-particle emitting devices, with 0.5 and 100 MBq activity, were designed and constructed to perform such experiments irradiating monolayers of cells. Estimates of dose rate at the cell surface were obtained from measurements by a PIPS alpha-particle spectrometer and from calculations by the SRIM 2000, Monte Carlo charged particle transport code. Particle fluence area distributions were measured by solid state nuclear track detectors. The design and dosimetric characterisation of the devices are discussed. c2002 Elsevier Science Ltd. All rights reserved.

Cell Culture in Microgravity: Opening the Door to Space Cell Biology

NASA Technical Reports Server (NTRS)

Pellis, Neal R.; Dawson, David L. (Technical Monitor)

1999-01-01

Adaptational response of human cell populations to microgravity is investigated using simulation, short-term Shuttle experiments, and long-term microgravity. Simulation consists of a clinostatically-rotated cell culture system. The system is a horizontally-rotated cylinder completely filled with culture medium. Low speed rotation results in continuous-fall of the cells through the fluid medium. In this setting, cells: 1) aggregate, 2) propagate in three dimensions, 3) synthesize matrix, 4) differentiate, and 5) form sinusoids that facilitate mass transfer. Space cell culture is conducted in flight bioreactors and in static incubators. Cells grown in microgravity are: bovine cartilage, promyelocytic leukemia, kidney proximal tubule cells, adrenal medulla, breast and colon cancer, and endothelium. Cells were cultured in space to test specific hypotheses. Cartilage cells were used to determine structural differences in cartilage grown in space compared to ground-based bioreactors. Results from a 130-day experiment on Mir revealed that cartilage grown in space was substantially more compressible due to insufficient glycosaminoglycan in the matrix. Interestingly, earth-grown cartilage conformed better to the dimensions of the scaffolding material, while the Mir specimens were spherical. The other cell populations are currently being analyzed for cell surface properties, gene expression, and differentiation. Results suggest that some cells spontaneously differentiate in microgravity. Additionally, vast changes in gene expression may occur in response to microgravity. In conclusion, the transition to microgravity may constitute a physical perturbation in cells resulting in unique gene expressions, the consequences of which may be useful in tissue engineering, disease modeling, and space cell biology.

Synthesis and anticancer activity of novel curcumin-quinolone hybrids.

PubMed

Raghavan, Saiharish; Manogaran, Prasath; Gadepalli Narasimha, Krishna Kumari; Kalpattu Kuppusami, Balasubramanian; Mariyappan, Palanivelu; Gopalakrishnan, Anjana; Venkatraman, Ganesh

2015-09-01

A number of new curcumin-quinolone hybrids were synthesised from differently substituted 3-formyl-2-quinolones and vanillin and their in vitro cytotoxicity was determined on a panel of representative cell lines (A549, MCF7, SKOV3 and H460) using MTT assay. The most potent compound 14, was analysed for its mode of action using various cell biology experiments. SKOV3 cells treated with compound 14 showed distorted cell morphology under phase contrast imaging and induction of apoptosis was confirmed by Annexin V/PE assay. Further experiments on generation of reactive oxygen species (ROS) and cell cycle analysis revealed that these hybrids induce apoptosis by ROS generation and arrest cell cycle progression in S and G2/M phase. Copyright © 2015 Elsevier Ltd. All rights reserved.

The German ISS-experiment Cellular Responses to Radiation in Space (CERASP): The effects of single and combined space flight conditions on mammalian cells

NASA Astrophysics Data System (ADS)

Hellweg, C. E.; Thelen, M.; Arenz, A.; Baumstark-Khan, C.

The combined action of ionizing radiation and microgravity will continue to influence future manned space missions, with special risks for astronauts on the Moon surface or for long duration missions to Mars. There is increasing evidence that basic cellular functions are sensitive not only to radiation but also to microgravity. Previous space flight experiments gave contradictory results: from inhibition of DNA repair by microgravity to enhancement, whereas others did not detect any influence of microgravity on repair. At the Radiation Biology Department of the German Aerospace Center (DLR), recombinant bacterial and mammalian cell systems were developed as reporters for cellular signal transduction modulation by genotoxic environmental conditions. The space experiment “Cellular Responses to Radiation in Space” (CERASP) to be performed at the International Space Station (ISS) will make use of such reporter cell lines thereby supplying basic information on the cellular response to radiation applied in microgravity. One of the biological endpoints will be survival reflected by radiation-dependent reduction of constitutive expression of the enhanced variant of green fluorescent protein (EGFP). A second end-point will be gene activation by space flight conditions in mammalian cells, based on fluorescent promoter reporter systems using the destabilized d2EGFP variant. The promoter element to be investigated reflects the activity of the nuclear factor kappa B (NF-κB) pathway. The NF-κB family of proteins plays a major role in the inflammatory and immune response, cell proliferation and differentiation, apoptosis and tumor genesis. Results obtained with X-rays and accelerated heavy ions produced at the French heavy ion accelerator GANIL imply that densely ionizing radiation has a stronger potential to activate NF-κB dependent gene expression than sparsely ionizing radiation. The correlation of NF-κB activation to negative regulation of apoptosis could favor survival of cells with damaged DNA. A third endpoint to be examined will be DNA damage induced by combined exposure to radiation and microgravity and its repair. In the current work, preparatory experiments for the space experiment CERASP were performed. For radiation exposure on the ISS, an artificial radiation source is necessary since long-term exposure to cosmic radiation of frozen cells for damage accumulation will not be feasible. The biological activity of the designated space radiation source, the β-emitter promethium-147, was evaluated. Different shielding scenarios according to the experiment and safety requirements were evaluated. As growth surface for the human embryonic kidney cells, polytetrafluoroethylene and polyolefin foils were tested. For protection issues, the shielding effect of titanium foils was evaluated. With the prototype Pm-147 radiation source, the requirements of CERASP can be fulfilled with cells growing on the polytetrafluoroethylene foil and titanium foils for safety issues. In this setting, β-rays activated NF-κB-dependent reporter gene expression in human embryonic kidney cells. Regarding cell survival and NF-κB activation, the Pm-147 radiation source meets the requirements of the space experiment CERASP.

Keith's MAGIC: Cloning and the Cell Cycle.

PubMed

Wells, D N

2013-10-01

Abstract Professor Keith Campbell's critical contribution to the discovery that a somatic cell from an adult animal can be fully reprogrammed by oocyte factors to form a cloned individual following nuclear transfer (NT)(Wilmut et al., 1997 ) overturned a dogma concerning the reversibility of cell fate that many scientists had considered to be biologically impossible. This seminal experiment proved the totipotency of adult somatic nuclei and finally confirmed that adult cells could differentiate without irreversible changes to the genetic material.

[Further studies of continuous human and animal cell lines for the manufacture of viral vaccines and diagnostic kits].

PubMed

Mironova, L L; Koniushko, O I; Popova, V D

2005-01-01

Long-term experiments have provided conditions for the optimal conditions for reproduction of vaccine strains of poliomyelitis, measles, tick-borne and Japan encephalitis on the continuous cell lines. This makes it possible to solve one of the most urgent problems of modern biotechnology, namely to refuse to use primary cell cultures in vaccinology and to apply a more accessible, safe, and reference biological substrate that are stable cell lines.

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

PubMed Central

Landry, Jonathan J. M.; Pyl, Paul Theodor; Rausch, Tobias; Zichner, Thomas; Tekkedil, Manu M.; Stütz, Adrian M.; Jauch, Anna; Aiyar, Raeka S.; Pau, Gregoire; Delhomme, Nicolas; Gagneur, Julien; Korbel, Jan O.; Huber, Wolfgang; Steinmetz, Lars M.

2013-01-01

HeLa is the most widely used model cell line for studying human cellular and molecular biology. To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome. Effective design and interpretation of molecular genetic studies performed using HeLa cells require accurate genomic information. Here we present a detailed genomic and transcriptomic characterization of a HeLa cell line. We performed DNA and RNA sequencing of a HeLa Kyoto cell line and analyzed its mutational portfolio and gene expression profile. Segmentation of the genome according to copy number revealed a remarkably high level of aneuploidy and numerous large structural variants at unprecedented resolution. Some of the extensive genomic rearrangements are indicative of catastrophic chromosome shattering, known as chromothripsis. Our analysis of the HeLa gene expression profile revealed that several pathways, including cell cycle and DNA repair, exhibit significantly different expression patterns from those in normal human tissues. Our results provide the first detailed account of genomic variants in the HeLa genome, yielding insight into their impact on gene expression and cellular function as well as their origins. This study underscores the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments, and has implications for the use of HeLa as a model of human biology. PMID:23550136

The role of electron irradiation history in liquid cell transmission electron microscopy.

PubMed

Moser, Trevor H; Mehta, Hardeep; Park, Chiwoo; Kelly, Ryan T; Shokuhfar, Tolou; Evans, James E

2018-04-01

In situ liquid cell transmission electron microscopy (LC-TEM) allows dynamic nanoscale characterization of systems in a hydrated state. Although powerful, this technique remains impaired by issues of repeatability that limit experimental fidelity and hinder the identification and control of some variables underlying observed dynamics. We detail new LC-TEM devices that improve experimental reproducibility by expanding available imaging area and providing a platform for investigating electron flux history on the sample. Irradiation history is an important factor influencing LC-TEM results that has, to this point, been largely qualitatively and not quantitatively described. We use these devices to highlight the role of cumulative electron flux history on samples from both nanoparticle growth and biological imaging experiments and demonstrate capture of time zero, low-dose images on beam-sensitive samples. In particular, the ability to capture pristine images of biological samples, where the acquired image is the first time that the cell experiences significant electron flux, allowed us to determine that nanoparticle movement compared to the cell membrane was a function of cell damage and therefore an artifact rather than visualizing cell dynamics in action. These results highlight just a subset of the new science that is accessible with LC-TEM through the new multiwindow devices with patterned focusing aides.

The role of electron irradiation history in liquid cell transmission electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Trevor H.; Mehta, Hardeep; Park, Chiwoo

In situ liquid cell transmission electron microscopy (LC-TEM) allows dynamic nanoscale characterization of systems in a hydrated state. Although powerful, this technique remains impaired by issues of repeatability that limit experimental fidelity and hinder the identification and control of some variables underlying observed dynamics. We detail new LC- TEM devices that improve experimental reproducibility by expanding available imaging area and providing a platform for investigating electron flux history on the sample. Irradiation history is an important factor influencing LC-TEM results that has, to this point, been largely qualitatively and not quantitatively described. We use these devices to highlight the rolemore » of cumulative electron flux history on samples from both nanoparticle growth and biological imaging experiments and demonstrate capture of time zero, low-dose images on beam-sensitive samples. In particular, the ability to capture pristine images of biological samples, where the acquired image is the first time that the cell experiences significant electron flux, allowed us to determine that nanoparticle movement compared to the cell membrane was a function of cell damage and therefore an artifact rather than visualizing cell dynamics in action. These results highlight just a subset of the new science that is accessible with LC-TEM through the new multiwindow devices with patterned focusing aides.« less

The role of electron irradiation history in liquid cell transmission electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Trevor H.; Mehta, Hardeep; Park, Chiwoo

In situ liquid cell transmission electron microscopy (LC-TEM) allows dynamic nanoscale characterization of systems in a hydrated state. Although powerful, this technique remains impaired by issues of repeatability that limit experimental fidelity and hinder the identification and control of some variables underlying observed dynamics. We detail new LC-TEM devices that improve experimental reproducibility by expanding available imaging area and providing a platform for investigating electron flux history on the sample. Irradiation history is an important factor influencing LC-TEM results that has, to this point, been largely qualitatively and not quantitatively described. We use these devices to highlight the role ofmore » cumulative electron flux history on samples from both nanoparticle growth and biological imaging experiments and demonstrate capture of time zero, low-dose images on beam-sensitive samples. In particular, the ability to capture pristine images of biological samples, where the acquired image is the first time that the cell experiences significant electron flux, allowed us to determine that nanoparticle movement compared to the cell membrane was a function of cell damage and therefore an artifact rather than visualizing cell dynamics in action. Lastly, these results highlight just a subset of the new science that is accessible with LC-TEM through the new multiwindow devices with patterned focusing aides.« less

The role of electron irradiation history in liquid cell transmission electron microscopy

PubMed Central

Mehta, Hardeep

2018-01-01

In situ liquid cell transmission electron microscopy (LC-TEM) allows dynamic nanoscale characterization of systems in a hydrated state. Although powerful, this technique remains impaired by issues of repeatability that limit experimental fidelity and hinder the identification and control of some variables underlying observed dynamics. We detail new LC-TEM devices that improve experimental reproducibility by expanding available imaging area and providing a platform for investigating electron flux history on the sample. Irradiation history is an important factor influencing LC-TEM results that has, to this point, been largely qualitatively and not quantitatively described. We use these devices to highlight the role of cumulative electron flux history on samples from both nanoparticle growth and biological imaging experiments and demonstrate capture of time zero, low-dose images on beam-sensitive samples. In particular, the ability to capture pristine images of biological samples, where the acquired image is the first time that the cell experiences significant electron flux, allowed us to determine that nanoparticle movement compared to the cell membrane was a function of cell damage and therefore an artifact rather than visualizing cell dynamics in action. These results highlight just a subset of the new science that is accessible with LC-TEM through the new multiwindow devices with patterned focusing aides. PMID:29725619

The role of electron irradiation history in liquid cell transmission electron microscopy

DOE PAGES

Moser, Trevor H.; Mehta, Hardeep; Park, Chiwoo; ...

2018-04-20

In situ liquid cell transmission electron microscopy (LC-TEM) allows dynamic nanoscale characterization of systems in a hydrated state. Although powerful, this technique remains impaired by issues of repeatability that limit experimental fidelity and hinder the identification and control of some variables underlying observed dynamics. We detail new LC-TEM devices that improve experimental reproducibility by expanding available imaging area and providing a platform for investigating electron flux history on the sample. Irradiation history is an important factor influencing LC-TEM results that has, to this point, been largely qualitatively and not quantitatively described. We use these devices to highlight the role ofmore » cumulative electron flux history on samples from both nanoparticle growth and biological imaging experiments and demonstrate capture of time zero, low-dose images on beam-sensitive samples. In particular, the ability to capture pristine images of biological samples, where the acquired image is the first time that the cell experiences significant electron flux, allowed us to determine that nanoparticle movement compared to the cell membrane was a function of cell damage and therefore an artifact rather than visualizing cell dynamics in action. Lastly, these results highlight just a subset of the new science that is accessible with LC-TEM through the new multiwindow devices with patterned focusing aides.« less

In silico nanodosimetry: new insights into nontargeted biological responses to radiation.

PubMed

Kuncic, Zdenka; Byrne, Hilary L; McNamara, Aimee L; Guatelli, Susanna; Domanova, Westa; Incerti, Sébastien

2012-01-01

The long-held view that radiation-induced biological damage must be initiated in the cell nucleus, either on or near DNA itself, is being confronted by mounting evidence to suggest otherwise. While the efficacy of cell death may be determined by radiation damage to nuclear DNA, a plethora of less deterministic biological responses has been observed when DNA is not targeted. These so-called nontargeted responses cannot be understood in the framework of DNA-centric radiobiological models; what is needed are new physically motivated models that address the damage-sensing signalling pathways triggered by the production of reactive free radicals. To this end, we have conducted a series of in silico experiments aimed at elucidating the underlying physical processes responsible for nontargeted biological responses to radiation. Our simulation studies implement new results on very low-energy electromagnetic interactions in liquid water (applicable down to nanoscales) and we also consider a realistic simulation of extranuclear microbeam irradiation of a cell. Our results support the idea that organelles with important functional roles, such as mitochondria and lysosomes, as well as membranes, are viable targets for ionizations and excitations, and their chemical composition and density are critical to determining the free radical yield and ensuing biological responses.

Microgravity

NASA Image and Video Library

2001-05-31

This diagram shows the general arrangement of the payloads to be carried by the multidisciplinary STS-107 Research-1 Space Shuttle mission in 2002. The Spacehab module will host experiments that require direct operation by the flight crew. Others with special requirements will be on the GAS Bridge Assembly sparning the payload bay. The Extended Duration Orbiter kit carries additional oxygen and hydrogen for the electricity-producing fuel cells. Research-1 experiments will cover space biology, life science, microgravity research, and commercial space product development, research sponsored by NASA's Office of Biological and Physical Research. An alternative view without callouts is available at 0101765.

Microgravity

NASA Image and Video Library

2001-05-31

Thisdiagram shows the general arrangement of the payloads to be carried by the multidisciplinary STS-107 Research-1 Space Shuttle mission in 2002. The Spacehab module will host experiments that require direct operation by the flight crew. Others with special requirements will be on the GAS Bridge Assembly sparning the payload bay. The Extended Duration Orbiter kit carries additional oxygen and hydrogen for the electricity-producing fuel cells. Research-1 experiments will cover space biology, life science, microgravity research, and commercial space product development, research sponsored by NASA's Office of Biological and Physical Research. An alternative view with callouts is available at 0101764.

STS-107 payload arrangement

NASA Technical Reports Server (NTRS)

2001-01-01

Thisdiagram shows the general arrangement of the payloads to be carried by the multidisciplinary STS-107 Research-1 Space Shuttle mission in 2002. The Spacehab module will host experiments that require direct operation by the flight crew. Others with special requirements will be on the GAS Bridge Assembly sparning the payload bay. The Extended Duration Orbiter kit carries additional oxygen and hydrogen for the electricity-producing fuel cells. Research-1 experiments will cover space biology, life science, microgravity research, and commercial space product development, research sponsored by NASA's Office of Biological and Physical Research. An alternative view with callouts is available at 0101764.

STS-107 payload arrangement

NASA Technical Reports Server (NTRS)

2001-01-01

This diagram shows the general arrangement of the payloads to be carried by the multidisciplinary STS-107 Research-1 Space Shuttle mission in 2002. The Spacehab module will host experiments that require direct operation by the flight crew. Others with special requirements will be on the GAS Bridge Assembly sparning the payload bay. The Extended Duration Orbiter kit carries additional oxygen and hydrogen for the electricity-producing fuel cells. Research-1 experiments will cover space biology, life science, microgravity research, and commercial space product development, research sponsored by NASA's Office of Biological and Physical Research. An alternative view without callouts is available at 0101765.

Isolation, characterization and propagation of mitotically active germ cells from adult mouse and human ovaries

PubMed Central

Woods, Dori C; Tilly, Jonathan L

2017-01-01

Accruing evidence indicates that production of new oocytes (oogenesis) and their enclosure by somatic cells (folliculogenesis) are processes not limited to the perinatal period in mammals. Endpoints ranging from oocyte counts to genetic lineage tracing and transplantation experiments support a paradigm shift in reproductive biology involving active renewal of oocyte-containing follicles during postnatal life. The recent purification of mitotically active oocyte progenitor cells, termed female germline stem cells (fGSCs) or oogonial stem cells (OSCs), from mouse and human ovaries opens up new avenues for research into the biology and clinical utility of these cells. Here we detail methods for the isolation of mouse and human OSCs from adult ovarian tissue, cultivation of the cells after purification, and characterization of the cells before and after ex vivo expansion. The latter methods include analysis of germ cell–specific markers and in vitro oogenesis, as well as the use of intraovarian transplantation to test the oocyte-forming potential of OSCs in vivo. PMID:23598447

Droplet microfluidics--a tool for single-cell analysis.

PubMed

Joensson, Haakan N; Andersson Svahn, Helene

2012-12-03

Droplet microfluidics allows the isolation of single cells and reagents in monodisperse picoliter liquid capsules and manipulations at a throughput of thousands of droplets per second. These qualities allow many of the challenges in single-cell analysis to be overcome. Monodispersity enables quantitative control of solute concentrations, while encapsulation in droplets provides an isolated compartment for the single cell and its immediate environment. The high throughput allows the processing and analysis of the tens of thousands to millions of cells that must be analyzed to accurately describe a heterogeneous cell population so as to find rare cell types or access sufficient biological space to find hits in a directed evolution experiment. The low volumes of the droplets make very large screens economically viable. This Review gives an overview of the current state of single-cell analysis involving droplet microfluidics and offers examples where droplet microfluidics can further biological understanding. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The development of the hardware for studying biological clock systems under microgravity conditions, using scorpions as animal models

NASA Astrophysics Data System (ADS)

Serafini, L.; Viganò, W.; Donati, A.; Porciani, M.; Zolesi, V.; Schulze-Varnholt, D.; Manieri, P.; El-Din Sallam, A.; Schmäh, M.; Horn, E. R.

2007-02-01

The study of internal clock systems of scorpions in weightless conditions is the goal of the SCORPI experiment. SCORPI was selected for flight on the International Space Station (ISS) and will be mounted in the European facility BIOLAB, the European Space Agency (ESA) laboratory designed to support biological experiments on micro-organisms, cells, tissue, cultures, small plants and small invertebrates. This paper outlines the main features of a breadboard designed and developed in order to allow the analysis of critical aspects of the experiment. It is a complete tool to simulate the experiment mission on ground and it can be customised, adapted and tuned to the scientific requirements. The paper introduces the SCORPI-T experiment which represents an important precursor for the success of the SCORPI on BIOLAB. The capabilities of the hardware developed show its potential use for future similar experiments in space.

Perturbation Biology: Inferring Signaling Networks in Cellular Systems

PubMed Central

Miller, Martin L.; Gauthier, Nicholas P.; Jing, Xiaohong; Kaushik, Poorvi; He, Qin; Mills, Gordon; Solit, David B.; Pratilas, Christine A.; Weigt, Martin; Braunstein, Alfredo; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

2013-01-01

We present a powerful experimental-computational technology for inferring network models that predict the response of cells to perturbations, and that may be useful in the design of combinatorial therapy against cancer. The experiments are systematic series of perturbations of cancer cell lines by targeted drugs, singly or in combination. The response to perturbation is quantified in terms of relative changes in the measured levels of proteins, phospho-proteins and cellular phenotypes such as viability. Computational network models are derived de novo, i.e., without prior knowledge of signaling pathways, and are based on simple non-linear differential equations. The prohibitively large solution space of all possible network models is explored efficiently using a probabilistic algorithm, Belief Propagation (BP), which is three orders of magnitude faster than standard Monte Carlo methods. Explicit executable models are derived for a set of perturbation experiments in SKMEL-133 melanoma cell lines, which are resistant to the therapeutically important inhibitor of RAF kinase. The resulting network models reproduce and extend known pathway biology. They empower potential discoveries of new molecular interactions and predict efficacious novel drug perturbations, such as the inhibition of PLK1, which is verified experimentally. This technology is suitable for application to larger systems in diverse areas of molecular biology. PMID:24367245

Primary culture of glial cells from mouse sympathetic cervical ganglion: a valuable tool for studying glial cell biology.

PubMed

de Almeida-Leite, Camila Megale; Arantes, Rosa Maria Esteves

2010-12-15

Central nervous system glial cells as astrocytes and microglia have been investigated in vitro and many intracellular pathways have been clarified upon various stimuli. Peripheral glial cells, however, are not as deeply investigated in vitro despite its importance role in inflammatory and neurodegenerative diseases. Based on our previous experience of culturing neuronal cells, our objective was to standardize and morphologically characterize a primary culture of mouse superior cervical ganglion glial cells in order to obtain a useful tool to study peripheral glial cell biology. Superior cervical ganglia from neonatal C57BL6 mice were enzymatically and mechanically dissociated and cells were plated on diluted Matrigel coated wells in a final concentration of 10,000cells/well. Five to 8 days post plating, glial cell cultures were fixed for morphological and immunocytochemical characterization. Glial cells showed a flat and irregular shape, two or three long cytoplasm processes, and round, oval or long shaped nuclei, with regular outline. Cell proliferation and mitosis were detected both qualitative and quantitatively. Glial cells were able to maintain their phenotype in our culture model including immunoreactivity against glial cell marker GFAP. This is the first description of immunocytochemical characterization of mouse sympathetic cervical ganglion glial cells in primary culture. This work discusses the uses and limitations of our model as a tool to study many aspects of peripheral glial cell biology. Copyright © 2010 Elsevier B.V. All rights reserved.

Studies on the effects of microgravity on the ultrastructure and functions of cultured mammalian cells (L-6)

NASA Technical Reports Server (NTRS)

Sato, Atsushige

1993-01-01

The human body consists of 10(exp 13) cells. Understanding the mechanisms by which the cells sense and respond to microgravity is very important as the basis for space biology. The cells were originally isolated aseptically from mammalian bodies and cultured in vitro. A set of cell culture vessels was developed to be applied to three kinds of space flight experiments. Experiment 1 is to practice the cell culture technique in a space laboratory and obtain favorable growth of the cells. Aseptic handling in tryspin treatment and medium renewal will be tested. The cells, following space flight, will be returned to the ground and cultured continuously to investigate the effects of space flight on the cellular characteristics. Experiment 2 is to examine the cytoskeletal structure of the cells under microgravity conditions. The cytoskeletal structure plays essential roles in the morphological construction, movements, axonal transport, and differentiation of the cells. The cells fixed during space flight will be returned and the cytoskeleton and ultrastructure observed using electron microscopy and fluorescence microscopy. Experiment 3 is to study the cellular productivity of valuable substances. The waste medium harvested during space flight are returned and quantitated for the cellular products. The effects of microgravity on mammalian cells will be clarified from the various aspects.

Volumetric Stress-Strain Analysis of Optohydrodynamically Suspended Biological Cells

PubMed Central

Liang, Yu; Saha, Asit K.

2011-01-01

Ongoing investigations are exploring the biomechanical properties of isolated and suspended biological cells in pursuit of understanding single-cell mechanobiology. An optical tweezer with minimal applied laser power has positioned biologic cells at the geometric center of a microfluidic cross-junction, creating a novel optohydrodynamic trap. The resulting fluid flow environment facilitates unique multiaxial loading of single cells with site-specific normal and shear stresses resulting in a physical albeit extensional state. A recent two-dimensional analysis has explored the cytoskeletal strain response due to these fluid-induced stresses [Wilson and Kohles, 2010, “Two-Dimensional Modeling of Nanomechanical Stresses-Strains in Healthy and Diseased Single-Cells During Microfluidic Manipulation,” J Nanotechnol Eng Med, 1(2), p. 021005]. Results described a microfluidic environment having controlled nanometer and piconewton resolution. In this present study, computational fluid dynamics combined with multiphysics modeling has further characterized the applied fluid stress environment and the solid cellular strain response in three dimensions to accompany experimental cell stimulation. A volumetric stress-strain analysis was applied to representative living cell biomechanical data. The presented normal and shear stress surface maps will guide future microfluidic experiments as well as provide a framework for characterizing cytoskeletal structure influencing the stress to strain response. PMID:21186894

An Introduction to Lipid Analysis in the Cell Biology Laboratory.

ERIC Educational Resources Information Center

Schuh, Timothy J.

2002-01-01

Explains a thin-layer chromatography (TLC) experiment that allows students to study complex mixtures of lipids using small volumes. Uses a water-soluble dye to stain lipids that is fast and safe. (YDS)

First Materials Processing Test in the Science Operation Area (SOA) During STS-47 Spacelab-J Mission

NASA Technical Reports Server (NTRS)

1992-01-01

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Featured together in the Science Operation Area (SOA) are payload specialists' first Materials Processing Test during NASA/NASDA joint ground activities at the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC) at Marshall Space Fight Center (MSFC).

First Materials Processing Test in the Science Operation Area (SOA) During STS-47 Spacelab-J Mission

NASA Technical Reports Server (NTRS)

1992-01-01

The science laboratory, Spacelab-J (SL-J), flown aboard the STS-47 flight was a joint venture between NASA and the National Space Development Agency of Japan (NASDA) utilizing a manned Spacelab module. The mission conducted 24 materials science and 20 life science experiments, of which 35 were sponsored by NASDA, 7 by NASA, and two collaborative efforts. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, and frogs and frog eggs. Featured together in the Science Operation Area (SOA) are payload specialists' first Materials Processing Test during NASA/NASDA joint ground activities at the Huntsville Operations Support Center (HOSC) Spacelab Payload Operations Control Center (SL POCC) at Marshall Space Flight Center (MSFC).

Ion beam modification of biological materials in nanoscale

NASA Astrophysics Data System (ADS)

Yu, L. D.; Anuntalabhochai, S.

2012-07-01

Ion interaction with biological objects in nanoscale is a novel research area stemming from applications of low-energy ion beams in biotechnology and biomedicine. Although the ion beam applications in biotechnology and biomedicine have achieved great successes, many mechanisms remain unclear and many new applications are to be explored. We have carried out some research on exploring the mechanisms and new applications besides attaining ion beam induction of mutation breeding and gene transformation. In the studies on the mechanisms, we focused our investigations on the direct interaction in nanoscale between ions and biological living materials. Our research topics have included the low-energy ion range in DNA, low-energy ion or neutral beam bombardment effect on DNA topological form change and mutation, low-energy ion or neutral beam bombardment effect on the cell envelope and gene transformation, and molecular dynamics simulation of ultra-low-energy ion irradiation of DNA. In the exploration of new applications, we have started experiments on ion irradiation or bombardment, in the nanoscaled depth or area, of human cells for biomedical research. This paper introduces our experiments and reports interesting results.

The citrus methoxyflavone tangeretin affects human cell-cell interactions.

PubMed

Brack, Marc E; Boterberg, Tom; Depypere, Herman T; Stove, Christophe; Leclercq, Georges; Mareel, Marc M

2002-01-01

Two effects of the citrus methoxyflavone tangeretin on cell-cell interactions are biologically relevant. Firstly, tangeretin upregulates the function of the E-cadherin/catenin complex in human MCF-7/6 breast carcinoma cells. This leads to firm cell-cell adhesion and inhibition of invasion in vitro. Secondly, tangeretin downregulates the interleukin-2 receptor on T-lymphocytes and natural killer cells. This leads to a decrease in the cytotoxic competence of these immunocytes against cancer cells. The second effect can become important when high doses of tangeretin are combined with adjuvant tamoxifen treatment for breast cancer. Experiments with nude mice bearing MCF-7/6 tumors showed that tangeretin given orally at high doses, abrogated the therapeutic suppression of tumor growth exerted by tamoxifen. No evidence for a tumor promoting effect of tangeretin by itself was found in these experiments. Tangeretin may be an interesting molecule for application in cases where immunosuppression could be clinically beneficial.

Cell proliferation inhibition in reduced gravity

NASA Technical Reports Server (NTRS)

Moos, P. J.; Fattaey, H. K.; Johnson, T. C.; Spooner, B. S. (Principal Investigator)

1994-01-01

Extended durations of spaceflight have been shown to be deleterious on an organismic level; however, mechanisms underlying cellular sensitivity to the gravitational environment remain to be elucidated. The majority of the gravitational studies to date indicates that cell regulatory pathways may be influenced by their gravitational environment. Still, few cell biology experiments have been performed in space flight and even fewer experiments have been repeated on subsequent flights. With flight opportunities on STS-50, 54, and 57, Sf9 cells were flown in the BioServe Fluids Processing Apparatus and cell proliferation was measured with and without exposure to a cell regulatory sialoglycopeptide (CeReS) inhibitor. Results from these flights indicate that the Sf9 cells grew comparable to ground controls, that the CeReS inhibitor bound to its specific receptor, and that its signal transduction cascade was not gravity sensitive.

On-chip Magnetic Separation and Cell Encapsulation in Droplets

NASA Astrophysics Data System (ADS)

Chen, A.; Byvank, T.; Bharde, A.; Miller, B. L.; Chalmers, J. J.; Sooryakumar, R.; Chang, W.-J.; Bashir, R.

2012-02-01

The demand for high-throughput single cell assays is gaining importance because of the heterogeneity of many cell suspensions, even after significant initial sorting. These suspensions may display cell-to-cell variability at the gene expression level that could impact single cell functional genomics, cancer, stem-cell research and drug screening. The on-chip monitoring of individual cells in an isolated environment could prevent cross-contamination, provide high recovery yield and ability to study biological traits at a single cell level These advantages of on-chip biological experiments contrast to conventional methods, which require bulk samples that provide only averaged information on cell metabolism. We report on a device that integrates microfluidic technology with a magnetic tweezers array to combine the functionality of separation and encapsulation of objects such as immunomagnetically labeled cells or magnetic beads into pico-liter droplets on the same chip. The ability to control the separation throughput that is independent of the hydrodynamic droplet generation rate allows the encapsulation efficiency to be optimized. The device can potentially be integrated with on-chip labeling and/or bio-detection to become a powerful single-cell analysis device.

Temperate bacterial viruses as double-edged swords in bacterial warfare.

PubMed

Gama, João Alves; Reis, Ana Maria; Domingues, Iolanda; Mendes-Soares, Helena; Matos, Ana Margarida; Dionisio, Francisco

2013-01-01

It has been argued that bacterial cells may use their temperate viruses as biological weapons. For instance, a few bacterial cells among a population of lysogenic cells could release the virus and kill susceptible non-lysogenic competitors, while their clone mates would be immune. Because viruses replicate inside their victims upon infection, this process would amplify their number in the arena. Sometimes, however, temperate viruses spare recipient cells from death by establishing themselves in a dormant state inside cells. This phenomenon is called lysogenization and, for some viruses such as the λ virus, the probability of lysogenization increases with the multiplicity of infection. Therefore, the amplification of viruses leads to conflicting predictions about the efficacy of temperate viruses as biological weapons: amplification can increase the relative advantage of clone mates of lysogens but also the likelihood of saving susceptible cells from death, because the probability of lysogenization is higher. To test the usefulness of viruses as biological weapons, we performed competition experiments between lysogenic Escherichia coli cells carrying the λ virus and susceptible λ-free E. coli cells, either in a structured or unstructured habitat. In structured and sometimes in unstructured habitats, the λ virus qualitatively behaved as a "replicating toxin". However, such toxic effect of λ viruses ceased after a few days of competition. This was due to the fact that many of initially susceptible cells became lysogenic. Massive lysogenization of susceptible cells occurred precisely under the conditions where the amplification of the virus was substantial. From then on, these cells and their descendants became immune to the λ virus. In conclusion, if at short term bacterial cells may use temperate viruses as biological weapons, after a few days only the classical view of temperate bacterial viruses as parasitic agents prevails.

Temperate Bacterial Viruses as Double-Edged Swords in Bacterial Warfare

PubMed Central

Gama, João Alves; Reis, Ana Maria; Domingues, Iolanda; Mendes-Soares, Helena; Matos, Ana Margarida; Dionisio, Francisco

2013-01-01

It has been argued that bacterial cells may use their temperate viruses as biological weapons. For instance, a few bacterial cells among a population of lysogenic cells could release the virus and kill susceptible non-lysogenic competitors, while their clone mates would be immune. Because viruses replicate inside their victims upon infection, this process would amplify their number in the arena. Sometimes, however, temperate viruses spare recipient cells from death by establishing themselves in a dormant state inside cells. This phenomenon is called lysogenization and, for some viruses such as the λ virus, the probability of lysogenization increases with the multiplicity of infection. Therefore, the amplification of viruses leads to conflicting predictions about the efficacy of temperate viruses as biological weapons: amplification can increase the relative advantage of clone mates of lysogens but also the likelihood of saving susceptible cells from death, because the probability of lysogenization is higher. To test the usefulness of viruses as biological weapons, we performed competition experiments between lysogenic Escherichia coli cells carrying the λ virus and susceptible λ-free E. coli cells, either in a structured or unstructured habitat. In structured and sometimes in unstructured habitats, the λ virus qualitatively behaved as a “replicating toxin”. However, such toxic effect of λ viruses ceased after a few days of competition. This was due to the fact that many of initially susceptible cells became lysogenic. Massive lysogenization of susceptible cells occurred precisely under the conditions where the amplification of the virus was substantial. From then on, these cells and their descendants became immune to the λ virus. In conclusion, if at short term bacterial cells may use temperate viruses as biological weapons, after a few days only the classical view of temperate bacterial viruses as parasitic agents prevails. PMID:23536852

Critical Analysis of Primary Literature in a Master's-Level Class: Effects on Self-Efficacy and Science-Process Skills.

PubMed

Abdullah, Christopher; Parris, Julian; Lie, Richard; Guzdar, Amy; Tour, Ella

2015-01-01

The ability to think analytically and creatively is crucial for success in the modern workforce, particularly for graduate students, who often aim to become physicians or researchers. Analysis of the primary literature provides an excellent opportunity to practice these skills. We describe a course that includes a structured analysis of four research papers from diverse fields of biology and group exercises in proposing experiments that would follow up on these papers. To facilitate a critical approach to primary literature, we included a paper with questionable data interpretation and two papers investigating the same biological question yet reaching opposite conclusions. We report a significant increase in students' self-efficacy in analyzing data from research papers, evaluating authors' conclusions, and designing experiments. Using our science-process skills test, we observe a statistically significant increase in students' ability to propose an experiment that matches the goal of investigation. We also detect gains in interpretation of controls and quantitative analysis of data. No statistically significant changes were observed in questions that tested the skills of interpretation, inference, and evaluation. © 2015 C. Abdullah et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Tissue Engineering Under Microgravity Conditions-Use of Stem Cells and Specialized Cells.

PubMed

Grimm, Daniela; Egli, Marcel; Krüger, Marcus; Riwaldt, Stefan; Corydon, Thomas J; Kopp, Sascha; Wehland, Markus; Wise, Petra; Infanger, Manfred; Mann, Vivek; Sundaresan, Alamelu

2018-03-29

Experimental cell research studying three-dimensional (3D) tissues in space and on Earth using new techniques to simulate microgravity is currently a hot topic in Gravitational Biology and Biomedicine. This review will focus on the current knowledge of the use of stem cells and specialized cells for tissue engineering under simulated microgravity conditions. We will report on recent advancements in the ability to construct 3D aggregates from various cell types using devices originally created to prepare for spaceflights such as the random positioning machine (RPM), the clinostat, or the NASA-developed rotating wall vessel (RWV) bioreactor, to engineer various tissues such as preliminary vessels, eye tissue, bone, cartilage, multicellular cancer spheroids, and others from different cells. In addition, stem cells had been investigated under microgravity for the purpose to engineer adipose tissue, cartilage, or bone. Recent publications have discussed different changes of stem cells when exposed to microgravity and the relevant pathways involved in these biological processes. Tissue engineering in microgravity is a new technique to produce organoids, spheroids, or tissues with and without scaffolds. These 3D aggregates can be used for drug testing studies or for coculture models. Multicellular tumor spheroids may be interesting for radiation experiments in the future and to reduce the need for in vivo experiments. Current achievements using cells from patients engineered on the RWV or on the RPM represent an important step in the advancement of techniques that may be applied in translational Regenerative Medicine.

Aniso Tubule

NASA Image and Video Library

2015-04-03

ISS043E087335 (04/03/2015) --- ESA (European Space Agency) astronaut Samantha Cristoforetti works to retrieve samples for the Aniso Tubule experiment from the Cell Biology Experiment Facility (CBEF) on Apr. 3, 2015. Aniso Tubule examines growth modifications of Arabidopsis hypocotyls in space. Scientists will analyze the changes in dynamics of cortical microtubules and microtubule associated proteins with a fluorescence microscope.

Integrated experimental platforms to study blast injuries: a bottom-up approach

NASA Astrophysics Data System (ADS)

Bo, C.; Williams, A.; Rankin, S.; Proud, W. G.; Brown, K. A.

2014-05-01

We are developing experimental models of blast injury using data from live biological samples. An integrated research strategy is followed to study material and biological properties of cells, tissues and organs, that are subjected to dynamic and static pressures, relevant to those of battlefield blast. We have developed a confined Split Hopkinson Pressure Bar (SHPB) system, which allows cells, either in suspension or as a monolayer, to be subjected to compression waves with pressures on the order of a few MPa and durations of hundreds of microseconds. The chamber design enables recovery of biological samples for cellular and molecular analysis. The SHPB platform, coupled with Quasi-Static experiments, is used to determine stress-strain curves of soft biological tissues under compression at low, medium and high strain rates. Tissue samples are examined, using histological techniques, to study macro- and microscopic changes induced by compression waves. In addition, a shock tube enables application of single or multiple air blasts with pressures on the order of kPa and a few milliseconds duration; this platform was used for initial studies on mesenchymal stem cells responses to blast pressures.

Using synthetic biology to make cells tomorrow's test tubes.

PubMed

Garcia, Hernan G; Brewster, Robert C; Phillips, Rob

2016-04-18

The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.

Gravitational Biology Facility on Space Station: Meeting the needs of space biology

NASA Technical Reports Server (NTRS)

Allen, Katherine; Wade, Charles

1992-01-01

The Gravitational Biology Facility (GBF) is a set of generic laboratory equipment needed to conduct research on Space Station Freedom (SSF), focusing on Space Biology Program science (Cell and Developmental Biology and Plant Biology). The GBF will be functional from the earliest utilization flights through the permanent manned phase. Gravitational biology research will also make use of other Life Sciences equipment on the space station as well as existing equipment developed for the space shuttle. The facility equipment will be developed based on requirements derived from experiments proposed by the scientific community to address critical questions in the Space Biology Program. This requires that the facility have the ability to house a wide variety of species, various methods of observation, and numerous methods of sample collection, preservation, and storage. The selection of the equipment will be done by the members of a scientific working group (5 members representing cell biology, 6 developmental biology, and 6 plant biology) who also provide requirements to design engineers to ensure that the equipment will meet scientific needs. All equipment will undergo extensive ground based experimental validation studies by various investigators addressing a variety of experimental questions. Equipment will be designed to be adaptable to other space platforms. The theme of the Gravitational Biology Facility effort is to provide optimal and reliable equipment to answer the critical questions in Space Biology as to the effects of gravity on living systems.

Coarse-Grained Models for Protein-Cell Membrane Interactions

PubMed Central

Bradley, Ryan; Radhakrishnan, Ravi

2015-01-01

The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes. PMID:26613047

Isolation of hair follicle bulge stem cells from YFP-expressing reporter mice.

PubMed

Nakrieko, Kerry-Ann; Irvine, Timothy S; Dagnino, Lina

2013-01-01

In this article we provide a method to isolate hair follicle stem cells that have undergone targeted gene inactivation. The mice from which these cells are isolated are bred into a Rosa26-yellow fluorescent protein (YFP) reporter background, which results in YFP expression in the targeted stem cell population. These cells are isolated and purified by fluorescence-activated cell sorting, using epidermal stem cell-specific markers in conjunction with YFP fluorescence. The purified cells can be used for gene expression studies, clonogenic experiments, and biological assays, such as viability and capacity for directional migration.

Estimating the Size of Onion Epidermal Cells from Diffraction Patterns

NASA Astrophysics Data System (ADS)

Groff, Jeffrey R.

2012-10-01

Bioscience and premedical profession students are a major demographic served by introductory physics courses at many colleges and universities. Exposing these students to biological applications of physical principles will help them to appreciate physics as a useful tool for their future professions. Here I describe an experiment suitable for introductory physics where principles of wave optics are applied to probe the size of onion epidermal cells. The epidermis tissue is composed of cells of relatively uniform size and shape (Fig. 1) so the tissue acts like a one-dimensional transmission diffraction grating. The diffraction patterns generated when a laser beam passes through the tissue (Fig. 2) are analyzed and an estimate of the average width of individual onion epidermal cells is calculated. The results are compared to direct measurements taken using a light microscope. The use of microscopes and plant-cell tissue slides creates opportunities for cross-discipline collaboration between physics and biology instructors.

Copper isotope fractionation during surface adsorption and intracellular incorporation by bacteria

PubMed Central

Navarrete, Jesica U.; Borrok, David M.; Viveros, Marian; Ellzey, Joanne T.

2011-01-01

Copper isotopes may prove to be a useful tool for investigating bacteria–metal interactions recorded in natural waters, soils, and rocks. However, experimental data which attempt to constrain Cu isotope fractionation in biologic systems are limited and unclear. In this study, we utilized Cu isotopes (δ65Cu) to investigate Cu–bacteria interactions, including surface adsorption and intracellular incorporation. Experiments were conducted with individual representative species of Gram-positive (Bacillus subtilis) and Gram-negative (Escherichia coli) bacteria, as well as with wild-type consortia of microorganisms from several natural environments. Ph-dependent adsorption experiments were conducted with live and dead cells over the pH range 2.5–6. Surface adsorption experiments of Cu onto live bacterial cells resulted in apparent separation factors (Δ65Cusolution–solid = δ65Cusolution – δ65Cusolid) ranging from +0.3‰ to +1.4‰ for B. subtilis and +0.2‰ to +2.6‰ for E. coli. However, because heat-killed bacterial cells did not exhibit this behavior, the preference of the lighter Cu isotope by the cells is probably not related to reversible surface adsorption, but instead is a metabolically-driven phenomenon. Adsorption experiments with heat-killed cells yielded apparent separation factors ranging from +0.3‰ to –0.69‰ which likely reflects fractionation from complexation with organic acid surface functional group sites. For intracellular incorporation experiments the lab strains and natural consortia preferentially incorporated the lighter Cu isotope with an apparent Δ65Cusolution–solid ranging from ~+1.0‰ to +4.4‰. Our results indicate that live bacterial cells preferentially sequester the lighter Cu isotope regardless of the experimental conditions. The fractionation mechanisms involved are likely related to active cellular transport and regulation, including the reduction of Cu(II) to Cu(I). Because similar intracellular Cu machinery is shared by fungi, plants, and higher organisms, the influence of biological processes on the δ65Cu of natural waters and soils is probably considerable. PMID:21785492

Untangling cell tracks: Quantifying cell migration by time lapse image data analysis.

PubMed

Svensson, Carl-Magnus; Medyukhina, Anna; Belyaev, Ivan; Al-Zaben, Naim; Figge, Marc Thilo

2018-03-01

Automated microscopy has given researchers access to great amounts of live cell imaging data from in vitro and in vivo experiments. Much focus has been put on extracting cell tracks from such data using a plethora of segmentation and tracking algorithms, but further analysis is normally required to draw biologically relevant conclusions. Such relevant conclusions may be whether the migration is directed or not, whether the population has homogeneous or heterogeneous migration patterns. This review focuses on the analysis of cell migration data that are extracted from time lapse images. We discuss a range of measures and models used to analyze cell tracks independent of the biological system or the way the tracks were obtained. For single-cell migration, we focus on measures and models giving examples of biological systems where they have been applied, for example, migration of bacteria, fibroblasts, and immune cells. For collective migration, we describe the model systems wound healing, neural crest migration, and Drosophila gastrulation and discuss methods for cell migration within these systems. We also discuss the role of the extracellular matrix and subsequent differences between track analysis in vitro and in vivo. Besides methods and measures, we are putting special focus on the need for openly available data and code, as well as a lack of common vocabulary in cell track analysis. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

The Neural Development Section (NDS) headed by Dr. Lino Tessarollo has an open postdoctoral fellow position. The candidate should have a background in neurobiology and basic expertise in molecular biology, cell biology, immunoistochemistry and biochemistry.  Experience in confocal analysis is desired. The NDS study the biology of neurotrophin and Trk receptors function by using both in vitro and in vivo approaches. Our group makes extensive use of engineered mouse models and cell culture models. The current research emphasis is on understanding the molecular mechanisms by which activated trk receptor function. Specifically, we are dissecting the molecular mechanism responsible for modulating Trk receptors activity, including their interaction with specific scaffold proteins and proteins leading to de-activation of Trk signaling. Moreover, we are attempting to identify new signaling pathways activated by truncated Trk receptors.

Bioinformatic analysis of primary endothelial cell gene array data illustrated by the analysis of transcriptome changes in endothelial cells exposed to VEGF-A and PlGF.

PubMed

Schoenfeld, Jonathan; Lessan, Khashayar; Johnson, Nicola A; Charnock-Jones, D Stephen; Evans, Amanda; Vourvouhaki, Ekaterini; Scott, Laurie; Stephens, Richard; Freeman, Tom C; Saidi, Samir A; Tom, Brian; Weston, Gareth C; Rogers, Peter; Smith, Stephen K; Print, Cristin G

2004-01-01

We recently published a review in this journal describing the design, hybridisation and basic data processing required to use gene arrays to investigate vascular biology (Evans et al. Angiogenesis 2003; 6: 93-104). Here, we build on this review by describing a set of powerful and robust methods for the analysis and interpretation of gene array data derived from primary vascular cell cultures. First, we describe the evaluation of transcriptome heterogeneity between primary cultures derived from different individuals, and estimation of the false discovery rate introduced by this heterogeneity and by experimental noise. Then, we discuss the appropriate use of Bayesian t-tests, clustering and independent component analysis to mine the data. We illustrate these principles by analysis of a previously unpublished set of gene array data in which human umbilical vein endothelial cells (HUVEC) cultured in either rich or low-serum media were exposed to vascular endothelial growth factor (VEGF)-A165 or placental growth factor (PlGF)-1(131). We have used Affymetrix U95A gene arrays to map the effects of these factors on the HUVEC transcriptome. These experiments followed a paired design and were biologically replicated three times. In addition, one experiment was repeated using serial analysis of gene expression (SAGE). In contrast to some previous studies, we found that VEGF-A and PlGF consistently regulated only small, non-overlapping and culture media-dependant sets of HUVEC transcripts, despite causing significant cell biological changes.

Membrane Fluidity Changes, A Basic Mechanism of Interaction of Gravity with Cells?

NASA Astrophysics Data System (ADS)

Kohn, Florian; Hauslage, Jens; Hanke, Wolfgang

2017-10-01

All life on earth has been established under conditions of stable gravity of 1g. Nevertheless, in numerous experiments the direct gravity dependence of biological processes has been shown on all levels of organization, from single molecules to humans. According to the underlying mechanisms a variety of questions, especially about gravity sensation of single cells without specialized organelles or structures for gravity sensing is being still open. Biological cell membranes are complex structures containing mainly lipids and proteins. Functional aspects of such membranes are usually attributed to membrane integral proteins. This is also correct for the gravity dependence of cells and organisms which is well accepted since long for a wide range of biological systems. However, it is as well established that parameters of the lipid matrix are directly modifying the function of proteins. Thus, the question must be asked, whether, and how far plain lipid membranes are affected by gravity directly. In principle it can be said that up to recently no real basic mechanism for gravity perception in single cells has been presented or verified. However, it now has been shown that as a basic membrane parameter, membrane fluidity, is significantly dependent on gravity. This finding might deliver a real basic mechanism for gravity perception of living organisms on all scales. In this review we summarize older and more recent results to demonstrate that the finding of membrane fluidity being gravity dependent is consistent with a variety of published laboratory experiments. We additionally point out to the consequences of these recent results for research in the field life science under space condition.

Single-cell photoacoustic thermometry

PubMed Central

Gao, Liang; Wang, Lidai; Li, Chiye; Liu, Yan; Ke, Haixin; Zhang, Chi

2013-01-01

Abstract. A novel photoacoustic thermometric method is presented for simultaneously imaging cells and sensing their temperature. With three-seconds-per-frame imaging speed, a temperature resolution of 0.2°C was achieved in a photo-thermal cell heating experiment. Compared to other approaches, the photoacoustic thermometric method has the advantage of not requiring custom-developed temperature-sensitive biosensors. This feature should facilitate the conversion of single-cell thermometry into a routine lab tool and make it accessible to a much broader biological research community. PMID:23377004

VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development.

PubMed

Merks, Roeland M H; Guravage, Michael; Inzé, Dirk; Beemster, Gerrit T S

2011-02-01

Plant organs, including leaves and roots, develop by means of a multilevel cross talk between gene regulation, patterned cell division and cell expansion, and tissue mechanics. The multilevel regulatory mechanisms complicate classic molecular genetics or functional genomics approaches to biological development, because these methodologies implicitly assume a direct relation between genes and traits at the level of the whole plant or organ. Instead, understanding gene function requires insight into the roles of gene products in regulatory networks, the conditions of gene expression, etc. This interplay is impossible to understand intuitively. Mathematical and computer modeling allows researchers to design new hypotheses and produce experimentally testable insights. However, the required mathematics and programming experience makes modeling poorly accessible to experimental biologists. Problem-solving environments provide biologically intuitive in silico objects ("cells", "regulation networks") required for setting up a simulation and present those to the user in terms of familiar, biological terminology. Here, we introduce the cell-based computer modeling framework VirtualLeaf for plant tissue morphogenesis. The current version defines a set of biologically intuitive C++ objects, including cells, cell walls, and diffusing and reacting chemicals, that provide useful abstractions for building biological simulations of developmental processes. We present a step-by-step introduction to building models with VirtualLeaf, providing basic example models of leaf venation and meristem development. VirtualLeaf-based models provide a means for plant researchers to analyze the function of developmental genes in the context of the biophysics of growth and patterning. VirtualLeaf is an ongoing open-source software project (http://virtualleaf.googlecode.com) that runs on Windows, Mac, and Linux.

Using yeast to determine the functional consequences of mutations in the human p53 tumor suppressor gene: An introductory course‐based undergraduate research experience in molecular and cell biology

PubMed Central

Brownell, Sara E.; Seawell, Patricia Chandler; Malladi, Shyamala; Imam, Jamie F. Conklin; Singla, Veena; Bradon, Nicole; Cyert, Martha S.; Stearns, Tim

2016-01-01

Abstract The opportunity to engage in scientific research is an important, but often neglected, component of undergraduate training in biology. We describe the curriculum for an innovative, course‐based undergraduate research experience (CURE) appropriate for a large, introductory cell and molecular biology laboratory class that leverages students′ high level of interest in cancer. The course is highly collaborative and emphasizes the analysis and interpretation of original scientific data. During the course, students work in teams to characterize a collection of mutations in the human p53 tumor suppressor gene via expression and analysis in yeast. Initially, student pairs use both qualitative and quantitative assays to assess the ability of their p53 mutant to activate expression of reporter genes, and they localize their mutation within the p53 structure. Through facilitated discussion, students suggest possible molecular explanations for the transactivation defects displayed by their p53 mutants and propose experiments to test these hypotheses that they execute during the second part of the course. They use a western blot to determine whether mutant p53 levels are reduced, a DNA‐binding assay to test whether recognition of any of three p53 target sequences is compromised, and fluorescence microscopy to assay nuclear localization. Students studying the same p53 mutant periodically convene to discuss and interpret their combined data. The course culminates in a poster session during which students present their findings to peers, instructors, and the greater biosciences community. Based on our experience, we provide recommendations for the development of similar large introductory lab courses. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(2):161–178, 2017. PMID:27873457

Science Notes.

ERIC Educational Resources Information Center

Shaw, G. W.; And Others

1989-01-01

Provides a reading list for A- and S-level biology. Contains several experiments and demonstrations with topics on: the intestine, bullock corneal cells, valences, the science of tea, automated hydrolysis, electronics characteristics, bromine diffusion, enthalpy of vaporization determination, thermometers, pendulums, hovercraft, Bernoulli fluid…

Agent-Based Phytoplankton Models of Cellular and Population Processes: Fostering Individual-Based Learning in Undergraduate Research

NASA Astrophysics Data System (ADS)

Berges, J. A.; Raphael, T.; Rafa Todd, C. S.; Bate, T. C.; Hellweger, F. L.

2016-02-01

Engaging undergraduate students in research projects that require expertise in multiple disciplines (e.g. cell biology, population ecology, and mathematical modeling) can be challenging because they have often not developed the expertise that allows them to participate at a satisfying level. Use of agent-based modeling can allow exploration of concepts at more intuitive levels, and encourage experimentation that emphasizes processes over computational skills. Over the past several years, we have involved undergraduate students in projects examining both ecological and cell biological aspects of aquatic microbial biology, using the freely-downloadable, agent-based modeling environment NetLogo (https://ccl.northwestern.edu/netlogo/). In Netlogo, actions of large numbers of individuals can be simulated, leading to complex systems with emergent behavior. The interface features appealing graphics, monitors, and control structures. In one example, a group of sophomores in a BioMathematics program developed an agent-based model of phytoplankton population dynamics in a pond ecosystem, motivated by observed macroscopic changes in cell numbers (due to growth and death), and driven by responses to irradiance, temperature and a limiting nutrient. In a second example, junior and senior undergraduates conducting Independent Studies created a model of the intracellular processes governing stress and cell death for individual phytoplankton cells (based on parameters derived from experiments using single-cell culturing and flow cytometry), and then this model was embedded in the agents in the pond ecosystem model. In our experience, students with a range of mathematical abilities learned to code quickly and could use the software with varying degrees of sophistication, for example, creation of spatially-explicit two and three-dimensional models. Skills developed quickly and transferred readily to other platforms (e.g. Matlab).

Humidity-controlled preparation of frozen-hydrated biological samples for cryogenic coherent x-ray diffraction microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takayama, Yuki; Nakasako, Masayoshi; RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo 679-5148

2012-05-15

Coherent x-ray diffraction microscopy (CXDM) has the potential to visualize the structures of micro- to sub-micrometer-sized biological particles, such as cells and organelles, at high resolution. Toward advancing structural studies on the functional states of such particles, here, we developed a system for the preparation of frozen-hydrated biological samples for cryogenic CXDM experiments. The system, which comprised a moist air generator, microscope, micro-injector mounted on a micromanipulator, custom-made sample preparation chamber, and flash-cooling device, allowed for the manipulation of sample particles in the relative humidity range of 20%-94%rh at 293 K to maintain their hydrated and functional states. Here, wemore » report the details of the system and the operation procedure, including its application to the preparation of a frozen-hydrated chloroplast sample. Sample quality was evaluated through a cryogenic CXDM experiment conducted at BL29XUL of SPring-8. Taking the performance of the system and the quality of the sample, the system was suitable to prepare frozen-hydrated biological samples for cryogenic CXDM experiments.« less

Role of Conserved Oligomeric Golgi Complex in the Abnormalities of Glycoprotein Processing in Breast Cancer Cells

DTIC Science & Technology

2006-05-01

terminal oligosaccharide units serve as highly specific biological recognition molecules implicated in major regulatory processes of the cell...treatment or mock-treated for 9 days. To study the glycosylation process in COG complex depleted cells series of Pulse -Chase experiments have been...DAMD17-03-1-0243 TITLE: Role of the Conserved Oligomeric Golgi Complex in the Abnormalities of Glycoprotein Processing in Breast Cancer

Biological cell controllable patch-clamp microchip

NASA Astrophysics Data System (ADS)

Penmetsa, Siva; Nagrajan, Krithika; Gong, Zhongcheng; Mills, David; Que, Long

2010-12-01

A patch-clamp (PC) microchip with cell sorting and positioning functions is reported, which can avoid drawbacks of random cell selection or positioning for a PC microchip. The cell sorting and positioning are enabled by air bubble (AB) actuators. AB actuators are pneumatic actuators, in which air pressure is generated by microheaters within sealed microchambers. The sorting, positioning, and capturing of 3T3 cells by this type of microchip have been demonstrated. Using human breast cancer cells MDA-MB-231 as the model, experiments have been demonstrated by this microchip as a label-free technical platform for real-time monitoring of the cell viability.

Synthesis, biological evaluation, and live cell imaging of novel fluorescent duocarmycin analogs.

PubMed

Tietze, Lutz F; Behrendt, Frank; Pestel, Galina F; Schuberth, Ingrid; Mitkovski, Mišo

2012-11-01

For a better understanding of the mode of action of duocarmycin and its analogs, the novel fluorescent duocarmycin derivatives 13-15 and 17b-19b were synthesized, and their bioactivity as well as their cellular uptake investigated using confocal laser scanning microscopy (CLSM) in live-cell imaging experiments. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.

Fluorescence Quantum Yield Measurements of Fluorescent Proteins: A Laboratory Experiment for a Biochemistry or Molecular Biophysics Laboratory Course

ERIC Educational Resources Information Center

Wall, Kathryn P.; Dillon, Rebecca; Knowles, Michelle K.

2015-01-01

Fluorescent proteins are commonly used in cell biology to assess where proteins are within a cell as a function of time and provide insight into intracellular protein function. However, the usefulness of a fluorescent protein depends directly on the quantum yield. The quantum yield relates the efficiency at which a fluorescent molecule converts…

On the Roots of Difficulties in Learning about Cell Division: Process-Based Analysis of Students' Conceptual Development in Teaching Experiments

ERIC Educational Resources Information Center

Riemeier, Tanja; Gropengiesser, Harald

2008-01-01

Empirical investigations on students' conceptions of cell biology indicate major misunderstandings of scientific concepts even after thorough teaching. Therefore, the main aim of our research project was to investigate students' difficulties in learning this topic and to study the impact of learning activities on students' conceptions. Using the…

Problem-Solving Test: RNA and Protein Synthesis in Bacteriophage-Infected "E. coli" Cells

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2008-01-01

The classic experiment presented in this problem-solving test was designed to identify the template molecules of translation by analyzing the synthesis of phage proteins in "Escherichia coli" cells infected with bacteriophage T4. The work described in this test led to one of the most seminal discoveries of early molecular biology: it dealt a…

Biological characteristics of human-urine-derived stem cells: potential for cell-based therapy in neurology.

PubMed

Guan, Jun-Jie; Niu, Xin; Gong, Fei-Xiang; Hu, Bin; Guo, Shang-Chun; Lou, Yuan-Lei; Zhang, Chang-Qing; Deng, Zhi-Feng; Wang, Yang

2014-07-01

Stem cells in human urine have gained attention in recent years; however, urine-derived stem cells (USCs) are far from being well elucidated. In this study, we compared the biological characteristics of USCs with adipose-derived stem cells (ASCs) and investigated whether USCs could serve as a potential cell source for neural tissue engineering. USCs were isolated from voided urine with a modified culture medium. Through a series of experiments, we examined the growth rate, surface antigens, and differentiation potential of USCs, and compared them with ASCs. USCs showed robust proliferation ability. After serial propagation, USCs retained normal karyotypes. Cell surface antigen expression of USCs was similar to ASCs. With lineage-specific induction factors, USCs could differentiate toward the osteogenic, chondrogenic, adipogenic, and neurogenic lineages. To assess the ability of USCs to survive, differentiate, and migrate, they were seeded onto hydrogel scaffold and transplanted into rat brain. The results showed that USCs were able to survive in the lesion site, migrate to other areas, and express proteins that were associated with neural phenotypes. The results of our study demonstrate that USCs possess similar biological characteristics with ASCs and have multilineage differentiation potential. Moreover USCs can differentiate to neuron-like cells in rat brain. The present study shows that USCs are a promising cell source for tissue engineering and regenerative medicine.

Nano-textured fluidic biochip as biological filter for selective survival of neuronal cells.

PubMed

Han, Hsieh-Cheng; Lo, Hung-Chun; Wu, Chia-Yu; Chen, Kuei-Hsien; Chen, Li-Chyong; Ou, Keng-Liang; Hosseinkhani, Hossein

2015-06-01

This is an innovative study to engineer biological filter to evaluate the effect of template surface structure and physiochemical properties that can be used for wide variety of applications in biological, health care as well as environmental protection. Specifically, planar silicon (Si) wafer and arrayed Si nano-tips (SiNT) templates were fabricated and coated with gold for various lengths of time to study the effect of surface charge, surface roughness, and hydrophilicity on biological activity of rat pheochromocytoma cell lines PC12. The initial growth and proliferation of PC12 cells on Si and SiNT templates showed an antipathy for the ultra-sharp SiNTs templates. In contrast, the same cells demonstrated a preferable adherence to and proliferation on planar Si templates, resulting in higher cell densities by three orders of magnitude than those on SiNT templates. It is hypothesized that SiNTs array does generate nano-fluidic effect such that the effective contact region for aqueous solution on SiNTs is lower than that on planar Si templates, thus decreasing adsorbable area for cell viability and survival. Moreover, the effect of the gold coating on cell number density was analyzed in terms of the surface roughness, zeta potential and wetting properties of the templates. It was determined that surface charge, as measured by the zeta potential, strongly correlated with the trend observed in the surface cell density, whereas no such correlation was observed for surface roughness or wetting properties in the ranges of our experiment conditions. © 2014 Wiley Periodicals, Inc.

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

PubMed

Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

2016-10-20

The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

Biological Applications Of Fourier Transform Infrared (FTIR) Or Bloody FTIR

NASA Astrophysics Data System (ADS)

Jakobsen, R. J.; Winters, S.; Gendreau, R. M.

1981-10-01

An ex vivo FT-IR/ATR experiment for studying blood protein adsorption at the molecular level is described. This experiment involves the use of live dogs pumping the blood through a arterial-veinal shunt to the ATR cell and back into the animal. The results from these live dog experiments are compared to results obtained using donated whole blood. These experiments demonstrate that FT-IR can be used to study aqueous, physiological, flowing solutions in real time with the sensitivity necessary to detect minor changes.

Materials of the final reports on the joint Soviet-American experiment on the Kosmos-936 biosatellite

NASA Technical Reports Server (NTRS)

Timofeyev-Resolskiy, N. V.; Parfenov, G. P.; Tairbekov, M.; Platonova, R. N.; Rostopshina, A. V.; Zhvalikovskaya, V. P.; Mosgovaya, I. Y.; Shvets, V. N.; Kovalev, Y. Y.; Dudkin, V. Y.

1978-01-01

Biological experiments onboard the Kosmos-936 investigated the effect of weightlessness on the basic components of cells, the genetic structure and energy apparatus. Genetic studies were made on the Drosophila melanogaster. Experiments were made on higher vegetation and fungi as well. The results indicate that weightlessness cannot be the principal barrier for normal development. An experiment with ectopic osteogenesis in weightlessness was carried out. Measurements were made of cosmic radiation inside and outside the biosatellite.

Opposite actions of transforming growth factor-beta 1 on the gene expression of atrial natriuretic peptide biological and clearance receptors in a murine thymic stromal cell line.

PubMed

Agui, T; Xin, X; Cai, Y; Shim, G; Muramatsu, Y; Yamada, T; Fujiwara, H; Matsumoto, K

1995-09-01

The regulation of the gene expression of the atrial natriuretic peptide receptor (ANPR) subtypes, ANPR-A, ANPR-B, and ANPR-C, was investigated in a murine thymic stromal cell line, MRL 104.8a. When MRL 104.8a cells were cultured with transforming growth factor (TGF)-beta1, [125I]ANP binding sites increased with increasing dose of TGF-beta1. These binding sites were identified as ANPR-C by a displacement experiment with ANPR-C-specific ligand, C-ANF, and by the affinity cross-linking of the [125I]ANP binding sites with a chemical cross-linker to determine the molecular weight of the ANPR. This augmentation of the ANPR-C expression was elucidated to occur at the transcriptional level by Northern blot experiment, comparison of the relative amounts of mRNA by reverse transcription (RT)-PCR, and in vitro nuclear transcription assay. Conversely, the expression of the ANP biological receptors, ANPR-A and ANPR-B, was shown to be down-regulated by TGF-beta1. These data suggest that TGF-beta1 regulates the gene expression of ANPRs in the thymic stromal cells and that ANP and TGF-beta1 might affect the thymic stromal cell functions.

Discovery of functional interactions among actin regulators by analysis of image fluctuations in an unperturbed motile cell system.

PubMed

Isogai, Tadamoto; Danuser, Gaudenz

2018-05-26

Cell migration is driven by propulsive forces derived from polymerizing actin that pushes and extends the plasma membrane. The underlying actin network is constantly undergoing adaptation to new mechano-chemical environments and intracellular conditions. As such, mechanisms that regulate actin dynamics inherently contain multiple feedback loops and redundant pathways. Given the highly adaptable nature of such a system, studies that use only perturbation experiments (e.g. knockdowns, overexpression, pharmacological activation/inhibition, etc.) are challenged by the nonlinearity and redundancy of the pathway. In these pathway configurations, perturbation experiments at best describe the function(s) of a molecular component in an adapting (e.g. acutely drug-treated) or fully adapted (e.g. permanent gene silenced) cell system, where the targeted component now resides in a non-native equilibrium. Here, we propose how quantitative live-cell imaging and analysis of constitutive fluctuations of molecular activities can overcome these limitations. We highlight emerging actin filament barbed-end biology as a prime example of a complex, nonlinear molecular process that requires a fluctuation analytic approach, especially in an unperturbed cellular system, to decipher functional interactions of barbed-end regulators, actin polymerization and membrane protrusion.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

Biological and Clinical Significance of MAD2L1 and BUB1, Genes Frequently Appearing in Expression Signatures for Breast Cancer Prognosis

PubMed Central

Wang, Zhanwei; Katsaros, Dionyssios; Shen, Yi; Fu, Yuanyuan; Canuto, Emilie Marion; Benedetto, Chiara; Lu, Lingeng; Chu, Wen-Ming; Risch, Harvey A.; Yu, Herbert

2015-01-01

To investigate the biologic relevance and clinical implication of genes involved in multiple gene expression signatures for breast cancer prognosis, we identified 16 published gene expression signatures, and selected two genes, MAD2L1 and BUB1. These genes appeared in 5 signatures and were involved in cell-cycle regulation. We analyzed the expression of these genes in relation to tumor features and disease outcomes. In vitro experiments were also performed in two breast cancer cell lines, MDA-MB-231 and MDA-MB-468, to assess cell proliferation, migration and invasion after knocking down the expression of these genes. High expression of these genes was found to be associated with aggressive tumors and poor disease-free survival of 203 breast cancer patients in our study, and the association with survival was confirmed in an online database consisting of 914 patients. In vitro experiments demonstrated that lowering the expression of these genes by siRNAs reduced tumor cell growth and inhibited cell migration and invasion. Our investigation suggests that MAD2L1 and BUB1 may play important roles in breast cancer progression, and measuring the expression of these genes may assist the prediction of breast cancer prognosis. PMID:26287798

FE Furukawa poses for a photo during VolSci Session

NASA Image and Video Library

2011-06-25

ISS028-E-009727 (25 June 2011) --- Japan Aerospace Exploration Agency astronaut Satoshi Furukawa, Expedition 28 flight engineer, is pictured near the Cell Biology Experiment Facility (CBEF) in the Kibo laboratory of the International Space Station.

Purification and Cultivation of Human Pituitary Growth Hormones Secreting Cells

NASA Technical Reports Server (NTRS)

Hymer, W. C.; Todd, P.; Grindeland, R.; Lanham, W.; Morrison, D.

1985-01-01

The rat and human pituitary gland contains a mixture of hormone producing cell types. The separation of cells which make growth hormone (GH) is attempted for the purpose of understanding how the hormone molecule is made within the pituitary cell; what form(s) it takes within the cell; and what form(s) GH assumes as it leaves the cell. Since GH has a number of biological targets (e.g., muscle, liver, bone), the assessment of the activities of the intracellular/extracellular GH by new and sensitive bioassays. GH cells contained in the mixture was separated by free flow electrophoresis. These experiments show that GH cells have different electrophoretic mobilities. This is relevant to NASA since a lack of GH could be a prime causative factor in muscle atrophy. Further, GH has recently been implicated in the etiology of motion sickness in space. Continous flow electrophoresis experiment on STS-8 showed that GH cells could be partially separated in microgravity. However, definitive cell culture studies could not be done due to insufficient cell recoveries.

Relativistic parameters of senescence.

PubMed

Stathatos, Marios A

2005-01-01

The laws of biochemistry and biology are governed by parameters whose description in mathematical formulas is based on the three-dimensional space. It is a fact, however, that the life span of a cell and its specific functions, though limited, can be extended or diminished depending on the genetic code but also, on the natural pressure of the environment. The plasticity exhibited by a cellular system has been attributed to the change of the three-dimensional structure of the cell, with time being a simple measure of this change. The model of biological relativity proposed here, considers time as a flexible fourth dimension that corresponds directly to the inertial status of the cells. Two types of clocks are defined: the relativistic biological clock (RBC) and the mechanical clock (MC). In contrast to the MCs that show the astrological reference time, the time shown by the RBCs delay because it depends on cellular activity. The maximum and the expected life span of the cells and/or the organisms can be therefore relied on time transformation. One of the most important factors that can affect time flow is the energy that is produced during metabolic work. Based on this observation, RBCs can be constructed following series of theoretical experiments in order to assess biological time and life span changes.

Lessons we learned from high-throughput and top-down systems biology analyses about glioma stem cells.

PubMed

Mock, Andreas; Chiblak, Sara; Herold-Mende, Christel

2014-01-01

A growing body of evidence suggests that glioma stem cells (GSCs) account for tumor initiation, therapy resistance, and the subsequent regrowth of gliomas. Thus, continuous efforts have been undertaken to further characterize this subpopulation of less differentiated tumor cells. Although we are able to enrich GSCs, we still lack a comprehensive understanding of GSC phenotypes and behavior. The advent of high-throughput technologies raised hope that incorporation of these newly developed platforms would help to tackle such questions. Since then a couple of comparative genome-, transcriptome- and proteome-wide studies on GSCs have been conducted giving new insights in GSC biology. However, lessons had to be learned in designing high-throughput experiments and some of the resulting conclusions fell short of expectations because they were performed on only a few GSC lines or at one molecular level instead of an integrative poly-omics approach. Despite these shortcomings, our knowledge of GSC biology has markedly expanded due to a number of survival-associated biomarkers as well as glioma-relevant signaling pathways and therapeutic targets being identified. In this article we review recent findings obtained by comparative high-throughput analyses of GSCs. We further summarize fundamental concepts of systems biology as well as its applications for glioma stem cell research.

Towards a perceptive understanding of size in cellular biology.

PubMed

Zoppè, Monica

2017-06-29

Cells are minute-typically too small to be seen by the human eye. Even so, the cellular world encompasses a range of scales, from roughly a tenth of a nanometer (10 -10 m) to a millimeter (10 -3 m) or larger, spanning seven orders of magnitude or more. Because they are so far from our experience, it is difficult for us to envision such scales. To help our imagination grasp such dimensions, I propose the adoption of a 'perceptive scale' that can facilitate a more direct experience of cellular sizes. From this, as I argue below, will stem a new perception also of biological shape, cellular space and dynamic processes.

Bacterial Microcolonies in Gel Beads for High-Throughput Screening of Libraries in Synthetic Biology.

PubMed

Duarte, José M; Barbier, Içvara; Schaerli, Yolanda

2017-11-17

Synthetic biologists increasingly rely on directed evolution to optimize engineered biological systems. Applying an appropriate screening or selection method for identifying the potentially rare library members with the desired properties is a crucial step for success in these experiments. Special challenges include substantial cell-to-cell variability and the requirement to check multiple states (e.g., being ON or OFF depending on the input). Here, we present a high-throughput screening method that addresses these challenges. First, we encapsulate single bacteria into microfluidic agarose gel beads. After incubation, they harbor monoclonal bacterial microcolonies (e.g., expressing a synthetic construct) and can be sorted according their fluorescence by fluorescence activated cell sorting (FACS). We determine enrichment rates and demonstrate that we can measure the average fluorescent signals of microcolonies containing phenotypically heterogeneous cells, obviating the problem of cell-to-cell variability. Finally, we apply this method to sort a pBAD promoter library at ON and OFF states.

Crambescin C1 Exerts a Cytoprotective Effect on HepG2 Cells through Metallothionein Induction

PubMed Central

Roel, María; Rubiolo, Juan A.; Ternon, Eva; Thomas, Olivier P.; Vieytes, Mercedes R.; Botana, Luis M.

2015-01-01

The Mediterranean marine sponge Crambe crambe is the source of two families of guanidine alkaloids known as crambescins and crambescidins. Some of the biological effects of crambescidins have been previously reported while crambescins have undergone little study. Taking this into account, we performed comparative transcriptome analysis to examine the effect of crambescin-C1 (CC1) on human tumor hepatocarcinoma cells HepG2 followed by validation experiments to confirm its predicted biological activities. We report herein that, while crambescin-A1 has a minor effect on these cells, CC1 protects them against oxidative injury by means of metallothionein induction even at low concentrations. Additionally, at high doses, CC1 arrests the HepG2 cell cycle in G0/G1 and thus inhibits tumor cell proliferation. The findings presented here provide the first detailed approach regarding the different effects of crambescins on tumor cells and provide a basis for future studies on other possible cellular mechanisms related to these bioactivities. PMID:26225985

In Vitro Bioluminescence Assay to Characterize Circadian Rhythm in Mammary Epithelial Cells.

PubMed

Fang, Mingzhu; Kang, Hwan-Goo; Park, Youngil; Estrella, Brian; Zarbl, Helmut

2017-09-28

The circadian rhythm is a fundamental physiological process present in all organisms that regulates biological processes ranging from gene expression to sleep behavior. In vertebrates, circadian rhythm is controlled by a molecular oscillator that functions in both the suprachiasmatic nucleus (SCN; central pacemaker) and individual cells comprising most peripheral tissues. More importantly, disruption of circadian rhythm by exposure to light-at-night, environmental stressors and/or toxicants is associated with increased risk of chronic diseases and aging. The ability to identify agents that can disrupt central and/or peripheral biological clocks, and agents that can prevent or mitigate the effects of circadian disruption, has significant implications for prevention of chronic diseases. Although rodent models can be used to identify exposures and agents that induce or prevent/mitigate circadian disruption, these experiments require large numbers of animals. In vivo studies also require significant resources and infrastructure, and require researchers to work all night. Thus, there is an urgent need for a cell-type appropriate in vitro system to screen for environmental circadian disruptors and enhancers in cell types from different organs and disease states. We constructed a vector that drives transcription of the destabilized luciferase in eukaryotic cells under the control of the human PERIOD 2 gene promoter. This circadian reporter construct was stably transfected into human mammary epithelial cells, and circadian responsive reporter cells were selected to develop the in vitro bioluminescence assay. Here, we present a detailed protocol to establish and validate the assay. We further provide details for proof of concept experiments demonstrating the ability of our in vitro assay to recapitulate the in vivo effects of various chemicals on the cellular biological clock. The results indicate that the assay can be adapted to a variety of cell types to screen for both environmental disruptors and chemopreventive enhancers of circadian clocks.

Real-Time Cellular Exometabolome Analysis with a Microfluidic-Mass Spectrometry Platform

PubMed Central

Marasco, Christina C.; Enders, Jeffrey R.; Seale, Kevin T.; McLean, John A.; Wikswo, John P.

2015-01-01

To address the challenges of tracking the multitude of signaling molecules and metabolites that is the basis of biological complexity, we describe a strategy to expand the analytical techniques for dynamic systems biology. Using microfluidics, online desalting, and mass spectrometry technologies, we constructed and validated a platform well suited for sampling the cellular microenvironment with high temporal resolution. Our platform achieves success in: automated cellular stimulation and microenvironment control; reduced non-specific adsorption to polydimethylsiloxane due to surface passivation; real-time online sample collection; near real-time sample preparation for salt removal; and real-time online mass spectrometry. When compared against the benchmark of “in-culture” experiments combined with ultraperformance liquid chromatography-electrospray ionization-ion mobility-mass spectrometry (UPLC-ESI-IM-MS), our platform alleviates the volume challenge issues caused by dilution of autocrine and paracrine signaling and dramatically reduces sample preparation and data collection time, while reducing undesirable external influence from various manual methods of manipulating cells and media (e.g., cell centrifugation). To validate this system biologically, we focused on cellular responses of Jurkat T cells to microenvironmental stimuli. Application of these stimuli, in conjunction with the cell’s metabolic processes, results in changes in consumption of nutrients and secretion of biomolecules (collectively, the exometabolome), which enable communication with other cells or tissues and elimination of waste. Naïve and experienced T-cell metabolism of cocaine is used as an exemplary system to confirm the platform’s capability, highlight its potential for metabolite discovery applications, and explore immunological memory of T-cell drug exposure. Our platform proved capable of detecting metabolomic variations between naïve and experienced Jurkat T cells and highlights the dynamics of the exometabolome over time. Upregulation of the cocaine metabolite, benzoylecgonine, was noted in experienced T cells, indicating potential cellular memory of cocaine exposure. These metabolomics distinctions were absent from the analogous, traditional “in-culture” UPLC-ESI-IM-MS experiment, further demonstrating this platform’s capabilities. PMID:25723555

Nano-ranged low-energy ion-beam-induced DNA transfer in biological cells

NASA Astrophysics Data System (ADS)

Yu, L. D.; Wongkham, W.; Prakrajang, K.; Sangwijit, K.; Inthanon, K.; Thongkumkoon, P.; Wanichapichart, P.; Anuntalabhochai, S.

2013-06-01

Low-energy ion beams at a few tens of keV were demonstrated to be able to induce exogenous macromolecules to transfer into plant and bacterial cells. In the process, the ion beam with well controlled energy and fluence bombarded living cells to cause certain degree damage in the cell envelope in nanoscales to facilitate the macromolecules such as DNA to pass through the cell envelope and enter the cell. Consequently, the technique was applied for manipulating positive improvements in the biological species. This physical DNA transfer method was highly efficient and had less risk of side-effects compared with chemical and biological methods. For better understanding of mechanisms involved in the process, a systematic study on the mechanisms was carried out. Applications of the technique were also expanded from DNA transfer in plant and bacterial cells to DNA transfection in human cancer cells potentially for the stem cell therapy purpose. Low-energy nitrogen and argon ion beams that were applied in our experiments had ranges of 100 nm or less in the cell envelope membrane which was majorly composed of polymeric cellulose. The ion beam bombardment caused chain-scission dominant damage in the polymer and electrical property changes such as increase in the impedance in the envelope membrane. These nano-modifications of the cell envelope eventually enhanced the permeability of the envelope membrane to favor the DNA transfer. The paper reports details of our research in this direction.

A thiazolo[4,5-b]pyridine-based fluorescent probe for detection of zinc ions and application for in vitro and in vivo bioimaging.

PubMed

Gong, Jiao; Li, Yuan-Heng; Zhang, Chan-Juan; Huang, Jian; Sun, Qi

2018-08-01

2-HPTP, a novel thiazolo [4, 5-b] pyridine-based Zn 2+ selective fluorescent probe has been synthesized and investigated. This probe exhibited a high selectivity towards Zn 2+ over other biologically essential cations such as Na + , K + , Ca 2+ , or Mg 2+ . 2-HPTP formed a 1:1 complex with Zn 2+ and showed a fluorescent enhancement with a long emission wavelength red-shift (85 nm) upon complex formation with Zn 2+ . The detection limit and association constant were calculated as 3.48 × 10 -7 M and 2.40 × 10 6 M -1 by a fluorescence titration experiment. Furthermore, the live cell imaging experiment showed that 2-HPTP was membrane permeable and photostable, and hence, could be used to monitor the concentration changes of intracellular Zn 2+ . The co-staining experiments in the cells demonstrated that 2-HPTP possessed high lysosomal selectivity in living cells. Finally, using the nematode C. elegans as an experimental model, we established that 2-HPTP could be successful in imaging Zn 2+ concentration changes in living tissues. Therefore, this molecule should be useful for studies on the biological functions of Zn 2+ . Copyright © 2018 Elsevier B.V. All rights reserved.

Development of the Neuron Assessment for Measuring Biology Students' Use of Experimental Design Concepts and Representations.

PubMed

Dasgupta, Annwesa P; Anderson, Trevor R; Pelaez, Nancy J

2016-01-01

Researchers, instructors, and funding bodies in biology education are unanimous about the importance of developing students' competence in experimental design. Despite this, only limited measures are available for assessing such competence development, especially in the areas of molecular and cellular biology. Also, existing assessments do not measure how well students use standard symbolism to visualize biological experiments. We propose an assessment-design process that 1) provides background knowledge and questions for developers of new "experimentation assessments," 2) elicits practices of representing experiments with conventional symbol systems, 3) determines how well the assessment reveals expert knowledge, and 4) determines how well the instrument exposes student knowledge and difficulties. To illustrate this process, we developed the Neuron Assessment and coded responses from a scientist and four undergraduate students using the Rubric for Experimental Design and the Concept-Reasoning Mode of representation (CRM) model. Some students demonstrated sound knowledge of concepts and representations. Other students demonstrated difficulty with depicting treatment and control group data or variability in experimental outcomes. Our process, which incorporates an authentic research situation that discriminates levels of visualization and experimentation abilities, shows potential for informing assessment design in other disciplines. © 2016 A. P. Dasgupta et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

The Principles of Engineering Immune Cells to Treat Cancer

PubMed Central

Lim, Wendell A.; June, Carl H.

2017-01-01

Chimeric antigen receptor (CAR) T cells have proven that engineered immune cells can serve as a powerful new class of cancer therapeutics. Clinical experience has helped to define the major challenges that must be met to make engineered T cells a reliable, safe, and effective platform that can be deployed against a broad range of tumors. The emergence of synthetic biology approaches for cellular engineering is providing us with a broadly expanded set of tools for programming immune cells. We discuss how these tools could be used to design the next generation of smart T cell precision therapeutics. PMID:28187291

Microvalve controlled multi-functional microfluidic chip for divisional cell co-culture.

PubMed

Li, Rui; Zhang, Xingjian; Lv, Xuefei; Geng, Lina; Li, Yongrui; Qin, Kuiwei; Deng, Yulin

2017-12-15

Pneumatic micro-valve controlled microfluidic chip provides precise fluidic control for cell manipulation. In this paper, a multi-functional microfluidic chip was designed for three separate experiments: 1. Different cell lines were dispensed and cultured; 2. Three transfected SH-SY5Y cells were introduced and treated with methyl-phenyl-pyridinium (MPP + ) as drug delivery mode; 3. Specific protection and interaction were observed among cell co-culture after nerve damage. The outcomes revealed the potential and practicability of our entire multi-functional pneumatic chip system on different cell biology applications. Copyright © 2017. Published by Elsevier Inc.

Effects of hypergravity on immunologic function

NASA Technical Reports Server (NTRS)

Sonnenfeld, G.; Koebel, D. A.; Davis, S.

1995-01-01

The purpose of this study was to compare the effects of hypergravity exposure (2g) with those of exposure to space flight in the Cosmos 2044 flight. To do so, rats were centrifuged continuously for 14 days. Two different experiments were carried out on tissue obtained from the centrifuged rats. In the first experiment, rat bone marrow cells were examined for their response to recombinant murine colony stimulating factor-granulocyte/monocyte (GM-CSF). In the second experiment, rat spleen and bone marrow cells were stained in with a variety of antibodies directed against cell surface antigenic markers. These cells were preserved and analyzed on a flow cytometer. The results of the studies indicated that bone marrow cells from centrifuged rats showed no significant change in response to GM-CSF as compared to bone marrow cells from control rats. Spleen cells from flown rats showed some statistically significant changes in leukocytes subset distribution, but no differences that appeared to be of biological significance. These results indicate that hypergravity did not greatly affect the same immunological parameters affected by space flight in the Cosmos 2044 mission.

Effects of hypergravity on immunologic function

NASA Technical Reports Server (NTRS)

Sonnenfeld, G.; Koebel, D. A.; Davis, S.

1994-01-01

The purpose of this study was to compare the effects of hypergravity exposure (2g) with those of exposure to space flight in the Cosmos 2044 flight. To do so, rats were centrifuged continuously for 14 days. Two different experiments were carried out on tissue obtained from the centrifuged rats. In the first experiment, rat bone marrow cells were examined for their response to recombinant murine colony stimulating factor-granulocyte/monocyte (GM-CSF). In the second experiment, rate spleen and bone marrow cells were stained in with a variety of antibodies directed against cell surface antigenic markers. These cells were preserved and analyzed on a flow cytometer. The results of the studies indicated that bone marrow cells from centrifuged rats showed no significant change in response to GM-CSF as compared to bone marrow cells from control rats. Spleen cells from flown rats showed some statistically significant changes in leukocytes subset distribution, but no differences that appeared to be of biological significance. These results indicate that hypergravity did not greatly affect the same immunological parameters affected by space flight in the Cosmos 2044 mission.

Theories and models of the biology of the cell in space--an introduction

NASA Technical Reports Server (NTRS)

Cogoli, A.; Cogoli-Greuter, M.

1994-01-01

The World Space Congress 1992 took place after two Spacelab flights with important biological payloads on board, the SLS-1 (June 1991) and IML-1 (January 1992) missions respectively. Interesting experiments were carried out in 1991 also on the Shuttle middeck and on the sounding rocket MASER 4. The highlights of the investigations on these missions together with the results of relevant ground-based research were presented at the symposium.

The Pleurodele, an animal model for space biology studies

NASA Astrophysics Data System (ADS)

Gualandris, L.; Grinfeld, S.; Foulquier, F.; Kan, P.; Duprat, A. M.

Pleurodeles waltl, an Urodele amphibian is proposed as a model for space biology studies. Our laboratory is developing three types of experiments in space using this animal: 1) in vivo fertilization and development (``FERTILE'' project); 2) influence of microgravity and space radiation on the organization and preservation of spacialized structures in the neurons and muscle cells (in vitro; ``CELIMENE'' PROJECT); 3) influence of microgravity on tissue regeneration (muscle, bone, epidermis and spinal cord).

Localization of single biological molecules out of the focal plane

NASA Astrophysics Data System (ADS)

Gardini, L.; Capitanio, M.; Pavone, F. S.

2014-03-01

Since the behaviour of proteins and biological molecules is tightly related to the cell's environment, more and more microscopy techniques are moving from in vitro to in living cells experiments. Looking at both diffusion and active transportation processes inside a cell requires three-dimensional localization over a few microns range, high SNR images and high temporal resolution (ms order of magnitude). We developed an apparatus that combines different microscopy techniques to satisfy all the technical requirements for 3D tracking of single fluorescent molecules inside living cells with nanometer accuracy. To account for the optical sectioning of thick samples we built up a HILO (Highly Inclined and Laminated Optical sheet) microscopy system through which we can excite the sample in a widefield (WF) configuration by a thin sheet of light that can follow the molecule up and down along the z axis spanning the entire thickness of the cell with a SNR much higher than traditional WF microscopy. Since protein dynamics inside a cell involve all three dimensions, we included a method to measure the x, y, and z coordinates with nanometer accuracy, exploiting the properties of the point-spread-function of out-of-focus quantum dots bound to the protein of interest. Finally, a feedback system stabilizes the microscope from thermal drifts, assuring accurate localization during the entire duration of the experiment.

A plasmid-based Escherichia coli gene expression system with cell-to-cell variation below the extrinsic noise limit

PubMed Central

2017-01-01

Experiments in synthetic biology and microbiology can benefit from protein expression systems with low cell-to-cell variability (noise) and expression levels precisely tunable across a useful dynamic range. Despite advances in understanding the molecular biology of microbial gene regulation, many experiments employ protein-expression systems exhibiting high noise and nearly all-or-none responses to induction. I present an expression system that incorporates elements known to reduce gene expression noise: negative autoregulation and bicistronic transcription. I show by stochastic simulation that while negative autoregulation can produce a more gradual response to induction, bicistronic expression of a repressor and gene of interest can be necessary to reduce noise below the extrinsic limit. I synthesized a plasmid-based system incorporating these principles and studied its properties in Escherichia coli cells, using flow cytometry and fluorescence microscopy to characterize induction dose-response, induction/repression kinetics and gene expression noise. By varying ribosome binding site strengths, expression levels from 55–10,740 molecules/cell were achieved with noise below the extrinsic limit. Individual strains are inducible across a dynamic range greater than 20-fold. Experimental comparison of different regulatory networks confirmed that bicistronic autoregulation reduces noise, and revealed unexpectedly high noise for a conventional expression system with a constitutively expressed transcriptional repressor. I suggest a hybrid, low-noise expression system to increase the dynamic range. PMID:29084263

Single-cell printer: automated, on demand, and label free.

PubMed

Gross, Andre; Schöndube, Jonas; Niekrawitz, Sonja; Streule, Wolfgang; Riegger, Lutz; Zengerle, Roland; Koltay, Peter

2013-12-01

Within the past years, single-cell analysis has developed into a key topic in cell biology to study cellular functions that are not accessible by investigation of larger cell populations. Engineering approaches aiming to access single cells to extract information about their physiology, phenotype, and genotype at the single-cell level are going manifold ways, meanwhile allowing separation, sorting, culturing, and analysis of individual cells. Based on our earlier research toward inkjet-like printing of single cells, this article presents further characterization results obtained with a fully automated prototype instrument for printing of single living cells in a noncontact inkjet-like manner. The presented technology is based on a transparent microfluidic drop-on-demand dispenser chip coupled with a camera-assisted automatic detection system. Cells inside the chip are detected and classified with this detection system before they are expelled from the nozzle confined in microdroplets, thus enabling a "one cell per droplet" printing mode. To demonstrate the prototype instrument's suitability for biological and biomedical applications, basic experiments such as printing of single-bead and cell arrays as well as deposition and culture of single cells in microwell plates are presented. Printing efficiencies greater than 80% and viability rates about 90% were achieved.

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.

PubMed

Vallejos, Catalina A; Marioni, John C; Richardson, Sylvia

2015-06-01

Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of unexplained technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model where: (i) cell-specific normalisation constants are estimated as part of the model parameters, (ii) technical variability is quantified based on spike-in genes that are artificially introduced to each analysed cell's lysate and (iii) the total variability of the expression counts is decomposed into technical and biological components. BASiCS also provides an intuitive detection criterion for highly (or lowly) variable genes within the population of cells under study. This is formalised by means of tail posterior probabilities associated to high (or low) biological cell-to-cell variance contributions, quantities that can be easily interpreted by users. We demonstrate our method using gene expression measurements from mouse Embryonic Stem Cells. Cross-validation and meaningful enrichment of gene ontology categories within genes classified as highly (or lowly) variable supports the efficacy of our approach.

openBEB: open biological experiment browser for correlative measurements

PubMed Central

2014-01-01

Background New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis. Results We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS. OpenBEB consists of two main parts: A core program and a plug-in manager. Whereas the data-type independent core of openBEB maintains a local container of raw-data and metadata and provides annotation and data management tools, all data-specific tasks are performed by plug-ins. The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization. A macro-interpreter allows the automation and coordination of the different modules. An update and deployment mechanism keeps the core program, the plug-ins and the metadata definition files in sync with a central repository. Conclusions The versatility, the simple deployment and update mechanism, and the scalability in terms of module integration offered by openBEB make this software interesting for a large scientific community. OpenBEB targets three types of researcher, ideally working closely together: (i) Engineers and scientists developing new methods and instruments, e.g., for systems-biology, (ii) scientists performing biological experiments, (iii) theoreticians and mathematicians analyzing data. The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the “house keeping” abilities of the core program. We report the use of openBEB to combine live cell microscopy, microfluidic control and visual proteomics. In this example, measurements from diverse complementary techniques are combined and correlated. PMID:24666611

Preferential binding of positive nanoparticles on cell membranes is due to electrostatic interactions: A too simplistic explanation that does not take into account the nanoparticle protein corona.

PubMed

Forest, Valérie; Pourchez, Jérémie

2017-01-01

The internalization of nanoparticles by cells (and more broadly the nanoparticle/cell interaction) is a crucial issue both for biomedical applications (for the design of nanocarriers with enhanced cellular uptake to reach their intracellular therapeutic targets) and in a nanosafety context (as the internalized dose is one of the key factors in cytotoxicity). Many parameters can influence the nanoparticle/cell interaction, among them, the nanoparticle physico-chemical features, and especially the surface charge. It is generally admitted that positive nanoparticles are more uptaken by cells than neutral or negative nanoparticles. It is supposedly due to favorable electrostatic interactions with negatively charged cell membrane. However, this theory seems too simplistic as it does not consider a fundamental element: the nanoparticle protein corona. Indeed, once introduced in a biological medium nanoparticles adsorb proteins at their surface, forming a new interface defining the nanoparticle "biological identity". This adds a new level of complexity in the interactions with biological systems that cannot be any more limited to electrostatic binding. These interactions will then influence cell behavior. Based on a literature review and on an example of our own experience the parameters involved in the nanoparticle protein corona formation as well as in the nanoparticle/cell interactions are discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Analysis of results of ASTP experiment in electrophoresis

NASA Technical Reports Server (NTRS)

Vanderhoff, J. W.; Micale, F. J.; Krumrine, P. H.

1977-01-01

The Apollo-Soyuz Test Project (ASTP) included an electrophoretic separation experiment of biological cells. The nature separation results of aldehyde-fixed rabbit, human and horse red blood cells, which were taken in the form of photographs taken at three-minute intervals, are the subject of this report. The electrophoretic separation was successful in that fractionation according to mobility did occur and was found in the sliced samples. Photographic evidence indicates that the low electroosmotic methylcellulose coating was successful in reducing the electroosmosis to a near zero value. Also, the flight film shows that the bands migrated down the column as theory would predict, producing two bands of high cell concentration separated and surrounded by regions of lower cell concentration. However, most likely some clumping of cells occurred to cause the trailing band to be larger than expected from theory. Overall, the experiment was a success in demonstrating a static electrophoresis separation under microgravity conditions with a resolution not possible on earth.

Influence of cell printing on biological characters of chondrocytes

PubMed Central

Qu, Miao; Gao, Xiaoyan; Hou, Yikang; Shen, Congcong; Xu, Yourong; Zhu, Ming; Wang, Hengjian; Xu, Haisong; Chai, Gang; Zhang, Yan

2015-01-01

Objective: To establish a two-dimensional biological printing technique of chondrocytes and compare the difference of related biological characters between printed chondrocytes and unprinted cells so as to control the cell transfer process and keep cell viability after printing. Methods: Primary chondrocytes were obtained from human mature and fetal cartilage tissues and then were regularly sub-cultured to harvest cells at passage 2 (P2), which were adjusted to the single cell suspension at a density of 1×106/mL. The experiment was divided into 2 groups: experimental group P2 chondrocytes were transferred by rapid prototype biological printer (driving voltage value 50 V, interval in x-axis 300 μm, interval in y-axis 1500 μm). Afterwards Live/Dead viability Kit and flow cytometry were respectively adopted to detect cell viability; CCK-8 Kit was adopted to detect cell proliferation viability; immunocytochemistry, immunofluorescence and RT-PCR was employed to identify related markers of chondrocytes; control group steps were the same as the printing group except that cell suspension received no printing. Results: Fluorescence microscopy and flow cytometry analyses showed that there was no significant difference between experimental group and control group in terms of cell viability. After 7-day in vitro culture, control group exhibited higher O.D values than experimental group from 2nd day to 7th day but there was no distinct difference between these two groups (P>0.05). Inverted microscope observation demonstrated that the morphology of these two groups had no significant difference either. Similarly, Immunocytochemistry, immunofluorescence and RT-PCR assays also showed that there was no significant difference in the protein and gene expression of type II collagen and aggrecan between these two groups (P>0.05). Conclusion Cell printing has no distinctly negative effect on cell vitality, proliferation and phenotype of chondrocytes. Biological printing technique may provide a novel approach for realizing the oriented, quantificational and regular distribution of chondrocytes in a two-dimensional plane and lay the foundation for the construction of three-dimensional cell printing or even organ printing system. PMID:26770337

Genetically encoded fluorescent tags

PubMed Central

Thorn, Kurt

2017-01-01

Genetically encoded fluorescent tags are protein sequences that can be fused to a protein of interest to render it fluorescent. These tags have revolutionized cell biology by allowing nearly any protein to be imaged by light microscopy at submicrometer spatial resolution and subsecond time resolution in a live cell or organism. They can also be used to measure protein abundance in thousands to millions of cells using flow cytometry. Here I provide an introduction to the different genetic tags available, including both intrinsically fluorescent proteins and proteins that derive their fluorescence from binding of either endogenous or exogenous fluorophores. I discuss their optical and biological properties and guidelines for choosing appropriate tags for an experiment. Tools for tagging nucleic acid sequences and reporter molecules that detect the presence of different biomolecules are also briefly discussed. PMID:28360214

Quantitative analyses for elucidating mechanisms of cell fate commitment in the mouse blastocyst

NASA Astrophysics Data System (ADS)

Saiz, Néstor; Kang, Minjung; Puliafito, Alberto; Schrode, Nadine; Xenopoulos, Panagiotis; Lou, Xinghua; Di Talia, Stefano; Hadjantonakis, Anna-Katerina

2015-03-01

In recent years we have witnessed a shift from qualitative image analysis towards higher resolution, quantitative analyses of imaging data in developmental biology. This shift has been fueled by technological advances in both imaging and analysis software. We have recently developed a tool for accurate, semi-automated nuclear segmentation of imaging data from early mouse embryos and embryonic stem cells. We have applied this software to the study of the first lineage decisions that take place during mouse development and established analysis pipelines for both static and time-lapse imaging experiments. In this paper we summarize the conclusions from these studies to illustrate how quantitative, single-cell level analysis of imaging data can unveil biological processes that cannot be revealed by traditional qualitative studies.

Imaging modes of atomic force microscopy for application in molecular and cell biology.

PubMed

Dufrêne, Yves F; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J

2017-04-06

Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

Design and Analysis of Single-Cell Sequencing Experiments.

PubMed

Grün, Dominic; van Oudenaarden, Alexander

2015-11-05

Recent advances in single-cell sequencing hold great potential for exploring biological systems with unprecedented resolution. Sequencing the genome of individual cells can reveal somatic mutations and allows the investigation of clonal dynamics. Single-cell transcriptome sequencing can elucidate the cell type composition of a sample. However, single-cell sequencing comes with major technical challenges and yields complex data output. In this Primer, we provide an overview of available methods and discuss experimental design and single-cell data analysis. We hope that these guidelines will enable a growing number of researchers to leverage the power of single-cell sequencing. Copyright © 2015 Elsevier Inc. All rights reserved.

Exosome secretion promotes chemotaxis of cancer cells.

PubMed

Sung, Bong Hwan; Weaver, Alissa M

2017-03-04

Migration of cells toward chemical cues, or chemotaxis, is important for many biologic processes such as immune defense, wound healing and cancer metastasis. Although chemotaxis is thought to occur in cancer cells, it is less well characterized than chemotaxis of professional immune cells such as neutrophils. Here, we show that cancer cell chemotaxis relies on secretion of exosome-type extracellular vesicles. Migration of fibrosarcoma cells toward a gradient of exosome-depleted serum was diminished by knockdown of the exosome secretion regulator Rab27a. Rescue experiments in which chemotaxis chambers were coated with purified extracellular vesicles demonstrate that exosomes but not microvesicles affect both speed and directionality of migrating cells. Chamber coating with purified fibronectin and fibronectin-depleted exosomes demonstrates that the exosome cargo fibronectin promotes cell speed but cannot account for the role of exosomes in promoting directionality of fibrosarcoma cell movement during chemotaxis. These experiments indicate that exosomes contain multiple motility-promoting cargoes that contribute to different aspects of cell motility.

Simultaneous extraction of proteins and metabolites from cells in culture

PubMed Central

Sapcariu, Sean C.; Kanashova, Tamara; Weindl, Daniel; Ghelfi, Jenny; Dittmar, Gunnar; Hiller, Karsten

2014-01-01

Proper sample preparation is an integral part of all omics approaches, and can drastically impact the results of a wide number of analyses. As metabolomics and proteomics research approaches often yield complementary information, it is desirable to have a sample preparation procedure which can yield information for both types of analyses from the same cell population. This protocol explains a method for the separation and isolation of metabolites and proteins from the same biological sample, in order for downstream use in metabolomics and proteomics analyses simultaneously. In this way, two different levels of biological regulation can be studied in a single sample, minimizing the variance that would result from multiple experiments. This protocol can be used with both adherent and suspension cell cultures, and the extraction of metabolites from cellular medium is also detailed, so that cellular uptake and secretion of metabolites can be quantified. Advantages of this technique includes:1.Inexpensive and quick to perform; this method does not require any kits.2.Can be used on any cells in culture, including cell lines and primary cells extracted from living organisms.3.A wide variety of different analysis techniques can be used, adding additional value to metabolomics data analyzed from a sample; this is of high value in experimental systems biology. PMID:26150938

Ultrathin Ceramic Membranes as Scaffolds for Functional Cell Coculture Models on a Biomimetic Scale

PubMed Central

Jud, Corinne; Ahmed, Sher; Müller, Loretta; Kinnear, Calum; Vanhecke, Dimitri; Umehara, Yuki; Frey, Sabine; Liley, Martha; Angeloni, Silvia; Petri-Fink, Alke; Rothen-Rutishauser, Barbara

2015-01-01

Abstract Epithelial tissue serves as an interface between biological compartments. Many in vitro epithelial cell models have been developed as an alternative to animal experiments to answer a range of research questions. These in vitro models are grown on permeable two-chamber systems; however, commercially available, polymer-based cell culture inserts are around 10 μm thick. Since the basement membrane found in biological systems is usually less than 1 μm thick, the 10-fold thickness of cell culture inserts is a major limitation in the establishment of realistic models. In this work, an alternative insert, accommodating an ultrathin ceramic membrane with a thickness of only 500 nm (i.e., the Silicon nitride Microporous Permeable Insert [SIMPLI]-well), was produced and used to refine an established human alveolar barrier coculture model by both replacing the conventional inserts with the SIMPLI-well and completing it with endothelial cells. The structural–functional relationship of the model was evaluated, including the translocation of gold nanoparticles across the barrier, revealing a higher translocation if compared to corresponding polyethylene terephthalate (PET) membranes. This study demonstrates the power of the SIMPLI-well system as a scaffold for epithelial tissue cell models on a truly biomimetic scale, allowing construction of more functionally accurate models of human biological barriers. PMID:26713225

Digital biology and chemistry.

PubMed

Witters, Daan; Sun, Bing; Begolo, Stefano; Rodriguez-Manzano, Jesus; Robles, Whitney; Ismagilov, Rustem F

2014-09-07

This account examines developments in "digital" biology and chemistry within the context of microfluidics, from a personal perspective. Using microfluidics as a frame of reference, we identify two areas of research within digital biology and chemistry that are of special interest: (i) the study of systems that switch between discrete states in response to changes in chemical concentration of signals, and (ii) the study of single biological entities such as molecules or cells. In particular, microfluidics accelerates analysis of switching systems (i.e., those that exhibit a sharp change in output over a narrow range of input) by enabling monitoring of multiple reactions in parallel over a range of concentrations of signals. Conversely, such switching systems can be used to create new kinds of microfluidic detection systems that provide "analog-to-digital" signal conversion and logic. Microfluidic compartmentalization technologies for studying and isolating single entities can be used to reconstruct and understand cellular processes, study interactions between single biological entities, and examine the intrinsic heterogeneity of populations of molecules, cells, or organisms. Furthermore, compartmentalization of single cells or molecules in "digital" microfluidic experiments can induce switching in a range of reaction systems to enable sensitive detection of cells or biomolecules, such as with digital ELISA or digital PCR. This "digitizing" offers advantages in terms of robustness, assay design, and simplicity because quantitative information can be obtained with qualitative measurements. While digital formats have been shown to improve the robustness of existing chemistries, we anticipate that in the future they will enable new chemistries to be used for quantitative measurements, and that digital biology and chemistry will continue to provide further opportunities for measuring biomolecules, understanding natural systems more deeply, and advancing molecular and cellular analysis. Microfluidics will impact digital biology and chemistry and will also benefit from them if it becomes massively distributed.

Electrophoresis experiments in microgravity

NASA Technical Reports Server (NTRS)

Snyder, Robert S.; Rhodes, Percy H.

1991-01-01

The use of the microgravity environment to separate and purify biological cells and proteins has been a major activity since the beginning of the NASA Microgravity Science and Applications program. Purified populations of cells are needed for research, transplantation and analysis of specific cell constituents. Protein purification is a necessary step in research areas such as genetic engineering where the new protein has to be separated from the variety of other proteins synthesized from the microorganism. Sufficient data are available from the results of past electrophoresis experiments in space to show that these experiments were designed with incomplete knowledge of the fluid dynamics of the process including electrohydrodynamics. However, electrophoresis is still an important separation tool in the laboratory and thermal convection does limit its performance. Thus, there is a justification for electrophoresis but the emphasis of future space experiments must be directed toward basic research with model experiments to understand the microgravity environment and fluid analysis to test the basic principles of the process.

Identification of common coexpression modules based on quantitative network comparison.

PubMed

Jo, Yousang; Kim, Sanghyeon; Lee, Doheon

2018-06-13

Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression network or modules may reveal the molecular mechanism of complex disease or the relationship between biological processes. However, there has been no quantitative network comparison method for coexpression networks and we examined previous methods for other networks that cannot be applied to coexpression network. Therefore, we aimed to propose quantitative comparison methods for coexpression networks and to find common biological mechanisms between Huntington's disease and brain aging by the new method. We proposed two similarity measures for quantitative comparison of coexpression networks. Then, we performed experiments using known coexpression networks. We showed the validity of two measures and evaluated threshold values for similar coexpression network pairs from experiments. Using these similarity measures and thresholds, we quantitatively measured the similarity between disease-specific and aging-related coexpression modules and found similar Huntington's disease-aging coexpression module pairs. We identified similar Huntington's disease-aging coexpression module pairs and found that these modules are related to brain development, cell death, and immune response. It suggests that up-regulated cell signalling related cell death and immune/ inflammation response may be the common molecular mechanisms in the pathophysiology of HD and normal brain aging in the frontal cortex.

Inference is bliss: using evolutionary relationship to guide categorical inferences.

PubMed

Novick, Laura R; Catley, Kefyn M; Funk, Daniel J

2011-01-01

Three experiments, adopting an evolutionary biology perspective, investigated subjects' inferences about living things. Subjects were told that different enzymes help regulate cell function in two taxa and asked which enzyme a third taxon most likely uses. Experiment 1 and its follow-up, with college students, used triads involving amphibians, reptiles, and mammals (reptiles and mammals are most closely related evolutionarily) and plants, fungi, and animals (fungi are more closely related to animals than to plants). Experiment 2, with 10th graders, also included triads involving mammals, birds, and snakes/crocodilians (birds and snakes/crocodilians are most closely related). Some subjects received cladograms (hierarchical diagrams) depicting the evolutionary relationships among the taxa. The effect of providing cladograms depended on students' background in biology. The results illuminate students' misconceptions concerning common taxa and constraints on their willingness to override faulty knowledge when given appropriate evolutionary evidence. Implications for introducing tree thinking into biology curricula are discussed. Copyright © 2011 Cognitive Science Society, Inc.

A beginner's guide to atomic force microscopy probing for cell mechanics

PubMed Central

2016-01-01

Abstract Atomic Force microscopy (AFM) is becoming a prevalent tool in cell biology and biomedical studies, especially those focusing on the mechanical properties of cells and tissues. The newest generation of bio‐AFMs combine ease of use and seamless integration with live‐cell epifluorescence or more advanced optical microscopies. As a unique feature with respect to other bionanotools, AFM provides nanometer‐resolution maps for cell topography, stiffness, viscoelasticity, and adhesion, often overlaid with matching optical images of the probed cells. This review is intended for those about to embark in the use of bio‐AFMs, and aims to assist them in designing an experiment to measure the mechanical properties of adherent cells. In addition to describing the main steps in a typical cell mechanics protocol and explaining how data is analysed, this review will also discuss some of the relevant contact mechanics models available and how they have been used to characterize specific features of cellular and biological samples. Microsc. Res. Tech. 80:75–84, 2017. © 2016 Wiley Periodicals, Inc. PMID:27676584

Imaging of human differentiated 3D neural aggregates using light sheet fluorescence microscopy.

PubMed

Gualda, Emilio J; Simão, Daniel; Pinto, Catarina; Alves, Paula M; Brito, Catarina

2014-01-01

The development of three dimensional (3D) cell cultures represents a big step for the better understanding of cell behavior and disease in a more natural like environment, providing not only single but multiple cell type interactions in a complex 3D matrix, highly resembling physiological conditions. Light sheet fluorescence microscopy (LSFM) is becoming an excellent tool for fast imaging of such 3D biological structures. We demonstrate the potential of this technique for the imaging of human differentiated 3D neural aggregates in fixed and live samples, namely calcium imaging and cell death processes, showing the power of imaging modality compared with traditional microscopy. The combination of light sheet microscopy and 3D neural cultures will open the door to more challenging experiments involving drug testing at large scale as well as a better understanding of relevant biological processes in a more realistic environment.

Innovative molecular-based fluorescent nanoparticles for multicolor single particle tracking in cells

NASA Astrophysics Data System (ADS)

Daniel, Jonathan; Godin, Antoine G.; Palayret, Matthieu; Lounis, Brahim; Cognet, Laurent; Blanchard-Desce, Mireille

2016-03-01

Based on an original molecular-based design, we present bright and photostable fluorescent organic nanoparticles (FONs) showing excellent colloidal stability in various aqueous environments. Complementary near-infrared emitting and green emitting FONs were prepared using a simple, fast and robust protocol. Both types of FONs could be simultaneously imaged at the single-particle level in solution as well as in biological environments using a monochromatic excitation and a dual-color fluorescence microscope. No evidence of acute cytotoxicity was found upon incubation of live cells with mixed solutions of FONs, and both types of nanoparticles were found internalized in the cells where their motion could be simultaneously tracked at video-rate up to minutes. These fluorescent organic nanoparticles open a novel non-toxic alternative to existing nanoparticles for imaging biological structures, compatible with live-cell experiments and specially fitted for multicolor single particle tracking.

Imaging of human differentiated 3D neural aggregates using light sheet fluorescence microscopy

PubMed Central

Gualda, Emilio J.; Simão, Daniel; Pinto, Catarina; Alves, Paula M.; Brito, Catarina

2014-01-01

The development of three dimensional (3D) cell cultures represents a big step for the better understanding of cell behavior and disease in a more natural like environment, providing not only single but multiple cell type interactions in a complex 3D matrix, highly resembling physiological conditions. Light sheet fluorescence microscopy (LSFM) is becoming an excellent tool for fast imaging of such 3D biological structures. We demonstrate the potential of this technique for the imaging of human differentiated 3D neural aggregates in fixed and live samples, namely calcium imaging and cell death processes, showing the power of imaging modality compared with traditional microscopy. The combination of light sheet microscopy and 3D neural cultures will open the door to more challenging experiments involving drug testing at large scale as well as a better understanding of relevant biological processes in a more realistic environment. PMID:25161607

BIOLAB

NASA Image and Video Library

2013-08-27

ISS036-E-037859 (27 Aug. 2013) --- European Space Agency astronaut Luca Parmitano, Expedition 36 flight engineer, works with the Biolab in the Columbus laboratory of the International Space Station. Biolab is used to perform space biology experiments on microorganisms, cells, tissue cultures, plants and small invertebrates.

Preparation and operation of space-based experiment on plant growth in KIBO, named Space Seed

NASA Astrophysics Data System (ADS)

Yano, Sachiko; Tanigaki, Fumiaki; Shimazu, Toru; Kasahara, Haruo; Nakamura, Tai; Karahara, Ichirou; Hoson, Takayuki; Kamisaka, Seiichiro

The Japan Aerospace Exploration Agency (JAXA) recently carried out plant growth experiment using the Plant Experiment Unit (PEU) installed in the Cell Biology Experiment Facility (CBEF) onboard KIBO. This experiment named Space Seed was designed to investigate the effect of microgravity on plant growth, especially seed to seed life cycle. Space shuttle STS-128 (17A) carrying eight PEU's was launched to the International Space Station (ISS) on August 28, 2009. The experiment was started on September 10 and terminated on November 11, 2009. The control system of environment in PEU and CBEF worked successfully as planned. In KIBO, Arabidopsis seeds germinated, and bolting and flowering were observed in the PEU's. In the end of March, 2010, Arabidopsis plants harvested in Kibo will be recovered to Earth by the space shuttle mission STS-131(19A) and analyzed for their biological characteristics such as seed fertility, cell wall properties, and gene expression. In this presentation, we describe the outline of the Space Seed experiment. We also describe experimental data such as the control of temperature and humidity in PEUs and CBEF, the onboard operations by the ISS crew, the procedure by which the experiment was monitored from the ground, and brief information about seed germination and subsequent growth under microgravity condition in space. We also succeeded in comparing the results of plant growth in PEUs on onboard 1-G control (Centrifuge) with results in microgravity condition and in ground control.

Stem cell education for medical students at Tongji University: Primary cell culture and directional differentiation of rat bone marrow mesenchymal stem cells.

PubMed

Jin, Caixia; Tian, Haibin; Li, Jiao; Jia, Song; Li, Siguang; Xu, Guo-Tong; Xu, Lei; Lu, Lixia

2018-03-01

Stem cells are cells that can self-renew and differentiate into a variety of cell types under certain conditions. Stem cells have great potential in regenerative medicine and cell therapy for the treatment of certain diseases. To deliver knowledge about this frontier in science and technology to medical undergraduate students, we designed an innovative practical experiment for freshmen in their second semester. The lab exercise focused on rat bone marrow mesenchymal stem cell (BMSC) isolation, cell culture and differentiation, and it aimed to help students master the aseptic techniques for cell culture, the basic methods and procedures for the primary culture and passage of BMSCs, the basic procedure for the directional differentiation of BMSCs into adipocytes and their subsequent identification by oil-red-O staining. This lab exercise is a very meaningful and useful introduction to stem cell collection and manipulation and inspires medical students to deepen their understanding of translational medicine and regenerative medicine. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(2):151-154, 2018. © 2017 The International Union of Biochemistry and Molecular Biology.

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

PubMed Central

Vallejos, Catalina A.; Marioni, John C.; Richardson, Sylvia

2015-01-01

Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of unexplained technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model where: (i) cell-specific normalisation constants are estimated as part of the model parameters, (ii) technical variability is quantified based on spike-in genes that are artificially introduced to each analysed cell’s lysate and (iii) the total variability of the expression counts is decomposed into technical and biological components. BASiCS also provides an intuitive detection criterion for highly (or lowly) variable genes within the population of cells under study. This is formalised by means of tail posterior probabilities associated to high (or low) biological cell-to-cell variance contributions, quantities that can be easily interpreted by users. We demonstrate our method using gene expression measurements from mouse Embryonic Stem Cells. Cross-validation and meaningful enrichment of gene ontology categories within genes classified as highly (or lowly) variable supports the efficacy of our approach. PMID:26107944

Modeling mammary organogenesis from biological first principles: Cells and their physical constraints.

PubMed

Montévil, Maël; Speroni, Lucia; Sonnenschein, Carlos; Soto, Ana M

2016-10-01

In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing non-identical cells, which organize in tri-dimensional patterns. These association patterns and cells types change as tissues and organs are formed. This contextuality and circularity makes it difficult to establish detailed cause and effect relationships. Here we propose an approach to overcome these intrinsic difficulties by combining the use of two models; 1) an experimental one that employs 3D culture technology to obtain the structures of the mammary gland, namely, ducts and acini, and 2) a mathematical model based on biological principles. The typical approach for mathematical modeling in biology is to apply mathematical tools and concepts developed originally in physics or computer sciences. Instead, we propose to construct a mathematical model based on proper biological principles. Specifically, we use principles identified as fundamental for the elaboration of a theory of organisms, namely i) the default state of cell proliferation with variation and motility and ii) the principle of organization by closure of constraints. This model has a biological component, the cells, and a physical component, a matrix which contains collagen fibers. Cells display agency and move and proliferate unless constrained; they exert mechanical forces that i) act on collagen fibers and ii) on other cells. As fibers organize, they constrain the cells on their ability to move and to proliferate. The model exhibits a circularity that can be interpreted in terms of closure of constraints. Implementing the mathematical model shows that constraints to the default state are sufficient to explain ductal and acinar formation, and points to a target of future research, namely, to inhibitors of cell proliferation and motility generated by the epithelial cells. The success of this model suggests a step-wise approach whereby additional constraints imposed by the tissue and the organism could be examined in silico and rigorously tested by in vitro and in vivo experiments, in accordance with the organicist perspective we embrace. Copyright © 2016. Published by Elsevier Ltd.

Modeling mammary organogenesis from biological first principles: Cells and their physical constraints

PubMed Central

Montévil, Maël; Speroni, Lucia; Sonnenschein, Carlos; Soto, Ana M.

2017-01-01

In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing non-identical cells, which organize in tri-dimensional patterns. These association patterns and cells types change as tissues and organs are formed. This contextuality and circularity makes it difficult to establish detailed cause and effect relationships. Here we propose an approach to overcome these intrinsic difficulties by combining the use of two models; 1) an experimental one that employs 3D culture technology to obtain the structures of the mammary gland, namely, ducts and acini, and 2) a mathematical model based on biological principles. The typical approach for mathematical modeling in biology is to apply mathematical tools and concepts developed originally in physics or computer sciences. Instead, we propose to construct a mathematical model based on proper biological principles. Specifically, we use principles identified as fundamental for the elaboration of a theory of organisms, namely i) the default state of cell proliferation with variation and motility and ii) the principle of organization by closure of constraints. This model has a biological component, the cells, and a physical component, a matrix which contains collagen fibers. Cells display agency and move and proliferate unless constrained; they exert mechanical forces that i) act on collagen fibers and ii) on other cells. As fibers organize, they constrain the cells on their ability to move and to proliferate. The model exhibits a circularity that can be interpreted in terms of closure of constraints. Implementing the mathematical model shows that constraints to the default state are sufficient to explain ductal and acinar formation, and points to a target of future research, namely, to inhibitors of cell proliferation and motility generated by the epithelial cells. The success of this model suggests a step-wise approach whereby additional constraints imposed by the tissue and the organism could be examined in silico and rigorously tested by in vitro and in vivo experiments, in accordance with the organicist perspective we embrace. PMID:27544910

Bacterial cell-free expression technology to in vitro systems engineering and optimization.

PubMed

Caschera, Filippo

2017-06-01

Cell-free expression system is a technology for the synthesis of proteins in vitro . The system is a platform for several bioengineering projects, e.g. cell-free metabolic engineering, evolutionary design of experiments, and synthetic minimal cell construction. Bacterial cell-free protein synthesis system (CFPS) is a robust tool for synthetic biology. The bacteria lysate, the DNA, and the energy module, which are the three optimized sub-systems for in vitro protein synthesis, compose the integrated system. Currently, an optimized E. coli cell-free expression system can produce up to ∼2.3 mg/mL of a fluorescent reporter protein. Herein, I will describe the features of ATP-regeneration systems for in vitro protein synthesis, and I will present a machine-learning experiment for optimizing the protein yield of E. coli cell-free protein synthesis systems. Moreover, I will introduce experiments on the synthesis of a minimal cell using liposomes as dynamic containers, and E. coli cell-free expression system as biochemical platform for metabolism and gene expression. CFPS can be further integrated with other technologies for novel applications in environmental, medical and material science.

Integrated multiscale biomaterials experiment and modelling: a perspective

PubMed Central

Buehler, Markus J.; Genin, Guy M.

2016-01-01

Advances in multiscale models and computational power have enabled a broad toolset to predict how molecules, cells, tissues and organs behave and develop. A key theme in biological systems is the emergence of macroscale behaviour from collective behaviours across a range of length and timescales, and a key element of these models is therefore hierarchical simulation. However, this predictive capacity has far outstripped our ability to validate predictions experimentally, particularly when multiple hierarchical levels are involved. The state of the art represents careful integration of multiscale experiment and modelling, and yields not only validation, but also insights into deformation and relaxation mechanisms across scales. We present here a sampling of key results that highlight both challenges and opportunities for integrated multiscale experiment and modelling in biological systems. PMID:28981126

U.S. biological experiments in space

NASA Technical Reports Server (NTRS)

Klein, H. P.

1981-01-01

The history of biologic experimentation in space is traced. Early balloon and rocket borne animals showed no abnormalities on the macroscale, and biosatellite launches with bacteria and amoebae revealed no microscopic dysfunctions. Adult Drosophila flies on board Cosmos spacecraft died with a shortened lifespan, while their offspring lived full lifespans. Green pepper plants grown in weightlessness showed a different orientation, but no physiological disturbances. Normal bone growth in rats has been found to almost cease after 11 days in space, and the mean life span of red blood cells decreases by four days. A series of experiments designed by U.S. scientists will be performed on primates provided and flown by the U.S.S.R. Finally, experiments on board Spacelab will involve determination of the persistence of circadian rhythms in bacteria and humans.

Biological effects of combined resveratrol and vitamin D3 on ovarian tissue.

PubMed

Uberti, Francesca; Morsanuto, Vera; Aprile, Silvio; Ghirlanda, Sabrina; Stoppa, Ian; Cochis, Andrea; Grosa, Giorgio; Rimondini, Lia; Molinari, Claudio

2017-09-15

Resveratrol (3,5,4'-trihydroxy-trans-stilbene) is a natural antioxidant polyphenol able to exert a wide range of biological effect on several tissues. Despite its important beneficial properties, it has a low water solubility, which limits its therapeutic applications in humans. Resveratrol also acts as a phytoestrogen that modulates estrogen receptor (ER)-mediated transcription. In addition, it has been shown that ovarian tissues benefit greatly from vitamin D3, which exerts its beneficial effects through VDR receptors. The aim was to evaluate the cooperative effects of resveratrol combined with vitamin D3 on ovarian cells and tissues and some other organs as well. Moreover, the modulation of specific intracellular pathways involving ER and VDR receptors has been studied. The experiments were performed both in vitro and in vivo, to analyze cell viability, radical oxygen species production, signal transductions through Western Blot, and resveratrol quantification by HPLC. Cell viability, radical oxygen species production, and intracellular pathways have been studied on CHO-K1 cells. Also, the relative mechanism activated following oral intake in female Wistar rats as animal model was investigated, evaluating bioavailability, biodistribution and signal transduction in heart, kidney, liver and ovarian tissues. Both in in vitro and in vivo experiments, resveratrol exerts more evident effects when administered in combination with vitD in ovarian cells, showing a common biphasic cooperative effect: The role of vitamin D3 in maintaining and supporting the biological activity of resveratrol has been clearly observed. Moreover, resveratrol plus vitamin D3 blood concentrations showed a biphasic absorption rate. Such results could be used as a fundamental data for the development of new therapies for gynecological conditions, such as hot-flashes.

FUSION-Guided Hypothesis Development Leads to the Identification of N6,N6-Dimethyladenosine, a Marine-Derived AKT Pathway Inhibitor

PubMed Central

Vaden, Rachel M.; Oswald, Nathaniel W.; Potts, Malia B.; MacMillan, John B.; White, Michael A.

2017-01-01

Chemicals found in nature have evolved over geological time scales to productively interact with biological molecules, and thus represent an effective resource for pharmaceutical development. Marine-derived bacteria are rich sources of chemically diverse, bioactive secondary metabolites, but harnessing this diversity for biomedical benefit is limited by challenges associated with natural product purification and determination of biochemical mechanism. Using Functional Signature Ontology (FUSION), we report the parallel isolation and characterization of a marine-derived natural product, N6,N6-dimethyladenosine, that robustly inhibits AKT signaling in a variety of non-small cell lung cancer cell lines. Upon validation of the elucidated structure by comparison with a commercially available sample, experiments were initiated to understand the small molecule’s breadth of effect in a biological setting. One such experiment, a reverse phase protein array (RPPA) analysis of >50 kinases, indicated a specific cellular response to treatment. In all, leveraging the FUSION platform allowed for the rapid generation and validation of a biological mechanism of action hypothesis for an unknown natural product and permitted accelerated purification of the bioactive component from a chemically complex fraction. PMID:28294973

Spacelab

NASA Image and Video Library

1992-09-12

The group of Japanese researchers of the Spacelab-J (SL-J) were thumbs-up in the Payload Operations Control Center (POCC) at the Marshall Space Flight Center after the successful launch of Space Shuttle Orbiter Endeavour that carried their experiments. The SL-J was a joint mission of NASA and the National Space Development Agency of Japan (NASDA) utilizing a marned Spacelab module. The mission conducted microgravity investigations in materials and life sciences. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, frogs, and frog eggs. The POCC was the air/ground communications channel between the astronauts and ground control teams during the Spacelab missions. The Spacelab science operations were a cooperative effort between the science astronaut crew in orbit and their colleagues in the POCC. Spacelab-J was launched aboard the Space Shuttle Orbiter Endeavour on September 12, 1992.

Aligning Goals, Assessments, and Activities: An Approach to Teaching PCR and Gel Electrophoresis

PubMed Central

Robertson, Amber L.; Batzli, Janet; Harris, Michelle; Miller, Sarah

2008-01-01

Polymerase chain reaction (PCR) and gel electrophoresis have become common techniques used in undergraduate molecular and cell biology labs. Although students enjoy learning these techniques, they often cannot fully comprehend and analyze the outcomes of their experiments because of a disconnect between concepts taught in lecture and experiments done in lab. Here we report the development and implementation of novel exercises that integrate the biological concepts of DNA structure and replication with the techniques of PCR and gel electrophoresis. Learning goals were defined based on concepts taught throughout the cell biology lab course and learning objectives specific to the PCR and gel electrophoresis lab. Exercises developed to promote critical thinking and target the underlying concepts of PCR, primer design, gel analysis, and troubleshooting were incorporated into an existing lab unit based on the detection of genetically modified organisms. Evaluative assessments for each exercise were aligned with the learning goals and used to measure student learning achievements. Our analysis found that the exercises were effective in enhancing student understanding of these concepts as shown by student performance across all learning goals. The new materials were particularly helpful in acquiring relevant knowledge, fostering critical-thinking skills, and uncovering prevalent misconceptions. PMID:18316813

Activities During Spacelab-J Mission at Payload Operations and Control Center

NASA Technical Reports Server (NTRS)

1992-01-01

The group of Japanese researchers of the Spacelab-J (SL-J) were thumbs-up in the Payload Operations Control Center (POCC) at the Marshall Space Flight Center after the successful launch of Space Shuttle Orbiter Endeavour that carried their experiments. The SL-J was a joint mission of NASA and the National Space Development Agency of Japan (NASDA) utilizing a marned Spacelab module. The mission conducted microgravity investigations in materials and life sciences. Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glasses and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi and plant seeds, frogs, and frog eggs. The POCC was the air/ground communications channel between the astronauts and ground control teams during the Spacelab missions. The Spacelab science operations were a cooperative effort between the science astronaut crew in orbit and their colleagues in the POCC. Spacelab-J was launched aboard the Space Shuttle Orbiter Endeavour on September 12, 1992.

Micro-chromatin Immunoprecipation (μChIP) Protocol for Real-time PCR Analysis of a Limited Amount of Cells.

PubMed

Gillotin, Sébastien; Guillemot, François

2016-06-20

Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is an important strategy to study gene regulation. When availability of cells is limited, however, it can be useful to focus on specific genes to investigate in depth the role of transcription factors or histone marks. Unfortunately, performing ChIP experiments to study transcription factors' binding to DNA can be difficult when biological material is restricted. This protocol describes a robust method to perform μChIP for over-expressed or endogenous transcription factors using ~100,000 cells per ChIP experiment (Masserdotti et al ., 2015). We also describe optimization steps, which we think are critical for this protocol to work and which can be used to further reduce the number of cells.

Micromechanics of human mitotic chromosomes

NASA Astrophysics Data System (ADS)

Sun, Mingxuan; Kawamura, Ryo; Marko, John F.

2011-02-01

Eukaryote cells dramatically reorganize their long chromosomal DNAs to facilitate their physical segregation during mitosis. The internal organization of folded mitotic chromosomes remains a basic mystery of cell biology; its understanding would likely shed light on how chromosomes are separated from one another as well as into chromosome structure between cell divisions. We report biophysical experiments on single mitotic chromosomes from human cells, where we combine micromanipulation, nano-Newton-scale force measurement and biochemical treatments to study chromosome connectivity and topology. Results are in accord with previous experiments on amphibian chromosomes and support the 'chromatin network' model of mitotic chromosome structure. Prospects for studies of chromosome-organizing proteins using siRNA expression knockdowns, as well as for differential studies of chromosomes with and without mutations associated with genetic diseases, are also discussed.

Engineer Medium and Feed for Modulating N-Glycosylation of Recombinant Protein Production in CHO Cell Culture.

PubMed

Fan, Yuzhou; Kildegaard, Helene Faustrup; Andersen, Mikael Rørdam

2017-01-01

Chinese hamster ovary (CHO) cells have become the primary expression system for the production of complex recombinant proteins due to their long-term success in industrial scale production and generating appropriate protein N-glycans similar to that of humans. Control and optimization of protein N-glycosylation is crucial, as the structure of N-glycans can largely influence both biological and physicochemical properties of recombinant proteins. Protein N-glycosylation in CHO cell culture can be controlled and tuned by engineering medium, feed, culture process, as well as genetic elements of the cell. In this chapter, we will focus on how to carry out experiments for N-glycosylation modulation through medium and feed optimization. The workflow and typical methods involved in the experiment process will be presented.

Suspension cell culture in microgravity and development of a space bioreactor

NASA Technical Reports Server (NTRS)

Morrison, Dennis R.

1987-01-01

NASA has methodically developed unique suspension type cell and recovery apparatus culture systems for bioprocess technology experiments and production of biological products in microgravity. The first space bioreactor has been designed for microprocessor control, no gaseous headspace, circulation and resupply of culture medium, and slow mixing in very low shear regimes. Various ground based bioreactors are being used to test reactor vessel design, on-line sensors, effects of shear, nutrient supply, and waste removal from continuous culture of human cells attached to microcarriers. The small (500 ml) bioreactor is being constructed for flight experiments in the Shuttle middeck to verify systems operation under microgravity conditions and to measure the efficiencies of mass transport, gas transfer, oxygen consumption, and control of low shear stress on cells.

Beller Lectureship Talk: Active response of biological cells to mechanical stress

NASA Astrophysics Data System (ADS)

Safran, Samuel

2009-03-01

Forces exerted by and on adherent cells are important for many physiological processes such as wound healing and tissue formation. In addition, recent experiments have shown that stem cell differentiation is controlled, at least in part, by the elasticity of the surrounding matrix. We present a simple and generic theoretical model for the active response of biological cells to mechanical stress. The theory includes cell activity and mechanical forces as well as random forces as factors that determine the polarizability that relates cell orientation to stress. This allows us to explain the puzzling observation of parallel (or sometimes random) alignment of cells for static and quasi-static stresses and of nearly perpendicular alignment for dynamically varying stresses. In addition, we predict the response of the cellular orientation to a sinusoidally varying applied stress as a function of frequency and compare the theory with recent experiments. The dependence of the cell orientation angle on the Poisson ratio of the surrounding material distinguishes cells whose activity is controlled by stress from those controlled by strain. We have extended the theory to generalize the treatment of elastic inclusions in solids to ''living'' inclusions (cells) whose active polarizability, analogous to the polarizability of non-living matter, results in the feedback of cellular forces that develop in response to matrix stresses. We use this to explain recent observations of the non-monotonic dependence of stress-fiber polarization in stem cells on matrix rigidity. These findings provide a mechanical correlate for the existence of an optimal substrate elasticity for cell differentiation and function. [3pt] *In collaboration with R. De (Brown University), Y. Biton (Weizmann Institute), and A. Zemel (Hebrew University) and the experimental groups: Max Planck Institute, Stuttgart: S. Jungbauer, R. Kemkemer, J. Spatz; University of Pennsylvania: A. Brown, D. Discher, F. Rehfeldt.

Covariation of metabolic rates and cell size in coccolithophores

NASA Astrophysics Data System (ADS)

Aloisi, G.

2015-08-01

Coccolithophores are sensitive recorders of environmental change. The size of their coccosphere varies in the ocean along gradients of environmental conditions and provides a key for understanding the fate of this important phytoplankton group in the future ocean. But interpreting field changes in coccosphere size in terms of laboratory observations is hard, mainly because the marine signal reflects the response of multiple morphotypes to changes in a combination of environmental variables. In this paper I examine the large corpus of published laboratory experiments with coccolithophores looking for relations between environmental conditions, metabolic rates and cell size (a proxy for coccosphere size). I show that growth, photosynthesis and, to a lesser extent, calcification covary with cell size when pCO2, irradiance, temperature, nitrate, phosphate and iron conditions change. With the exception of phosphate and temperature, a change from limiting to non-limiting conditions always results in an increase in cell size. An increase in phosphate or temperature (below the optimum temperature for growth) produces the opposite effect. The magnitude of the coccosphere-size changes observed in the laboratory is comparable to that observed in the ocean. If the biological reasons behind the environment-metabolism-size link are understood, it will be possible to use coccosphere-size changes in the modern ocean and in marine sediments to investigate the fate of coccolithophores in the future ocean. This reasoning can be extended to the size of coccoliths if, as recent experiments are starting to show, coccolith size reacts to environmental change proportionally to coccosphere size. The coccolithophore database is strongly biased in favour of experiments with the coccolithophore Emiliania huxleyi (E. huxleyi; 82 % of database entries), and more experiments with other species are needed to understand whether these observations can be extended to coccolithophores in general. I introduce a simple model that simulates the growth rate and the size of cells forced by nitrate and phosphate concentrations. By considering a simple rule that allocates the energy flow from nutrient acquisition to cell structure (biomass) and cell maturity (biological complexity, eventually leading to cell division), the model is able to reproduce the covariation of growth rate and cell size observed in laboratory experiments with E. huxleyi when these nutrients become limiting. These results support ongoing efforts to interpret coccosphere and coccolith size measurements in the context of climate change.

New Horizons in Enhancing the Proliferation and Differentiation of Neural Stem Cells Using Stimulatory Effects of the Short Time Exposure to Radiofrequency Radiation

PubMed Central

Eghlidospour, M.; Mortazavi, S. M. J.; Yousefi, F.; Mortazavi, S. A. R.

2015-01-01

Mobile phone use and wireless communication technology have grown explosively over the past decades. This rapid growth has caused widespread global concern about the potential detrimental effects of this technology on human health. Stem cells generate specialized cell types of the tissue in which they reside through normal differentiation pathways. Considering the undeniable importance of stem cells in modern medicine, numerous studies have been performed on the effects of ionizing and non-ionizing radiation on cellular processes such as: proliferation, differentiation, cell cycle and DNA repair processes. We have conducted extensive studies on beneficial (stimulatory) or detrimental biological effects of exposure to different sources of electromagnetic fields such as mobile phones, mobile phone base stations, mobile phone jammers, radar systems, magnetic resonance imaging (MRI) systems and dentistry cavitrons over the past years. In this article, recent studies on the biological effects of non-ionizing electromagnetic radiation in the range of radiofrequency (RF) on some important features of stem cells such as their proliferation and differentiation are reviewed. Studies reviewed in this paper indicate that the stimulatory or inhibitory effects of RF radiation on the proliferation and differentiation of stem cells depend on various factors such as the biological systems, experiment conditions, the frequency and intensity of RF and the duration of exposure. PMID:26396965

New Horizons in Enhancing the Proliferation and Differentiation of Neural Stem Cells Using Stimulatory Effects of the Short Time Exposure to Radiofrequency Radiation.

PubMed

Eghlidospour, M; Mortazavi, S M J; Yousefi, F; Mortazavi, S A R

2015-09-01

Mobile phone use and wireless communication technology have grown explosively over the past decades. This rapid growth has caused widespread global concern about the potential detrimental effects of this technology on human health. Stem cells generate specialized cell types of the tissue in which they reside through normal differentiation pathways. Considering the undeniable importance of stem cells in modern medicine, numerous studies have been performed on the effects of ionizing and non-ionizing radiation on cellular processes such as: proliferation, differentiation, cell cycle and DNA repair processes. We have conducted extensive studies on beneficial (stimulatory) or detrimental biological effects of exposure to different sources of electromagnetic fields such as mobile phones, mobile phone base stations, mobile phone jammers, radar systems, magnetic resonance imaging (MRI) systems and dentistry cavitrons over the past years. In this article, recent studies on the biological effects of non-ionizing electromagnetic radiation in the range of radiofrequency (RF) on some important features of stem cells such as their proliferation and differentiation are reviewed. Studies reviewed in this paper indicate that the stimulatory or inhibitory effects of RF radiation on the proliferation and differentiation of stem cells depend on various factors such as the biological systems, experiment conditions, the frequency and intensity of RF and the duration of exposure.

Model-based design of experiments for cellular processes.

PubMed

Chakrabarty, Ankush; Buzzard, Gregery T; Rundell, Ann E

2013-01-01

Model-based design of experiments (MBDOE) assists in the planning of highly effective and efficient experiments. Although the foundations of this field are well-established, the application of these techniques to understand cellular processes is a fertile and rapidly advancing area as the community seeks to understand ever more complex cellular processes and systems. This review discusses the MBDOE paradigm along with applications and challenges within the context of cellular processes and systems. It also provides a brief tutorial on Fisher information matrix (FIM)-based and Bayesian experiment design methods along with an overview of existing software packages and computational advances that support MBDOE application and adoption within the Systems Biology community. As cell-based products and biologics progress into the commercial sector, it is anticipated that MBDOE will become an essential practice for design, quality control, and production. Copyright © 2013 Wiley Periodicals, Inc.

Cell growth, division, and death in cohesive tissues: A thermodynamic approach

NASA Astrophysics Data System (ADS)

Yabunaka, Shunsuke; Marcq, Philippe

2017-08-01

Cell growth, division, and death are defining features of biological tissues that contribute to morphogenesis. In hydrodynamic descriptions of cohesive tissues, their occurrence implies a nonzero rate of variation of cell density. We show how linear nonequilibrium thermodynamics allows us to express this rate as a combination of relevant thermodynamic forces: chemical potential, velocity divergence, and activity. We illustrate the resulting effects of the nonconservation of cell density on simple examples inspired by recent experiments on cell monolayers, considering first the velocity of a spreading front, and second an instability leading to mechanical waves.

Convolutional Deep Belief Networks for Single-Cell/Object Tracking in Computational Biology and Computer Vision.

PubMed

Zhong, Bineng; Pan, Shengnan; Zhang, Hongbo; Wang, Tian; Du, Jixiang; Chen, Duansheng; Cao, Liujuan

2016-01-01

In this paper, we propose deep architecture to dynamically learn the most discriminative features from data for both single-cell and object tracking in computational biology and computer vision. Firstly, the discriminative features are automatically learned via a convolutional deep belief network (CDBN). Secondly, we design a simple yet effective method to transfer features learned from CDBNs on the source tasks for generic purpose to the object tracking tasks using only limited amount of training data. Finally, to alleviate the tracker drifting problem caused by model updating, we jointly consider three different types of positive samples. Extensive experiments validate the robustness and effectiveness of the proposed method.

Convolutional Deep Belief Networks for Single-Cell/Object Tracking in Computational Biology and Computer Vision

PubMed Central

Pan, Shengnan; Zhang, Hongbo; Wang, Tian; Du, Jixiang; Chen, Duansheng; Cao, Liujuan

2016-01-01

In this paper, we propose deep architecture to dynamically learn the most discriminative features from data for both single-cell and object tracking in computational biology and computer vision. Firstly, the discriminative features are automatically learned via a convolutional deep belief network (CDBN). Secondly, we design a simple yet effective method to transfer features learned from CDBNs on the source tasks for generic purpose to the object tracking tasks using only limited amount of training data. Finally, to alleviate the tracker drifting problem caused by model updating, we jointly consider three different types of positive samples. Extensive experiments validate the robustness and effectiveness of the proposed method. PMID:27847827

Raman tweezers in microfluidic systems for analysis and sorting of living cells

NASA Astrophysics Data System (ADS)

Pilát, Zdeněk.; Ježek, Jan; Kaňka, Jan; Zemánek, Pavel

2014-12-01

We have devised an analytical and sorting system combining optical trapping with Raman spectroscopy in microfluidic environment, dedicated to identification and sorting of biological objects, such as living cells of various unicellular organisms. Our main goal was to create a robust and universal platform for non-destructive and non-contact sorting of micro-objects based on their Raman spectral properties. This approach allowed us to collect spectra containing information about the chemical composition of the objects, such as the presence and composition of pigments, lipids, proteins, or nucleic acids, avoiding artificial chemical probes such as fluorescent markers. The non-destructive nature of this optical analysis and manipulation allowed us to separate individual living cells of our interest in a sterile environment and provided the possibility to cultivate the selected cells for further experiments. We used a mixture of polystyrene micro-particles and algal cells to test and demonstrate the function of our analytical and sorting system. The devised system could find its use in many medical, biotechnological, and biological applications.

Raman tweezers in microfluidic systems for analysis and sorting of living cells

NASA Astrophysics Data System (ADS)

Pilát, Zdenëk; Ježek, Jan; Kaňka, Jan; Zemánek, Pavel

2014-03-01

We have devised an analytical and sorting system combining optical trapping with Raman spectroscopy in microfluidic environment in order to identify and sort biological objects, such as living cells of various prokaryotic and eukaryotic organisms. Our main objective was to create a robust and universal platform for non-contact sorting of microobjects based on their Raman spectral properties. This approach allowed us to collect information about the chemical composition of the objects, such as the presence and composition of lipids, proteins, or nucleic acids without using artificial chemical probes such as fluorescent markers. The non-destructive and non-contact nature of this optical analysis and manipulation allowed us to separate individual living cells of our interest in a sterile environment and provided the possibility to cultivate the selected cells for further experiments. We used differently treated cells of algae to test and demonstrate the function of our analytical and sorting system. The devised system could find its use in many medical, biotechnological, and biological applications.

Computational Biology Methods for Characterization of Pluripotent Cells.

PubMed

Araúzo-Bravo, Marcos J

2016-01-01

Pluripotent cells are a powerful tool for regenerative medicine and drug discovery. Several techniques have been developed to induce pluripotency, or to extract pluripotent cells from different tissues and biological fluids. However, the characterization of pluripotency requires tedious, expensive, time-consuming, and not always reliable wet-lab experiments; thus, an easy, standard quality-control protocol of pluripotency assessment remains to be established. Here to help comes the use of high-throughput techniques, and in particular, the employment of gene expression microarrays, which has become a complementary technique for cellular characterization. Research has shown that the transcriptomics comparison with an Embryonic Stem Cell (ESC) of reference is a good approach to assess the pluripotency. Under the premise that the best protocol is a computer software source code, here I propose and explain line by line a software protocol coded in R-Bioconductor for pluripotency assessment based on the comparison of transcriptomics data of pluripotent cells with an ESC of reference. I provide advice for experimental design, warning about possible pitfalls, and guides for results interpretation.

Pitting Corrosion Within Bioreactors for Space Cell-Culture Contaminated by Paenibacillus glucanolyticus, a Case Report

NASA Astrophysics Data System (ADS)

Barravecchia, Ivana; Cesari, Chiara De; Pyankova, Olga V.; Scebba, Francesca; Mascherpa, Marco Carlo; Vecchione, Alessandra; Tavanti, Arianna; Tedeschi, Lorena; Angeloni, Debora

2018-02-01

Performing cell biology experiments in space imposes the use of hardware that essentially allows fluid exchange in a contained environment. Given the technical and logistical peculiarities, the limited opportunities and the high cost of access to space, a great effort during mission preparation of scientific studies is devoted to preventing loss of the experiment. The European Space Agency (ESA) requires, at the end of the preparation phase, the execution of an Experiment Sequence Test (EST), a dry-run version of the space experiment to check all procedures. At conclusion of the EST of our experiment `ENDO' (ESA ILSRA-2009-1026), we found pitting corrosion of metal parts and biofilm formation within the cell-culture devices. The subsequent chemical (spectral assays), instrumental (OGP SmartScope) and microbiological (MALDI-TOF, 16S rRNA gene sequencing) investigations allowed the identification in contaminated material of Paenibacillus glucanolyticus, a ubiquitous, aerobic, facultative anaerobic, endospore forming, acid-producing, Gram-positive microorganism. A concurrence of P. glucanolyticus contamination and galvanic corrosion determined massive fouling, rust precipitation and damage to cells and cell-culture devices being, to our knowledge, the association between this microbe and corrosion never reported before in literature. As a consequence of the episode a critical procedure of experiment set up, i.e. hardware sterilization, was modified. The ENDO experiment was successfully launched to the International Space Station on September 2nd 2015 and returned to the PI laboratory on September 13th, with all cell culture samples in optimal condition.

Pitting Corrosion Within Bioreactors for Space Cell-Culture Contaminated by Paenibacillus glucanolyticus, a Case Report

NASA Astrophysics Data System (ADS)

Barravecchia, Ivana; Cesari, Chiara De; Pyankova, Olga V.; Scebba, Francesca; Mascherpa, Marco Carlo; Vecchione, Alessandra; Tavanti, Arianna; Tedeschi, Lorena; Angeloni, Debora

2018-05-01

Performing cell biology experiments in space imposes the use of hardware that essentially allows fluid exchange in a contained environment. Given the technical and logistical peculiarities, the limited opportunities and the high cost of access to space, a great effort during mission preparation of scientific studies is devoted to preventing loss of the experiment. The European Space Agency (ESA) requires, at the end of the preparation phase, the execution of an Experiment Sequence Test (EST), a dry-run version of the space experiment to check all procedures. At conclusion of the EST of our experiment `ENDO' (ESA ILSRA-2009-1026), we found pitting corrosion of metal parts and biofilm formation within the cell-culture devices. The subsequent chemical (spectral assays), instrumental (OGP SmartScope) and microbiological (MALDI-TOF, 16S rRNA gene sequencing) investigations allowed the identification in contaminated material of Paenibacillus glucanolyticus, a ubiquitous, aerobic, facultative anaerobic, endospore forming, acid-producing, Gram-positive microorganism. A concurrence of P. glucanolyticus contamination and galvanic corrosion determined massive fouling, rust precipitation and damage to cells and cell-culture devices being, to our knowledge, the association between this microbe and corrosion never reported before in literature. As a consequence of the episode a critical procedure of experiment set up, i.e. hardware sterilization, was modified. The ENDO experiment was successfully launched to the International Space Station on September 2nd 2015 and returned to the PI laboratory on September 13th, with all cell culture samples in optimal condition.

Analysis of undergraduate cell biology contents in Brazilian public universities.

PubMed

Mermelstein, Claudia; Costa, Manoel Luis

2017-04-01

The enormous amount of information available in cell biology has created a challenge in selecting the core concepts we should be teaching our undergraduates. One way to define a set of essential core ideas in cell biology is to analyze what a specific cell biology community is teaching their students. Our main objective was to analyze the cell biology content currently being taught in Brazilian universities. We collected the syllabi of cell biology courses from public universities in Brazil and analyzed the frequency of cell biology topics in each course. We also compared the Brazilian data with the contents of a major cell biology textbook. Our analysis showed that while some cell biology topics such as plasma membrane and cytoskeleton was present in ∼100% of the Brazilian curricula analyzed others such as cell signaling and cell differentiation were present in only ∼35%. The average cell biology content taught in the Brazilian universities is quite different from what is presented in the textbook. We discuss several possible explanations for these observations. We also suggest a list with essential cell biology topics for any biological or biomedical undergraduate course. The comparative discussion of cell biology topics presented here could be valuable in other educational contexts. © 2017 The Authors. Cell Biology International Published by John Wiley & Sons Ltd on behalf of International Federation of Cell Biology.

Electrophysiological experiments in microgravity: lessons learned and future challenges.

PubMed

Wuest, Simon L; Gantenbein, Benjamin; Ille, Fabian; Egli, Marcel

2018-01-01

Advances in electrophysiological experiments have led to the discovery of mechanosensitive ion channels (MSCs) and the identification of the physiological function of specific MSCs. They are believed to play important roles in mechanosensitive pathways by allowing for cells to sense their mechanical environment. However, the physiological function of many MSCs has not been conclusively identified. Therefore, experiments have been developed that expose cells to various mechanical loads, such as shear flow, membrane indentation, osmotic challenges and hydrostatic pressure. In line with these experiments, mechanical unloading, as experienced in microgravity, represents an interesting alternative condition, since exposure to microgravity leads to a series of physiological adaption processes. As outlined in this review, electrophysiological experiments performed in microgravity have shown an influence of gravity on biological functions depending on ion channels at all hierarchical levels, from the cellular level to organs. In this context, calcium signaling represents an interesting cellular pathway, as it involves the direct action of calcium-permeable ion channels, and specific gravitatic cells have linked graviperception to this pathway. Multiple key proteins in the graviperception pathways have been identified. However, measurements on vertebrae cells have revealed controversial results. In conclusion, electrophysiological experiments in microgravity have shown that ion-channel-dependent physiological processes are altered in mechanically unloaded conditions. Future experiments may provide a better understanding of the underlying mechanisms.

Carbofluoresceins and Carborhodamines as Scaffolds for High-Contrast Fluorogenic Probes

PubMed Central

2013-01-01

Fluorogenic molecules are important tools for advanced biochemical and biological experiments. The extant collection of fluorogenic probes is incomplete, however, leaving regions of the electromagnetic spectrum unutilized. Here, we synthesize green-excited fluorescent and fluorogenic analogues of the classic fluorescein and rhodamine 110 fluorophores by replacement of the xanthene oxygen with a quaternary carbon. These anthracenyl “carbofluorescein” and “carborhodamine 110” fluorophores exhibit excellent fluorescent properties and can be masked with enzyme- and photolabile groups to prepare high-contrast fluorogenic molecules useful for live cell imaging experiments and super-resolution microscopy. Our divergent approach to these red-shifted dye scaffolds will enable the preparation of numerous novel fluorogenic probes with high biological utility. PMID:23557713

Radiation biology of HZE particles

NASA Technical Reports Server (NTRS)

Nelson, Gregory A.

1990-01-01

The biological effects of heavy charged particle (HZE) radiation are of particular interest to travellers and planners for long duration space flights where exposure levels represent a potential health hazard. The unique feature of HZE radiation is the structured pattern of its energy deposition in targets which may be related to charge, velocity, or rate of energy loss. There are many consequences of this feature to biological endpoints when compared to effects of ionizing photons. Dose vs response and dose rate kinetics are modified, DNA and cellular repair systems are altered in their abilities to cope with damage and, the qualitative features of damage are unique for different ions. These features must be incorporated into any risk assessment system for radiation health management. HZE induced mutation, cell inactivation and altered organogenesis will be discussed emphasizing studies with the nematode Caenorhabditis elegans and cultured cells. Observations from radiobiology experiments in space will also be reviewed along with plans for future space-based studies.

Construction of a ratiometric fluorescent probe with an extremely large emission shift for imaging hypochlorite in living cells

NASA Astrophysics Data System (ADS)

Song, Xuezhen; Dong, Baoli; Kong, Xiuqi; Wang, Chao; Zhang, Nan; Lin, Weiying

2018-01-01

Hypochlorite is one of the important reactive oxygen species (ROS) and plays critical roles in many biologically vital processes. Herein, we present a unique ratiometric fluorescent probe (CBP) with an extremely large emission shift for detecting hypochlorite in living cells. Utilizing positively charged α,β-unsaturated carbonyl group as the reaction site, the probe CBP itself exhibited near-infrared (NIR) fluorescence at 662 nm, and can display strong blue fluorescence at 456 nm when responded to hypochlorite. Notably, the extremely large emission shift of 206 nm could enable the precise measurement of the fluorescence peak intensities and ratios. CBP showed high sensitivity, excellent selectivity, desirable performance at physiological pH, and low cytotoxicity. The bioimaging experiments demonstrate the biological application of CBP for the ratiometric imaging of hypochlorite in living cells.

Erythrocyte Membrane Failure by Electromechanical Stress.

PubMed

Du, E; Qiang, Yuhao; Liu, Jia

2018-01-01

We envision that electrodeformation of biological cells through dielectrophoresis as a new technique to elucidate the mechanistic details underlying membrane failure by electrical and mechanical stresses. Here we demonstrate the full control of cellular uniaxial deformation and tensile recovery in biological cells via amplitude-modified electric field at radio frequency by an interdigitated electrode array in microfluidics. Transient creep and cyclic experiments were performed on individually tracked human erythrocytes. Observations of the viscoelastic-to-viscoplastic deformation behavior and the localized plastic deformations in erythrocyte membranes suggest that electromechanical stress results in irreversible membrane failure. Examples of membrane failure can be separated into different groups according to the loading scenarios: mechanical stiffening, physical damage, morphological transformation from discocyte to echinocyte, and whole cell lysis. These results show that this technique can be potentially utilized to explore membrane failure in erythrocytes affected by other pathophysiological processes.

Corylin increases the sensitivity of hepatocellular carcinoma cells to chemotherapy through long noncoding RNA RAD51-AS1-mediated inhibition of DNA repair.

PubMed

Chen, Chin-Chuan; Chen, Chi-Yuan; Ueng, Shir-Hwa; Hsueh, Chuen; Yeh, Chau-Ting; Ho, Jar-Yi; Chou, Li-Fang; Wang, Tong-Hong

2018-05-10

Corylin, a biologically active agent extracted from Psoralea corylifolia L. (Fabaceae), promotes bone differentiation and inhibits inflammation. Currently, few reports have addressed the biological functions that are regulated by corylin, and to date, no studies have investigated its antitumor activity. In this study, we used cell functional assays to analyze the antitumor activity of corylin in hepatocellular carcinoma (HCC). Furthermore, whole-transcriptome assays were performed to identify the downstream genes that were regulated by corylin, and gain-of-function and loss-of-function experiments were conducted to examine the regulatory roles of the above genes. We found that corylin significantly inhibited the proliferation, migration, and invasion of HCC cells and increased the toxic effects of chemotherapeutic agents against HCC cells. These properties were due to the induction of a long noncoding RNA, RAD51-AS1, which bound to RAD51 mRNA, thereby inhibiting RAD51 protein expression, thus inhibiting the DNA damage repair ability of HCC cells. Animal experiments also showed that a combination treatment with corylin significantly increased the inhibitory effects of the chemotherapeutic agent etoposide (VP16) on tumor growth. These findings indicate that corylin has strong potential as an adjuvant drug in HCC treatment and that corylin can strengthen the therapeutic efficacy of chemotherapy and radiotherapy.

Isolation, Culture, and Motility Measurements of Epidermal Melanocytes from GFP-Expressing Reporter Mice.

PubMed

Dagnino, Lina; Crawford, Melissa

2018-03-27

In this article, we provide a method to isolate primary epidermal melanocytes from reporter mice, which also allow targeted gene inactivation. The mice from which these cells are isolated are bred into a Rosa26 mT/mG reporter background, which results in GFP expression in the targeted melanocytic cell population. These cells are isolated and cultured to >95% purity. The cells can be used for gene expression studies, clonogenic experiments, and biological assays, such as capacity for migration. Melanocytes are slow moving cells, and we also provide a method to measure motility using individual cell tracking and data analysis.

Bortezomib in Kidney Transplantation

PubMed Central

Raghavan, Rajeev; Jeroudi, Abdallah; Achkar, Katafan; Gaber, A. Osama; Patel, Samir J.; Abdellatif, Abdul

2010-01-01

Although current therapies for pretransplant desensitization and treatment of antibody-mediated rejection (AMR) have had some success, they do not specifically deplete plasma cells that produce antihuman leukocyte antigen (HLA) antibodies. Bortezomib, a proteasome inhibitor approved for the treatment of multiple myeloma (a plasma cell neoplasm), induces plasma cell apoptosis. In this paper we review the current body of literature regarding the use of this biological agent in the field of transplantation. Although limited experience with bortezomib may seem to show promise in the realm of transplant recipients desensitization and treatment of AMR, there is also experience that may suggest otherwise. Bortezomib's role in desensitization protocols and treatment of AMR will be defined better as more clinical data and trials become available. PMID:20953363

Towards monitoring real-time cellular response using an integrated microfluidics-MALDI/nESI-ion mobility-mass spectrometry platform

PubMed Central

Enders, Jeffrey R.; Marasco, Christina C.; Kole, Ayeeshik; Nguyen, Bao; Sundarapandian, Sevugarajan; Seale, Kevin T.; Wikswo, John P.; McLean, John A.

2014-01-01

The combination of microfluidic cell trapping devices with ion mobility-mass spectrometry offers the potential for elucidating in real time the dynamic responses of small populations of cells to paracrine signals, changes in metabolite levels, and delivery of drugs and toxins. Preliminary experiments examining peptides in methanol and recording the interactions of yeast and Jurkat cells with their superfusate have identified instrumental setup and control parameters and on-line desalting procedures. Numerous initial experiments demonstrate and validate this new instrumental platform. Future outlooks and potential applications are addressed, specifically how this instrumentation may be used for fully automated systems biology studies of the significantly interdependent, dynamic internal workings of cellular metabolic and signaling pathways. PMID:21073240

A minimal physical model for crawling cells

NASA Astrophysics Data System (ADS)

Tiribocchi, Adriano; Tjhung, Elsen; Marenduzzo, Davide; Cates, Michael E.

Cell motility in higher organisms (eukaryotes) is fundamental to biological functions such as wound healing or immune response, and is also implicated in diseases such as cancer. For cells crawling on solid surfaces, considerable insights into motility have been gained from experiments replicating such motion in vitro. Such experiments show that crawling uses a combination of actin treadmilling (polymerization), which pushes the front of a cell forward, and myosin-induced stress (contractility), which retracts the rear. We present a simplified physical model of a crawling cell, consisting of a droplet of active polar fluid with contractility throughout, but treadmilling connected to a thin layer near the supporting wall. The model shows a variety of shapes and/or motility regimes, some closely resembling cases seen experimentally. Our work supports the view that cellular motility exploits autonomous physical mechanisms whose operation does not need continuous regulatory effort.

A minimal physical model captures the shapes of crawling cells

NASA Astrophysics Data System (ADS)

Tjhung, E.; Tiribocchi, A.; Marenduzzo, D.; Cates, M. E.

2015-01-01

Cell motility in higher organisms (eukaryotes) is crucial to biological functions ranging from wound healing to immune response, and also implicated in diseases such as cancer. For cells crawling on hard surfaces, significant insights into motility have been gained from experiments replicating such motion in vitro. Such experiments show that crawling uses a combination of actin treadmilling (polymerization), which pushes the front of a cell forward, and myosin-induced stress (contractility), which retracts the rear. Here we present a simplified physical model of a crawling cell, consisting of a droplet of active polar fluid with contractility throughout, but treadmilling connected to a thin layer near the supporting wall. The model shows a variety of shapes and/or motility regimes, some closely resembling cases seen experimentally. Our work strongly supports the view that cellular motility exploits autonomous physical mechanisms whose operation does not need continuous regulatory effort.

Differential equation methods for simulation of GFP kinetics in non-steady state experiments.

PubMed

Phair, Robert D

2018-03-15

Genetically encoded fluorescent proteins, combined with fluorescence microscopy, are widely used in cell biology to collect kinetic data on intracellular trafficking. Methods for extraction of quantitative information from these data are based on the mathematics of diffusion and tracer kinetics. Current methods, although useful and powerful, depend on the assumption that the cellular system being studied is in a steady state, that is, the assumption that all the molecular concentrations and fluxes are constant for the duration of the experiment. Here, we derive new tracer kinetic analytical methods for non-steady state biological systems by constructing mechanistic nonlinear differential equation models of the underlying cell biological processes and linking them to a separate set of differential equations governing the kinetics of the fluorescent tracer. Linking the two sets of equations is based on a new application of the fundamental tracer principle of indistinguishability and, unlike current methods, supports correct dependence of tracer kinetics on cellular dynamics. This approach thus provides a general mathematical framework for applications of GFP fluorescence microscopy (including photobleaching [FRAP, FLIP] and photoactivation to frequently encountered experimental protocols involving physiological or pharmacological perturbations (e.g., growth factors, neurotransmitters, acute knockouts, inhibitors, hormones, cytokines, and metabolites) that initiate mechanistically informative intracellular transients. When a new steady state is achieved, these methods automatically reduce to classical steady state tracer kinetic analysis. © 2018 Phair. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Towards a quantitative understanding of stem cell-niche interaction: experiments, models, and technologies.

PubMed

Roeder, Ingo; Loeffler, Markus; Glauche, Ingmar

2011-04-15

Here we report about an interdisciplinary workshop focusing on the effects of the local growth-environment on the regulation of stem cell development. Under the title "Towards a quantitative understanding of stem cell/ niche interaction: Experiments, models, and technologies", 33 experts from eight countries discussed current knowledge, new experimental and theoretical results as well as innovative measurement technologies. Specifically, the workshop addressed the following questions: What defines a stem cell niche? What are functional/regulatory characteristics of stem cell- microenvironment interactions? What experimental systems and technologies for quantifying niche function are available? As a consensus result it was recorded that there is no unique niche architecture across tissues but that there are generic principles of niche organization guaranteeing a proper function of stem cells. This functional aspect, as the major defining criterion, leads to the conclusion that stem cells and their niches need to be considered as an inseparable pair with implications for their experimental assessment: To be able to study any of those two components, the other component has to be accounted for. In this context, a number of classical in vitro assays using co-cultures of stem and stroma cells, but also new, specifically bioengineered culture systems have been discussed with respect to their advantages and disadvantages. Finally, there was a general agreement that the comprehensive understanding of niche-mediated stem cell regulation will, due to the complexity of involved mechanisms, require an interdisciplinary, systems biological approach. In addition to cell and molecular biology, biochemistry, biophysics and bioengineering also bioinformatics and mathematical modeling will play a major role in the future of this field. Copyright © 2011 Elsevier Inc. All rights reserved.

Leveraging advances in biology to design biomaterials

NASA Astrophysics Data System (ADS)

Darnell, Max; Mooney, David J.

2017-12-01

Biomaterials have dramatically increased in functionality and complexity, allowing unprecedented control over the cells that interact with them. From these engineering advances arises the prospect of improved biomaterial-based therapies, yet practical constraints favour simplicity. Tools from the biology community are enabling high-resolution and high-throughput bioassays that, if incorporated into a biomaterial design framework, could help achieve unprecedented functionality while minimizing the complexity of designs by identifying the most important material parameters and biological outputs. However, to avoid data explosions and to effectively match the information content of an assay with the goal of the experiment, material screens and bioassays must be arranged in specific ways. By borrowing methods to design experiments and workflows from the bioprocess engineering community, we outline a framework for the incorporation of next-generation bioassays into biomaterials design to effectively optimize function while minimizing complexity. This framework can inspire biomaterials designs that maximize functionality and translatability.

Fifteen symposia on microdosimetry: implications for modern particle-beam cancer radiotherapy.

PubMed

Wambersie, A; Menzel, H; Gueulette, J; Pihet, P

2015-09-01

The objective of microdosimetry was, and still is, to identify physical descriptions of the initial physical processes of ionising radiation interacting with biological matter which correlate with observed radiobiological effects with a view to improve the understanding of radiobiological mechanisms and effects. The introduction of therapy with particles starting with fast neutrons followed by negative pions, protons and light ions necessitated the application of biological weighting factors for absorbed dose in order to account for differences of the relative biological effectiveness (RBE). Dedicated radiobiological experiments in therapy beams with mammalian cells and with laboratory animals provided sets of RBE values which are used to evaluate empirical 'clinical RBE values'. The combination of such experiments with microdosimetric measurements in identical conditions offered the possibility to establish semi-empirical relationships between microdosimetric parameters and results of RBE studies. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

SU-E-T-146: Effects of Uncertainties of Radiation Sensitivity of Biological Modelling for Treatment Planning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oita, M; Department of Life System, Institute of Technology and Science, Graduate School, The Tokushima University; Uto, Y

Purpose: The aim of this study was to evaluate the distribution of uncertainty of cell survival by radiation, and assesses the usefulness of stochastic biological model applying for gaussian distribution. Methods: For single cell experiments, exponentially growing cells were harvested from the standard cell culture dishes by trypsinization, and suspended in test tubes containing 1 ml of MEM(2x10{sup 6} cells/ml). The hypoxic cultures were treated with 95% N{sub 2}−5% CO{sub 2} gas for 30 minutes. In vitro radiosensitization was also measured in EMT6/KU single cells to add radiosensitizer under hypoxic conditions. X-ray irradiation was carried out by using an Xraymore » unit (Hitachi X-ray unit, model MBR-1505R3) with 0.5 mm Al/1.0 mm Cu filter, 150 kV, 4 Gy/min). In vitro assay, cells on the dish were irradiated with 1 Gy to 24 Gy, respectively. After irradiation, colony formation assays were performed. Variations of biological parameters were investigated at standard cell culture(n=16), hypoxic cell culture(n=45) and hypoxic cell culture(n=21) with radiosensitizers, respectively. The data were obtained by separate schedule to take account for the variation of radiation sensitivity of cell cycle. Results: At standard cell culture, hypoxic cell culture and hypoxic cell culture with radiosensitizers, median and standard deviation of alpha/beta ratio were 37.1±73.4 Gy, 9.8±23.7 Gy, 20.7±21.9 Gy, respectively. Average and standard deviation of D{sub 50} were 2.5±2.5 Gy, 6.1±2.2 Gy, 3.6±1.3 Gy, respectively. Conclusion: In this study, we have challenged to apply these uncertainties of parameters for the biological model. The variation of alpha values, beta values, D{sub 50} as well as cell culture might have highly affected by probability of cell death. Further research is in progress for precise prediction of the cell death as well as tumor control probability for treatment planning.« less

Morphological observation and analysis using automated image cytometry for the comparison of trypan blue and fluorescence-based viability detection method.

PubMed

Chan, Leo Li-Ying; Kuksin, Dmitry; Laverty, Daniel J; Saldi, Stephanie; Qiu, Jean

2015-05-01

The ability to accurately determine cell viability is essential to performing a well-controlled biological experiment. Typical experiments range from standard cell culturing to advanced cell-based assays that may require cell viability measurement for downstream experiments. The traditional cell viability measurement method has been the trypan blue (TB) exclusion assay. However, since the introduction of fluorescence-based dyes for cell viability measurement using flow or image-based cytometry systems, there have been numerous publications comparing the two detection methods. Although previous studies have shown discrepancies between TB exclusion and fluorescence-based viability measurements, image-based morphological analysis was not performed in order to examine the viability discrepancies. In this work, we compared TB exclusion and fluorescence-based viability detection methods using image cytometry to observe morphological changes due to the effect of TB on dead cells. Imaging results showed that as the viability of a naturally-dying Jurkat cell sample decreased below 70 %, many TB-stained cells began to exhibit non-uniform morphological characteristics. Dead cells with these characteristics may be difficult to count under light microscopy, thus generating an artificially higher viability measurement compared to fluorescence-based method. These morphological observations can potentially explain the differences in viability measurement between the two methods.

Apollo Soyuz pamphlet No. 7: Biology in zero-G

NASA Technical Reports Server (NTRS)

Page, L. W.; Page, T.

1977-01-01

The effects of weightlessness on small living organisms, and methods for improving biological techniques were investigated in the seven experiments reported in this pamphlet which is intended as a curriculum supplement for secondary schools. Topics include: (1) killfish hatching and orientation; (2) microbial growth and changes in biorhythm; (3) cell separation by electrophoresis; (4) microbial exchange in the space raft; and (5) changes in astronaut immunity during spaceflight. The pamphlet is intended as a curriculum supplement for secondary schools.

Trends in modeling Biomedical Complex Systems

PubMed Central

Milanesi, Luciano; Romano, Paolo; Castellani, Gastone; Remondini, Daniel; Liò, Petro

2009-01-01

In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments, informatics tools and technologies suitable for biological and biomedical research, which are becoming increasingly multidisciplinary, multidimensional and information-driven. The most important concepts on mathematical modeling methodologies and statistical inference, bioinformatics and standards tools to investigate complex biomedical systems are discussed and the prominent literature useful to both the practitioner and the theoretician are presented. PMID:19828068

Human cell culture in a space bioreactor

NASA Technical Reports Server (NTRS)

Morrison, Dennis R.

1988-01-01

Microgravity offers new ways of handling fluids, gases, and growing mammalian cells in efficient suspension cultures. In 1976 bioreactor engineers designed a system using a cylindrical reactor vessel in which the cells and medium are slowly mixed. The reaction chamber is interchangeable and can be used for several types of cell cultures. NASA has methodically developed unique suspension type cell and recovery apparatus culture systems for bioprocess technology experiments and production of biological products in microgravity. The first Space Bioreactor was designed for microprocessor control, no gaseous headspace, circulation and resupply of culture medium, and slow mixing in very low shear regimes. Various ground based bioreactors are being used to test reactor vessel design, on-line sensors, effects of shear, nutrient supply, and waste removal from continuous culture of human cells attached to microcarriers. The small Bioreactor is being constructed for flight experiments in the Shuttle Middeck to verify systems operation under microgravity conditions and to measure the efficiencies of mass transport, gas transfer, oxygen consumption and control of low shear stress on cells.

Development and Validation of a Rubric for Diagnosing Students' Experimental Design Knowledge and Difficulties.

PubMed

Dasgupta, Annwesa P; Anderson, Trevor R; Pelaez, Nancy

2014-01-01

It is essential to teach students about experimental design, as this facilitates their deeper understanding of how most biological knowledge was generated and gives them tools to perform their own investigations. Despite the importance of this area, surprisingly little is known about what students actually learn from designing biological experiments. In this paper, we describe a rubric for experimental design (RED) that can be used to measure knowledge of and diagnose difficulties with experimental design. The development and validation of the RED was informed by a literature review and empirical analysis of undergraduate biology students' responses to three published assessments. Five areas of difficulty with experimental design were identified: the variable properties of an experimental subject; the manipulated variables; measurement of outcomes; accounting for variability; and the scope of inference appropriate for experimental findings. Our findings revealed that some difficulties, documented some 50 yr ago, still exist among our undergraduate students, while others remain poorly investigated. The RED shows great promise for diagnosing students' experimental design knowledge in lecture settings, laboratory courses, research internships, and course-based undergraduate research experiences. It also shows potential for guiding the development and selection of assessment and instructional activities that foster experimental design. © 2014 A. P. Dasgupta et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Investigating the Role of an Inquiry-Based Biology Lab Course on Student Attitudes and Views toward Science.

PubMed

Jeffery, Erica; Nomme, Kathy; Deane, Thomas; Pollock, Carol; Birol, Gülnur

2016-01-01

Students' academic experiences can influence their conceptualization of science. In contrast experts hold particular beliefs, perceptions, opinions, and attitudes about science that are often absent in first-year undergraduate students. Shifts toward more expert-like attitudes and views have been linked to improved student engagement, critical-thinking ability, conceptual understanding, and academic performance. In this study, we investigate shifts in attitudes and views toward science by students in four biology classes with differences in student enrollment, academic support, and instruction. We observe significant, positive effects of enrollment in a guided-inquiry lab course and academic performance on the percentage of expert-like student attitudes and views at the end of term. We also identify variation in two aspects of student attitudes and views: 1) confidence and interest and 2) understanding and acceptance. In particular, enrollment in the lab course boosts student confidence and interest in scientific inquiry in the short term, even for students with low academic performance or little English-language experience. Our results suggest that low-performing students in particular may require additional opportunities for experiential learning or greater academic support to develop expert-like perceptions of biology as a science. © 2016 E. Jeffery et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Undergraduates achieve learning gains in plant genetics through peer teaching of secondary students.

PubMed

Chrispeels, H E; Klosterman, M L; Martin, J B; Lundy, S R; Watkins, J M; Gibson, C L; Muday, G K

2014-01-01

This study tests the hypothesis that undergraduates who peer teach genetics will have greater understanding of genetic and molecular biology concepts as a result of their teaching experiences. Undergraduates enrolled in a non-majors biology course participated in a service-learning program in which they led middle school (MS) or high school (HS) students through a case study curriculum to discover the cause of a green tomato variant. The curriculum explored plant reproduction and genetic principles, highlighting variation in heirloom tomato fruits to reinforce the concept of the genetic basis of phenotypic variation. HS students were taught additional activities related to mole-cular biology techniques not included in the MS curriculum. We measured undergraduates' learning outcomes using pre/postteaching content assessments and the course final exam. Undergraduates showed significant gains in understanding of topics related to the curriculum they taught, compared with other course content, on both types of assessments. Undergraduates who taught HS students scored higher on questions specific to the HS curriculum compared with undergraduates who taught MS students, despite identical lecture content, on both types of assessments. These results indicate the positive effect of service-learning peer-teaching experiences on undergraduates' content knowledge, even for non-science major students. © 2014 H. E. Chrispeels et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Proteomic analysis of effects by x-rays and heavy ion in HeLa cells.

PubMed

Bing, Zhitong; Yang, Guanghui; Zhang, Yanan; Wang, Fengling; Ye, Caiyong; Sun, Jintu; Zhou, Guangming; Yang, Lei

2014-06-01

Carbon ion therapy may be better against cancer than the effects of a photon beam. To investigate a biological advantage of carbon ion beam over X-rays, the radioresistant cell line HeLa cells were used. Radiation-induced changes in the biological processes were investigated post-irradiation at 1 h by a clinically relevant radiation dose (2 Gy X-ray and 2 Gy carbon beam). The differential expression proteins were collected for analysing biological effects. The radioresistant cell line Hela cells were used. In our study, the stable isotope labelling with amino acids (SILAC) method coupled with 2D-LC-LTQ Orbitrap mass spectrometry was applied to identity and quantify the differentially expressed proteins after irradiation. The Western blotting experiment was used to validate the data. A total of 123 and 155 significantly changed proteins were evaluated with treatment of 2 Gy carbon and X-rays after radiation 1 h, respectively. These deregulated proteins were found to be mainly involved in several kinds of metabolism processes through Gene Ontology (GO) enrichment analysis. The two groups perform different response to different types of irradiation. The radioresistance of the cancer cells treated with 2 Gy X-rays irradiation may be largely due to glycolysis enhancement, while the greater killing effect of 2 Gy carbon may be due to unchanged glycolysis and decreased amino acid metabolism.

Interaction between pancreatic β cell and electromagnetic fields: A systematic study toward finding the natural frequency spectrum of β cell system.

PubMed

Farashi, Sajjad

2017-01-01

Interaction between biological systems and environmental electric or magnetic fields has gained attention during the past few decades. Although there are a lot of studies that have been conducted for investigating such interaction, the reported results are considerably inconsistent. Besides the complexity of biological systems, the important reason for such inconsistent results may arise due to different excitation protocols that have been applied in different experiments. In order to investigate carefully the way that external electric or magnetic fields interact with a biological system, the parameters of excitation, such as intensity or frequency, should be selected purposefully due to the influence of these parameters on the system response. In this study, pancreatic β cell, the main player of blood glucose regulating system, is considered and the study is focused on finding the natural frequency spectrum of the system using modeling approach. Natural frequencies of a system are important characteristics of the system when external excitation is applied. The result of this study can help researchers to select proper frequency parameter for electrical excitation of β cell system. The results show that there are two distinct frequency ranges for natural frequency of β cell system, which consist of extremely low (or near zero) and 100-750 kHz frequency ranges. There are experimental works on β cell exposure to electromagnetic fields that support such finding.

Elastic light scattering from single cells: orientational dynamics in optical trap.

PubMed

Watson, Dakota; Hagen, Norbert; Diver, Jonathan; Marchand, Philippe; Chachisvilis, Mirianas

2004-08-01

Light-scattering diagrams (phase functions) from single living cells and beads suspended in an optical trap were recorded with 30-ms time resolution. The intensity of the scattered light was recorded over an angular range of 0.5-179.5 degrees using an optical setup based on an elliptical mirror and rotating aperture. Experiments revealed that light-scattering diagrams from biological cells exhibit significant and complex time dependence. We have attributed this dependence to the cell's orientational dynamics within the trap. We have also used experimentally measured phase function information to calculate the time dependence of the optical radiation pressure force on the trapped particle and show how it changes depending on the orientation of the particle. Relevance of these experiments to potential improvement in the sensitivity of label-free flow cytometry is discussed.

Evaluation of the health impact of nanoparticles emitted from combustion sources: Comprehensive characterization of the physicochemical properties of nanoparticle emissions from wood combustion compliances, car- and ship diesel-engines as well as investigation of their toxicological effects on human lung cells and macrophages.

NASA Astrophysics Data System (ADS)

Zimmermann, R.; Dittmar, G.; Kanashova, T.; Buters, J.; Öder, S.; Paur, H. R.; Mülhopt, S.; Dilger, M.; Weiss, C.; Harndorf, H.; Stengel, B.; Hirvonen, M. R.; Jokiniemi, J.; Hiller, K.; Sapcariu, S.; Sippula, O.; Streibel, T.; Karg, E.; Weggler, B.; Schnelle-Kreis, J.; Lintelmann, J.; Sklorz, M.; Orasche, J.; Müller, L.; Passig, J.; Gröger, T.; BéruBé, K.; Krebs, T.

2016-12-01

Combustion emissions cause health effects. The HICE-Aerosol and Health project team studies the physicochemical properties as well as biological and toxicological effects on lung cells of combustion particle emissions. The chemical composition and physical parameters thoroughly characterized. Human lung cells are exposed to the diluted combustion exhaust fumes at the air-liquid interface (ALI), allowing a realistic lung-cell exposure by simulation of the lung situation. After exposure, cellular responses of the exposed lung cells are studied by multi-omics molecular biological analyses on transcriptomic, proteomic and metabolomic level. Emissions of wood combustion (log wood, pellet heater), ship diesel engines and car gasoline engines are addressed. Special field deployable ALI-exposition systems in a mobile S2-biological laboratory were set up and applied. Human alveolar epithelial cells (A549, BEAS2B and primary cells) as well as murine macrophages were ALI-exposed to diluted emissions. The cellular effects were then comprehensively characterized (viability, cyto-toxicology, multi-omics effects monitoring) and put in context with the chemical and physical aerosol data. The following order of overall cellular response-strength was observed: A relatively mild cellular effect is observed for the diluted wood combustion emissions. Interestingly the effects-strength for log-wood and pellet burner emissions are similar, although PM-concentrations are much higher for the log-wood heater. Similar mild biological effects are observed for the gasoline car emissions. The ship diesel engine emissions induced the most intense biological responses. A surprising result in this context is, that heavy fuel oil (HFO)-emissions showed lower biological effect strengths than the supposedly cleaner diesel fuel emissions (DF). The HFO-emission contain high concentrations of known toxicants (transition metals, polycyclic aromatics). This result was recently confirmed by experiments with murine RAW macrophages. Detailed analyses of the activated cellular response pathways, such as pro-inflammatory responses, xenobiotic metabolism, phagocytosis and oxidative stress were performed. The data is suggesting a large difference in relative toxicity for different combustion sources.

The Current Status of the Space Station Biological Research Project: a Core Facility Enabling Multi-Generational Studies under Slectable Gravity Levels

NASA Astrophysics Data System (ADS)

Santos, O.

2002-01-01

The Space Station Biological Research Project (SSBRP) has developed a new plan which greatly reduces the development costs required to complete the facility. This new plan retains core capabilities while allowing for future growth. The most important piece of equipment required for quality biological research, the 2.5 meter diameter centrifuge capable of accommodating research specimen habitats at simulated gravity levels ranging from microgravity to 2.0 g, is being developed by NASDA, the Japanese space agency, for the SSBRP. This is scheduled for flight to the ISS in 2007. The project is also developing a multi-purpose incubator, an automated cell culture unit, and two microgravity habitat holding racks, currently scheduled for launch in 2005. In addition the Canadian Space Agency is developing for the project an insect habitat, which houses Drosophila melanogaster, and provides an internal centrifuge for 1 g controls. NASDA is also developing for the project a glovebox for the contained manipulation and analysis of biological specimens, scheduled for launch in 2006. This core facility will allow for experimentation on small plants (Arabidopsis species), nematode worms (C. elegans), fruit flies (Drosophila melanogaster), and a variety of microorganisms, bacteria, yeast, and mammalian cells. We propose a plan for early utilization which focuses on surveys of changes in gene expression and protein structure due to the space flight environment. In the future, the project is looking to continue development of a rodent habitat and a plant habitat that can be accommodated on the 2.5 meter centrifuge. By utilizing the early phases of the ISS to broadly answer what changes occur at the genetic and protein level of cells and organisms exposed to the ISS low earth orbit environment, we can generate interest for future experiments when the ISS capabilities allow for direct manipulation and intervention of experiments. The ISS continues to hold promise for high quality, long term, multi-generational biological studies with large sample sizes and appropriate controls.

Biological 2-Input Decoder Circuit in Human Cells

PubMed Central

2015-01-01

Decoders are combinational circuits that convert information from n inputs to a maximum of 2n outputs. This operation is of major importance in computing systems yet it is vastly underexplored in synthetic biology. Here, we present a synthetic gene network architecture that operates as a biological decoder in human cells, converting 2 inputs to 4 outputs. As a proof-of-principle, we use small molecules to emulate the two inputs and fluorescent reporters as the corresponding four outputs. The experiments are performed using transient transfections in human kidney embryonic cells and the characterization by fluorescence microscopy and flow cytometry. We show a clear separation between the ON and OFF mean fluorescent intensity states. Additionally, we adopt the integrated mean fluorescence intensity for the characterization of the circuit and show that this metric is more robust to transfection conditions when compared to the mean fluorescent intensity. To conclude, we present the first implementation of a genetic decoder. This combinational system can be valuable toward engineering higher-order circuits as well as accommodate a multiplexed interface with endogenous cellular functions. PMID:24694115

Biological 2-input decoder circuit in human cells.

PubMed

Guinn, Michael; Bleris, Leonidas

2014-08-15

Decoders are combinational circuits that convert information from n inputs to a maximum of 2(n) outputs. This operation is of major importance in computing systems yet it is vastly underexplored in synthetic biology. Here, we present a synthetic gene network architecture that operates as a biological decoder in human cells, converting 2 inputs to 4 outputs. As a proof-of-principle, we use small molecules to emulate the two inputs and fluorescent reporters as the corresponding four outputs. The experiments are performed using transient transfections in human kidney embryonic cells and the characterization by fluorescence microscopy and flow cytometry. We show a clear separation between the ON and OFF mean fluorescent intensity states. Additionally, we adopt the integrated mean fluorescence intensity for the characterization of the circuit and show that this metric is more robust to transfection conditions when compared to the mean fluorescent intensity. To conclude, we present the first implementation of a genetic decoder. This combinational system can be valuable toward engineering higher-order circuits as well as accommodate a multiplexed interface with endogenous cellular functions.

Planar MEMS bio-chip for recording ion-channel currents in biological cells

NASA Astrophysics Data System (ADS)

Pandey, Santosh; Ferdous, Zannatul; White, Marvin H.

2003-10-01

We describe a planar MEMS silicon structure to record ion-channel currents in biological cells. The conventional method of performing an electrophysiological experiment, 'patch-clamping,' employs a glass micropipette. Despite careful treatments of the micropipette tip, such as fire polishing and surface coating, the latter is a source of thermal noise because of its inherent, tapered, conical structure, which gives rise to a large pipette resistance. This pipette resistance, when coupled with the self-capacitance of the biological cell, limits the available bandwidth and processing of fast transient, ion channel current pulses. In this work, we reduce considerably the pipette resistance with a planar micropipette on a silicon chip to permit the resolution of sub-millisecond, ion-channel pulses. We discuss the design topology of the device, describe the fabrication sequence, and highlight important critical issues. The design of an integrated on-chip CMOS instrumentation amplifier is described, which has a low-noise front-end, input-offset cancellation, correlated double sampling (CDS), and an ultra-high gain in the order of 1012V/A.

Recommendations for the validation of cell-based assays used for the detection of neutralizing antibody immune responses elicited against biological therapeutics.

PubMed

Gupta, Shalini; Devanarayan, Viswanath; Finco, Deborah; Gunn, George R; Kirshner, Susan; Richards, Susan; Rup, Bonita; Song, An; Subramanyam, Meena

2011-07-15

The administration of biological therapeutics may result in the development of anti-drug antibodies (ADAs) in treated subjects. In some cases, ADA responses may result in the loss of therapeutic efficacy due to the formation of neutralizing ADAs (NAbs). An important characteristic of anti-drug NAbs is their direct inhibitory effect on the pharmacological activity of the therapeutic. Neutralizing antibody responses are of particular concern for biologic products with an endogenous homolog whose activity can be potentially dampened or completely inhibited by the NAbs leading to an autoimmune-type deficiency syndrome. Therefore, it is important that ADAs are detected and characterized appropriately using sensitive and reliable methods. The design, development and optimization of cell-based assays used for detection of NAbs have been published previously by Gupta et al. 2007 [1]. This paper provides recommendations on best practices for the validation of cell-based NAb assay and suggested validation parameters based on the experience of the authors. Copyright © 2011 Elsevier B.V. All rights reserved.

[Establishment and application of mechanical strain loading system of multi-channel cells].

PubMed

Li, Yongming; Wang, Hua; Zhang, Xiaodong; Tang, Lin

2012-02-01

Based on single-chip microcomputer, we have established a mechanical strain loading system with multi-channel to study the biological behavior of cultured cells in vitro under mechanical strain. We developed a multi-channel cell strain loading device controlled by single-chip microcomputer. We controlled the vacuum pump with vacuum chamber to make negative pressure changing periodically in the vacuum chamber. The tested cells were seeded on the surface of an elastic membrane mounted on the vacuum chamber, and could be strained or relaxed by cyclic pressure. Since the cells are attached to the surface of the membrane, they presumably experience the same deformation as that was applied to the membrane. The system was easy to carry and to operate, with deformation rate (1%-21%) and frequency (0-0. 5Hz) which could be adjusted correctly according to experimental requirement, and could compare different deformation rate of three channels at the same time. The system ran stably and completely achieved design aims, and provided a method to study the biological behavior of cultured cells attached to the surface of the elastic membrane under mechanical strain in vitro.

Microscopy Images as Interactive Tools in Cell Modeling and Cell Biology Education

PubMed Central

Araújo-Jorge, Tania C.; Cardona, Tania S.; Mendes, Cláudia L. S.; Henriques-Pons, Andrea; Meirelles, Rosane M. S.; Coutinho, Cláudia M. L. M.; Aguiar, Luiz Edmundo V.; Meirelles, Maria de Nazareth L.; de Castro, Solange L.; Barbosa, Helene S.; Luz, Mauricio R. M. P.

2004-01-01

The advent of genomics, proteomics, and microarray technology has brought much excitement to science, both in teaching and in learning. The public is eager to know about the processes of life. In the present context of the explosive growth of scientific information, a major challenge of modern cell biology is to popularize basic concepts of structures and functions of living cells, to introduce people to the scientific method, to stimulate inquiry, and to analyze and synthesize concepts and paradigms. In this essay we present our experience in mixing science and education in Brazil. For two decades we have developed activities for the science education of teachers and undergraduate students, using microscopy images generated by our work as cell biologists. We describe open-air outreach education activities, games, cell modeling, and other practical and innovative activities presented in public squares and favelas. Especially in developing countries, science education is important, since it may lead to an improvement in quality of life while advancing understanding of traditional scientific ideas. We show that teaching and research can be mutually beneficial rather than competing pursuits in advancing these goals. PMID:15257338

How Do You Like Your Science, Wet or Dry? How Two Lab Experiences Influence Student Understanding of Science Concepts and Perceptions of Authentic Scientific Practice.

PubMed

Munn, Maureen; Knuth, Randy; Van Horne, Katie; Shouse, Andrew W; Levias, Sheldon

2017-01-01

This study examines how two kinds of authentic research experiences related to smoking behavior-genotyping human DNA (wet lab) and using a database to test hypotheses about factors that affect smoking behavior (dry lab)-influence students' perceptions and understanding of scientific research and related science concepts. The study used pre and post surveys and a focus group protocol to compare students who conducted the research experiences in one of two sequences: genotyping before database and database before genotyping. Students rated the genotyping experiment to be more like real science than the database experiment, in spite of the fact that they associated more scientific tasks with the database experience than genotyping. Independent of the order of completing the labs, students showed gains in their understanding of science concepts after completion of the two experiences. There was little change in students' attitudes toward science pre to post, as measured by the Scientific Attitude Inventory II. However, on the basis of their responses during focus groups, students developed more sophisticated views about the practices and nature of science after they had completed both research experiences, independent of the order in which they experienced them. © 2017 M. Munn et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Variation of gene expression in Bacillus subtilis samples of fermentation replicates.

PubMed

Zhou, Ying; Yu, Wen-Bang; Ye, Bang-Ce

2011-06-01

The application of comprehensive gene expression profiling technologies to compare wild and mutated microorganism samples or to assess molecular differences between various treatments has been widely used. However, little is known about the normal variation of gene expression in microorganisms. In this study, an Agilent customized microarray representing 4,106 genes was used to quantify transcript levels of five-repeated flasks to assess normal variation in Bacillus subtilis gene expression. CV analysis and analysis of variance were employed to investigate the normal variance of genes and the components of variance, respectively. The results showed that above 80% of the total variation was caused by biological variance. For the 12 replicates, 451 of 4,106 genes exhibited variance with CV values over 10%. The functional category enrichment analysis demonstrated that these variable genes were mainly involved in cell type differentiation, cell type localization, cell cycle and DNA processing, and spore or cyst coat. Using power analysis, the minimal biological replicate number for a B. subtilis microarray experiment was determined to be six. The results contribute to the definition of the baseline level of variability in B. subtilis gene expression and emphasize the importance of replicate microarray experiments.

ChemBank: a small-molecule screening and cheminformatics resource database.

PubMed

Seiler, Kathleen Petri; George, Gregory A; Happ, Mary Pat; Bodycombe, Nicole E; Carrinski, Hyman A; Norton, Stephanie; Brudz, Steve; Sullivan, John P; Muhlich, Jeremy; Serrano, Martin; Ferraiolo, Paul; Tolliday, Nicola J; Schreiber, Stuart L; Clemons, Paul A

2008-01-01

ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

Micro-magnetic Structures for Biological Applications

NASA Astrophysics Data System (ADS)

Howdyshell, Marci L.

Developments in single-molecule and single-cell experiments over the past century have provided researchers with many tools to probe the responses of cells to stresses such as physical force or to the injection of foreign genes. Often these techniques target the cell membrane, although many are now advancing to probe within the cell. As these techniques are improved upon and the investigations advance toward clinical applications, it has become more critical to achieve high-throughput outcomes which in turn lead to statistically significant results. The technologies developed in this thesis are targeted at transfecting large populations of cells with controlled doses of specific exogenic material without adversely affecting cell viability. Underlying this effort is a platform of lithographically patterned ferromagnetic thin films capable of remotely manipulating and localizing magnetic microbeads attached to biological entities. A novel feature of this approach, as demonstrated here with both DNA and cells, is the opportunity for multiplexed operations on targeted biological specimens. This thesis includes two main thrusts: (1) the advancement of the trapping platforms through experimental verification of mathematical models providing the energy landscapes associated with the traps and (2) implementation of the platform as a basis for rapid and effective high-throughput microchannel and nanochannel cell electroporation devices. The electroporation devices have, in our studies, not only been demonstrated to sustain cell viability with extremely low cell mortality rates, but are also found to be effective for various types of cells. The advances over current electroporation technologies that are achieved in these efforts demonstrate the potential for detection of mRNA expression in heterogeneous cell populations and probing intracellular responses to the introduction of foreign genes into cells.

Fluorescent proteins such as eGFP lead to catalytic oxidative stress in cells.

PubMed

Ganini, Douglas; Leinisch, Fabian; Kumar, Ashutosh; Jiang, JinJie; Tokar, Erik J; Malone, Christine C; Petrovich, Robert M; Mason, Ronald P

2017-08-01

Fluorescent proteins are an important tool that has become omnipresent in life sciences research. They are frequently used for localization of proteins and monitoring of cells [1,2]. Green fluorescent protein (GFP) was the first and has been the most used fluorescent protein. Enhanced GFP (eGFP) was optimized from wild-type GFP for increased fluorescence yield and improved expression in mammalian systems [3]. Many GFP-like fluorescent proteins have been discovered, optimized or created, such as the red fluorescent protein TagRFP [4]. Fluorescent proteins are expressed colorless and immature and, for eGFP, the conversion to the fluorescent form, mature, is known to produce one equivalent of hydrogen peroxide (H 2 O 2 ) per molecule of chromophore [5,6]. Even though it has been proposed that this process is non-catalytic and generates nontoxic levels of H 2 O 2 [6], this study investigates the role of fluorescent proteins in generating free radicals and inducing oxidative stress in biological systems. Immature eGFP and TagRFP catalytically generate the free radical superoxide anion (O 2 •- ) and H 2 O 2 in the presence of NADH. Generation of the free radical O 2 •- and H 2 O 2 by eGFP in the presence of NADH affects the gene expression of cells. Many biological pathways are altered, such as a decrease in HIF1α stabilization and activity. The biological pathways altered by eGFP are known to be implicated in the pathophysiology of many diseases associated with oxidative stress; therefore, it is critical that such experiments using fluorescent proteins are validated with alternative methodologies and the results are carefully interpreted. Since cells inevitably experience oxidative stress when fluorescent proteins are expressed, the use of this tool for cell labeling and in vivo cell tracing also requires validation using alternative methodologies. Published by Elsevier B.V.

A Bridge to Active Learning: A Summer Bridge Program Helps Students Maximize Their Active-Learning Experiences and the Active-Learning Experiences of Others.

PubMed

Cooper, Katelyn M; Ashley, Michael; Brownell, Sara E

2017-01-01

National calls to improve student academic success in college have sparked the development of bridge programs designed to help students transition from high school to college. We designed a 2-week Summer Bridge program that taught introductory biology content in an active-learning way. Through a set of exploratory interviews, we unexpectedly identified that Bridge students had developed sophisticated views of active learning, even though this was not an explicit goal of the program. We conducted an additional set of semistructured interviews that focused on active learning and compared the interviews of Bridge students with those from non-Bridge students who had been eligible for but did not participate in the program. We used the constant comparative method to identify themes from the interviews. We found that Bridge students perceived that, because they knew how to approach active learning and viewed it as important, they benefited more from active learning in introductory biology than non-Bridge students. Specifically, Bridge students seemed to be more aware of their own learning gains from participating in active learning. Compared with the majority of non-Bridge students, the majority of Bridge students described using a greater variety of strategies to maximize their experiences in active learning. Finally, in contrast to non-Bridge students, Bridge students indicated that they take an equitable approach to group work. These findings suggest that we may be able to prime students to maximize their own and other's experiences in active learning. © 2017 K. M. Cooper et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Measuring the elasticity of plant cells with atomic force microscopy.

PubMed

Braybrook, Siobhan A

2015-01-01

The physical properties of biological materials impact their functions. This is most evident in plants where the cell wall contains each cell's contents and connects each cell to its neighbors irreversibly. Examining the physical properties of the plant cell wall is key to understanding how plant cells, tissues, and organs grow and gain the shapes important for their respective functions. Here, we present an atomic force microscopy-based nanoindentation method for examining the elasticity of plant cells at the subcellular, cellular, and tissue level. We describe the important areas of experimental design to be considered when planning and executing these types of experiments and provide example data as illustration. Copyright © 2015 Elsevier Inc. All rights reserved.

Bioengineering and Bioinformatics Summer Institutes: Meeting Modern Challenges in Undergraduate Summer Research

PubMed Central

Dong, Cheng; Snyder, Alan J.; Jones, A. Daniel; Sheets, Erin D.

2008-01-01

Summer undergraduate research programs in science and engineering facilitate research progress for faculty and provide a close-ended research experience for students, which can prepare them for careers in industry, medicine, and academia. However, ensuring these outcomes is a challenge when the students arrive ill-prepared for substantive research or if projects are ill-defined or impractical for a typical 10-wk summer. We describe how the new Bioengineering and Bioinformatics Summer Institutes (BBSI), developed in response to a call for proposals by the National Institutes of Health (NIH) and the National Science Foundation (NSF), provide an impetus for the enhancement of traditional undergraduate research experiences with intense didactic training in particular skills and technologies. Such didactic components provide highly focused and qualified students for summer research with the goal of ensuring increased student satisfaction with research and mentor satisfaction with student productivity. As an example, we focus on our experiences with the Penn State Biomaterials and Bionanotechnology Summer Institute (PSU-BBSI), which trains undergraduates in core technologies in surface characterization, computational modeling, cell biology, and fabrication to prepare them for student-centered research projects in the role of materials in guiding cell biology. PMID:18316807

Water without windows: Evaluating the performance of open cell transmission electron microscopy under saturated water vapor conditions, and assessing its potential for microscopy of hydrated biological specimens.

PubMed

Cassidy, Cathal; Yamashita, Masao; Cheung, Martin; Kalale, Chola; Adaniya, Hidehito; Kuwahara, Ryusuke; Shintake, Tsumoru

2017-01-01

We have performed open cell transmission electron microscopy experiments through pure water vapor in the saturation pressure regime (>0.6 kPa), in a modern microscope capable of sub-Å resolution. We have systematically studied achievable pressure levels, stability and gas purity, effective thickness of the water vapor column and associated electron scattering processes, and the effect of gas pressure on electron optical resolution and image contrast. For example, for 1.3 kPa pure water vapor and 300kV electrons, we report pressure stability of ± 20 Pa over tens of minutes, effective thickness of 0.57 inelastic mean free paths, lattice resolution of 0.14 nm on a reference Au specimen, and no significant degradation in contrast or stability of a biological specimen (M13 virus, with 6 nm body diameter). We have also done some brief experiments to confirm feasibility of loading specimens into an in situ water vapor ambient without exposure to intermediate desiccating conditions. Finally, we have also checked if water experiments had any discernible impact on the microscope performance, and report pertinent vacuum and electron optical data, for reference purposes.

Biological Effects of Nonionizing Electromagnetic Radiation. Volume III, Number 3.

DTIC Science & Technology

1979-03-01

experimental errors psychic healing, dowsing, and telepathy . In addi- inherent in these experiments , there was no dif- tion , tests of human sensitivity... synthetic and naturall y occurring cellular surface area of rat liver cells tha t phospholipid membranes were studied using Reman perturb water suggest

Multichannel microformulators for massively parallel machine learning and automated design of biological experiments

NASA Astrophysics Data System (ADS)

Wikswo, John; Kolli, Aditya; Shankaran, Harish; Wagoner, Matthew; Mettetal, Jerome; Reiserer, Ronald; Gerken, Gregory; Britt, Clayton; Schaffer, David

Genetic, proteomic, and metabolic networks describing biological signaling can have 102 to 103 nodes. Transcriptomics and mass spectrometry can quantify 104 different dynamical experimental variables recorded from in vitro experiments with a time resolution approaching 1 s. It is difficult to infer metabolic and signaling models from such massive data sets, and it is unlikely that causality can be determined simply from observed temporal correlations. There is a need to design and apply specific system perturbations, which will be difficult to perform manually with 10 to 102 externally controlled variables. Machine learning and optimal experimental design can select an experiment that best discriminates between multiple conflicting models, but a remaining problem is to control in real time multiple variables in the form of concentrations of growth factors, toxins, nutrients and other signaling molecules. With time-division multiplexing, a microfluidic MicroFormulator (μF) can create in real time complex mixtures of reagents in volumes suitable for biological experiments. Initial 96-channel μF implementations control the exposure profile of cells in a 96-well plate to different temporal profiles of drugs; future experiments will include challenge compounds. Funded in part by AstraZeneca, NIH/NCATS HHSN271201600009C and UH3TR000491, and VIIBRE.

Registered report: tumour vascularization via endothelial differentiation of glioblastoma stem-like cells.

PubMed

Chroscinski, Denise; Sampey, Darryl; Maherali, Nimet

2015-02-25

The Nature in 2010 (Ricci-Vitiani et al., 2010). The experiments that will be replicated are those reported in Figure 4B and Supplementary Figure 10B (Ricci-Vitiani et al., 2010), which demonstrate that glioblastoma stem-like cells can derive into endothelial cells, and can be selectively ablated to reduce tumor progression in vivo, and Supplementary Figures S10C and S10D (Ricci-Vitiani et al., 2010), which demonstrate that fully differentiated glioblastoma cells cannot form functionally relevant endothelium. The Reproducibility Project: Cancer Biology is a collaboration between the eLife.

Laser biostimulation of patients suffering from multiple sclerosis in respect to the biological influence of laser light

NASA Astrophysics Data System (ADS)

Peszynski-Drews, Cezary; Klimek, Andrzej; Sopinski, Marek; Obrzejta, Dominik

2003-10-01

The authors discuss the results, obtained so far during three years' clinical examination, of laser therapy in the treatment of patients suffering from multiple sclerosis. They regard both the results of former laboratory experiments and so far discovered mechanisms of biological influence of laser light as an objective explanation of high effectiveness of laser therapy in the csae of this so far incurable disease. They discuss wide range of biological mechanisms of laser therapy, examined so far on different levels (cell, tissue, organ), allowing the explanation of beneficial influence of laser light in pathogenetically different morbidities.

3D-modelling of radon-induced cellular radiobiological effects in bronchial airway bifurcations: direct versus bystander effects.

PubMed

Szőke, István; Farkas, Arpád; Balásházy, Imre; Hofmann, Werner; Madas, Balázs G; Szőke, Réka

2012-06-01

The primary objective of this paper was to investigate the distribution of radiation doses and the related biological responses in cells of a central airway bifurcation of the human lung of a hypothetical worker of the New Mexico uranium mines during approximately 12 hours of exposure to short-lived radon progenies. State-of-the-art computational modelling techniques were applied to simulate the relevant biophysical and biological processes in a central human airway bifurcation. The non-uniform deposition pattern of inhaled radon daughters caused a non-uniform distribution of energy deposition among cells, and of related cell inactivation and cell transformation probabilities. When damage propagation via bystander signalling was assessed, it produced more cell killing and cell transformation events than did direct effects. If bystander signalling was considered, variations of the average probabilities of cell killing and cell transformation were supra-linear over time. Our results are very sensitive to the radiobiological parameters, derived from in vitro experiments (e.g., range of bystander signalling), applied in this work and suggest that these parameters may not be directly applicable to realistic three-dimensional (3D) epithelium models.

Spot Scanning and Passive Scattering Proton Therapy: Relative Biological Effectiveness and Oxygen Enhancement Ratio in Cultured Cells.

PubMed

Iwata, Hiromitsu; Ogino, Hiroyuki; Hashimoto, Shingo; Yamada, Maho; Shibata, Hiroki; Yasui, Keisuke; Toshito, Toshiyuki; Omachi, Chihiro; Tatekawa, Kotoha; Manabe, Yoshihiko; Mizoe, Jun-etsu; Shibamoto, Yuta

2016-05-01

To determine the relative biological effectiveness (RBE), oxygen enhancement ratio (OER), and contribution of the indirect effect of spot scanning proton beams, passive scattering proton beams, or both in cultured cells in comparison with clinically used photons. The RBE of passive scattering proton beams at the center of the spread-out Bragg peak (SOBP) was determined from dose-survival curves in 4 cell lines using 6-MV X rays as controls. Survival of 2 cell lines after spot scanning and passive scattering proton irradiation was then compared. Biological effects at the distal end region of the SOBP were also investigated. The OER of passive scattering proton beams and 6 MX X rays were investigated in 2 cell lines. The RBE and OER values were estimated at a 10% cell survival level. The maximum degree of protection of radiation effects by dimethyl sulfoxide was determined to estimate the contribution of the indirect effect against DNA damage. All experiments comparing protons and X rays were made under the same biological conditions. The RBE values of passive scattering proton beams in the 4 cell lines examined were 1.01 to 1.22 (average, 1.14) and were almost identical to those of spot scanning beams. Biological effects increased at the distal end of the SOBP. In the 2 cell lines examined, the OER was 2.74 (95% confidence interval, 2.56-2.80) and 3.08 (2.84-3.11), respectively, for X rays, and 2.39 (2.38-2.43) and 2.72 (2.69-2.75), respectively, for protons (P<.05 for both cells between X rays and protons). The maximum degree of protection was significantly higher for X rays than for proton beams (P<.05). The RBE values of spot scanning and passive scattering proton beams were almost identical. The OER was lower for protons than for X rays. The lower contribution of the indirect effect may partly account for the lower OER of protons. Copyright © 2016 Elsevier Inc. All rights reserved.

Varying iron release from transferrin and lactoferrin proteins. A laboratory experiment.

PubMed

Carmona, Fernando; González, Ana; Sánchez, Manu; Gálvez, Natividad; Cuesta, Rafael; Capdevila, Mercè; Dominguez-Vera, Jose M

2017-11-01

Iron metabolism is an important subject of study for undergraduate students of chemistry and biochemistry. Relevant laboratory exercises are scarce in the literature but would be very helpful in assisting students grasp key concepts. The experiment described here deals with different iron release mechanisms of two protagonists in iron metabolism: serum transferrin (Tf) and lactoferrin (Lf). Despite having very similar structures and iron-binding sites, Tf releases practically all its iron at pH 5.5 while Lf requires a significantly lower pH of 3. This difference in behavior is directly related to their respective biological functions as Tf blood-borne iron into the cell, while Lf competes with pathogens to sequester iron in biological fluids at more acidic pHs.  During this experiment, the students will carry out iron loading and unloading on both human Lf and Tf and monitor the iron release at different pHs using UV-Vis spectroscopy. With this simple approach, the students will discover the different patterns of iron release of Tf and Lf and how this variance in behavior relates to their biological functions. Furthermore, this laboratory practice can be expanded to allow students to investigate a variety of iron proteins. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):521-527, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

Research on the preparation, biocompatibility and bioactivity of magnesium matrix hydroxyapatite composite material.

PubMed

Linsheng, Li; Guoxiang, Lin; Lihui, Li

2016-08-12

In this paper, magnesium matrix hydroxyapatite composite material was prepared by electrophoretic deposition method. The optimal process parameters of electrophoretic deposition were HA suspension concentration of 0.02 kg/L, aging time of 10 days and voltage of 60 V. Animal experiment and SBF immersion experiment were used to test the biocompatibility and bioactivity of this material respectively. The SD rats were divided into control group and implant group. The implant surrounding tissue was taken to do tissue biopsy, HE dyed and organizational analysis after a certain amount of time in the SD rat body. The biological composite material was soaked in SBF solution under homeothermic condition. After 40 days, the bioactivity of the biological composite material was evaluated by testing the growth ability of apatite on composite material. The experiment results showed that magnesium matrix hydroxyapatite biological composite material was successfully prepared by electrophoretic deposition method. Tissue hyperplasia, connective tissue and new blood vessels appeared in the implant surrounding soft tissue. No infiltration of inflammatory cells of lymphocytes and megakaryocytes around the implant was found. After soaked in SBF solution, a layer bone-like apatite was found on the surface of magnesium matrix hydroxyapatite biological composite material. The magnesium matrix hydroxyapatite biological composite material could promot calcium deposition and induce bone-like apatite formation with no cytotoxicity and good biocompatibility and bioactivity.

Role of the p53 Tumor Suppressor Homolog, p63, in Breast Cancer

DTIC Science & Technology

2007-05-01

paradigms. To understand the mechanisms of transcriptional regulation by p63, we analyzed p63 DNA-binding sites in vivo across the entire human ...biological function in human cells. Molecular Cell 24, 593-602 (*these authors contributed equally). Suh EK*, YANG A*, Kettenbach A*, Bamberger C... human genes. Results and details of these experiments are described in Yang et al., (2006), “Relationships between p63 binding, DNA sequence

Length and activity of the root apical meristem revealed in vivo by infrared imaging.

PubMed

Bizet, François; Hummel, Irène; Bogeat-Triboulot, Marie-Béatrice

2015-03-01

Understanding how cell division and cell elongation influence organ growth and development is a long-standing issue in plant biology. In plant roots, most of the cell divisions occur in a short and specialized region, the root apical meristem (RAM). Although RAM activity has been suggested to be of high importance to understand how roots grow and how the cell cycle is regulated, few experimental and numeric data are currently available. The characterization of the RAM is difficult and essentially based upon cell length measurements through destructive and time-consuming microscopy approaches. Here, a new non-invasive method is described that couples infrared light imaging and kinematic analyses and that allows in vivo measurements of the RAM length. This study provides a detailed description of the RAM activity, especially in terms of cell flux and cell division rate. We focused on roots of hydroponic grown poplars and confirmed our method on maize roots. How the RAM affects root growth rate is studied by taking advantage of the high inter-individual variability of poplar root growth. An osmotic stress was applied and did not significantly affect the RAM length, highlighting its homeostasis in short to middle-term responses. The methodology described here simplifies a lot experimental procedures, allows an increase in the number of individuals that can be taken into account in experiments, and means new experiments can be formulated that allow temporal monitoring of the RAM length. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Gene Chips: A New Tool for Biology

NASA Astrophysics Data System (ADS)

Botstein, David

2005-03-01

The knowledge of many complete genomic sequences has led to a ``grand unification of biology,'' consisting of direct evidence that most of the basic cellular functions of all organisms are carried out by genes and proteins whose primary sequences are directly related by descent (i.e. orthologs). Further, genome sequences have made it possible to study all the genes of a single organism simultaneously. We have been using DNA microarrays (sometime referred to as ``gene chips'') to study patterns of gene expression and genome rearrangement in yeast and human cells under a variety of conditions and in human tumors and normal tissues. These experiments produce huge volumes of data; new computational and statistical methods are required to analyze them properly. Examples from this work will be presented to illustrate how genome-scale experiments and analysis can result in new biological insights not obtainable by traditional analyses of genes and proteins one by one. For lymphomas, breast tumors, lung tumors, liver tumors, gastric tumors, brain tumors and soft tissue tumors we have been able, by the application of clustering algorithms, to subclassify tumors of similar anatomical origin on the basis of their gene expression patterns. These subclassifications appear to be reproducible and clinically as well as biologically meaningful. By studying synchronized cells growing in culture, we have identified many hundreds of yeast and human genes that are expressed periodically, at characteristically different points in the cell division cycle. In humans, it turns out that most of these genes are the same genes that comprise the ``proliferation cluster,'' i.e. the genes whose expression is specifically associated with the proliferativeness of tumors and tumor cell lines. Finally, we have been applying a variant of our DNA microarray technology (which we call ``array comparative hybridization'') to follow the DNA copy number of genes, both in tumors and in yeast cells undergoing adaptive evolution during hundreds of generations of growth in continuous culture. These studies suggest a basic similarity in mechanism between adaptive evolution in yeast and tumor progression in humans.

Survey of cell biology experiments in reduced gravity

NASA Technical Reports Server (NTRS)

Taylor, G. R.

1977-01-01

The effects of spaceflight on terrestrial cell systems are discussed. With some important exceptions, static cell systems carried aboard U.S.A. and U.S.S.R. space flights have failed to reveal space related anomalies. Some sophisticated devices which were developed for viewing directly, or continuously recording, the growth of cells, tissue cultures and eggs in flight, are described and the results summarized. The unique presence of high energy, multicharged (HZE) particles and full-range ultraviolet irradiation in space prompted evaluation of the response of single cells to these factors. Summary results and general conclusions are presented. Potential areas of research in future space flights are identified.

Toward synthesizing executable models in biology.

PubMed

Fisher, Jasmin; Piterman, Nir; Bodik, Rastislav

2014-01-01

Over the last decade, executable models of biological behaviors have repeatedly provided new scientific discoveries, uncovered novel insights, and directed new experimental avenues. These models are computer programs whose execution mechanistically simulates aspects of the cell's behaviors. If the observed behavior of the program agrees with the observed biological behavior, then the program explains the phenomena. This approach has proven beneficial for gaining new biological insights and directing new experimental avenues. One advantage of this approach is that techniques for analysis of computer programs can be applied to the analysis of executable models. For example, one can confirm that a model agrees with experiments for all possible executions of the model (corresponding to all environmental conditions), even if there are a huge number of executions. Various formal methods have been adapted for this context, for example, model checking or symbolic analysis of state spaces. To avoid manual construction of executable models, one can apply synthesis, a method to produce programs automatically from high-level specifications. In the context of biological modeling, synthesis would correspond to extracting executable models from experimental data. We survey recent results about the usage of the techniques underlying synthesis of computer programs for the inference of biological models from experimental data. We describe synthesis of biological models from curated mutation experiment data, inferring network connectivity models from phosphoproteomic data, and synthesis of Boolean networks from gene expression data. While much work has been done on automated analysis of similar datasets using machine learning and artificial intelligence, using synthesis techniques provides new opportunities such as efficient computation of disambiguating experiments, as well as the ability to produce different kinds of models automatically from biological data.

Experimental Monitoring of Cr(VI) Bio-reduction Using Electrochemical Geophysics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Birsen Canan; Gary R. Olhoeft; William A. Smith

2007-09-01

Many Department of Energy (DOE) sites are contaminated with highly carcinogenic hexavalent chromium (Cr(VI)). In this research, we explore the feasibility of applying complex resistivity to the detection and monitoring of microbially-induced reduction of hexavalent chromium (Cr(VI)) to a less toxic form (Cr(III)). We hope to measure the change in ionic concentration that occurs during this reduction reaction. This form of reduction promises to be an attractive alternative to more expensive remedial treatment methods. The specific goal of this research is to define the minimum and maximum concentration of the chemical and biological compounds in contaminated samples for which themore » Cr(VI) - Cr(III) reduction processes could be detected via complex resistivity. There are three sets of experiments, each comprised of three sample columns. The first experiment compares three concentrations of Cr(VI) at the same bacterial cell concentration. The second experiment establishes background samples with, and without, Cr(VI) and bacterial cells. The third experiment examines the influence of three different bacterial cell counts on the same concentration of Cr(VI). A polarization relaxation mechanism was observed between 10 and 50 Hz. The polarization mechanism, unfortunately, was not unique to bio-chemically active samples. Spectral analysis of complex resistivity data, however, showed that the frequency where the phase minimum occurred was not constant for bio-chemically active samples throughout the experiment. A significant shifts in phase minima occurred between 10 to 20 Hz from the initiation to completion of Cr(VI) reduction. This phenomena was quantified using the Cole-Cole model and the Marquardt-Levenberg nonlinear least square minimization method. The data suggests that the relaxation time and the time constant of this relaxation are the Cole-Cole parameters most sensitive to changes in biologically-induced reduction of Cr(VI).« less

Using PCR-RFLP technology to teach single nucleotide polymorphism for undergraduates.

PubMed

Zhang, Bo; Wang, Yan; Xu, Xiaofeng; Guan, Xingying; Bai, Yun

2013-01-01

Recent studies indicated that the aberrant gene expression of peroxiredoxin-6 (prdx6) was found in various kinds of cancers. Because of its biochemical function and gene expression pattern in cancer cells, the association between genetic polymorphism of Prdx6 and cancer onset is interesting. In this report, we have developed and implemented a serial experiment in molecular biology laboratory course to teach single nucleotide polymorphism (SNP) to undergraduate students majoring in molecular biology or genetics. The flanking sequence of rs4382766 was located in Prdx6 gene, which contained a restriction site of SspI, and was used as a target in this lab course. The students could mimic real research by integrating different techniques, such as database retrieving, genomic DNA isolation, PCR, and restriction enzyme assay. This serial experiment of PCR-RFLP helps students set up intact idea of molecular biology and understand the relation among individual experiments. Students were found to be more enthusiastic during the laboratory classes than those in the former curriculum. Copyright © 2013 Wiley Periodicals, Inc.

Transport of the highly charged myo-inositol hexakisphosphate molecule across the red blood cell membrane: a phase transfer and biological study.

PubMed

Vincent, Stéphane P; Lehn, Jean-Marie; Lazarte, Jaime; Nicolau, Claude

2002-09-01

To address the problem of delivering highly charged small molecules, such as phytic acid (InsP(6) or IHP), across biological membranes, we investigated an approach based on a non-covalent interaction between transport molecule(s) and IHP. Thus, we synthesized a collection of compounds containing IHP ionically bound to lipophilic (but non-lipidic) ammonium or poly-ammonium cations. First, we assessed the ability of these water-soluble salts to cross a biological membrane by measuring the partition coefficients between human serum and 1-octanol. In view of the ability of IHP to act as potent effector for oxygen release, the O(2)-hemoglobin dissociation curves were then measured for the most efficient salts on whole blood. From both the biological and the physical properties of IHP-ammonium salts we determined that cycloalkylamines (or poly-amines) were the best transport molecules, especially cycloheptyl- and cyclooctylamine. Indeed, the octanol/serum partition coefficient of IHP undecacyclooctylammonium salt, is superior to 1, which is very favorable for potential uptake into the red blood cell membrane. A qualitative correlation was found between the partitioning experiments and the biological evaluations performed on whole blood.

Visualization in simulation tools: requirements and a tool specification to support the teaching of dynamic biological processes.

PubMed

Jørgensen, Katarina M; Haddow, Pauline C

2011-08-01

Simulation tools are playing an increasingly important role behind advances in the field of systems biology. However, the current generation of biological science students has either little or no experience with such tools. As such, this educational glitch is limiting both the potential use of such tools as well as the potential for tighter cooperation between the designers and users. Although some simulation tool producers encourage their use in teaching, little attempt has hitherto been made to analyze and discuss their suitability as an educational tool for noncomputing science students. In general, today's simulation tools assume that the user has a stronger mathematical and computing background than that which is found in most biological science curricula, thus making the introduction of such tools a considerable pedagogical challenge. This paper provides an evaluation of the pedagogical attributes of existing simulation tools for cell signal transduction based on Cognitive Load theory. Further, design recommendations for an improved educational simulation tool are provided. The study is based on simulation tools for cell signal transduction. However, the discussions are relevant to a broader biological simulation tool set.

Teaching Cell Biology to Nonscience Majors Through Forensics, or How to Design a Killer Course

PubMed Central

Arwood, Laura

2004-01-01

Nonscience majors often do not respond to traditional lecture-only biology courses. However, these students still need exposure to basic biological concepts. To accomplish this goal, forensic science was paired with compatible cell biology subjects. Several topics such as human development and molecular biology were found to fulfill this purpose. Another goal was to maximize the hands-on experience of the nonscience major students. This objective was fulfilled by specific activities such as fingerprinting and DNA typing. One particularly effective teaching tool was a mock murder mystery complete with a Grand Jury trial. Another objective was to improve students' attitudes toward science. This was successful in that students felt more confident in their own scientific abilities after taking the course. In pre/post tests, students answered four questions about their ability to conduct science. All four statements showed a positive shift after the course (p values ranging from .001 to .036, df = 23; n = 24). The emphasis on experiential pedagogy was also shown to increase critical thinking skills. In pre/post testing, students in this course significantly increased their performance on critical thinking assessment tests from 33.3% correct to 45.3% (p = .008, df = 4; n = 24). PMID:15257341

In vitro studies of actin filament and network dynamics

PubMed Central

Mullins, R Dyche; Hansen, Scott D

2013-01-01

Now that many genomes have been sequenced, a central concern of cell biology is to understand how the proteins they encode work together to create living matter. In vitro studies form an essential part of this program because understanding cellular functions of biological molecules often requires isolating them and reconstituting their activities. In particular, many elements of the actin cytoskeleton were first discovered by biochemical methods and their cellular functions deduced from in vitro experiments. We highlight recent advances that have come from in vitro studies, beginning with studies of actin filaments, and ending with multi-component reconstitutions of complex actin-based processes, including force-generation and cell spreading. We describe both scientific results and the technical innovations that made them possible. PMID:23267766

Investigating Cell Criticality

NASA Astrophysics Data System (ADS)

Serra, R.; Villani, M.; Damiani, C.; Graudenzi, A.; Ingrami, P.; Colacci, A.

Random Boolean networks provide a way to give a precise meaning to the notion that living beings are in a critical state. Some phenomena which are observed in real biological systems (distribution of "avalanches" in gene knock-out experiments) can be modeled using random Boolean networks, and the results can be analytically proven to depend upon the Derrida parameter, which also determines whether the network is critical. By comparing observed and simulated data one can then draw inferences about the criticality of biological cells, although with some care because of the limited number of experimental observations. The relationship between the criticality of a single network and that of a set of interacting networks, which simulate a tissue or a bacterial colony, is also analyzed by computer simulations.

Multi-scale modeling in cell biology

PubMed Central

Meier-Schellersheim, Martin; Fraser, Iain D. C.; Klauschen, Frederick

2009-01-01

Biomedical research frequently involves performing experiments and developing hypotheses that link different scales of biological systems such as, for instance, the scales of intracellular molecular interactions to the scale of cellular behavior and beyond to the behavior of cell populations. Computational modeling efforts that aim at exploring such multi-scale systems quantitatively with the help of simulations have to incorporate several different simulation techniques due to the different time and space scales involved. Here, we provide a non-technical overview of how different scales of experimental research can be combined with the appropriate computational modeling techniques. We also show that current modeling software permits building and simulating multi-scale models without having to become involved with the underlying technical details of computational modeling. PMID:20448808

A study on biological activity of marine fungi from different habitats in coastal regions.

PubMed

Zhou, Songlin; Wang, Min; Feng, Qi; Lin, Yingying; Zhao, Huange

2016-01-01

In recent years, marine fungi have become an important source of active marine natural products. Former researches are limited in habitats selection of fungi with bioactive compounds. In this paper were to measure antibacterial and antitumor cell activity for secondary metabolites of marine fungi, which were isolated from different habitats in coastal regions. 195 strains of marine fungi were isolated and purified from three different habitats. They biologically active experiment results showed that fungi isolation from the mangrove habitats had stronger antibacterial activity than others, and the stains isolated from the estuarial habitats had the least antibacterial activity. However, the strains separated from beach habitats strongly inhibited tumor cell proliferation in vitro, and fungi of mangrove forest habitats had the weakest activity of inhibiting tumor. Meanwhile, 195 fungal strains belonged to 46 families, 84 genera, 142 species and also showed 137 different types of activity combinations by analyzing the inhibitory activity of the metabolites fungi for 4 strains of pathogenic bacteria and B-16 cells. The study investigated the biological activity of marine fungi isolated from different habitats in Haikou coastal regions. The results help us to understand bioactive metabolites of marine fungi from different habitats, and how to selected biological activity fungi from various marine habitats effectively.

Comprehensive analysis of miRNAs expression profiles revealed potential key miRNA/mRNAs regulating colorectal cancer stem cell self-renewal.

PubMed

Xu, Peng; Wang, Junhua; Sun, Bo; Xiao, Zhongdang

2018-05-20

Self-renewal is essential for the malignant biological behaviors of colorectal cancer stem cells. While the self-renewal molecular mechanisms of colorectal cancer stem cells are not yet fully understood. Recently, miRNAs are reported to be relevant to the self-renewal ability of cancer stem cells. In this study, we first isolated colorectal cancer stem cell from colorectal cancer cell line HCT-116 by 1% low serum culture. Then we conducted a comprehensive analysis based on the miRNAs profiles data of both colorectal cancer stem cells and normal cultured colorectal cancer cells. Pathway analysis revealed multiple pathways including Jak-STAT, TGF-beta, PI3K-Akt and MAPK signaling pathway that are correlated to colorectal cancer. Further, we constructed a miRNA-mRNA network, based on which, several miRNA/mRNA pairs were ranked according to their impact index to the self-renewal of colorectal cancer stem cells. Further biological experiment showed that up-regulation of miR-92a-3p led to cell cycle arrest and reduced colony formation. This work provides clues to find the new potential biomarkers for colorectal cancer stem cell diagnosis and select effective miRNAs for targeted therapy. Copyright © 2018 Elsevier B.V. All rights reserved.

The in vivo structure of biological membranes and evidence for lipid domains.

PubMed

Nickels, Jonathan D; Chatterjee, Sneha; Stanley, Christopher B; Qian, Shuo; Cheng, Xiaolin; Myles, Dean A A; Standaert, Robert F; Elkins, James G; Katsaras, John

2017-05-01

Examining the fundamental structure and processes of living cells at the nanoscale poses a unique analytical challenge, as cells are dynamic, chemically diverse, and fragile. A case in point is the cell membrane, which is too small to be seen directly with optical microscopy and provides little observational contrast for other methods. As a consequence, nanoscale characterization of the membrane has been performed ex vivo or in the presence of exogenous labels used to enhance contrast and impart specificity. Here, we introduce an isotopic labeling strategy in the gram-positive bacterium Bacillus subtilis to investigate the nanoscale structure and organization of its plasma membrane in vivo. Through genetic and chemical manipulation of the organism, we labeled the cell and its membrane independently with specific amounts of hydrogen (H) and deuterium (D). These isotopes have different neutron scattering properties without altering the chemical composition of the cells. From neutron scattering spectra, we confirmed that the B. subtilis cell membrane is lamellar and determined that its average hydrophobic thickness is 24.3 ± 0.9 Ångstroms (Å). Furthermore, by creating neutron contrast within the plane of the membrane using a mixture of H- and D-fatty acids, we detected lateral features smaller than 40 nm that are consistent with the notion of lipid rafts. These experiments-performed under biologically relevant conditions-answer long-standing questions in membrane biology and illustrate a fundamentally new approach for systematic in vivo investigations of cell membrane structure.

Cell biology perspectives in phage biology.

PubMed

Ansaldi, Mireille

2012-01-01

Cellular biology has long been restricted to large cellular organisms. However, as the resolution of microscopic methods increased, it became possible to study smaller cells, in particular bacterial cells. Bacteriophage biology is one aspect of bacterial cell biology that has recently gained insight from cell biology. Despite their small size, bacteriophages could be successfully labeled and their cycle studied in the host cells. This review aims to put together, although non-extensively, several cell biology studies that recently pushed the elucidation of key mechanisms in phage biology, such as the lysis-lysogeny decision in temperate phages or genome replication and transcription, one step further.

Biological Effects of Particles with Very High Energy Deposition on Mammalian Cells Utilizing the Brookhaven Tandem Van de Graaff Accelerator

NASA Technical Reports Server (NTRS)

Saha, Janapriya; Cucinotta, Francis A.; Wang, Minli

2013-01-01

High LET radiation from GCR (Galactic Cosmic Rays) consisting mainly of high charge and energy (HZE) nuclei and secondary protons and neutrons, and secondaries from protons in SPE (Solar Particle Event) pose a major health risk to astronauts due to induction of DNA damage and oxidative stress. Experiments with high energy particles mimicking the space environment for estimation of radiation risk are being performed at NASA Space Radiation Laboratory at BNL. Experiments with low energy particles comparing to high energy particles of similar LET are of interest for investigation of the role of track structure on biological effects. For this purpose, we report results utilizing the Tandem Van de Graaff accelerator at BNL. The primary objective of our studies is to elucidate the influence of high vs low energy deposition on track structure, delta ray contribution and resulting biological responses. These low energy ions are of special relevance as these energies may occur following absorption through the spacecraft and shielding materials in human tissues and nuclear fragments produced in tissues by high energy protons and neutrons. This study will help to verify the efficiency of these low energy particles and better understand how various cell types respond to them.

Physical Model of the Dynamic Instability in an Expanding Cell Culture

PubMed Central

Mark, Shirley; Shlomovitz, Roie; Gov, Nir S.; Poujade, Mathieu; Grasland-Mongrain, Erwan; Silberzan, Pascal

2010-01-01

Abstract Collective cell migration is of great significance in many biological processes. The goal of this work is to give a physical model for the dynamics of cell migration during the wound healing response. Experiments demonstrate that an initially uniform cell-culture monolayer expands in a nonuniform manner, developing fingerlike shapes. These fingerlike shapes of the cell culture front are composed of columns of cells that move collectively. We propose a physical model to explain this phenomenon, based on the notion of dynamic instability. In this model, we treat the first layers of cells at the front of the moving cell culture as a continuous one-dimensional membrane (contour), with the usual elasticity of a membrane: curvature and surface-tension. This membrane is active, due to the forces of cellular motility of the cells, and we propose that this motility is related to the local curvature of the culture interface; larger convex curvature correlates with a stronger cellular motility force. This shape-force relation gives rise to a dynamic instability, which we then compare to the patterns observed in the wound healing experiments. PMID:20141748

PVP-coated, negatively charged silver nanoparticles: A multi-center study of their physicochemical characteristics, cell culture and in vivo experiments

PubMed Central

Ahlberg, Sebastian; Antonopulos, Alexandra; Diendorf, Jörg; Dringen, Ralf; Flöck, Rebekka; Goedecke, Wolfgang; Graf, Christina; Haberl, Nadine; Helmlinger, Jens; Herzog, Fabian; Heuer, Frederike; Hirn, Stephanie; Johannes, Christian; Kittler, Stefanie; Köller, Manfred; Korn, Katrin; Kreyling, Wolfgang G; Krombach, Fritz; Lademann, Jürgen; Loza, Kateryna; Luther, Eva M; Malissek, Marcelina; Meinke, Martina C; Nordmeyer, Daniel; Pailliart, Anne; Raabe, Jörg; Rancan, Fiorenza; Rothen-Rutishauser, Barbara; Rühl, Eckart; Schleh, Carsten; Seibel, Andreas; Sengstock, Christina; Treuel, Lennart; Vogt, Annika; Weber, Katrin; Zellner, Reinhard

2014-01-01

Summary PVP-capped silver nanoparticles with a diameter of the metallic core of 70 nm, a hydrodynamic diameter of 120 nm and a zeta potential of −20 mV were prepared and investigated with regard to their biological activity. This review summarizes the physicochemical properties (dissolution, protein adsorption, dispersability) of these nanoparticles and the cellular consequences of the exposure of a broad range of biological test systems to this defined type of silver nanoparticles. Silver nanoparticles dissolve in water in the presence of oxygen. In addition, in biological media (i.e., in the presence of proteins) the surface of silver nanoparticles is rapidly coated by a protein corona that influences their physicochemical and biological properties including cellular uptake. Silver nanoparticles are taken up by cell-type specific endocytosis pathways as demonstrated for hMSC, primary T-cells, primary monocytes, and astrocytes. A visualization of particles inside cells is possible by X-ray microscopy, fluorescence microscopy, and combined FIB/SEM analysis. By staining organelles, their localization inside the cell can be additionally determined. While primary brain astrocytes are shown to be fairly tolerant toward silver nanoparticles, silver nanoparticles induce the formation of DNA double-strand-breaks (DSB) and lead to chromosomal aberrations and sister-chromatid exchanges in Chinese hamster fibroblast cell lines (CHO9, K1, V79B). An exposure of rats to silver nanoparticles in vivo induced a moderate pulmonary toxicity, however, only at rather high concentrations. The same was found in precision-cut lung slices of rats in which silver nanoparticles remained mainly at the tissue surface. In a human 3D triple-cell culture model consisting of three cell types (alveolar epithelial cells, macrophages, and dendritic cells), adverse effects were also only found at high silver concentrations. The silver ions that are released from silver nanoparticles may be harmful to skin with disrupted barrier (e.g., wounds) and induce oxidative stress in skin cells (HaCaT). In conclusion, the data obtained on the effects of this well-defined type of silver nanoparticles on various biological systems clearly demonstrate that cell-type specific properties as well as experimental conditions determine the biocompatibility of and the cellular responses to an exposure with silver nanoparticles. PMID:25383306

Advances in microfluidic devices made from thermoplastics used in cell biology and analyses.

PubMed

Gencturk, Elif; Mutlu, Senol; Ulgen, Kutlu O

2017-09-01

Silicon and glass were the main fabrication materials of microfluidic devices, however, plastics are on the rise in the past few years. Thermoplastic materials have recently been used to fabricate microfluidic platforms to perform experiments on cellular studies or environmental monitoring, with low cost disposable devices. This review describes the present state of the development and applications of microfluidic systems used in cell biology and analyses since the year 2000. Cultivation, separation/isolation, detection and analysis, and reaction studies are extensively discussed, considering only microorganisms (bacteria, yeast, fungi, zebra fish, etc.) and mammalian cell related studies in the microfluidic platforms. The advantages/disadvantages, fabrication methods, dimensions, and the purpose of creating the desired system are explained in detail. An important conclusion of this review is that these microfluidic platforms are still open for research and development, and solutions need to be found for each case separately.

A role for the geomagnetic field in cell regulation.

PubMed

Liboff, A R

2010-08-01

We advance the hypothesis that biological systems utilize the geomagnetic field (GMF) for functional purposes by means of ion cyclotron resonance-like (ICR) mechanisms. Numerous ICR-designed experiments have demonstrated that living things are sensitive, in varying degrees, to magnetic fields that are equivalent to both changes in the general magnetostatic intensity of the GMF, as well as its temporal perturbations. We propose the existence of ICR-like cell regulation processes, homologous to the way that biochemical messengers alter the net biological state through competing processes of enhancement and inhibition. In like manner, combinations of different resonance frequencies all coupled to the same local magnetic field provide a unique means for cell regulation. Recent work on ultraweak ICR magnetic fields by Zhadin and others fits into our proposed framework if one assumes that cellular systems generate time-varying electric fields of the order 100 mV/cm with bandwidths that include relevant ICR frequencies.

Trends in fluorescence imaging and related techniques to unravel biological information.

PubMed

Haustein, Elke; Schwille, Petra

2007-09-01

Optical microscopy is among the most powerful tools that the physical sciences have ever provided biology. It is indispensable for basic lab work, as well as for cutting edge research, as the visual monitoring of life processes still belongs to the most compelling evidences for a multitude of biomedical applications. Along with the rapid development of new probes and methods for the analysis of laser induced fluorescence, optical microscopy over past years experienced a vast increase of both new techniques and novel combinations of established methods to study biological processes with unprecedented spatial and temporal precision. On the one hand, major technical advances have significantly improved spatial resolution. On the other hand, life scientists are moving toward three- and even four-dimensional cell biology and biophysics involving time as a crucial coordinate to quantitatively understand living specimen. Monitoring the whole cell or tissue in real time, rather than producing snap-shot-like two-dimensional projections, will enable more physiological and, thus, more clinically relevant experiments, whereas an increase in temporal resolution facilitates monitoring fast nonperiodic processes as well as the quantitative analysis of characteristic dynamics.

Trends in fluorescence imaging and related techniques to unravel biological information

PubMed Central

Haustein, Elke; Schwille, Petra

2007-01-01

Optical microscopy is among the most powerful tools that the physical sciences have ever provided biology. It is indispensable for basic lab work, as well as for cutting edge research, as the visual monitoring of life processes still belongs to the most compelling evidences for a multitude of biomedical applications. Along with the rapid development of new probes and methods for the analysis of laser induced fluorescence, optical microscopy over past years experienced a vast increase of both new techniques and novel combinations of established methods to study biological processes with unprecedented spatial and temporal precision. On the one hand, major technical advances have significantly improved spatial resolution. On the other hand, life scientists are moving toward three- and even four-dimensional cell biology and biophysics involving time as a crucial coordinate to quantitatively understand living specimen. Monitoring the whole cell or tissue in real time, rather than producing snap-shot-like two-dimensional projections, will enable more physiological and, thus, more clinically relevant experiments, whereas an increase in temporal resolution facilitates monitoring fast nonperiodic processes as well as the quantitative analysis of characteristic dynamics. PMID:19404444

Dynamic, mechanical integration between nucleus and cell- where physics meets biology.

PubMed

Dickinson, Richard B; Neelam, Srujana; Lele, Tanmay P

2015-01-01

Nuclear motions like rotation, translation and deformation suggest that the nucleus is acted upon by mechanical forces. Molecular linkages with the cytoskeleton are thought to transfer forces to the nuclear surface. We developed an approach to apply reproducible, known mechanical forces to the nucleus in spread adherent cells and quantified the elastic response of the mechanically integrated nucleus-cell. The method is sensitive to molecular perturbations and revealed new insight into the function of the LINC complex. While these experiments revealed elastic behaviors, turnover of the cytoskeleton by assembly/disassembly and binding/unbinding of linkages are expected to dissipate any stored mechanical energy in the nucleus or the cytoskeleton. Experiments investigating nuclear forces over longer time scales demonstrated the mechanical principle that expansive/compressive stresses on the nuclear surface arise from the movement of the cell boundaries to shape and position the nucleus. Such forces can shape the nucleus to conform to cell shapes during cell movements with or without myosin activity.

Dynamic, mechanical integration between nucleus and cell- where physics meets biology

PubMed Central

Dickinson, Richard B; Neelam, Srujana; Lele, Tanmay P

2015-01-01

Nuclear motions like rotation, translation and deformation suggest that the nucleus is acted upon by mechanical forces. Molecular linkages with the cytoskeleton are thought to transfer forces to the nuclear surface. We developed an approach to apply reproducible, known mechanical forces to the nucleus in spread adherent cells and quantified the elastic response of the mechanically integrated nucleus-cell. The method is sensitive to molecular perturbations and revealed new insight into the function of the LINC complex. While these experiments revealed elastic behaviors, turnover of the cytoskeleton by assembly/disassembly and binding/unbinding of linkages are expected to dissipate any stored mechanical energy in the nucleus or the cytoskeleton. Experiments investigating nuclear forces over longer time scales demonstrated the mechanical principle that expansive/compressive stresses on the nuclear surface arise from the movement of the cell boundaries to shape and position the nucleus. Such forces can shape the nucleus to conform to cell shapes during cell movements with or without myosin activity. PMID:26338356

Estimating the Size of Onion Epidermal Cells from Diffraction Patterns

ERIC Educational Resources Information Center

Groff, Jeffrey R.

2012-01-01

Bioscience and premedical profession students are a major demographic served by introductory physics courses at many colleges and universities. Exposing these students to biological applications of physical principles will help them to appreciate physics as a useful tool for their future professions. Here I describe an experiment suitable for…

Measuring the mechanical properties of plant cells by combining micro-indentation with osmotic treatments.

PubMed

Weber, Alain; Braybrook, Siobhan; Huflejt, Michal; Mosca, Gabriella; Routier-Kierzkowska, Anne-Lise; Smith, Richard S

2015-06-01

Growth in plants results from the interaction between genetic and signalling networks and the mechanical properties of cells and tissues. There has been a recent resurgence in research directed at understanding the mechanical aspects of growth, and their feedback on genetic regulation. This has been driven in part by the development of new micro-indentation techniques to measure the mechanical properties of plant cells in vivo. However, the interpretation of indentation experiments remains a challenge, since the force measures results from a combination of turgor pressure, cell wall stiffness, and cell and indenter geometry. In order to interpret the measurements, an accurate mechanical model of the experiment is required. Here, we used a plant cell system with a simple geometry, Nicotiana tabacum Bright Yellow-2 (BY-2) cells, to examine the sensitivity of micro-indentation to a variety of mechanical and experimental parameters. Using a finite-element mechanical model, we found that, for indentations of a few microns on turgid cells, the measurements were mostly sensitive to turgor pressure and the radius of the cell, and not to the exact indenter shape or elastic properties of the cell wall. By complementing indentation experiments with osmotic experiments to measure the elastic strain in turgid cells, we could fit the model to both turgor pressure and cell wall elasticity. This allowed us to interpret apparent stiffness values in terms of meaningful physical parameters that are relevant for morphogenesis. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

[Construction of rAAV2-GPIIb/IIIa vector and test of its expression and function in vitro].

PubMed

Wang, Kai; Peng, Jian-Qiang; Chen, Fang-Ping; Wu, Xiao-Bin

2006-04-01

This study was aimed to explore the possibility of rAAV2 vector-mediating gene therapy for Glanzmann' s thrombasthenia. The rAAV2-GPIIb/IIIa vector was constructed. The GPIIb/IIIa gene expression in mammal cell were examined by different methods, such as: detection of mRNA expression in BHK-21 cells after 24 hours of infection (MOI = 1 x 10(5) v.g/cell) was performed by RT-PCR; the relation between MOI and quantity of GPII6/IIIa gene expression was detected by FACS after 48 hours of infection; GPIIb/IIIa protein expression in BHK-21 cells after 48 hours of infection (MOI = 10(5) v x g/cell) was assayed by Western blot, GPIIb/IIIa protein expression on cell surface was detected by immunofluorescence, and the biological function of expressing product was determined by PAC-1 conjunct experiments. The results showed that GPIIb/IIIa gene expression in mRNA level could be detected in BHK-21 cells after 24 hours of infection at MOI = 1 x 10(5) v x g/cell and the GPIIb/IIIa gene expression in protein level could be detected in BHK-21 cells after 48 hours of infection at MOI = 1 x 10(5) v x g/cell. In certain range, quantity of GPIIb/IIIa gene expression increased with MOI, but overdose of MOI decreased quantity of GPIIb/IIIa gene expression. Activated product of GPIIb/IIIa gene expression could combined with PAC-I, and possesed normal biological function. In conclusion, rAAV2 vactor can effectively mediate GPIIb and GPIIIa gene expressing in mammal cells, and the products of these genes exhibit biological function. This result may provide a basis for application of rAAV2 vector in Glanzmann's thrombasthenia gene therapy in furture.

An Improved Model of Nonuniform Coleochaete Cell Division.

PubMed

Wang, Yuandi; Cong, Jinyu

2016-08-01

Cell division is a key biological process in which cells divide forming new daughter cells. In the present study, we investigate continuously how a Coleochaete cell divides by introducing a modified differential equation model in parametric equation form. We discuss both the influence of "dead" cells and the effects of various end-points on the formation of the new cells' boundaries. We find that the boundary condition on the free end-point is different from that on the fixed end-point; the former has a direction perpendicular to the surface. It is also shown that the outer boundaries of new cells are arc-shaped. The numerical experiments and theoretical analyses for this model to construct the outer boundary are given.

An in silico DNA cloning experiment for the biochemistry laboratory.

PubMed

Elkins, Kelly M

2011-01-01

This laboratory exercise introduces students to concepts in recombinant DNA technology while accommodating a major semester project in protein purification, structure, and function in a biochemistry laboratory for junior- and senior-level undergraduate students. It is also suitable for forensic science courses focused in DNA biology and advanced high school biology classes. Students begin by examining a plasmid map with the goal of identifying which restriction enzymes may be used to clone a piece of foreign DNA containing a gene of interest into the vector. From the National Center for Biotechnology Initiative website, students are instructed to retrieve a protein sequence and use Expasy's Reverse Translate program to reverse translate the protein to cDNA. Students then use Integrated DNA Technologies' OligoAnalyzer to predict the complementary DNA strand and obtain DNA recognition sequences for the desired restriction enzymes from New England Biolabs' website. Students add the appropriate DNA restriction sequences to the double-stranded foreign DNA for cloning into the plasmid and infecting Escherichia coli cells. Students are introduced to computational biology tools, molecular biology terminology and the process of DNA cloning in this valuable single session, in silico experiment. This project develops students' understanding of the cloning process as a whole and contrasts with other laboratory and internship experiences in which the students may be involved in only a piece of the cloning process/techniques. Students interested in pursuing postgraduate study and research or employment in an academic biochemistry or molecular biology laboratory or industry will benefit most from this experience. Copyright © 2010 Wiley Periodicals, Inc.

The evolution of phase holographic imaging from a research idea to publicly traded company

NASA Astrophysics Data System (ADS)

Egelberg, Peter

2018-02-01

Recognizing the value and unmet need for label-free kinetic cell analysis, Phase Holograhic Imaging defines its market segment as automated, easy to use and affordable time-lapse cytometry. The process of developing new technology, meeting customer expectations, sources of corporate funding and R&D adjustments prompted by field experience will be reviewed. Additionally, it is discussed how relevant biological information can be extracted from a sequence of quantitative phase images, with negligible user assistance and parameter tweaking, to simultaneously provide cell culture characteristics such as cell growth rate, viability, division rate, mitosis duration, phagocytosis rate, migration, motility and cell-cell adherence without requiring any artificial cell manipulation.

Biological implications of polydimethylsiloxane-based microfluidic cell culture†

PubMed Central

Regehr, Keil J.; Domenech, Maribella; Koepsel, Justin T.; Carver, Kristopher C.; Ellison-Zelski, Stephanie J.; Murphy, William L.; Schuler, Linda A.; Alarid, Elaine T.; Beebe, David J.

2009-01-01

Polydimethylsiloxane (PDMS) has become a staple of the microfluidics community by virtue of its simple fabrication process and material attributes, such as gas permeability, optical transparency, and flexibility. As microfluidic systems are put toward biological problems and increasingly utilized as cell culture platforms, the material properties of PDMS must be considered in a biological context. Two properties of PDMS were addressed in this study: the leaching of uncured oligomers from the polymer network into microchannel media, and the absorption of small, hydrophobic molecules (i.e. estrogen) from serum-containing media into the polymer bulk. Uncured PDMS oligomers were detectable via MALDI-MS in microchannel media both before and after Soxhlet extraction of PDMS devices in ethanol. Additionally, PDMS oligomers were identified in the plasma membranes of NMuMG cells cultured in PDMS microchannels for 24 hours. Cells cultured in extracted microchannels also contained a detectable amount of uncured PDMS. It was shown that MCF-7 cells seeded directly on PDMS inserts were responsive to hydrophilic prolactin but not hydrophobic estrogen, reflecting its specificity for absorbing small, hydrophobic molecules; and the presence of PDMS floating in wells significantly reduced cellular response to estrogen in a serum-dependent manner. Quantification of estrogen via ELISA revealed that microchannel estrogen partitioned rapidly into the surrounding PDMS to a ratio of approximately 9:1. Pretreatments such as blocking with serum or pre-absorbing estrogen for 24 hours did not affect estrogen loss from PDMS-based microchannels. These findings highlight the importance of careful consideration of culture system properties when determining an appropriate environment for biological experiments. PMID:19606288

Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty.

PubMed

Mdluli, Thembi; Buzzard, Gregery T; Rundell, Ann E

2015-09-01

This model-based design of experiments (MBDOE) method determines the input magnitudes of an experimental stimuli to apply and the associated measurements that should be taken to optimally constrain the uncertain dynamics of a biological system under study. The ideal global solution for this experiment design problem is generally computationally intractable because of parametric uncertainties in the mathematical model of the biological system. Others have addressed this issue by limiting the solution to a local estimate of the model parameters. Here we present an approach that is independent of the local parameter constraint. This approach is made computationally efficient and tractable by the use of: (1) sparse grid interpolation that approximates the biological system dynamics, (2) representative parameters that uniformly represent the data-consistent dynamical space, and (3) probability weights of the represented experimentally distinguishable dynamics. Our approach identifies data-consistent representative parameters using sparse grid interpolants, constructs the optimal input sequence from a greedy search, and defines the associated optimal measurements using a scenario tree. We explore the optimality of this MBDOE algorithm using a 3-dimensional Hes1 model and a 19-dimensional T-cell receptor model. The 19-dimensional T-cell model also demonstrates the MBDOE algorithm's scalability to higher dimensions. In both cases, the dynamical uncertainty region that bounds the trajectories of the target system states were reduced by as much as 86% and 99% respectively after completing the designed experiments in silico. Our results suggest that for resolving dynamical uncertainty, the ability to design an input sequence paired with its associated measurements is particularly important when limited by the number of measurements.

Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty

PubMed Central

Mdluli, Thembi; Buzzard, Gregery T.; Rundell, Ann E.

2015-01-01

This model-based design of experiments (MBDOE) method determines the input magnitudes of an experimental stimuli to apply and the associated measurements that should be taken to optimally constrain the uncertain dynamics of a biological system under study. The ideal global solution for this experiment design problem is generally computationally intractable because of parametric uncertainties in the mathematical model of the biological system. Others have addressed this issue by limiting the solution to a local estimate of the model parameters. Here we present an approach that is independent of the local parameter constraint. This approach is made computationally efficient and tractable by the use of: (1) sparse grid interpolation that approximates the biological system dynamics, (2) representative parameters that uniformly represent the data-consistent dynamical space, and (3) probability weights of the represented experimentally distinguishable dynamics. Our approach identifies data-consistent representative parameters using sparse grid interpolants, constructs the optimal input sequence from a greedy search, and defines the associated optimal measurements using a scenario tree. We explore the optimality of this MBDOE algorithm using a 3-dimensional Hes1 model and a 19-dimensional T-cell receptor model. The 19-dimensional T-cell model also demonstrates the MBDOE algorithm’s scalability to higher dimensions. In both cases, the dynamical uncertainty region that bounds the trajectories of the target system states were reduced by as much as 86% and 99% respectively after completing the designed experiments in silico. Our results suggest that for resolving dynamical uncertainty, the ability to design an input sequence paired with its associated measurements is particularly important when limited by the number of measurements. PMID:26379275

Identification of HYPK-Interacting Proteins Reveals Involvement of HYPK in Regulating Cell Growth, Cell Cycle, Unfolded Protein Response and Cell Death

PubMed Central

Choudhury, Kamalika Roy; Raychaudhuri, Swasti; Bhattacharyya, Nitai P.

2012-01-01

Huntingtin Yeast Two-Hybrid Protein K (HYPK) is an intrinsically unstructured huntingtin (HTT)-interacting protein with chaperone-like activity. To obtain more information about the function(s) of the protein, we identified 27 novel interacting partners of HYPK by pull-down assay coupled with mass spectrometry and, further, 9 proteins were identified by co-localization and co-immunoprecipitation (co-IP) assays. In neuronal cells, (EEF1A1 and HSPA1A), (HTT and LMNB2) and (TP53 and RELA) were identified in complex with HYPK in different experiments. Various Gene Ontology (GO) terms for biological processes, like protein folding (GO: 0006457), response to unfolded protein (GO: 0006986), cell cycle arrest (GO: 0007050), anti-apoptosis (GO: 0006916) and regulation of transcription (GO: 0006355) were significantly enriched with the HYPK-interacting proteins. Cell growth and the ability to refold heat-denatured reporter luciferase were decreased, but cytotoxicity was increased in neuronal cells where HYPK was knocked-down using HYPK antisense DNA construct. The proportion of cells in different phases of cell cycle was also altered in cells with reduced levels of HYPK. These results show that HYPK is involved in several biological processes, possibly through interaction with its partners. PMID:23272104

In vitro biological outcome of laser application for modification or processing of titanium dental implants.

PubMed

Hindy, Ahmed; Farahmand, Farzam; Tabatabaei, Fahimeh Sadat

2017-07-01

There are numerous functions for laser in modern implant dentistry including surface treatment, surface coating, and implant manufacturing. As laser application may potentially improve osseointegration of dental implants, we systematically reviewed the literature for in vitro biological responses to laser-modified or processed titanium dental implants. The literature was searched in PubMed, ISI Web, and Scopus, using keywords "titanium dental implants," "laser," "biocompatibility," and their synonyms. After screening the 136 references obtained, 28 articles met the inclusion criteria. We found that Nd:YAG laser was the most commonly used lasers in the treatment or processing of titanium dental implants. Most of the experiments used cell attachment and cell proliferation to investigate bioresponses of the implants. The most commonly used cells in these assays were osteoblast-like cells. Only one study was conducted in stem cells. These in vitro studies reported higher biocompatibility in laser-modified titanium implants. It seems that laser radiation plays a vital role in cell response to dental implants; however, it is necessary to accomplish more studies using different laser types and parameters on various cells to offer a more conclusive result.

Specimen Sample Preservation for Cell and Tissue Cultures

NASA Technical Reports Server (NTRS)

Meeker, Gabrielle; Ronzana, Karolyn; Schibner, Karen; Evans, Robert

1996-01-01

The era of the International Space Station with its longer duration missions will pose unique challenges to microgravity life sciences research. The Space Station Biological Research Project (SSBRP) is responsible for addressing these challenges and defining the science requirements necessary to conduct life science research on-board the International Space Station. Space Station will support a wide range of cell and tissue culture experiments for durations of 1 to 30 days. Space Shuttle flights to bring experimental samples back to Earth for analyses will only occur every 90 days. Therefore, samples may have to be retained for periods up to 60 days. This presents a new challenge in fresh specimen sample storage for cell biology. Fresh specimen samples are defined as samples that are preserved by means other than fixation and cryopreservation. The challenge of long-term storage of fresh specimen samples includes the need to suspend or inhibit proliferation and metabolism pending return to Earth-based laboratories. With this challenge being unique to space research, there have not been any ground based studies performed to address this issue. It was decided hy SSBRP that experiment support studies to address the following issues were needed: Fixative Solution Management; Media Storage Conditions; Fresh Specimen Sample Storage of Mammalian Cell/Tissue Cultures; Fresh Specimen Sample Storage of Plant Cell/Tissue Cultures; Fresh Specimen Sample Storage of Aquatic Cell/Tissue Cultures; and Fresh Specimen Sample Storage of Microbial Cell/Tissue Cultures. The objective of these studies was to derive a set of conditions and recommendations that can be used in a long duration microgravity environment such as Space Station that will permit extended storage of cell and tissue culture specimens in a state consistent with zero or minimal growth, while at the same time maintaining their stability and viability.

Dynamic speckle interferometry of microscopic processes in solid state and thin biological objects

NASA Astrophysics Data System (ADS)

Vladimirov, A. P.

2015-08-01

Modernized theory of dynamic speckle interferometry is considered. It is shown that the time-average radiation intensity has the parameters characterizing the wave phase changes. It also brings forward an expression for time autocorrelation function of the radiation intensity. It is shown that with the vanishing averaging time value the formulas transform to the prior expressions. The results of experiments with high-cycle material fatigue and cell metabolism analysis conducted using the time-averaging technique are discussed. Good reproducibility of the results is demonstrated. It is specified that the upgraded technique allows analyzing accumulation of fatigue damage, detecting the crack start moment and determining its growth velocity with uninterrupted cyclic load. It is also demonstrated that in the experiments with a cell monolayer the technique allows studying metabolism change both in an individual cell and in a group of cells.

Biomaterials and computation: a strategic alliance to investigate emergent responses of neural cells.

PubMed

Sergi, Pier Nicola; Cavalcanti-Adam, Elisabetta Ada

2017-03-28

Topographical and chemical cues drive migration, outgrowth and regeneration of neurons in different and crucial biological conditions. In the natural extracellular matrix, their influences are so closely coupled that they result in complex cellular responses. As a consequence, engineered biomaterials are widely used to simplify in vitro conditions, disentangling intricate in vivo behaviours, and narrowing the investigation on particular emergent responses. Nevertheless, how topographical and chemical cues affect the emergent response of neural cells is still unclear, thus in silico models are used as additional tools to reproduce and investigate the interactions between cells and engineered biomaterials. This work aims at presenting the synergistic use of biomaterials-based experiments and computation as a strategic way to promote the discovering of complex neural responses as well as to allow the interactions between cells and biomaterials to be quantitatively investigated, fostering a rational design of experiments.

A simple polymeric model describes cell nuclear mechanical response

NASA Astrophysics Data System (ADS)

Banigan, Edward; Stephens, Andrew; Marko, John

The cell nucleus must continually resist inter- and intracellular mechanical forces, and proper mechanical response is essential to basic cell biological functions as diverse as migration, differentiation, and gene regulation. Experiments probing nuclear mechanics reveal that the nucleus stiffens under strain, leading to two characteristic regimes of force response. This behavior depends sensitively on the intermediate filament protein lamin A, which comprises the outer layer of the nucleus, and the properties of the chromatin interior. To understand these mechanics, we study a simulation model of a polymeric shell encapsulating a semiflexible polymer. This minimalistic model qualitatively captures the typical experimental nuclear force-extension relation and observed nuclear morphologies. Using a Flory-like theory, we explain the simulation results and mathematically estimate the force-extension relation. The model and experiments suggest that chromatin organization is a dominant contributor to nuclear mechanics, while the lamina protects cell nuclei from large deformations.

Modeling marrow damage from response data: Evolution from radiation biology to benzene toxicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, T.D.; Morris, M.D.; Hasan, J.S.

1996-12-01

Consensus principles from radiation biology were used to describe a generic set of nonlinear, first-order differential equations for modeling toxicity-induced compensatory cell kinetics in terms of sublethal injury, repair, direct killing, killing of cells with unrepaired sublethal injury, and repopulation. This cellular model was linked to a probit model of hematopoietic mortality that describes death from infection and/or hemorrhage between 5 and 30 days. Mortality data from 27 experiments with 851 dose-response groups, in which doses were protracted by rate and/or fractionation, were used to simultaneously estimate all rate constants by maximum-likelihood methods. Data used represented 18,940 test animals: 12,827more » mice, 2925 rats, 1676 sheep, 829 swine, 479 dogs, and 204 burros. Although a long-term, repopulating hematopoietic stem cell is ancestral to all lineages needed to restore normal homeostasis, the dose-response data from the protracted irradiations indicate clearly that the particular lineage that is critical to hematopoietic recovery does not resemble stemlike cells with regard to radiosensitivity and repopulation rates. Instead, the weakest link in the chain of hematopoiesis was found to have an intrinsic radioresistance equal to or greater than stromal cells and to repopulate at the same rates. Model validation has been achieved by predicting the LD50 and/or fractional group mortality in 38 protracted-dose experiments (rats and mice) that were not used in the fitting of model coefficients. 29 refs., 5 figs., 5 tabs.« less

Cellular Aspects of Prion Replication In Vitro

PubMed Central

Grassmann, Andrea; Wolf, Hanna; Hofmann, Julia; Graham, James; Vorberg, Ina

2013-01-01

Prion diseases or transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative disorders in mammals that are caused by unconventional agents predominantly composed of aggregated misfolded prion protein (PrP). Prions self-propagate by recruitment of host-encoded PrP into highly ordered β-sheet rich aggregates. Prion strains differ in their clinical, pathological and biochemical characteristics and are likely to be the consequence of distinct abnormal prion protein conformers that stably replicate their alternate states in the host cell. Understanding prion cell biology is fundamental for identifying potential drug targets for disease intervention. The development of permissive cell culture models has greatly enhanced our knowledge on entry, propagation and dissemination of TSE agents. However, despite extensive research, the precise mechanism of prion infection and potential strain effects remain enigmatic. This review summarizes our current knowledge of the cell biology and propagation of prions derived from cell culture experiments. We discuss recent findings on the trafficking of cellular and pathologic PrP, the potential sites of abnormal prion protein synthesis and potential co-factors involved in prion entry and propagation. PMID:23340381

Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology

PubMed Central

Udy, Dylan B.; Voorhies, Mark; Chan, Patricia P.; Lowe, Todd M.; Dumont, Sophie

2015-01-01

The rat kangaroo (long-nosed potoroo, Potorous tridactylus) is a marsupial native to Australia. Cultured rat kangaroo kidney epithelial cells (PtK) are commonly used to study cell biological processes. These mammalian cells are large, adherent, and flat, and contain large and few chromosomes—and are thus ideal for imaging intra-cellular dynamics such as those of mitosis. Despite this, neither the rat kangaroo genome nor transcriptome have been sequenced, creating a challenge for probing the molecular basis of these cellular dynamics. Here, we present the sequencing, assembly and annotation of the draft rat kangaroo de novo transcriptome. We sequenced 679 million reads that mapped to 347,323 Trinity transcripts and 20,079 Unigenes. We present statistics emerging from transcriptome-wide analyses, and analyses suggesting that the transcriptome covers full-length sequences of most genes, many with multiple isoforms. We also validate our findings with a proof-of-concept gene knockdown experiment. We expect that this high quality transcriptome will make rat kangaroo cells a more tractable system for linking molecular-scale function and cellular-scale dynamics. PMID:26252667

Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology.

PubMed

Udy, Dylan B; Voorhies, Mark; Chan, Patricia P; Lowe, Todd M; Dumont, Sophie

2015-01-01

The rat kangaroo (long-nosed potoroo, Potorous tridactylus) is a marsupial native to Australia. Cultured rat kangaroo kidney epithelial cells (PtK) are commonly used to study cell biological processes. These mammalian cells are large, adherent, and flat, and contain large and few chromosomes-and are thus ideal for imaging intra-cellular dynamics such as those of mitosis. Despite this, neither the rat kangaroo genome nor transcriptome have been sequenced, creating a challenge for probing the molecular basis of these cellular dynamics. Here, we present the sequencing, assembly and annotation of the draft rat kangaroo de novo transcriptome. We sequenced 679 million reads that mapped to 347,323 Trinity transcripts and 20,079 Unigenes. We present statistics emerging from transcriptome-wide analyses, and analyses suggesting that the transcriptome covers full-length sequences of most genes, many with multiple isoforms. We also validate our findings with a proof-of-concept gene knockdown experiment. We expect that this high quality transcriptome will make rat kangaroo cells a more tractable system for linking molecular-scale function and cellular-scale dynamics.

Consistency of the Proteome in Primary Human Keratinocytes With Respect to Gender, Age, and Skin Localization*

PubMed Central

Sprenger, Adrian; Weber, Sebastian; Zarai, Mostafa; Engelke, Rudolf; Nascimento, Juliana M.; Gretzmeier, Christine; Hilpert, Martin; Boerries, Melanie; Has, Cristina; Busch, Hauke; Bruckner-Tuderman, Leena; Dengjel, Jörn

2013-01-01

Keratinocytes account for 95% of all cells of the epidermis, the stratified squamous epithelium forming the outer layer of the skin, in which a significant number of skin diseases takes root. Immortalized keratinocyte cell lines are often used as research model systems providing standardized, reproducible, and homogenous biological material. Apart from that, primary human keratinocytes are frequently used for medical studies because the skin provides an important route for drug administration and is readily accessible for biopsies. However, comparability of these cell systems is not known. Cell lines may undergo phenotypic shifts and may differ from the in vivo situation in important aspects. Primary cells, on the other hand, may vary in biological functions depending on gender and age of the donor and localization of the biopsy specimen. Here we employed metabolic labeling in combination with quantitative mass spectrometry-based proteomics to assess A431 and HaCaT cell lines for their suitability as model systems. Compared with cell lines, comprehensive profiling of the primary human keratinocyte proteome with respect to gender, age, and skin localization identified an unexpected high proteomic consistency. The data were analyzed by an improved ontology enrichment analysis workflow designed for the study of global proteomics experiments. It enables a quick, comprehensive and unbiased overview of altered biological phenomena and links experimental data to literature. We guide through our workflow, point out its advantages compared with other methods and apply it to visualize differences of cell lines compared with primary human keratinocytes. PMID:23722187

BiologicalNetworks 2.0 - an integrative view of genome biology data

PubMed Central

2010-01-01

Background A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Results Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other) and their relations (interactions, co-expression, co-citations, and other). The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. Conclusions The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org. PMID:21190573