Determination of Ammonia Oxidizing Bacteria and Nitrate Oxidizing Bacteria in Wastewater and Bioreactors

NASA Technical Reports Server (NTRS)

Francis, Somilez Asya

2014-01-01

The process of water purification has many different physical, chemical, and biological processes. One part of the biological process is the task of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB). Both play critical roles in the treatment of wastewater by oxidizing toxic compounds. The broad term is nitrification, a naturally occurring process that is carried out by AOB and NOB by using oxidation to convert ammonia to nitrite and nitrite to nitrate. To monitor this biological activity, bacterial staining was performed on wastewater contained in inoculum tanks and biofilm samples from bioreactors. Using microscopy and qPCR, the purpose of this experiment was to determine if the population of AOB and NOB in wastewater and membrane bioreactors changed depending on temperature and hibernation conditions to determine the optimal parameters for AOB/NOB culture to effectively clean wastewater.

Do Primary Students Understand How Pregnancy Can Occur? A Comparison of Students in Jakarta, West Java, West Nusa Tenggara and South Sulawesi, Indonesia

ERIC Educational Resources Information Center

Utomo, Iwu Dwisetyani; McDonald, Peter; Reimondos, Anna; Utomo, Ariane; Hull, Terence H.

2014-01-01

In Indonesian primary schools, sex education is implicitly integrated into various related subjects, such as science, biology, social studies and religion. The technical facts of ovulation and sperm are mentioned in biology, although little or no connection is made between this process and sexual intercourse. By the end of primary school,…

Understanding Randomness and its Impact on Student Learning: Lessons Learned from Building the Biology Concept Inventory (BCI)

PubMed Central

Garvin-Doxas, Kathy

2008-01-01

While researching student assumptions for the development of the Biology Concept Inventory (BCI; http://bioliteracy.net), we found that a wide class of student difficulties in molecular and evolutionary biology appears to be based on deep-seated, and often unaddressed, misconceptions about random processes. Data were based on more than 500 open-ended (primarily) college student responses, submitted online and analyzed through our Ed's Tools system, together with 28 thematic and think-aloud interviews with students, and the responses of students in introductory and advanced courses to questions on the BCI. Students believe that random processes are inefficient, whereas biological systems are very efficient. They are therefore quick to propose their own rational explanations for various processes, from diffusion to evolution. These rational explanations almost always make recourse to a driver, e.g., natural selection in evolution or concentration gradients in molecular biology, with the process taking place only when the driver is present, and ceasing when the driver is absent. For example, most students believe that diffusion only takes place when there is a concentration gradient, and that the mutational processes that change organisms occur only in response to natural selection pressures. An understanding that random processes take place all the time and can give rise to complex and often counterintuitive behaviors is almost totally absent. Even students who have had advanced or college physics, and can discuss diffusion correctly in that context, cannot make the transfer to biological processes, and passing through multiple conventional biology courses appears to have little effect on their underlying beliefs. PMID:18519614

A Thermo-Poromechanics Finite Element Model for Predicting Arterial Tissue Fusion

NASA Astrophysics Data System (ADS)

Fankell, Douglas P.

This work provides modeling efforts and supplemental experimental work performed towards the ultimate goal of modeling heat transfer, mass transfer, and deformation occurring in biological tissue, in particular during arterial fusion and cutting. Developing accurate models of these processes accomplishes two goals. First, accurate models would enable engineers to design devices to be safer and less expensive. Second, the mechanisms behind tissue fusion and cutting are widely unknown; models with the ability to accurately predict physical phenomena occurring in the tissue will allow for insight into the underlying mechanisms of the processes. This work presents three aims and the efforts in achieving them, leading to an accurate model of tissue fusion and more broadly the thermo-poromechanics (TPM) occurring within biological tissue. Chapters 1 and 2 provide the motivation for developing accurate TPM models of biological tissue and an overview of previous modeling efforts. In Chapter 3, a coupled thermo-structural finite element (FE) model with the ability to predict arterial cutting is offered. From the work presented in Chapter 3, it became obvious a more detailed model was needed. Chapter 4 meets this need by presenting small strain TPM theory and its implementation in an FE code. The model is then used to simulate thermal tissue fusion. These simulations show the model's promise in predicting the water content and temperature of arterial wall tissue during the fusion process, but it is limited by its small deformation assumptions. Chapters 5-7 attempt to address this limitation by developing and implementing a large deformation TPM FE model. Chapters 5, 6, and 7 present a thermodynamically consistent, large deformation TPM FE model and its ability to simulate tissue fusion. Ultimately, this work provides several methods of simulating arterial tissue fusion and the thermo-poromechanics of biological tissue. It is the first work, to the author's knowledge, to simulate the fully coupled TPM of biological tissue and the first to present a fully coupled large deformation TPM FE model. In doing so, a stepping stone for more advanced modeling of biological tissue has been laid.

Population processes during establishment and spread of invading species: implications for survey and detection programs

Treesearch

Andrew Liebhold

2000-01-01

Three important population processes occur during any biological invasion: arrival, establishment, and spread. Arrival is the process by which individual(s) of the invading organism are transported to their new habitat. Establishment can be considered the opposite of extinction and represents the growth of a newly arrived population sufficient such that extinction is...

Slowly switching between environments facilitates reverse evolution in small populations

NASA Astrophysics Data System (ADS)

Tan, Longzhi; Gore, Jeff

2011-03-01

The rate at which a physical process occurs usually changes the behavior of a system. In thermodynamics, the reversibility of a process generally increases when it occurs at an infinitely slow rate. In biological evolution, adaptations to a new environment may be reversed by evolution in the ancestral environment. Such fluctuating environments are ubiquitous in nature, although how the rate of switching affects reverse evolution is unknown. Here we use a computational approach to quantify evolutionary reversibility as a function of the rate of switching between two environments. For small population sizes, which travel on landscapes as random walkers, we find that both genotypic and phenotypic reverse evolution increase at slow switching rates. However, slow switching of environments decreases evolutionary reversibility for a greedy walker, corresponding to large populations (extensive clonal interference). We conclude that the impact of the switching rate for biological evolution is more complicated than other common physical processes, and that a quantitative approach may yield significant insight into reverse evolution.

The biology of deception: emotion and morphine.

PubMed

Stefano, G B; Fricchione, G L

1995-01-01

The biology of deception suggests that denial-like processes are at the core of the cognitive coping. In this regard, with cognitive ability, one associates or assumes that this process occurs by way of a 'rational' mind. Such a detailed cognitive process as being rational would also lead, counter intuitively, to inactivity and or major delays in conclusion reaching. Thus, our perceived rationality may also be a deceptive behavioral response. Of equal noteworthyness, man is also 'emotional'. We surmise that emotion represents the pre-cognitive short-cut to overcome this potential for excessive rationality. In this light, we may explain certain psychiatric disorders such as obsessive-compulsive behavior as emotional extremes dealing with cognitive habits used to bind anxiety operating most probably at the pre-cognitive level. Given recent discoveries in neuroimmunology and an understanding of naturally occurring morphine as both an immune and neurological down-regulatory substance we hypothesize that abnormalities associated with emotional extremes may be due, in part, to morphinergic imbalances.

Incorporating ecogeomorphic feedbacks to better understand resiliency in streams: A review and directions forward

NASA Astrophysics Data System (ADS)

Atkinson, Carla L.; Allen, Daniel C.; Davis, Lisa; Nickerson, Zachary L.

2018-03-01

Decades of interdisciplinary research show river form and function depends on interactions between the living and nonliving world, but a dominant paradigm underlying ecogeomorphic work consists of a top-down, unidirectional approach with abiotic forces driving biotic systems. Stream form and location within the stream network does dictate the habitat and resources available for organisms and overall community structure. Yet this traditional hierarchal framework on its own is inadequate in communicating information regarding the influence of biological systems on fluvial geomorphology that lead to changes in channel morphology, sediment cycling, and system-scale functions (e.g., sediment yield, biogeochemical nutrient cycling). Substantial evidence that organisms influence fluvial geomorphology exists, specifically the ability of aquatic vegetation and lotic animals to modify flow velocities and sediment deposition and transport - thus challenging the traditional hierarchal framework. Researchers recognize the need for ecogeomorphic frameworks that conceptualize feedbacks between organisms, sediment transport, and geomorphic structure. Furthermore, vital ecosystem processes, such as biogeochemical nutrient cycling represent the conversations that are occurring between geomorphological and biological systems. Here we review and synthesize selected case studies highlighting the role organisms play in moderating geomorphic processes and likely interact with these processes to have an impact on an essential ecosystem process, biogeochemical nutrient recycling. We explore whether biophysical interactions can provide information essential to improving predictions of system-scale river functions, specifically sediment transport and biogeochemical cycling, and discuss tools used to study these interactions. We suggest that current conceptual frameworks should acknowledge that hydrologic, geomorphologic, and ecologic processes operate on different temporal scales, generating bidirectional feedback loops over space and time. Hydro- and geomorphologic processes, operating episodically during bankfull conditions, influence ecological processes (e.g., biogeochemical cycling) occurring over longer time periods during base-flow conditions. This ecological activity generates the antecedent conditions that influence the hydro- and geomorphologic processes occurring during the next high flow event, creating a bidirectional feedback. This feedback should enhance the resiliency of fluvial landforms and ecosystem processes, allowing physical and biological processes to pull and push against each other over time.

Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology.

PubMed

Koutinas, Michalis; Kiparissides, Alexandros; Pistikopoulos, Efstratios N; Mantalaris, Athanasios

2012-01-01

The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology

PubMed Central

Koutinas, Michalis; Kiparissides, Alexandros; Pistikopoulos, Efstratios N.; Mantalaris, Athanasios

2013-01-01

The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals. PMID:24688682

Systems biology of personalized nutrition

PubMed Central

van Ommen, Ben; van den Broek, Tim; de Hoogh, Iris; van Erk, Marjan; van Someren, Eugene; Rouhani-Rankouhi, Tanja; Anthony, Joshua C; Hogenelst, Koen; Pasman, Wilrike; Boorsma, André; Wopereis, Suzan

2017-01-01

Abstract Personalized nutrition is fast becoming a reality due to a number of technological, scientific, and societal developments that complement and extend current public health nutrition recommendations. Personalized nutrition tailors dietary recommendations to specific biological requirements on the basis of a person’s health status and goals. The biology underpinning these recommendations is complex, and thus any recommendations must account for multiple biological processes and subprocesses occurring in various tissues and must be formed with an appreciation for how these processes interact with dietary nutrients and environmental factors. Therefore, a systems biology–based approach that considers the most relevant interacting biological mechanisms is necessary to formulate the best recommendations to help people meet their wellness goals. Here, the concept of “systems flexibility” is introduced to personalized nutrition biology. Systems flexibility allows the real-time evaluation of metabolism and other processes that maintain homeostasis following an environmental challenge, thereby enabling the formulation of personalized recommendations. Examples in the area of macro- and micronutrients are reviewed. Genetic variations and performance goals are integrated into this systems approach to provide a strategy for a balanced evaluation and an introduction to personalized nutrition. Finally, modeling approaches that combine personalized diagnosis and nutritional intervention into practice are reviewed. PMID:28969366

Deciphering the Interdependence between Ecological and Evolutionary Networks.

PubMed

Melián, Carlos J; Matthews, Blake; de Andreazzi, Cecilia S; Rodríguez, Jorge P; Harmon, Luke J; Fortuna, Miguel A

2018-05-24

Biological systems consist of elements that interact within and across hierarchical levels. For example, interactions among genes determine traits of individuals, competitive and cooperative interactions among individuals influence population dynamics, and interactions among species affect the dynamics of communities and ecosystem processes. Such systems can be represented as hierarchical networks, but can have complex dynamics when interdependencies among levels of the hierarchy occur. We propose integrating ecological and evolutionary processes in hierarchical networks to explore interdependencies in biological systems. We connect gene networks underlying predator-prey trait distributions to food webs. Our approach addresses longstanding questions about how complex traits and intraspecific trait variation affect the interdependencies among biological levels and the stability of meta-ecosystems. Copyright © 2018 Elsevier Ltd. All rights reserved.

The model of drugs distribution dynamics in biological tissue

NASA Astrophysics Data System (ADS)

Ginevskij, D. A.; Izhevskij, P. V.; Sheino, I. N.

2017-09-01

The dose distribution by Neutron Capture Therapy follows the distribution of 10B in the tissue. The modern models of pharmacokinetics of drugs describe the processes occurring in conditioned "chambers" (blood-organ-tumor), but fail to describe the spatial distribution of the drug in the tumor and in normal tissue. The mathematical model of the spatial distribution dynamics of drugs in the tissue, depending on the concentration of the drug in the blood, was developed. The modeling method is the representation of the biological structure in the form of a randomly inhomogeneous medium in which the 10B distribution occurs. The parameters of the model, which cannot be determined rigorously in the experiment, are taken as the quantities subject to the laws of the unconnected random processes. The estimates of 10B distribution preparations in the tumor and healthy tissue, inside/outside the cells, are obtained.

Förster resonance energy transfer as a tool to study photoreceptor biology

PubMed Central

Hovan, Stephanie C.; Howell, Scott; Park, Paul S.-H.

2010-01-01

Vision is initiated in photoreceptor cells of the retina by a set of biochemical events called phototransduction. These events occur via coordinated dynamic processes that include changes in secondary messenger concentrations, conformational changes and post-translational modifications of signaling proteins, and protein-protein interactions between signaling partners. A complete description of the orchestration of these dynamic processes is still unavailable. Described in this work is the first step in the development of tools combining fluorescent protein technology, Förster resonance energy transfer (FRET), and transgenic animals that have the potential to reveal important molecular insights about the dynamic processes occurring in photoreceptor cells. We characterize the fluorescent proteins SCFP3A and SYFP2 for use as a donor-acceptor pair in FRET assays, which will facilitate the visualization of dynamic processes in living cells. We also demonstrate the targeted expression of these fluorescent proteins to the rod photoreceptor cells of Xenopus laevis, and describe a general method for detecting FRET in these cells. The general approaches described here can address numerous types of questions related to phototransduction and photoreceptor biology by providing a platform to visualize dynamic processes in molecular detail within a native context. PMID:21198205

Laser-induced dissociation processes of protonated glucose: dehydration reactions vs cross-ring dissociation

NASA Astrophysics Data System (ADS)

Dyakov, Y. A.; Kazaryan, M. A.; Golubkov, M. G.; Gubanova, D. P.; Bulychev, N. A.; Kazaryan, S. M.

2018-04-01

Studying the processes occurring in biological systems under irradiation is critically important for understanding the principles of working of biological systems. One of the main problems, which stimulate interest to the processes of photo-induced excitation and ionization of biomolecules, is the necessity of their identification by various mass spectrometry (MS) methods. While simple analysis of small molecules became a standard MS technique long time ago, recognition of large molecules, especially carbohydrates, is still a difficult problem, and requires sophisticated techniques and complicated computer analysis. Due to the large variety of substances in the samples, as far as the complexity of the processes occurring after excitation/ionization of the molecules, the recognition efficiency of MS technique in terms of carbohydrates is still not high enough. Additional theoretical and experimental analysis of ionization and dissociation processes in various kinds of polysaccharides, beginning from the simplest ones, is necessary. In our work, we extent previous theoretical and experimental studies of saccharides, and concentrate our attention to protonated glucose. In this article we paid the most attention to the cross-ring dissociation and water loss reactions due to their importance for identification of various isomers of hydrocarbon molecules (for example, distinguish α- and β-glucose).

Root resorption after orthodontic treatment: a review.

PubMed

Jatania, Archana; Shivalinga, B M; Kiran, Jyothi

2012-01-01

Root resorption that occurs in permanent teeth is an unwanted process and is considered pathologic. Although apical root resorption occurs in individuals who have never experienced orthodontic tooth movement, the incidence among treated individuals is seen to be significantly higher. Some resorption occurs in most orthodontic patients, but because of repair the changes are difficult to detect with radiographic examination and therefore are clinically insignificant. This article gives a review of the various types of root resorption, the etiological factors, the biology and the identification of root resorption.

Quantum biological channel modeling and capacity calculation.

PubMed

Djordjevic, Ivan B

2012-12-10

Quantum mechanics has an important role in photosynthesis, magnetoreception, and evolution. There were many attempts in an effort to explain the structure of genetic code and transfer of information from DNA to protein by using the concepts of quantum mechanics. The existing biological quantum channel models are not sufficiently general to incorporate all relevant contributions responsible for imperfect protein synthesis. Moreover, the problem of determination of quantum biological channel capacity is still an open problem. To solve these problems, we construct the operator-sum representation of biological channel based on codon basekets (basis vectors), and determine the quantum channel model suitable for study of the quantum biological channel capacity and beyond. The transcription process, DNA point mutations, insertions, deletions, and translation are interpreted as the quantum noise processes. The various types of quantum errors are classified into several broad categories: (i) storage errors that occur in DNA itself as it represents an imperfect storage of genetic information, (ii) replication errors introduced during DNA replication process, (iii) transcription errors introduced during DNA to mRNA transcription, and (iv) translation errors introduced during the translation process. By using this model, we determine the biological quantum channel capacity and compare it against corresponding classical biological channel capacity. We demonstrate that the quantum biological channel capacity is higher than the classical one, for a coherent quantum channel model, suggesting that quantum effects have an important role in biological systems. The proposed model is of crucial importance towards future study of quantum DNA error correction, developing quantum mechanical model of aging, developing the quantum mechanical models for tumors/cancer, and study of intracellular dynamics in general.

Engineering Design and Operation Report: Biological Treatment Process for the Removal of Ammonia from a Small Drinking Water System in Iowa: Pilot to Full-Scale

EPA Science Inventory

Many regions in the United States have excessive levels of ammonia in their drinking water sources (e.g., ground and surface waters) as a result of naturally occurring processes, agricultural and urban runoff, concentrated animal feeding operations, municipal wastewater treatment...

Innovative Biological Treatment Process for the Removal of Ammonia, Arsenic, Iron and Manganese from a Small Drinking Water System in Gilbert, Iowa (Phase 1: Pilot Evaluation)

EPA Science Inventory

Many regions in the United States have excessive levels of ammonia in their drinking water sources (e.g., ground and surface waters) as a result of naturally occurring processes, agricultural and urban runoff, concentrated animal feeding operations, municipal wastewater treatment...

Forest health in the Blue Mountains: an plant ecologist's perspective on ecosystem processes and biological diversity.

Treesearch

Charles G. Johnson

1994-01-01

Natural disturbances are important to ecosystem processes. Disturbances historically have occurred in the vegetation of the Blue Mountain area of northeastern Oregon and southeastern Washington. The primary modifying events that historically have cycled through most of its plant communities are fire, grazing and browsing, insect and disease epidemics, windthrow,...

Hormesis and adaptive cellular control systems

EPA Science Inventory

Hormetic dose response occurs for many endpoints associated with exposures of biological organisms to environmental stressors. Cell-based U- or inverted U-shaped responses may derive from common processes involved in activation of adaptive responses required to protect cells from...

Engineered biosealant producing inorganic and organic biopolymers

USDA-ARS?s Scientific Manuscript database

Microbiologically induced calcium carbonate precipitation (MICCP) is a naturally occurring biological process that has shown its potential in remediation of a wide range of structural damages including concrete cracks. MICCP involves sequential microbiological and chemical reactions, such as urea h...

When galectins recognize glycans: from biochemistry to physiology and back again.

PubMed

Di Lella, Santiago; Sundblad, Victoria; Cerliani, Juan P; Guardia, Carlos M; Estrin, Dario A; Vasta, Gerardo R; Rabinovich, Gabriel A

2011-09-20

In the past decade, increasing efforts have been devoted to the study of galectins, a family of evolutionarily conserved glycan-binding proteins with multifunctional properties. Galectins function, either intracellularly or extracellularly, as key biological mediators capable of monitoring changes occurring on the cell surface during fundamental biological processes such as cellular communication, inflammation, development, and differentiation. Their highly conserved structures, exquisite carbohydrate specificity, and ability to modulate a broad spectrum of biological processes have captivated a wide range of scientists from a wide spectrum of disciplines, including biochemistry, biophysics, cell biology, and physiology. However, in spite of enormous efforts to dissect the functions and properties of these glycan-binding proteins, limited information about how structural and biochemical aspects of these proteins can influence biological functions is available. In this review, we aim to integrate structural, biochemical, and functional aspects of this bewildering and ancient family of glycan-binding proteins and discuss their implications in physiologic and pathologic settings. © 2011 American Chemical Society

Practicing safe cell culture: applied process designs for minimizing virus contamination risk.

PubMed

Kiss, Robert D

2011-01-01

CONFERENCE PROCEEDING Proceedings of the PDA/FDA Adventitious Viruses in Biologics: Detection and Mitigation Strategies Workshop in Bethesda, MD, USA; December 1-3, 2010 Guest Editors: Arifa Khan (Bethesda, MD), Patricia Hughes (Bethesda, MD) and Michael Wiebe (San Francisco, CA) Genentech responded to a virus contamination in its biologics manufacturing facility by developing and implementing a series of barriers specifically designed to prevent recurrence of this significant and impactful event. The barriers included steps to inactivate or remove potential virus particles from the many raw materials used in cell culture processing. Additionally, analytical testing barriers provided protection of the downstream processing areas should a culture contamination occur, and robust virus clearance capability provided further assurance of virus safety should a low level contamination go undetected. This conference proceeding will review Genentech's approach, and lessons learned, in minimizing virus contamination risk in cell culture processes through multiple layers of targeted barriers designed to deliver biologics products with high success rates.

Twelve testable hypotheses on the geobiology of weathering.

PubMed

Brantley, S L; Megonigal, J P; Scatena, F N; Balogh-Brunstad, Z; Barnes, R T; Bruns, M A; Van Cappellen, P; Dontsova, K; Hartnett, H E; Hartshorn, A S; Heimsath, A; Herndon, E; Jin, L; Keller, C K; Leake, J R; McDowell, W H; Meinzer, F C; Mozdzer, T J; Petsch, S; Pett-Ridge, J; Pregitzer, K S; Raymond, P A; Riebe, C S; Shumaker, K; Sutton-Grier, A; Walter, R; Yoo, K

2011-03-01

Critical Zone (CZ) research investigates the chemical, physical, and biological processes that modulate the Earth's surface. Here, we advance 12 hypotheses that must be tested to improve our understanding of the CZ: (1) Solar-to-chemical conversion of energy by plants regulates flows of carbon, water, and nutrients through plant-microbe soil networks, thereby controlling the location and extent of biological weathering. (2) Biological stoichiometry drives changes in mineral stoichiometry and distribution through weathering. (3) On landscapes experiencing little erosion, biology drives weathering during initial succession, whereas weathering drives biology over the long term. (4) In eroding landscapes, weathering-front advance at depth is coupled to surface denudation via biotic processes. (5) Biology shapes the topography of the Critical Zone. (6) The impact of climate forcing on denudation rates in natural systems can be predicted from models incorporating biogeochemical reaction rates and geomorphological transport laws. (7) Rising global temperatures will increase carbon losses from the Critical Zone. (8) Rising atmospheric P(CO2) will increase rates and extents of mineral weathering in soils. (9) Riverine solute fluxes will respond to changes in climate primarily due to changes in water fluxes and secondarily through changes in biologically mediated weathering. (10) Land use change will impact Critical Zone processes and exports more than climate change. (11) In many severely altered settings, restoration of hydrological processes is possible in decades or less, whereas restoration of biodiversity and biogeochemical processes requires longer timescales. (12) Biogeochemical properties impart thresholds or tipping points beyond which rapid and irreversible losses of ecosystem health, function, and services can occur. © 2011 Blackwell Publishing Ltd.

Microgravity research in plant biological systems: Realizing the potential of molecular biology

NASA Technical Reports Server (NTRS)

Lewis, Norman G.; Ryan, Clarence A.

1993-01-01

The sole all-pervasive feature of the environment that has helped shape, through evolution, all life on Earth is gravity. The near weightlessness of the Space Station Freedom space environment allows gravitational effects to be essentially uncoupled, thus providing an unprecedented opportunity to manipulate, systematically dissect, study, and exploit the role of gravity in the growth and development of all life forms. New and exciting opportunities are now available to utilize molecular biological and biochemical approaches to study the effects of microgravity on living organisms. By careful experimentation, we can determine how gravity perception occurs, how the resulting signals are produced and transduced, and how or if tissue-specific differences in gene expression occur. Microgravity research can provide unique new approaches to further our basic understanding of development and metabolic processes of cells and organisms, and to further the application of this new knowledge for the betterment of humankind.

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.

Pectin in foods

USDA-ARS?s Scientific Manuscript database

Pectin, a complex polysaccharide, is a major component of non-lignified cell walls of dicotyledonous and some monocotyledonous plants. Its food-related technological functions are numerous and mirror many of its biological functions. As a naturally occurring component of raw or processed foods and a...

Developments and departures in the philosophy of soil science

USDA-ARS?s Scientific Manuscript database

Traditional soil science curriculums provide comprehensive instruction on soil properties, soil classification, and the physical, chemical, and biological processes that occur in soils. This reductionist perspective is sometimes balanced with a more holistic perspective that focuses on soils as natu...

Treatment of winery wastewater by physicochemical, biological and advanced processes: a review.

PubMed

Ioannou, L A; Li Puma, G; Fatta-Kassinos, D

2015-04-09

Winery wastewater is a major waste stream resulting from numerous cleaning operations that occur during the production stages of wine. The resulting effluent contains various organic and inorganic contaminants and its environmental impact is notable, mainly due to its high organic/inorganic load, the large volumes produced and its seasonal variability. Several processes for the treatment of winery wastewater are currently available, but the development of alternative treatment methods is necessary in order to (i) maximize the efficiency and flexibility of the treatment process to meet the discharge requirements for winery effluents, and (ii) decrease both the environmental footprint, as well as the investment/operational costs of the process. This review, presents the state-of-the-art of the processes currently applied and/or tested for the treatment of winery wastewater, which were divided into five categories: i.e., physicochemical, biological, membrane filtration and separation, advanced oxidation processes, and combined biological and advanced oxidation processes. The advantages and disadvantages, as well as the main parameters/factors affecting the efficiency of winery wastewater treatment are discussed. Both bench- and pilot/industrial-scale processes have been considered for this review. Copyright © 2014 Elsevier B.V. All rights reserved.

Inhibition of microbiological sulfide oxidation by methanethiol and dimethyl polysulfides at natron-alkaline conditions.

PubMed

van den Bosch, Pim L F; de Graaff, Marco; Fortuny-Picornell, Marc; van Leerdam, Robin C; Janssen, Albert J H

2009-06-01

To avoid problems related to the discharge of sulfidic spent caustics, a biotechnological process is developed for the treatment of gases containing both hydrogen sulfide and methanethiol. The process operates at natron-alkaline conditions (>1 mol L(-1) of sodium- and potassium carbonates and a pH of 8.5-10) to enable the treatment of gases with a high partial CO(2) pressure. In the process, methanethiol reacts with biologically produced sulfur particles to form a complex mixture predominantly consisting of inorganic polysulfides, dimethyl disulfide (DMDS), and dimethyl trisulfide (DMTS). The effect of these organic sulfur compounds on the biological oxidation of sulfide to elemental sulfur was studied with natron-alkaliphilic bacteria belonging to the genus Thioalkalivibrio. Biological oxidation rates were reduced by 50% at 0.05 mM methanethiol, while for DMDS and DMTS, this was estimated to occur at 1.5 and 1.0 mM, respectively. The inhibiting effect of methanethiol on biological sulfide oxidation diminished due to its reaction with biologically produced sulfur particles. This reaction increases the feasibility of biotechnological treatment of gases containing both hydrogen sulfide and methanethiol at natron-alkaline conditions.

Atomic Force Microscopy of Biological Membranes

PubMed Central

Frederix, Patrick L.T.M.; Bosshart, Patrick D.; Engel, Andreas

2009-01-01

Abstract Atomic force microscopy (AFM) is an ideal method to study the surface topography of biological membranes. It allows membranes that are adsorbed to flat solid supports to be raster-scanned in physiological solutions with an atomically sharp tip. Therefore, AFM is capable of observing biological molecular machines at work. In addition, the tip can be tethered to the end of a single membrane protein, and forces acting on the tip upon its retraction indicate barriers that occur during the process of protein unfolding. Here we discuss the fundamental limitations of AFM determined by the properties of cantilevers, present aspects of sample preparation, and review results achieved on reconstituted and native biological membranes. PMID:19167286

300 mm arrays and 30 nm Features: Frontiers in Sorting Biological Objects

NASA Astrophysics Data System (ADS)

Austin, Robert; Comella, Brandon; D'Silva, Joseph; Sturm, James

2014-03-01

One of the great challenges in prediction of metastasis is determining when the metastatic process actually begins. It is presumed that this process occurs due to passage of biological objects in the blood from tumor to remote sites. We will discuss our attempts to find both very large objects (circulating tumor cell clumps) and very small (exosomes) using a combination of extremely large scale photolithography on 300 mm wafers and deep-UV lithography to produce sub-100 nm arrays to sort exosomes. These technologies push the envelope of present day academic facilities . Supported by the National Science Foundation and the National Cancer Institute.

Investigating Processes of Materials Formation via Liquid Phase and Cryogenic TEM

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

De Yoreo, James J.; Sommerdijk, Nico

2016-06-14

The formation of materials in solutions is a widespread phenomenon in synthetic, biological and geochemical systems, occurring through dynamic processes of nucleation, self-assembly, crystal growth, and coarsening. The recent advent of liquid phase TEM and advances in cryogenic TEM are transforming our understanding of these phenomena by providing new insights into the underlying physical and chemical mechanisms. The techniques have been applied to metallic and semiconductor nanoparticles, geochemical and biological minerals, electrochemical systems, macromolecular complexes, and selfassembling systems, both organic and inorganic. New instrumentation and methodologies currently on the horizon promise new opportunities for advancing the science of materials synthesis.

Biologically controlled minerals as potential indicators of life

NASA Technical Reports Server (NTRS)

Schwartz, D. E.; Mancinelli, R. L.; Kaneshiro, E.

1991-01-01

Minerals can be produced and deposited either by abiotic or biologic means. Regardless of their origin, mineral crystals reflect the environment conditions (e.g., temperature, pressure, chemical composition, and redox potential) present during crystal formation. Biologically-produced mineral crystals are grown or reworked under the control of their host organism and reflect an environment different from the abiotic environment. In addition, minerals of either biologic or abiotic origin have great longevities. For these reasons, biologically produced minerals have been proposed as biomarkers. Biomarkers are key morphological, chemical, and isotopic signatures of living systems that can be used to determine if life processes have occurred. Studies of biologically controlled minerals produced by the protist, Paramecium tetraurelia, were initiated since techniques have already been developed to culture them and isolate their crystalline material, and methods are already in place to analyze this material. Two direct crystalline phases were identified. One phase, whose chemical composition is high in Mg, was identified as struvite. The second phase, whose chemical composition is high in Ca, has not been previously found occurring naturally and may be considered a newly discovered material. Analyses are underway to determine the characteristics of these minerals in order to compare them with characteristics of these minerals in order to compare them with characteristics of minerals formed abiotically, but with the same chemical composition.

A Multi-isotope Tracer Approach Linking Land Use With Carbon and Nitrogen Cycling in the San Joaquin River System

NASA Astrophysics Data System (ADS)

Young, M. B.; Kendall, C.; Silva, S. R.; Dahlgren, R. A.; Stringfellow, W. T.

2008-12-01

The San Joaquin River (SJR) is a large hypereutrophic river located in the Central Valley, California, a major agricultural region. Nutrient subsidies, algae, and other organic material from the San Joaquin River contribute to periods of low dissolved oxygen in the Stockton Deep Water Ship Channel, inhibiting salmon migration. We used a multi-isotope approach to link nitrate and particulate organic matter (POM) to different sources and related land uses. The isotope data was also used to better understand the physical and biological processes controlling the distribution of nitrate and POM throughout the river system. Samples collected from the mainstem SJR and tributaries twice-monthly to monthly between March 2005 and December 2007 were analyzed for nitrate, POM, and water isotopes. There are many land uses surrounding the SJR and its tributaries, including multiple types of agriculture, dairies, wetlands, and urban areas. Samples from SJR tributaries containing both major and minor contributions of wetland discharge generally had distinct nitrate and POM isotope signatures compared to other tributaries. Unique nitrate and POM isotope signatures associated with wetland discharges may reflect anaerobic biological processes occurring in flooded soils. For the mainstem SJR, we applied an isotope mass balance approach using nitrate and water isotopes to calculate the expected downstream isotope values based upon measured inputs from known water sources such as drains and tributaries. Differences between the calculated downstream isotope values and the measured values indicate locations and time periods when either biological processes such as algal uptake, or physical process such as the input of unidentified water sources, significantly altered the isotope signatures of water, POM, or nitrate within the SJR. This research will provide a better understanding of how different land uses affect the delivery of carbon and nitrogen to the SJR, and will provide a better understanding of the physical and biological processes occurring within the mainstem SJR.

Biological embedding: evaluation and analysis of an emerging concept for nursing scholarship.

PubMed

Nist, Marliese Dion

2017-02-01

The purpose of this paper was to report the analysis of the concept of biological embedding. Research that incorporates a life course perspective is becoming increasingly prominent in the health sciences. Biological embedding is a central concept in life course theory and may be important for nursing theories to enhance our understanding of health states in individuals and populations. Before the concept of biological embedding can be used in nursing theory and research, an analysis of the concept is required to advance it towards full maturity. Concept analysis. PubMed, CINAHL and PsycINFO were searched for publications using the term 'biological embedding' or 'biological programming' and published through 2015. An evaluation of the concept was first conducted to determine the concept's level of maturity and was followed by a concept comparison, using the methods for concept evaluation and comparison described by Morse. A consistent definition of biological embedding - the process by which early life experience alters biological processes to affect adult health outcomes - was found throughout the literature. The concept has been used in several theories that describe the mechanisms through which biological embedding might occur and highlight its role in the development of health trajectories. Biological embedding is a partially mature concept, requiring concept comparison with an overlapping concept - biological programming - to more clearly establish the boundaries of biological embedding. Biological embedding has significant potential for theory development and application in multiple academic disciplines, including nursing. © 2016 John Wiley & Sons Ltd.

Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity.

PubMed

Hateley, Shannon; Hosamani, Ravikumar; Bhardwaj, Shilpa R; Pachter, Lior; Bhattacharya, Sharmila

2016-10-01

Altered gravity can perturb normal development and induce corresponding changes in gene expression. Understanding this relationship between the physical environment and a biological response is important for NASA's space travel goals. We use RNA-Seq and qRT-PCR techniques to profile changes in early Drosophila melanogaster pupae exposed to chronic hypergravity (3g, or three times Earth's gravity). During the pupal stage, D. melanogaster rely upon gravitational cues for proper development. Assessing gene expression changes in the pupae under altered gravity conditions helps highlight gravity-dependent genetic pathways. A robust transcriptional response was observed in hypergravity-treated pupae compared to controls, with 1513 genes showing a significant (q<0.05) difference in gene expression. Five major biological processes were affected: ion transport, redox homeostasis, immune response, proteolysis, and cuticle development. This outlines the underlying molecular and biological changes occurring in Drosophila pupae in response to hypergravity; gravity is important for many biological processes on Earth. Published by Elsevier Inc.

A Biobehavioral Model of Cancer Stress and Disease Course

PubMed Central

Andersen, Barbara L.; Kiecolt-Glaser, Janice K.; Glaser, Ronald

2009-01-01

Approximately 1 million Americans are diagnosed with cancer each year and must cope with the disease and treatments. Many studies have documented the deteriorations in quality of life that occur. These data suggest that the adjustment process is burdensome and lengthy. There is ample evidence showing that adults experiencing other long-term stressors experience not only high rates of adjustment difficulties (e.g., syndromal depression) but important biologic effects, such as persistent downregulation of elements of the immune system, and adverse health outcomes, such as higher rates of respiratory tract infections. Thus, deteriorations in quality of life with cancer are underscored if they have implications for biological processes, such as the immune system, relating to disease progression and spread. Considering these and other data, a biobehavioral model of adjustment to the stresses of cancer is offered, and mechanisms by which psychological and behavioral responses may influence biological processes and, perhaps, health outcomes are proposed. Finally, strategies for testing the model via experiments testing psychological interventions are offered. PMID:8024167

FIRST ORDER KINETIC GAS GENERATION MODEL PARAMETERS FOR WET LANDFILLS

EPA Science Inventory

Landfill gas is produced as a result of a sequence of physical, chemical, and biological processes occurring within an anaerobic landfill. Landfill operators, energy recovery project owners, regulators, and energy users need to be able to project the volume of gas produced and re...

The Interaction of Nitrites with Food, Drugs, and Contaminants.

ERIC Educational Resources Information Center

Greenland, Sander

1978-01-01

Nitrites commonly occur in food and drinking water as additives, contaminants, or products of biological processes. These highly reactive substances combine with other commonly ingested substances to form potent carcinogens. Controls are needed on levels of nitrites and reactive contaminants in food and drinking water. (RE)

Biological Remediation of Petroleum Contaminants

NASA Astrophysics Data System (ADS)

Kuhad, Ramesh Chander; Gupta, Rishi

Large volumes of hazardous wastes are generated in the form of oily sludges and contaminated soils during crude oil transportation and processing. Although many physical, chemical and biological treatment technologies are available for petroleum contaminants petroleum contaminants in soil, biological methods have been considered the most cost-effective. Practical biological remediation methods typically involve direct use of the microbes naturally occurring in the contaminated environment and/or cultured indigenous or modified microorganisms. Environmental and nutritional factors, including the properties of the soil, the chemical structure of the hydrocarbon(s), oxygen, water, nutrient availability, pH, temperature, and contaminant bioavailability, can significantly affect the rate and the extent of hydrocarbon biodegradation hydrocarbon biodegradation by microorganisms in contaminated soils. This chapter concisely discusses the major aspects of bioremediation of petroleum contaminants.

[The Biology of Learning].

PubMed

Campo-Cabal, Gerardo

2012-01-01

The effort to relate mental and biological functioning has fluctuated between two doctrines: 1) an attempt to explain mental functioning as a collective property of the brain and 2) as one relatied to other mental processes associated with specific regions of the brain. The article reviews the main theories developed over the last 200 years: phrenology, the psuedo study of the brain, mass action, cellular connectionism and distributed processing among others. In addition, approaches have emerged in recent years that allows for an understanding of the biological determinants and individual differences in complex mental processes through what is called cognitive neuroscience. Knowing the definition of neuroscience, the learning of memory, the ways in which learning occurs, the principles of the neural basis of memory and learning and its effects on brain function, among other things, allows us the basic understanding of the processes of memory and learning and is an important requirement to address the best manner to commit to the of training future specialists in Psychiatry. Copyright © 2012 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Planar optical waveguide based sandwich assay sensors and processes for the detection of biological targets including protein markers, pathogens and cellular debris

DOEpatents

Martinez, Jennifer S [Santa Fe, NM; Swanson, Basil I [Los Alamos, NM; Grace, Karen M [Los Alamos, NM; Grace, Wynne K [Los Alamos, NM; Shreve, Andrew P [Santa Fe, NM

2009-06-02

An assay element is described including recognition ligands bound to a film on a single mode planar optical waveguide, the film from the group of a membrane, a polymerized bilayer membrane, and a self-assembled monolayer containing polyethylene glycol or polypropylene glycol groups therein and an assay process for detecting the presence of a biological target is described including injecting a biological target-containing sample into a sensor cell including the assay element, with the recognition ligands adapted for binding to selected biological targets, maintaining the sample within the sensor cell for time sufficient for binding to occur between selected biological targets within the sample and the recognition ligands, injecting a solution including a reporter ligand into the sensor cell; and, interrogating the sample within the sensor cell with excitation light from the waveguide, the excitation light provided by an evanescent field of the single mode penetrating into the biological target-containing sample to a distance of less than about 200 nanometers from the waveguide thereby exciting the fluorescent-label in any bound reporter ligand within a distance of less than about 200 nanometers from the waveguide and resulting in a detectable signal.

Bone fracture healing in mechanobiological modeling: A review of principles and methods.

PubMed

Ghiasi, Mohammad S; Chen, Jason; Vaziri, Ashkan; Rodriguez, Edward K; Nazarian, Ara

2017-06-01

Bone fracture is a very common body injury. The healing process is physiologically complex, involving both biological and mechanical aspects. Following a fracture, cell migration, cell/tissue differentiation, tissue synthesis, and cytokine and growth factor release occur, regulated by the mechanical environment. Over the past decade, bone healing simulation and modeling has been employed to understand its details and mechanisms, to investigate specific clinical questions, and to design healing strategies. The goal of this effort is to review the history and the most recent work in bone healing simulations with an emphasis on both biological and mechanical properties. Therefore, we provide a brief review of the biology of bone fracture repair, followed by an outline of the key growth factors and mechanical factors influencing it. We then compare different methodologies of bone healing simulation, including conceptual modeling (qualitative modeling of bone healing to understand the general mechanisms), biological modeling (considering only the biological factors and processes), and mechanobiological modeling (considering both biological aspects and mechanical environment). Finally we evaluate different components and clinical applications of bone healing simulation such as mechanical stimuli, phases of bone healing, and angiogenesis.

Biodegradation of phytosanitary products in biological wastewater treatment.

PubMed

Massot, A; Estève, K; Noilet, P; Méoule, C; Poupot, C; Mietton-Peuchot, M

2012-04-15

Agricultural activity generates two types of waste: firstly, biodegradable organic effluents generally treated by biological processes and, secondly, phytosanitary effluents which contain residues of plant protection products. The latter are collected and treated. Current technological solutions are essentially based on concentration or physical-chemical processes. However, recent improvements in the biodegradability of pesticides open the way to the consideration of alternative, biological, treatment using mixed liquor from wastewater plant activated sludge. The feasibility of the biological treatment of viticultural effluents has been evaluated by the application of pesticides to activated sludge. The necessity for selection of a pesticide-resistant biomass has been highlighted. The elimination of the phytosanitary products shows the potential of a resistant biomass in the treatment of pesticides. The aerated biological storage ponds at three wineries, followed by a sand or reed-bed filter, were used for the treatment of the total annual volume of the viticulture effluents and validate the laboratory experiments. The results show that the biological purification of pesticides by activated sludge is possible by allowing approximately 8 days for biomass adaptation. Stability of purification occurs between 20 and 30 days. Copyright © 2012 Elsevier Ltd. All rights reserved.

Unusual glycosylation of proteins: Beyond the universal sequon and other amino acids.

PubMed

Dutta, Devawati; Mandal, Chhabinath; Mandal, Chitra

2017-12-01

Glycosylation of proteins is the most common, multifaceted co- and post-translational modification responsible for many biological processes and cellular functions. Significant alterations and aberrations of these processes are related to various pathological conditions, and often turn out to be disease biomarkers. Conventional N-glycosylation occurs through the recognition of the consensus sequon, asparagine (Asn)-X-serine (Ser)/threonine (Thr), where X is any amino acid except for proline, with N-acetylglucosamine (GlcNAc) as the first glycosidic linkage. Usually, O-glycosylation adds a glycan to the hydroxyl group of Ser or Thr beginning with N-acetylgalactosamine (GalNAc). Protein glycosylation is further governed by additional diversifications in sequon and structure, which are yet to be fully explored. This review mainly focuses on the occurrence of N-glycosylation in non-consensus motifs, where Ser/Thr at the +2 position is substituted by other amino acids. Additionally, N-glycosylation is also observed in other amide/amine group-containing amino acids. Similarly, O-glycosylation occurs at hydroxyl group-containing amino acids other than serine/threonine. The neighbouring amino acids and local structural features around the potential glycosylation site also play a significant role in determining the extent of glycosylation. All of these phenomena that yield glycosylation at the atypical sites are reported in a variety of biological systems, including different pathological conditions. Therefore, the discovery of more novel sequence patterns for N- and O-glycosylation may help in understanding the functions of complex biological processes and cellular functions. Taken together, all these information provided in this review would be helpful for the biological readers. Copyright © 2017 Elsevier B.V. All rights reserved.

Extraction, Characterization, Stability and Biological Activity of Flavonoids Isolated from Chamomile Flowers

PubMed Central

Srivastava, Janmejai K; Gupta, Sanjay

2009-01-01

Dried flowers of Chamomile (Matricaria chamomilla) are largely used for their medicinal properties. In the present study, we examined the pharmacological properties of aqueous and methanolic fraction isolated from two varieties of German chamomile. HPLC-MS analysis of chamomile extract confirmed apigenin-7-O-glucoside as the major constituent of chamomile; some minor glycoside components were observed along with essential oils. These glucosides are highly stable in solution at different temperature range and their degradation occurs after long-term storage and extraction conditions at different pH and solvent. Methanolic fraction isolated from chamomile flowers demonstrated higher biologic response in inhibiting cell growth and causing induction of apoptosis in various human cancer cell lines compared to aqueous chamomile fraction. Apigenin glucosides inhibited cancer cell growth through deconjugation of glycosides that occurs in the cellular compartment to produce aglycone, apigenin. Taken together, the pharmacological profile of chamomile extract was dependent upon extraction process, storage conditions which affected the biological activity. PMID:20098626

A meta-analysis to evaluate the cellular processes regulated by the interactome of endogenous and over-expressed estrogen receptor alpha.

PubMed

Simões, Joana; Amado, Francisco M; Vitorino, Rui; Helguero, Luisa A

2015-01-01

The nature of the proteins complexes that regulate ERα subcellular localization and activity is still an open question in breast cancer biology. Identification of such complexes will help understand development of endocrine resistance in ER+ breast cancer. Mass spectrometry (MS) has allowed comprehensive analysis of the ERα interactome. We have compared six published works analyzing the ERα interactome of MCF-7 and HeLa cells in order to identify a shared or different pathway-related fingerprint. Overall, 806 ERα interacting proteins were identified. The cellular processes were differentially represented according to the ERα purification methodology, indicating that the methodologies used are complementary. While in MCF-7 cells, the interactome of endogenous and over-expressed ERα essentially represents the same biological processes and cellular components, the proteins identified were not over-lapping; thus, suggesting that the biological response may differ as the regulatory/participating proteins in these complexes are different. Interestingly, biological processes uniquely associated to ERα over-expressed in HeLa cell line included L-serine biosynthetic process, cellular amino acid biosynthetic process and cell redox homeostasis. In summary, all the approaches analyzed in this meta-analysis are valid and complementary; in particular, for those cases where the processes occur at low frequency with normal ERα levels, and can be identified when the receptor is over-expressed. However special effort should be put into validating these findings in cells expressing physiological ERα levels.

New insights into metabolic signaling and cell survival: the role of beta-O-linkage of N-acetylglucosamine.

PubMed

Ngoh, Gladys A; Jones, Steven P

2008-12-01

The involvement of glucose in fundamental metabolic pathways represents a core element of biology. Late in the 20th century, a unique glucose-derived signal was discovered, which appeared to be involved in a variety of cellular processes, including mitosis, transcription, insulin signaling, stress responses, and potentially, Alzheimer's disease, and diabetes. By definition, this glucose-fed signaling system was a post-translational modification to proteins. However, unlike classical cotranslational N-glycosylation occurring in the endoplasmic reticulum and Golgi apparatus, this process occurs elsewhere throughout the cell in a highly dynamic fashion, similar to the quintessential post-translational modification, phosphorylation. This more recently described post-translational modification, the beta-O-linkage of N-acetylglucosamine (i.e., O-GlcNAc) to nucleocytoplasmic proteins, represents an under-investigated area of biology. This signaling system operates in all of the tissues examined and seems to have persisted throughout all multicellular eukaryotes. Thus, it comes with little surprise that O-GlcNAc signaling is an integral system and viable target for biomedical investigation. This system may be a boundless source for insight into a variety of diseases and yield numerous opportunities for drug design. This Perspective will address recent insights into O-GlcNAc signaling in the cardiovascular system as a paradigm for its involvement in other biological systems.

Students' Conceptions of Water Transport

ERIC Educational Resources Information Center

Rundgren, Carl-Johan; Rundgren, Shu-Nu Chang; Schonborn, Konrad J.

2010-01-01

Understanding diffusion of water into and out of the cell through osmosis is fundamental to the learning and teaching of biology. Although this process is thought of as occurring directly across the lipid bilayer, the majority of water transport is actually mediated by specialised transmembrane water-channels called aquaporins. This study…

Antiviral Innate Immunity through the lens of Systems Biology

PubMed Central

Tripathi, Shashank; García-Sastre, Adolfo

2015-01-01

Cellular innate immunity poses the first hurdle against invading viruses in their attempt to establish infection. This antiviral response is manifested with the detection of viral components by the host cell, followed by transduction of antiviral signals, transcription and translation of antiviral effectors and leads to the establishment of an antiviral state. These events occur in a rather branched and interconnected sequence than a linear path. Traditionally, these processes were studied in the context of a single virus and a host component. However, with the advent of rapid and affordable OMICS technologies it has become feasible to address such questions on a global scale. In the discipline of Systems Biology’, extensive omics datasets are assimilated using computational tools and mathematical models to acquire deeper understanding of complex biological processes. In this review we have catalogued and discussed the application of Systems Biology approaches in dissecting the antiviral innate immune responses. PMID:26657882

Biological Embedding: Evaluation and Analysis of an Emerging Concept for Nursing Scholarship

PubMed Central

Nist, Marliese Dion

2016-01-01

Aim The purpose of this paper is to report the analysis of the concept of biological embedding. Background Research that incorporates a life course perspective is becoming increasingly prominent in the health sciences. Biological embedding is a central concept in life course theory and may be important for nursing theories to enhance our understanding of health states in individuals and populations. Before the concept of biological embedding can be used in nursing theory and research, an analysis of the concept is required to advance it toward full maturity. Design Concept analysis. Data Sources PubMed, CINAHL and PsycINFO were searched for publications using the term ‘biological embedding’ or ‘biological programming’ and published through 2015. Methods An evaluation of the concept was first conducted to determine the concept’s level of maturity and was followed by a concept comparison, using the methods for concept evaluation and comparison described by Morse. Results A consistent definition of biological embedding – the process by which early life experience alters biological processes to affect adult health outcomes – was found throughout the literature. The concept has been used in several theories that describe the mechanisms through which biological embedding might occur and highlight its role in the development of health trajectories. Biological embedding is a partially mature concept, requiring concept comparison with an overlapping concept – biological programming – to more clearly establish the boundaries of biological embedding. Conclusions Biological embedding has significant potential for theory development and application in multiple academic disciplines, including nursing. PMID:27682606

Method for identifying biochemical and chemical reactions and micromechanical processes using nanomechanical and electronic signal identification

DOEpatents

Holzrichter, J.F.; Siekhaus, W.J.

1997-04-15

A scanning probe microscope, such as an atomic force microscope (AFM) or a scanning tunneling microscope (STM), is operated in a stationary mode on a site where an activity of interest occurs to measure and identify characteristic time-varying micromotions caused by biological, chemical, mechanical, electrical, optical, or physical processes. The tip and cantilever assembly of an AFM is used as a micromechanical detector of characteristic micromotions transmitted either directly by a site of interest or indirectly through the surrounding medium. Alternatively, the exponential dependence of the tunneling current on the size of the gap in the STM is used to detect micromechanical movement. The stationary mode of operation can be used to observe dynamic biological processes in real time and in a natural environment, such as polymerase processing of DNA for determining the sequence of a DNA molecule. 6 figs.

Method for identifying biochemical and chemical reactions and micromechanical processes using nanomechanical and electronic signal identification

DOEpatents

Holzrichter, John F.; Siekhaus, Wigbert J.

1997-01-01

A scanning probe microscope, such as an atomic force microscope (AFM) or a scanning tunneling microscope (STM), is operated in a stationary mode on a site where an activity of interest occurs to measure and identify characteristic time-varying micromotions caused by biological, chemical, mechanical, electrical, optical, or physical processes. The tip and cantilever assembly of an AFM is used as a micromechanical detector of characteristic micromotions transmitted either directly by a site of interest or indirectly through the surrounding medium. Alternatively, the exponential dependence of the tunneling current on the size of the gap in the STM is used to detect micromechanical movement. The stationary mode of operation can be used to observe dynamic biological processes in real time and in a natural environment, such as polymerase processing of DNA for determining the sequence of a DNA molecule.

Is There a Relationship Between Tic Frequency and Physiological Arousal? Examination in a Sample of Children with Co-Occurring Tic and Anxiety Disorders

PubMed Central

Conelea, Christine A.; Ramanujam, Krishnapriya; Walther, Michael R.; Freeman, Jennifer B.; Garcia, Abbe M.

2014-01-01

Stress is the contextual variable most commonly implicated in tic exacerbations. However, research examining associations between tics, stressors, and the biological stress response has yielded mixed results. This study examined whether tics occur at a greater frequency during discrete periods of heightened physiological arousal. Children with co-occurring tic and anxiety disorders (n = 8) completed two stress induction tasks (discussion of family conflict, public speech). Observational (tic frequencies) and physiological (heart rate) data were synchronized using The Observer XT, and tic frequencies were compared across periods of high and low heart rate. Tic frequencies across the entire experiment did not increase during periods of higher heart rate. During the speech task, tic frequencies were significantly lower during periods of higher heart rate. Results suggest that tic exacerbations may not be associated with heightened physiological arousal and highlight the need for further tic research using integrated measurement of behavioral and biological processes. PMID:24662238

Is There a Relationship Between Tic Frequency and Physiological Arousal? Examination in a Sample of Children With Co-Occurring Tic and Anxiety Disorders.

PubMed

Conelea, Christine A; Ramanujam, Krishnapriya; Walther, Michael R; Freeman, Jennifer B; Garcia, Abbe M

2014-03-01

Stress is the contextual variable most commonly implicated in tic exacerbations. However, research examining associations between tics, stressors, and the biological stress response has yielded mixed results. This study examined whether tics occur at a greater frequency during discrete periods of heightened physiological arousal. Children with co-occurring tic and anxiety disorders (n = 8) completed two stress-induction tasks (discussion of family conflict, public speech). Observational (tic frequencies) and physiological (heart rate [HR]) data were synchronized using The Observer XT, and tic frequencies were compared across periods of high and low HR. Tic frequencies across the entire experiment did not increase during periods of higher HR. During the speech task, tic frequencies were significantly lower during periods of higher HR. Results suggest that tic exacerbations may not be associated with heightened physiological arousal and highlight the need for further tic research using integrated measurement of behavioral and biological processes. © The Author(s) 2014.

Geochemistry of the Amazon Estuary

USGS Publications Warehouse

Smoak, Joseph M.; Krest, James M.; Swarzenski, Peter W

2006-01-01

The Amazon River supplies more freshwater to the ocean than any other river in the world. This enormous volume of freshwater forces the estuarine mixing out of the river channel and onto the continental shelf. On the continental shelf, the estuarine mixing occurs in a very dynamic environment unlike that of a typical estuary. The tides, the wind, and the boundary current that sweeps the continental shelf have a pronounced influence on the chemical and biological processes occurring within the estuary. The dynamic environment, along with the enormous supply of water, solutes and particles makes the Amazon estuary unique. This chapter describes the unique features of the Amazon estuary and how these features influence the processes occurring within the estuary. Examined are the supply and cycling of major and minor elements, and the use of naturally occurring radionuclides to trace processes including water movement, scavenging, sediment-water interaction, and sediment accumulation rates. The biogeochemical cycling of carbon, nitrogen, and phosphorus, and the significances of the Amazon estuary in the global mass balance of these elements are examined.

Modeling biological problems in computer science: a case study in genome assembly.

PubMed

Medvedev, Paul

2018-01-30

As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment and assembly. In this tutorial, we use the example of the genome assembly problem to demonstrate how to go from a question in the biological realm to a solution in the computer science realm. We show the modeling process step-by-step, including all the intermediate failed attempts. Please note this is not an introduction to how genome assembly algorithms work and, if treated as such, would be incomplete and unnecessarily long-winded. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Beyond the hydrophobic effect: Critical function of water at biological phase boundaries--A hypothesis.

PubMed

Damodaran, Srinivasan

2015-07-01

Many life-sustaining processes in living cells occur at the membrane-water interface. The pertinent questions that need to be asked are what is the evolutionary reason for biology to choose the membrane-water interface as the site for performing and/or controlling crucial biological reactions and what is the key physical principle that is singular to the membrane-water interface that biology exploits for regulating metabolic processes in cells? In this review, a hypothesis is developed, which espouses that cells control activities of membrane-bound enzymes and receptor activated processes via manipulating the thermodynamic activity of water at the membrane-water interfacial region. In support of this hypothesis, first we establish that the surface pressure of a lipid monolayer is a direct measure of a reduction in the thermodynamic activity of interfacial water. Second, we show that the surface pressure-dependent activation/inactivation of interfacial enzymes is fundamentally related to their dependence on interfacial water activity. We extend this argument to infer that cells might manipulate activities of membrane-associated biological processes via manipulating the activity of interfacial water via localized compression or expansion of the interface. In this paper, we critically analyze literature data on mechano-activation of large pore ion channels in Escherichia coli spheroplasts and G-proteins in reconstituted lipid vesicles, and show that these pressure-induced activation processes are fundamentally and quantitatively related to changes in the thermodynamic state of interfacial water, caused by mechanical stretching of the bilayer. Copyright © 2015 Elsevier B.V. All rights reserved.

A Ratiometric Two-Photon Fluorescent Probe for Tracking the Lysosomal ATP Level: Direct in cellulo Observation of Lysosomal Membrane Fusion Processes.

PubMed

Jun, Yong Woong; Wang, Taejun; Hwang, Sekyu; Kim, Dokyoung; Ma, Donghee; Kim, Ki Hean; Kim, Sungjee; Jung, Junyang; Ahn, Kyo Han

2018-06-05

Vesicles exchange its contents through membrane fusion processes-kiss-and-run and full-collapse fusion. Indirect observation of these fusion processes using artificial vesicles enhanced our understanding on the molecular mechanisms involved. Direct observation of the fusion processes in a real biological system, however, remains a challenge owing to many technical obstacles. We disclose a ratiometric two-photon probe offering real-time tracking of lysosomal ATP with quantitative information for the first time. By applying the probe to two-photon live-cell imaging technique, lysosomal membrane fusion process in cells has been directly observed along with the concentration of its content-lysosomal ATP. Results show that the kiss-and-run process between lysosomes proceeds through repeating transient interactions with gradual content mixing, whereas the full-fusion process occurs at once. Furthermore, it is confirmed that both the fusion processes proceed with conservation of the content. Such a small-molecule probe exerts minimal disturbance and hence has potential for studying various biological processes associated with lysosomal ATP. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Developmental biology in marine invertebrate symbioses.

PubMed

McFall-Ngai, M J; Ruby, E G

2000-12-01

Associations between marine invertebrates and their cooperative bacterial symbionts offer access to an understanding of the roots of host-microbe interaction; for example, several symbioses like the squid-vibrio light organ association serve as models for investigating how each partner affects the developmental biology of the other. Previous results have identified a program of specific developmental events that unfolds as the association is initiated. In the past year, published studies have focused primarily on describing the mechanisms underlying the signaling processes that occur between the juvenile squid and the luminous bacteria that colonize it.

What have humans done for evolutionary biology? Contributions from genes to populations.

PubMed

Briga, Michael; Griffin, Robert M; Berger, Vérane; Pettay, Jenni E; Lummaa, Virpi

2017-11-15

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future. © 2017 The Author(s).

What have humans done for evolutionary biology? Contributions from genes to populations

PubMed Central

Briga, Michael; Griffin, Robert M.; Berger, Vérane; Pettay, Jenni E.

2017-01-01

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future. PMID:29118130

Winging It: Using Digital Imaging To Investigate Butterfly Metamorphosis

ERIC Educational Resources Information Center

Bowen, Anne; Bell, Randy L.

2004-01-01

One of the best ways to inspire interest in biology is through observations of living things. Unfortunately, this important component of science methodology is often left out because of the difficulty of including it in the classroom. Additionally, amazing processes occur in nature that few have the chance to observe. This article reviews a…

Prototype-Distortion Category Learning: A Two-Phase Learning Process across a Distributed Network

ERIC Educational Resources Information Center

Little, Deborah M.; Thulborn, Keith R.

2006-01-01

This paper reviews a body of work conducted in our laboratory that applies functional magnetic resonance imaging (fMRI) to better understand the biological response and change that occurs during prototype-distortion learning. We review results from two experiments (Little, Klein, Shobat, McClure, & Thulborn, 2004; Little & Thulborn, 2005) that…

Fire effects on belowground sustainability: A review and synthesis

Treesearch

Daniel G. Neary; Carole C. Klopatek; Leonard F. DeBano; Peter F. Ffolliott

1999-01-01

The overall effects of the fire on ecosystems are complex, ranging from the reduction or elimination of aboveground biomass to impacts on belowground physical, chemical and microbial mediated processes. Since a key component of overall ecosystem sustainability occurs belowground, recovery is tied to the soil's physical, chemical, and biological functions and...

A Contemporary, Laboratory-Intensive Course on Messenger RNA Transcription and Processing

ERIC Educational Resources Information Center

Carson, Sue; Miller, Heather

2012-01-01

Messenger ribonucleic acid (mRNA) plays a pivotal role in the central dogma of molecular biology. Importantly, molecular events occurring during and after mRNA synthesis have the potential to create multiple proteins from one gene, leading to some of the remarkable protein diversity that genomes hold. The North Carolina State University…

Aqua mediated synthesis of bio-active compounds.

PubMed

Panda, Siva S

2013-05-01

Recently the aqueous medium has attracted the interest of organic chemists, and many. Moreover, in the past 20 years, the drug-discovery process has undergone extraordinary changes, and high-throughput biological screening of potential drug candidates has led to an ever-increasing demand for novel drug-like compounds. Noteworthy advantages were observed during the course of study on aqua mediated synthesis of compounds of medicinal importance. The established advantages of water as a solvent for reactions are, water is the most abundant and available resource on the planet and many biochemical processes occur in aqueous medium. This review will focus on describing new developments in the application of water in medicinal chemistry for the synthesis of bio-active compounds possessing various biological properties.

Potentials of biological oxidation processes for the treatment of spent sulfidic caustics containing thiols.

PubMed

Sipma, Jan; Svitelskaya, Anna; van der Mark, Bart; Pol, Look W Hulshoff; Lettinga, Gatze; Buisman, Cees J N; Janssen, Albert J H

2004-12-01

This research focused on the biological treatment of sulfidic spent caustics from refineries, which contain mainly hydrogen sulfide, methanethiol (MT) and ethanethiol (ET). Also various organic compounds can be present such as BTEX. Biological oxidation of 2.5 mM MT in batch experiments occurred after MT was first auto-oxidized into dimethyldisulfide (DMDS) whereafter oxidation into sulfate was completed in 350 h. DMDS as sole substrate was completely oxidized within 40 h. Therefore, DMDS formation seems to play an important role in detoxification of MT. Biological oxidation of ET and buthanethiol was not successful in batch experiments. Complete oxidation of MT and ET was observed in flow-through reactor experiments. Simultaneous oxidation of sulfide and MT was achieved when treating a synthetic spent caustic, containing 10 mM sulfide and 2.5 mM MT, in a bubble column reactor with carrier material at a hydraulic retention time of 6 h. Addition of 7.5 mM phenol, a common pollutant of spent caustics, did not adversely affect the biological oxidation process and phenol was completely removed from the effluent. Finally, three different spent caustics solutions from refineries were successfully treated.

The effect of carbon as an energy source for biological denitrification through Pseudomonas stutzeri.

PubMed

Shivran, Hari Singh; Kumar, S; Kumar, Dinesh; Singh, R V

2005-04-01

The biological denitrification processes possess many advantages in comparison to other denitrification processes. The present study was undertaken to observe the effect of quantity of carbon on biological denitrification with Pseudomonas stutzeri at different C/N ratios. The results obtained in the present investigations show that the pH and alkalinity of the effluent increased with increase in C/N ratio due to alkalinity generated during denitrification. The COD of the influent was increased with increase in C/N ratio. The effluent COD was nil under pseudo-steady state condition up to the C/N ratio of 2.5. Above this C/N ratio, the organics started entering in the treated water. The maximum feasible economic reduction of NO(3-)N from 51.6 mg/l to 1.2 mg/l occurred at C/N ratio of 2.5 and the obtained concentration of NO(3-)N was found to be lower than the tolerance limit (10 mg/l) prescribed by the WHO. The present work provides a feasible approach for a more efficient NO(3-)N removal process.

Cellular processing and destinies of artificial DNA nanostructures.

PubMed

Lee, Di Sheng; Qian, Hang; Tay, Chor Yong; Leong, David Tai

2016-08-07

Since many bionanotechnologies are targeted at cells, understanding how and where their interactions occur and the subsequent results of these interactions is important. Changing the intrinsic properties of DNA nanostructures and linking them with interactions presents a holistic and powerful strategy for understanding dual nanostructure-biological systems. With the recent advances in DNA nanotechnology, DNA nanostructures present a great opportunity to understand the often convoluted mass of information pertaining to nanoparticle-biological interactions due to the more precise control over their chemistry, sizes, and shapes. Coupling just some of these designs with an understanding of biological processes is both a challenge and a source of opportunities. Despite continuous advances in the field of DNA nanotechnology, the intracellular fate of DNA nanostructures has remained unclear and controversial. Because understanding its cellular processing and destiny is a necessary prelude to any rational design of exciting and innovative bionanotechnology, in this review, we will discuss and provide a comprehensive picture relevant to the intracellular processing and the fate of various DNA nanostructures which have been remained elusive for some time. We will also link the unique capabilities of DNA to some novel ideas for developing next-generation bionanotechnologies.

Stabilization of flux during dead-end ultra-low pressure ultrafiltration.

PubMed

Peter-Varbanets, Maryna; Hammes, Frederik; Vital, Marius; Pronk, Wouter

2010-06-01

Gravity driven ultrafiltration was operated in dead-end mode without any flushing or cleaning. In contrary to general expectations, the flux value stabilized after about one week of operation and remained constant during an extended period of time (several months). Different surface water types and diluted wastewater were used as feed water and, depending on the feed water composition, stable flux values were in the range of 4-10 L h(-1) m(-2). When sodium azide was added to the feed water to diminish the biological activity, no stabilization of flux occurred, indicating that biological processes play an important role in the flux stabilization process. Confocal laser scanning microscopy revealed the presence of a biofouling layer, of which the structure changed over time, leading to relatively heterogeneous structures. It is assumed that the stabilization of flux is related to the development of heterogeneous structures in the fouling layer, due to biological processes in the layer. The phenomenon of flux stabilization opens interesting possibilities for application, for instance in simple and low-cost ultrafiltration systems for decentralized drinking water treatment in developing and transition countries, independent of energy supply, chemicals, or complex process control. 2010 Elsevier Ltd. All rights reserved.

Serum angiotensin-1 converting enzyme activity processes a human immunodeficiency virus 1 gp160 peptide for presentation by major histocompatibility complex class I molecules

PubMed Central

1992-01-01

T cell stimulation by the human immunodeficiency virus 1 gp160-derived peptide p18 presented by H-2Dd class I major histocompatibility complex molecules in a cell-free system was found to require proteolytic cleavage. This extracellular processing was mediated by peptidases present in fetal calf serum. In vitro processing of p18 resulted in a distinct reverse phase high performance liquid chromatography profile, from which a biologically active product was isolated and sequenced. This peptide processing can be specifically blocked by the angiotensin- 1 converting enzyme (ACE) inhibitor captopril, and can occur by exposing p18 to purified ACE. The ability of naturally occurring extracellular proteases to convert inactive peptides to T cell antigens has important implications for understanding cytotoxic T lymphocyte responses in vivo, and for rational peptide vaccine design. PMID:1316930

[Non-nitrification pathway for NH4+ -N removal in pilot-scale drinking water biological processes].

PubMed

Yu, Xin; Ye, Lin; Li, Xu-dong; Zhang, Xiao-jian; Shi, Xu; Liu, Bo; Li, Rui-hua

2008-04-01

The non-nitrification pathway for NH4+ -N removal in pilot-scale drinking water biological treatment processes and its possible mechanism were investigated through calculating N and DO stoichiometric balance. With more than 2 mg/L NH4+ -N in the influent, for the fluidized bed bioreactor (FBBR), the total of NH4+ -N, NO2(-) -N, NO3(-) -N in the influent was 0.91 mg/L higher than that in the effluent, and for the biofilter, its DO consumption was 2.90 mg/L less than the stoichiometric amount. The results suggested that nitrogen loss occurred in both reactors and a part of NH4+ -N was removed through non-nitrification pathway. Because the utilization of phosphorus and organic matters was independent of nitrogen loss, the assimilation and denitrification could be excluded from the possible mechanisms. Because the very low C/N in the influent and the accumulation of NO2(-) -N in the reactors were similar with the wastewater biological processes, the "autotrophic removal of nitrogen" was regarded as the most probable non-nitrification pathway. In this mechanism, the couple of short-cut nitrification and ANAMMOX (or OLAND) leading to the transformation of NH4+ -N and NO2(-) -N into gaseous N2 was responsible for the nitrogen loss in drinking water biological processes.

Modeling nitrous oxide production during biological nitrogen removal via nitrification and denitrification: extensions to the general ASM models.

PubMed

Ni, Bing-Jie; Ruscalleda, Maël; Pellicer-Nàcher, Carles; Smets, Barth F

2011-09-15

Nitrous oxide (N(2)O) can be formed during biological nitrogen (N) removal processes. In this work, a mathematical model is developed that describes N(2)O production and consumption during activated sludge nitrification and denitrification. The well-known ASM process models are extended to capture N(2)O dynamics during both nitrification and denitrification in biological N removal. Six additional processes and three additional reactants, all involved in known biochemical reactions, have been added. The validity and applicability of the model is demonstrated by comparing simulations with experimental data on N(2)O production from four different mixed culture nitrification and denitrification reactor study reports. Modeling results confirm that hydroxylamine oxidation by ammonium oxidizers (AOB) occurs 10 times slower when NO(2)(-) participates as final electron acceptor compared to the oxic pathway. Among the four denitrification steps, the last one (N(2)O reduction to N(2)) seems to be inhibited first when O(2) is present. Overall, N(2)O production can account for 0.1-25% of the consumed N in different nitrification and denitrification systems, which can be well simulated by the proposed model. In conclusion, we provide a modeling structure, which adequately captures N(2)O dynamics in autotrophic nitrification and heterotrophic denitrification driven biological N removal processes and which can form the basis for ongoing refinements.

A finite element simulation of biological conversion processes in landfills.

PubMed

Robeck, M; Ricken, T; Widmann, R

2011-04-01

Landfills are the most common way of waste disposal worldwide. Biological processes convert the organic material into an environmentally harmful landfill gas, which has an impact on the greenhouse effect. After the depositing of waste has been stopped, current conversion processes continue and emissions last for several decades and even up to 100years and longer. A good prediction of these processes is of high importance for landfill operators as well as for authorities, but suitable models for a realistic description of landfill processes are rather poor. In order to take the strong coupled conversion processes into account, a constitutive three-dimensional model based on the multiphase Theory of Porous Media (TPM) has been developed at the University of Duisburg-Essen. The theoretical formulations are implemented in the finite element code FEAP. With the presented calculation concept we are able to simulate the coupled processes that occur in an actual landfill. The model's theoretical background and the results of the simulations as well as the meantime successfully performed simulation of a real landfill body will be shown in the following. Copyright © 2010 Elsevier Ltd. All rights reserved.

Molybdenum isotope fractionation in scleractinian corals and its implications on biological activities

NASA Astrophysics Data System (ADS)

Wei, G.; Wang, Z.; Li, J.; Deng, W.; Chen, X.; Ma, J.; Zeng, T.

2017-12-01

Molybdenum can actively involve in many biological processes on coral reefs, and its isotope fractionation in coral skeleton is possibly linked to some biological activities. We have performed a 3-days' time-series observation in a time interval of 4 hours on both Mo concentrations and δ98/85Mo of the seawater of the Luhuitou Reef in Sanya of Southern Hainan Islands in the northern South China Sea. Both Mo concentrations and δ98/85Mo show in pace diurnal variations with temperature, pH, dissolved oxygen (DO) contents, dissolved inorganic carbon (DIC) contents and its δ13C. High Mo concentrations and low δ98/85Mo generally occur during day time, and low Mo concentrations and high δ98/85Mo occur at night, suggesting that respiration of coral dominated at night tends to uptake more Mo from seawater. A further analysis on the Mo isotopic compositions of 6 different coral species on the Luhuitou Reef indicates that different coral species has different δ98/85Mo values in their skeleton. The lowest δ98/85Mo value occurs in Fungia of 0.34 ‰, and the highest occurs in Acropora sp of 1.91 ‰. These are all lower than that of the seawater, 2.04 ‰, suggesting a specie-depended Mo fractionation on coral skeleton. Meanwhile, we measured a 32-year time series of both Mo concentrations and δ98/85Mo of a Porites coral from the Great Barrier Reefs of Australia in annual resolution. The Mo concentrations vary from 12.5 to 78.0 ng/g, with an average of 21.4 ± 0.02 ng/g, and the δ98/95Mo values change from 0.46 to 1.83‰, with an average of 1.34 ± 0.09‰. A significant negative correlation occurs between the δ98/95Mo and the Mo concentration, and a positive correlation occurs between the δ98/95Mo and the seawater surface temperature. All these suggest that Mo isotope fractionation in coral skeleton is associated with biological activities of coral, such as respiration, and the δ98/95Mo values may be used to indicate changes in the related biological activities.

Ceratopteris richardii: a productive model for revealing secrets of signaling and development

NASA Technical Reports Server (NTRS)

Chatterjee, A.; Roux, S. J.

2000-01-01

Ceratopteris richardii is an aquatic fern grown in tropical and subtropical regions of the world. It is proven to be a productive model system for studies in the genetics, biochemistry, and cell biology of basic biologic processes that occur in early gametophytic development. It provides several advantages to biologists, especially those interested in gravitational biology, polarity development, and in the genetics of sexual development. It is easy to culture, has a relatively short life cycle, and offers an array of attractive features that facilitate genetic studies. The germination and early development of large populations of genetically identical spores are easy to synchronize, and both the direction of polarity development and cell-level gravity responses can be measured and readily manipulated within the first 24 h of spore development. Although there is no reliable transformation system available yet in Ceratopteris, recent studies suggest that the technique of RNA interference can be used to block translation of specific genes in a related fern, Marsilea, and current studies will soon reveal the applicability of this approach, as well as of other transformation approaches, in Ceratopteris. A recently completed expressed sequence tag (EST) sequencing project makes available the partial sequence of more than 2000 cDNAs, representing a significant percentage of the genes being expressed during the first 24 h of spore germination, when many developmentally interesting processes are occurring. A microarray of these ESTs is being constructed, so especially for those scientists interested in basic cellular phenomena that occur early in spore germination, the availability of the ESTs and of the microarray will make Ceratopteris an even more attractive model system.

Ceratopteris richardii: a productive model for revealing secrets of signaling and development.

PubMed

Chatterjee, A; Roux, S J

2000-09-01

Ceratopteris richardii is an aquatic fern grown in tropical and subtropical regions of the world. It is proven to be a productive model system for studies in the genetics, biochemistry, and cell biology of basic biologic processes that occur in early gametophytic development. It provides several advantages to biologists, especially those interested in gravitational biology, polarity development, and in the genetics of sexual development. It is easy to culture, has a relatively short life cycle, and offers an array of attractive features that facilitate genetic studies. The germination and early development of large populations of genetically identical spores are easy to synchronize, and both the direction of polarity development and cell-level gravity responses can be measured and readily manipulated within the first 24 h of spore development. Although there is no reliable transformation system available yet in Ceratopteris, recent studies suggest that the technique of RNA interference can be used to block translation of specific genes in a related fern, Marsilea, and current studies will soon reveal the applicability of this approach, as well as of other transformation approaches, in Ceratopteris. A recently completed expressed sequence tag (EST) sequencing project makes available the partial sequence of more than 2000 cDNAs, representing a significant percentage of the genes being expressed during the first 24 h of spore germination, when many developmentally interesting processes are occurring. A microarray of these ESTs is being constructed, so especially for those scientists interested in basic cellular phenomena that occur early in spore germination, the availability of the ESTs and of the microarray will make Ceratopteris an even more attractive model system.

Is there a shadow biosphere of silicon utilizing organisms on earth?

NASA Astrophysics Data System (ADS)

Das, P.; Das, S.

2012-12-01

The idea of shadow biosphere was first visualized by Carol Cleland and Shelley Copley of the University of Colorado in 2005. Since that time many scientists were interested in this subject and the basis of this paper is also correlated with this novel idea. A shadow biosphere essentially consists of self replicating bodies utilizing one or more chemicals which are not exploited to such extent by organisms of the real biosphere. Silicon-utilizing organisms mainly belong to the diatoms, some other algae, sponges, monocotyledon plants in this category are classified by us. They can survive in extremes of temperature, pressure, radiation, pH, salinity and nutrient conditions and this unusual tolerance to stress depends on their silicon biomineralization occurring either as a biologically controlled process or as a biologically induced process. In the control process silicate is sequestered and transferred to the intracellular silica deposition vesicle by energy driven pump mechanism in presence of specific transporter protein. In induced silicon mineralization, initial amorphous nucleation of silicon is gradually transformed to a crystalline phase. Besides these two methods, there are also other processes in which formation of silanol and siloxane can occur from oligomers of silica originating from monomers by Hydrogen bonding, cation bridging and direct electrostatic interactions. The structure of the silica biomineralised cell wall in silicon utilizing organisms is very complex, but this may explain their ability to stress tolerance and their possible coordinating role with other essential bioactive elements in nature. When electropositive elements are less, then polymerization of silicon-oxygen excess may occur easily, particularly in carbon and nitrogen paucity in the environment. Thus all these features indicate possibility of a shadow biosphere of these organisms on earth.

A model for microbially induced precipitation of vadose-zone calcites in fractures at LOS Alamos, New Mexico, USA

NASA Astrophysics Data System (ADS)

Newman, Brent D.; Campbell, Andrew R.; Norman, David I.; Ringelberg, David B.

1997-05-01

Fractures are unique environments that can concentrate the flow of water, nutrients, and contaminants. As such, fractures play an important role in controlling the flux of various substances into and through the vadose zone. Calcite fracture fillings are present in the near surface in the Bandelier Tuff Formation at Los Alamos, New Mexico, and provide a record of the geochemical and hydrologic processes that have occurred in fractures. The objective of this study was to examine calcite fracture fills in order to improve understanding of processes within fractures, and in particular those that lead to precipitation of calcite. Samples of calcite fillings were collected from vertical and horizontal fractures exposed in a shallow waste-burial pit. Scanning electron microscopy show morphologies which suggest that plants, fungi, and bacteria were important in the precipitation process. Quadrupole mass spectrometric analyses of fluid inclusion gases show predominantly methane (17-99%) and little to no oxygen (0-8%), suggesting the development of anaerobic conditions in the fractures. Ester-linked phospholipid biomarkers are evidence for a diverse microbial community in the fractures, and the presence of di-ether lipids indicate that the methane was generated by anaerobic bacteria. The calcite fillings apparently resulted from multiple biological and chemical processes in which plant roots in the fractures were converted to calcite. Roots grew into the fractures, eventually died, and were decomposed by bacteria and fungi. Anaerobic gases were generated from encapsulated organic material within the calcite via microbial decomposition, or were generated by microbes simultaneously with calcite precipitation. It is likely that the biological controls on calcite formation that occurred in the Los Alamos fractures also occurs in soils, and may explain the occurrence of other types of pedogenic calcites.

Research into acetone removal from air by biofiltration using a biofilter with straight structure plates

PubMed Central

Baltrėnas, Pranas; Zagorskis, Alvydas; Misevičius, Antonas

2015-01-01

The biological air treatment method is based on the biological destruction of organic compounds using certain cultures of microorganisms. This method is simple and may be applied in many branches of industry. The main element of biological air treatment devices is a filter charge. Tests were carried out using a new-generation laboratory air purifier with a plate structure. This purifier is called biofilter. The biofilter has a special system for packing material humidification which does not require additional energy inputs. In order to extend the packing material's durability, it was composed of thermally treated birch fibre. Pollutant (acetone) biodegradation occurred on thermally treated wood fibre in this research. According to the performed tests and the received results, the process of biodestruction was highly efficient. When acetone was passed through biofilter's packing material at 0.08 m s−1 rate, the efficiency of the biofiltration process was from 70% up to 90%. The species of bacteria capable of removing acetone vapour from the air, i.e. Bacillus (B. cereus, B. subtilis), Pseudomonas (P. aeruginosa, P. putida), Stapylococcus (S. aureus) and Rhodococcus sp., was identified in this study during the process of biofiltration. Their amount in the biological packing material changed from 1.6 × 107 to 3.7 × 1011 CFU g−1. PMID:26019659

Research into acetone removal from air by biofiltration using a biofilter with straight structure plates.

PubMed

Baltrėnas, Pranas; Zagorskis, Alvydas; Misevičius, Antonas

2015-03-04

The biological air treatment method is based on the biological destruction of organic compounds using certain cultures of microorganisms. This method is simple and may be applied in many branches of industry. The main element of biological air treatment devices is a filter charge. Tests were carried out using a new-generation laboratory air purifier with a plate structure. This purifier is called biofilter. The biofilter has a special system for packing material humidification which does not require additional energy inputs. In order to extend the packing material's durability, it was composed of thermally treated birch fibre. Pollutant (acetone) biodegradation occurred on thermally treated wood fibre in this research. According to the performed tests and the received results, the process of biodestruction was highly efficient. When acetone was passed through biofilter's packing material at 0.08 m s -1 rate, the efficiency of the biofiltration process was from 70% up to 90%. The species of bacteria capable of removing acetone vapour from the air, i.e. Bacillus ( B. cereus , B. subtilis ), Pseudomonas ( P. aeruginosa , P. putida ), Stapylococcus ( S. aureus ) and Rhodococcus sp., was identified in this study during the process of biofiltration. Their amount in the biological packing material changed from 1.6 × 10 7 to 3.7 × 10 11 CFU g -1 .

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.

Design-Based Learning for Biology: Genetic Engineering Experience Improves Understanding of Gene Expression

ERIC Educational Resources Information Center

Ellefson, Michelle R.; Brinker, Rebecca A.; Vernacchio, Vincent J.; Schunn, Christian D.

2008-01-01

Gene expression is a difficult topic for students to learn and comprehend, at least partially because it involves various biochemical structures and processes occurring at the microscopic level. Designer Bacteria, a design-based learning (DBL) unit for high-school students, applies principles of DBL to the teaching of gene expression. Throughout…

MICHIGAN SOIL VAPOR EXTRACTION REMEDIATION (MISER) MODEL: A COMPUTER PROGRAM TO MODEL SOIL VAPOR EXTRACTION AND BIOVENTING OF ORGANIC CHEMICALS IN UNSATURATED GEOLOGICAL MATERIAL

EPA Science Inventory

Soil vapor extraction (SVE) and bioventing (BV) are proven strategies for remediation of unsaturated zone soils. Mathematical models are powerful tools that can be used to integrate and quantify the interaction of physical, chemical, and biological processes occurring in field sc...

Microarray gene-expression study in fibroblast and lymphoblastoid cell lines from antipsychotic-naïve first-episode schizophrenia patients.

PubMed

Gassó, Patricia; Mas, Sergi; Rodríguez, Natalia; Boloc, Daniel; García-Cerro, Susana; Bernardo, Miquel; Lafuente, Amalia; Parellada, Eduard

2017-12-01

Schizophrenia (SZ) is a chronic psychiatric disorder whose onset of symptoms occurs in late adolescence and early adulthood. The etiology is complex and involves important gene-environment interactions. Microarray gene-expression studies on SZ have identified alterations in several biological processes. The heterogeneity in the results can be attributed to the use of different sample types and other important confounding factors including age, illness chronicity and antipsychotic exposure. The aim of the present microarray study was to analyze, for the first time to our knowledge, differences in gene expression profiles in 18 fibroblast (FCLs) and 14 lymphoblastoid cell lines (LCLs) from antipsychotic-naïve first-episode schizophrenia (FES) patients and healthy controls. We used an analytical approach based on protein-protein interaction network construction and functional annotation analysis to identify the biological processes that are altered in SZ. Significant differences in the expression of 32 genes were found when LCLs were assessed. The network and gene set enrichment approach revealed the involvement of similar biological processes in FCLs and LCLs, including apoptosis and related biological terms such as cell cycle, autophagy, cytoskeleton organization and response to stress and stimulus. Metabolism and other processes, including signal transduction, kinase activity and phosphorylation, were also identified. These results were replicated in two independent cohorts using the same analytical approach. This provides more evidence for altered apoptotic processes in antipsychotic-naïve FES patients and other important biological functions such as cytoskeleton organization and metabolism. The convergent results obtained in both peripheral cell models support their usefulness for transcriptome studies on SZ. Copyright © 2017 Elsevier Ltd. All rights reserved.

Adaptive neural coding: from biological to behavioral decision-making

PubMed Central

Louie, Kenway; Glimcher, Paul W.; Webb, Ryan

2015-01-01

Empirical decision-making in diverse species deviates from the predictions of normative choice theory, but why such suboptimal behavior occurs is unknown. Here, we propose that deviations from optimality arise from biological decision mechanisms that have evolved to maximize choice performance within intrinsic biophysical constraints. Sensory processing utilizes specific computations such as divisive normalization to maximize information coding in constrained neural circuits, and recent evidence suggests that analogous computations operate in decision-related brain areas. These adaptive computations implement a relative value code that may explain the characteristic context-dependent nature of behavioral violations of classical normative theory. Examining decision-making at the computational level thus provides a crucial link between the architecture of biological decision circuits and the form of empirical choice behavior. PMID:26722666

Biomolecular computing systems: principles, progress and potential.

PubMed

Benenson, Yaakov

2012-06-12

The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing.

Stable-isotope fingerprints of biological agents as forensic tools.

PubMed

Horita, Juske; Vass, Arpad A

2003-01-01

Naturally occurring stable isotopes of light elements in chemical and biological agents may possess unique "stable-isotope fingerprints" depending on their sources and manufacturing processes. To test this hypothesis, two strains of bacteria (Bacillus globigii and Erwinia agglomerans) were grown under controlled laboratory conditions. We observed that cultured bacteria cells faithfully inherited the isotopic composition (hydrogen, carbon, and nitrogen) of media waters and substrates in predictable manners in terms of bacterial metabolism and that even bacterial cells of the same strain, which grew in media water and substrates of different isotopic compositions, have readily distinguishable isotopic signatures. These "stable-isotopic fingerprints" of chemical and biological agents can be used as forensic tools in the event of biochemical terrorist attacks.

Computing the origin and evolution of the ribosome from its structure — Uncovering processes of macromolecular accretion benefiting synthetic biology

PubMed Central

Caetano-Anollés, Gustavo; Caetano-Anollés, Derek

2015-01-01

Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules. PMID:27096056

Evolution of proteins.

NASA Technical Reports Server (NTRS)

Dayhoff, M. O.

1971-01-01

The amino acid sequences of proteins from living organisms are dealt with. The structure of proteins is first discussed; the variation in this structure from one biological group to another is illustrated by the first halves of the sequences of cytochrome c, and a phylogenetic tree is derived from the cytochrome c data. The relative geological times associated with the events of this tree are discussed. Errors which occur in the duplication of cells during the evolutionary process are examined. Particular attention is given to evolution of mutant proteins, globins, ferredoxin, and transfer ribonucleic acids (tRNA's). Finally, a general outline of biological evolution is presented.

Nanopipettes as Monitoring Probes for the Single Living Cell: State of the Art and Future Directions in Molecular Biology.

PubMed

Bulbul, Gonca; Chaves, Gepoliano; Olivier, Joseph; Ozel, Rifat Emrah; Pourmand, Nader

2018-06-06

Examining the behavior of a single cell within its natural environment is valuable for understanding both the biological processes that control the function of cells and how injury or disease lead to pathological change of their function. Single-cell analysis can reveal information regarding the causes of genetic changes, and it can contribute to studies on the molecular basis of cell transformation and proliferation. By contrast, whole tissue biopsies can only yield information on a statistical average of several processes occurring in a population of different cells. Electrowetting within a nanopipette provides a nanobiopsy platform for the extraction of cellular material from single living cells. Additionally, functionalized nanopipette sensing probes can differentiate analytes based on their size, shape or charge density, making the technology uniquely suited to sensing changes in single-cell dynamics. In this review, we highlight the potential of nanopipette technology as a non-destructive analytical tool to monitor single living cells, with particular attention to integration into applications in molecular biology.

Context clues: the importance of stem cell-material interactions

PubMed Central

Murphy, William L.

2014-01-01

Understanding the processes by which stem cells give rise to de novo tissues is an active focus of stem cell biology and bioengineering disciplines. Instructive morphogenic cues surrounding the stem cell during morphogenesis create what is referred to as the stem cell microenvironment. An emerging paradigm in stem cell bioengineering involves “biologically driven assembly,” in which stem cells are encouraged to largely define their own morphogenesis processes. However, even in the case of biologically driven assembly, stem cells do not act alone. The properties of the surrounding microenvironment can be critical regulators of cell fate. Stem cell-material interactions are among the most well-characterized microenvironmental effectors of stem cell fate, and they establish a signaling “context” that can define the mode of influence for morphogenic cues. Here we describe illustrative examples of cell-material interactions that occur during in vitro stem cell studies, with an emphasis on how cell-material interactions create instructive contexts for stem cell differentiation and morphogenesis. PMID:24369691

Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy.

PubMed

Kedrov, Alexej; Janovjak, Harald; Sapra, K Tanuj; Müller, Daniel J

2007-01-01

Molecular interactions are the basic language of biological processes. They establish the forces interacting between the building blocks of proteins and other macromolecules, thus determining their functional roles. Because molecular interactions trigger virtually every biological process, approaches to decipher their language are needed. Single-molecule force spectroscopy (SMFS) has been used to detect and characterize different types of molecular interactions that occur between and within native membrane proteins. The first experiments detected and localized molecular interactions that stabilized membrane proteins, including how these interactions were established during folding of alpha-helical secondary structure elements into the native protein and how they changed with oligomerization, temperature, and mutations. SMFS also enables investigators to detect and locate molecular interactions established during ligand and inhibitor binding. These exciting applications provide opportunities for studying the molecular forces of life. Further developments will elucidate the origins of molecular interactions encoded in their lifetimes, interaction ranges, interplay, and dynamics characteristic of biological systems.

Protein-protein recognition control by modulating electrostatic interactions.

PubMed

Han, Song; Yin, Shijin; Yi, Hong; Mouhat, Stéphanie; Qiu, Su; Cao, Zhijian; Sabatier, Jean-Marc; Wu, Yingliang; Li, Wenxin

2010-06-04

Protein-protein control recognition remains a huge challenge, and its development depends on understanding the chemical and biological mechanisms by which these interactions occur. Here we describe a protein-protein control recognition technique based on the dominant electrostatic interactions occurring between the proteins. We designed a potassium channel inhibitor, BmP05-T, that was 90.32% identical to wild-type BmP05. Negatively charged residues were translocated from the nonbinding interface to the binding interface of BmP05 inhibitor, such that BmP05-T now used BmP05 nonbinding interface as the binding interface. This switch demonstrated that nonbinding interfaces were able to control the orientation of protein binding interfaces in the process of protein-protein recognition. The novel function findings of BmP05-T peptide suggested that the control recognition technique described here had the potential for use in designing and utilizing functional proteins in many biological scenarios.

Optical Sensing of Polarization States Changes in Meat due to the Ageing

NASA Astrophysics Data System (ADS)

Tománek, Pavel; Mikláš, Jan; Abubaker, Hamed Mohamed; Grmela, Lubomír

2010-11-01

Food materials or biological materials display large compositional variations, inhomogeneities, and anisotropic structures. The biological tissues consist of cells which dimensions are bigger than a wavelength of visible light, therefore Mie scattering of transmitted and reflected light occurs and different polarization states arise. The meat industry needs reliable meat quality information throughout the production process in order to guarantee high-quality meat products for consumers. The minor importance is still given to the food quality control and inspection during processing operations or storing conditions. The paper presents a quite simple optical method allowing measure the freshness or ageing of products. The principle is to study temporal characteristics of polarization states of forward or backward scattered laser light in the samples in function of meat ageing.

The role of aluminum in slow sand filtration.

PubMed

Weber-Shirk, Monroe L; Chan, Kwok Loon

2007-03-01

Engineering enhancement of slow sand filtration has been an enigma in large part because the mechanisms responsible for particle removal have not been well characterized. The presumed role of biological processes in the filter ripening process nearly precluded the possibility of enhancing filter performance since interventions to enhance biological activity would have required decreasing the quality of the influent water. In previous work, we documented that an acid soluble polymer controls filter performance. The new understanding that particle removal is controlled in large part by physical chemical mechanisms has expanded the possibilities of engineering slow sand filter performance. Herein, we explore the role of naturally occurring aluminum as a ripening agent for slow sand filters and the possibility of using a low dose of alum to improve filter performance or to ripen slow sand filters.

Biological Niches within Human Calcified Aortic Valves: Towards Understanding of the Pathological Biomineralization Process

PubMed Central

Cottignoli, Valentina; Agrosì, Giovanna; Familiari, Giuseppe; Salvador, Loris

2015-01-01

Despite recent advances, mineralization site, its microarchitecture, and composition in calcific heart valve remain poorly understood. A multiscale investigation, using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and energy dispersive X-ray spectrometry (EDS), from micrometre up to nanometre, was conducted on human severely calcified aortic and mitral valves, to provide new insights into calcification process. Our aim was to evaluate the spatial relationship existing between bioapatite crystals, their local growing microenvironment, and the presence of a hierarchical architecture. Here we detected the presence of bioapatite crystals in two different mineralization sites that suggest the action of two different growth processes: a pathological crystallization process that occurs in biological niches and is ascribed to a purely physicochemical process and a matrix-mediated mineralized process in which the extracellular matrix acts as the template for a site-directed nanocrystals nucleation. Different shapes of bioapatite crystallization were observed at micrometer scale in each microenvironment but at the nanoscale level crystals appear to be made up by the same subunits. PMID:26509159

Process-based network decomposition reveals backbone motif structure

PubMed Central

Wang, Guanyu; Du, Chenghang; Chen, Hao; Simha, Rahul; Rong, Yongwu; Xiao, Yi; Zeng, Chen

2010-01-01

A central challenge in systems biology today is to understand the network of interactions among biomolecules and, especially, the organizing principles underlying such networks. Recent analysis of known networks has identified small motifs that occur ubiquitously, suggesting that larger networks might be constructed in the manner of electronic circuits by assembling groups of these smaller modules. Using a unique process-based approach to analyzing such networks, we show for two cell-cycle networks that each of these networks contains a giant backbone motif spanning all the network nodes that provides the main functional response. The backbone is in fact the smallest network capable of providing the desired functionality. Furthermore, the remaining edges in the network form smaller motifs whose role is to confer stability properties rather than provide function. The process-based approach used in the above analysis has additional benefits: It is scalable, analytic (resulting in a single analyzable expression that describes the behavior), and computationally efficient (all possible minimal networks for a biological process can be identified and enumerated). PMID:20498084

Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology.

PubMed

Li, Jinyang; Liu, Yi; Kim, Eunkyoung; March, John C; Bentley, William E; Payne, Gregory F

2017-04-01

The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O 2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H 2 O 2 ) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this electrochemical tool for in vitro redox-probing. Copyright © 2017 Elsevier Inc. All rights reserved.

Biosurveillance: A Review and Update

PubMed Central

Kman, Nicholas E.; Bachmann, Daniel J.

2012-01-01

Since the terrorist attacks and anthrax release in 2001, almost $32 billion has been allocated to biodefense and biosurveillance in the USA alone. Surveillance in health care refers to the continual systematic collection, analysis, interpretation, and dissemination of data. When attempting to detect agents of bioterrorism, surveillance can occur in several ways. Syndromic surveillance occurs by monitoring clinical manifestations of certain illnesses. Laboratory surveillance occurs by looking for certain markers or laboratory data, and environmental surveillance is the process by which the ambient air or environment is continually sampled for the presence of biological agents. This paper focuses on the ways by which we detect bioterrorism agents and the effectiveness of these systems. PMID:22242207

Recent biological trends in management of fracture non-union

PubMed Central

Emara, Khaled M; Diab, Ramy Ahmed; Emara, Ahmed Khaled

2015-01-01

Bone regeneration is a complex, well-orchestrated physiological process of bone formation, which can be seen during normal fracture healing, and is involved in continuous remodelling throughout adult life. Currently, there is a plethora of different strategies to augment the impaired or “insufficient” bone-regeneration process, including the “gold standard” autologous bone graft, free fibula vascularised graft, allograft implantation, and use of growth factors, osteoconductive scaffolds, osteoprogenitor cells and distraction osteogenesis. Improved “local” strategies in terms of tissue engineering and gene therapy, or even “systemic” enhancement of bone repair, are under intense investigation, in an effort to overcome the limitations of the current methods, to produce bone-graft substitutes with biomechanical properties that are as identical to normal bone as possible, to accelerate the overall regeneration process, or even to address systemic conditions, such as skeletal disorders and osteoporosis. An improved understanding of the molecular and cellular events that occur during bone repair and remodeling has led to the development of biologic agents that can augment the biological microenvironment and enhance bone repair. Orthobiologics, including stem cells, osteoinductive growth factors, osteoconductive matrices, and anabolic agents, are available clinically for accelerating fracture repair and treatment of compromised bone repair situations like delayed unions and nonunions. A lack of standardized outcome measures for comparison of biologic agents in clinical fracture repair trials, frequent off-label use, and a limited understanding of the biological activity of these agents at the bone repair site have limited their efficacy in clinical applications. PMID:26396938

Beyond the Cell: Using Multiscalar Topics to Bring Interdisciplinarity into Undergraduate Cellular Biology Courses

PubMed Central

Weber, Carolyn F.

2016-01-01

Western science has grown increasingly reductionistic and, in parallel, the undergraduate life sciences curriculum has become disciplinarily fragmented. While reductionistic approaches have led to landmark discoveries, many of the most exciting scientific advances in the late 20th century have occurred at disciplinary interfaces; work at these interfaces is necessary to manage the world’s looming problems, particularly those that are rooted in cellular-level processes but have ecosystem- and even global-scale ramifications (e.g., nonsustainable agriculture, emerging infectious diseases). Managing such problems requires comprehending whole scenarios and their emergent properties as sums of their multiple facets and complex interrelationships, which usually integrate several disciplines across multiple scales (e.g., time, organization, space). This essay discusses bringing interdisciplinarity into undergraduate cellular biology courses through the use of multiscalar topics. Discussing how cellular-level processes impact large-scale phenomena makes them relevant to everyday life and unites diverse disciplines (e.g., sociology, cell biology, physics) as facets of a single system or problem, emphasizing their connections to core concepts in biology. I provide specific examples of multiscalar topics and discuss preliminary evidence that using such topics may increase students’ understanding of the cell’s position within an ecosystem and how cellular biology interfaces with other disciplines. PMID:27146162

Dupuytren's: a systems biology disease

PubMed Central

2011-01-01

Dupuytren's disease (DD) is an ill-defined fibroproliferative disorder of the palm of the hands leading to digital contracture. DD commonly occurs in individuals of northern European extraction. Cellular components and processes associated with DD pathogenesis include altered gene and protein expression of cytokines, growth factors, adhesion molecules, and extracellular matrix components. Histology has shown increased but varying levels of particular types of collagen, myofibroblasts and myoglobin proteins in DD tissue. Free radicals and localised ischaemia have been suggested to trigger the proliferation of DD tissue. Although the existing available biological information on DD may contain potentially valuable (though largely uninterpreted) information, the precise aetiology of DD remains unknown. Systems biology combines mechanistic modelling with quantitative experimentation in studies of networks and better understanding of the interaction of multiple components in disease processes. Adopting systems biology may be the ideal approach for future research in order to improve understanding of complex diseases of multifactorial origin. In this review, we propose that DD is a disease of several networks rather than of a single gene, and show that this accounts for the experimental observations obtained to date from a variety of sources. We outline how DD may be investigated more effectively by employing a systems biology approach that considers the disease network as a whole rather than focusing on any specific single molecule. PMID:21943049

The biology of cultural conflict

PubMed Central

Berns, Gregory S.; Atran, Scott

2012-01-01

Although culture is usually thought of as the collection of knowledge and traditions that are transmitted outside of biology, evidence continues to accumulate showing how biology and culture are inseparably intertwined. Cultural conflict will occur only when the beliefs and traditions of one cultural group represent a challenge to individuals of another. Such a challenge will elicit brain processes involved in cognitive decision-making, emotional activation and physiological arousal associated with the outbreak, conduct and resolution of conflict. Key targets to understand bio-cultural differences include primitive drives—how the brain responds to likes and dislikes, how it discounts the future, and how this relates to reproductive behaviour—but also higher level functions, such as how the mind represents and values the surrounding physical and social environment. Future cultural wars, while they may bear familiar labels of religion and politics, will ultimately be fought over control of our biology and our environment. PMID:22271779

The biology of cultural conflict.

PubMed

Berns, Gregory S; Atran, Scott

2012-03-05

Although culture is usually thought of as the collection of knowledge and traditions that are transmitted outside of biology, evidence continues to accumulate showing how biology and culture are inseparably intertwined. Cultural conflict will occur only when the beliefs and traditions of one cultural group represent a challenge to individuals of another. Such a challenge will elicit brain processes involved in cognitive decision-making, emotional activation and physiological arousal associated with the outbreak, conduct and resolution of conflict. Key targets to understand bio-cultural differences include primitive drives-how the brain responds to likes and dislikes, how it discounts the future, and how this relates to reproductive behaviour-but also higher level functions, such as how the mind represents and values the surrounding physical and social environment. Future cultural wars, while they may bear familiar labels of religion and politics, will ultimately be fought over control of our biology and our environment.

Developmental Processes across the First Two Years of Parenthood: Stability and Change in Adult Attachment Style

ERIC Educational Resources Information Center

Stern, Jessica A.; Fraley, R. Chris; Jones, Jason D.; Gross, Jacquelyn T.; Shaver, Phillip R.; Cassidy, Jude

2018-01-01

The first months after becoming a new parent are a unique and important period in human development. Despite substantial research on the many social and biological changes that occur during the first months of parenthood, little is known about changes in mothers' attachment. The present study examines developmental stability and change in…

MICHIGAN SOIL VAPOR EXTRACTION REMEDIATION (MISER) MODEL: A COMPUTER PROGRAM TO MODEL SOIL VAPORT EXTRACTION AND BIOVENTING OF ORGANIC MATERIALS IN UNSATURATED GEOLO-GICAL MATERIAL (EPA/600/SR-97/099)

EPA Science Inventory

Soil vapor extraction (SVE) and bioventing (BV) are proven strategies for remediation of unsaturated zone soils. Mathematical models are powerful tools that can be used to integrate and quantify the interaction of physical, chemical, and biological processes occurring in field sc...

Mismatch in the distribution of floral ecotypes and pollinators: insights into the evolution of sexually deceptive orchids.

PubMed

Phillips, R D; Bohman, B; Anthony, J M; Krauss, S L; Dixon, K W; Peakall, R

2015-03-01

Plants are predicted to show floral adaptation to geographic variation in the most effective pollinator, potentially leading to reproductive isolation and genetic divergence. Many sexually deceptive orchids attract just a single pollinator species, limiting opportunities to experimentally investigate pollinator switching. Here, we investigate Drakaea concolor, which attracts two pollinator species. Using pollinator choice tests, we detected two morphologically similar ecotypes within D. concolor. The common ecotype only attracted Zaspilothynnus gilesi, whereas the rare ecotype also attracted an undescribed species of Pogonothynnus. The rare ecotype occurred at populations nested within the distribution of the common ecotype, with no evidence of ecotypes occurring sympatrically. Surveying for pollinators at over 100 sites revealed that ecotype identity was not correlated with wasp availability, with most orchid populations only attracting the rare Z. gilesi. Using microsatellite markers, genetic differentiation among populations was very low (GST = 0.011) regardless of ecotype, suggestive of frequent gene flow. Taken together, these results may indicate that the ability to attract Pogonothynnus has evolved recently, but this ecotype is yet to spread. The nested distribution of ecotypes, rather than the more typical formation of ecotypes in allopatry, illustrates that in sexually deceptive orchids, pollinator switching could occur throughout a species' range, resulting from multiple potentially suitable but unexploited pollinators occurring in sympatry. This unusual case of sympatric pollinators highlights D. concolor as a promising study system for further understanding the process of pollinator switching from ecological, chemical and genetic perspectives. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Effect of Methanethiol Concentration on Sulfur Production in Biological Desulfurization Systems under Haloalkaline Conditions.

PubMed

Roman, Pawel; Veltman, René; Bijmans, Martijn F M; Keesman, Karel J; Janssen, Albert J H

2015-08-04

Bioremoval of H2S from gas streams became popular in recent years because of high process efficiency and low operational costs. To expand the scope of these processes to gas streams containing volatile organic sulfur compounds, like thiols, it is necessary to provide new insights into their impact on overall biodesulfurization process. Published data on the effect of thiols on biodesulfurization processes are scarce. In this study, we investigated the effect of methanethiol on the selectivity for sulfur production in a bioreactor integrated with a gas absorber. This is the first time that the inhibition of biological sulfur formation by methanethiol is investigated. In our reactor system, inhibition of sulfur production started to occur at a methanethiol loading rate of 0.3 mmol L(-1) d(-1). The experimental results were also described by a mathematical model that includes recent findings on the mode of biomass inhibition by methanethiol. We also found that the negative effect of methanethiol can be mitigated by lowering the salinity of the bioreactor medium. Furthermore, we developed a novel approach to measure the biological activity by sulfide measurements using UV-spectrophotometry. On the basis of this measurement method, it is possible to accurately estimate the unknown kinetic parameters in the mathematical model.

Comprehensive proteomic profiling of adult Angiostrongylus costaricensis, a human parasitic nematode.

PubMed

Rebello, Karina M; Barros, Juliana S L; Mota, Ester M; Carvalho, Paulo C; Perales, Jonas; Lenzi, Henrique L; Neves-Ferreira, Ana G C

2011-08-24

Angiostrongylus costaricensis is a nematode helminth that causes an intestinal acute inflammatory process known as abdominal angiostrongyliasis, which is a poorly understood human disease occurring in Latin America. Our aim was to study the proteomic profiles of adult parasites focusing on immunogenic proteins. Total cellular extracts from both genders showed similar 2-DE profiles, with 60% of all protein spots focused between pH 5-7 and presenting molecular masses from 20.1 to 66 kDa. A total of 53 different dominant proteins were identified in our dataset and were mainly associated with the following over-represented Gene Ontology Biological Process terms: "macromolecule metabolic process", "developmental process", "response to stress", and "biological regulation". Female and male immunoblots showed similar patterns of reactive proteins. Immunoreactive spots identified by MALDI-PSD were found to represent heat shock proteins, a putative abnormal DAuer Formation family member, and galectins. To date, very few biochemical analyses have focused on the nematode Angiostrongylus costaricensis. As such, our results contribute to a better understanding of its biology and the mechanisms underlying the host-parasite relationship associated with this species. Moreover, our findings represent a first step in the search for candidate proteins for diagnostic assays and the treatment of this parasitic infection. Copyright © 2011 Elsevier B.V. All rights reserved.

Risk analysis for biological hazards: What we need to know about invasive species

USGS Publications Warehouse

Stohlgren, T.J.; Schnase, J.L.

2006-01-01

Risk analysis for biological invasions is similar to other types of natural and human hazards. For example, risk analysis for chemical spills requires the evaluation of basic information on where a spill occurs; exposure level and toxicity of the chemical agent; knowledge of the physical processes involved in its rate and direction of spread; and potential impacts to the environment, economy, and human health relative to containment costs. Unlike typical chemical spills, biological invasions can have long lag times from introduction and establishment to successful invasion, they reproduce, and they can spread rapidly by physical and biological processes. We use a risk analysis framework to suggest a general strategy for risk analysis for invasive species and invaded habitats. It requires: (1) problem formation (scoping the problem, defining assessment endpoints); (2) analysis (information on species traits, matching species traits to suitable habitats, estimating exposure, surveys of current distribution and abundance); (3) risk characterization (understanding of data completeness, estimates of the “potential” distribution and abundance; estimates of the potential rate of spread; and probable risks, impacts, and costs); and (4) risk management (containment potential, costs, and opportunity costs; legal mandates and social considerations and information science and technology needs).

Capillary absorption spectrometer and process for isotopic analysis of small samples

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

Alexander, M. Lizabeth; Kelly, James F.; Sams, Robert L.

A capillary absorption spectrometer and process are described that provide highly sensitive and accurate stable absorption measurements of analytes in a sample gas that may include isotopologues of carbon and oxygen obtained from gas and biological samples. It further provides isotopic images of microbial communities that allow tracking of nutrients at the single cell level. It further targets naturally occurring variations in carbon and oxygen isotopes that avoids need for expensive isotopically labeled mixtures which allows study of samples taken from the field without modification. The process also permits sampling in vivo permitting real-time ambient studies of microbial communities.

The dynamics of correlated novelties.

PubMed

Tria, F; Loreto, V; Servedio, V D P; Strogatz, S H

2014-07-31

Novelties are a familiar part of daily life. They are also fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called "expanding the adjacent possible". The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological, or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (Heaps' law) and for the probability distribution on the space explored (Zipf's law), as well as signatures of the process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit events of Wikipedia pages, the emergence of tags in annotation systems, the sequence of words in texts, and listening to new songs in online music catalogues. By quantifying the dynamics of correlated novelties, our results provide a starting point for a deeper understanding of the adjacent possible and its role in biological, cultural, and technological evolution.

The dynamics of correlated novelties

NASA Astrophysics Data System (ADS)

Tria, F.; Loreto, V.; Servedio, V. D. P.; Strogatz, S. H.

2014-07-01

Novelties are a familiar part of daily life. They are also fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called ``expanding the adjacent possible''. The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological, or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (Heaps' law) and for the probability distribution on the space explored (Zipf's law), as well as signatures of the process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit events of Wikipedia pages, the emergence of tags in annotation systems, the sequence of words in texts, and listening to new songs in online music catalogues. By quantifying the dynamics of correlated novelties, our results provide a starting point for a deeper understanding of the adjacent possible and its role in biological, cultural, and technological evolution.

Platelets and cancer: a casual or causal relationship: revisited

PubMed Central

Menter, David G.; Tucker, Stephanie C.; Kopetz, Scott; Sood, Anil K.; Crissman, John D.; Honn, Kenneth V.

2014-01-01

Human platelets arise as subcellular fragments of megakaryocytes in bone marrow. The physiologic demand, presence of disease such as cancer, or drug effects can regulate the production circulating platelets. Platelet biology is essential to hemostasis, vascular integrity, angiogenesis, inflammation, innate immunity, wound healing, and cancer biology. The most critical biological platelet response is serving as “First Responders” during the wounding process. The exposure of extracellular matrix proteins and intracellular components occurs after wounding. Numerous platelet receptors recognize matrix proteins that trigger platelet activation, adhesion, aggregation, and stabilization. Once activated, platelets change shape and degranulate to release growth factors and bioactive lipids into the blood stream. This cyclic process recruits and aggregates platelets along with thrombogenesis. This process facilitates wound closure or can recognize circulating pathologic bodies. Cancer cell entry into the blood stream triggers platelet-mediated recognition and is amplified by cell surface receptors, cellular products, extracellular factors, and immune cells. In some cases, these interactions suppress immune recognition and elimination of cancer cells or promote arrest at the endothelium, or entrapment in the microvasculature, and survival. This supports survival and spread of cancer cells and the establishment of secondary lesions to serve as important targets for prevention and therapy. PMID:24696047

The dynamics of correlated novelties

PubMed Central

Tria, F.; Loreto, V.; Servedio, V. D. P.; Strogatz, S. H.

2014-01-01

Novelties are a familiar part of daily life. They are also fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called “expanding the adjacent possible”. The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological, or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (Heaps' law) and for the probability distribution on the space explored (Zipf's law), as well as signatures of the process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit events of Wikipedia pages, the emergence of tags in annotation systems, the sequence of words in texts, and listening to new songs in online music catalogues. By quantifying the dynamics of correlated novelties, our results provide a starting point for a deeper understanding of the adjacent possible and its role in biological, cultural, and technological evolution. PMID:25080941

Reinforcement in plants.

PubMed

Hopkins, Robin

2013-03-01

A major goal of evolutionary biology is to understand how diverging populations become species. The evolution of reproductive isolation (RI) halts the genomic homogenization caused by gene flow and recombination, and enables differentiation and local adaptations to become fixed between newly forming species. Selection can favor the strengthening of RI through a process termed reinforcement. Reinforcement occurs when selection favors traits that decrease mating between two incipient species in response to costly mating or the production of maladapted hybrids. Although this process has been investigated more frequently in animals, there is also evidence of reinforcement in plants. There are three strategies for the investigation of the process of reinforcement: case studies of species or diverging taxa; experimental evolution studies; and comparative studies. Here, I discuss how all three strategies find evidence consistent with reinforcement occurring in plants. I focus largely on case studies, and use research on Phlox drummondii to illustrate the importance of testing alternative hypotheses. Although the existing evidence suggests that reinforcement can occur, further investigations, particularly using large-scale comparative studies, are needed to determine the importance of reinforcement in plant speciation.

Bifurcation-based approach reveals synergism and optimal combinatorial perturbation.

PubMed

Liu, Yanwei; Li, Shanshan; Liu, Zengrong; Wang, Ruiqi

2016-06-01

Cells accomplish the process of fate decisions and form terminal lineages through a series of binary choices in which cells switch stable states from one branch to another as the interacting strengths of regulatory factors continuously vary. Various combinatorial effects may occur because almost all regulatory processes are managed in a combinatorial fashion. Combinatorial regulation is crucial for cell fate decisions because it may effectively integrate many different signaling pathways to meet the higher regulation demand during cell development. However, whether the contribution of combinatorial regulation to the state transition is better than that of a single one and if so, what the optimal combination strategy is, seem to be significant issue from the point of view of both biology and mathematics. Using the approaches of combinatorial perturbations and bifurcation analysis, we provide a general framework for the quantitative analysis of synergism in molecular networks. Different from the known methods, the bifurcation-based approach depends only on stable state responses to stimuli because the state transition induced by combinatorial perturbations occurs between stable states. More importantly, an optimal combinatorial perturbation strategy can be determined by investigating the relationship between the bifurcation curve of a synergistic perturbation pair and the level set of a specific objective function. The approach is applied to two models, i.e., a theoretical multistable decision model and a biologically realistic CREB model, to show its validity, although the approach holds for a general class of biological systems.

Adaptation aftereffects in the perception of gender from biological motion.

PubMed

Troje, Nikolaus F; Sadr, Javid; Geyer, Henning; Nakayama, Ken

2006-07-28

Human visual perception is highly adaptive. While this has been known and studied for a long time in domains such as color vision, motion perception, or the processing of spatial frequency, a number of more recent studies have shown that adaptation and adaptation aftereffects also occur in high-level visual domains like shape perception and face recognition. Here, we present data that demonstrate a pronounced aftereffect in response to adaptation to the perceived gender of biological motion point-light walkers. A walker that is perceived to be ambiguous in gender under neutral adaptation appears to be male after adaptation with an exaggerated female walker and female after adaptation with an exaggerated male walker. We discuss this adaptation aftereffect as a tool to characterize and probe the mechanisms underlying biological motion perception.

Biopharmaceuticals: From peptide to drug

NASA Astrophysics Data System (ADS)

Hannappel, Margarete

2017-08-01

Biologics are therapeutic proteins or peptides that are produced by means of biological processes within living organisms and cells. They are highly specific molecules and play a crucial role as therapeutics for the treatment of severe and chronic diseases (e.g. cancer, rheumatoid arthritis, diabetes, autoimmune disorders). The development of new biologics and biologics-based drugs gains more and more importance in the fight against various diseases. A short overview on biotherapeutical drug development is given. Cone snails are a large group of poisonous, predatory sea snails with more than 700 species. They use a very powerful venom which rapidly inactivates and paralyzes their prey. Most bioactive venom components are small peptides (conotoxins, conopeptides) which are precisely directed towards a specific target (e.g. ion channel, receptors). Due to their small size, their precision and speed of action, naturally occurring cone snail venom peptides represent an attractive source for the identification and design of novel biological drug entities. The Jagna cone snail project is an encouraging initiative to map the ecological variety of cone snails around the island of Bohol (Philippines) and to conserve the biological information for potential future application.

Isotopic inferences of ancient biochemistries - Carbon, sulfur, hydrogen, and nitrogen

NASA Technical Reports Server (NTRS)

Schidlowski, M.; Hayes, J. M.; Kaplan, I. R.

1983-01-01

In processes of biological incorporation and subsequent biochemical processing sizable isotope effects occur as a result of both thermodynamic and kinetic fractionations which take place during metabolic and biosynthetic reactions. In this chapter a review is provided of earlier work and recent studies on isotope fractionations in the biogeochemical cycles of carbon, sulfur, hydrogen, and nitrogen. Attention is given to the biochemistry of carbon isotope fractionation, carbon isotope fractionation in extant plants and microorganisms, isotope fractionation in the terrestrial carbon cycle, the effects of diagenesis and metamorphism on the isotopic composition of sedimentary carbon, the isotopic composition of sedimentary carbon through time, implications of the sedimentary carbon isotope record, the biochemistry of sulfur isotope fractionation, pathways of the biogeochemical cycle of nitrogen, and the D/H ratio in naturally occurring materials.

Truncated cystatin C in cerebrospiral fluid: Technical [corrected] artefact or biological process?

PubMed

Carrette, Odile; Burkhard, Pierre R; Hughes, Severine; Hochstrasser, Denis F; Sanchez, Jean-Charles

2005-08-01

Cystatin C, a low molecular weight cysteine proteinase inhibitor present in human body fluids at physiological concentrations, is more expressed in cerebrospinal fluid (CSF) than in plasma. Mass spectrometric characterization showed that after 3 months of storage of human CSF at -20 degrees C, cystatin C was cleaved in the peptide bond between R8 and L9 and lost its eight N-termini amino acids, whereas this cleavage did not occur when stored at -80 degrees C. This truncation occurred in all CSF samples studied irrespective of the underlying neurological status, indicating a storage-related artefact rather than a physiological or pathological processing of the protein. These results stress the importance of optimal preanalytical storage conditions of any sample prior to proteomics studies.

Immune remodeling: lessons from repertoire alterations during chronological aging and in immune-mediated disease.

PubMed

Vallejo, Abbe N

2007-03-01

Immunological studies of aging and of patients with chronic immune-mediated diseases document overlap of immune phenotypes. Here, the term "immune remodeling" refers to these phenotypes that are indicative of biological processes of deterioration and repair. This concept is explored through lessons from studies about the changes in the T-cell repertoire and the functional diversity of otherwise oligoclonal, senescent T cells. Immune remodeling suggests a gradual process that occurs throughout life. However, similar but more drastic remodeling occurs disproportionately among young patients with chronic disease. In this article, I propose that immune remodeling is a beneficial adaptation of aging to promote healthy survival beyond reproductive performance, but acute remodeling poses risk of premature exhaustion of the immune repertoire and, thus, is detrimental in young individuals.

The process defines the product: what really matters in biosimilar design and production?

PubMed

Vulto, Arnold G; Jaquez, Orlando A

2017-08-01

Biologic drugs are highly complex molecules produced by living cells through a multistep manufacturing process. The key characteristics of these molecules, known as critical quality attributes (CQAs), can vary based on post-translational modifications that occur in the cellular environment or during the manufacturing process. The extent of the variation in each of the CQAs must be characterized for the originator molecule and systematically matched as closely as possible by the biosimilar developer to ensure bio-similarity. The close matching of the originator fingerprint is the foundation of the biosimilarity exercise, as the analytical tools designed to measure differences at the molecular level are far more sensitive and specific than tools available to physicians during clinical trials. Biosimilar development, therefore, has a greater focus on preclinical attributes compared with the development of an original biological agent. As changes in CQAs can occur at different stages of the manufacturing process, even small modifications to the process can alter biosimilar attributes beyond the point of similarity and impact clinical effectiveness and safety. The manufacturer's ability to provide consistent production and quality control will greatly influence the acceptance of biosimilars. To this end, preventing drift from the required specifications over time and avoiding the various implications brought by product shortage will enhance biosimilar integration into daily practice. As most prescribers are not familiar with this new drug development paradigm, educational programmes will be needed so that prescribers see biosimilars as fully equivalent, efficacious and safe medicines when compared with originator products. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Rheumatology.

The process defines the product: what really matters in biosimilar design and production?

PubMed Central

Jaquez, Orlando A.

2017-01-01

Abstract Biologic drugs are highly complex molecules produced by living cells through a multistep manufacturing process. The key characteristics of these molecules, known as critical quality attributes (CQAs), can vary based on post-translational modifications that occur in the cellular environment or during the manufacturing process. The extent of the variation in each of the CQAs must be characterized for the originator molecule and systematically matched as closely as possible by the biosimilar developer to ensure bio-similarity. The close matching of the originator fingerprint is the foundation of the biosimilarity exercise, as the analytical tools designed to measure differences at the molecular level are far more sensitive and specific than tools available to physicians during clinical trials. Biosimilar development, therefore, has a greater focus on preclinical attributes compared with the development of an original biological agent. As changes in CQAs can occur at different stages of the manufacturing process, even small modifications to the process can alter biosimilar attributes beyond the point of similarity and impact clinical effectiveness and safety. The manufacturer’s ability to provide consistent production and quality control will greatly influence the acceptance of biosimilars. To this end, preventing drift from the required specifications over time and avoiding the various implications brought by product shortage will enhance biosimilar integration into daily practice. As most prescribers are not familiar with this new drug development paradigm, educational programmes will be needed so that prescribers see biosimilars as fully equivalent, efficacious and safe medicines when compared with originator products. PMID:28903544

A fractal model for nuclear organization: current evidence and biological implications

PubMed Central

Bancaud, Aurélien; Lavelle, Christophe; Huet, Sébastien; Ellenberg, Jan

2012-01-01

Chromatin is a multiscale structure on which transcription, replication, recombination and repair of the genome occur. To fully understand any of these processes at the molecular level under physiological conditions, a clear picture of the polymorphic and dynamic organization of chromatin in the eukaryotic nucleus is required. Recent studies indicate that a fractal model of chromatin architecture is consistent with both the reaction-diffusion properties of chromatin interacting proteins and with structural data on chromatin interminglement. In this study, we provide a critical overview of the experimental evidence that support a fractal organization of chromatin. On this basis, we discuss the functional implications of a fractal chromatin model for biological processes and propose future experiments to probe chromatin organization further that should allow to strongly support or invalidate the fractal hypothesis. PMID:22790985

The Approach to Study the Kama Reservoir Basin Deformation in the Zone of a Variable Backwater

NASA Astrophysics Data System (ADS)

Dvinskikh, S. A.; Kitaev, A. B.; Shaydulina, A. A.

2018-01-01

A reservoir floor starts to change since it has been filled up to a normal headwater level (NHL) under the impact of hydrosphere and lithosphere interactions as well as under the impact of chemical and biological processes that occur in its water masses. At that complicated and often contradictory “relations” between features of geo- and hydrodynamic processes are created. The consequences of these relations are the alterations of values of morphometric indices of the reservoir water surface, depth and volume. We observe two processes that are oppositely directed. They are accumulation and erosion. They are more complex at the upper area of the reservoir - the zone of a variable backwater. The basin deformation observed there is lop-sided and relatively quiet, but with time these deformations make difficulties for water users. To provide good navigation and to reduce harmful effect of waters on other water consumption objects, it is necessary to study and to forecast constantly the basin transformation processes that occur at this zone.

Low Pressure Greenhouse Concepts for Mars

NASA Technical Reports Server (NTRS)

Fowler, Philip A.; Wheeler, Raymond M.; Bucklin, Ray A.; Corey, Kenneth A.

2000-01-01

A project was initiated to begin testing some environmental limits for managing plant growth systems. These limits will help determine some of the concepts for building plant enclosures for use on Mars. In particular, this study focuses on the effects of reduced atmospheric pressures. Structural design is considered as it relates to the biological processes that would occur within that structure. The design must be closely tied to the functionality of the biological system and has a few primary concerns that need to be tested to resolve the question as to the path of the design. Early tests indicate that plants can survive and grow at low (greater than 76 mb) pressure.

[Genetics and criminology: a new concept].

PubMed

Jeffery, C R; Jeffery, I A

1975-01-01

The early history of criminology was one of interaction with genetics and biology, but since the sociological school emerged in the 1920's there has occurred a major split between sociological criminology and biology. Behavioral genetics as it has developed since 1950 has great relevance to criminology in terms of neurological and brain functioning, learning processes, violence and the XYY syndrome, and the sociopathy. A new interdisciplinary research effort must be undertaken in order to look at the interaction of genetics, human behavior, criminal law and criminology. If criminology is interested in learning, motivation, aggression and behavior, it must incorporate the new genetics into its theoretical structure.

Caenorhabditis elegans - A model system for space biology studies

NASA Technical Reports Server (NTRS)

Johnson, Thomas E.; Nelson, Gregory A.

1991-01-01

The utility of the nematode Caenorhabditis elegans in studies spanning aspects of development, aging, and radiobiology is reviewed. These topics are interrelated via cellular and DNA repair processes especially in the context of oxidative stress and free-radical metabolism. The relevance of these research topics to problems in space biology is discussed and properties of the space environment are outlined. Exposure to the space-flight environment can induce rapid changes in living systems that are similar to changes occurring during aging; manipulation of these environmental parameters may represent an experimental strategy for studies of development and senescence. The current and future opportunities for such space-flight experimentation are presented.

Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum

PubMed Central

Grace, Miriam; Hütt, Marc-Thorsten

2015-01-01

Spatiotemporal patterns often emerge from local interactions in a self-organizing fashion. In biology, the resulting patterns are also subject to the influence of the systematic differences between the system’s constituents (biological variability). This regulation of spatiotemporal patterns by biological variability is the topic of our review. We discuss several examples of correlations between cell properties and the self-organized spatiotemporal patterns, together with their relevance for biology. Our guiding, illustrative example will be spiral waves of cAMP in a colony of Dictyostelium discoideum cells. Analogous processes take place in diverse situations (such as cardiac tissue, where spiral waves occur in potentially fatal ventricular fibrillation) so a deeper understanding of this additional layer of self-organized pattern formation would be beneficial to a wide range of applications. One of the most striking differences between pattern-forming systems in physics or chemistry and those in biology is the potential importance of variability. In the former, system components are essentially identical with random fluctuations determining the details of the self-organization process and the resulting patterns. In biology, due to variability, the properties of potentially very few cells can have a driving influence on the resulting asymptotic collective state of the colony. Variability is one means of implementing a few-element control on the collective mode. Regulatory architectures, parameters of signaling cascades, and properties of structure formation processes can be "reverse-engineered" from observed spatiotemporal patterns, as different types of regulation and forms of interactions between the constituents can lead to markedly different correlations. The power of this biology-inspired view of pattern formation lies in building a bridge between two scales: the patterns as a collective state of a very large number of cells on the one hand, and the internal parameters of the single cells on the other. PMID:26562406

The viking biological investigation: preliminary results.

PubMed

Klein, H P; Horowitz, N H; Levin, G V; Oyama, V I; Lederberg, J; Rich, A; Hubbard, J S; Hobby, G L; Straat, P A; Berdahl, B J; Carle, G C; Brown, F S; Johnson, R D

1976-10-01

Three different types of biological experiments on samples of martian surface material ("soil") were conducted inside the Viking lander. In the carbon assimilation or pyrolytic release experiment, (14)CO(2) and (14)CO were exposed to soil in the presence of light. A small amount of gas was found to be converted into organic material. Heat treatment of a duplicate sample prevented such conversion. In the gas exchange experiment, soil was first humidified (exposed to water vapor) for 6 sols and then wet with a complex aqueous solution of metabolites. The gas above the soil was monitored by gas chromatography. A substantial amount of O(2) was detected in the first chromatogram taken 2.8 hours after humidification. Subsequent analyses revealed that significant increases in CO(2) and only small changes in N(2) had also occurred. In the labeled release experiment, soil was moistened with a solution containing several (14)C-labeled organic compounds. A substantial evolution of radioactive gas was registered but did not occur with a duplicate heat-treated sample. Alternative chemical and biological interpretations are possible for these preliminary data. The experiments are still in process, and these results so far do not allow a decision regarding the existence of life on the plonet Mars.

Dental caries - not just holes in teeth! A perspective.

PubMed

Bowen, W H

2016-06-01

Cavitation in teeth results from a pathogenic process termed dental caries that has occurred on the tooth surface for weeks or even years. Accumulation of dental plaque (biofilm) on the tooth is usually the first manifestation of the disease. Although acid production is the immediate and proximal cause of dissolution of teeth; it is the milieu within which the acid is formed that should be of primary concern. Focusing on the 'critical pH' has detracted attention from the more biological aspects (biofilm formation) of dental caries. Dental caries is unique; it is a biological process occurring on essentially an inert surface. Investigation of the multitude of interactions occurring in plaque ranging from enamel interfaces to surfaces of bacteria and matrices poses challenges worthy of the best scientific minds. The mouth clearly offers unique opportunities to investigate the multi facets of biofilm formation in vivo, generating data that have relevance way beyond the mouth. Prevention of this ubiquitous disease, dental caries, continues to present serious challenges. The public health benefits of fluoride delivered in its various formats are well recognized. Nevertheless, additional preventive approaches are required. Overcoming the rapid clearance of agents from the mouth is particularly challenging. Building on the polymerizing capacity of glucosyltransferases it may be possible to incorporate a therapeutic agent into the matrix plaque, thereby delivering therapeutic agents precisely to where they are needed. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours | Office of Cancer Genomics

Cancer.gov

Analysis of molecular aberrations across multiple cancer types, known as pan-cancer analysis, identifies commonalities and differences in key biological processes that are dysregulated in cancer cells from diverse lineages. Pan-cancer analyses have been performed for adult1–4 but not paediatric cancers, which commonly occur in developing mesodermic rather than adult epithelial tissues5.

Interaction of biological systems with static and ELF electric and magnetic fields

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

Anderson, L.E.; Kelman, B.J.; Weigel, R.J.

1987-01-01

Although background levels of atmospheric electric and geomagnetic field levels are extremely low, over the past several decades, human beings and other life forms on this planet have been subjected to a dramatically changing electromagnetic milieu. An exponential increase in exposure to electromagnetic fields has occurred, largely because of such technological advances as the growth of electrical power generation and transmission systems, the increased use of wireless communications, and the use of radar. In addition, electromagnetic field generating devices have proliferated in industrial plants, office buildings, homes, public transportation systems, and elsewhere. Although significant increases have occurred in electromagnetic fieldmore » strenghths spanning all frequency ranges, this symposium addresses only the impact of these fields at static and extremely low frequencies (ELF), primarily 50 and 60 Hz. This volume contains the proceedings of the symposium entitled /open quotes/Interaction of biological systems with static and ELF electric and magnetic fields/close quotes/. The purpose of the symposium was to provide a forum for discussions of all aspects of research on the interaction of static and ELF electromagnetic fields with biological systems. These systems include simple biophysical models, cell and organ preparations, whole animals, and man. Dosimetry, exposure system design, and artifacts in ELF bioeffects research were also addressed, along with current investigations that examine fundamental mechanisms of interactions between the fields and biological processes. Papers are indexed separately.« less

A taxonomy of visualization tasks for the analysis of biological pathway data.

PubMed

Murray, Paul; McGee, Fintan; Forbes, Angus G

2017-02-15

Understanding complicated networks of interactions and chemical components is essential to solving contemporary problems in modern biology, especially in domains such as cancer and systems research. In these domains, biological pathway data is used to represent chains of interactions that occur within a given biological process. Visual representations can help researchers understand, interact with, and reason about these complex pathways in a number of ways. At the same time, these datasets offer unique challenges for visualization, due to their complexity and heterogeneity. Here, we present taxonomy of tasks that are regularly performed by researchers who work with biological pathway data. The generation of these tasks was done in conjunction with interviews with several domain experts in biology. These tasks require further classification than is provided by existing taxonomies. We also examine existing visualization techniques that support each task, and we discuss gaps in the existing visualization space revealed by our taxonomy. Our taxonomy is designed to support the development and design of future biological pathway visualization applications. We conclude by suggesting future research directions based on our taxonomy and motivated by the comments received by our domain experts.

Comparative genomic hybridization.

PubMed

Pinkel, Daniel; Albertson, Donna G

2005-01-01

Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals ( 14, 35, 103 ), others occur in the course of normal processes in some species ( 33 ), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results.

What experimental approaches (eg, in vivo, in vitro, tissue retrieval) are effective in investigating the biologic effects of particles?

PubMed Central

Bostrom, Mathias; O'Keefe, Regis

2009-01-01

Understanding the complex cellular and tissue mechanisms and interactions resulting in periprosthetic osteolysis requires a number of experimental approaches, each of which has its own set of advantages and limitations. In vitro models allow for the isolation of individual cell populations and have furthered our understanding of particle-cell interactions; however, they are limited because they do not mimic the complex tissue environment in which multiple cell interactions occur. In vivo animal models investigate the tissue interactions associated with periprosthetic osteolysis, but the choice of species and whether the implant system is subjected to mechanical load or to unloaded conditions are critical in assessing whether these models can be extrapolated to the clinical condition. Rigid analysis of retrieved tissue from clinical cases of osteolysis offers a different approach to studying the biologic process of osteolysis, but it is limited in that the tissue analyzed represents the end-stage of this process and, thus, may not reflect this process adequately. PMID:18612016

What experimental approaches (eg, in vivo, in vitro, tissue retrieval) are effective in investigating the biologic effects of particles?

PubMed

Bostrom, Mathias; O'Keefe, Regis

2008-01-01

Understanding the complex cellular and tissue mechanisms and interactions resulting in periprosthetic osteolysis requires a number of experimental approaches, each of which has its own set of advantages and limitations. In vitro models allow for the isolation of individual cell populations and have furthered our understanding of particle-cell interactions; however, they are limited because they do not mimic the complex tissue environment in which multiple cell interactions occur. In vivo animal models investigate the tissue interactions associated with periprosthetic osteolysis, but the choice of species and whether the implant system is subjected to mechanical load or to unloaded conditions are critical in assessing whether these models can be extrapolated to the clinical condition. Rigid analysis of retrieved tissue from clinical cases of osteolysis offers a different approach to studying the biologic process of osteolysis, but it is limited in that the tissue analyzed represents the end-stage of this process and, thus, may not reflect this process adequately.

Top 10 research questions related to growth and maturation of relevance to physical activity, performance, and fitness.

PubMed

Malina, Robert M

2014-06-01

Growth, maturation, and development dominate the daily lives of children and adolescents for approximately the first 2 decades of life. Growth and maturation are biological processes, while development is largely a behavioral process. The 3 processes occur simultaneously and interact. They can be influenced by physical activity and also can influence activity, performance, and fitness. Allowing for these potential interactions, 10 questions on growth and maturation that have relevance to physical activity, performance, and fitness are presented. The questions are not mutually exclusive and address several broadly defined topical areas: exercise and growth, body weight status (body mass index, adiposity rebound, "unhealthy weight gain"), movement proficiency (hypothesized barrier, role in obesity), individual differences, tracking, maturity-associated variation in performance, and corresponding variation in physical activity. Central to the discussion of each is the need for a biocultural approach recognizing the interactions of biology and behavior as potential influences on the variables of interest.

Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes

PubMed Central

Mus, Florence; Crook, Matthew B.; Garcia, Kevin; Garcia Costas, Amaya; Geddes, Barney A.; Kouri, Evangelia D.; Paramasivan, Ponraj; Ryu, Min-Hyung; Oldroyd, Giles E. D.; Poole, Philip S.; Udvardi, Michael K.; Voigt, Christopher A.

2016-01-01

Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology. PMID:27084023

Inter-annual variability of transparent exopolymer particles in the Arctic Ocean reveals high sensitivity to ecosystem changes.

PubMed

Engel, Anja; Piontek, Judith; Metfies, Katja; Endres, Sonja; Sprong, Pim; Peeken, Ilka; Gäbler-Schwarz, Steffi; Nöthig, Eva-Maria

2017-06-23

Transparent exopolymer particles (TEP) are a class of marine gel particles and important links between surface ocean biology and atmospheric processes. Derived from marine microorganisms, these particles can facilitate the biological pumping of carbon dioxide to the deep sea, or act as cloud condensation and ice nucleation particles in the atmosphere. Yet, environmental controls on TEP abundance in the ocean are poorly known. Here, we investigated some of these controls during the first multiyear time-series on TEP abundance for the Fram Strait, the Atlantic gateway to the Central Arctic Ocean. Data collected at the Long-Term Ecological Research observatory HAUSGARTEN during 2009 to 2014 indicate a strong biological control with highest abundance co-occurring with the prymnesiophyte Phaeocystis pouchetii. Higher occurrence of P. pouchetii in the Arctic Ocean has previously been related to northward advection of warmer Atlantic waters, which is expected to increase in the future. Our study highlights the role of plankton key species in driving climate relevant processes; thus, changes in plankton distribution need to be accounted for when estimating the ocean's biogeochemical response to global change.

[Parametabolism as Non-Specific Modifier of Supramolecular Interactions in Living Systems].

PubMed

Kozlov, V A; Sapozhnikov, S P; Sheptuhina, A I; Golenkov, A V

2015-01-01

As it became known recently, in addition to the enzyme (enzymes and/or ribozymes) in living organisms occur a large number of ordinary chemical reactions without the participation of biological catalysts. These reactions are distinguished by low speed and, as a rule, the irreversibility. For example, along with diabetes mellitus, glycation and fructosilation of proteins are observed resulted in posttranslational modification with the low- or nonfunctioning protein formation which is poorly exposed to enzymatic proteolysis and therefore accumulates in the body. In addition, the known processes such as the nonenzymatic carbomoylation, pyridoxylation and thiamiation proteins. There is a reasonable basis to believe that alcoholic injury also realized through parametabolic secondary metabolites synthesis such as acetaldehyde. At the same time, the progress in supramolecular chemistry proves that in biological objects there is another large group ofparametabolic reactions caused by the formation of supramolecular complexes. Obviously, known parameterizes interactions can modify the formation of supramolecular complexes in living objects. These processes are of considerable interest for fundamental biology and fundamental and practical medicine, but they remain unexplored due to a lack of awareness of a wide range of researchers.

Metabolic profiling of body fluids and multivariate data analysis.

PubMed

Trezzi, Jean-Pierre; Jäger, Christian; Galozzi, Sara; Barkovits, Katalin; Marcus, Katrin; Mollenhauer, Brit; Hiller, Karsten

2017-01-01

Metabolome analyses of body fluids are challenging due pre-analytical variations, such as pre-processing delay and temperature, and constant dynamical changes of biochemical processes within the samples. Therefore, proper sample handling starting from the time of collection up to the analysis is crucial to obtain high quality samples and reproducible results. A metabolomics analysis is divided into 4 main steps: 1) Sample collection, 2) Metabolite extraction, 3) Data acquisition and 4) Data analysis. Here, we describe a protocol for gas chromatography coupled to mass spectrometry (GC-MS) based metabolic analysis for biological matrices, especially body fluids. This protocol can be applied on blood serum/plasma, saliva and cerebrospinal fluid (CSF) samples of humans and other vertebrates. It covers sample collection, sample pre-processing, metabolite extraction, GC-MS measurement and guidelines for the subsequent data analysis. Advantages of this protocol include: •Robust and reproducible metabolomics results, taking into account pre-analytical variations that may occur during the sampling process•Small sample volume required•Rapid and cost-effective processing of biological samples•Logistic regression based determination of biomarker signatures for in-depth data analysis.

Electro-autotrophic synthesis of higher alcohols

DOEpatents

Liao, James C.; Cho, Kwang Myung

2016-11-01

The disclosure provides a process that converts CO.sub.2 to higher alcohols (e.g. isobutanol) using electricity as the energy source. This process stores electricity (e.g. from solar energy, nuclear energy, and the like) in liquid fuels that can be used as high octane number gasoline substitutes. Instead of deriving reducing power from photosynthesis, this process derives reducing power from electrically generated mediators, either H.sub.2 or formate. H.sub.2 can be derived from electrolysis of water. Formate can be generated by electrochemical reduction of CO.sub.2. After delivering the reducing power in the cell, formate becomes CO.sub.2 and recycles back. Therefore, the biological CO.sub.2 fixation process can occur in the dark.

Electro-autotrophic synthesis of higher alcohols

DOEpatents

Liao, James C.; Cho, Kwang Myung

2015-10-06

The disclosure provides a process that converts CO.sub.2 to higher alcohols (e.g. isobutanol) using electricity as the energy source. This process stores electricity (e.g. from solar energy, nuclear energy, and the like) in liquid fuels that can be used as high octane number gasoline substitutes. Instead of deriving reducing power from photosynthesis, this process derives reducing power from electrically generated mediators, either H.sub.2 or formate. H.sub.2 can be derived from electrolysis of water. Formate can be generated by electrochemical reduction of CO.sub.2. After delivering the reducing power in the cell, formate becomes CO.sub.2 and recycles back. Therefore, the biological CO.sub.2 fixation process can occur in the dark.

Environmental Implications of Maritime Vessel Intensification in Arctic Waters

NASA Astrophysics Data System (ADS)

Stevenson, T. C.; Banis, D.; Sheard, W.

2016-12-01

In 2016, the Arctic experienced some of the warmest monthly temperatures on record. Record high temperatures in the Arctic continue to cause rapid sea ice declines, opening new areas of ocean to commercial exploitation and transportation and causing significant reductions in critical sea ice habitats used by iconic species. Elevated maritime vessel traffic in the Arctic is projected to increase black carbon emissions, encourage the spread of invasive species, increase mammal strikes, intensify conflict with smaller subsistence boats, and heighten oil spill risks. The Arctic Council, an intergovernmental organization concerned with sustainable development and environmental protection, is working with member countries, indigenous participants and other groups on developing networks of marine protected areas within ecologically or biologically important areas. To help inform that process, we analyzed vessel traffic and marine protected area coverage occurring within ecologically or biologically significant areas in the circumpolar Arctic. Our preliminary findings suggest vessel traffic within ecologically or biologically significant areas were highest around Iceland, Norway, Russia and United States but differed by vessel type. The density of fishing vessels occurring within ecologically or biologically important areas were highest near Norway, Iceland, Faroe Islands, parts of Greenland and United States, whereas vessels carrying liquefied natural gas and oil were concentrated near Norway and Russia. The percentage of area covered by marine protected areas within ecologically or biologically significant areas was low, with the exception of places like Wrangel Island, Svalbard, and areas around Greenland. These findings are important because it illustrates ecologically or biologically significant areas in the Arctic are vulnerable to projected vessel traffic intensification and the level of protection afforded by marine protected areas is relatively low.

Charge Transport in Trehalose-Derived Sugar Glasses

NASA Astrophysics Data System (ADS)

Nemzer, Louis; Navati, Mahantesh; Friedman, Joel; Epstein, Arthur

2013-03-01

Trehalose is a naturally occurring disaccharide with a well-known ability to preserve the biological function of proteins and cell membranes during periods of stress, including dehydration, by stabilizing the conformations of the macromolecules within a glassy matrix. This phenomenon makes use of the propensity of trehalose to interact strongly with protein functional groups and solvating water molecules via hydrogen bonding. Recently, it has been shown that trehalose sugar glasses also support long range charge transport in the form of oxidation-reduction reactions occurring between spatially separated donors and acceptors. Based on an Arrhenius conductivity analysis, along with IR-absorption and dielectric spectroscopy data, we propose that a Grotthuss-like proton hopping mechanism is responsible for the high charge carrier mobility and observed bias-dependent apparent activation energy. The possibility is raised for novel redox reactions to be performed on proteins constrained to specific 3D conformations. This could lead to a deeper understanding of biological processes, such as anhydrobiosis, as well as the development of new biomimetic photovoltaic devices.

Mechanisms of Tooth Eruption and Orthodontic Tooth Movement

PubMed Central

Wise, G.E.; King, G.J.

2008-01-01

Teeth move through alveolar bone, whether through the normal process of tooth eruption or by strains generated by orthodontic appliances. Both eruption and orthodontics accomplish this feat through similar fundamental biological processes, osteoclastogenesis and osteogenesis, but there are differences that make their mechanisms unique. A better appreciation of the molecular and cellular events that regulate osteoclastogenesis and osteogenesis in eruption and orthodontics is not only central to our understanding of how these processes occur, but also is needed for ultimate development of the means to control them. Possible future studies in these areas are also discussed, with particular emphasis on translation of fundamental knowledge to improve dental treatments. PMID:18434571

Single-Molecule Sensing with Nanopore Confinement: From Chemical Reactions to Biological Interactions.

PubMed

Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

2018-03-25

The nanopore can generate an electrochemical confinement for single-molecule sensing that help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this Concept article, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improving anaerobic and aerobic degradation by ultrasonic disintegration of biomass.

PubMed

Neis, Uwe; Nickel, Klaus; Lundén, Anna

2008-11-01

Biological cell lysis is known to be the rate-limiting step of anaerobic biosolids degradation. Due to the slow pace by which this reaction occurs, it is necessary to equip treatment plants with large digesters or alternatively incorporate technological aids. High-power ultrasound used to disintegrate bacterial cells has been utilized as a pre-treatment process prior to anaerobic digestion. Through this application, as seen on pilot- and full-scales, it is possible to attain up to 30% more biogas, an increase in VS-destruction of up to 30% and a reduced sludge mass for disposal. Utilizing ultrasound technology in aerobic applications is a new and innovative approach. Improved denitrification through a more readily available internal carbon source, and less excess sludge mass can be traced to the positive effects that sonication of sludge has on the overall biological wastewater treatment process. Reference full-scale installations suggest that the technology is both technically feasible and economically sound.

Onset of meso-scale turbulence in active nematics

NASA Astrophysics Data System (ADS)

Doostmohammadi, Amin; Shendruk, Tyler N.; Thijssen, Kristian; Yeomans, Julia M.

2017-05-01

Meso-scale turbulence is an innate phenomenon, distinct from inertial turbulence, that spontaneously occurs at low Reynolds number in fluidized biological systems. This spatiotemporal disordered flow radically changes nutrient and molecular transport in living fluids and can strongly affect the collective behaviour in prominent biological processes, including biofilm formation, morphogenesis and cancer invasion. Despite its crucial role in such physiological processes, understanding meso-scale turbulence and any relation to classical inertial turbulence remains obscure. Here we show how the motion of active matter along a micro-channel transitions to meso-scale turbulence through the evolution of locally disordered patches (active puffs) from an ordered vortex-lattice flow state. We demonstrate that the stationary critical exponents of this transition to meso-scale turbulence in a channel coincide with the directed percolation universality class. This finding bridges our understanding of the onset of low-Reynolds-number meso-scale turbulence and traditional scale-invariant turbulence in confinement.

Interplay between social experiences and the genome: epigenetic consequences for behavior.

PubMed

Champagne, Frances A

2012-01-01

Social experiences can have a persistent effect on biological processes leading to phenotypic diversity. Variation in gene regulation has emerged as a mechanism through which the interplay between DNA and environments leads to the biological encoding of these experiences. Epigenetic modifications-molecular pathways through which transcription is altered without altering the underlying DNA sequence-play a critical role in the normal process of development and are being increasingly explored as a mechanism linking environmental experiences to long-term biobehavioral outcomes. In this review, evidence implicating epigenetic factors, such as DNA methylation and histone modifications, in the link between social experiences occurring during the postnatal period and in adulthood and altered neuroendocrine and behavioral outcomes will be highlighted. In addition, the role of epigenetic mechanisms in shaping variation in social behavior and the implications of epigenetics for our understanding of the transmission of traits across generations will be discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

Modelling the collective response of heterogeneous cell populations to stationary gradients and chemical signal relay

NASA Astrophysics Data System (ADS)

Pineda, M.; Eftimie, R.

2017-12-01

The directed motion of cell aggregates toward a chemical source occurs in many relevant biological processes. Understanding the mechanisms that control this complex behavior is of great relevance for our understanding of developmental biological processes and many diseases. In this paper, we consider a self-propelled particle model for the movement of heterogeneous subpopulations of chemically interacting cells towards an imposed stable chemical gradient. Our simulations show explicitly how self-organisation of cell populations (which could lead to engulfment or complete cell segregation) can arise from the heterogeneity of chemotactic responses alone. This new result complements current theoretical and experimental studies that emphasise the role of differential cell-cell adhesion on self-organisation and spatial structure of cellular aggregates. We also investigate how the speed of individual cell aggregations increases with the chemotactic sensitivity of the cells, and decreases with the number of cells inside the aggregates

The cytoskeletal arrangements necessary to neurogenesis

PubMed Central

Compagnucci, Claudia; Piemonte, Fiorella; Sferra, Antonella; Piermarini, Emanuela; Bertini, Enrico

2016-01-01

During the process of neurogenesis, the stem cell committed to the neuronal cell fate starts a series of molecular and morphological changes. The understanding of the physio-pathology of mechanisms controlling the molecular and morphological changes occurring during neuronal differentiation is fundamental to the development of effective therapies for many neurologic diseases. Unfortunately, our knowledge of the biological events occurring in the cell during neuronal differentiation is still poor. In this study, we focus preliminarily on the relevance of the cytoskeletal rearrangements, which earlier drive the morphology of the neuronal precursors, and later the migrating/mature neurons. In fact, neuritogenesis, neurite branching, outgrowth and retraction are seminal to the development of a fully functional nervous system. With this in mind, we highlight the importance of iPSC technology to study the processes of cytoskeletal-driven morphological changes during neuronal differentiation. PMID:26760504

Remediation of water contaminated with diesel oil using a coupled process: Biological degradation followed by heterogeneous Fenton-like oxidation.

PubMed

Chen, Yuan; Lin, Jiajiang; Chen, Zuliang

2017-09-01

The treatment of a synthetically prepared wastewater containing diesel oil has been investigated using combined treatment schemes based on the biological treatment followed by an advanced oxidation process. 78% of diesel oil was degraded by Acinetobacter venetianus in 96 h, while the removal efficiency of chemical oxygen demand (COD) in the aqueous phase was only 56.8%, indicating that degraded metabolites existed in solution. To solve this problem, a Fenton-like system consisting of nanoscale zero-valent iron (nZVI) and hydrogen peroxide was used for further oxidation of the metabolites after biodegradation. Results showed that the total COD removal increased from 56.8% to 89% under the optimal condition. In addition, effects of initial pH (2.0-9.0), ZVI dosage (0-2.0 g L-1), hydrogen peroxide (H 2 O 2 ) dosage concentration (0-15 mmol L-1) and temperature (298-308 K) on the treatment efficiency of the combined process were studied. Scanning electron microscopy (SEM) demonstrated that changes to the surface of nZVI occurred. GC-MS revealed that the degraded metabolites were mineralized practically by nZVI/H 2 O 2 system. The results points towards the potential of Fenton-like oxidation as a short post-treatment after a biological process for the treatment of organic pollutants in wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

Processes regulating progressive nitrogen limitation under elevated carbon dioxide: a meta-analysis

NASA Astrophysics Data System (ADS)

Liang, J.; Qi, X.; Souza, L.; Luo, Y.

2015-10-01

Nitrogen (N) cycle has the potential to regulate climate change through its influence on carbon (C) sequestration. Although extensive researches have been done to explore whether or not progressive N limitation (PNL) occurs under CO2 enrichment, a comprehensive assessment of the processes that regulate PNL is still lacking. Here, we quantitatively synthesized the responses of all major processes and pools in terrestrial N cycle with meta-analysis of CO2 experimental data available in the literature. The results showed that CO2 enrichment significantly increased N sequestration in plant and litter pools but not in soil pool. Thus, the basis of PNL occurrence partially exists. However, CO2 enrichment also significantly increased the N influx via biological N fixation, but decreased the N efflux via leaching. In addition, no general diminished CO2 fertilization effect on plant growth over time was observed. Overall, our analyses suggest that the extra N supply by the increased biological N fixation and decreased leaching may potentially alleviate PNL under elevated CO2 conditions. Moreover, our synthesis showed that CO2 enrichment increased soil ammonium (NH4+) but decreased nitrate (NO3-). The different responses of NH4+ and NO3-, and the consequent biological processes, may result in changes in soil microenvironment, community structures and above-belowground interactions, which could potentially affect the terrestrial biogeochemical cycles and the feedback to climate change.

Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths

PubMed Central

Li, Chunhe; Wang, Jin

2013-01-01

Cellular reprogramming has been recently intensively studied experimentally. We developed a global potential landscape and kinetic path framework to explore a human stem cell developmental network composed of 52 genes. We uncovered the underlying landscape for the stem cell network with two basins of attractions representing stem and differentiated cell states, quantified and exhibited the high dimensional biological paths for the differentiation and reprogramming process, connecting the stem cell state and differentiated cell state. Both the landscape and non-equilibrium curl flux determine the dynamics of cell differentiation jointly. Flux leads the kinetic paths to be deviated from the steepest descent gradient path, and the corresponding differentiation and reprogramming paths are irreversible. Quantification of paths allows us to find out how the differentiation and reprogramming occur and which important states they go through. We show the developmental process proceeds as moving from the stem cell basin of attraction to the differentiation basin of attraction. The landscape topography characterized by the barrier heights and transition rates quantitatively determine the global stability and kinetic speed of cell fate decision process for development. Through the global sensitivity analysis, we provided some specific predictions for the effects of key genes and regulation connections on the cellular differentiation or reprogramming process. Key links from sensitivity analysis and biological paths can be used to guide the differentiation designs or reprogramming tactics. PMID:23935477

Proteomic analysis of Bombyx mori molting fluid: Insights into the molting process.

PubMed

Liu, Hua-Wei; Wang, Luo-Ling; Tang, Xin; Dong, Zhao-Ming; Guo, Peng-Chao; Zhao, Dong-Chao; Xia, Qing-You; Zhao, Ping

2018-02-20

Molting is an essential biological process occurring multiple times throughout the life cycle of most Ecdysozoa. Molting fluids accumulate and function in the exuvial space during the molting process. In this study, we used liquid chromatography-tandem mass spectrometry to investigate the molting fluids to analyze the molecular mechanisms of molting in the silkworm, Bombyx mori. In total, 375 proteins were identified in molting fluids from the silkworm at 14-16h before pupation and eclosion, including 12 chitin metabolism-related enzymes, 35 serine proteases, 15 peptidases, and 38 protease inhibitors. Gene ontology analysis indicated that "catalytic" constitutes the most enriched function in the molting fluid. Gene expression patterns and bioinformatic analyses suggested that numerous enzymes are involved in the degradation of cuticle proteins and chitin. Protein-protein interaction network and activity analyses showed that protease inhibitors are involved in the regulation of multiple pathways in molting fluid. Additionally, many immune-related proteins may be involved in the immune defense during molting. These results provide a comprehensive proteomic insight into proteolytic enzymes and protease inhibitors in molting fluid, and will likely improve the current understanding of physiological processes in insect molting. Insect molting constitutes a dynamic physiological process. To better understand this process, we used LC-MS/MS to investigate the proteome of silkworm molting fluids and identified key proteins involved in silkworm molting. The biological processes of the old cuticle degradation pathway and immune defense response were analyzed in the proteome of silkworm molting fluid. We report that protease inhibitors serve as key factors in the regulation of the molting process. The proteomic results provide new insight into biological molting processes in insects. Copyright © 2017 Elsevier B.V. All rights reserved.

Inter-species investigation of the mechano-regulation of bone healing: comparison of secondary bone healing in sheep and rat.

PubMed

Checa, Sara; Prendergast, Patrick J; Duda, Georg N

2011-04-29

Inter-species differences in regeneration exist in various levels. One aspect is the dynamics of bone regeneration and healing, e.g. small animals show a faster healing response when compared to large animals. Mechanical as well as biological factors are known to play a key role in the process. However, it remains so far unknown whether different animals follow at all comparable mechano-biological rules during tissue regeneration, and in particular during bone healing. In this study, we investigated whether differences observed in vivo in the dynamics of bone healing between rat and sheep are only due to differences in the animal size or whether these animals have a different mechano-biological response during the healing process. Histological sections from in vivo experiments were compared to in silico predictions of a mechano-biological computer model for the simulation of bone healing. Investigations showed that the healing processes in both animal models occur under significantly different levels of mechanical stimuli within the callus region, which could explain histological observations of early intramembranous ossification at the endosteal side. A species-specific adaptation of a mechano-biological model allowed a qualitative match of model predictions with histological observations. Specifically, when keeping cell activity processes at the same rate, the amount of tissue straining defining favorable mechanical conditions for the formation of bone had to be increased in the large animal model, with respect to the small animal, to achieve a qualitative agreement of model predictions with histological data. These findings illustrate that geometrical (size) differences alone cannot explain the distinctions seen in the histological appearance of secondary bone healing in sheep and rat. It can be stated that significant differences in the mechano-biological regulation of the healing process exist between these species. Future investigations should aim towards understanding whether these differences are due to differences in cell behavior, material properties of the newly formed tissues within the callus and/or differences in response to the mechanical environment. Copyright © 2011 Elsevier Ltd. All rights reserved.

Allosteric Learning Model in English Lesson: Teachers' Views, the Instructions of Curriculum and Course Book, a Sample of Daily Lesson Plan

ERIC Educational Resources Information Center

Berkant, Hasan Güner; Baysal, Seda

2017-01-01

The changes which occur during the learning process have been explained by many teaching-learning models and theories. One of these models is allosteric learning model (ALM) which was developed by André Giordan in 1989. This model was derived from a biological metaphor related to proteins. The interaction between individual and environment in a…

The universality of the von Bertalanffy growth curve. Comment on: ;Physics of metabolic organization; by Marko Jusup et al.

NASA Astrophysics Data System (ADS)

Maino, James L.; Kearney, Michael R.

2017-03-01

A key strength of the DEB approach, in contrast to other metabolic theories, is that its foundational principles are general to all of life. Other theories have attempted to explain patterns in metabolism in terms of taxon-specific processes, such as the geometry of vascular network supply constraints [1,2], or heat dissipation requirements of endotherms [3], but DEB theory presents constraints on metabolic processes that apply to a wide range of taxa, including bacteria, invertebrates, birds, or mammals [4]. The price of this generalisability is abstraction, but there is much to gain from a general and unifying metabolic theory. Abstracting individuals into simple energy processors would seem to overlook many other important aspects of their biology, such as their unique phylogeny, physiology, or ethology, but this strategy has facilitated great advances in one of the grand challenges in biology: making sense of interacting phenomena occurring across wide scales in space, time, and organisational complexity. The study of cells, individuals, communities and ecosystems have benefited from such a regime [5,6]. Similarly, the simple abstraction of partitioning individual organisms into compartments of reserve biomass and structural biomass allows one to account for an astounding variety of energetic transformations that occur between species and as an organism develops.

MIMO: an efficient tool for molecular interaction maps overlap

PubMed Central

2013-01-01

Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

Emergence of biological organization through thermodynamic inversion.

PubMed

Kompanichenko, Vladimir

2014-01-01

Biological organization arises under thermodynamic inversion in prebiotic systems that provide the prevalence of free energy and information contribution over the entropy contribution. The inversion might occur under specific far-from-equilibrium conditions in prebiotic systems oscillating around the bifurcation point. At the inversion moment, (physical) information characteristic of non-biological systems acquires the new features: functionality, purposefulness, and control over the life processes, which transform it into biological information. Random sequences of amino acids and nucleotides, spontaneously synthesized in the prebiotic microsystem, in the primary living unit (probiont) re-assemble into functional sequences, involved into bioinformation circulation through nucleoprotein interaction, resulted in the genetic code emergence. According to the proposed concept, oscillating three-dimensional prebiotic microsystems transformed into probionts in the changeable hydrothermal medium of the early Earth. The inversion concept states that spontaneous (accidental, random) transformations in prebiotic systems cannot produce life; it is only non-spontaneous (perspective, purposeful) transformations, which are the result of thermodynamic inversion, that lead to the negentropy conversion of prebiotic systems into initial living units.

Biological and Organic Chemical Decomposition of Silicates. Chapter 7.2

NASA Technical Reports Server (NTRS)

Silverman, M. P.

1979-01-01

The weathering of silicate rocks and minerals, an important concern of geologists and geochemists for many years, traditionally has been approached from strictly physical and chemical points of view. Biological effects were either unrecognized, ignored, or were mentioned in passing to account for such phenomena as the accumulation of organic matter in sediments or the generation of reducing environments. A major exception occurred in soil science where agricultural scientists, studying the factors important in the development of soils and their ability to nourish and sustain various crops, laid the foundation for much of what is known of the biological breakdown of silicate rocks and minerals. The advent of the space age accelerated the realization that many environmental problems and geo- chemical processes on Earth can only be understood in terms of ecosystems. This in turn, spurred renewed interest and activity among modem biologists, geologists and soil scientists attempting to unravel the intimate relations between biology and the weathering of silicate rocks and minerals of the earth surface.

Synthetic fossilization of soft biological tissues and their shape-preserving transformation into silica or electron-conductive replicas

DOE PAGES

Townson, Jason L.; Lin, Yu-Shen; Chou, Stanley S.; ...

2014-12-08

Structural preservation of complex biological systems from the subcellular to whole organism level in robust forms, enabling dissection and imaging while preserving 3D context, represents an enduring grand challenge in biology. Here we report a simple immersion method for structurally preserving intact organisms via conformal stabilization within silica. This self-limiting process, which we refer to as silica bioreplication, occurs by condensation of water-soluble silicic acid proximally to biomolecular interfaces throughout the organism. Conformal nanoscopic silicification of all biomolecular features imparts structural rigidity enabling the preservation of shape and nano-to-macroscale dimensional features upon drying to form a biocomposite and further highmore » temperature oxidative calcination to form silica replicas or reductive pyrolysis to form electrically conductive carbon replicas of complete organisms. Ultimately, the simplicity and generalizability of this approach should facilitate efforts in biological preservation and analysis and could enable the development of new classes of biomimetic composite materials.« less

System Analysis of LWDH Related Genes Based on Text Mining in Biological Networks

PubMed Central

Miao, Yingbo; Zhang, Liangcai; Wang, Yang; Feng, Rennan; Yang, Lei; Zhang, Shihua; Jiang, Yongshuai; Liu, Guiyou

2014-01-01

Liuwei-dihuang (LWDH) is widely used in traditional Chinese medicine (TCM), but its molecular mechanism about gene interactions is unclear. LWDH genes were extracted from the existing literatures based on text mining technology. To simulate the complex molecular interactions that occur in the whole body, protein-protein interaction networks (PPINs) were constructed and the topological properties of LWDH genes were analyzed. LWDH genes have higher centrality properties and may play important roles in the complex biological network environment. It was also found that the distances within LWDH genes are smaller than expected, which means that the communication of LWDH genes during the biological process is rapid and effectual. At last, a comprehensive network of LWDH genes, including the related drugs and regulatory pathways at both the transcriptional and posttranscriptional levels, was constructed and analyzed. The biological network analysis strategy used in this study may be helpful for the understanding of molecular mechanism of TCM. PMID:25243143

Biological and Organic Chemical Decomposition of Silicates. Chapter 7.2

NASA Technical Reports Server (NTRS)

Sliverman, M. P.

1979-01-01

The weathering of silicate rocks and minerals, an important concern of geologists and geochemists for many years, traditionally has been approached from strictly physical and chemical points of view. Biological effects were either unrecognized, ignored, or were mentioned in passing to account for such phenomena as the accumulation of organic matter in sediments or the generation of reducing environments. A major exception occurred in soil science where agricultural scientists, studying the factors important in the development of soils and their ability to nourish and sustain various crops, laid the foundation for much of what is known of the biological breakdown of silicate rocks and minerals. The advent of the space age accelerated the realization that many environmental problems and geochemical processes on Earth can only be understood in terms of ecosystems. This in turn, spurred renewed interest and activity among modem biologists, geologists and soil scientists attempting to unravel the intimate relations between biology and the weathering of silicate rocks and minerals of the earth's surface.

Exponential evolution: implications for intelligent extraterrestrial life.

PubMed

Russell, D A

1983-01-01

Some measures of biologic complexity, including maximal levels of brain development, are exponential functions of time through intervals of 10(6) to 10(9) yrs. Biological interactions apparently stimulate evolution but physical conditions determine the time required to achieve a given level of complexity. Trends in brain evolution suggest that other organisms could attain human levels within approximately 10(7) yrs. The number (N) and longevity (L) terms in appropriate modifications of the Drake Equation, together with trends in the evolution of biological complexity on Earth, could provide rough estimates of the prevalence of life forms at specified levels of complexity within the Galaxy. If life occurs throughout the cosmos, exponential evolutionary processes imply that higher intelligence will soon (10(9) yrs) become more prevalent than it now is. Changes in the physical universe become less rapid as time increases from the Big Bang. Changes in biological complexity may be most rapid at such later times. This lends a unique and symmetrical importance to early and late universal times.

Biological enhancement of graft-tunnel healing in anterior cruciate ligament reconstruction

PubMed Central

SACCOMANNO, MARISTELLA F.; CAPASSO, LUIGI; FRESTA, LUCA; MILANO, GIUSEPPE

2016-01-01

The sites where graft healing occurs within the bone tunnel and where the intra-articular ligamentization process takes place are the two most important sites of biological incorporation after anterior cruciate ligament (ACL) reconstruction, since they help to determine the mechanical behavior of the femur-ACL graft-tibia complex. Graft-tunnel healing is a complex process influenced by several factors, such as type of graft, preservation of remnants, bone quality, tunnel length and placement, fixation techniques and mechanical stress. In recent years, numerous experimental and clinical studies have been carried out to evaluate potential strategies designed to enhance and optimize the biological environment of the graft-tunnel interface. Modulation of inflammation, tissue engineering and gene transfer techniques have been applied in order to obtain a direct-type fibrocartilaginous insertion of the ACL graft, similar to that of native ligament, and to accelerate the healing process of tendon grafts within the bone tunnel. Although animal studies have given encouraging results, clinical studies are lacking and their results do not really support the use of the various strategies in clinical practice. Further investigations are therefore needed to optimize delivery techniques, therapeutic concentrations, maintenance of therapeutic effects over time, and to reduce the risk of undesirable effects in clinical practice. PMID:27900311

Biological iron oxidation by Gallionella spp. in drinking water production under fully aerated conditions.

PubMed

de Vet, W W J M; Dinkla, I J T; Rietveld, L C; van Loosdrecht, M C M

2011-11-01

Iron oxidation under neutral conditions (pH 6.5-8) may be a homo- or heterogeneous chemically- or a biologically-mediated process. The chemical oxidation is supposed to outpace the biological process under slightly alkaline conditions (pH 7-8). The iron oxidation kinetics and growth of Gallionella spp. - obligatory chemolithotrophic iron oxidizers - were assessed in natural, organic carbon-containing water, in continuous lab-scale reactors and full-scale groundwater trickling filters in the Netherlands. From Gallionella cell numbers determined by qPCR, balances were made for all systems. The homogeneous chemical iron oxidation occurred in accordance with the literature, but was retarded by a low water temperature (13 °C). The contribution of the heterogeneous chemical oxidation was, despite the presence of freshly formed iron oxyhydroxides, much lower than in previous studies in ultrapure water. This could be caused by the adsorption of natural organic matter (NOM) on the iron oxide surfaces. In the oxygen-saturated natural water with a pH ranging from 6.5 to 7.7, Gallionella spp. grew uninhibited and biological iron oxidation was an important, and probably the dominant, process. Gallionella growth was not even inhibited in a full-scale filter after plate aeration. From this we conclude that Gallionella spp. can grow under neutral pH and fully aerated conditions when the chemical iron oxidation is retarded by low water temperature and inhibition of the autocatalytic iron oxidation. Copyright © 2011 Elsevier Ltd. All rights reserved.

1H NMR-based metabolic profiling for evaluating poppy seed rancidity and brewing.

PubMed

Jawień, Ewa; Ząbek, Adam; Deja, Stanisław; Łukaszewicz, Marcin; Młynarz, Piotr

2015-12-01

Poppy seeds are widely used in household and commercial confectionery. The aim of this study was to demonstrate the application of metabolic profiling for industrial monitoring of the molecular changes which occur during minced poppy seed rancidity and brewing processes performed on raw seeds. Both forms of poppy seeds were obtained from a confectionery company. Proton nuclear magnetic resonance (1H NMR) was applied as the analytical method of choice together with multivariate statistical data analysis. Metabolic fingerprinting was applied as a bioprocess control tool to monitor rancidity with the trajectory of change and brewing progressions. Low molecular weight compounds were found to be statistically significant biomarkers of these bioprocesses. Changes in concentrations of chemical compounds were explained relative to the biochemical processes and external conditions. The obtained results provide valuable and comprehensive information to gain a better understanding of the biology of rancidity and brewing processes, while demonstrating the potential for applying NMR spectroscopy combined with multivariate data analysis tools for quality control in food industries involved in the processing of oilseeds. This precious and versatile information gives a better understanding of the biology of these processes.

Synergy and Interactions Among Biological Pathways Leading to Preterm Premature Rupture of Membranes

PubMed Central

Lannon, Sophia M. R.; Vanderhoeven, Jeroen P.; Eschenbach, David A.; Gravett, Michael G.; Waldorf, Kristina M. Adams

2014-01-01

Preterm premature rupture of membranes (PPROM) occurs in 1% to 2% of births. Impact of PPROM is greatest in low- and middle-income countries where prematurity-related deaths are most common. Recent investigations identify cytokine and matrix metalloproteinase activation, oxidative stress, and apoptosis as primary pathways to PPROM. These biological processes are initiated by heterogeneous etiologies including infection/inflammation, placental bleeding, uterine overdistention, and genetic polymorphisms. We hypothesize that pathways to PPROM overlap and act synergistically to weaken membranes. We focus our discussion on membrane composition and strength, pathways linking risk factors to membrane weakening, and future research directions to reduce the global burden of PPROM. PMID:24840939

Human evolution, life history theory, and the end of biological reproduction.

PubMed

Last, Cadell

2014-01-01

Throughout primate history there have been three major life history transitions towards increasingly delayed sexual maturation and biological reproduction, as well as towards extended life expectancy. Monkeys reproduce later and live longer than do prosimians, apes reproduce later and live longer than do monkeys, and humans reproduce later and live longer than do apes. These life history transitions are connected to increased encephalization. During the last life history transition from apes to humans, increased encephalization co-evolved with increased dependence on cultural knowledge for energy acquisition. This led to a dramatic pressure for more energy investment in growth over current biological reproduction. Since the industrial revolution socioeconomic development has led to even more energy being devoted to growth over current biological reproduction. I propose that this is the beginning of an ongoing fourth major primate life history transition towards completely delayed biological reproduction and an extension of the evolved human life expectancy. I argue that the only fundamental difference between this primate life history transition and previous life history transitions is that this transition is being driven solely by cultural evolution, which may suggest some deeper evolutionary transition away from biological evolution is already in the process of occurring.

The behavioural characteristics of sediment properties and their implications for sediment fingerprinting as an approach for identifying sediment sources in river basins

NASA Astrophysics Data System (ADS)

Koiter, A. J.; Owens, P. N.; Petticrew, E. L.; Lobb, D. A.

2013-10-01

Sediment fingerprinting is a technique that is increasingly being used to improve the understanding of sediment dynamics within river basins. At present, one of the main limitations of the technique is the ability to link sediment back to their sources due to the non-conservative nature of many of the sediment properties. The processes that occur between the sediment source locations and the point of collection downstream are not well understood or quantified and currently represent a black-box in the sediment fingerprinting approach. The literature on sediment fingerprinting tends to assume that there is a direct connection between sources and sinks, while much of the broader environmental sedimentology literature identifies that numerous chemical, biological and physical transformations and alterations can occur as sediment moves through the landscape. The focus of this paper is on the processes that drive particle size and organic matter selectivity and biological, geochemical and physical transformations and how understanding these processes can be used to guide sampling protocols, fingerprint selection and data interpretation. The application of statistical approaches without consideration of how unique sediment fingerprints have developed and how robust they are within the environment is a major limitation of many recent studies. This review summarises the current information, identifies areas that need further investigation and provides recommendations for sediment fingerprinting that should be considered for adoption in future studies if the full potential and utility of the approach are to be realised.

Plasmonic-based nanoprobes for dynamic sensing of single tumor cells (Conference Presentation)

NASA Astrophysics Data System (ADS)

Chen, Zixuan

2017-02-01

We described here two plasmonic-based nanoprobes with purpose of imaging dynamic biologic process of single tumor cells. At first, we proposed a multi-modified core-shell gold@silver nanorods for real-time monitoring the entire autophagy process at single-cell level. Autophagy is vital for understanding the mechanisms of human pathologies, developing novel drugs and exploring approaches for autophagy controlling. The plasmon resonance scattering spectra of the nanoprobes was superoxide radicals (O2•-)-dependent, a major indicator of cell autophagy, and suitable for real-time monitoring at single-cell level. More importantly, with the introduction of `relay probe' operation, two types of O2•-regulating autophagy processes were successfully traced from the beginning to the end, and the possible mechanism was also proposed. According to our results, intracellular O2•- level controlled the autophagy process by mediating the autolysosome generation. Different starvation approaches can induce different autophagy processes, such as diverse steady state time-consuming. In addition, a plasmonic-based nanothermometer was prepared via dense thermosensitive polymer (pNIPAAm) capping on gold nanorods, of which the plasmon resonance spectra was linearly dependent on adjacent temperature. In this work, the white light transmitted dark-field illuminator was replaced by a laser total internal reflection dark-field microscope (LTIR-DFM) system in order to overcome the low-throughput and inexorable biological scattering background of DFM, as well as interference from mechanic noise, nanoprobe direction, optical system drift, etc. With this nanothermometer, we have successfully captured temporal biological thermal process (thermogenesis) occurred in single tumor cells, providing a new potential strategy for in-situ cellular analysis.

Ontology of physics for biology: representing physical dependencies as a basis for biological processes.

PubMed

Cook, Daniel L; Neal, Maxwell L; Bookstein, Fred L; Gennari, John H

2013-12-02

In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based biosimulation models. We introduced OPB:Physical entity and OPB:Physical property classes that extend available spatiotemporal representations of physical entities and processes to explicitly represent the thermodynamics and dynamics of physiological processes. Our utilitarian, long-term aim is to develop computational tools for creating and querying formalized physiological knowledge for use by multiscale "physiome" projects such as the EU's Virtual Physiological Human (VPH) and NIH's Virtual Physiological Rat (VPR). Here we describe the OPB:Physical dependency taxonomy of classes that represent of the laws of classical physics that are the "rules" by which physical properties of physical entities change during occurrences of physical processes. For example, the fluid analog of Ohm's law (as for electric currents) is used to describe how a blood flow rate depends on a blood pressure gradient. Hooke's law (as in elastic deformations of springs) is used to describe how an increase in vascular volume increases blood pressure. We classify such dependencies according to the flow, transformation, and storage of thermodynamic energy that occurs during processes governed by the dependencies. We have developed the OPB and annotation methods to represent the meaning-the biophysical semantics-of the mathematical statements of physiological analysis and the biophysical content of models and datasets. Here we describe and discuss our approach to an ontological representation of physical laws (as dependencies) and properties as encoded for the mathematical analysis of biophysical processes.

Review of wildlife resources of Vandenberg Air Force Base, California

NASA Technical Reports Server (NTRS)

Breininger, David R.

1989-01-01

Wildlife resources are reviewed for purposes of developing a Base Biological Monitoring Program (BMP) for Vandenberg Air Force Base (VAFB) in Santa Barbara County, California. The review and recommendations were prepared by review of applicable scientific literature and environmental documents for VAFB, discussing information needs with natural resource management professionals at VAFB, and observations of base field conditions. This process found that there are 29 federally listed vertebrates (endangered, threatened, or Category 2) that occur or may occur in the vicinity of VAFB. There are also 63 other state listed or regionally declining species that may occur in the vicinity of VAFB. Habitats of VAFB represent a very valuable environmental resource for rare and declining wildlife in California. However, little information is available on VAFB wildlife resources other than lists of species that occur or are expected to occur. Recommendations are presented to initiate a long-term wildlife monitoring program at VAFB to provide information for environmental impact assessment and wise land use planning.

UV fluorescence excitation spectroscopy as a non-invasive predictor of epidermal proliferation and clinical performance of cosmetic formulations

NASA Astrophysics Data System (ADS)

Maidhof, Robert; Liebel, Frank; Hwang, Cheng; Ruvolo, Eduardo; Lyga, John

2017-02-01

The epidermis is the outermost layer of skin and is composed of cells primarily containing keratin. It consists of about ten layers of living cells (keratinocytes) and ten layers of dead cells (corneocytes). These cells are continually shed from the outside and replaced from the inside in a process called desquamation which is controlled by two biological events - proliferation and differentiation. One method to non-invasively study biological changes in the skin is using fluorescence excitation spectroscopy. Several characteristic excitation-emission peaks occur in skin that have been related to the epidermal and dermal composition. The magnitude of the peak that occurs at 295nm excitation (F295) has been linked to changes in skin proliferation, cell turnover, epidermal thickening, and skin aging. We hypothesize that changes in this fluorescent signal could be used to assess the potential activity of cosmetic anti-aging compounds to deliver a benefit to skin. Previous work with retinol and glycolic acid, two commonly used actives that effect epidermal proliferation and exfoliation, has demonstrated an increase in F295 (attributed to tryptophan excitation fluorescence). In this study we present the results of a placebo controlled study that aims to correlate changes in F295 with biological performance (epidermal thickening and Ki67 expression).

Understanding the immune response to seasonal influenza vaccination in older adults: a systems biology approach.

PubMed

Lambert, Nathaniel D; Ovsyannikova, Inna G; Pankratz, V Shane; Jacobson, Robert M; Poland, Gregory A

2012-08-01

Annual vaccination against seasonal influenza is recommended to decrease disease-related mortality and morbidity. However, one population that responds suboptimally to influenza vaccine is adults over the age of 65 years. The natural aging process is associated with a complex deterioration of multiple components of the host immune system. Research into this phenomenon, known as immunosenescence, has shown that aging alters both the innate and adaptive branches of the immune system. The intricate mechanisms involved in immune response to influenza vaccine, and how these responses are altered with age, have led us to adopt a more encompassing systems biology approach to understand exactly why the response to vaccination diminishes with age. Here, the authors review what changes occur with immunosenescence, and some immunogenetic factors that influence response, and outline the systems biology approach to understand the immune response to seasonal influenza vaccination in older adults.

Molecular imaging and the unification of multilevel mechanisms and data in medical physics.

PubMed

Nikiforidis, George C; Sakellaropoulos, George C; Kagadis, George C

2008-08-01

Molecular imaging (MI) constitutes a recently developed approach of imaging, where modalities and agents have been reinvented and used in novel combinations in order to expose and measure biologic processes occurring at molecular and cellular levels. It is an approach that bridges the gap between modalities acquiring data from high (e.g., computed tomography, magnetic resonance imaging, and positron-emitting isotopes) and low (e.g., PCR, microarrays) levels of a biological organization. While data integration methodologies will lead to improved diagnostic and prognostic performance, interdisciplinary collaboration, triggered by MI, will result in a better perception of the underlying biological mechanisms. Toward the development of a unifying theory describing these mechanisms, medical physicists can formulate new hypotheses, provide the physical constraints bounding them, and consequently design appropriate experiments. Their new scientific and working environment calls for interventions in their syllabi to educate scientists with enhanced capabilities for holistic views and synthesis.

Managing shifting species: Ancient DNA reveals conservation conundrums in a dynamic world.

PubMed

Waters, Jonathan M; Grosser, Stefanie

2016-11-01

The spread of exotic species represents a major driver of biological change across the planet. While dispersal and colonization are natural biological processes, we suggest that the failure to recognize increasing rates of human-facilitated self-introductions may represent a threat to native lineages. Notably, recent biogeographic analyses have revealed numerous cases of biological range shifts in response to anthropogenic impacts and climate change. In particular, ancient DNA analyses have revealed several cases in which lineages traditionally thought to be long-established "natives" are in fact recent colonizers. Such range expansion events have apparently occurred in response to human-mediated native biodiversity declines and ecosystem change, particularly in recently colonized, isolated ecosystems such as New Zealand. While such events can potentially boost local biodiversity, the spread of exotic lineages may also hasten the decline of indigenous species, so it is essential that conservation managers recognize these rapid biotic shifts.​. © 2016 WILEY Periodicals, Inc.

Rapid Start-up and Loading of an Attached Growth, Simultaneous Nitrification/Denitrification Membrane Aerated Bioreactor

NASA Technical Reports Server (NTRS)

Meyer, Caitlin E.; Pensinger, Stuart; Pickering, Karen D.; Barta, Daniel; Shull, Sarah A.; Vega, Letticia M.; Christenson, Dylan; Jackson, W. Andrew

2015-01-01

Membrane aerated bioreactors (MABR) are attached-growth biological systems used for simultaneous nitrification and denitrification to reclaim water from waste. This design is an innovative approach to common terrestrial wastewater treatments for nitrogen and carbon removal and implementing a biologically-based water treatment system for long-duration human exploration is an attractive, low energy alternative to physiochemical processes. Two obstacles to implementing such a system are (1) the "start-up" duration from inoculation to steady-state operations and (2) the amount of surface area needed for the biological activity to occur. The Advanced Water Recovery Systems (AWRS) team at JSC explored these two issues through two tests; a rapid inoculation study and a wastewater loading study. Results from these tests demonstrate that the duration from inoculation to steady state can be reduced to under two weeks, and that despite low ammonium removal rates, the MABRs are oversized.

Bioinspired Functional Surfaces for Technological Applications

NASA Astrophysics Data System (ADS)

Sharma, Vipul; Kumar, Suneel; Reddy, Kumbam Lingeshwar; Bahuguna, Ashish; Krishnan, Venkata

2016-08-01

Biological matters have been in continuous encounter with extreme environmental conditions leading to their evolution over millions of years. The fittest have survived through continuous evolution, an ongoing process. Biological surfaces are the important active interfaces between biological matters and the environment, and have been evolving over time to a higher state of intelligent functionality. Bioinspired surfaces with special functionalities have grabbed attention in materials research in the recent times. The microstructures and mechanisms behind these functional biological surfaces with interesting properties have inspired scientists to create artificial materials and surfaces which possess the properties equivalent to their counterparts. In this review, we have described the interplay between unique multiscale (micro- and nano-scale) structures of biological surfaces with intrinsic material properties which have inspired researchers to achieve the desired wettability and functionalities. Inspired by naturally occurring surfaces, researchers have designed and fabricated novel interfacial materials with versatile functionalities and wettability, such as superantiwetting surfaces (superhydrophobic and superoleophobic), omniphobic, switching wettability and water collecting surfaces. These strategies collectively enable functional surfaces to be utilized in different applications such as fog harvesting, surface-enhanced Raman spectroscopy (SERS), catalysis, sensing and biological applications. This paper delivers a critical review of such inspiring biological surfaces and artificial bioinspired surfaces utilized in different applications, where material science and engineering have merged by taking inspiration from the natural systems.

Increased electrical conductivity of peptides through annealing process

NASA Astrophysics Data System (ADS)

Namgung, Seok Daniel; Lee, Jaehun; Choe, Ik Rang; Sung, Taehoon; Kim, Young-O.; Lee, Yoon-Sik; Nam, Ki Tae; Kwon, Jang-Yeon

2017-08-01

Biocompatible biologically occurring polymer is suggested as a component of human implantable devices since conventional inorganic materials are apt to trigger inflammation and toxicity problem within human body. Peptides consisting of aromatic amino acid, tyrosine, are chosen, and enhancement on electrical conductivity is studied. Annealing process gives rise to the decrease on resistivity of the peptide films and the growth of the carrier concentration is a plausible reason for such a decrease on resistivity. The annealed peptides are further applied to an active layer of field effect transistor, in which low on/off current ratio (˜10) is obtained.

Capillary absorption spectrometer and process for isotopic analysis of small samples

DOEpatents

Alexander, M. Lizabeth; Kelly, James F.; Sams, Robert L.; Moran, James J.; Newburn, Matthew K.; Blake, Thomas A.

2016-03-29

A capillary absorption spectrometer and process are described that provide highly sensitive and accurate stable absorption measurements of analytes in a sample gas that may include isotopologues of carbon and oxygen obtained from gas and biological samples. It further provides isotopic images of microbial communities that allow tracking of nutrients at the single cell level. It further targets naturally occurring variations in carbon and oxygen isotopes that avoids need for expensive isotopically labeled mixtures which allows study of samples taken from the field without modification. The method also permits sampling in vivo permitting real-time ambient studies of microbial communities.

Hyporheic zone as a bioreactor: sediment heterogeneity influencing biogeochemical processes

NASA Astrophysics Data System (ADS)

Perujo, Nuria; Romani, Anna M.; Sanchez-Vila, Xavier

2017-04-01

Mediterranean fluvial systems are characterized by frequent periods of low flow or even drought. During low flow periods, water from wastewater treatment plants (WWTPs) is proportionally large in fluvial systems. River water might be vertically transported through the hyporheic zone, and then porous medium acts as a complementary treatment system since, as water infiltrates, a suite of biogeochemical processes occurs. Subsurface sediment heterogeneity plays an important role since it influences the interstitial fluxes of the medium and drives biomass growing, determining biogeochemical reactions. In this study, WWTP water was continuously infiltrated for 3 months through two porous medium tanks: one consisting of 40 cm of fine sediment (homogeneous); and another comprised of two layers of different grain size sediments (heterogeneous), 20 cm of coarse sediment in the upper part and 20 cm of fine one in the bottom. Several hydrological, physicochemical and biological parameters were measured periodically (weekly at the start of the experiment and biweekly at the end). Analysed parameters include dissolved nitrogen, phosphorus, organic carbon, and oxygen all measured at the surface, and at 5, 20 and 40 cm depth. Variations in hydraulic conductivity with time were evaluated. Sediment samples were also analysed at three depths (surface, 20 and 40 cm) to determine bacterial density, chlorophyll content, extracellular polymeric substances, and biofilm function (extracellular enzyme activities and carbon substrate utilization profiles). Preliminary results suggest hydraulic conductivity to be the main driver of the differences in the biogeochemical processes occurring in the subsurface. At the heterogeneous tank, a low nutrient reduction throughout the whole medium is measured. In this medium, high hydraulic conductivity allows for a large amount of infiltrating water, but with a small residence time. Since some biological processes are largely time-dependent, small water residence time results in low nutrient reduction. Moreover, high nitrification and low ammonium concentration in the interface of the two grain-size layers are measured, probably related to high dissolved oxygen concentration at the coarse-fine sediment interface, further promoting accumulation of bacteria and algae. In contrast, the homogeneous tank shows low dissolved oxygen values and high denitrification in depth which could be related to lower overall hydraulic conductivity, as compared to the heterogeneous tank. The preliminary analysis of our results indicates a key role of hydraulic conductivity on biogeochemical processes in the porous medium but, at the same time that it is strongly interacting with sediment grain-size distribution and the development of biofilm. The final scope of this study is to know the interactions between physicochemical and biological components in sediments in order to understand in detail the biogeochemical processes occurring.

Mind the gap: non-biological processes contributing to soil CO2 efflux.

PubMed

Rey, Ana

2015-05-01

Widespread recognition of the importance of soil CO2 efflux as a major source of CO2 to the atmosphere has led to active research. A large soil respiration database and recent reviews have compiled data, methods, and current challenges. This study highlights some deficiencies for a proper understanding of soil CO2 efflux focusing on processes of soil CO2 production and transport that have not received enough attention in the current soil respiration literature. It has mostly been assumed that soil CO2 efflux is the result of biological processes (i.e. soil respiration), but recent studies demonstrate that pedochemical and geological processes, such as geothermal and volcanic CO2 degassing, are potentially important in some areas. Besides the microbial decomposition of litter, solar radiation is responsible for photodegradation or photochemical degradation of litter. Diffusion is considered to be the main mechanism of CO2 transport in the soil, but changes in atmospheric pressure and thermal convection may also be important mechanisms driving soil CO2 efflux greater than diffusion under certain conditions. Lateral fluxes of carbon as dissolved organic and inorganic carbon occur and may cause an underestimation of soil CO2 efflux. Traditionally soil CO2 efflux has been measured with accumulation chambers assuming that the main transport mechanism is diffusion. New techniques are available such as improved automated chambers, CO2 concentration profiles and isotopic techniques that may help to elucidate the sources of carbon from soils. We need to develop specific and standardized methods for different CO2 sources to quantify this flux on a global scale. Biogeochemical models should include biological and non-biological CO2 production processes before we can predict the response of soil CO2 efflux to climate change. Improving our understanding of the processes involved in soil CO2 efflux should be a research priority given the importance of this flux in the global carbon budget. © 2014 John Wiley & Sons Ltd.

[Arterial media calcification in patients with type 2 diabetes mellitus].

PubMed

Belovici, Maria Isabela; Pandele, G I

2008-01-01

Arterial calcification was previously viewed as an inevitable, passive, and degenerative process that occurred at the end stages of atherosclerosis. Recent studies, however, have demonstrated that calcification of arteries is a complex and regulated process. It may occur in conjunction with atherosclerosis or in an isolated form that is commonly associated with diabetes and renal failure. Higher artery calcium scores are associated with increased cardiovascular events, and some aspects of arterial calcification are similar to the biology of forming bone. Arterial calcification can thus be viewed as a distinct inflammatory arteriopathy, much like atherosclerosis and aneurysms, with its own contribution to cardiovascular morbidity and mortality. Current research involves efforts to define the complex interactions between cellular and molecular mediators of arterial calcification and, in particular, the role of endogenous calcification inhibitors. This review discusses the clinical relevance, cellular events, and suspected molecular pathways that control arterial calcification.

Landscape associations of birds during migratory stopover

NASA Astrophysics Data System (ADS)

Diehl, Robert Howard

The challenge for migratory bird conservation is habitat preservation that sustains breeding, migration, and non-breeding biological processes. In choosing an appropriately scaled conservation arena for habitat preservation, a conservative and thorough examination of stopover habitat use patterns by migrants works back from the larger scales at which such relationships may occur. Because the use of stopover habitats by migrating birds occurs at spatial scales larger than traditional field techniques can easily accommodate, I quantify these relationship using the United States system of weather surveillance radars (popularly known as NEXRAD). To provide perspective on use of this system for biologists, I first describe the technical challenges as well as some of the biological potential of these radars for ornithological research. Using data from these radars, I then examined the influence of Lake Michigan and the distribution of woodland habitat on migrant concentrations in northeastern Illinois habitats during stopover. Lake Michigan exerted less influence on migrant abundance and density than the distribution and availability of habitat for stopover. There was evidence of post-migratory movement resulting in habitats within suburban landscapes experiencing higher migrant abundance but lower migrant density than habitats within nearby urban and agricultural landscapes. Finally, in the context of hierarchy theory, I examined the influence of landscape ecological and behavioral processes on bird density during migratory stopover. Migrant abundance did not vary across landscapes that differed considerably in the amount of habitat available for stopover. As a result, smaller, more isolated patches held higher densities of birds. Spatial models of migrant habitat selection based on migrant proximity to a patch explained nearly as much variance in the number of migrants occupying patches (R2 = 0.88) as selection models based on migrant interception of patches during flight (R2 = 0.90). Because migrant densities in specific patches were the consequence of biological processes operating at larger spatial scales, sound conservation strategies for migrating landbirds should consider the landscape context of stopover habitats that are potential targets for preservation.

4D Biofabrication of Branching Multicellular Structures: A Morphogenesis Simulation Based on Turing’s Reaction-Diffusion Dynamics

NASA Astrophysics Data System (ADS)

Zhu, Xiaolu; Yang, Hao

2017-12-01

The recently emerged four-dimensional (4D) biofabrication technique aims to create dynamic three-dimensional (3D) biological structures that can transform their shapes or functionalities with time when an external stimulus is imposed or when cell postprinting self-assembly occurs. The evolution of 3D pattern of branching geometry via self-assembly of cells is critical for 4D biofabrication of artificial organs or tissues with branched geometry. However, it is still unclear that how the formation and evolution of these branching pattern are biologically encoded. We study the 4D fabrication of lung branching structures utilizing a simulation model on the reaction-diffusion mechanism, which is established using partial differential equations of four variables, describing the reaction and diffusion process of morphogens with time during the development process of lung branching. The simulation results present the forming process of 3D branching pattern, and also interpret the behaviors of side branching and tip splitting as the stalk growing, through 3D visualization of numerical simulation.

Pathway of FeEDTA transformation and its impact on performance of NOx removal in a chemical absorption-biological reduction integrated process

PubMed Central

Li, Wei; Zhao, Jingkai; Zhang, Lei; Xia, Yinfeng; Liu, Nan; Li, Sujing; Zhang, Shihan

2016-01-01

A novel chemical absorption-biological reduction (CABR) integrated process, employing ferrous ethylenediaminetetraacetate (Fe(II)EDTA) as a solvent, is deemed as a potential option for NOx removal from the flue gas. Previous work showed that the Fe(II)EDTA concentration was critical for the NOx removal in the CABR process. In this work, the pathway of FeEDTA (Fe(III)/Fe(II)-EDTA) transformation was investigated to assess its impact on the NOx removal in a biofilter. Experimental results revealed that the FeEDTA transformation involved iron precipitation and EDTA degradation. X-ray photoelectron spectroscopy analysis confirmed the iron was precipitated in the form of Fe(OH)3. The iron mass balance analysis showed 44.2% of the added iron was precipitated. The EDTA degradation facilitated the iron precipitation. Besides chemical oxidation, EDTA biodegradation occurred in the biofilter. The addition of extra EDTA helped recover the iron from the precipitation. The transformation of FeEDTA did not retard the NO removal. In addition, EDTA rather than the iron concentration determined the NO removal efficiency. PMID:26743930

Active control of complex, multicomponent self-assembly processes

NASA Astrophysics Data System (ADS)

Schulman, Rebecca

The kinetics of many complex biological self-assembly processes such as cytoskeletal assembly are precisely controlled by cells. Spatiotemporal control over rates of filament nucleation, growth and disassembly determine how self-assembly occurs and how the assembled form changes over time. These reaction rates can be manipulated by changing the concentrations of the components needed for assembly by activating or deactivating them. I will describe how we can use these principles to design driven self-assembly processes in which we assemble and disassemble multiple types of components to create micron-scale networks of semiflexible filaments assembled from DNA. The same set of primitive components can be assembled into many different, structures depending on the concentrations of different components and how designed, DNA-based chemical reaction networks manipulate these concentrations over time. These chemical reaction networks can in turn interpret environmental stimuli to direct complex, multistage response. Such a system is a laboratory for understanding complex active material behaviors, such as metamorphosis, self-healing or adaptation to the environment that are ubiquitous in biological systems but difficult to quantitatively characterize or engineer.

Developmental mechanisms underlying variation in craniofacial disease and evolution.

PubMed

Fish, Jennifer L

2016-07-15

Craniofacial disease phenotypes exhibit significant variation in penetrance and severity. Although many genetic contributions to phenotypic variation have been identified, genotype-phenotype correlations remain imprecise. Recent work in evolutionary developmental biology has exposed intriguing developmental mechanisms that potentially explain incongruities in genotype-phenotype relationships. This review focuses on two observations from work in comparative and experimental animal model systems that highlight how development structures variation. First, multiple genetic inputs converge on relatively few developmental processes. Investigation of when and how variation in developmental processes occurs may therefore help predict potential genetic interactions and phenotypic outcomes. Second, genetic mutation is typically associated with an increase in phenotypic variance. Several models outlining developmental mechanisms underlying mutational increases in phenotypic variance are discussed using Satb2-mediated variation in jaw size as an example. These data highlight development as a critical mediator of genotype-phenotype correlations. Future research in evolutionary developmental biology focusing on tissue-level processes may help elucidate the "black box" between genotype and phenotype, potentially leading to novel treatment, earlier diagnoses, and better clinical consultations for individuals affected by craniofacial anomalies. Copyright © 2015 Elsevier Inc. All rights reserved.

A model for improving endangered species recovery programs

NASA Astrophysics Data System (ADS)

Miller, Brian; Reading, Richard; Conway, Courtney; Jackson, Jerome A.; Hutchins, Michael; Snyder, Noel; Forrest, Steve; Frazier, Jack; Derrickson, Scott

1994-09-01

This paper discusses common organizational problems that cause inadequate planning and implementation processes of endangered species recovery across biologically dissimilar species. If these problems occur, even proven biological conservation techniques are jeopardized. We propose a solution that requires accountability in all phases of the restoration process and is based on cooperative input among government agencies, nongovernmental conservation organizations, and the academic community. The first step is formation of a task-oriented recovery team that integrates the best expertise into the planning process. This interdisciplinary team should be composed of people whose skills directly address issues critical for recovery. Once goals and procedures are established, the responsible agency (for example, in the United States, the US Fish and Wildlife Service) could divest some or all of its obligation for implementing the plan, yet still maintain oversight by holding implementing entities contractually accountable. Regular, periodic outside review and public documentation of the recovery team, lead agency, and the accomplishments of implementing bodies would permit evaluation necessary to improve performance. Increased cooperation among agency and nongovernmental organizations provided by this model promises a more efficient use of limited resources toward the conservation of biodiversity.

Infections on the move: how transient phases of host movement influence disease spread

PubMed Central

Fenton, A.; Dell, A. I.

2017-01-01

Animal movement impacts the spread of human and wildlife diseases, and there is significant interest in understanding the role of migrations, biological invasions and other wildlife movements in spatial infection dynamics. However, the influence of processes acting on infections during transient phases of host movement is poorly understood. We propose a conceptual framework that explicitly considers infection dynamics during transient phases of host movement to better predict infection spread through spatial host networks. Accounting for host transient movement captures key processes that occur while hosts move between locations, which together determine the rate at which hosts spread infections through networks. We review theoretical and empirical studies of host movement and infection spread, highlighting the multiple factors that impact the infection status of hosts. We then outline characteristics of hosts, parasites and the environment that influence these dynamics. Recent technological advances provide disease ecologists unprecedented ability to track the fine-scale movement of organisms. These, in conjunction with experimental testing of the factors driving infection dynamics during host movement, can inform models of infection spread based on constituent biological processes. PMID:29263283

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

PubMed Central

Milacic, Marija; Haw, Robin; Rothfels, Karen; Wu, Guanming; Croft, David; Hermjakob, Henning; D’Eustachio, Peter; Stein, Lincoln

2012-01-01

Reactome describes biological pathways as chemical reactions that closely mirror the actual physical interactions that occur in the cell. Recent extensions of our data model accommodate the annotation of cancer and other disease processes. First, we have extended our class of protein modifications to accommodate annotation of changes in amino acid sequence and the formation of fusion proteins to describe the proteins involved in disease processes. Second, we have added a disease attribute to reaction, pathway, and physical entity classes that uses disease ontology terms. To support the graphical representation of “cancer” pathways, we have adapted our Pathway Browser to display disease variants and events in a way that allows comparison with the wild type pathway, and shows connections between perturbations in cancer and other biological pathways. The curation of pathways associated with cancer, coupled with our efforts to create other disease-specific pathways, will interoperate with our existing pathway and network analysis tools. Using the Epidermal Growth Factor Receptor (EGFR) signaling pathway as an example, we show how Reactome annotates and presents the altered biological behavior of EGFR variants due to their altered kinase and ligand-binding properties, and the mode of action and specificity of anti-cancer therapeutics. PMID:24213504

Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

PubMed Central

de Graaf, Albert A.; Freidig, Andreas P.; De Roos, Baukje; Jamshidi, Neema; Heinemann, Matthias; Rullmann, Johan A.C.; Hall, Kevin D.; Adiels, Martin; van Ommen, Ben

2009-01-01

The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the consideration and interpretation of experimental data at widely differing scales of space and time. In this review, we discuss a selection of available modeling approaches and applications relevant for nutrition. We then put these models into perspective by categorizing them according to their space and time domain. Through this categorization process, we identified a dearth of models that consider processes occurring between the microscopic and macroscopic scale. We propose a “middle-out” strategy to develop the required full-scale, multilevel computational models. Exhaustive and accurate phenotyping, the use of the virtual patient concept, and the development of biomarkers from “-omics” signatures are identified as key elements of a successful systems biology modeling approach in nutrition research—one that integrates physiological mechanisms and data at multiple space and time scales. PMID:19956660

Disentangling physical and biological drivers of phytoplankton dynamics in a coastal system.

PubMed

Cianelli, Daniela; D'Alelio, Domenico; Uttieri, Marco; Sarno, Diana; Zingone, Adriana; Zambianchi, Enrico; d'Alcalà, Maurizio Ribera

2017-11-20

This proof-of-concept study integrates the surface currents measured by high-frequency coastal radars with plankton time-series data collected at a fixed sampling point from the Mediterranean Sea (MareChiara Long Term Ecological Research site in the Gulf of Naples) to characterize the spatial origin of phytoplankton assemblages and to scrutinize the processes ruling their dynamics. The phytoplankton community generally originated from the coastal waters whereby species succession was mainly regulated by biological factors (life-cycle processes, species-specific physiological performances and inter-specific interactions). Physical factors, e.g. the alternation between coastal and offshore waters and the horizontal mixing, were also important drivers of phytoplankton dynamics promoting diversity maintenance by i) advecting species from offshore and ii) diluting the resident coastal community so as to dampen resource stripping by dominant species and thereby increase the numerical importance of rarer species. Our observations highlight the resilience of coastal communities, which may favour their persistence over time and the prevalence of successional events over small time and space scales. Although coastal systems may act differently from one another, our findings provide a conceptual framework to address physical-biological interactions occurring in coastal basins, which can be generalised to other areas.

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology.

PubMed

Price, S A; Schmitz, L

2016-04-05

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. © 2016 The Author(s).

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

Olsen, C.R.; Larsen, I.L.; Lowry, P.D.

Radionuclides released into the Susquehanna--Chesapeake System from the Three Mile Island, Peach Bottom, and Calvert Cliffs nuclear power plants are partitioned among dissolved, particulate, and biological phases and may thus exist in a number of physical and chemical forms. In this project, we have measured the dissolved and particulate distributions of fallout /sup 137/Cs; reactor-released /sup 137/Cs, /sup 134/Cs, /sup 65/Zn, /sup 60/Co, and /sup 58/Co; and naturally occurring /sup 7/Be and /sup 210/Pb in the lower Susquehanna River and Upper Chesapeake Bay. In addition, we chemically leached suspended particles and bottom sediments in the laboratory to determine radionuclide partitioningmore » among different particulate-sorbing phases to complement the site-specific field data. This information has been used to document the important geochemical processes that affect the transport, sorption, distribution, and fate of reactor-released radionuclides (and by analogy, other trace contaminants) in this river-estuarine system. Knowledge of the mechanisms, kinetic factors, and processes that affect radionuclide distributions is crucial for predicting their biological availability, toxicity, chemical behavior, physical transport, and accumulation in aquatic systems. The results from this project provide the information necessary for developing accurate radionuclide-transport and biological-uptake models. 76 refs., 12 figs.« less

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

PubMed Central

Schmitz, L.

2016-01-01

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. PMID:26977068

Real-Time Analysis of Magnetic Hyperthermia Experiments on Living Cells under a Confocal Microscope.

PubMed

Connord, Vincent; Clerc, Pascal; Hallali, Nicolas; El Hajj Diab, Darine; Fourmy, Daniel; Gigoux, Véronique; Carrey, Julian

2015-05-01

Combining high-frequency alternating magnetic fields (AMF) and magnetic nanoparticles (MNPs) is an efficient way to induce biological responses through several approaches: magnetic hyperthermia, drug release, controls of gene expression and neurons, or activation of chemical reactions. So far, these experiments cannot be analyzed in real-time during the AMF application. A miniaturized electromagnet fitting under a confocal microscope is built, which produces an AMF of frequency and amplitude similar to the ones used in magnetic hyperthermia. AMF application induces massive damages to tumoral cells having incorporated nanoparticles into their lysosomes without affecting the others. Using this setup, real-time analyses of molecular events occurring during AMF application are performed. Lysosome membrane permeabilization and reactive oxygen species production are detected after only 30 min of AMF application, demonstrating they occur at an early stage in the cascade of events leading eventually to cell death. Additionally, lysosomes self-assembling into needle-shaped organization under the influence of AMF is observed in real-time. This experimental approach will permit to get a deeper insight into the physical, molecular, and biological process occurring in several innovative techniques used in nanomedecine based on the combined use of MNPs and high-frequency magnetic fields. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A biologically inspired neural network for dynamic programming.

PubMed

Francelin Romero, R A; Kacpryzk, J; Gomide, F

2001-12-01

An artificial neural network with a two-layer feedback topology and generalized recurrent neurons, for solving nonlinear discrete dynamic optimization problems, is developed. A direct method to assign the weights of neural networks is presented. The method is based on Bellmann's Optimality Principle and on the interchange of information which occurs during the synaptic chemical processing among neurons. The neural network based algorithm is an advantageous approach for dynamic programming due to the inherent parallelism of the neural networks; further it reduces the severity of computational problems that can occur in methods like conventional methods. Some illustrative application examples are presented to show how this approach works out including the shortest path and fuzzy decision making problems.

The role of animal models in tendon research

PubMed Central

Hast, M. W.; Zuskov, A.; Soslowsky, L. J.

2014-01-01

Tendinopathy is a debilitating musculoskeletal condition which can cause significant pain and lead to complete rupture of the tendon, which often requires surgical repair. Due in part to the large spectrum of tendon pathologies, these disorders continue to be a clinical challenge. Animal models are often used in this field of research as they offer an attractive framework to examine the cascade of processes that occur throughout both tendon pathology and repair. This review discusses the structural, mechanical, and biological changes that occur throughout tendon pathology in animal models, as well as strategies for the improvement of tendon healing. Cite this article: Bone Joint Res 2014;3:193–202. PMID:24958818

Self-Organization Processes at the Intracellular Level

NASA Astrophysics Data System (ADS)

Ponce Dawson, Silvina

2003-03-01

In spite of their relatively small sizes, cells are incredibly complex objects in which various sorts of self-organizing processes occur. Cell division is an example of a process that nearly all cells undergo in which a concerted sequence of events takes place. What are the signals that tell the cell to move along this sequence? Clearly, this is a self-organized process. Microtubules (long polymers that are part of the cytoskeleton) and calcium signals play a major role during cell division. In this course we will focus on some features of microtubule dynamics and calcium signals that are amenable to modeling. In both of these biological systems, behaviors at a single molecule level are key determinants of the self-organized dynamics that is observed at larger scales. Thus, the modeling of these systems presents interesting challenges which require novel strategies. Their study may not only provide answers for biologically motivated questions, but is also a natural setting in which the transition between particle-like and mean-field models can be explored. In this course we will first give a brief biological introduction on the structure of eukaryotic cells, microtubule dynamics and intracellular calcium signals. We will then describe some of the models that have been presented in the literature and discuss the spatio-temporal dynamics that they predict, comparing them with observed behaviors in vitro or in vivo. We will end with a discussion on the virtues and limitations of the various modeling strategies described.

Inflammatory, metabolic, and genetic mechanisms of vascular calcification

PubMed Central

Demer, Linda L.; Tintut, Yin

2014-01-01

This review centers on updating the active research area of vascular calcification. This pathology underlies substantial cardiovascular morbidity and mortality, through adverse mechanical effects on vascular compliance, vasomotion, and, most likely, plaque stability. Biomineralization is a complex, regulated process occurring widely throughout nature. Decades ago, its presence in the vasculature was considered a mere curiosity and an unregulated, “dystrophic” process that does not involve biological mechanisms. While it remains controversial whether the process has any adaptive value or past evolutionary advantage, substantial advances have been made in understanding the biological mechanisms driving the process. Different types of calcific vasculopathy, such as inflammatory vs. metabolic, have parallel mechanisms in skeletal bone calcification, such as intramembranous and endochondral ossification. Recent work has identified important regulatory roles for inflammation, oxidized lipids, elastin, alkaline phosphatase, osteoprogenitor cells, matrix gamma-carboxyglutamic acid protein (MGP), transglutaminase, osteoclastic regulatory factors, phosphate regulatory hormones and receptors, apoptosis, prelamin A, autophagy, and microvesicles or microparticles similar to the matrix vesicles of skeletal bone. Recent work has uncovered fascinating interactions between MGP, vitamin K, warfarin and transport proteins. And, lastly, recent breakthroughs in inherited forms of calcific vasculopathy, have identified the genes responsible as well as an unexpected overlap of phenotypes. PMID:24665125

Proteomics Insights into Autophagy.

PubMed

Cudjoe, Emmanuel K; Saleh, Tareq; Hawkridge, Adam M; Gewirtz, David A

2017-10-01

Autophagy, a conserved cellular process by which cells recycle their contents either to maintain basal homeostasis or in response to external stimuli, has for the past two decades become one of the most studied physiological processes in cell biology. The 2016 Nobel Prize in Medicine and Biology awarded to Dr. Ohsumi Yoshinori, one of the first scientists to characterize this cellular mechanism, attests to its importance. The induction and consequent completion of the process of autophagy results in wide ranging changes to the cellular proteome as well as the secretome. MS-based proteomics affords the ability to measure, in an unbiased manner, the ubiquitous changes that occur when autophagy is initiated and progresses in the cell. The continuous improvements and advances in mass spectrometers, especially relating to ionization sources and detectors, coupled with advances in proteomics experimental design, has made it possible to study autophagy, among other process, in great detail. Innovative labeling strategies and protein separation techniques as well as complementary methods including immuno-capture/blotting/staining have been used in proteomics studies to provide more specific protein identification. In this review, we will discuss recent advances in proteomics studies focused on autophagy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coexpression network based on natural variation in human gene expression reveals gene interactions and functions

PubMed Central

Nayak, Renuka R.; Kearns, Michael; Spielman, Richard S.; Cheung, Vivian G.

2009-01-01

Genes interact in networks to orchestrate cellular processes. Analysis of these networks provides insights into gene interactions and functions. Here, we took advantage of normal variation in human gene expression to infer gene networks, which we constructed using correlations in expression levels of more than 8.5 million gene pairs in immortalized B cells from three independent samples. The resulting networks allowed us to identify biological processes and gene functions. Among the biological pathways, we found processes such as translation and glycolysis that co-occur in the same subnetworks. We predicted the functions of poorly characterized genes, including CHCHD2 and TMEM111, and provided experimental evidence that TMEM111 is part of the endoplasmic reticulum-associated secretory pathway. We also found that IFIH1, a susceptibility gene of type 1 diabetes, interacts with YES1, which plays a role in glucose transport. Furthermore, genes that predispose to the same diseases are clustered nonrandomly in the coexpression network, suggesting that networks can provide candidate genes that influence disease susceptibility. Therefore, our analysis of gene coexpression networks offers information on the role of human genes in normal and disease processes. PMID:19797678

Mathematical modeling of cell adhesion in shear flow: application to targeted drug delivery in inflammation and cancer metastasis.

PubMed

Jadhav, Sameer; Eggleton, Charles D; Konstantopoulos, Konstantinos

2007-01-01

Cell adhesion plays a pivotal role in diverse biological processes that occur in the dynamic setting of the vasculature, including inflammation and cancer metastasis. Although complex, the naturally occurring processes that have evolved to allow for cell adhesion in the vasculature can be exploited to direct drug carriers to targeted cells and tissues. Fluid (blood) flow influences cell adhesion at the mesoscale by affecting the mechanical response of cell membrane, the intercellular contact area and collisional frequency, and at the nanoscale level by modulating the kinetics and mechanics of receptor-ligand interactions. Consequently, elucidating the molecular and biophysical nature of cell adhesion requires a multidisciplinary approach involving the synthesis of fundamentals from hydrodynamic flow, molecular kinetics and cell mechanics with biochemistry/molecular cell biology. To date, significant advances have been made in the identification and characterization of the critical cell adhesion molecules involved in inflammatory disorders, and, to a lesser degree, in cancer metastasis. Experimental work at the nanoscale level to determine the lifetime, interaction distance and strain responses of adhesion receptor-ligand bonds has been spurred by the advent of atomic force microscopy and biomolecular force probes, although our current knowledge in this area is far from complete. Micropipette aspiration assays along with theoretical frameworks have provided vital information on cell mechanics. Progress in each of the aforementioned research areas is key to the development of mathematical models of cell adhesion that incorporate the appropriate biological, kinetic and mechanical parameters that would lead to reliable qualitative and quantitative predictions. These multiscale mathematical models can be employed to predict optimal drug carrier-cell binding through isolated parameter studies and engineering optimization schemes, which will be essential for developing effective drug carriers for delivery of therapeutic agents to afflicted sites of the host.

Peatlands as a unique climatic hotspots

NASA Astrophysics Data System (ADS)

Slowinska, S.; Marcisz, K.; Slowinski, M. M.; Blazejczyk, K.; Lamentowicz, M.

2017-12-01

Peatlands are unique environments, often acting as microrefugia of various taxa. High groundwater table, organic soils, specific vegetation and topography are important determinants of their local climatic conditions. However, relations between those determinants are not stable. For example, seasonal changes in weather patterns, hydrological dynamics, and local vegetation may alter microclimate. Additionally, long-term changes are important factor, as for example overgrowing due to significant change of microclimate conditions, what in turn changes geochemical and biological processes in the peat layer. We have been investigating interactions between abiotic and biotic factors of a small Sphagnum mire (ca. 6.0 ha) for over ten years now. The mire is located in Poland in transitional temperate climate and is the only place in polish lowlands where glacial relict Betula nana occurs. Identification of local climate of the mire, its microclimatic differentiation and its influence on surroundings were objectives of the study. We recorded water level fluctuations, photosynthetically active radiation (PAR), air temperature and humidity, and peat temperature at five monitoring plots at the mire and observed significant differences between them. We also investigated Sphagnum mosses growth and testate amoeba diversity and community structure to understand biological response of those differences. We observed that local climate of the mire was significantly different from open area reference place, it was much colder especially during nights. The average minimal temperature at the height 30 cm for growing seasons 2010-2012 was 3.7oC lower there and ground frosts occurred even in the summer. The climate of the mire affected the forest directly adjacent to it, and depending on weather conditions the strength and the distance of this interaction was different. Our results show that micro-environmental changes affects on biological processes and should be taken into consideration in palaeoecological investigations.

Physical-biological coupling induced aggregation mechanism for the formation of high biomass red tides in low nutrient waters.

PubMed

Lai, Zhigang; Yin, Kedong

2014-01-01

Port Shelter is a semi-enclosed bay in northeast Hong Kong where high biomass red tides are observed to occur frequently in narrow bands along the local bathymetric isobars. Previous study showed that nutrients in the Bay are not high enough to support high biomass red tides. The hypothesis is that physical aggregation and vertical migration of dinoflagellates appear to be the driving mechanism to promote the formation of red tides in this area. To test this hypothesis, we used a high-resolution estuarine circulation model to simulate the near-shore water dynamics based on in situ measured temperature/salinity profiles, winds and tidal constitutes taken from a well-validated regional tidal model. The model results demonstrated that water convergence occurs in a narrow band along the west shore of Port Shelter under a combined effect of stratified tidal current and easterly or northeasterly wind. Using particles as dinoflagellate cells and giving diel vertical migration, the model results showed that the particles aggregate along the convergent zone. By tracking particles in the model predicted current field, we estimated that the physical-biological coupled processes induced aggregation of the particles could cause 20-45 times enhanced cell density in the convergent zone. This indicated that a high cell density red tide under these processes could be initialized without very high nutrients concentrations. This may explain why Port Shelter, a nutrient-poor Bay, is the hot spot for high biomass red tides in Hong Kong in the past 25 years. Our study explains why red tide occurrences are episodic events and shows the importance of taking the physical-biological aggregation mechanism into consideration in the projection of red tides for coastal management. Copyright © 2013 Elsevier B.V. All rights reserved.

Theory of long-range diffusion of proteins on a spherical biological membrane: application to protein cluster formation and actin-comet tail growth.

PubMed

Amatore, Christian; Oleinick, Alexander I; Klymenko, Oleksiy V; Svir, Irina

2009-07-13

Breaking of symmetry is often required in biology in order to produce a specific function. In this work we address the problem of protein diffusion over a spherical vesicle surface towards one pole of the vesicle in order to produce ultimately an active protein cluster performing a specific biological function. Such a process is, for example, prerequisite for the assembling of proteins which then cooperatively catalyze the polymerization of actin monomers to sustain the growth of actin tails as occurs in natural vesicles such as those contained in Xenopus eggs. By this process such vesicles may propel themselves within the cell by the principle of action-reaction. In this work the physicochemical treatment of diffusion of large biomolecules within a cellular membrane is extended to encompass the case when proteins may be transiently poised by corral-like structures partitioning the membrane as has been recently documented in the literature. In such case the exchange of proteins between adjacent corrals occurs by energy-gated transitions instead of classical Brownian motion, yet the present analysis shows that long-range movements of the biomolecules may still be described by a classical diffusion law though the diffusion coefficient has then a different physical meaning. Such a model explains why otherwise classical diffusion of proteins may give rise to too small diffusion coefficients compared to predictions based on the protein dimension. This model is implemented to examine the rate of proteins clustering at one pole of a spherical vesicle and its outcome is discussed in relevance to the mechanism of actin comet tails growth.

Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control.

PubMed

Kent, Lisa M; Loo, Trevor S; Melton, Laurence D; Mercadante, Davide; Williams, Martin A K; Jameson, Geoffrey B

2016-01-15

Many pectin methylesterases (PMEs) are expressed in plants to modify plant cell-wall pectins for various physiological roles. These pectins are also attacked by PMEs from phytopathogens and phytophagous insects. The de-methylesterification by PMEs of the O6-methyl ester groups of the homogalacturonan component of pectin, exposing galacturonic acids, can occur processively or non-processively, respectively, describing sequential versus single de-methylesterification events occurring before enzyme-substrate dissociation. The high resolution x-ray structures of a PME from Aspergillus niger in deglycosylated and Asn-linked N-acetylglucosamine-stub forms reveal a 10⅔-turn parallel β-helix (similar to but with less extensive loops than bacterial, plant, and insect PMEs). Capillary electrophoresis shows that this PME is non-processive, halophilic, and acidophilic. Molecular dynamics simulations and electrostatic potential calculations reveal very different behavior and properties compared with processive PMEs. Specifically, uncorrelated rotations are observed about the glycosidic bonds of a partially de-methyl-esterified decasaccharide model substrate, in sharp contrast to the correlated rotations of processive PMEs, and the substrate-binding groove is negatively not positively charged. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Global report on preterm birth and stillbirth (2 of 7): discovery science

PubMed Central

2010-01-01

Background Normal and abnormal processes of pregnancy and childbirth are poorly understood. This second article in a global report explains what is known about the etiologies of preterm births and stillbirths and identifies critical gaps in knowledge. Two important concepts emerge: the continuum of pregnancy, beginning at implantation and ending with uterine involution following birth; and the multifactorial etiologies of preterm birth and stillbirth. Improved tools and data will enable discovery scientists to identify causal pathways and cost-effective interventions. Pregnancy and parturition continuum The biological process of pregnancy and childbirth begins with implantation and, after birth, ends with the return of the uterus to its previous state. The majority of pregnancy is characterized by rapid uterine and fetal growth without contractions. Yet most research has addressed only uterine stimulation (labor) that accounts for <0.5% of pregnancy. Etiologies The etiologies of preterm birth and stillbirth differ by gestational age, genetics, and environmental factors. Approximately 30% of all preterm births are indicated for either maternal or fetal complications, such as maternal illness or fetal growth restriction. Commonly recognized pathways leading to preterm birth occur most often during the gestational ages indicated: (1) inflammation caused by infection (22-32 weeks); (2) decidual hemorrhage caused by uteroplacental thrombosis (early or late preterm birth); (3) stress (32-36 weeks); and (4) uterine overdistention, often caused by multiple fetuses (32-36 weeks). Other contributors include cervical insufficiency, smoking, and systemic infections. Many stillbirths have similar causes and mechanisms. About two-thirds of late fetal deaths occur during the antepartum period; the other third occur during childbirth. Intrapartum asphyxia is a leading cause of stillbirths in low- and middle-income countries. Recommendations Utilizing new systems biology tools, opportunities now exist for researchers to investigate various pathways important to normal and abnormal pregnancies. Improved access to quality data and biological specimens are critical to advancing discovery science. Phenotypes, standardized definitions, and uniform criteria for assessing preterm birth and stillbirth outcomes are other immediate research needs. Conclusion Preterm birth and stillbirth have multifactorial etiologies. More resources must be directed toward accelerating our understanding of these complex processes, and identifying upstream and cost-effective solutions that will improve these pregnancy outcomes. PMID:20233383

Effects of predation efficiencies on the dynamics of a tritrophic food chain.

PubMed

Cassinari, Maria Paola; Groppi, Maria; Tebaldi, Claudio

2007-07-01

In this paper the dynamics of a tritrophic food chain (resource, consumer, top predator) is investigated, with particular attention not only to equilibrium states but also to cyclic behaviours that the system may exhibit. The analysis is performed in terms of two bifurcation parameters, denoted by p and q, which measure the efficiencies of the interaction processes. The persistence of the system is discussed, characterizing in the (p; q) plane the regions of existence and stability of biologically significant steady states and those of existence of limit cycles. The bifurcations occurring are discussed, and their implications with reference to biological control problems are considered. Examples of the rich dynamics exhibited by the model, including a chaotic regime, are described.

Fibrosis and diseases of the eye

PubMed Central

Friedlander, Martin

2007-01-01

Most diseases that cause catastrophic loss of vision do so as a result of abnormal angiogenesis and wound healing, often in response to tissue ischemia or inflammation. Disruption of the highly ordered tissue architecture in the eye caused by vascular leakage, hemorrhage, and concomitant fibrosis can lead to mechanical disruption of the visual axis and/or biological malfunctioning. An increased understanding of inflammation, wound healing, and angiogenesis has led to the development of drugs effective in modulating these biological processes and, in certain circumstances, the preservation of vision. Unfortunately, such pharmacological interventions often are too little, too late, and progression of vision loss frequently occurs. The recent development of progenitor and/or stem cell technologies holds promise for the treatment of currently incurable ocular diseases. PMID:17332885

Quantitative imaging biomarker ontology (QIBO) for knowledge representation of biomedical imaging biomarkers.

PubMed

Buckler, Andrew J; Liu, Tiffany Ting; Savig, Erica; Suzek, Baris E; Ouellette, M; Danagoulian, J; Wernsing, G; Rubin, Daniel L; Paik, David

2013-08-01

A widening array of novel imaging biomarkers is being developed using ever more powerful clinical and preclinical imaging modalities. These biomarkers have demonstrated effectiveness in quantifying biological processes as they occur in vivo and in the early prediction of therapeutic outcomes. However, quantitative imaging biomarker data and knowledge are not standardized, representing a critical barrier to accumulating medical knowledge based on quantitative imaging data. We use an ontology to represent, integrate, and harmonize heterogeneous knowledge across the domain of imaging biomarkers. This advances the goal of developing applications to (1) improve precision and recall of storage and retrieval of quantitative imaging-related data using standardized terminology; (2) streamline the discovery and development of novel imaging biomarkers by normalizing knowledge across heterogeneous resources; (3) effectively annotate imaging experiments thus aiding comprehension, re-use, and reproducibility; and (4) provide validation frameworks through rigorous specification as a basis for testable hypotheses and compliance tests. We have developed the Quantitative Imaging Biomarker Ontology (QIBO), which currently consists of 488 terms spanning the following upper classes: experimental subject, biological intervention, imaging agent, imaging instrument, image post-processing algorithm, biological target, indicated biology, and biomarker application. We have demonstrated that QIBO can be used to annotate imaging experiments with standardized terms in the ontology and to generate hypotheses for novel imaging biomarker-disease associations. Our results established the utility of QIBO in enabling integrated analysis of quantitative imaging data.

Evolution viewed from physics, physiology and medicine.

PubMed

Noble, Denis

2017-10-06

Stochasticity is harnessed by organisms to generate functionality. Randomness does not, therefore, necessarily imply lack of function or 'blind chance' at higher levels. In this respect, biology must resemble physics in generating order from disorder. This fact is contrary to Schrödinger's idea of biology generating phenotypic order from molecular- level order, which inspired the central dogma of molecular biology. The order originates at higher levels, which constrain the components at lower levels. We now know that this includes the genome, which is controlled by patterns of transcription factors and various epigenetic and reorganization mechanisms. These processes can occur in response to environmental stress, so that the genome becomes 'a highly sensitive organ of the cell' (McClintock). Organisms have evolved to be able to cope with many variations at the molecular level. Organisms also make use of physical processes in evolution and development when it is possible to arrive at functional development without the necessity to store all information in DNA sequences. This view of development and evolution differs radically from that of neo-Darwinism with its emphasis on blind chance as the origin of variation. Blind chance is necessary, but the origin of functional variation is not at the molecular level. These observations derive from and reinforce the principle of biological relativity, which holds that there is no privileged level of causation. They also have important implications for medical science.

The Key Events Dose-Response Framework: a cross-disciplinary mode-of-action based approach to examining dose-response and thresholds.

PubMed

Julien, Elizabeth; Boobis, Alan R; Olin, Stephen S

2009-09-01

The ILSI Research Foundation convened a cross-disciplinary working group to examine current approaches for assessing dose-response and identifying safe levels of intake or exposure for four categories of bioactive agents-food allergens, nutrients, pathogenic microorganisms, and environmental chemicals. This effort generated a common analytical framework-the Key Events Dose-Response Framework (KEDRF)-for systematically examining key events that occur between the initial dose of a bioactive agent and the effect of concern. Individual key events are considered with regard to factors that influence the dose-response relationship and factors that underlie variability in that relationship. This approach illuminates the connection between the processes occurring at the level of fundamental biology and the outcomes observed at the individual and population levels. Thus, it promotes an evidence-based approach for using mechanistic data to reduce reliance on default assumptions, to quantify variability, and to better characterize biological thresholds. This paper provides an overview of the KEDRF and introduces a series of four companion papers that illustrate initial application of the approach to a range of bioactive agents.

Biological effects of weightlessness and clinostatic conditions registered in cells of root meristem and cap of higher plants

NASA Astrophysics Data System (ADS)

Sytnik, K. M.; Kordyum, E. L.; Belyavskaya, N. A.; Nedukha, E. M.; Tarasenko, V. A.

Research in cellular reproduction, differentiation and vital activity, i.e. processes underlying the development and functioning of organisms, plants included, is essential for solving fundamental and applied problems of space biology. Detailed anatomical analysis of roots of higher plants grown on board the Salyut 6 orbital research station show that under conditions of weightlessness for defined duration mitosis, cytokinesis and tissue differentiation in plant vegetative organs occur essentially normally. At the same time, certain rearrangements in the structural organization of cellular organelles - mainly the plastid apparatus, mitochondria, Golgi apparatus and nucleus - are established in the root meristem and cap of the experimental plants. This is evidence for considerable changes in cellular metabolism. The structural changes in the subcellular level arising under spaceflight conditions are partially absent in clinostat experiments designed to simulate weightlessness. Various clinostatic conditions have different influences on the cell structural and functional organization than does space flight. It is suggested that alterations of cellular metabolism under weightlessness and clinostatic conditions occur within existing genetic programs.

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

Holt, Allison M; Standaert, Robert F; Jubb, Aaron M

Biological membranes, formed primarily by the self-assembly of complex mixtures of phospholipids, provide a structured scaffold for compartmentalization and structural processes in living cells. The specific physical properties of phospholipid species present in a given membrane play a key role in mediating these processes. Phosphatidylethanolamine (PE), a zwitterionic lipid present in bacterial, yeast, and mammalian cell membranes, is exceptional. In addition to undergoing the standard lipid polymorphic transition between the gel and liquid-crystalline phase, it can also assume an unusual polymorphic state, the inverse hexagonal phase (HII). Divalent cations are among the factors that drive the formation of the HIImore » phase, wherein the lipid molecules form stacked tubular structures by burying the hydrophilic head groups and exposing the hydrophobic tails to the bulk solvent. Most biological membranes contain a lipid species capable of forming the HII state suggesting that such lipid polymorphic structural states play an important role in structural biological processes such as membrane fusion. In this study, the interactions between Mg2+ and biomimetic bacterial cell membranes composed of PE and phosphatidylglycerol (PG) were probed using differential scanning calorimetry (DSC), small-angle x-ray scattering (SAXS), and fluorescence spectroscopy. The lipid phase transitions were examined at varying ratios of PE to PG and upon exposure to physiologically relevant concentrations of Mg2+. An understanding of these basic interactions enhances our understanding of membrane dynamics and how membrane-mediated structural changes may occur in vivo.« less

A single-stage biological process for municipal sewage treatment in tourist areas.

PubMed

Di Iaconi, C; De Sanctis, M; Lopez, A

2014-11-01

This pilot scale study aims to test the effectiveness of an innovative compact biological system (SBBGR - Sequencing Batch Biofilter Granular Reactor) for treating municipal wastewater in tourist areas characterised by intense seasonal water demand and wastewater discharge. The results obtained after a long term operation of 463 days have shown that the proposed system is able to assure average removal efficiencies higher than 90% for COD (chemical oxygen demand), total suspended solids and TKN (total Kjeldahl nitrogen) independently of the influent concentration values and organic loading, which ranged from 0.2 to 5.1 kgCOD/m(3)biofilter.d Furthermore, the plant showed a high degree of operation flexibility and stability in response to the organic load variations occurring in tourist areas. In fact, no significant deterioration in the plant's effluent quality was observed even during a sudden several-fold increase in organic loading. High nitrogen removal efficiencies (80%, on average) were also achieved thanks to the establishment of simultaneous nitrification-denitrification process favoured by the plant's high biomass concentration and operating conditions. Finally, the system was characterized by an excess sludge production much lower (60-80% lower) than that of conventional biological systems operating without a primary clarifier. An acceptable level of stabilization of excess sludge was also obtained so that a further stabilization process was no longer required. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Food safety of GMOs].

PubMed

Joudrier, P

2009-01-01

In this presentation, we review the complexity of the different biological events which occur during life cell cycles. Indeed transgenesis is not an unknown event for cells. In the second part of this article, the complex and complete evaluation process destined to assure the food safety of GMOs, before they are released on the market, is describd. Some ansers to questions frequently asked about the GMOs are given. It is concludedthat GMOs are probably more safe than their conventional non-GM counterpart.

[Prospects for Application of Gases and Gas Hydrates to Cryopreservation].

PubMed

Shishova, N V; Fesenko, E E

2015-01-01

In the present review, we tried to evaluate the known properties of gas hydrates and gases participating in the formation of gas hydrates from the point of view of the mechanisms of cryoinjury and cryoprotection, to consider the papers on freezing biological materials in the presence of inert gases, and to analyze the perspectives for the development of this direction. For the purpose, we searched for the information on the physical properties of gases and gas hydrates, compared processes occured during the formation of gas hydrates and water ice, analyzed the influence of the formation and growth of gas hydrates on the structure of biological objects. We prepared a short review on the biological effects of xenon, krypton, argon, carbon dioxide, hydrogen sulfide, and carbon monoxide especially on hypothermal conditions and probable application of these properties in cryopreservation technologies. The description of the existing experiments on cryopreservation of biological objects with the use of gases was analyzed. On the basis of the information we found, the most perspective directions of work in the field of cryopreservation of biological objects with the use of gases were outlined. An attempt was made to forecast the potential problems in this field.

The use of selective adsorbents in capillary electrophoresis-mass spectrometry for analyte preconcentration and microreactions: a powerful three-dimensional tool for multiple chemical and biological applications.

PubMed

Guzman, N A; Stubbs, R J

2001-10-01

Much attention has recently been directed to the development and application of online sample preconcentration and microreactions in capillary electrophoresis using selective adsorbents based on chemical or biological specificity. The basic principle involves two interacting chemical or biological systems with high selectivity and affinity for each other. These molecular interactions in nature usually involve noncovalent and reversible chemical processes. Properly bound to a solid support, an "affinity ligand" can selectively adsorb a "target analyte" found in a simple or complex mixture at a wide range of concentrations. As a result, the isolated analyte is enriched and highly purified. When this affinity technique, allowing noncovalent chemical interactions and biochemical reactions to occur, is coupled on-line to high-resolution capillary electrophoresis and mass spectrometry, a powerful tool of chemical and biological information is created. This paper describes the concept of biological recognition and affinity interaction on-line with high-resolution separation, the fabrication of an "analyte concentrator-microreactor", optimization conditions of adsorption and desorption, the coupling to mass spectrometry, and various applications of clinical and pharmaceutical interest.

Challenges in the Development of Functional Assays of Membrane Proteins

PubMed Central

Tiefenauer, Louis; Demarche, Sophie

2012-01-01

Lipid bilayers are natural barriers of biological cells and cellular compartments. Membrane proteins integrated in biological membranes enable vital cell functions such as signal transduction and the transport of ions or small molecules. In order to determine the activity of a protein of interest at defined conditions, the membrane protein has to be integrated into artificial lipid bilayers immobilized on a surface. For the fabrication of such biosensors expertise is required in material science, surface and analytical chemistry, molecular biology and biotechnology. Specifically, techniques are needed for structuring surfaces in the micro- and nanometer scale, chemical modification and analysis, lipid bilayer formation, protein expression, purification and solubilization, and most importantly, protein integration into engineered lipid bilayers. Electrochemical and optical methods are suitable to detect membrane activity-related signals. The importance of structural knowledge to understand membrane protein function is obvious. Presently only a few structures of membrane proteins are solved at atomic resolution. Functional assays together with known structures of individual membrane proteins will contribute to a better understanding of vital biological processes occurring at biological membranes. Such assays will be utilized in the discovery of drugs, since membrane proteins are major drug targets.

Post-traumatic stress disorder.

PubMed

Yehuda, Rachel; Hoge, Charles W; McFarlane, Alexander C; Vermetten, Eric; Lanius, Ruth A; Nievergelt, Caroline M; Hobfoll, Stevan E; Koenen, Karestan C; Neylan, Thomas C; Hyman, Steven E

2015-10-08

Post-traumatic stress disorder (PTSD) occurs in 5-10% of the population and is twice as common in women as in men. Although trauma exposure is the precipitating event for PTSD to develop, biological and psychosocial risk factors are increasingly viewed as predictors of symptom onset, severity and chronicity. PTSD affects multiple biological systems, such as brain circuitry and neurochemistry, and cellular, immune, endocrine and metabolic function. Treatment approaches involve a combination of medications and psychotherapy, with psychotherapy overall showing greatest efficacy. Studies of PTSD pathophysiology initially focused on the psychophysiology and neurobiology of stress responses, and the acquisition and the extinction of fear memories. However, increasing emphasis is being placed on identifying factors that explain individual differences in responses to trauma and promotion of resilience, such as genetic and social factors, brain developmental processes, cumulative biological and psychological effects of early childhood and other stressful lifetime events. The field of PTSD is currently challenged by fluctuations in diagnostic criteria, which have implications for epidemiological, biological, genetic and treatment studies. However, the advent of new biological methodologies offers the possibility of large-scale approaches to heterogeneous and genetically complex brain disorders, and provides optimism that individualized approaches to diagnosis and treatment will be discovered.

Seasonal controls of the short term variability of pCO2 at the Scotian Shelf

NASA Astrophysics Data System (ADS)

Thomas, H.; Craig, S.; Greenan, B. J. W.; Burt, W.; Herndl, G. J.; Higginson, S.; Salt, L.; Shadwick, E. H.; Urrego-Blanco, J.

2012-04-01

Much of the surface ocean carbon cycle variability can be attributed to the availability of sunlight, through processes such as heat fluxes or photosynthesis, which regulate the ocean carbon cycle over a wide range of time scales. The critical processes occurring on timescales of a day or less, however, have undergone few investigations, and most of those have been limited to a time span of several days to months, or exceptionally, for longer periods. Optical methods have helped to infer short-term biological variability, however lacking corresponding investigations of oceanic CO2 system. Here, we employ high-frequency CO2 system and optical observations covering the full seasonal cycle on the Scotian Shelf, Northwestern Atlantic Ocean, in order to unravel daily periodicity of the surface ocean carbon cycle and its effects on annual budgets. We show that significant daily periodicity occurs only if the water column is sufficiently stable as observed during seasonal warming. During that time biological CO2 drawdown, or net community production (NCP), is delayed for several hours relative to the daylight cycle due the daily build-up of essential Chlorophyll a, to cell physiology and to grazing effects, all restricting or hindering photosynthesis in the early morning hours. NCP collapses in summer by more than 90%, when the mixed layer depth reaches the seasonal minimum, which eventually makes the observed daily periodicity of the CO2 system vanish.

Ontology of physics for biology: representing physical dependencies as a basis for biological processes

PubMed Central

2013-01-01

Background In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based biosimulation models. We introduced OPB:Physical entity and OPB:Physical property classes that extend available spatiotemporal representations of physical entities and processes to explicitly represent the thermodynamics and dynamics of physiological processes. Our utilitarian, long-term aim is to develop computational tools for creating and querying formalized physiological knowledge for use by multiscale “physiome” projects such as the EU’s Virtual Physiological Human (VPH) and NIH’s Virtual Physiological Rat (VPR). Results Here we describe the OPB:Physical dependency taxonomy of classes that represent of the laws of classical physics that are the “rules” by which physical properties of physical entities change during occurrences of physical processes. For example, the fluid analog of Ohm’s law (as for electric currents) is used to describe how a blood flow rate depends on a blood pressure gradient. Hooke’s law (as in elastic deformations of springs) is used to describe how an increase in vascular volume increases blood pressure. We classify such dependencies according to the flow, transformation, and storage of thermodynamic energy that occurs during processes governed by the dependencies. Conclusions We have developed the OPB and annotation methods to represent the meaning—the biophysical semantics—of the mathematical statements of physiological analysis and the biophysical content of models and datasets. Here we describe and discuss our approach to an ontological representation of physical laws (as dependencies) and properties as encoded for the mathematical analysis of biophysical processes. PMID:24295137

[Therapy for childhood uveitis: biologics: too often--too late?].

PubMed

Mackensen, F; Lutz, T

2011-03-01

Pediatric uveitis differs from uveitis seen in adulthood not only because of the uveitis presentation and severity of disease but also by a worse prognosis and age-specific problems that may occur under therapy. Biologics are selective acting proteins that are manufactured by biotechnology. The greatest amount of knowledge to date exists for the TNF alpha blocking agents. Experimental and clinical studies showed that TNF alpha plays a significant role in the process of intraocular inflammation, so it was a logical step to use TNF blocking agents in uveitis therapy. Randomized controlled studies are rare, but pooled data (as presented here) of case series published show good evidence for the efficacy especially of infliximab and adalimumab. It is to be hoped that blindness and severe sight disabilities can be further reduced by this treatment in the future. From pediatric rheumatology we have learned about even newer biologics. With this review we want to show the weaknesses and strengths of therapy with biologics and want to help in choosing this treatment at the indicated time point in the disease.

Recent developments on ultrasound-assisted one-pot multicomponent synthesis of biologically relevant heterocycles.

PubMed

Banerjee, Bubun

2017-03-01

Heterocycles are the backbone of organic compounds. Specially, N- &O-containing heterocycles represent privileged structural subunits well distributed in naturally occurring compounds with immense biological activities. Multicomponent reactions (MCRs) are becoming valuable tool for synthesizing structurally diverse molecular entities. On the other hand, the last decade has seen a tremendous outburst in modifying chemical processes to make them sustainable for the betterment of our environment. The application of ultrasound in organic synthesis is fulfilling some of the goals of 'green and sustainable chemistry' as it has some advantages over the traditional thermal methods in terms of reaction rates, yields, purity of the products, product selectivity, etc. Therefore the synthesis of biologically relevant heterocycles using one-pot multi-component technique coupled with the application of ultrasound is one of the thrusting areas in the 21st Century among the organic chemists. The present review deals with the "up to date" developments on ultrasound assisted one-pot multi-component synthesis of biologically relevant heterocycles reported so far. Copyright © 2016 Elsevier B.V. All rights reserved.

Biological Potential in Serpentinizing Systems

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.

2016-01-01

Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

In Situ Biodosimetric Experiment for Space Applications

NASA Astrophysics Data System (ADS)

Goldschmidt, Gergely; Kovaliczky, Éva; Szabó, József; Rontó, Györgyi; Bérces, Attila

2012-06-01

This paper presents the principles and application of DNA based biological UV dosimeters, as developed by Research Group for Biophysics (RGB). These dosimeters are used for assessing the biological hazard of living systems on the Earth's surface and in different waters (rivers, lakes, seas, etc.). The UV dosimetry system has also been used in the space. In dosimeters a bacterial virus, bacteriophage T7 and polycrystalline uracil thin layers have been used as biological detectors. On the Earth's surface the UV radiation induces dimer formation in phage T7 and in the uracil detector, which was evaluated by loss of viability of the phage particles and by the decrease of the characteristic optical density (OD) of uracil thin layers. Recently the development of human space activities has also increased the need to measure the biological effect of extraterrestrial solar radiation, too. The evaluation of the space samples occurred on ground, thus only the starting and the final state were taken into account. A new improved, automated method is presented below which makes data collection more efficient and also makes the dynamics of the process observable.

Cell autonomous expression of inflammatory genes in biologically aged fibroblasts associated with elevated NF-kappaB activity.

PubMed

Kriete, Andres; Mayo, Kelli L; Yalamanchili, Nirupama; Beggs, William; Bender, Patrick; Kari, Csaba; Rodeck, Ulrich

2008-07-16

Chronic inflammation is a well-known corollary of the aging process and is believed to significantly contribute to morbidity and mortality of many age-associated chronic diseases. However, the mechanisms that cause age-associated inflammatory changes are not well understood. Particularly, the contribution of cell stress responses to age-associated inflammation in 'non-inflammatory' cells remains poorly defined. The present cross-sectional study focused on differences in molecular signatures indicative of inflammatory states associated with biological aging of human fibroblasts from donors aged 22 to 92 years. Gene expression profiling revealed elevated steady-state transcript levels consistent with a chronic inflammatory state in fibroblast cell-strains obtained from older donors. We also observed enhanced NF-kappaB DNA binding activity in a subset of strains, and the NF-kappaB profile correlated with mRNA expression levels characteristic of inflammatory processes, which include transcripts coding for cytokines, chemokines, components of the complement cascade and MHC molecules. This intrinsic low-grade inflammatory state, as it relates to aging, occurs in cultured cells irrespective of the presence of other cell types or the in vivo context. Our results are consistent with the view that constitutive activation of inflammatory pathways is a phenomenon prevalent in aged fibroblasts. It is possibly part of a cellular survival process in response to compromised mitochondrial function. Importantly, the inflammatory gene expression signature described here is cell autonomous, i.e. occurs in the absence of prototypical immune or pro-inflammatory cells, growth factors, or other inflammatory mediators.

Exploiting Fast-Variables to Understand Population Dynamics and Evolution

NASA Astrophysics Data System (ADS)

Constable, George W. A.; McKane, Alan J.

2018-07-01

We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

Live-cell Imaging of Platelet Degranulation and Secretion Under Flow.

PubMed

Barendrecht, Arjan D; Verhoef, Johan J F; Pignatelli, Silvia; Pasterkamp, Gerard; Heijnen, Harry F G; Maas, Coen

2017-07-10

Blood platelets are essential players in hemostasis, the formation of thrombi to seal vascular breaches. They are also involved in thrombosis, the formation of thrombi that occlude the vasculature and injure organs, with life-threatening consequences. This motivates scientific research on platelet function and the development of methods to track cell-biological processes as they occur under flow conditions. A variety of flow models are available for the study of platelet adhesion and aggregation, two key phenomena in platelet biology. This work describes a method to study real-time platelet degranulation under flow during activation. The method makes use of a flow chamber coupled to a syringe-pump setup that is placed under a wide-field, inverted, LED-based fluorescence microscope. The setup described here allows for the simultaneous excitation of multiple fluorophores that are delivered by fluorescently labeled antibodies or fluorescent dyes. After live-cell imaging experiments, the cover glasses can be further processed and analyzed using static microscopy (i.e., confocal microscopy or scanning electron microscopy).

Exploiting Fast-Variables to Understand Population Dynamics and Evolution

NASA Astrophysics Data System (ADS)

Constable, George W. A.; McKane, Alan J.

2017-11-01

We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

Dance expertise modulates visual sensitivity to complex biological movements.

PubMed

Orlandi, Andrea; Zani, Alberto; Proverbio, Alice Mado

2017-09-01

Motor resonance processes that occur when observing an individual perform an action may be modulated by acquired visuomotor expertise. We used the event-related potential (EEG/ERP) technique to investigate the ability to automatically recognize a subtle difference between very similar novel contemporary dance movements. Twelve professional dancers and twelve non-dancers were shown 212 pairs of videos of complex whole-body movements that lasted 3s. The second of each pair was the repetition of the previous movement or a slight variation of it (deviance). The participants were engaged in a secondary attentional task. Modulation of a larger centro-parietal N400 effect and a reduction of the Late Positivity amplitude (repetition suppression effect) were identified in response to deviant stimuli only in the dancers. Source reconstruction (swLORETA) showed activations in biological motion, body and face processing related areas, and fronto-parietal and limbic systems. The current findings provide evidence that acquired dance expertise modifies the ability to visually code whole-body complex movements. Copyright © 2017 Elsevier Ltd. All rights reserved.

Enhanced biological nutrient removal in sequencing batch reactors operated as static/oxic/anoxic (SOA) process.

PubMed

Xu, Dechao; Chen, Hongbo; Li, Xiaoming; Yang, Qi; Zeng, Tianjing; Luo, Kun; Zeng, Guangming

2013-09-01

An innovative static/oxic/anoxic (SOA) activated sludge process characterized by static phase as a substitute for conventional anaerobic stage was developed to enhance biological nutrient removal (BNR) with influent ammonia of 20 and 40 mg/L in R1 and R2 reactors, respectively. The results demonstrated that static phase could function as conventional anaerobic stage. In R1 lower influent ammonia concentration facilitated more polyphosphate accumulating organisms (PAOs) growth, but secondary phosphorus release occurred due to NOx(-) depletion during post-anoxic period. In R2, however, denitrifying phosphorus removal proceeded with sufficient NOx(-). Both R1 and R2 saw simultaneous nitrification-denitrification. Glycogen was utilized to drive post-denitrification with denitrification rates in excess of typical endogenous decay rates. The anoxic stirring duration could be shortened from 3 to 1.5h to avoid secondary phosphorus release in R1 and little adverse impact was found on nutrients removal in R2. Copyright © 2013 Elsevier Ltd. All rights reserved.

Regulated bioluminescence as a tool for bioremediation process monitoring and control of bacterial cultures

NASA Technical Reports Server (NTRS)

Burlage, Robert S.; Heitzer, Armin; Digrazia, Philip M.

1991-01-01

An effective on-line monitoring technique for toxic waste bioremediation using bioluminescent microorganisms has shown great potential for the description and optimization of biological processes. The lux genes of the bacterium Vibrio fischeri are used by this species to produce visible light. The lux genes can be genetically fused to the control region of a catabolic gene, with the result that bioluminescence is produced whenever the catabolic gene is induced. Thus the detection of light from a sample indicates that genetic expression from a specific gene is occurring. This technique was used to monitor biodegradation of specific contaminants from waste sites. For these studies, fusions between the lux genes and the operons for naphthalene and toluene/xylene degradation were constructed. Strains carrying one of these fusions respond sensitively and specifically to target substrates. Bioluminescence from these cultures can be rapidly measured in a nondestructive and noninvasive manner. The potential for this technique in this and other biological systems is discussed.

Identification and super-resolution imaging of ligand-activated receptor dimers in live cells

NASA Astrophysics Data System (ADS)

Winckler, Pascale; Lartigue, Lydia; Giannone, Gregory; de Giorgi, Francesca; Ichas, François; Sibarita, Jean-Baptiste; Lounis, Brahim; Cognet, Laurent

2013-08-01

Molecular interactions are key to many chemical and biological processes like protein function. In many signaling processes they occur in sub-cellular areas displaying nanoscale organizations and involving molecular assemblies. The nanometric dimensions and the dynamic nature of the interactions make their investigations complex in live cells. While super-resolution fluorescence microscopies offer live-cell molecular imaging with sub-wavelength resolutions, they lack specificity for distinguishing interacting molecule populations. Here we combine super-resolution microscopy and single-molecule Förster Resonance Energy Transfer (FRET) to identify dimers of receptors induced by ligand binding and provide super-resolved images of their membrane distribution in live cells. By developing a two-color universal-Point-Accumulation-In-the-Nanoscale-Topography (uPAINT) method, dimers of epidermal growth factor receptors (EGFR) activated by EGF are studied at ultra-high densities, revealing preferential cell-edge sub-localization. This methodology which is specifically devoted to the study of molecules in interaction, may find other applications in biological systems where understanding of molecular organization is crucial.

Development of HA/Ag-NPs Composite Coating from Green Process for Hip Applications.

PubMed

Lozoya-Rodríguez, Denisse A; de Lima, Renata; Fraceto, Leonardo F; Ledezma Pérez, Antonio; Bazaldua Domínguez, Mercedes; Gómez Batres, Roberto; Reyes Rojas, Armando; Orozco Carmona, Víctor

2017-08-08

In the present study, biological hydroxyapatite (HA) was obtained from bovine bones through a thermal process. A total of 0% and 1% of silver nanoparticles (Ag-NPs) synthesized from Opuntia ficus (nopal) were added to the biological hydroxyapatite coatings using an atmospheric plasma spray (APS) on a Ti6Al4V substrate. Following this, its antimicrobial efficiency was evaluated against the following bacterial strains: Escherichia coli , Staphylococcus aureus , and Pseudomonas aeruginosa . This was conducted according to the Japanese Industrial Standard (JIS) Z2801:2000 "Antimicrobial Product-Test for Antimicrobial Activity and Efficacy". Scanning electron microscopy (SEM) showed that the silver nanoparticles (Ag-NPs) were evenly distributed on the coating surface. Energy dispersive X-ray spectroscopy (EDX) shows that apatite deposition occurs on a daily basis, maintaining a Ca/P rate between 2.12 and 1.45. Biocompatibility properties were evaluated with osteoblast-like cells (MC3T3-E1) by single-cell gel electrophoresis assay and Tali image cytometry.

Using the brain's fight-or-flight response for predicting mental illness on the human space flight program

NASA Astrophysics Data System (ADS)

Losik, L.

A predictive medicine program allows disease and illness including mental illness to be predicted using tools created to identify the presence of accelerated aging (a.k.a. disease) in electrical and mechanical equipment. When illness and disease can be predicted, actions can be taken so that the illness and disease can be prevented and eliminated. A predictive medicine program uses the same tools and practices from a prognostic and health management program to process biological and engineering diagnostic data provided in analog telemetry during prelaunch readiness and space exploration missions. The biological and engineering diagnostic data necessary to predict illness and disease is collected from the pre-launch spaceflight readiness activities and during space flight for the ground crew to perform a prognostic analysis on the results from a diagnostic analysis. The diagnostic, biological data provided in telemetry is converted to prognostic (predictive) data using the predictive algorithms. Predictive algorithms demodulate telemetry behavior. They illustrate the presence of accelerated aging/disease in normal appearing systems that function normally. Mental illness can predicted using biological diagnostic measurements provided in CCSDS telemetry from a spacecraft such as the ISS or from a manned spacecraft in deep space. The measurements used to predict mental illness include biological and engineering data from an astronaut's circadian and ultranian rhythms. This data originates deep in the brain that is also damaged from the long-term exposure to cortisol and adrenaline anytime the body's fight or flight response is activated. This paper defines the brain's FOFR; the diagnostic, biological and engineering measurements needed to predict mental illness, identifies the predictive algorithms necessary to process the behavior in CCSDS analog telemetry to predict and thus prevent mental illness from occurring on human spaceflight missions.

Sensor Web in Antarctica: Developing an Intelligent, Autonomous Platform for Locating Biological Flourishes in Cryogenic Environments

NASA Technical Reports Server (NTRS)

Delin, K. A.; Harvey, R. P.; Chabot, N. A.; Jackson, S. P.; Adams, Mike; Johnson, D. W.; Britton, J. T.

2003-01-01

The most rigorous tests of the ability to detect extant life will occur where biotic activity is limited by severe environmental conditions. Cryogenic environments are among the most severe-the energy and nutrients needed for biological activity are in short supply while the climate itself is actively destructive to biological mechanisms. In such settings biological activity is often limited to brief flourishes, occurring only when and where conditions are at their most favorable. The closer that typical regional conditions approach conditions that are actively hostile , the more widely distributed biological blooms will be in both time and space. On a spatial dimension of a few meters or a time dimension of a few days, biological activity becomes much more difficult to detect. One way to overcome this difficulty is to establish a Sensor Web that can monitor microclimates over appropriate scales of time and distance, allowing a continuous virtual presence for instant recognition of favorable conditions. A more sophisticated Sensor Web, incorporating metabolic sensors, can effectively meet the challenge to be in "the right place in the right time". This is particularly of value in planetary surface missions, where limited mobility and mission timelines require extremely efficient sample and data acquisition. Sensor Webs can be an effective way to fill the gap between broad scale orbital data collection and fine-scale surface lander science. We are in the process of developing an intelligent, distributed and autonomous Sensor Web that will allow us to monitor microclimate under severe cryogenic conditions, approaching those extant on the surface of Mars. Ultimately this Sensor Web will include the ability to detect and/or establish limits on extant microbiological activity through incorporation of novel metabolic gas sensors. Here we report the results of our first deployment of a Sensor Web prototype in a previously unexplored high altitude East Antarctic Plateau "micro-oasis" at the MacAlpine Hills, Law Glacier, Antarctica.

Cell phenotypic variation in normal and damaged tendons

PubMed Central

Clegg, Peter D; Strassburg, Sandra; Smith, Roger K

2007-01-01

Injuries to tendons are common in both human athletes as well as in animals, such as the horse, which are used for competitive purposes. Furthermore, such injuries are also increasing in prevalence in the ageing, sedentary population. Tendon diseases often respond poorly to treatment and require lengthy periods of rehabilitation. The tendon has a unique extracellular matrix, which has developed to withstand the mechanical demands of such tensile-load bearing structures. Following injury, any repair process is inadequate and results in tissue that is distinct from original tendon tissue. There is growing evidence for the key role of the tendon cell (tenocyte) in both the normal physiological homeostasis and regulation of the tendon matrix and the pathological derangements that occur in disease. In particular, the tenocyte is considered to have a major role in effecting the subclinical matrix degeneration that is thought to occur prior to clinical disease, as well as in the severe degradative events that occur in the tendon at the onset of clinical disease. Furthermore, the tenocyte is likely to have a central role in the production of the biologically inadequate fibrocartilaginous repair tissue that develops subsequent to tendinopathy. Understanding the biology of the tenocyte is central to the development of appropriate interventions and drug therapies that will either prevent the onset of disease, or lead to more rapid and appropriate repair of injured tendon. Central to this is a full understanding of the proteolytic response in the tendon in disease by such enzymes as metalloproteinases, as well as the control of the inappropriate fibrocartilaginous differentiation. Finally, it is important that we understand the role of both intrinsic and extrinsic cellular elements in the repair process in the tendon subsequent to injury. PMID:17696903

Stable carbon and sulfur isotopes as records of the early biosphere

NASA Technical Reports Server (NTRS)

Desmarais, David J.

1989-01-01

The abundance ratios of the stable isotopes of light elements such as carbon and sulfur can differ between various naturally-occurring chemical compounds. If coexisting compounds have achieved mutual chemical and isotopic equilibrium, then the relative isotopic composition can record the conditions at which equilibrium was last maintained. If coexisting chemical compounds indeed formed simultaneously but had not achieved mutual equilibrium, then their relative isotopic compositions often reflect the conditions and mechanisms associated with the kinetically controlled reactions responsible for their production. In the context of Mars, the stable isotopic compositions of various minerals might record not only the earlier environmental conditions of the planet, but also whether or not the chemistry of life ever occurred there. Two major geochemical reservoirs occur in Earth's crust, both for carbon and sulfur. In rocks formed in low temperature sedimentary environments, the oxidized forms of these elements tend to be enriched in the isotope having the larger mass, relative to the reduced forms. In sediments where the organics and sulfides were formed by biological processes, these isotopic contrasts were caused by the processes of biological CO2 fixation and dissimilatory sulfate reduction. Such isotopic contrasts between oxidized and reduced forms of carbon and sulfur are permitted by thermodynamics at ambient temperatures. However, nonbiological chemical reactions associated with the production of organic matter and the reduction of organics and sulfides are extremely slow at ambient temperatures. Thus the synthesis of organics and sulfides under ambient conditions illustrates life's profound role as a chemical catalyst that has altered the chemistry of Earth's crust. Because the stable isotopes of carbon and sulfur can reflect their chemistry, they are useful probes of the Martian surface.

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

Pomeroy, L.R.

There are three distinct but not mutually exclusive areas of research in this contract, studies of intrusions of the west wall of the Gulf Stream onto the outer continental shelf, studies of the flux of materials across nearshore density fronts, and advances in understanding of the planktonic food web of the continental shelf. Studies of frontal events on the outer and inner continental shelf involve distinctive physical and chemical regimes and have proven to require distinctive biological approaches. The studies of the food web run through our work on both of the frontal regimes, but certain aspects have become subjectsmore » in their own right. We have developed a simulation model of the flux of energy through the continental shelf food web which we believe to be more realistic than previous ones of its type. We have examined several of the many roles of dissolved organic compounds in sea water which originate either from release by phytoplankton, digestive processes or metabolites of zooplankton, or extracellular digestion of microorganisms. Methods have been developed under this contract to measure both the chelating capacity of naturally occurring organic materials and the copper concentration in the water. It has been possible to characterize the effects, both toxic and stimulatory, of copper on photosynthesis of naturally occurring phytoplankton populations. It is possible to characterize in considerable detail the course of biological events associated with meanders of the Gulf Stream. We are now in a position to explain the limits to biological productivity of the outer continental shelf of the southeastern US and the reasons why that biological production moves through the food web in the characteristic way that it does.« less

Atmospheric Nitrogen Deposition in the Western United States: Sources, Sinks and Changes over Time

NASA Astrophysics Data System (ADS)

Anderson, Sarah Marie

Anthropogenic activities have greatly modified the way nitrogen moves through the atmosphere and terrestrial and aquatic environments. Excess reactive nitrogen generated through fossil fuel combustion, industrial fixation, and intensification of agriculture is not confined to anthropogenic systems but leaks into natural ecosystems with consequences including acidification, eutrophication, and biodiversity loss. A better understanding of where excess nitrogen originates and how that changes over time is crucial to identifying when, where, and to what degree environmental impacts occur. A major route into ecosystems for excess nitrogen is through atmospheric deposition. Excess nitrogen is emitted to the atmosphere where it can be transported great distances before being deposited back to the Earth's surface. Analyzing the composition of atmospheric nitrogen deposition and biological indicators that reflect deposition can provide insight into the emission sources as well as processes and atmospheric chemistry that occur during transport and what drives variation in these sources and processes. Chapter 1 provides a review and proof of concept of lichens to act as biological indicators and how their elemental and stable isotope composition can elucidate variation in amounts and emission sources of nitrogen over space and time. Information on amounts and emission sources of nitrogen deposition helps inform natural resources and land management decisions by helping to identify potentially impacted areas and causes of those impacts. Chapter 2 demonstrates that herbaria lichen specimens and field lichen samples reflect historical changes in atmospheric nitrogen deposition from urban and agricultural sources across the western United States. Nitrogen deposition increases throughout most of the 20 th century because of multiple types of emission sources until the implementation of the Clean Air Act Amendments of 1990 eventually decrease nitrogen deposition around the turn of the 21st century. Chapter 3 focuses on how nitrogen emissions and subsequent deposition are affected by processes and chemistry during atmospheric transport through analysis of the oxygen isotope composition of nitrate in wet deposition. Local emission sources drive spatial variation, changes in solar radiation drive seasonal variation, and variability in atmospheric conditions and transport drive interannual variation in the processes and chemistry occurring during atmospheric transport of reactive nitrogen.

Isotope Variations in Terrestrial Carbonates and Thermal Springs as Biomarkers: Analogs for Martian Processes

NASA Technical Reports Server (NTRS)

Socki, Richard A.; Gibson, Everett K., Jr.; Bissada, K. K.

2006-01-01

Stable isotope measurements of carbonate minerals contained within ALH84001 [1] suggest that fluids were present at 3.9 Gy on Mars [2, 3, 4, 5]. Both oxygen and carbon isotopes provide independent means of deciphering paleoenvironmental conditions at the time of carbonate mineral precipitation. In terrestrial carbonate rocks oxygen isotopes not only indicate the paleotemperature of the precipitating fluid, but also provide clues to environmental conditions that affected the fluid chemistry. Carbon isotopes, on the other hand, can indicate the presence or absence of organic compounds during precipitation (i.e. biogenically vs. thermogenically-generated methane), thus serving as a potential biomarker. We have undertaken a study of micro scale stable isotope variations measured in some terrestrial carbonates and the influence of organic compounds associated with the formation of these carbonates. Preliminary results indicate that isotope variations occur within narrow and discrete intervals, providing clues to paleoenvironmental conditions that include both biological and non-biological activity. These results carry implications for deciphering Martian isotope data and therefore potential biological prospecting on the planet Mars. Recently, Fourier Transform Spectrometer observations have detected methane occurring in the Martian atmosphere [6] that could be attributed to a possible biogenic source. Indeed, Mars Express has detected the presence of methane in the Martian atmosphere [7], with evidence indicating that methane abundances are greatest above those basins with high water concentrations.

Quantitative imaging of mammalian transcriptional dynamics: from single cells to whole embryos.

PubMed

Zhao, Ziqing W; White, Melanie D; Bissiere, Stephanie; Levi, Valeria; Plachta, Nicolas

2016-12-23

Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos.

Estimating species-specific suvival and movement when species identification is uncertain

USGS Publications Warehouse

Runge, J.P.; Hines, J.E.; Nichols, J.D.

2007-01-01

Incorporating uncertainty in the investigation of ecological studies has been the topic of an increasing body of research. In particular, mark?recapture methodology has shown that incorporating uncertainty in the probability of detecting individuals in populations enables accurate estimation of population-level processes such as survival, reproduction, and dispersal. Recent advances in mark?recapture methodology have included estimating population-level processes for biologically important groups despite the misassignment of individuals to those groups. Examples include estimating rates of apparent survival despite less than perfect accuracy when identifying individuals to gender or breeding state. Here we introduce a method for estimating apparent survival and dispersal in species that co-occur but that are difficult to distinguish. We use data from co-occurring populations of meadow voles (Microtus pennsylvanicus) and montane voles (M. montanus) in addition to simulated data to show that ignoring species uncertainty can lead to biased estimates of population processes. The incorporation of species uncertainty in mark?recapture studies should aid future research investigating ecological concepts such as interspecific competition, niche differentiation, and spatial population dynamics in sibling species.

The intrinsic role of nanoconfinement in chemical equilibrium: evidence from DNA hybridization.

PubMed

Rubinovich, Leonid; Polak, Micha

2013-05-08

Recently we predicted that when a reaction involving a small number of molecules occurs in a nanometric-scale domain entirely segregated from the surrounding media, the nanoconfinement can shift the position of equilibrium toward products via reactant-product reduced mixing. In this Letter, we demonstrate how most-recently reported single-molecule fluorescence measurements of partial hybridization of ssDNA confined within nanofabricated chambers provide the first experimental confirmation of this entropic nanoconfinement effect. Thus, focusing separately on each occupancy-specific equilibrium constant, quantitatively reveals extra stabilization of the product upon decreasing the chamber occupancy or size. Namely, the DNA hybridization under nanoconfined conditions is significantly favored over the identical reaction occurring in bulk media with the same reactant concentrations. This effect, now directly verified for DNA, can be relevant to actual biological processes, as well as to diverse reactions occurring within molecular capsules, nanotubes, and other functional nanospaces.

Zooplankton data: Vertical distributions of zooplankton in the Norweigian and Greenland Seas during summer, 1989

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

Lane, P.V.Z.; Smith, S.L.; Schwarting, E.M.

1993-08-01

Recent studies of zooplankton populations in the Greenland Sea have focused on processes at the Marginal Ice Zone (MIZ) and the areas immediately adjacent to it under the ice and in open water. These studies have shown a relatively short period of intense secondary productivity which is closely linked temporally and spatially to phytoplankton blooms occurring near the ice edge in spring and early summer. During the summer of 1989 we participated in a project focusing on benthic and water column processes in the basins of the Norwegian and Greenland Seas. This study allowed us to compare biological processes atmore » the MIZ with those occurring in the open waters of the Greenland Sea, and to compare processes at both of these locations with those in the Norwegian Sea. The data presented in this report are the results of zooplankton net tows covering the upper 1000 meters of the water column over the Norwegian Sea basin and the Greenland Sea basin, and the upper 500 meters of open water adjacent to the MIZ in the Greenland Sea. Sampling was conducted between 12 and 29 July 1989.« less

The cell biology of Drosophila wing metamorphosis in vitro.

PubMed

Milner, Martin J; Muir, Jonathan

1987-03-01

We have examined the metamorphosis of the wing imaginal disc of Drosophila during culture in vitro in the continuous presence of 20-hydroxy ecdysone (0.1 μg/ ml). We find that the sequence of cellular changes in the wing blade during culture closely match those occurring in situ, involving two periods at which the dorsal and ventral surfaces are joined only by cell processes containing trans-alar microtubule arrays. Good pupal and imaginal cuticle secretion is found in this system.

An Adaptive Method of Lines with Error Control for Parabolic Equations of the Reaction-Diffusion Type.

DTIC Science & Technology

1984-06-01

space discretization error . 1. I 3 1. INTRODUCTION Reaction- diffusion processes occur in many branches of biology and physical chemistry. Examples...to model reaction- diffusion phenomena. The primary goal of this adaptive method is to keep a particular norm of the space discretization error less...AD-A142 253 AN ADAPTIVE MET6 OFD LNES WITH ERROR CONTROL FOR 1 INST FOR PHYSICAL SCIENCE AND TECH. I BABUSKAAAO C7 EA OH S UMR AN UNVC EEP R

A review of phosphate mineral nucleation in biology and geobiology.

PubMed

Omelon, Sidney; Ariganello, Marianne; Bonucci, Ermanno; Grynpas, Marc; Nanci, Antonio

2013-10-01

Relationships between geological phosphorite deposition and biological apatite nucleation have often been overlooked. However, similarities in biological apatite and phosphorite mineralogy suggest that their chemical formation mechanisms may be similar. This review serves to draw parallels between two newly described phosphorite mineralization processes, and proposes a similar novel mechanism for biologically controlled apatite mineral nucleation. This mechanism integrates polyphosphate biochemistry with crystal nucleation theory. Recently, the roles of polyphosphates in the nucleation of marine phosphorites were discovered. Marine bacteria and diatoms have been shown to store and concentrate inorganic phosphate (Pi) as amorphous, polyphosphate granules. Subsequent release of these P reserves into the local marine environment as Pi results in biologically induced phosphorite nucleation. Pi storage and release through an intracellular polyphosphate intermediate may also occur in mineralizing oral bacteria. Polyphosphates may be associated with biologically controlled apatite nucleation within vertebrates and invertebrates. Historically, biological apatite nucleation has been attributed to either a biochemical increase in local Pi concentration or matrix-mediated apatite nucleation control. This review proposes a mechanism that integrates both theories. Intracellular and extracellular amorphous granules, rich in both calcium and phosphorus, have been observed in apatite-biomineralizing vertebrates, protists, and atremate brachiopods. These granules may represent stores of calcium-polyphosphate. Not unlike phosphorite nucleation by bacteria and diatoms, polyphosphate depolymerization to Pi would be controlled by phosphatase activity. Enzymatic polyphosphate depolymerization would increase apatite saturation to the level required for mineral nucleation, while matrix proteins would simultaneously control the progression of new biological apatite formation.

[Research on removal efficiency of Cd (II)-bearing wastewater by sulfate-reducing biological filter].

PubMed

Wu, Xuan; Tan, Ke-Yan; Hu, Xi-Jia; Gu, Yun; Yang, Hong

2014-04-01

At the temperature of 18.0-22.3 degrees C, biological carriers were produce from pure SRB and zeolite by the embedding immobilized method, and a sulfate-reducing biological filter filled with filter carriers was built to treat cadmium-containing wastewater. Experimental research on removal efficiency of Cd2+, COD and SO4(2-) in wastewater by the biological filter was carried out after SRB domestication. Results show that cadmium can be removed satisfactorily from wastewater using SRB by the biological filter filled with sulfate-reducing bacteria. When the filtration rate was 0.4 m x h(-1) and the cadmium concentration in wastewater was not more than 15 mg x L(-1), the processing efficiency was the best. In the formal running period, the removal rates of Cd2+, COD and SO4(2-) by the biological filter were more than 99%, 75% and 50%. The effluent Cd2+ concentration was less than 0.1 mg x L(-1), which could meet the cadmium emission requirements in the wastewater quality standards for discharge to municipal sewers (CJ 343-2010). The removal of Cd2+, COD and SO4(2-) by biological filter mainly occurs in the top 60 cm of the filter bed during stable operation. When the filtration rate was less than 0.6 m x h(-1), Cd(2+) can be removed by the biological filter with high efficiency and stability.

Environmental Designer Drugs: When Transformation May Not Eliminate Risk

PubMed Central

2015-01-01

Environmental transformation processes, including those occurring in natural and engineered systems, do not necessarily drastically alter molecular structures of bioactive organic contaminants. While the majority of generated transformation products are likely benign, substantial conservation of structure in transformation products can imply conservation or even creation of bioactivity across multiple biological end points and thus incomplete mitigation of ecological risk. Therefore, focusing solely on parent compound removal for contaminants of higher relative risk, the most common approach to fate characterization, provides no mechanistic relationship to potential biological effects and is inadequate as a comprehensive metric for reduction of ecological risks. Here, we explore these phenomena for endocrine-active steroid hormones, focusing on examples of conserved bioactivity and related implications for fate assessment, regulatory approaches, and research opportunities. PMID:25216024

Engineering of routes to heparin and related polysaccharides.

PubMed

Bhaskar, Ujjwal; Sterner, Eric; Hickey, Anne Marie; Onishi, Akihiro; Zhang, Fuming; Dordick, Jonathan S; Linhardt, Robert J

2012-01-01

Anticoagulant heparin has been shown to possess important biological functions that vary according to its fine structure. Variability within heparin's structure occurs owing to its biosynthesis and animal tissue-based recovery and adds another dimension to its complex polymeric structure. The structural variations in chain length and sulfation patterns mediate its interaction with many heparin-binding proteins, thereby eliciting complex biological responses. The advent of novel chemical and enzymatic approaches for polysaccharide synthesis coupled with high throughput combinatorial approaches for drug discovery have facilitated an increased effort to understand heparin's structure-activity relationships. An improved understanding would offer potential for new therapeutic development through the engineering of polysaccharides. Such a bioengineering approach requires the amalgamation of several different disciplines, including carbohydrate synthesis, applied enzymology, metabolic engineering, and process biochemistry.

Mesoscale modeling: solving complex flows in biology and biotechnology.

PubMed

Mills, Zachary Grant; Mao, Wenbin; Alexeev, Alexander

2013-07-01

Fluids are involved in practically all physiological activities of living organisms. However, biological and biorelated flows are hard to analyze due to the inherent combination of interdependent effects and processes that occur on a multitude of spatial and temporal scales. Recent advances in mesoscale simulations enable researchers to tackle problems that are central for the understanding of such flows. Furthermore, computational modeling effectively facilitates the development of novel therapeutic approaches. Among other methods, dissipative particle dynamics and the lattice Boltzmann method have become increasingly popular during recent years due to their ability to solve a large variety of problems. In this review, we discuss recent applications of these mesoscale methods to several fluid-related problems in medicine, bioengineering, and biotechnology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Status of miniature integrated UV resonance fluorescence and Raman sensors for detection and identification of biochemical warfare agents

NASA Astrophysics Data System (ADS)

Hug, William F.; Bhartia, Rohit; Taspin, Alexandre; Lane, Arthur; Conrad, Pamela; Sijapati, Kripa; Reid, Ray D.

2005-11-01

Laser induced native fluorescence (LINF) is the most sensitive method of detection of biological material including microorganisms, virus', and cellular residues. LINF is also a sensitive method of detection for many non-biological materials as well. The specificity with which these materials can be classified depends on the excitation wavelength and the number and location of observation wavelengths. Higher levels of specificity can be obtained using Raman spectroscopy but a much lower levels of sensitivity. Raman spectroscopy has traditionally been employed in the IR to avoid fluorescence. Fluorescence rarely occurs at wavelength below about 270nm. Therefore, when excitation occurs at a wavelength below 250nm, no fluorescence background occurs within the Raman fingerprint region for biological materials. When excitation occurs within electronic resonance bands of the biological target materials, Raman signal enhancement over one million typically occurs. Raman sensitivity within several hundred times fluorescence are possible in the deep UV where most biological materials have strong absorption. Since the Raman and fluorescence emissions occur at different wavelength, both spectra can be observed simultaneously, thereby providing a sensor with unique sensitivity and specificity capability. We will present data on our integrated, deep ultraviolet, LINF/Raman instruments that are being developed for several applications including life detection on Mars as well as biochemical warfare agents on Earth. We will demonstrate the ability to discriminate organic materials based on LINF alone. Together with UV resonance Raman, higher levels of specificity will be demonstrated. In addition, these instruments are being developed as on-line chemical sensors for industrial and municipal waste streams and product quality applications.

The Role of Laboratory-Based Studies of the Physical and Biological Properties of Sea Ice in Supporting the Observation and Modeling of Ice Covered Seas

NASA Astrophysics Data System (ADS)

Light, B.; Krembs, C.

2003-12-01

Laboratory-based studies of the physical and biological properties of sea ice are an essential link between high latitude field observations and existing numerical models. Such studies promote improved understanding of climatic variability and its impact on sea ice and the structure of ice-dependent marine ecosystems. Controlled laboratory experiments can help identify feedback mechanisms between physical and biological processes and their response to climate fluctuations. Climatically sensitive processes occurring between sea ice and the atmosphere and sea ice and the ocean determine surface radiative energy fluxes and the transfer of nutrients and mass across these boundaries. High temporally and spatially resolved analyses of sea ice under controlled environmental conditions lend insight to the physics that drive these transfer processes. Techniques such as optical probing, thin section photography, and microscopy can be used to conduct experiments on natural sea ice core samples and laboratory-grown ice. Such experiments yield insight on small scale processes from the microscopic to the meter scale and can be powerful interdisciplinary tools for education and model parameterization development. Examples of laboratory investigations by the authors include observation of the response of sea ice microstructure to changes in temperature, assessment of the relationships between ice structure and the partitioning of solar radiation by first-year sea ice covers, observation of pore evolution and interfacial structure, and quantification of the production and impact of microbial metabolic products on the mechanical, optical, and textural characteristics of sea ice.

Sex that moves mountains: The influence of spawning fish on river profiles over geologic timescales

NASA Astrophysics Data System (ADS)

Fremier, Alexander K.; Yanites, Brian J.; Yager, Elowyn M.

2018-03-01

A key component of resilience is to understand feedbacks among components of biophysical systems, such as physical drivers, ecological responses and the subsequent feedbacks onto physical process. While physically based explanations of biological speciation are common (e.g., mountains separating a species can lead to speciation), less common is the inverse process examined: can a speciation event have significant influence on physical processes and patterns in a landscape? When such processes are considered, such as with 'ecosystem engineers', many studies have focused on the short-term physical and biological effects rather than the long-term impacts. Here, we formalized the physical influence of salmon spawning on stream beds into a model of channel profile evolution by altering the critical shear stress required to move stream bed particles. We then asked if spawning and an adaptive radiation event (similar to the one that occurred in Pacific salmon species) could have an effect on channel erosion processes and stream profiles over geological timescales. We found that spawning can profoundly influence the longitudinal profiles of stream beds and thereby the evolution of entire watersheds. The radiation of five Pacific salmon from a common ancestor, additionally, could also cause significant geomorphic change by altering a wider section of the profile for a given distribution of grain sizes. This modeling study suggests that biological evolution can impact landscape evolution by increasing the sediment transport and erosion efficiency of mountain streams. Moreover, the physical effects of a species on its environment might be a complementary explanation for rapid radiation events in species through the creation of new habitat types. This example provides an illustrative case for thinking about the long- and short-term coupling of biotic and abiotic systems.

Real-Time Intracellular Measurements of ROS and RNS in Living Cells with Single Core-Shell Nanowire Electrodes.

PubMed

Zhang, Xin-Wei; Qiu, Quan-Fa; Jiang, Hong; Zhang, Fu-Li; Liu, Yan-Lin; Amatore, Christian; Huang, Wei-Hua

2017-10-09

Nanoelectrodes allow precise and quantitative measurements of important biological processes at the single living-cell level in real time. Cylindrical nanowire electrodes (NWEs) required for intracellular measurements create a great challenge for achieving excellent electrochemical and mechanical performances. Herein, we present a facile and robust solution to this problem based on a unique SiC-core-shell design to produce cylindrical NWEs with superior mechanical toughness provided by the SiC nano-core and an excellent electrochemical performance provided by the ultrathin carbon shell that can be used as such or platinized. The use of such NWEs for biological applications is illustrated by the first quantitative measurements of ROS/RNS in individual phagolysosomes of living macrophages. As the shell material can be varied to meet any specific detection purpose, this work opens up new opportunities to monitor quantitatively biological functions occurring inside cells and their organelles. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design of SGLT2 Inhibitors for the Treatment of Type 2 Diabetes: A History Driven by Biology to Chemistry.

PubMed

Cai, Wenqing; Jiang, Linlin; Xie, Yafei; Liu, Yuqiang; Liu, Wei; Zhao, Guilong

2015-01-01

A brief history of the design of sodium-dependent glucose cotransporter 2 (SGLT2) inhibitors is reviewed. The design of O-glucoside SGLT2 inhibitors by structural modification of phlorizin, a naturally occurring O-glucoside, in the early stage was a process mainly driven by biology with anticipation of improving SGLT2/SGLT1 selectivity and increasing metabolic stability. Discovery of dapagliflozin, a pioneering C-glucoside SGLT2 inhibitor developed by Bristol-Myers Squibb, represents an important milestone in this history. In the second stage, the design of C-glycoside SGLT2 inhibitors by modifications of the aglycone and glucose moiety of dapagliflozin, an original structural template for almost all C-glycoside SGLT2 inhibitors, was mainly driven by synthetic organic chemistry due to the challenge of designing dapagliflozin derivatives that are patentable, biologically active and synthetically accessible. Structure-activity relationships (SAR) of the SGLT2 inhibitors are also discussed.

Chemistry and biology of natural and designed enediynes.

PubMed Central

Nicolaou, K C; Smith, A L; Yue, E W

1993-01-01

Ever since the initial reports of the enediyne anticancer antibiotics in the late 1980s, researchers from a number of disciplines have been devoting increasing attention to their chemistry, biology, and potential medical applications. Synthetic chemists and molecular designers have been engaged in attempts to synthesize these molecules and to model their unique architecture. Considerable efforts have been directed at understanding and mimicking the various processes involved in the targeting, activation, and DNA cleavage associated with these natural products. This review summarizes the main contributions to the field, with particular emphasis on work from our laboratories. Highlights include studies of the Bergman reaction, which is central to the mechanism of action of enediynes, the design and chemical synthesis of a number of these systems, and biological studies with selected molecules. Finally, the total synthesis of calicheamicin gamma 1I, the most prominent member of this class of naturally occurring compounds, is discussed. Images Fig. 2 Fig. 5 Fig. 6 PMID:8327459

The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology.

PubMed

O'Malley, Maureen A

2018-06-01

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.

The Rise of Radicals in Bioinorganic Chemistry.

PubMed

Gray, Harry B; Winkler, Jay R

2016-10-01

Prior to 1950, the consensus was that biological transformations occurred in two-electron steps, thereby avoiding the generation of free radicals. Dramatic advances in spectroscopy, biochemistry, and molecular biology have led to the realization that protein-based radicals participate in a vast array of vital biological mechanisms. Redox processes involving high-potential intermediates formed in reactions with O 2 are particularly susceptible to radical formation. Clusters of tyrosine (Tyr) and tryptophan (Trp) residues have been found in many O 2 -reactive enzymes, raising the possibility that they play an antioxidant protective role. In blue copper proteins with plastocyanin-like domains, Tyr/Trp clusters are uncommon in the low-potential single-domain electron-transfer proteins and in the two-domain copper nitrite reductases. The two-domain muticopper oxidases, however, exhibit clusters of Tyr and Trp residues near the trinuclear copper active site where O 2 is reduced. These clusters may play a protective role to ensure that reactive oxygen species are not liberated during O 2 reduction.

High-contrast 3D microscopic imaging of deep layers in a biological medium

NASA Astrophysics Data System (ADS)

Faridian, Ahmad; Pedrini, Giancarlo; Osten, Wolfgang

2014-03-01

Multilayer imaging of biological specimens is a demanding field of research, but scattering is one of the major obstacles in imaging the internal layers of a specimen. Although in many studies the biological object is assumed to be a weak scatterer, this condition is hardly satisfied for sub-millimeter sized organisms. The scattering medium is inhomogeneously distributed inside the specimen. Therefore, the scattering which occurs in the upper layers of a given internal layer of interest is different from the lower layers. That results in a different amount of collectable information for a specific point in the layer from each view. An opposed view dark-field digital holographic microscope (DHM) has been implemented in this work to collect the information concurrently from both views and increase the image quality. Implementing a DHM system gives the possibility to perform digital refocusing process and obtain multilayer images from each side without depth scanning of the object. The results have been presented and discussed here for a Drosophila embryo.

Rapid Startup and Loading of an Attached Growth, Simultaneous Nitrification/Denitrification Membrane Aerated Bioreactor

NASA Technical Reports Server (NTRS)

Meyer, Caitlin; Vega, Leticia

2014-01-01

The Membrane Aerated Bioreactor (MABR) is an attached-growth biological system for simultaneous nitrification and denitrification. This design is an innovative approach to common terrestrial wastewater treatments for nitrogen and carbon removal. Implementing a biologically-based water treatment system for long-duration human exploration is an attractive, low energy alternative to physiochemical processes. Two obstacles to implementing such a system are (1) the "start-up" duration from inoculation to steady-state operations and (2) the amount of surface area needed for the biological activity to occur. The Advanced Water Recovery Systems (AWRS) team at JSC explored these two issues through two tests; a rapid inoculation study and a wastewater loading study. Results from these tests demonstrate that the duration from inoculation to steady state can be reduced to two weeks and that the surface area to volume ratio baseline used in the Alternative Water Processor (AWP) test was higher than what was needed to remove the organic carbon and ammonium from the system.

Paracrystalline Disorder from Phosphate Ion Orientation and Substitution in Synthetic Bone Mineral.

PubMed

Marisa, Mary E; Zhou, Shiliang; Melot, Brent C; Peaslee, Graham F; Neilson, James R

2016-12-05

Hydroxyapatite is an inorganic mineral closely resembling the mineral phase in bone. However, as a biological mineral, it is highly disordered, and its composition and atomistic structure remain poorly understood. Here, synchrotron X-ray total scattering and pair distribution function analysis methods provide insight into the nature of atomistic disorder in a synthetic bone mineral analogue, chemically substituted hydroxyapatite. By varying the effective hydrolysis rate and/or carbonate concentration during growth of the mineral, compounds with varied degrees of paracrystallinity are prepared. From advanced simulations constrained by the experimental pair distribution function and density functional theory, the paracrystalline disorder prevalent in these materials appears to result from accommodation of carbonate in the lattice through random displacement of the phosphate groups. Though many substitution modalities are likely to occur in concert, the most predominant substitution places carbonate into the mirror plane of an ideal phosphate site. Understanding the mineralogical imperfections of a biologically analogous hydroxyapatite is important not only to potential bone grafting applications but also to biological mineralization processes themselves.

Nutrient budgets in the subtropical ocean gyres dominated by lateral transport

NASA Astrophysics Data System (ADS)

Letscher, Robert T.; Primeau, François; Moore, J. Keith

2016-11-01

Ocean circulation replenishes surface nutrients depleted by biological production and export. Vertical processes are thought to dominate, but estimated vertical nutrient fluxes are insufficient to explain observed net productivity in the subtropical ocean gyres. Lateral inputs help balance the North Atlantic nutrient budget, but their importance for other gyres has not been demonstrated. Here we use an ocean model that couples circulation and ecosystem dynamics to show that lateral transport and biological uptake of inorganic and organic forms of nitrogen and phosphorus from the gyre margins exceeds the vertical delivery of nutrients, supplying 24-36% of the nitrogen and 44-67% of the phosphorus required to close gyre nutrient budgets. At the Bermuda and Hawaii time-series sites, nearly half of the annual lateral supply by lateral transport occurs during the summer-to-fall stratified period, helping explain seasonal patterns of inorganic carbon drawdown and nitrogen fixation. Our study confirms the importance of upper-ocean lateral nutrient transport for understanding the biological cycles of carbon and nutrients in the ocean's largest biome.

Systems Toxicology: From Basic Research to Risk Assessment

PubMed Central

2014-01-01

Systems Toxicology is the integration of classical toxicology with quantitative analysis of large networks of molecular and functional changes occurring across multiple levels of biological organization. Society demands increasingly close scrutiny of the potential health risks associated with exposure to chemicals present in our everyday life, leading to an increasing need for more predictive and accurate risk-assessment approaches. Developing such approaches requires a detailed mechanistic understanding of the ways in which xenobiotic substances perturb biological systems and lead to adverse outcomes. Thus, Systems Toxicology approaches offer modern strategies for gaining such mechanistic knowledge by combining advanced analytical and computational tools. Furthermore, Systems Toxicology is a means for the identification and application of biomarkers for improved safety assessments. In Systems Toxicology, quantitative systems-wide molecular changes in the context of an exposure are measured, and a causal chain of molecular events linking exposures with adverse outcomes (i.e., functional and apical end points) is deciphered. Mathematical models are then built to describe these processes in a quantitative manner. The integrated data analysis leads to the identification of how biological networks are perturbed by the exposure and enables the development of predictive mathematical models of toxicological processes. This perspective integrates current knowledge regarding bioanalytical approaches, computational analysis, and the potential for improved risk assessment. PMID:24446777

Recent advances in lipid separations and structural elucidation using mass spectrometry combined with ion mobility spectrometry, ion-molecule reactions and fragmentation approaches

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

Zheng, Xueyun; Smith, Richard D.; Baker, Erin S.

Lipids are a vital class of molecules that play important and varied roles in biological processes. Fully understanding lipid roles, however, is extremely difficult since the number and diversity of lipid species is immense, with cells expressing hundreds of enzymes that synthesize tens of thousands of different lipids. While recent advances in chromatography and high resolution mass spectrometry have greatly progressed the understanding of lipid species and functions, effectively separating many lipids still remains problematic. Isomeric lipids have made lipid characterization especially difficult and occur due to subclasses having the same chemical composition, or species having multiple acyl chains connectivitiesmore » (sn-1, sn-2, or sn-3), double bond positions and orientations (cis or trans), and functional group stereochemistry (R versus S). Fully understanding the roles of lipids in biological processes therefore requires separating and evaluating how isomers change in biological and environmental samples. To address this challenge, ion mobility spectrometry separations, ion-molecule reactions and fragmentation techniques have increasingly been added to lipid analysis workflows to improve identifications. In this manuscript, we review the current state of these approaches and their capabilities for improving the identification of specific lipid species.« less

BMDExpress Data Viewer: A Visualization Tool to Analyze ...

EPA Pesticide Factsheets

Regulatory agencies increasingly apply benchmark dose (BMD) modeling to determine points of departure in human risk assessments. BMDExpress applies BMD modeling to transcriptomics datasets and groups genes to biological processes and pathways for rapid assessment of doses at which biological perturbations occur. However, graphing and analytical capabilities within BMDExpress are limited, and the analysis of output files is challenging. We developed a web-based application, BMDExpress Data Viewer, for visualization and graphical analyses of BMDExpress output files. The software application consists of two main components: ‘Summary Visualization Tools’ and ‘Dataset Exploratory Tools’. We demonstrate through two case studies that the ‘Summary Visualization Tools’ can be used to examine and assess the distributions of probe and pathway BMD outputs, as well as derive a potential regulatory BMD through the modes or means of the distributions. The ‘Functional Enrichment Analysis’ tool presents biological processes in a two-dimensional bubble chart view. By applying filters of pathway enrichment p-value and minimum number of significant genes, we showed that the Functional Enrichment Analysis tool can be applied to select pathways that are potentially sensitive to chemical perturbations. The ‘Multiple Dataset Comparison’ tool enables comparison of BMDs across multiple experiments (e.g., across time points, tissues, or organisms, etc.). The ‘BMDL-BM

Systems toxicology: from basic research to risk assessment.

PubMed

Sturla, Shana J; Boobis, Alan R; FitzGerald, Rex E; Hoeng, Julia; Kavlock, Robert J; Schirmer, Kristin; Whelan, Maurice; Wilks, Martin F; Peitsch, Manuel C

2014-03-17

Systems Toxicology is the integration of classical toxicology with quantitative analysis of large networks of molecular and functional changes occurring across multiple levels of biological organization. Society demands increasingly close scrutiny of the potential health risks associated with exposure to chemicals present in our everyday life, leading to an increasing need for more predictive and accurate risk-assessment approaches. Developing such approaches requires a detailed mechanistic understanding of the ways in which xenobiotic substances perturb biological systems and lead to adverse outcomes. Thus, Systems Toxicology approaches offer modern strategies for gaining such mechanistic knowledge by combining advanced analytical and computational tools. Furthermore, Systems Toxicology is a means for the identification and application of biomarkers for improved safety assessments. In Systems Toxicology, quantitative systems-wide molecular changes in the context of an exposure are measured, and a causal chain of molecular events linking exposures with adverse outcomes (i.e., functional and apical end points) is deciphered. Mathematical models are then built to describe these processes in a quantitative manner. The integrated data analysis leads to the identification of how biological networks are perturbed by the exposure and enables the development of predictive mathematical models of toxicological processes. This perspective integrates current knowledge regarding bioanalytical approaches, computational analysis, and the potential for improved risk assessment.

Classification of climate-change-induced stresses on biological diversity.

PubMed

Geyer, Juliane; Kiefer, Iris; Kreft, Stefan; Chavez, Veronica; Salafsky, Nick; Jeltsch, Florian; Ibisch, Pierre L

2011-08-01

Conservation actions need to account for and be adapted to address changes that will occur under global climate change. The identification of stresses on biological diversity (as defined in the Convention on Biological Diversity) is key in the process of adaptive conservation management. We considered any impact of climate change on biological diversity a stress because such an effect represents a change (negative or positive) in key ecological attributes of an ecosystem or parts of it. We applied a systemic approach and a hierarchical framework in a comprehensive classification of stresses to biological diversity that are caused directly by global climate change. Through analyses of 20 conservation sites in 7 countries and a review of the literature, we identified climate-change-induced stresses. We grouped the identified stresses according to 3 levels of biological diversity: stresses that affect individuals and populations, stresses that affect biological communities, and stresses that affect ecosystem structure and function. For each stress category, we differentiated 3 hierarchical levels of stress: stress class (thematic grouping with the coarsest resolution, 8); general stresses (thematic groups of specific stresses, 21); and specific stresses (most detailed definition of stresses, 90). We also compiled an overview of effects of climate change on ecosystem services using the categories of the Millennium Ecosystem Assessment and 2 additional categories. Our classification may be used to identify key climate-change-related stresses to biological diversity and may assist in the development of appropriate conservation strategies. The classification is in list format, but it accounts for relations among climate-change-induced stresses. © 2011 Society for Conservation Biology.

Consciousness in the universe: a review of the 'Orch OR' theory.

PubMed

Hameroff, Stuart; Penrose, Roger

2014-03-01

The nature of consciousness, the mechanism by which it occurs in the brain, and its ultimate place in the universe are unknown. We proposed in the mid 1990's that consciousness depends on biologically 'orchestrated' coherent quantum processes in collections of microtubules within brain neurons, that these quantum processes correlate with, and regulate, neuronal synaptic and membrane activity, and that the continuous Schrödinger evolution of each such process terminates in accordance with the specific Diósi-Penrose (DP) scheme of 'objective reduction' ('OR') of the quantum state. This orchestrated OR activity ('Orch OR') is taken to result in moments of conscious awareness and/or choice. The DP form of OR is related to the fundamentals of quantum mechanics and space-time geometry, so Orch OR suggests that there is a connection between the brain's biomolecular processes and the basic structure of the universe. Here we review Orch OR in light of criticisms and developments in quantum biology, neuroscience, physics and cosmology. We also introduce a novel suggestion of 'beat frequencies' of faster microtubule vibrations as a possible source of the observed electro-encephalographic ('EEG') correlates of consciousness. We conclude that consciousness plays an intrinsic role in the universe. Copyright © 2013 Elsevier B.V. All rights reserved.

Conformational plasticity of JRAB/MICAL-L2 provides "law and order" in collective cell migration.

PubMed

Sakane, Ayuko; Yoshizawa, Shin; Nishimura, Masaomi; Tsuchiya, Yuko; Matsushita, Natsuki; Miyake, Kazuhisa; Horikawa, Kazuki; Imoto, Issei; Mizuguchi, Chiharu; Saito, Hiroyuki; Ueno, Takato; Matsushita, Sachi; Haga, Hisashi; Deguchi, Shinji; Mizuguchi, Kenji; Yokota, Hideo; Sasaki, Takuya

2016-10-15

In fundamental biological processes, cells often move in groups, a process termed collective cell migration. Collectively migrating cells are much better organized than a random assemblage of individual cells. Many molecules have been identified as factors involved in collective cell migration, and no one molecule is adequate to explain the whole picture. Here we show that JRAB/MICAL-L2, an effector protein of Rab13 GTPase, provides the "law and order" allowing myriad cells to behave as a single unit just by changing its conformation. First, we generated a structural model of JRAB/MICAL-L2 by a combination of bioinformatic and biochemical analyses and showed how JRAB/MICAL-L2 interacts with Rab13 and how its conformational change occurs. We combined cell biology, live imaging, computational biology, and biomechanics to show that impairment of conformational plasticity in JRAB/MICAL-L2 causes excessive rigidity and loss of directionality, leading to imbalance in cell group behavior. This multidisciplinary approach supports the concept that the conformational plasticity of a single molecule provides "law and order" in collective cell migration. © 2016 Sakane et al. 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).

Examining the Role of Leadership in an Undergraduate Biology Institutional Reform Initiative.

PubMed

Matz, Rebecca L; Jardeleza, Sarah E

Undergraduate science, technology, engineering, and mathematics (STEM) education reform continues to be a national priority. We studied a reform process in undergraduate biology at a research-intensive university to explore what leadership issues arose in implementation of the initiative when characterized with a descriptive case study method. The data were drawn from transcripts of meetings that occurred over the first 2 years of the reform process. Two literature-based models of change were used as lenses through which to view the data. We find that easing the burden of an undergraduate education reform initiative on faculty through articulating clear outcomes, developing shared vision across stakeholders on how to achieve those outcomes, providing appropriate reward systems, and ensuring faculty have ample opportunity to influence the initiative all appear to increase the success of reform. The two literature-based models were assessed, and an extended model of change is presented that moves from change in STEM instructional strategies to STEM organizational change strategies. These lessons may be transferable to other institutions engaging in education reform. © 2016 R. L. Matz and S. E. Jardeleza. 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).

Potential coordination role between O-GlcNAcylation and epigenetics.

PubMed

Wu, Donglu; Cai, Yong; Jin, Jingji

2017-10-01

Dynamic changes of the post-translational O-GlcNAc modification (O-GlcNAcylation) are controlled by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) and the glycoside hydrolase O-GlcNAcase (OGA) in cells. O-GlcNAcylation often occurs on serine (Ser) and threonine (Thr) residues of the specific substrate proteins via the addition of O-GlcNAc group by OGT. It has been known that O-GlcNAcylation is not only involved in many fundamental cellular processes, but also plays an important role in cancer development through various mechanisms. Recently, accumulating data reveal that O-GlcNAcylation at histones or non-histone proteins can lead to the start of the subsequent biological processes, suggesting that O-GlcNAcylation as 'protein code' or 'histone code' may provide recognition platforms or executive instructions for subsequent recruitment of proteins to carry out the specific functions. In this review, we summarize the interaction of O-GlcNAcylation and epigenetic changes, introduce recent research findings that link crosstalk between O-GlcNAcylation and epigenetic changes, and speculate on the potential coordination role of O-GlcNAcylation with epigenetic changes in intracellular biological processes.

From single steps to mass migration: the problem of scale in the movement ecology of the Serengeti wildebeest.

PubMed

Torney, Colin J; Hopcraft, J Grant C; Morrison, Thomas A; Couzin, Iain D; Levin, Simon A

2018-05-19

A central question in ecology is how to link processes that occur over different scales. The daily interactions of individual organisms ultimately determine community dynamics, population fluctuations and the functioning of entire ecosystems. Observations of these multiscale ecological processes are constrained by various technological, biological or logistical issues, and there are often vast discrepancies between the scale at which observation is possible and the scale of the question of interest. Animal movement is characterized by processes that act over multiple spatial and temporal scales. Second-by-second decisions accumulate to produce annual movement patterns. Individuals influence, and are influenced by, collective movement decisions, which then govern the spatial distribution of populations and the connectivity of meta-populations. While the field of movement ecology is experiencing unprecedented growth in the availability of movement data, there remain challenges in integrating observations with questions of ecological interest. In this article, we present the major challenges of addressing these issues within the context of the Serengeti wildebeest migration, a keystone ecological phenomena that crosses multiple scales of space, time and biological complexity.This article is part of the theme issue 'Collective movement ecology'. © 2018 The Author(s).

Biological properties

Treesearch

Rebecca E. Ibach

2005-01-01

There are numerous biological degradations that wood is exposed to in various environments. Biological damage occurs when a log, sawn product, or final product is not stored, handled, or designed properly. Biological organisms, such as bacteria, mold, stain, decay fungi, insects, and marine borers, depend heavily on temperature and moisture conditions to grow. A higher...

[Anoxic bioremediation of urban polluted river water with biofilm].

PubMed

Zhang, Yong-Ming; Hu, Yi-Zhen; Yan, Rong; Liu, Fang

2009-07-15

Reactor like oxidation ditch was used for anaerobic bioremediation of urban river water, in which biofilm formed on ceramic honeycomb carrier was used instated of activated sludge. The dissolved oxygen in the wastewater was controlled under 0.5 mg/L for anoxic oxidation, and ammonia nitrogen was removed 40 to 60 percent, and total nitrogen removed 40 to 45 percent, that is ammonia nitrogen and total nitrogen were removed at the same time, also, nitrite was not any accumulated during the process. The biofilm was taken into flask to culture under anoxic oxidation condition in order to prove if anaerobic ammonium oxidation (ANAMMOX) occurred in the process, and ammonia and nitrite nitrogen were also removed at the same time in the experiment, which suggested that nitrification-denitrification and ANAMMOX occurred in bioremediation of urban surface water with low ratio of carbon and nitrogen at the same time. The anammox bacteria were existed in the biofilm according to molecular biological analysis. The experiment will be significant for bioremediation of eutrophication water body.

Prions, amyloids, and RNA: Pieces of a puzzle.

PubMed

Nizhnikov, Anton A; Antonets, Kirill S; Bondarev, Stanislav A; Inge-Vechtomov, Sergey G; Derkatch, Irina L

2016-05-03

Amyloids are protein aggregates consisting of fibrils rich in β-sheets. Growth of amyloid fibrils occurs by the addition of protein molecules to the tip of an aggregate with a concurrent change of a conformation. Thus, amyloids are self-propagating protein conformations. In certain cases these conformations are transmissible / infectious; they are known as prions. Initially, amyloids were discovered as pathological extracellular deposits occurring in different tissues and organs. To date, amyloids and prions have been associated with over 30 incurable diseases in humans and animals. However, a number of recent studies demonstrate that amyloids are also functionally involved in a variety of biological processes, from biofilm formation by bacteria, to long-term memory in animals. Interestingly, amyloid-forming proteins are highly overrepresented among cellular factors engaged in all stages of mRNA life cycle: from transcription and translation, to storage and degradation. Here we review rapidly accumulating data on functional and pathogenic amyloids associated with mRNA processing, and discuss possible significance of prion and amyloid networks in the modulation of key cellular functions.

Causes of the great mass extinction of marine organisms in the Late Devonian

NASA Astrophysics Data System (ADS)

Barash, M. S.

2016-11-01

The second of the five great mass extinctions of the Phanerozoic occurred in the Late Devonian. The number of species decreased by 70-82%. Major crises occurred at the Frasnian-Famennian and Devonian-Carboniferous boundary. The lithological and geochemical compositions of sediments, volcanic deposits, impactites, carbon and oxygen isotope ratios, evidence of climate variability, and sea level changes reflect the processes that led the critical conditions. Critical intervals are marked by layers of black shales, which were deposited in euxinic or anoxic environments. These conditions were the main direct causes of the extinctions. The Late Devonian mass extinction was determined by a combination of impact events and extensive volcanism. They produced similar effects: emissions of harmful chemical compounds and aerosols to cause greenhouse warming; darkening of the atmosphere, which prevented photosynthesis; and stagnation of oceans and development of anoxia. Food chains collapsed and biological productivity decreased. As a result, all vital processes were disturbed and a large portion of the biota became extinct.

Time-resolved observation of protein allosteric communication

PubMed Central

Buchenberg, Sebastian; Sittel, Florian; Stock, Gerhard

2017-01-01

Allostery represents a fundamental mechanism of biological regulation that is mediated via long-range communication between distant protein sites. Although little is known about the underlying dynamical process, recent time-resolved infrared spectroscopy experiments on a photoswitchable PDZ domain (PDZ2S) have indicated that the allosteric transition occurs on multiple timescales. Here, using extensive nonequilibrium molecular dynamics simulations, a time-dependent picture of the allosteric communication in PDZ2S is developed. The simulations reveal that allostery amounts to the propagation of structural and dynamical changes that are genuinely nonlinear and can occur in a nonlocal fashion. A dynamic network model is constructed that illustrates the hierarchy and exceeding structural heterogeneity of the process. In compelling agreement with experiment, three physically distinct phases of the time evolution are identified, describing elastic response (≲0.1 ns), inelastic reorganization (∼100 ns), and structural relaxation (≳1μs). Issues such as the similarity to downhill folding as well as the interpretation of allosteric pathways are discussed. PMID:28760989

Biological markers from Green River kerogen decomposition

NASA Astrophysics Data System (ADS)

Burnham, A. K.; Clarkson, J. E.; Singleton, M. F.; Wong, C. M.; Crawford, R. W.

1982-07-01

Isoprenoid and other carbon skeletons that are formed in living organisms and preserved essentially intact in ancient sediments are often called biological markers. The purpose of this paper is to develop improved methods of using isoprenoid hydrocarbons to relate petroleum or shale oil to its source rock. It is demonstrated that most, but not all, of the isoprenoid hydrocarbon structures are chemically bonded in kerogen (or to minerals) in Green River oil shale. The rate constant for thermally producing isoprenoid, cyclic, and aromatic hydrocarbons is substantially greater than for the bulk of shale oil. This may be related to the substantial quantity of CO 2 which is evolved coincident with the isoprenoid hydrocarbons but prior to substantial oil evolution. Although formation of isoprenoid alkenes is enhanced by rapid heating and high pyrolysis temperatures, the ratio of isoprenoid alkenes plus alkanes to normal alkenes plus alkanes is independent of heating rate. High-temperature laboratory pyrolysis experiments can thus be used to predict the distribution of aliphatic hydrocarbons in low temperature processes such as in situ shale oil production and perhaps petroleum formation. Finally, we demonstrate that significant variation in biological marker ratios occurs as a function of stratigraphy in the Green River formation. This information, combined with methods for measuring process yield from oil composition, enables one to relate time-dependent processing conditions to the corresponding time-dependent oil yield in a vertical modified- in situ retort even if there is a substantial and previously undetermined delay in drainage of shale oil from the retort.

Impact of TiO2 on the chemical and biological transformation of formulated chiral-metalaxyl in agricultural soils.

PubMed

Huang, Junxing; Zhang, Xu; Liang, Chuanzhou; Hu, Jun

2018-04-15

The impacts of TiO 2 on the chemical and biological transformation of racemic metalaxyl wettable powder (rac-metalaxyl WP) in agricultural soils, and soil microorganisms were investigated. Under simulated solar irradiation, TiO 2 highly promoted the transformation of rac-metalaxyl WP without changing the enantiomer fraction, with the promotion amplitude (60-1280%) being dependent on TiO 2 characteristics. TiO 2 characteristics showed different influence on the transformation of rac-metalaxyl WP in soils and aqueous solutions because their characteristics changed differently in soils. The impact of the mancozeb and other co-constituents on the transformation of rac-metalaxyl WP was smaller in soil media than in aqueous solution. Autoclave sterilization changed soil properties and subsequently weakened the promotion effects of TiO 2 on the chemical transformations of rac-metalaxyl WP to 0-233%. Microorganism biomass and bacterial community were not statistically significant changed by TiO 2 exposure regardless of rac-metalaxyl WP, suggesting that the promotional effects occurred mainly through chemical processes. The results also showed TiO 2 -soil interactions may be strengthened with TiO 2 (Degussa P25) aging time in soils, which decreased its promotion amplitude from 1060% (without aging) to 880% (aging for 20 days). Intermediate formed in soil biological transformation process was different from that in TiO 2 photocatalysis process. Copyright © 2018 Elsevier B.V. All rights reserved.

Biology-inspired AMO physics

NASA Astrophysics Data System (ADS)

Mathur, Deepak

2015-01-01

This Topical Review presents an overview of increasingly robust interconnects that are being established between atomic, molecular and optical (AMO) physics and the life sciences. AMO physics, outgrowing its historical role as a facilitator—a provider of optical methodologies, for instance—now seeks to partner biology in its quest to link systems-level descriptions of biological entities to insights based on molecular processes. Of course, perspectives differ when AMO physicists and biologists consider various processes. For instance, while AMO physicists link molecular properties and dynamics to potential energy surfaces, these have to give way to energy landscapes in considerations of protein dynamics. But there are similarities also: tunnelling and non-adiabatic transitions occur both in protein dynamics and in molecular dynamics. We bring to the fore some such differences and similarities; we consider imaging techniques based on AMO concepts, like 4D fluorescence microscopy which allows access to the dynamics of cellular processes, multiphoton microscopy which offers a built-in confocality, and microscopy with femtosecond laser beams to saturate the suppression of fluorescence in spatially controlled fashion so as to circumvent the diffraction limit. Beyond imaging, AMO physics contributes with optical traps that probe the mechanical and dynamical properties of single ‘live’ cells, highlighting differences between healthy and diseased cells. Trap methodologies have also begun to probe the dynamics governing of neural stem cells adhering to each other to form neurospheres and, with squeezed light to probe sub-diffusive motion of yeast cells. Strong field science contributes not only by providing a source of energetic electrons and γ-rays via laser-plasma accelerations schemes, but also via filamentation and supercontinuum generation, enabling mainstream collision physics into play in diverse processes like DNA damage induced by low-energy collisions to invoking dissociative attachment in quantification of stress levels in humans. The prognosis is extremely good for more intense interaction of AMO physics and biology; by way of future predictions attention is drawn to only two of very many opportunities for such interactions: application of attosecond techniques and tunnelling experiments to biological problems.

Animal models and conserved processes

PubMed Central

2012-01-01

Background The concept of conserved processes presents unique opportunities for using nonhuman animal models in biomedical research. However, the concept must be examined in the context that humans and nonhuman animals are evolved, complex, adaptive systems. Given that nonhuman animals are examples of living systems that are differently complex from humans, what does the existence of a conserved gene or process imply for inter-species extrapolation? Methods We surveyed the literature including philosophy of science, biological complexity, conserved processes, evolutionary biology, comparative medicine, anti-neoplastic agents, inhalational anesthetics, and drug development journals in order to determine the value of nonhuman animal models when studying conserved processes. Results Evolution through natural selection has employed components and processes both to produce the same outcomes among species but also to generate different functions and traits. Many genes and processes are conserved, but new combinations of these processes or different regulation of the genes involved in these processes have resulted in unique organisms. Further, there is a hierarchy of organization in complex living systems. At some levels, the components are simple systems that can be analyzed by mathematics or the physical sciences, while at other levels the system cannot be fully analyzed by reducing it to a physical system. The study of complex living systems must alternate between focusing on the parts and examining the intact whole organism while taking into account the connections between the two. Systems biology aims for this holism. We examined the actions of inhalational anesthetic agents and anti-neoplastic agents in order to address what the characteristics of complex living systems imply for inter-species extrapolation of traits and responses related to conserved processes. Conclusion We conclude that even the presence of conserved processes is insufficient for inter-species extrapolation when the trait or response being studied is located at higher levels of organization, is in a different module, or is influenced by other modules. However, when the examination of the conserved process occurs at the same level of organization or in the same module, and hence is subject to study solely by reductionism, then extrapolation is possible. PMID:22963674

B. F. Skinner and G. H. Mead: on biological science and social science.

PubMed Central

Blackman, D E

1991-01-01

Skinner's contributions to psychology provide a unique bridge between psychology conceptualized as a biological science and psychology conceptualized as a social science. Skinner focused on behavior as a naturally occurring biological phenomenon of interest in its own right, functionally related to surrounding events and, in particular (like phylogenesis), subject to selection by its consequences. This essentially biological orientation was further enhanced by Skinner's emphasis on the empirical foundations provided by laboratory-based experimental analyses of behavior, often with nonhuman subjects. Skinner's theoretical writings, however, also have affinity with the traditions of constructionist social science. The verbal behavior of humans is said to be subject, like other behavior, to functional analyses in terms of its environment, in this case its social context. Verbal behavior in turn makes it possible for us to relate to private events, a process that ultimately allows for the development of consciousness, which is thus said to be a social product. Such ideas make contact with aspects of G. H. Mead's social behaviorism and, perhaps of more contemporary impact in psychology, L. Vygotsky's general genetic law of cultural development. Failure to articulate both the biological and the social science aspects of Skinner's theoretical approach to psychology does a disservice to his unique contribution to a discipline that remains fragmented between two intellectual traditions. PMID:2037828

A decontamination study of simulated chemical and biological agents

NASA Astrophysics Data System (ADS)

Uhm, Han S.; Lee, Han Y.; Hong, Yong C.; Shin, Dong H.; Park, Yun H.; Hong, Yi F.; Lee, Chong K.

2007-07-01

A comprehensive decontamination scheme of the chemical and biological agents, including airborne agents and surface contaminating agents, is presented. When a chemical and biological attack occurs, it is critical to decontaminate facilities or equipments to an acceptable level in a very short time. The plasma flame presented here may provide a rapid and effective elimination of toxic substances in the interior air in isolated spaces. As an example, a reaction chamber, with the dimensions of a 22cm diameter and 30cm length, purifies air with an airflow rate of 5000l/min contaminated with toluene, the simulated chemical agent, and soot from a diesel engine, the simulated aerosol for biological agents. Although the airborne agents in an isolated space are eliminated to an acceptable level by the plasma flame, the decontamination of the chemical and biological agents cannot be completed without cleaning surfaces of the facilities. A simulated sterilization study of micro-organisms was carried out using the electrolyzed ozone water. The electrolyzed ozone water very effectively kills endospores of Bacillus atrophaeus (ATCC 9372) within 3min. The electrolyzed ozone water also kills the vegetative micro-organisms, fungi, and virus. The electrolyzed ozone water, after the decontamination process, disintegrates into ordinary water and oxygen without any trace of harmful materials to the environment.

Soluble Epidermal Growth Factor Receptors (sEGFRs) in Cancer: Biological Aspects and Clinical Relevance.

PubMed

Maramotti, Sally; Paci, Massimiliano; Manzotti, Gloria; Rapicetta, Cristian; Gugnoni, Mila; Galeone, Carla; Cesario, Alfredo; Lococo, Filippo

2016-04-19

The identification of molecules that can reliably detect the presence of a tumor or predict its behavior is one of the biggest challenges of research in cancer biology. Biological fluids are intriguing mediums, containing many molecules that express the individual health status and, accordingly, may be useful in establishing the potential risk of cancer, defining differential diagnosis and prognosis, predicting the response to treatment, and monitoring the disease progression. The existence of circulating soluble growth factor receptors (sGFRs) deriving from their membrane counterparts has stimulated the interest of researchers to investigate the use of such molecules as potential cancer biomarkers. But what are the origins of circulating sGFRs? Are they naturally occurring molecules or tumor-derived products? Among these, the epidermal growth factor receptor (EGFR) is a cell-surface molecule significantly involved in cancer development and progression; it can be processed into biological active soluble isoforms (sEGFR). We have carried out an extensive review of the currently available literature on the sEGFRs and their mechanisms of regulation and biological function, with the intent to clarify the role of these molecules in cancer (and other pathological conditions) and, on the basis of the retrieved evidences, speculate about their potential use in the clinical setting.

Space and time-resolved probing of heterogeneous catalysis reactions using lab-on-a-chip

NASA Astrophysics Data System (ADS)

Navin, Chelliah V.; Krishna, Katla Sai; Theegala, Chandra S.; Kumar, Challa S. S. R.

2016-03-01

Probing catalytic reactions on a catalyst surface in real time is a major challenge. Herein, we demonstrate the utility of a continuous flow millifluidic chip reactor coated with a nanostructured gold catalyst as an effective platform for in situ investigation of the kinetics of catalytic reactions by taking 5-(hydroxymethyl)furfural (HMF) to 2,5-furandicarboxylic acid (FDCA) conversion as a model reaction. The idea conceptualized in this paper can not only dramatically change the ability to probe the time-resolved kinetics of heterogeneous catalysis reactions but also used for investigating other chemical and biological catalytic processes, thereby making this a broad platform for probing reactions as they occur within continuous flow reactors.Probing catalytic reactions on a catalyst surface in real time is a major challenge. Herein, we demonstrate the utility of a continuous flow millifluidic chip reactor coated with a nanostructured gold catalyst as an effective platform for in situ investigation of the kinetics of catalytic reactions by taking 5-(hydroxymethyl)furfural (HMF) to 2,5-furandicarboxylic acid (FDCA) conversion as a model reaction. The idea conceptualized in this paper can not only dramatically change the ability to probe the time-resolved kinetics of heterogeneous catalysis reactions but also used for investigating other chemical and biological catalytic processes, thereby making this a broad platform for probing reactions as they occur within continuous flow reactors. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06752a

An autonomous chemically fuelled small-molecule motor

NASA Astrophysics Data System (ADS)

Wilson, Miriam R.; Solà, Jordi; Carlone, Armando; Goldup, Stephen M.; Lebrasseur, Nathalie; Leigh, David A.

2016-06-01

Molecular machines are among the most complex of all functional molecules and lie at the heart of nearly every biological process. A number of synthetic small-molecule machines have been developed, including molecular muscles, synthesizers, pumps, walkers, transporters and light-driven and electrically driven rotary motors. However, although biological molecular motors are powered by chemical gradients or the hydrolysis of adenosine triphosphate (ATP), so far there are no synthetic small-molecule motors that can operate autonomously using chemical energy (that is, the components move with net directionality as long as a chemical fuel is present). Here we describe a system in which a small molecular ring (macrocycle) is continuously transported directionally around a cyclic molecular track when powered by irreversible reactions of a chemical fuel, 9-fluorenylmethoxycarbonyl chloride. Key to the design is that the rate of reaction of this fuel with reactive sites on the cyclic track is faster when the macrocycle is far from the reactive site than when it is near to it. We find that a bulky pyridine-based catalyst promotes carbonate-forming reactions that ratchet the displacement of the macrocycle away from the reactive sites on the track. Under reaction conditions where both attachment and cleavage of the 9-fluorenylmethoxycarbonyl groups occur through different processes, and the cleavage reaction occurs at a rate independent of macrocycle location, net directional rotation of the molecular motor continues for as long as unreacted fuel remains. We anticipate that autonomous chemically fuelled molecular motors will find application as engines in molecular nanotechnology.

Ecohydrologic processes and soil thickness feedbacks control limestone-weathering rates in a karst landscape

DOE PAGES

Dong, Xiaoli; Cohen, Matthew J.; Martin, Jonathan B.; ...

2018-05-18

Here, chemical weathering of bedrock plays an essential role in the formation and evolution of Earth's critical zone. Over geologic time, the negative feedback between temperature and chemical weathering rates contributes to the regulation of Earth climate. The challenge of understanding weathering rates and the resulting evolution of critical zone structures lies in complicated interactions and feedbacks among environmental variables, local ecohydrologic processes, and soil thickness, the relative importance of which remains unresolved. We investigate these interactions using a reactive-transport kinetics model, focusing on a low-relief, wetland-dominated karst landscape (Big Cypress National Preserve, South Florida, USA) as a case study.more » Across a broad range of environmental variables, model simulations highlight primary controls of climate and soil biological respiration, where soil thickness both supplies and limits transport of biologically derived acidity. Consequently, the weathering rate maximum occurs at intermediate soil thickness. The value of the maximum weathering rate and the precise soil thickness at which it occurs depend on several environmental variables, including precipitation regime, soil inundation, vegetation characteristics, and rate of groundwater drainage. Simulations for environmental conditions specific to Big Cypress suggest that wetland depressions in this landscape began to form around beginning of the Holocene with gradual dissolution of limestone bedrock and attendant soil development, highlighting large influence of age-varying soil thickness on weathering rates and consequent landscape development. While climatic variables are often considered most important for chemical weathering, our results indicate that soil thickness and biotic activity are equally important. Weathering rates reflect complex interactions among soil thickness, climate, and local hydrologic and biotic processes, which jointly shape the supply and delivery of chemical reactants, and the resulting trajectories of critical zone and karst landscape development.« less

Ecohydrologic processes and soil thickness feedbacks control limestone-weathering rates in a karst landscape

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

Dong, Xiaoli; Cohen, Matthew J.; Martin, Jonathan B.

Here, chemical weathering of bedrock plays an essential role in the formation and evolution of Earth's critical zone. Over geologic time, the negative feedback between temperature and chemical weathering rates contributes to the regulation of Earth climate. The challenge of understanding weathering rates and the resulting evolution of critical zone structures lies in complicated interactions and feedbacks among environmental variables, local ecohydrologic processes, and soil thickness, the relative importance of which remains unresolved. We investigate these interactions using a reactive-transport kinetics model, focusing on a low-relief, wetland-dominated karst landscape (Big Cypress National Preserve, South Florida, USA) as a case study.more » Across a broad range of environmental variables, model simulations highlight primary controls of climate and soil biological respiration, where soil thickness both supplies and limits transport of biologically derived acidity. Consequently, the weathering rate maximum occurs at intermediate soil thickness. The value of the maximum weathering rate and the precise soil thickness at which it occurs depend on several environmental variables, including precipitation regime, soil inundation, vegetation characteristics, and rate of groundwater drainage. Simulations for environmental conditions specific to Big Cypress suggest that wetland depressions in this landscape began to form around beginning of the Holocene with gradual dissolution of limestone bedrock and attendant soil development, highlighting large influence of age-varying soil thickness on weathering rates and consequent landscape development. While climatic variables are often considered most important for chemical weathering, our results indicate that soil thickness and biotic activity are equally important. Weathering rates reflect complex interactions among soil thickness, climate, and local hydrologic and biotic processes, which jointly shape the supply and delivery of chemical reactants, and the resulting trajectories of critical zone and karst landscape development.« less

Drivers of inverse DOC-nitrate loss patterns in forest soils and streams

NASA Astrophysics Data System (ADS)

Goodale, C. L.

2013-12-01

Nitrate loss from forested catchments varies greatly across sites and over time, with few reliable correlates. One of the few recurring patterns, however, is the negative nonlinear relationship that occurs regularly between surface water nitrate and dissolved organic carbon (DOC) concentrations: that is, nitrate declines sharply as DOC concentrations increase, and high nitrate levels occur only at low DOC concentrations. Several hypotheses have been proposed to explain this pattern, but its cause has remained speculative. It is likely to be driven by C- or N-limitation of biological processes such as assimilation or denitrification, but the identity of which biological process or the main landscape position of their activity are not known. We examined whether DOC and nitrate are both driven by soil C content, at scales of both soil blocks and across catchments, by measuring soil, soil extract, and surface water chemistry across nine catchments selected from long-term monitoring networks in the Catskill and Adirondack Mountains. We measured soil C and N status and solution nitrate, DOC, bioavailable DOC (bDOC), and isotopic composition (13C-DOC, 15N- and 18O-NO3) to examine whether variation in stocks of soil C partly controls DOC and nitrate loss from forested catchments in New York State. These measurements showed that surface soil C and C:N ratio together determine soil production of DOC and nitrate, reflecting assimilative demand for N by heterotrophic microbes. Yet, they also show that these processes do not produce the inverse DOC-NO3 curve observed at the catchment scale. Rather, catchment-scale DOC-nitrate patterns are more likely to be governed by the balance between excess nitrate production and its bDOC-mediated loss to denitrification.

Novel method of extracting motion from natural movies.

PubMed

Suzuki, Wataru; Ichinohe, Noritaka; Tani, Toshiki; Hayami, Taku; Miyakawa, Naohisa; Watanabe, Satoshi; Takeichi, Hiroshige

2017-11-01

The visual system in primates can be segregated into motion and shape pathways. Interaction occurs at multiple stages along these pathways. Processing of shape-from-motion and biological motion is considered to be a higher-order integration process involving motion and shape information. However, relatively limited types of stimuli have been used in previous studies on these integration processes. We propose a new algorithm to extract object motion information from natural movies and to move random dots in accordance with the information. The object motion information is extracted by estimating the dynamics of local normal vectors of the image intensity projected onto the x-y plane of the movie. An electrophysiological experiment on two adult common marmoset monkeys (Callithrix jacchus) showed that the natural and random dot movies generated with this new algorithm yielded comparable neural responses in the middle temporal visual area. In principle, this algorithm provided random dot motion stimuli containing shape information for arbitrary natural movies. This new method is expected to expand the neurophysiological and psychophysical experimental protocols to elucidate the integration processing of motion and shape information in biological systems. The novel algorithm proposed here was effective in extracting object motion information from natural movies and provided new motion stimuli to investigate higher-order motion information processing. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Importance of vesicle release stochasticity in neuro-spike communication.

PubMed

Ramezani, Hamideh; Akan, Ozgur B

2017-07-01

Aim of this paper is proposing a stochastic model for vesicle release process, a part of neuro-spike communication. Hence, we study biological events occurring in this process and use microphysiological simulations to observe functionality of these events. Since the most important source of variability in vesicle release probability is opening of voltage dependent calcium channels (VDCCs) followed by influx of calcium ions through these channels, we propose a stochastic model for this event, while using a deterministic model for other variability sources. To capture the stochasticity of calcium influx to pre-synaptic neuron in our model, we study its statistics and find that it can be modeled by a distribution defined based on Normal and Logistic distributions.

To Replay, Perchance to Consolidate

PubMed Central

Genzel, Lisa; Robertson, Edwin M.

2015-01-01

After a memory is formed, it continues to be processed by the brain. These “off-line” processes consolidate the memory, leading to its enhancement and to changes in memory circuits. Potentially, these memory changes are driven by off-line replay of the pattern of neuronal activity present when the memory was being formed. A new study by Dhaksin Ramanathan and colleagues, published in PLOS Biology, demonstrates that replay occurs predominately after the acquisition of a new motor skill and that it is related to changes in memory performance and to the subsequent changes in memory circuits. Together, these observations reveal the importance of neuronal replay in the consolidation of novel motor skills. PMID:26496145

40 CFR 63.138 - Process wastewater provisions-performance standards for treatment processes managing Group 1...

Code of Federal Regulations, 2010 CFR

2010-07-01

.../or Table 9 compounds are similar and often identical. (3) Biological treatment processes. Biological treatment processes in compliance with this section may be either open or closed biological treatment processes as defined in § 63.111. An open biological treatment process in compliance with this section need...

Research About the Corosive Effects of FeCl3 in the Aeration Wastewater Basin

NASA Astrophysics Data System (ADS)

Panaitescu, C.; Petrescu, M. G.

2018-01-01

Biological aeration of industrial wastewater is a very impressive process in the treatment of wastewater. The involvement of chemical reagents in this process, however, implies the intensification of the corrosion processes due to both pollutants in the wastewater and the chemical reactions that occur when the coagulation / flocculation reagents are added. This paper explores the action of ferric chloride (FeCl3) on metallic parts in the aeration basin. The most affected structures are metal. At the classical basins the aeration systems were made of P295GH materials. The corrosion produced is uneven. The analysis of the high degree of corrosion was done according to the national and international standards. Finally, the paper supports the replacement of the existing aeration system with an anticorrosive material.

Oxidation of artificial sweetener sucralose by advanced oxidation processes: a review.

PubMed

Sharma, Virender K; Oturan, Mehmet; Kim, Hyunook

2014-01-01

Sucralose, a chlorinated carbohydrate, has shown its increased use as an artificial sweetener and persistently exists in wastewater treatment plant effluents and aquatic environment. This paper aims to review possible degradation of sucralose and related carbohydrates by biological, electrochemical, chemical, and advanced oxidation processes. Biodegradation of sucralose in waterworks did not occur significantly. Electrochemical oxidation of carbohydrates may be applied to seek degradation of sucralose. The kinetics of the oxidation of sucralose and the related carbohydrates by different oxidative species is compared. Free chlorine, ozone, and ferrate did not show any potential to degrade sucralose in water. Advanced oxidation processes, generating highly strong oxidizing agent hydroxyl radicals ((•)OH), have demonstrated effectiveness in transforming sucralose in water. The mechanism of oxidation of sucralose by (•)OH is briefly discussed.

COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets

PubMed Central

Lohmann, Ingrid

2012-01-01

In multi-cellular organisms, spatiotemporal activity of cis-regulatory DNA elements depends on their occupancy by different transcription factors (TFs). In recent years, genome-wide ChIP-on-Chip, ChIP-Seq and DamID assays have been extensively used to unravel the combinatorial interaction of TFs with cis-regulatory modules (CRMs) in the genome. Even though genome-wide binding profiles are increasingly becoming available for different TFs, single TF binding profiles are in most cases not sufficient for dissecting complex regulatory networks. Thus, potent computational tools detecting statistically significant and biologically relevant TF-motif co-occurrences in genome-wide datasets are essential for analyzing context-dependent transcriptional regulation. We have developed COPS (Co-Occurrence Pattern Search), a new bioinformatics tool based on a combination of association rules and Markov chain models, which detects co-occurring TF binding sites (BSs) on genomic regions of interest. COPS scans DNA sequences for frequent motif patterns using a Frequent-Pattern tree based data mining approach, which allows efficient performance of the software with respect to both data structure and implementation speed, in particular when mining large datasets. Since transcriptional gene regulation very often relies on the formation of regulatory protein complexes mediated by closely adjoining TF binding sites on CRMs, COPS additionally detects preferred short distance between co-occurring TF motifs. The performance of our software with respect to biological significance was evaluated using three published datasets containing genomic regions that are independently bound by several TFs involved in a defined biological process. In sum, COPS is a fast, efficient and user-friendly tool mining statistically and biologically significant TFBS co-occurrences and therefore allows the identification of TFs that combinatorially regulate gene expression. PMID:23272209

Intracellular Cadmium Isotope Fractionation

NASA Astrophysics Data System (ADS)

Horner, T. J.; Lee, R. B.; Henderson, G. M.; Rickaby, R. E.

2011-12-01

Recent stable isotope studies into the biological utilization of transition metals (e.g. Cu, Fe, Zn, Cd) suggest several stepwise cellular processes can fractionate isotopes in both culture and nature. However, the determination of fractionation factors is often unsatisfactory, as significant variability can exist - even between different organisms with the same cellular functions. Thus, it has not been possible to adequately understand the source and mechanisms of metal isotopic fractionation. In order to address this problem, we investigated the biological fractionation of Cd isotopes within genetically-modified bacteria (E. coli). There is currently only one known biological use or requirement of Cd, a Cd/Zn carbonic anhydrase (CdCA, from the marine diatom T. weissfloggii), which we introduce into the E. coli genome. We have also developed a cleaning procedure that allows for the treating of bacteria so as to study the isotopic composition of different cellular components. We find that whole cells always exhibit a preference for uptake of the lighter isotopes of Cd. Notably, whole cells appear to have a similar Cd isotopic composition regardless of the expression of CdCA within the E. coli. However, isotopic fractionation can occur within the genetically modified E. coli during Cd use, such that Cd bound in CdCA can display a distinct isotopic composition compared to the cell as a whole. Thus, the externally observed fractionation is independent of the internal uses of Cd, with the largest Cd isotope fractionation occurring during cross-membrane transport. A general implication of these experiments is that trace metal isotopic fractionation most likely reflects metal transport into biological cells (either actively or passively), rather than relating to expression of specific physiological function and genetic expression of different metalloenzymes.

A belowground perspective on the drought sensitivity of forests: Towards improved understanding and simulation

DOE PAGES

Phillips, Richard P.; Ibanez, Ines; D’Orangeville, Loic; ...

2016-09-13

Predicted increases in the frequency and intensity of droughts across the temperate biome have highlighted the need to examine the extent to which forests may differ in their sensitivity to water stress. At present, a rich body of literature exists on how leaf- and stem-level physiology influence tree drought responses; however, less is known regarding the dynamic interactions that occur below ground between roots and soil physical and biological factors. Hence, there is a need to better understand how and why processes occurring below ground influence forest sensitivity to drought. Here, we review what is known about tree species’ belowmore » ground strategies for dealing with drought, and how physical and biological characteristics of soils interact with rooting strategies to influence forest sensitivity to drought. Then, we highlight how a below ground perspective of drought can be used in models to reduce uncertainty in predicting the ecosystem consequences of droughts in forests. Lastly, we describe the challenges and opportunities associated with managing forests under conditions of increasing drought frequency and intensity, and explain how a below ground perspective on drought may facilitate improved forest management.« less

A belowground perspective on the drought sensitivity of forests: Towards improved understanding and simulation

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

Phillips, Richard P.; Ibanez, Ines; D’Orangeville, Loic

Predicted increases in the frequency and intensity of droughts across the temperate biome have highlighted the need to examine the extent to which forests may differ in their sensitivity to water stress. At present, a rich body of literature exists on how leaf- and stem-level physiology influence tree drought responses; however, less is known regarding the dynamic interactions that occur below ground between roots and soil physical and biological factors. Hence, there is a need to better understand how and why processes occurring below ground influence forest sensitivity to drought. Here, we review what is known about tree species’ belowmore » ground strategies for dealing with drought, and how physical and biological characteristics of soils interact with rooting strategies to influence forest sensitivity to drought. Then, we highlight how a below ground perspective of drought can be used in models to reduce uncertainty in predicting the ecosystem consequences of droughts in forests. Lastly, we describe the challenges and opportunities associated with managing forests under conditions of increasing drought frequency and intensity, and explain how a below ground perspective on drought may facilitate improved forest management.« less

On the role of the plasmodial cytoskeleton in facilitating intelligent behavior in slime mold Physarum polycephalum

PubMed Central

Mayne, Richard; Adamatzky, Andrew; Jones, Jeff

2015-01-01

The plasmodium of slime mold Physarum polycephalum behaves as an amorphous reaction-diffusion computing substrate and is capable of apparently ‘intelligent’ behavior. But how does intelligence emerge in an acellular organism? Through a range of laboratory experiments, we visualize the plasmodial cytoskeleton—a ubiquitous cellular protein scaffold whose functions are manifold and essential to life—and discuss its putative role as a network for transducing, transmitting and structuring data streams within the plasmodium. Through a range of computer modeling techniques, we demonstrate how emergent behavior, and hence computational intelligence, may occur in cytoskeletal communications networks. Specifically, we model the topology of both the actin and tubulin cytoskeletal networks and discuss how computation may occur therein. Furthermore, we present bespoke cellular automata and particle swarm models for the computational process within the cytoskeleton and observe the incidence of emergent patterns in both. Our work grants unique insight into the origins of natural intelligence; the results presented here are therefore readily transferable to the fields of natural computation, cell biology and biomedical science. We conclude by discussing how our results may alter our biological, computational and philosophical understanding of intelligence and consciousness. PMID:26478782

On the role of the plasmodial cytoskeleton in facilitating intelligent behavior in slime mold Physarum polycephalum.

PubMed

Mayne, Richard; Adamatzky, Andrew; Jones, Jeff

2015-01-01

The plasmodium of slime mold Physarum polycephalum behaves as an amorphous reaction-diffusion computing substrate and is capable of apparently 'intelligent' behavior. But how does intelligence emerge in an acellular organism? Through a range of laboratory experiments, we visualize the plasmodial cytoskeleton-a ubiquitous cellular protein scaffold whose functions are manifold and essential to life-and discuss its putative role as a network for transducing, transmitting and structuring data streams within the plasmodium. Through a range of computer modeling techniques, we demonstrate how emergent behavior, and hence computational intelligence, may occur in cytoskeletal communications networks. Specifically, we model the topology of both the actin and tubulin cytoskeletal networks and discuss how computation may occur therein. Furthermore, we present bespoke cellular automata and particle swarm models for the computational process within the cytoskeleton and observe the incidence of emergent patterns in both. Our work grants unique insight into the origins of natural intelligence; the results presented here are therefore readily transferable to the fields of natural computation, cell biology and biomedical science. We conclude by discussing how our results may alter our biological, computational and philosophical understanding of intelligence and consciousness.

Chapter 5:Biological Properties of Wood

Treesearch

Rebecca E. Ibach

2013-01-01

There are numerous biological degradations that wood is exposed to in various environments. Biological damage occurs when a log, sawn product, or final product is not stored, handled, or designed properly. Biological organisms such as bacteria, mold, stain, decay fungi, insects, and marine borers depend heavily on temperature and moisture conditions to grow. Figure 5.1...

In search of mitochondrial mechanisms: interfield excursions between cell biology and biochemistry.

PubMed

Bechtel, William; Abrahamsen, Adele

2007-01-01

Developing models of biological mechanisms, such as those involved in respiration in cells, often requires collaborative effort drawing upon techniques developed and information generated in different disciplines. Biochemists in the early decades of the 20th century uncovered all but the most elusive chemical operations involved in cellular respiration, but were unable to align the reaction pathways with particular structures in the cell. During the period 1940-1965 cell biology was emerging as a new discipline and made distinctive contributions to understanding the role of the mitochondrion and its component parts in cellular respiration. In particular, by developing techniques for localizing enzymes or enzyme systems in specific cellular components, cell biologists provided crucial information about the organized structures in which the biochemical reactions occurred. Although the idea that biochemical operations are intimately related to and depend on cell structures was at odds with the then-dominant emphasis on systems of soluble enzymes in biochemistry, a reconceptualization of energetic processes in the 1960s and 1970s made it clear why cell structure was critical to the biochemical account. This paper examines how numerous excursions between biochemistry and cell biology contributed a new understanding of the mechanism of cellular respiration.

Cooperation in Harsh Environments and the Emergence of Spatial Patterns.

PubMed

Smaldino, Paul E

2013-11-01

This paper concerns the confluence of two important areas of research in mathematical biology: spatial pattern formation and cooperative dilemmas. Mechanisms through which social organisms form spatial patterns are not fully understood. Prior work connecting cooperation and pattern formation has often included unrealistic assumptions that shed doubt on the applicability of those models toward understanding real biological patterns. I investigated a more biologically realistic model of cooperation among social actors. The environment is harsh, so that interactions with cooperators are strictly needed to survive. Harshness is implemented via a constant energy deduction. I show that this model can generate spatial patterns similar to those seen in many naturally-occuring systems. Moreover, for each payoff matrix there is an associated critical value of the energy deduction that separates two distinct dynamical processes. In low-harshness environments, the growth of cooperator clusters is impeded by defectors, but these clusters gradually expand to form dense dendritic patterns. In very harsh environments, cooperators expand rapidly but defectors can subsequently make inroads to form reticulated patterns. The resulting web-like patterns are reminiscent of transportation networks observed in slime mold colonies and other biological systems.

Why are living things sensitive to weak magnetic fields?

PubMed

Liboff, Abraham R

2014-09-01

There is evidence for robust interactions of weak ELF magnetic fields with biological systems. Quite apart from the difficulties attending a proper physical basis for such interactions, an equally daunting question asks why these should even occur, given the apparent lack of comparable signals in the long-term electromagnetic environment. We suggest that the biological basis is likely to be found in the weak (∼50 nT) daily swing in the geomagnetic field that results from the solar tidal force on free electrons in the upper atmosphere, a remarkably constant effect exactly in phase with the solar diurnal change. Because this magnetic change is locked into the solar-derived everyday diurnal response in living things, one can argue that it acts as a surrogate for the solar variation, and therefore plays a role in chronobiological processes. This implies that weak magnetic field interactions may have a chronodisruptive basis, homologous to the more familiar effects on the biological clock arising from sleep deprivation, phase-shift employment and light at night. It is conceivable that the widespread sensitivity of biological systems to weak ELF magnetic fields is vestigially derived from this diurnal geomagnetic effect.

Ion implantation modified stainless steel as a substrate for hydroxyapatite deposition. Part I. Surface modification and characterization.

PubMed

Pramatarova, L; Pecheva, E; Krastev, V; Riesz, F

2007-03-01

Material surfaces play critical role in biology and medicine since most biological reactions occur on surfaces and interfaces. There are many examples showing that the surface properties of the materials control and are directly involved in biological reactions and processes in-vitro like blood compatibility, protein absorption, cell development, etc. The rules that govern the diversity of biological surface phenomenon are fundamental physical laws. Stainless steel doped with Cr, Ni and Mo is widely used material in medicine and dentistry due to its excellent corrosion resistance and mechanical properties. The interest in this material has stimulated extensive studies on improving its bone-bonding properties. This paper describes the surface modification of Cr-Ni stainless steel (AISI 316) by a whole surface sequential implantation of Ca and P ions (the basic ions of hydroxyapatite). Three groups of stainless steel samples are prepared: (i) ion-implanted, (ii) ion-implanted and thermally treated at 600( composite function)C in air for 1 h and (iii) initials. The surface chemistry and topography before and after the surface modification are characterized by X-ray photoelectron spectroscopy, Auger electron spectroscopy, magic mirror method, atomic force microscopy and contact angle measurements.

BRAIN REGENERATION IN PHYSIOLOGY AND PATHOLOGY: THE IMMUNE SIGNATURE DRIVING THERAPEUTIC PLASTICITY OF NEURAL STEM CELLS

PubMed Central

Martino, Gianvito; Pluchino, Stefano; Bonfanti, Luca; Schwartz, Michal

2013-01-01

Regenerative processes occurring under physiological (maintenance) and pathological (reparative) conditions are a fundamental part of life and vary greatly among different species, individuals, and tissues. Physiological regeneration occurs naturally as a consequence of normal cell erosion, or as an inevitable outcome of any biological process aiming at the restoration of homeostasis. Reparative regeneration occurs as a consequence of tissue damage. Although the central nervous system (CNS) has been considered for years as a “perennial” tissue, it has recently become clear that both physiological and reparative regeneration occur also within the CNS to sustain tissue homeostasis and repair. Proliferation and differentiation of neural stem/progenitor cells (NPCs) residing within the healthy CNS, or surviving injury, are considered crucial in sustaining these processes. Thus a large number of experimental stem cell-based transplantation systems for CNS repair have recently been established. The results suggest that transplanted NPCs promote tissue repair not only via cell replacement but also through their local contribution to changes in the diseased tissue milieu. This review focuses on the remarkable plasticity of endogenous and exogenous (transplanted) NPCs in promoting repair. Special attention will be given to the cross-talk existing between NPCs and CNS-resident microglia as well as CNS-infiltrating immune cells from the circulation, as a crucial event sustaining NPC-mediated neuroprotection. Finally, we will propose the concept of the context-dependent potency of transplanted NPCs (therapeutic plasticity) to exert multiple therapeutic actions, such as cell replacement, neurotrophic support, and immunomodulation, in CNS repair. PMID:22013212

A mechano-biological model of multi-tissue evolution in bone

NASA Astrophysics Data System (ADS)

Frame, Jamie; Rohan, Pierre-Yves; Corté, Laurent; Allena, Rachele

2017-12-01

Successfully simulating tissue evolution in bone is of significant importance in predicting various biological processes such as bone remodeling, fracture healing and osseointegration of implants. Each of these processes involves in different ways the permanent or transient formation of different tissue types, namely bone, cartilage and fibrous tissues. The tissue evolution in specific circumstances such as bone remodeling and fracturing healing is currently able to be modeled. Nevertheless, it remains challenging to predict which tissue types and organization can develop without any a priori assumptions. In particular, the role of mechano-biological coupling in this selective tissue evolution has not been clearly elucidated. In this work, a multi-tissue model has been created which simultaneously describes the evolution of bone, cartilage and fibrous tissues. The coupling of the biological and mechanical factors involved in tissue formation has been modeled by defining two different tissue states: an immature state corresponding to the early stages of tissue growth and representing cell clusters in a weakly neo-formed Extra Cellular Matrix (ECM), and a mature state corresponding to well-formed connective tissues. This has allowed for the cellular processes of migration, proliferation and apoptosis to be described simultaneously with the changing ECM properties through strain driven diffusion, growth, maturation and resorption terms. A series of finite element simulations were carried out on idealized cantilever bending geometries. Starting from a tissue composition replicating a mid-diaphysis section of a long bone, a steady-state tissue formation was reached over a statically loaded period of 10,000 h (60 weeks). The results demonstrated that bone formation occurred in regions which are optimally physiologically strained. In two additional 1000 h bending simulations both cartilaginous and fibrous tissues were shown to form under specific geometrical and loading cases and cartilage was shown to lead to the formation of bone in a beam replicating a fracture healing initial tissue distribution. This finding is encouraging in that it is corroborated by similar experimental observations of cartilage leading bone formation during the fracture healing process. The results of this work demonstrate that a multi-tissue mechano-biological model of tissue evolution has the potential for predictive analysis in the design and implementations of implants, describing fracture healing and bone remodeling processes.

Infusing Bioethics into Biology and Microbiology Courses and Curricula: A Vertical Approach

PubMed Central

Jagger, Kathleen S.; Furlong, Jack

2014-01-01

With the rise of biomedicine and biotechnology, there has been a corresponding growth in the need for better understanding of consequent ethical questions. Increasingly, biologists are being asked not only to offer technical clarifications but also to venture ethical opinions, for which most feel poorly equipped. This expectation puts pressure on biology instructors at the university level to provide biology majors the skills and experience to discuss with some confidence and competence bioethical issues which may arise in either the workplace or through public discourse in everyday contexts. Many fine curricular resources about bioethics are available for varied pedagogical purposes, but few target undergraduate biology or microbiology student audiences. When it occurs in the context of a course, bioethics instruction often is taught by non-biologists outside standard biology curricula. We propose that biologists should strive to “infuse” bioethical thinking into their courses and major curricula but not in such a way as merely to point at ethical problems, treating them at a surface level. We suggest what we call “vertical infusion”: taking one bioethical issue per course and integrating this issue within the context of a relevant biological topic, challenging students to push their thinking beyond their initial intuitions toward underlying scientific and ethical principles. While the vertical approach lacks widespread coverage of ethical issues throughout a single course, it has the advantage of taking the bioethical dimension seriously and in intimate relation to contemporary discoveries in biology and to the biological principles, processes, or procedures that occasioned the ethical quandaries in the first place. PMID:25574281

Investigations on potential bacteria for the bioremediation treatment of environments contaminated with hydrocarbons

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

Lazar, I.; Voicu, A.; Dobrota, S.

1995-12-31

In Romania after more than 135 years of oil production and processing, some severe environmental pollution problems have accumulated. In this context a joint research group from Institute of Biology Bucharest and S.C. Petrostar S.A. Ploiesti became involved in a research project on bioremediation of an environment contaminated with hydrocarbon waste. In the first stage of this project, investigations on microbial communities occurring in environments contaminated with oil were carried out. In the second stage, the hundreds of bacterial strains and populations isolated from soils, slops, and water sites contaminated with waste oil and water waste oil mix were submittedmore » to a screening program, to select a naturally occurring mixed culture with a high ability to degrade hydrocarbons.« less

Superresolution Imaging using Single-Molecule Localization

PubMed Central

Patterson, George; Davidson, Michael; Manley, Suliana; Lippincott-Schwartz, Jennifer

2013-01-01

Superresolution imaging is a rapidly emerging new field of microscopy that dramatically improves the spatial resolution of light microscopy by over an order of magnitude (∼10–20-nm resolution), allowing biological processes to be described at the molecular scale. Here, we discuss a form of superresolution microscopy based on the controlled activation and sampling of sparse subsets of photoconvertible fluorescent molecules. In this single-molecule based imaging approach, a wide variety of probes have proved valuable, ranging from genetically encodable photoactivatable fluorescent proteins to photoswitchable cyanine dyes. These have been used in diverse applications of superresolution imaging: from three-dimensional, multicolor molecule localization to tracking of nanometric structures and molecules in living cells. Single-molecule-based superresolution imaging thus offers exciting possibilities for obtaining molecular-scale information on biological events occurring at variable timescales. PMID:20055680

Maintaining semen quality by improving cold chain equipment used in cattle artificial insemination

PubMed Central

Lieberman, Daniel; McClure, Elizabeth; Harston, Stephen; Madan, Damian

2016-01-01

Artificial insemination of dairy cattle is a common practice in the developing world that can improve farmer incomes and food security. Maintaining the fertilizing potential of frozen semen as it is manipulated, transported and stored is crucial to the success of this process. Here we describe simple technological improvements to protect semen from inadvertent thermal fluctuations that occur when users mishandle semen using standard equipment. We show that when frozen semen is mishandled, characteristics of semen biology associated with fertility are negatively affected. We describe several design modifications and results from thermal performance tests of several improved prototypes. Finally, we compare semen that has been mishandled in standard and improved equipment. The data suggest that our canister improvements can better maintain characteristics of semen biology that correlate with fertility when it is mishandled. PMID:27313137

Maintaining semen quality by improving cold chain equipment used in cattle artificial insemination.

PubMed

Lieberman, Daniel; McClure, Elizabeth; Harston, Stephen; Madan, Damian

2016-06-17

Artificial insemination of dairy cattle is a common practice in the developing world that can improve farmer incomes and food security. Maintaining the fertilizing potential of frozen semen as it is manipulated, transported and stored is crucial to the success of this process. Here we describe simple technological improvements to protect semen from inadvertent thermal fluctuations that occur when users mishandle semen using standard equipment. We show that when frozen semen is mishandled, characteristics of semen biology associated with fertility are negatively affected. We describe several design modifications and results from thermal performance tests of several improved prototypes. Finally, we compare semen that has been mishandled in standard and improved equipment. The data suggest that our canister improvements can better maintain characteristics of semen biology that correlate with fertility when it is mishandled.

The Antarctic dry valley lakes: Relevance to Mars

NASA Technical Reports Server (NTRS)

Wharton, R. A., Jr.; Mckay, Christopher P.; Mancinelli, Rocco L.; Clow, G. D.; Simmons, G. M., Jr.

1989-01-01

The similarity of the early environments of Mars and Earth, and the biological evolution which occurred on early Earth, motivates exobiologists to seriously consider the possiblity of an early Martian biota. Environments are being identified which could contain Martian life and areas which may presently contain evidence of this former life. Sediments which were thought to be deposited in large ice-covered lakes are present on Mars. Such localities were identified within some of the canyons of the Valles Marineris and more recently in the ancient terrain in the Southern Hemisphere. Perennially ice-covered Antarctic lakes are being studied in order to develop quantitative models that relate environmental factors to the nature of the biological community and sediment forming processes. These models will be applied to the Martian paleolakes to establish the scientific rationale for the exobiological study of ancient Martian sediments.

VEGF (Vascular Endothelial Growth Factor) and Fibrotic Lung Disease.

PubMed

Barratt, Shaney L; Flower, Victoria A; Pauling, John D; Millar, Ann B

2018-04-24

Interstitial lung disease (ILD) encompasses a group of heterogeneous diseases characterised by varying degrees of aberrant inflammation and fibrosis of the lung parenchyma. This may occur in isolation, such as in idiopathic pulmonary fibrosis (IPF) or as part of a wider disease process affecting multiple organs, such as in systemic sclerosis. Anti-Vascular Endothelial Growth Factor (anti-VEGF) therapy is one component of an existing broad-spectrum therapeutic option in IPF (nintedanib) and may become part of the emerging therapeutic strategy for other ILDs in the future. This article describes our current understanding of VEGF biology in normal lung homeostasis and how changes in its bioavailability may contribute the pathogenesis of ILD. The complexity of VEGF biology is particularly highlighted with an emphasis on the potential non-vascular, non-angiogenic roles for VEGF in the lung, in both health and disease.

A general mechanism for competitor-induced dissociation of molecular complexes

PubMed Central

Paramanathan, Thayaparan; Reeves, Daniel; Friedman, Larry J.; Kondev, Jane; Gelles, Jeff

2014-01-01

The kinetic stability of non-covalent macromolecular complexes controls many biological phenomena. Here we find that physical models of complex dissociation predict that competitor molecules will in general accelerate the breakdown of isolated bimolecular complexes by occluding rapid rebinding of the two binding partners. This prediction is largely independent of molecular details. We confirm the prediction with single-molecule fluorescence experiments on a well-characterized DNA strand dissociation reaction. Contrary to common assumptions, competitor–induced acceleration of dissociation can occur in biologically relevant competitor concentration ranges and does not necessarily implyternary association of competitor with the bimolecular complex. Thus, occlusion of complex rebinding may play a significant role in a variety of biomolecular processes. The results also show that single-molecule colocalization experiments can accurately measure dissociation rates despite their limited spatio temporal resolution. PMID:25342513

The Rules and Functions of Nucleocytoplasmic Shuttling Proteins.

PubMed

Fu, Xuekun; Liang, Chao; Li, Fangfei; Wang, Luyao; Wu, Xiaoqiu; Lu, Aiping; Xiao, Guozhi; Zhang, Ge

2018-05-12

Biological macromolecules are the basis of life activities. There is a separation of spatial dimension between DNA replication and RNA biogenesis, and protein synthesis, which is an interesting phenomenon. The former occurs in the cell nucleus, while the latter in the cytoplasm. The separation requires protein to transport across the nuclear envelope to realize a variety of biological functions. Nucleocytoplasmic transport of protein including import to the nucleus and export to the cytoplasm is a complicated process that requires involvement and interaction of many proteins. In recent years, many studies have found that proteins constantly shuttle between the cytoplasm and the nucleus. These shuttling proteins play a crucial role as transport carriers and signal transduction regulators within cells. In this review, we describe the mechanism of nucleocytoplasmic transport of shuttling proteins and summarize some important diseases related shuttling proteins.

Maintaining semen quality by improving cold chain equipment used in cattle artificial insemination

NASA Astrophysics Data System (ADS)

Lieberman, Daniel; McClure, Elizabeth; Harston, Stephen; Madan, Damian

2016-06-01

Artificial insemination of dairy cattle is a common practice in the developing world that can improve farmer incomes and food security. Maintaining the fertilizing potential of frozen semen as it is manipulated, transported and stored is crucial to the success of this process. Here we describe simple technological improvements to protect semen from inadvertent thermal fluctuations that occur when users mishandle semen using standard equipment. We show that when frozen semen is mishandled, characteristics of semen biology associated with fertility are negatively affected. We describe several design modifications and results from thermal performance tests of several improved prototypes. Finally, we compare semen that has been mishandled in standard and improved equipment. The data suggest that our canister improvements can better maintain characteristics of semen biology that correlate with fertility when it is mishandled.

The impact crater as a habitat: effects of impact processing of target materials.

PubMed

Cockell, Charles S; Osinski, Gordon R; Lee, Pascal

2003-01-01

Impact structures are a rare habitat on Earth. However, where they do occur they can potentially have an important influence on the local ecology. Some of the types of habitat created in the immediate post-impact environment are not specific to the impact phenomenon, such as hydrothermal systems and crater lakes that can be found, for instance, in post-volcanic environments, albeit with different thermal characteristics than those associated with impact. However, some of the habitats created are specifically linked to processes of impact processing. Two examples of how impact processing of target materials has created novel habitats that improve the opportunities for colonization are found in the Haughton impact structure in the Canadian High Arctic. Impact-shocked rocks have become a habitat for endolithic microorganisms, and large, impact-shattered blocks of rock are used as resting sites by avifauna. However, some materials produced by an impact, such as melt sheet rocks, can make craters more biologically depauperate than the area surrounding them. Although there are no recent craters with which to study immediate post-impact colonization, these data yield insights into generalized mechanisms of how impact processing can influence post-impact succession. Because impact events are one of a number of processes that can bring localized destruction to ecosystems, understanding the manner in which impact structures are recolonized is of ecological interest. Impact craters are a universal phenomenon on solid planetary surfaces, and so they are of potential biological relevance on other planetary surfaces, particularly Mars.

The impact crater as a habitat: effects of impact processing of target materials

NASA Technical Reports Server (NTRS)

Cockell, Charles S.; Osinski, Gordon R.; Lee, Pascal

2003-01-01

Impact structures are a rare habitat on Earth. However, where they do occur they can potentially have an important influence on the local ecology. Some of the types of habitat created in the immediate post-impact environment are not specific to the impact phenomenon, such as hydrothermal systems and crater lakes that can be found, for instance, in post-volcanic environments, albeit with different thermal characteristics than those associated with impact. However, some of the habitats created are specifically linked to processes of impact processing. Two examples of how impact processing of target materials has created novel habitats that improve the opportunities for colonization are found in the Haughton impact structure in the Canadian High Arctic. Impact-shocked rocks have become a habitat for endolithic microorganisms, and large, impact-shattered blocks of rock are used as resting sites by avifauna. However, some materials produced by an impact, such as melt sheet rocks, can make craters more biologically depauperate than the area surrounding them. Although there are no recent craters with which to study immediate post-impact colonization, these data yield insights into generalized mechanisms of how impact processing can influence post-impact succession. Because impact events are one of a number of processes that can bring localized destruction to ecosystems, understanding the manner in which impact structures are recolonized is of ecological interest. Impact craters are a universal phenomenon on solid planetary surfaces, and so they are of potential biological relevance on other planetary surfaces, particularly Mars.

Effective removal of the antibiotic Nafcillin from water by combining the Photoelectro-Fenton process and Anaerobic Biological Digestion.

PubMed

Vidal, Jorge; Huiliñir, Cesar; Santander, Rocío; Silva-Agredo, Javier; Torres-Palma, Ricardo A; Salazar, Ricardo

2018-05-15

The elimination of the antibiotic Nafcillin (NAF), which is usually used in hospitals and veterinary clinics around the world, was assessed through a combination of three advanced electrochemical oxidation processes followed by anaerobic digestion process. In the first stage different electrochemical advanced oxidation processes (EAOPs) were used: electro-oxidation with hydrogen peroxide (EO-H 2 O 2 ), electro-Fenton (EF) and Photo electro-Fenton (PEF). After PEF, almost complete and highly efficient degradation and elimination of NAF was achieved, with the concomitant elimination of the associated antimicrobial activity. The fast degradation rate produced by PEF is explained by the oxidative action of hydroxyl radicals (•OH) together with the direct UV photolysis of complexes formed between Fe 3+ and some organic intermediates. Total removal of NAF occurs after 90min of electrolysis by PEF, with the generation of organic intermediates that remain in solution. However, when this post PEF process solution was treated with an anaerobic biological process, the intermediates generated in the electrochemical degradation of NAF were completely eliminated after 24h. The kinetic degradation of NAF as well as the identification/quantification of products and intermediates formed during the degradation of antibiotic, such as inorganic ions, carboxylic acids and aromatic compounds, were determined by chromatographic and photometric methods. Finally, an oxidation pathway is proposed for the complete conversion to CO 2 . Copyright © 2017 Elsevier B.V. All rights reserved.

Functional Proteomic Analysis of Human NucleolusD⃞

PubMed Central

Scherl, Alexander; Couté, Yohann; Déon, Catherine; Callé, Aleth; Kindbeiter, Karine; Sanchez, Jean-Charles; Greco, Anna; Hochstrasser, Denis; Diaz, Jean-Jacques

2002-01-01

The notion of a “plurifunctional” nucleolus is now well established. However, molecular mechanisms underlying the biological processes occurring within this nuclear domain remain only partially understood. As a first step in elucidating these mechanisms we have carried out a proteomic analysis to draw up a list of proteins present within nucleoli of HeLa cells. This analysis allowed the identification of 213 different nucleolar proteins. This catalog complements that of the 271 proteins obtained recently by others, giving a total of ∼350 different nucleolar proteins. Functional classification of these proteins allowed outlining several biological processes taking place within nucleoli. Bioinformatic analyses permitted the assignment of hypothetical functions for 43 proteins for which no functional information is available. Notably, a role in ribosome biogenesis was proposed for 31 proteins. More generally, this functional classification reinforces the plurifunctional nature of nucleoli and provides convincing evidence that nucleoli may play a central role in the control of gene expression. Finally, this analysis supports the recent demonstration of a coupling of transcription and translation in higher eukaryotes. PMID:12429849

Bioterrorism and the Role of the Clinical Microbiology Laboratory

PubMed Central

2015-01-01

SUMMARY Regular review of the management of bioterrorism is essential for maintaining readiness for these sporadically occurring events. This review provides an overview of the history of biological disasters and bioterrorism. I also discuss the recent recategorization of tier 1 agents by the U.S. Department of Health and Human Services, the Laboratory Response Network (LRN), and specific training and readiness processes and programs, such as the College of American Pathologists (CAP) Laboratory Preparedness Exercise (LPX). LPX examined the management of cultivable bacterial vaccine and attenuated strains of tier 1 agents or close mimics. In the LPX program, participating laboratories showed improvement in the level of diagnosis required and referral of isolates to an appropriate reference laboratory. Agents which proved difficult to manage in sentinel laboratories included the more fastidious Gram-negative organisms, especially Francisella tularensis and Burkholderia spp. The recent Ebola hemorrhagic fever epidemic provided a check on LRN safety processes. Specific guidelines and recommendations for laboratory safety and risk assessment in the clinical microbiology are explored so that sentinel laboratories can better prepare for the next biological disaster. PMID:26656673

New Interest in Wild Forest Products in Europe as an Expression of Biocultural Dynamics.

PubMed

Wiersum, K F

2017-01-01

In Europe, interest in wild forest products is increasing. Such products may be interpreted in a biological sense as deriving from autonomously growing forest species or in a biocultural sense as reflecting dynamics in human living with biodiversity through re-wilding of earlier domesticated species. In this article I elaborate the idea that the new interests reflect biocultural dynamics. First, I identify these dynamics as involving both domestication and re-wilding and characterize these processes as involving biological, environmental, and cultural dimensions. Next, I present a comparative review of two approaches to re-wilding forest production in the Netherlands: meat production from new types of natural grazing systems, and food production from plants re-introduced to the wild. The first approach is based on the stimulation of naturally occurring ecological processes and the second on the stimulation of new forms of experiencing bio-cultural heritage. The examples demonstrate that the new interests in wild forest products involve both a return to earlier stages of domestication in an ecological sense and a new phase of acculturation to evolving socio-cultural conditions.

Examining the Role of Leadership in an Undergraduate Biology Institutional Reform Initiative

PubMed Central

Matz, Rebecca L.; Jardeleza, Sarah E.

2016-01-01

Undergraduate science, technology, engineering, and mathematics (STEM) education reform continues to be a national priority. We studied a reform process in undergraduate biology at a research-intensive university to explore what leadership issues arose in implementation of the initiative when characterized with a descriptive case study method. The data were drawn from transcripts of meetings that occurred over the first 2 years of the reform process. Two literature-based models of change were used as lenses through which to view the data. We find that easing the burden of an undergraduate education reform initiative on faculty through articulating clear outcomes, developing shared vision across stakeholders on how to achieve those outcomes, providing appropriate reward systems, and ensuring faculty have ample opportunity to influence the initiative all appear to increase the success of reform. The two literature-based models were assessed, and an extended model of change is presented that moves from change in STEM instructional strategies to STEM organizational change strategies. These lessons may be transferable to other institutions engaging in education reform. PMID:27856545

An Overview of Biomolecular Event Extraction from Scientific Documents

PubMed Central

Vanegas, Jorge A.; Matos, Sérgio; González, Fabio; Oliveira, José L.

2015-01-01

This paper presents a review of state-of-the-art approaches to automatic extraction of biomolecular events from scientific texts. Events involving biomolecules such as genes, transcription factors, or enzymes, for example, have a central role in biological processes and functions and provide valuable information for describing physiological and pathogenesis mechanisms. Event extraction from biomedical literature has a broad range of applications, including support for information retrieval, knowledge summarization, and information extraction and discovery. However, automatic event extraction is a challenging task due to the ambiguity and diversity of natural language and higher-level linguistic phenomena, such as speculations and negations, which occur in biological texts and can lead to misunderstanding or incorrect interpretation. Many strategies have been proposed in the last decade, originating from different research areas such as natural language processing, machine learning, and statistics. This review summarizes the most representative approaches in biomolecular event extraction and presents an analysis of the current state of the art and of commonly used methods, features, and tools. Finally, current research trends and future perspectives are also discussed. PMID:26587051

NADPH OXIDASE: STRUCTURE AND ACTIVATION MECHANISMS (REVIEW). NOTE I.

PubMed

Filip-Ciubotaru, Florina; Manciuc, Carmen; Stoleriu, Gabriela; Foia, Liliana

2016-01-01

NADPH oxidase (nicotinamide adenine dinucleotide phosphate-oxidase), with its generically termed NOX isoforms, is the major source of ROS (reactive oxigen species) in biological systems. ROS are small oxygen-derived molecules with an important role in various biological processes (physiological or pathological). If under physiological conditions some processes are beneficial and necessary for life, under pathophysiological conditions they are noxious, harmful. NADPH oxidases are present in phagocytes and in a wide variety of nonphagocytic cells. The enzyme generates superoxide by transferring electrons from NADPH inside the cell across the membrane and coupling them to molecular oxygen to produce superoxide anion, a reactive free-radical. Structurally, NADPH oxidase is a multicomponent enzyme which includes two integral membrane proteins, glycoprotein gp9 1 Phox and adaptor protein p22(phox), which together form the heterodimeric flavocytochrome b558 that constitutes the core of the enzyme. During the resting state, the multidomain regulatory subunits p40P(phox), p47(phox), p67(Phox) are located in the cytosol organized as a complex. The activation of phagocytic NADPH oxidase occurs through a complex series of protein interactions.

Processes regulating progressive nitrogen limitation under elevated carbon dioxide: a meta-analysis

NASA Astrophysics Data System (ADS)

Liang, Junyi; Qi, Xuan; Souza, Lara; Luo, Yiqi

2016-05-01

The nitrogen (N) cycle has the potential to regulate climate change through its influence on carbon (C) sequestration. Although extensive research has explored whether or not progressive N limitation (PNL) occurs under CO2 enrichment, a comprehensive assessment of the processes that regulate PNL is still lacking. Here, we quantitatively synthesized the responses of all major processes and pools in the terrestrial N cycle with meta-analysis of CO2 experimental data available in the literature. The results showed that CO2 enrichment significantly increased N sequestration in the plant and litter pools but not in the soil pool, partially supporting one of the basic assumptions in the PNL hypothesis that elevated CO2 results in more N sequestered in organic pools. However, CO2 enrichment significantly increased the N influx via biological N fixation and the loss via N2O emission, but decreased the N efflux via leaching. In addition, no general diminished CO2 fertilization effect on plant growth was observed over time up to the longest experiment of 13 years. Overall, our analyses suggest that the extra N supply by the increased biological N fixation and decreased leaching may potentially alleviate PNL under elevated CO2 conditions in spite of the increases in plant N sequestration and N2O emission. Moreover, our syntheses indicate that CO2 enrichment increases soil ammonium (NH4+) to nitrate (NO3-) ratio. The changed NH4+/NO3- ratio and subsequent biological processes may result in changes in soil microenvironments, above-belowground community structures and associated interactions, which could potentially affect the terrestrial biogeochemical cycles. In addition, our data synthesis suggests that more long-term studies, especially in regions other than temperate ones, are needed for comprehensive assessments of the PNL hypothesis.

Text-based Analytics for Biosurveillance

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

Charles, Lauren E.; Smith, William P.; Rounds, Jeremiah

The ability to prevent, mitigate, or control a biological threat depends on how quickly the threat is identified and characterized. Ensuring the timely delivery of data and analytics is an essential aspect of providing adequate situational awareness in the face of a disease outbreak. This chapter outlines an analytic pipeline for supporting an advanced early warning system that can integrate multiple data sources and provide situational awareness of potential and occurring disease situations. The pipeline, includes real-time automated data analysis founded on natural language processing (NLP), semantic concept matching, and machine learning techniques, to enrich content with metadata related tomore » biosurveillance. Online news articles are presented as an example use case for the pipeline, but the processes can be generalized to any textual data. In this chapter, the mechanics of a streaming pipeline are briefly discussed as well as the major steps required to provide targeted situational awareness. The text-based analytic pipeline includes various processing steps as well as identifying article relevance to biosurveillance (e.g., relevance algorithm) and article feature extraction (who, what, where, why, how, and when). The ability to prevent, mitigate, or control a biological threat depends on how quickly the threat is identified and characterized. Ensuring the timely delivery of data and analytics is an essential aspect of providing adequate situational awareness in the face of a disease outbreak. This chapter outlines an analytic pipeline for supporting an advanced early warning system that can integrate multiple data sources and provide situational awareness of potential and occurring disease situations. The pipeline, includes real-time automated data analysis founded on natural language processing (NLP), semantic concept matching, and machine learning techniques, to enrich content with metadata related to biosurveillance. Online news articles are presented as an example use case for the pipeline, but the processes can be generalized to any textual data. In this chapter, the mechanics of a streaming pipeline are briefly discussed as well as the major steps required to provide targeted situational awareness. The text-based analytic pipeline includes various processing steps as well as identifying article relevance to biosurveillance (e.g., relevance algorithm) and article feature extraction (who, what, where, why, how, and when).« less

Microbial trace-fossil formation, biogenous, and abiotic weathering in the Antarctic cold desert

NASA Technical Reports Server (NTRS)

Friedmann, E. Imre; Weed, Rebecca

1987-01-01

In the Antarctic cold desert (Ross Desert), the survival of the cryptoendolithic microorganisms that colonize the near-surface layer of porous sandstone rocks depends on a precarious equilibrium of biological and geological factors. An unfavorable shift of this equilibrium results in death, and this may be followed by formation of trace fossils that preserve the characteristic iron-leaching pattern caused by microbial activity. Similar microbial trace fossils may exist in the geological record. If life ever arose on early Mars, similar processes may have occurred there and left recognizable traces.

Structure and Function of TET Enzymes.

PubMed

Yin, Xiaotong; Xu, Yanhui

2016-01-01

Mammalian DNA methylation mainly occurs at the carbon-C5 position of cytosine (5mC). TET enzymes were discovered to successively oxidize 5mC to 5-hydromethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). TET enzymes and oxidized 5mC derivatives play important roles in various biological and pathological processes, including regulation of DNA demethylation, gene transcription, embryonic development, and oncogenesis. In this chapter, we will discuss the discovery of TET-mediated 5mC oxidation and the structure, function, and regulation of TET enzymes.

GAS-611 firefly in zero gravity

NASA Technical Reports Server (NTRS)

Williams, Tony

1988-01-01

The Get Away Special 611 (GAS-611) project will carry a small, self-contained biological experiment into a microgravity environment for a period of 120 hours. The payload will be a colony of Lampyridae (fireflies). The ability of this beetle to produce light with an efficiency of 98 pct will be evaluated in the micro-G environment. The chemical process that occurs could be assisted by the earth's gravitational pull and the very complex tracheae system found within this species of beetle. The effects of microgravity on mating and beetle larvae will also be studied.

Morphological and ecological preadaptations as the basis of bird synanthropization under transformed environment conditions

NASA Astrophysics Data System (ADS)

Rakhimov, I. I.; Ibragimova, K. K.

2018-01-01

Bird synanthropization is connected with a thorough and serious reconstruction of their biology and is a demonstration of changes currently occurring in the biosphere due to human influence. Nutritional and nesting conditions as well as protection due to urban characteristics are advantage factors that affect their populations. Under these conditions, the adaptive potential of species can be realized. Adaptations to a new and in-distinctive environment appear due to preadaptations. The synanthropization process of species happens without speciation by expression of existing genetic variation of morphological and ecological characteristics.

Preface: Special Topic on Ions in Water.

PubMed

Allen, Heather C; Tobias, Douglas J

2018-06-14

This special topic contains a diverse collection of 40 articles that span the vast range of subjects that fall under the heading "Ions in Water," a longstanding mainstay of chemical physics. The investigations reported herein employ state-of-the-art theoretical, computational, and experimental techniques, as well as combinations thereof, to provide new insights into the fundamental aspects of ion solvation and the important roles that ions play in mediating physicochemical processes occurring in solutions and at interfaces in a wide variety of settings relevant to biological, environmental, and technological applications.

Preface: Special Topic on Ions in Water

NASA Astrophysics Data System (ADS)

Allen, Heather C.; Tobias, Douglas J.

2018-06-01

This special topic contains a diverse collection of 40 articles that span the vast range of subjects that fall under the heading "Ions in Water," a longstanding mainstay of chemical physics. The investigations reported herein employ state-of-the-art theoretical, computational, and experimental techniques, as well as combinations thereof, to provide new insights into the fundamental aspects of ion solvation and the important roles that ions play in mediating physicochemical processes occurring in solutions and at interfaces in a wide variety of settings relevant to biological, environmental, and technological applications.

Nestedness across biological scales

PubMed Central

Marquitti, Flavia M. D.; Raimundo, Rafael L. G.; Sebastián-González, Esther; Coltri, Patricia P.; Perez, S. Ivan; Brandt, Débora Y. C.; Nunes, Kelly; Daura-Jorge, Fábio G.; Floeter, Sergio R.; Guimarães, Paulo R.

2017-01-01

Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness throughout biological scales can stimulate the debate on how pervasive nestedness may be in nature, while the theoretical emergent principles can aid further research on commonalities of biological networks. PMID:28166284

Quantification of the Bioturbation Activity of Lumbriculus Variegatus Worms Using Fluorescent Particulate Tracers

NASA Astrophysics Data System (ADS)

Hernandez-Gonzalez, L. M.; Roche, K. R.; Xie, M.; Packman, A. I.

2014-12-01

Important biological, physical and chemical processes, such as fluxes of oxygen, nutrients and contaminants, occur across sediment-water interfaces. These processes are influenced by bioturbation activities of benthic animals. Bioturbation is thought to be significant in releasing metals to the water column from contaminated sediments, but metals contamination also affects organism activity. Consequently, the aim of this study was to consider the interactions of biological activity, sediment chemistry, pore water transport, and chemical reactions in sediment mixing and the flux and toxicity of metals in sediments. Prior studies have modeled bioturbation as a diffusive process. However, diffusion models often do not describe accurately sediment mixing due to bioturbation. To this end, we used the continuous time random walk (CTRW) model to assess sediment mixing caused by bioturbation activity of Lumbriculus variegatus worms. We performed experiments using fine-grained sediments with different levels of zinc contamination from Lake DePue, which is a Superfund Site in Illinois. The tests were conducted in an aerated fresh water chamber. Fluorescent particulate tracers were added to the sediment surface to quantify mixing processes and the influence of metals contaminants on L. variegatus bioturbation activity. We observed sediment mixing and organism activity by time-lapse photography over 14 days. Then, we analyzed the images to characterize the fluorescent particle concentration as a function of sediment depth and time. Results reveal that sediment mixing caused by L. variegatus is subdiffusive in time and superdiffusive in space. These results suggest that anomalous sediment mixing is probably a ubiquitous process, as this behavior has only been observed previously in marine sediments. Also, the experiments indicate that bioturbation and sediment mixing decreased in the presence of higher metals concentrations in sediments. This process is expected to decrease efflux of metals from highly contaminated sediments by reducing biological activity.

Ecosystem function in waste stabilisation ponds: Improving water quality through a better understanding of biophysical coupling

NASA Astrophysics Data System (ADS)

Ghadouani, Anas; Reichwaldt, Elke S.; Coggins, Liah X.; Ivey, Gregory N.; Ghisalberti, Marco; Zhou, Wenxu; Laurion, Isabelle; Chua, Andrew

2014-05-01

Wastewater stabilisation ponds (WSPs) are highly productive systems designed to treat wastewater using only natural biological and chemical processes. Phytoplankton, microbial communities and hydraulics play important roles for ecosystem functionality of these pond systems. Although WSPs have been used for many decades, they are still considered as 'black box' systems as very little is known about the fundamental ecological processes which occur within them. However, a better understanding of how these highly productive ecosystems function is particularly important for hydrological processes, as treated wastewater is commonly discharged into streams, rivers, and oceans, and subject to strict water quality guidelines. WSPs are known to operate at different levels of efficiency, and treatment efficiency of WSPs is dependent on physical (flow characteristics and sludge accumulation and distribution) and biological (microbial and phytoplankton communities) characteristics. Thus, it is important to gain a better understanding of the role and influence of pond hydraulics and vital microbial communities on pond performance and WSP functional stability. The main aim of this study is to investigate the processes leading to differences in treatment performance of WSPs. This study uses a novel and innovative approach to understand these factors by combining flow cytometry and metabolomics to investigate various biochemical characteristics, including the metabolite composition and microbial community within WSPs. The results of these analyses will then be combined with results from the characterisation of pond hydrodynamics and hydraulic performance, which will be performed using advanced hydrodynamic modelling and advanced sludge profiling technology. By understanding how hydrodynamic and biological processes influence each other and ecosystem function and stability in WSPs, we will be able to propose ways to improve the quality of the treatment using natural processes, with less reliance on chemical treatment. This will in turn contribute to the reduction in the cost of operation, but more importantly reduce the impact on the environment (i.e., discharge, GHGs), and increase water quality and the potential for water reuse worldwide.

Integration of the Gene Ontology into an object-oriented architecture.

PubMed

Shegogue, Daniel; Zheng, W Jim

2005-05-10

To standardize gene product descriptions, a formal vocabulary defined as the Gene Ontology (GO) has been developed. GO terms have been categorized into biological processes, molecular functions, and cellular components. However, there is no single representation that integrates all the terms into one cohesive model. Furthermore, GO definitions have little information explaining the underlying architecture that forms these terms, such as the dynamic and static events occurring in a process. In contrast, object-oriented models have been developed to show dynamic and static events. A portion of the TGF-beta signaling pathway, which is involved in numerous cellular events including cancer, differentiation and development, was used to demonstrate the feasibility of integrating the Gene Ontology into an object-oriented model. Using object-oriented models we have captured the static and dynamic events that occur during a representative GO process, "transforming growth factor-beta (TGF-beta) receptor complex assembly" (GO:0007181). We demonstrate that the utility of GO terms can be enhanced by object-oriented technology, and that the GO terms can be integrated into an object-oriented model by serving as a basis for the generation of object functions and attributes.

Integration of the Gene Ontology into an object-oriented architecture

PubMed Central

Shegogue, Daniel; Zheng, W Jim

2005-01-01

Background To standardize gene product descriptions, a formal vocabulary defined as the Gene Ontology (GO) has been developed. GO terms have been categorized into biological processes, molecular functions, and cellular components. However, there is no single representation that integrates all the terms into one cohesive model. Furthermore, GO definitions have little information explaining the underlying architecture that forms these terms, such as the dynamic and static events occurring in a process. In contrast, object-oriented models have been developed to show dynamic and static events. A portion of the TGF-beta signaling pathway, which is involved in numerous cellular events including cancer, differentiation and development, was used to demonstrate the feasibility of integrating the Gene Ontology into an object-oriented model. Results Using object-oriented models we have captured the static and dynamic events that occur during a representative GO process, "transforming growth factor-beta (TGF-beta) receptor complex assembly" (GO:0007181). Conclusion We demonstrate that the utility of GO terms can be enhanced by object-oriented technology, and that the GO terms can be integrated into an object-oriented model by serving as a basis for the generation of object functions and attributes. PMID:15885145

40 CFR 62.14490 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... occur during combustion. Biologicals means preparations made from living organisms and their products... biologicals that is listed in paragraphs (1) through (7) of this definition. The definition of medical... § 261.4(a)(1) of this chapter. (1) Cultures and stocks of infectious agents and associated biologicals...

40 CFR 62.14490 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... occur during combustion. Biologicals means preparations made from living organisms and their products... biologicals that is listed in paragraphs (1) through (7) of this definition. The definition of medical... § 261.4(a)(1) of this chapter. (1) Cultures and stocks of infectious agents and associated biologicals...

ECOLOGICAL IMPACT OF INTEGRATED CHEMICAL AND BIOLOGICAL AQUATIC WEED CONTROL

EPA Science Inventory

This final report presents results of a four-year study of the ecological impacts of chemical, biological, and integrated methods of aquatic weed control. Biological and water quality changes occurred as abundance of macrophytic vegetation was altered by natural factors or manage...

Loss of trabeculae by mechano-biological means may explain rapid bone loss in osteoporosis.

PubMed

Mulvihill, Brianne M; McNamara, Laoise M; Prendergast, Patrick J

2008-10-06

Osteoporosis is characterized by rapid and irreversible loss of trabecular bone tissue leading to increased bone fragility. In this study, we hypothesize two causes for rapid loss of bone trabeculae; firstly, the perforation of trabeculae is caused by osteoclasts resorbing a cavity so deep that it cannot be refilled and, secondly, the increases in bone tissue elastic modulus lead to increased propensity for trabecular perforation. These hypotheses were tested using an algorithm that was based on two premises: (i) bone remodelling is a turnover process that repairs damaged bone tissue by resorbing and returning it to a homeostatic strain level and (ii) osteoblast attachment is under biochemical control. It was found that a mechano-biological algorithm based on these premises can simulate the remodelling cycle in a trabecular strut where damaged bone is resorbed to form a pit that is subsequently refilled with new bone. Furthermore, the simulation predicts that there is a depth of resorption cavity deeper than which refilling of the resorption pits is impossible and perforation inevitably occurs. However, perforation does not occur by a single fracture event but by continual removal of microdamage after it forms beneath the resorption pit. The simulation also predicts that perforations would occur more easily in trabeculae that are more highly mineralized (stiffer). Since both increased osteoclast activation rates and increased mineralization have been measured in osteoporotic bone, either or both may contribute to the rapid loss of trabecular bone mass observed in osteoporotic patients.

Distribution of biologic, anthropogenic, and volcanic constituents as a proxy for sediment transport in the San Francisco Bay Coastal System

USGS Publications Warehouse

McGann, Mary; Erikson, Li H.; Wan, Elmira; Powell, Charles; Maddocks, Rosalie F.; Barnard, P.L.; Jaffee, B.E.; Schoellhamer, D.H.

2013-01-01

Although conventional sediment parameters (mean grain size, sorting, and skewness) and provenance have typically been used to infer sediment transport pathways, most freshwater, brackish, and marine environments are also characterized by abundant sediment constituents of biological, and possibly anthropogenic and volcanic, origin that can provide additional insight into local sedimentary processes. The biota will be spatially distributed according to its response to environmental parameters such as water temperature, salinity, dissolved oxygen, organic carbon content, grain size, and intensity of currents and tidal flow, whereas the presence of anthropogenic and volcanic constituents will reflect proximity to source areas and whether they are fluvially- or aerially-transported. Because each of these constituents have a unique environmental signature, they are a more precise proxy for that source area than the conventional sedimentary process indicators. This San Francisco Bay Coastal System study demonstrates that by applying a multi-proxy approach, the primary sites of sediment transport can be identified. Many of these sites are far from where the constituents originated, showing that sediment transport is widespread in the region. Although not often used, identifying and interpreting the distribution of naturally-occurring and allochthonous biologic, anthropogenic, and volcanic sediment constituents is a powerful tool to aid in the investigation of sediment transport pathways in other coastal systems.

Howard Brenner's Legacy for Biological Transport Processes

NASA Astrophysics Data System (ADS)

Nitsche, Johannes

2014-11-01

This talk discusses the manner in which Howard Brenner's theoretical contributions have had, and long will have, strong and direct impact on the understanding of transport processes occurring in biological systems. His early work on low Reynolds number resistance/mobility coefficients of arbitrarily shaped particles, and particles near walls and in pores, is an essential component of models of hindered diffusion through many types of membranes and tissues, and convective transport in microfluidic diagnostic systems. His seminal contributions to macrotransport (coarse-graining, homogenization) theory presaged the growing discipline of multiscale modeling. For biological systems they represent the key to infusing diffusion models of a wide variety of tissues with a sound basis in their microscopic structure and properties, often over a hierarchy of scales. Both scientific currents are illustrated within the concrete context of diffusion models of drug/chemical diffusion through the skin. This area of theory, which is key to transdermal drug development and risk assessment of chemical exposure, has benefitted very directly from Brenner's contributions. In this as in other areas, Brenner's physicochemical insight, mathematical virtuosity, drive for fully justified analysis free of ad hoc assumptions, quest for generality, and impeccable exposition, have consistently elevated the level of theoretical understanding and presentation. We close with anecdotes showing how his personal qualities and warmth helped to impart high standards of rigor to generations of grateful research students. Authors are Johannes M. Nitsche, Ludwig C. Nitsche and Gerald B. Kasting.

Module-based multiscale simulation of angiogenesis in skeletal muscle

PubMed Central

2011-01-01

Background Mathematical modeling of angiogenesis has been gaining momentum as a means to shed new light on the biological complexity underlying blood vessel growth. A variety of computational models have been developed, each focusing on different aspects of the angiogenesis process and occurring at different biological scales, ranging from the molecular to the tissue levels. Integration of models at different scales is a challenging and currently unsolved problem. Results We present an object-oriented module-based computational integration strategy to build a multiscale model of angiogenesis that links currently available models. As an example case, we use this approach to integrate modules representing microvascular blood flow, oxygen transport, vascular endothelial growth factor transport and endothelial cell behavior (sensing, migration and proliferation). Modeling methodologies in these modules include algebraic equations, partial differential equations and agent-based models with complex logical rules. We apply this integrated model to simulate exercise-induced angiogenesis in skeletal muscle. The simulation results compare capillary growth patterns between different exercise conditions for a single bout of exercise. Results demonstrate how the computational infrastructure can effectively integrate multiple modules by coordinating their connectivity and data exchange. Model parameterization offers simulation flexibility and a platform for performing sensitivity analysis. Conclusions This systems biology strategy can be applied to larger scale integration of computational models of angiogenesis in skeletal muscle, or other complex processes in other tissues under physiological and pathological conditions. PMID:21463529

Reproductive biology of the black coral Antipathella wollastoni (Cnidaria: Antipatharia) in the Azores (NE Atlantic)

NASA Astrophysics Data System (ADS)

Rakka, Maria; Orejas, Covadonga; Sampaio, Iris; Monteiro, João; Parra, Hugo; Carreiro-Silva, Marina

2017-11-01

Antipathella wollastoni is an antipatharian species common to Macaronesia, occurring in depths between 20 and 1425 m. Despite its importance as a habitat-forming species, there is no information about its basic biology. The aim of the current study is to describe its reproductive strategy, gametogenic cycle and reproductive timing. Sampling was performed monthly on six tagged colonies during one year and specimens were histologically processed. A. wollastoni was found to be a gonochoric broadcast spawner. Gametogenesis took place within the primary transversal mesenteries, and followed an annual cycle. The reproductive season coincided with an increase in seawater temperature but spawning, inferred from the disappearance of gametes, likely happened after the sea surface temperature peak of the year (September 2009). Polyp fecundity ranged from 1 to 309 oocytes/polyp. A decrease in polyp fecundity was detected in samples at the higher pre-spawning maturity stage, indicating possible repetitive spawning or oocyte absorption. Intra-colonial comparisons revealed a longer duration of the reproductive cycle in the medial colony section, and a gradient of increased oocyte size towards the apical section, possibly due to intra-colonial differences in energy allocation between reproduction and other biological processes, or as a strategy against predation on gametes/larvae. Colony height was positively correlated with polyp fecundity indicating that the reproductive output increases with colony size.

An Integrated Framework for Process-Driven Model Construction in Disease Ecology and Animal Health

PubMed Central

Mancy, Rebecca; Brock, Patrick M.; Kao, Rowland R.

2017-01-01

Process models that focus on explicitly representing biological mechanisms are increasingly important in disease ecology and animal health research. However, the large number of process modelling approaches makes it difficult to decide which is most appropriate for a given disease system and research question. Here, we discuss different motivations for using process models and present an integrated conceptual analysis that can be used to guide the construction of infectious disease process models and comparisons between them. Our presentation complements existing work by clarifying the major differences between modelling approaches and their relationship with the biological characteristics of the epidemiological system. We first discuss distinct motivations for using process models in epidemiological research, identifying the key steps in model design and use associated with each. We then present a conceptual framework for guiding model construction and comparison, organised according to key aspects of epidemiological systems. Specifically, we discuss the number and type of disease states, whether to focus on individual hosts (e.g., cows) or groups of hosts (e.g., herds or farms), how space or host connectivity affect disease transmission, whether demographic and epidemiological processes are periodic or can occur at any time, and the extent to which stochasticity is important. We use foot-and-mouth disease and bovine tuberculosis in cattle to illustrate our discussion and support explanations of cases in which different models are used to address similar problems. The framework should help those constructing models to structure their approach to modelling decisions and facilitate comparisons between models in the literature. PMID:29021983

An Integrated Framework for Process-Driven Model Construction in Disease Ecology and Animal Health.

PubMed

Mancy, Rebecca; Brock, Patrick M; Kao, Rowland R

2017-01-01

Process models that focus on explicitly representing biological mechanisms are increasingly important in disease ecology and animal health research. However, the large number of process modelling approaches makes it difficult to decide which is most appropriate for a given disease system and research question. Here, we discuss different motivations for using process models and present an integrated conceptual analysis that can be used to guide the construction of infectious disease process models and comparisons between them. Our presentation complements existing work by clarifying the major differences between modelling approaches and their relationship with the biological characteristics of the epidemiological system. We first discuss distinct motivations for using process models in epidemiological research, identifying the key steps in model design and use associated with each. We then present a conceptual framework for guiding model construction and comparison, organised according to key aspects of epidemiological systems. Specifically, we discuss the number and type of disease states, whether to focus on individual hosts (e.g., cows) or groups of hosts (e.g., herds or farms), how space or host connectivity affect disease transmission, whether demographic and epidemiological processes are periodic or can occur at any time, and the extent to which stochasticity is important. We use foot-and-mouth disease and bovine tuberculosis in cattle to illustrate our discussion and support explanations of cases in which different models are used to address similar problems. The framework should help those constructing models to structure their approach to modelling decisions and facilitate comparisons between models in the literature.

Salvage logging, ecosystem processes, and biodiversity conservation.

PubMed

Lindenmayer, D B; Noss, R F

2006-08-01

We summarize the documented and potential impacts of salvage logging--a form of logging that removes trees and other biological material from sites after natural disturbance. Such operations may reduce or eliminate biological legacies, modify rare postdisturbance habitats, influence populations, alter community composition, impair natural vegetation recovery, facilitate the colonization of invasive species, alter soil properties and nutrient levels, increase erosion, modify hydrological regimes and aquatic ecosystems, and alter patterns of landscape heterogeneity These impacts can be assigned to three broad and interrelated effects: (1) altered stand structural complexity; (2) altered ecosystem processes and functions; and (3) altered populations of species and community composition. Some impacts may be different from or additional to the effects of traditional logging that is not preceded by a large natural disturbance because the conditions before, during, and after salvage logging may differ from those that characterize traditional timber harvesting. The potential impacts of salvage logging often have been overlooked, partly because the processes of ecosystem recovery after natural disturbance are still poorly understood and partly because potential cumulative effects of natural and human disturbance have not been well documented. Ecologically informed policies regarding salvage logging are needed prior to major natural disturbances so that when they occur ad hoc and crisis-mode decision making can be avoided. These policies should lead to salvage-exemption zones and limits on the amounts of disturbance-derived biological legacies (e.g., burned trees, logs) that are removed where salvage logging takes place. Finally, we believe new terminology is needed. The word salvage implies that something is being saved or recovered, whereas from an ecological perspective this is rarely the case.

On the thermodynamics of multilevel evolution.

PubMed

Tessera, Marc; Hoelzer, Guy A

2013-09-01

Biodiversity is hierarchically structured both phylogenetically and functionally. Phylogenetic hierarchy is understood as a product of branching organic evolution as described by Darwin. Ecosystem biologists understand some aspects of functional hierarchy, such as food web architecture, as a product of evolutionary ecology; but functional hierarchy extends to much lower scales of organization than those studied by ecologists. We argue that the more general use of the term "evolution" employed by physicists and applied to non-living systems connects directly to the narrow biological meaning. Physical evolution is best understood as a thermodynamic phenomenon, and this perspective comfortably includes all of biological evolution. We suggest four dynamical factors that build on each other in a hierarchical fashion and set the stage for the Darwinian evolution of biological systems: (1) the entropic erosion of structure; (2) the construction of dissipative systems; (3) the reproduction of growing systems and (4) the historical memory accrued to populations of reproductive agents by the acquisition of hereditary mechanisms. A particular level of evolution can underpin the emergence of higher levels, but evolutionary processes persist at each level in the hierarchy. We also argue that particular evolutionary processes can occur at any level of the hierarchy where they are not obstructed by material constraints. This theoretical framework provides an extensive basis for understanding natural selection as a multilevel process. The extensive literature on thermodynamics in turn provides an important advantage to this perspective on the evolution of higher levels of organization, such as the evolution of altruism that can accompany the emergence of social organization. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Metal-catalyzed protein tyrosine nitration in biological systems.

PubMed

Campolo, Nicolás; Bartesaghi, Silvina; Radi, Rafael

2014-11-01

Protein tyrosine nitration is an oxidative postranslational modification that can affect protein structure and function. It is mediated in vivo by the production of nitric oxide-derived reactive nitrogen species (RNS), including peroxynitrite (ONOO(-)) and nitrogen dioxide ((•)NO₂). Redox-active transition metals such as iron (Fe), copper (Cu), and manganese (Mn) can actively participate in the processes of tyrosine nitration in biological systems, as they catalyze the production of both reactive oxygen species and RNS, enhance nitration yields and provide site-specificity to this process. Early after the discovery that protein tyrosine nitration can occur under biologically relevant conditions, it was shown that some low molecular weight transition-metal centers and metalloproteins could promote peroxynitrite-dependent nitration. Later studies showed that nitration could be achieved by peroxynitrite-independent routes as well, depending on the transition metal-catalyzed oxidation of nitrite (NO₂(-)) to (•)NO₂ in the presence of hydrogen peroxide. Processes like these can be achieved either by hemeperoxidase-dependent reactions or by ferrous and cuprous ions through Fenton-type chemistry. Besides the in vitro evidence, there are now several in vivo studies that support the close relationship between transition metal levels and protein tyrosine nitration. So, the contribution of transition metals to the levels of tyrosine nitrated proteins observed under basal conditions and, specially, in disease states related with high levels of these metal ions, seems to be quite clear. Altogether, current evidence unambiguously supports a central role of transition metals in determining the extent and selectivity of protein tyrosine nitration mediated both by peroxynitrite-dependent and independent mechanisms.

Major Transcriptome Reprogramming Underlies Floral Mimicry Induced by the Rust Fungus Puccinia monoica in Boechera stricta

PubMed Central

Haugen, Riston H.; Saunders, Diane G. O.; Leonelli, Lauriebeth; MacLean, Dan; Hogenhout, Saskia A.; Kamoun, Sophien

2013-01-01

Pucciniamonoica is a spectacular plant parasitic rust fungus that triggers the formation of flower-like structures (pseudoflowers) in its Brassicaceae host plant Boechera stricta . Pseudoflowers mimic in shape, color, nectar and scent co-occurring and unrelated flowers such as buttercups. They act to attract insects thereby aiding spore dispersal and sexual reproduction of the rust fungus. Although much ecological research has been performed on P . monoica -induced pseudoflowers, this system has yet to be investigated at the molecular or genomic level. To date, the molecular alterations underlying the development of pseudoflowers and the genes involved have not been described. To address this, we performed gene expression profiling to reveal 256 plant biological processes that are significantly altered in pseudoflowers. Among these biological processes, plant genes involved in cell fate specification, regulation of transcription, reproduction, floral organ development, anthocyanin (major floral pigments) and terpenoid biosynthesis (major floral volatile compounds) were down-regulated in pseudoflowers. In contrast, plant genes involved in shoot, cotyledon and leaf development, carbohydrate transport, wax biosynthesis, cutin transport and L-phenylalanine metabolism (pathway that results in phenylethanol and phenylacetaldehyde volatile production) were up-regulated. These findings point to an extensive reprogramming of host genes by the rust pathogen to induce floral mimicry. We also highlight 31 differentially regulated plant genes that are enriched in the biological processes mentioned above, and are potentially involved in the formation of pseudoflowers. This work illustrates the complex perturbations induced by rust pathogens in their host plants, and provides a starting point for understanding the molecular mechanisms of pathogen-induced floral mimicry. PMID:24069397

Major transcriptome reprogramming underlies floral mimicry induced by the rust fungus Puccinia monoica in Boechera stricta.

PubMed

Cano, Liliana M; Raffaele, Sylvain; Haugen, Riston H; Saunders, Diane G O; Leonelli, Lauriebeth; MacLean, Dan; Hogenhout, Saskia A; Kamoun, Sophien

2013-01-01

Pucciniamonoica is a spectacular plant parasitic rust fungus that triggers the formation of flower-like structures (pseudoflowers) in its Brassicaceae host plant Boecherastricta. Pseudoflowers mimic in shape, color, nectar and scent co-occurring and unrelated flowers such as buttercups. They act to attract insects thereby aiding spore dispersal and sexual reproduction of the rust fungus. Although much ecological research has been performed on P. monoica-induced pseudoflowers, this system has yet to be investigated at the molecular or genomic level. To date, the molecular alterations underlying the development of pseudoflowers and the genes involved have not been described. To address this, we performed gene expression profiling to reveal 256 plant biological processes that are significantly altered in pseudoflowers. Among these biological processes, plant genes involved in cell fate specification, regulation of transcription, reproduction, floral organ development, anthocyanin (major floral pigments) and terpenoid biosynthesis (major floral volatile compounds) were down-regulated in pseudoflowers. In contrast, plant genes involved in shoot, cotyledon and leaf development, carbohydrate transport, wax biosynthesis, cutin transport and L-phenylalanine metabolism (pathway that results in phenylethanol and phenylacetaldehyde volatile production) were up-regulated. These findings point to an extensive reprogramming of host genes by the rust pathogen to induce floral mimicry. We also highlight 31 differentially regulated plant genes that are enriched in the biological processes mentioned above, and are potentially involved in the formation of pseudoflowers. This work illustrates the complex perturbations induced by rust pathogens in their host plants, and provides a starting point for understanding the molecular mechanisms of pathogen-induced floral mimicry.

A Different Approach for Usage of the Implant Materials: The Composite Graft Prefabrication.

PubMed

Deniz, Lutfi Murat; Ataman, Murat Görkem; Borman, Huseyin; Erinanç, Hilal

2016-10-01

With all implanted materials, a certain sequence of biological events occurs following the implantation. This process is destructive to the implant and peri-implant tissues. The aforementioned sequence of biological events may be responsible for the complications. In this study, the natural biologic process following implantation was completed in an area other than the final implantation area. The aim was to keep the peri-implant tissues in the final implantation area away from the process. In the control group, the porous polyethylene discs were implanted to subcutaneous area on the frontal bone of the rats. A month after the implantation, macroscopic and microscopic examinations were performed. In the study group, the discs were implanted primarily above the rectus abdominis muscle of the rats. It was named as "the composite graft prefabrication." Twenty-one days after the first implantation, the discs were removed from the rectus muscle and implanted to subcutaneous area on the frontal bone of the rats. A month after the final implantation, macroscopic and microscopic examinations were performed. In macroscopic examination, all possible complications were evaluated. In microscopic examination, apoptosis, fibrosis, inflammation, and fibrovascular in-growing were evaluated. In the control group, implant exposure was observed in 3 of the rats. In the study group, no complications were observed. Although there was no statistical difference between 2 groups in the microscopic findings, at first glance, the inflammation seemed to be the factor responsible for the complication in the control group. According to the macroscopic results, the composite graft prefabrication seemed to be effective in preventing complications.

Life on Earth is an individual.

PubMed

Hermida, Margarida

2016-06-01

Life is a self-maintaining process based on metabolism. Something is said to be alive when it exhibits organization and is actively involved in its own continued existence through carrying out metabolic processes. A life is a spatio-temporally restricted event, which continues while the life processes are occurring in a particular chunk of matter (or, arguably, when they are temporally suspended, but can be restarted at any moment), even though there is continuous replacement of parts. Life is organized in discrete packages, particular cells and multicellular organisms with differing degrees of individuality. Biological species, too, have been shown to be individuals, and not classes, as these collections of organisms are spatio-temporally localized, restricted, continuous, and somewhat cohesive entities, with a definite beginning and end. Assuming that all life on Earth has a common origin, all living organisms, cells, and tissues descending from this origin exhibit continuity of the life processes at the cellular level, as well as many of the features that define the individual character of species: spatio-temporal localization and restriction, continuity, historicity, and cohesiveness. Therefore, life on Earth is an ontological individual. Independent origins of life will have produced other such individuals. These provisionally called 'life-individuals' constitute a category of organization of life which has seldom been recognized. The discovery of at least one independent life-individual would go a long way toward the project of the universality of biology.

Mycoplasma pneumoniae, an Underutilized Model for Bacterial Cell Biology

PubMed Central

2014-01-01

In recent decades, bacterial cell biology has seen great advances, and numerous model systems have been developed to study a wide variety of cellular processes, including cell division, motility, assembly of macromolecular structures, and biogenesis of cell polarity. Considerable attention has been given to these model organisms, which include Escherichia coli, Bacillus subtilis, Caulobacter crescentus, and Myxococcus xanthus. Studies of these processes in the pathogenic bacterium Mycoplasma pneumoniae and its close relatives have also been carried out on a smaller scale, but this work is often overlooked, in part due to this organism's reputation as minimalistic and simple. In this minireview, I discuss recent work on the role of the M. pneumoniae attachment organelle (AO), a structure required for adherence to host cells, in these processes. The AO is constructed from proteins that generally lack homology to those found in other organisms, and this construction occurs in coordination with cell cycle events. The proteins of the M. pneumoniae AO share compositional features with proteins with related roles in model organisms. Once constructed, the AO becomes activated for its role in a form of gliding motility whose underlying mechanism appears to be distinct from that of other gliding bacteria, including Mycoplasma mobile. Together with the FtsZ cytoskeletal protein, motility participates in the cell division process. My intention is to bring this deceptively complex organism into alignment with the better-known model systems. PMID:25157081

QM/MM hybrid calculation of biological macromolecules using a new interface program connecting QM and MM engines

NASA Astrophysics Data System (ADS)

Hagiwara, Yohsuke; Ohta, Takehiro; Tateno, Masaru

2009-02-01

An interface program connecting a quantum mechanics (QM) calculation engine, GAMESS, and a molecular mechanics (MM) calculation engine, AMBER, has been developed for QM/MM hybrid calculations. A protein-DNA complex is used as a test system to investigate the following two types of QM/MM schemes. In a 'subtractive' scheme, electrostatic interactions between QM/MM regions are truncated in QM calculations; in an 'additive' scheme, long-range electrostatic interactions within a cut-off distance from QM regions are introduced into one-electron integration terms of a QM Hamiltonian. In these calculations, 338 atoms are assigned as QM atoms using Hartree-Fock (HF)/density functional theory (DFT) hybrid all-electron calculations. By comparing the results of the additive and subtractive schemes, it is found that electronic structures are perturbed significantly by the introduction of MM partial charges surrounding QM regions, suggesting that biological processes occurring in functional sites are modulated by the surrounding structures. This also indicates that the effects of long-range electrostatic interactions involved in the QM Hamiltonian are crucial for accurate descriptions of electronic structures of biological macromolecules.

Paracrystalline Disorder from Phosphate Ion Orientation and Substitution in Synthetic Bone Mineral

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

Marisa, Mary E.; Zhou, Shiliang; Melot, Brent C.

Hydroxyapatite is an inorganic mineral closely resembling the mineral phase in bone. However, as a biological mineral, it is highly disordered, and its composition and atomistic structure remain poorly understood. Here, synchrotron X-ray total scattering and pair distribution function analysis methods provide insight into the nature of atomistic disorder in a synthetic bone mineral analogue, chemically substituted hydroxyapatite. By varying the effective hydrolysis rate and/or carbonate concentration during growth of the mineral, compounds with varied degrees of paracrystallinity are prepared. From advanced simulations constrained by the experimental pair distribution function and density functional theory, the paracrystalline disorder prevalent in thesemore » materials appears to result from accommodation of carbonate in the lattice through random displacement of the phosphate groups. Though many substitution modalities are likely to occur in concert, the most predominant substitution places carbonate into the mirror plane of an ideal phosphate site. Understanding the mineralogical imperfections of a biologically analogous hydroxyapatite is important not only to potential bone grafting applications but also to biological mineralization processes themselves.« less

Entropic-elasticity-controlled dissociation and energetic-elasticity-controlled rupture induce catch-to-slip bonds in cell-adhesion molecules.

PubMed

Wei, YuJie

2008-03-01

We develop a physical model to describe the kinetic behavior in cell-adhesion molecules. Unbinding of noncovalent biological bonds is assumed to occur by both bond dissociation and bond rupture. Such a decomposition of debonding processes is a space decomposition of the debonding events. Dissociation under thermal fluctuation is nondirectional in a three-dimensional space, and its energy barrier to escape is not influenced by a tensile force, but the microstates that could lead to dissociation are changed by the tensile force; rupture happens along the tensile force direction. An applied force effectively lowers the energy barrier to escape along the loading direction. The lifetime of the biological bond, due to the two concurrent off rates, may grow with increasing tensile force to a moderate amount and then decrease with further increasing load. We hypothesize that a catch-to-slip bond transition is a generic feature in biological bonds. The model also predicts that catch bonds in a more flexible molecular structure have longer lifetimes and need less force to be fully activated.

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

Recent advances on biological production of difructose dianhydride III.

PubMed

Zhu, Yingying; Yu, Shuhuai; Zhang, Wenli; Zhang, Tao; Guang, Cuie; Mu, Wanmeng

2018-04-01

Difructose dianhydride III (DFA III) is a cyclic difructose containing two reciprocal glycosidic linkages. It is easily generated with a small amount by sucrose caramelization and thus occurs in a wide range of food-stuffs during food processing. DFA III has half sweetness but only 1/15 energy of sucrose, showing potential industrial application as low-calorie sucrose substitute. In addition, it displays many benefits including prebiotic effect, low cariogenicity property, and hypocholesterolemic effect, and improves absorption of minerals, flavonoids, and immunoglobulin G. DFA III is biologically produced from inulin by inulin fructotransferase (IFTase, EC 4.2.2.18). Plenty of DFA III-producing enzymes have been identified. The crystal structure of inulin fructotransferase has been determined, and its molecular modification has been performed to improve the catalytic activity and structural stability. Large-scale production of DFA III has been studied by various IFTases, especially using an ultrafiltration membrane bioreactor. In this article, the recent findings on physiological effects of DFA III are briefly summarized; the research progresses on identification, expression, and molecular modification of IFTase and large-scale biological production of DFA III by IFTase are reviewed in detail.

Mesoscale Eddies Are Oases for Higher Trophic Marine Life

PubMed Central

Godø, Olav R.; Samuelsen, Annette; Macaulay, Gavin J.; Patel, Ruben; Hjøllo, Solfrid Sætre; Horne, John; Kaartvedt, Stein; Johannessen, Johnny A.

2012-01-01

Mesoscale eddies stimulate biological production in the ocean, but knowledge of energy transfers to higher trophic levels within eddies remains fragmented and not quantified. Increasing the knowledge base is constrained by the inability of traditional sampling methods to adequately sample biological processes at the spatio-temporal scales at which they occur. By combining satellite and acoustic observations over spatial scales of 10 s of km horizontally and 100 s of m vertically, supported by hydrographical and biological sampling we show that anticyclonic eddies shape distribution and density of marine life from the surface to bathyal depths. Fish feed along density structures of eddies, demonstrating that eddies catalyze energy transfer across trophic levels. Eddies create attractive pelagic habitats, analogous to oases in the desert, for higher trophic level aquatic organisms through enhanced 3-D motion that accumulates and redistributes biomass, contributing to overall bioproduction in the ocean. Integrating multidisciplinary observation methodologies promoted a new understanding of biophysical interaction in mesoscale eddies. Our findings emphasize the impact of eddies on the patchiness of biomass in the sea and demonstrate that they provide rich feeding habitat for higher trophic marine life. PMID:22272294

Molecular chaperones as therapeutic targets to counteract proteostasis defects.

PubMed

Cattaneo, Monica; Dominici, Roberto; Cardano, Marina; Diaferia, Giuseppe; Rovida, Ermanna; Biunno, Ida

2012-03-01

The health of cells is preserved by the levels and correct folding states of the proteome, which is generated and maintained by the proteostasis network, an integrated biological system consisting of several cytoprotective and degradative pathways. Indeed, the health conditions of the proteostasis network is a fundamental prerequisite to life as the inability to cope with the mismanagement of protein folding arising from genetic, epigenetic, and micro-environment stress appears to trigger a whole spectrum of unrelated diseases. Here we describe the potential functional role of the proteostasis network in tumor biology and in conformational diseases debating on how the signaling branches of this biological system may be manipulated to develop more efficacious and selective therapeutic strategies. We discuss the dual strategy of these processes in modulating the folding activity of molecular chaperones in order to counteract the antithetic proteostasis deficiencies occurring in cancer and loss/gain of function diseases. Finally, we provide perspectives on how to improve the outcome of these disorders by taking advantage of proteostasis modeling. Copyright © 2011 Wiley Periodicals, Inc.

Enhancement of transmission of laser and other radiation by soft turbid physical and biological media

NASA Astrophysics Data System (ADS)

Askar'yan, G. A.

1982-07-01

An analysis is made and experimental results are reported of studies of the transmission of laser and other radiation by turbid physical and biological media, such as layers of a scattering medium or human tissue of thickness much greater than the characteristic attenuation length. It is reported that the transmission increases strongly as a result of depression and piercing of soft scattering media. A local pressure applied to a biological tissue produces a transmission enhancement considerably greater than compression of a layer of a physically turbid medium: this is due to the displacement of blood and of muscle out of the compressed region. A reduction in the scattering and absorption is expected to occur also in the case of rf and ionizing radiations, such as charged particles, x rays, gamma rays, etc. It is pointed out that this could be useful in deep irradiation carried out with the aim of inhibiting internal morbid processes (for example, in the spinal cord) and in treatment of neuroinfectious diseases (amyotrophic lateral sclerosis, multiple sclerosis, poliomyelitis, etc.), as well as in oncological conditions, ulcers, etc.

An experimental study of the biological effects of geomagnetic disturbances: The impact of a typical geomagnetic storm and its constituents on plants and animals

NASA Astrophysics Data System (ADS)

Krylov, Viacheslav V.; Zotov, Oleg D.; Klain, Boris I.; Ushakova, Natalia V.; Kantserova, Nadezhda P.; Znobisheva, Anna V.; Izyumov, Yuri G.; Kuz'mina, Victoria V.; Morozov, Alexey A.; Lysenko, Liudmila A.; Nemova, Nina N.; Osipova, Elena A.

2014-04-01

Naturally occurring geomagnetic storms have been shown to correlate with changes in organisms' biological processes. Changes in the geomagnetic field during a geomagnetic storm are complex and contain both slow changes of the geomagnetic field with frequencies of up to 0.001 Hz, and various geomagnetic pulsations observed in general to be within the range of 0.001-5 Hz. Little is known about what frequency constituent of geomagnetic storms has the strongest effect on living organisms. This paper uses an experimental approach to demonstrate that organisms from different taxa principally respond to slow changes of the geomagnetic field corresponding with the main phase and the initial period of the recovery phase of a geomagnetic storm. Pc1 type pulsations, which are commonly regarded as biologically effective elements of geomagnetic disturbances, did not affect controlled parameters in our experiments. This paper may serve as a starting point for a thorough inquiry into the influence of slow fluctuations of the geomagnetic field on organisms.

When things don't add up: quantifying impacts of multiple stressors from individual metabolism to ecosystem processing.

PubMed

Galic, Nika; Sullivan, Lauren L; Grimm, Volker; Forbes, Valery E

2018-04-01

Ecosystems are exposed to multiple stressors which can compromise functioning and service delivery. These stressors often co-occur and interact in different ways which are not yet fully understood. Here, we applied a population model representing a freshwater amphipod feeding on leaf litter in forested streams. We simulated impacts of hypothetical stressors, individually and in pairwise combinations that target the individuals' feeding, maintenance, growth and reproduction. Impacts were quantified by examining responses at three levels of biological organisation: individual-level body sizes and cumulative reproduction, population-level abundance and biomass and ecosystem-level leaf litter decomposition. Interactive effects of multiple stressors at the individual level were mostly antagonistic, that is, less negative than expected. Most population- and ecosystem-level responses to multiple stressors were stronger than expected from an additive model, that is, synergistic. Our results suggest that across levels of biological organisation responses to multiple stressors are rarely only additive. We suggest methods for efficiently quantifying impacts of multiple stressors at different levels of biological organisation. © 2018 John Wiley & Sons Ltd/CNRS.

Role of high molecular mass organics in colour formation during biological treatment of pulp and paper wastewater.

PubMed

Milestone, C B; Stuthridge, T R; Fulthorpe, R R

2007-01-01

This paper forms part of series of biological treatment colour behaviour studies. Surveys across a range of mills have observed colour increases in aerated stabilisation basins of 20-45%. Much of the colour formation has been demonstrated to occur in high molecular mass effluent organic constituents (HMM) present in bleach plant effluents. Removing material greater than 3000 Da essentially eliminated the colour forming ability in both E and D stage wastewaters. We have also shown that pulp and paper sludges contain anaerobic bacteria capable of reducing humic like materials. Colour formation was correlated to the anoxic conditions and the availability of readily biodegradable organic constituents during the wastewater treatment process. Overall, these studies suggest that colour formation in pulp and paper biological treatment systems may be caused by anaerobic bacteria using HMM material from the bleaching effluents as an electron acceptor for growth. This leads to the reduction of the material, which in turn leads to non-reversible internal changes, such as intra-molecular polymerisation or formation of chromophoric functional groups.

From urban municipalities to polar bioremediation: the characterisation and contribution of biogenic minerals for water treatment.

PubMed

Freidman, Benjamin L; Northcott, Kathy A; Thiel, Peta; Gras, Sally L; Snape, Ian; Stevens, Geoff W; Mumford, Kathryn A

2017-06-01

Minerals of biological origin have shown significant potential for the separation of contaminants from water worldwide. This study details the contribution of biologically derived minerals to water treatment operations, with a focus on filtration media from urban municipalities and remote cold regions. The results support biofilm-embedded iron and manganese to be the building blocks of biogenic mineral development on activated carbon and nutrient-amended zeolites. The presence of similar iron and manganese oxidising bacterial species across all filter media supports the analogous morphologies of biogenic minerals between sites and suggests that biological water treatment processes may be feasible across a range of climates. This is the first time the stages of biogenic mineral formation have been aligned with comprehensive imaging of the biofilm community and bacterial identification; especially with respect to cold regions. Where biogenic mineral formation occurs on filter media, the potential exists for enhanced adsorption for a range of organic and inorganic contaminants and improved longevity of filter media beyond the adsorption or exchange capacities of the raw material.

Extracellular Production of Reactive Oxygen Species by Marine Microbiota

NASA Astrophysics Data System (ADS)

Schneider, R. J.; Roe, K. L.; Voelker, B. M.; Hansel, C. M.

2016-02-01

The reactive oxygen species (ROS) superoxide (O2-) and hydrogen peroxide (H2O2) are important to the cycling of trace metals and carbon in marine systems. Previous studies have shown that biological ROS production in the ocean may be significant. We examined the ability of five common species of diatoms to produce and break down ROS in the presence and absence of light by suspending cells on filters and measuring downstream ROS concentrations using chemiluminescence probes. Results show a wide range of rates (undetectable to 7.3 x 10-16 mol cell-1 hr-1) and suggest that extracellular ROS production occurs through a variety of pathways. H2O2 decay appears to be mediated primarily by active cell processes, while O2- appears to occur through a combination of active and passive cell processes. Extracellular H2O2 production and decay were also determined for twelve species of heterotrophic bacteria using two different methodologies. Measured decay rates were consistent despite methodological differences. By contrast, large variability of production rates was observed could vary significantly even among between replicates of the same species measured using the same methodology. Although production rates cannot be stated with certainty, it is likely that extracellular H2O2 production occurs in most bacterial species.

Induction of interleukin 1 by synthetic and naturally occurring muramyl peptides.

PubMed

Dinarello, C A; Krueger, J M

1986-10-01

Like bacterial lipopolysaccharides (endotoxins), synthetic muramyl peptides (MPs) are thought to exert many of their biological effects by inducing the production of various mediators from host cells. Both synthetic muramyl dipeptide (MDP) and naturally occurring sleep factor (SF), which contains an MP structure, stimulate human monocytes to produce interleukin 1 (IL 1). IL 1 is a family of unique polypeptides that mediate a variety of host defense functions and possess several biological properties, many of which are shared with MPs. Endotoxins are potent inducers of IL 1, but polymyxin B, which blocks endotoxin's biological activities, has no effect on MP-induced IL 1 production. SF purified from human urine and SF isolated from the peritoneal fluid of patients undergoing chronic ambulatory peritoneal dialysis (CAPD) induce IL 1 when incubated with human mononuclear cells in vitro. SF from urine or CAPD fluid induces IL 1 production in the picrogram per milliliter range whereas synthetic MDP requires microgram per milliliter concentrations. Thus, both synthetic and naturally occurring MPs exert their biological effects, in part, by inducing IL 1.

The immersion freezing behavior of mineral dust particles mixed with biological substances

NASA Astrophysics Data System (ADS)

Augustin-Bauditz, S.; Wex, H.; Denjean, C.; Hartmann, S.; Schneider, J.; Schmidt, S.; Ebert, M.; Stratmann, F.

2015-10-01

Biological particles such as bacteria, fungal spores or pollen are known to be efficient ice nucleating particles. Their ability to nucleate ice is due to ice nucleation active macromolecules (INM). It has been suggested that these INM maintain their nucleating ability even when they are separated from their original carriers. This opens the possibility of an accumulation of such INM in e.g., soils, resulting in an internal mixture of mineral dust and INM. If particles from such soils which contain biological INM are then dispersed into the atmosphere due to wind erosion or agricultural processes, they could induce ice nucleation at temperatures typical for biological substances, i.e., above -20 up to almost 0 °C. To explore this hypothesis, we performed a measurement campaign within the research unit INUIT, where we investigated the ice nucleation behavior of mineral dust particles internally mixed with INM. Specifically, we mixed a pure mineral dust sample (illite-NX) with ice active biological material (birch pollen washing water) and quantified the immersion freezing behavior of the resulting particles utilizing the Leipzig Aerosol Cloud Interaction Simulator (LACIS). To characterize the mixing state of the generated aerosol we used different methods which will also be discussed. We found that internally mixed particles, containing ice active biological material, follow the ice nucleation behavior observed for the purely biological particles, i.e. freezing occurs at temperatures at which mineral dusts themselves are not yet ice active. It can be concluded that INM located on a mineral dust particle determine the freezing behavior of that particle.

[Caffeine and adaptive changes in the circulatory system during pregnancy].

PubMed

Cendrowska-Pinkosz, Monika; Dworzański, Wojciech; Krauze, Magdalena; Burdan, Franciszek

2017-01-23

Adaptive physiological changes that occur in pregnant women can fluctuate with the intake of substances with proven, adverse biological effect on the body. Due to the fact that caffeine is one of the most chronically used xenobiotics, the impact of consuming caffeine on adaptive processes in the circulatory system of a pregnant women required a research. Many researchers emphasise its negative effect on the circulatory system of the mother and her offspring. However, in spite of years of observation, there is no clear answer to what extent dose or in what period of time the caffeine modulates the adaptive processes during pregnancy. Because of the potential risk the supply of caffeine during pregnancy should be subjected to considerable restrictions.

Homo sapiens in the Americas. Overview of the earliest human expansion in the New World.

PubMed

Marangoni, Aurelio; Caramelli, David; Manzi, Giorgio

2014-01-01

Although it is widely recognised that America was the last continent to be populated by our species, researchers' views on various aspects of this process (e.g. the period in which it occurred, the area from which the colonizing populations came, the number of dispersal waves and the routes taken by these migrations) differ significantly. In this paper, we review both classical data and more recent findings from various research fields - including geology, paleoecology, archaeology, skeletal biology, and genetics - that may shed light on the dynamics of the colonization of the American continent, according to a critical reappraisal of the various hypotheses and models that have been advanced over time to explain this process.

Factors Affecting Wound Healing

PubMed Central

Guo, S.; DiPietro, L.A.

2010-01-01

Wound healing, as a normal biological process in the human body, is achieved through four precisely and highly programmed phases: hemostasis, inflammation, proliferation, and remodeling. For a wound to heal successfully, all four phases must occur in the proper sequence and time frame. Many factors can interfere with one or more phases of this process, thus causing improper or impaired wound healing. This article reviews the recent literature on the most significant factors that affect cutaneous wound healing and the potential cellular and/or molecular mechanisms involved. The factors discussed include oxygenation, infection, age and sex hormones, stress, diabetes, obesity, medications, alcoholism, smoking, and nutrition. A better understanding of the influence of these factors on repair may lead to therapeutics that improve wound healing and resolve impaired wounds. PMID:20139336

Shortcut nitrification/partial nitritation start-up for reject water treatment in a SBR

NASA Astrophysics Data System (ADS)

Muszyński-Huhajło, Mateusz; Miodoński, Stanisław

2017-11-01

For many wastewater treatment plants (WWTPs), side-stream treatment of reject water from digested sludge dewatering is a feasible opportunity to improve N-removal efficiency without costly plant expansion. Biological nitrogen removal over nitrite or combined partial nitritation (PN)-Anammox process has recently become a popular treatment method for such ammonium-rich streams. Shortcut nitrification and PN start-ups were successfully performed in a pilot-scale SBR treating real reject water. In all performed experiments, effective nitrate production inhibition occurred in less than 20 days due to operational conditions selection and without advanced control system. pH adjustment in the PN reactor allowed to achieve NO2-N /NH4-N ratio suitable for Anammox process (1.24±0.07).

Different Facets of Copy Number Changes: Permanent, Transient, and Adaptive

PubMed Central

Mishra, Sweta

2016-01-01

Chromosomal copy number changes are frequently associated with harmful consequences and are thought of as an underlying mechanism for the development of diseases. However, changes in copy number are observed during development and occur during normal biological processes. In this review, we highlight the causes and consequences of copy number changes in normal physiologic processes as well as cover their associations with cancer and acquired drug resistance. We discuss the permanent and transient nature of copy number gains and relate these observations to a new mechanism driving transient site-specific copy gains (TSSGs). Finally, we discuss implications of TSSGs in generating intratumoral heterogeneity and tumor evolution and how TSSGs can influence the therapeutic response in cancer. PMID:26755558

Factors affecting wound healing.

PubMed

Guo, S; Dipietro, L A

2010-03-01

Wound healing, as a normal biological process in the human body, is achieved through four precisely and highly programmed phases: hemostasis, inflammation, proliferation, and remodeling. For a wound to heal successfully, all four phases must occur in the proper sequence and time frame. Many factors can interfere with one or more phases of this process, thus causing improper or impaired wound healing. This article reviews the recent literature on the most significant factors that affect cutaneous wound healing and the potential cellular and/or molecular mechanisms involved. The factors discussed include oxygenation, infection, age and sex hormones, stress, diabetes, obesity, medications, alcoholism, smoking, and nutrition. A better understanding of the influence of these factors on repair may lead to therapeutics that improve wound healing and resolve impaired wounds.

Bioactive Molecules in Soil Ecosystems: Masters of the Underground

PubMed Central

Zhuang, Xuliang; Gao, Jie; Ma, Anzhou; Fu, Shenglei; Zhuang, Guoqiang

2013-01-01

Complex biological and ecological processes occur in the rhizosphere through ecosystem-level interactions between roots, microorganisms and soil fauna. Over the past decade, studies of the rhizosphere have revealed that when roots, microorganisms and soil fauna physically contact one another, bioactive molecular exchanges often mediate these interactions as intercellular signal, which prepare the partners for successful interactions. Despite the importance of bioactive molecules in sustainable agriculture, little is known of their numerous functions, and improving plant health and productivity by altering ecological processes remains difficult. In this review, we describe the major bioactive molecules present in below-ground ecosystems (i.e., flavonoids, exopolysaccharides, antibiotics and quorum-sensing signals), and we discuss how these molecules affect microbial communities, nutrient availability and plant defense responses. PMID:23615474

Dynamic nanoplatforms in biosensor and membrane constitutional systems.

PubMed

Mahon, Eugene; Aastrup, Teodor; Barboiu, Mihail

2012-01-01

Molecular recognition in biological systems occurs mainly at interfacial environments such as membrane surfaces, enzyme active sites, or the interior of the DNA double helix. At the cell membrane surface, carbohydrate-protein recognition principles apply to a range of specific non-covalent interactions including immune response, cell proliferation, adhesion and death, cell-cell interaction and communication. Protein-protein recognition meanwhile accounts for signalling processes and ion channel structure. In this chapter we aim to describe such constitutional dynamic interfaces for biosensing and membrane transport applications. Constitutionally adaptive interfaces may mimic the recognition capabilities intrinsic to natural recognition processes. We present some recent examples of 2D and 3D constructed sensors and membranes of this type and describe their sensing and transport capabilities.

Synthesis, structural characterization and biological activity of two diastereomeric JA-Ile macrolactones.

PubMed

Jimenez-Aleman, Guillermo H; Machado, Ricardo A R; Görls, Helmar; Baldwin, Ian T; Boland, Wilhelm

2015-06-07

Jasmonates are phytohormones involved in a wide range of plant processes, including growth, development, senescence, and defense. Jasmonoyl-L-isoleucine (JA-Ile, 2), an amino acid conjugate of jasmonic acid (JA, 1), has been identified as a bioactive endogenous jasmonate. However, JA-Ile (2) analogues trigger different responses in the plant. ω-Hydroxylation of the pentenyl side chain leads to the inactive 12-OH-JA-Ile (3) acting as a “stop” signal. On the other hand, a lactone derivative of 12-OH-JA (5) (jasmine ketolactone, JKL) occurs in nature, although with no known biological function. Inspired by the chemical structure of JKL (6) and in order to further explore the potential biological activities of 12-modified JA-Ile derivatives, we synthesized two macrolactones (JA-Ile-lactones (4a) and (4b)) derived from 12-OH-JA-Ile (3). The biological activity of (4a) and (4b) was tested for their ability to elicit nicotine production, a well-known jasmonate dependent secondary metabolite. Both macrolactones showed strong biological activity, inducing nicotine accumulation to a similar extent as methyl jasmonate does in Nicotiana attenuata leaves. Surprisingly, the highest nicotine contents were found in plants treated with the JA-Ile-lactone (4b), which has (3S,7S) configuration at the cyclopentanone not known from natural jasmonates. Macrolactone (4a) is a valuable standard to explore for its occurrence in nature.

Counting motifs in dynamic networks.

PubMed

Mukherjee, Kingshuk; Hasan, Md Mahmudul; Boucher, Christina; Kahveci, Tamer

2018-04-11

A network motif is a sub-network that occurs frequently in a given network. Detection of such motifs is important since they uncover functions and local properties of the given biological network. Finding motifs is however a computationally challenging task as it requires solving the costly subgraph isomorphism problem. Moreover, the topology of biological networks change over time. These changing networks are called dynamic biological networks. As the network evolves, frequency of each motif in the network also changes. Computing the frequency of a given motif from scratch in a dynamic network as the network topology evolves is infeasible, particularly for large and fast evolving networks. In this article, we design and develop a scalable method for counting the number of motifs in a dynamic biological network. Our method incrementally updates the frequency of each motif as the underlying network's topology evolves. Our experiments demonstrate that our method can update the frequency of each motif in orders of magnitude faster than counting the motif embeddings every time the network changes. If the network evolves more frequently, the margin with which our method outperforms the existing static methods, increases. We evaluated our method extensively using synthetic and real datasets, and show that our method is highly accurate(≥ 96%) and that it can be scaled to large dense networks. The results on real data demonstrate the utility of our method in revealing interesting insights on the evolution of biological processes.

In silico prediction of protein-protein interactions in human macrophages

PubMed Central

2014-01-01

Background Protein-protein interaction (PPI) network analyses are highly valuable in deciphering and understanding the intricate organisation of cellular functions. Nevertheless, the majority of available protein-protein interaction networks are context-less, i.e. without any reference to the spatial, temporal or physiological conditions in which the interactions may occur. In this work, we are proposing a protocol to infer the most likely protein-protein interaction (PPI) network in human macrophages. Results We integrated the PPI dataset from the Agile Protein Interaction DataAnalyzer (APID) with different meta-data to infer a contextualized macrophage-specific interactome using a combination of statistical methods. The obtained interactome is enriched in experimentally verified interactions and in proteins involved in macrophage-related biological processes (i.e. immune response activation, regulation of apoptosis). As a case study, we used the contextualized interactome to highlight the cellular processes induced upon Mycobacterium tuberculosis infection. Conclusion Our work confirms that contextualizing interactomes improves the biological significance of bioinformatic analyses. More specifically, studying such inferred network rather than focusing at the gene expression level only, is informative on the processes involved in the host response. Indeed, important immune features such as apoptosis are solely highlighted when the spotlight is on the protein interaction level. PMID:24636261

Positron follow-up in liquid water: I. A new Monte Carlo track-structure code.

PubMed

Champion, C; Le Loirec, C

2006-04-07

When biological matter is irradiated by charged particles, a wide variety of interactions occur, which lead to a deep modification of the cellular environment. To understand the fine structure of the microscopic distribution of energy deposits, Monte Carlo event-by-event simulations are particularly suitable. However, the development of these track-structure codes needs accurate interaction cross sections for all the electronic processes: ionization, excitation, positronium formation and even elastic scattering. Under these conditions, we have recently developed a Monte Carlo code for positrons in water, the latter being commonly used to simulate the biological medium. All the processes are studied in detail via theoretical differential and total cross-section calculations performed by using partial wave methods. Comparisons with existing theoretical and experimental data in terms of stopping powers, mean energy transfers and ranges show very good agreements. Moreover, thanks to the theoretical description of positronium formation, we have access, for the first time, to the complete kinematics of the electron capture process. Then, the present Monte Carlo code is able to describe the detailed positronium history, which will provide useful information for medical imaging (like positron emission tomography) where improvements are needed to define with the best accuracy the tumoural volumes.

AACR Centennial Series: The Biology of Cancer Metastasis: Historical Perspective

PubMed Central

Talmadge, James E; Fidler, Isaiah J

2014-01-01

Metastases resistant to therapy is the major cause of death from cancer. Despite almost 200 years of study, the process of tumor metastasis remains controversial. Stephen Paget initially identified the role of host-tumor interactions on the basis of a review of autopsy records. His “seed and soil” hypothesis was substantiated a century later with experimental studies and numerous reports have confirmed these seminal observations. Inarguably, an improved understanding of the metastatic process and the attributes of the cells selected by this process are critical to the treatment of patients with systemic disease. In many patients, metastasis has occurred by the time of diagnosis, such that metastasis prevention may not be relevant, and treatment of systemic disease, as well as the identity of patients with early disease, should be our goal. During the last three decades, revitalized research has focused on new discoveries in the biology of metastasis. While our understanding of the molecular events that regulate metastasis has improved; nonetheless, the relevant contributions and timing of molecular lesion(s) potentially involved in its pathogenesis remain unclear. The history of pioneering observations and discussion of current controversies should help investigators understand the complex and multifactorial interactions between the host and selected tumor cells that contribute to fatal metastasis and allow for the design of successful therapy. PMID:20610625

The Ocean's Vital Skin: Toward an Integrated Understanding of the Sea Surface Microlayer

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

Engel, Anja; Bange, Hermann W.; Cunliffe, Michael

Despite the huge extent of the ocean’s surface, until now relatively little attention has been paid to the sea surface microlayer (SML) as the ultimate interface where heat, momentum and mass exchange between the ocean and the atmosphere takes place. Via the SML, large-scale environmental changes in the ocean such as warming, acidification, deoxygenation, and eutrophication potentially influence cloud formation, precipitation, and the global radiation balance. Due to the deep connectivity between biological, chemical, and physical processes, studies of the SML may reveal multiple sensitivities to global and regional changes. Understanding the processes at the ocean’s surface, in particular involvingmore » the SML as an important and determinant interface, could therefore provide an essential contribution to the reduction of uncertainties regarding ocean-climate feedbacks. This review identifies gaps in our current knowledge of the SML and highlights a need to develop a holistic and mechanistic understanding of the diverse biological, chemical, and physical processes occurring at the ocean-atmosphere interface. We advocate the development of strong interdisciplinary expertise and collaboration in order to bridge between ocean and atmospheric sciences. Although this will pose significant methodological challenges, such an initiative would represent a new role model for interdisciplinary research in Earth System sciences.« less

The Ocean's Vital Skin: Toward an Integrated Understanding of the Sea Surface Microlayer

DOE PAGES

Engel, Anja; Bange, Hermann W.; Cunliffe, Michael; ...

2017-05-30

Despite the huge extent of the ocean’s surface, until now relatively little attention has been paid to the sea surface microlayer (SML) as the ultimate interface where heat, momentum and mass exchange between the ocean and the atmosphere takes place. Via the SML, large-scale environmental changes in the ocean such as warming, acidification, deoxygenation, and eutrophication potentially influence cloud formation, precipitation, and the global radiation balance. Due to the deep connectivity between biological, chemical, and physical processes, studies of the SML may reveal multiple sensitivities to global and regional changes. Understanding the processes at the ocean’s surface, in particular involvingmore » the SML as an important and determinant interface, could therefore provide an essential contribution to the reduction of uncertainties regarding ocean-climate feedbacks. This review identifies gaps in our current knowledge of the SML and highlights a need to develop a holistic and mechanistic understanding of the diverse biological, chemical, and physical processes occurring at the ocean-atmosphere interface. We advocate the development of strong interdisciplinary expertise and collaboration in order to bridge between ocean and atmospheric sciences. Although this will pose significant methodological challenges, such an initiative would represent a new role model for interdisciplinary research in Earth System sciences.« less

Biological Treatment of Water Disinfection Byproducts using ...

EPA Pesticide Factsheets

Major disinfection by-products (DBPs) from the chlorination process of drinking water include trihalomethanes (THMs) and haloacetic acides (HAA5). THMs mainly consist of chloroform, and other harsh chemicals. Prolonged consumptions of drinking water containing high levels of THMs has been linked with diseases of the liver, kidneys, bladder, or central nervous system and may increase likelihood of cancer. A risk also exists for THMs exposure via inhalation while showering, bathing or washing clothes and dishes. Due to these risks, the U.S. EPA regulate THMs content in drinking water. This research investigates biological degradation of THM using chloroform as a model compound. The study aims to decrease possible risks of THMs through filtration. Throughout this year’s presentations, there is a common theme of health and safety concerns. UC researchers are working hard to clean water ways of naturally occurring contaminates as well as man-made toxins found in our waterways. The significance of these presentations translates into the promise of safer environments, and more importantly saved lives, as UC’s faculty continues to produce real-world solutions to problems threatening the world around us. A biotech process has been developed and demonstrated that effectively remove and treat volatile disinfection by-products from drinking water. The process strips low concentration disinfection by-products, such as trihalomethanes, that are formed during the chlori

Electrobioremediation of oil spills.

PubMed

Daghio, Matteo; Aulenta, Federico; Vaiopoulou, Eleni; Franzetti, Andrea; Arends, Jan B A; Sherry, Angela; Suárez-Suárez, Ana; Head, Ian M; Bestetti, Giuseppina; Rabaey, Korneel

2017-05-01

Annually, thousands of oil spills occur across the globe. As a result, petroleum substances and petrochemical compounds are widespread contaminants causing concern due to their toxicity and recalcitrance. Many remediation strategies have been developed using both physicochemical and biological approaches. Biological strategies are most benign, aiming to enhance microbial metabolic activities by supplying limiting inorganic nutrients, electron acceptors or donors, thus stimulating oxidation or reduction of contaminants. A key issue is controlling the supply of electron donors/acceptors. Bioelectrochemical systems (BES) have emerged, in which an electrical current serves as either electron donor or acceptor for oil spill bioremediation. BES are highly controllable and can possibly also serve as biosensors for real time monitoring of the degradation process. Despite being promising, multiple aspects need to be considered to make BES suitable for field applications including system design, electrode materials, operational parameters, mode of action and radius of influence. The microbiological processes, involved in bioelectrochemical contaminant degradation, are currently not fully understood, particularly in relation to electron transfer mechanisms. Especially in sulfate rich environments, the sulfur cycle appears pivotal during hydrocarbon oxidation. This review provides a comprehensive analysis of the research on bioelectrochemical remediation of oil spills and of the key parameters involved in the process. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Paradox of Restoring Native River Landscapes and Restoring Native Ecosystems in the Colorado River System

NASA Astrophysics Data System (ADS)

Schmidt, J. C.

2014-12-01

Throughout the Colorado River basin (CRb), scientists and river managers collaborate to improve native ecosystems. Native ecosystems have deteriorated due to construction of dams and diversions that alter natural flow, sediment supply, and temperature regimes, trans-basin diversions that extract large amounts of water from some segments of the channel network, and invasion of non-native animals and plants. These scientist/manager collaborations occur in large, multi-stakeholder, adaptive management programs that include the Lower Colorado River Multi-Species Conservation Program, the Glen Canyon Dam Adaptive Management Program, and the Upper Colorado River Endangered Species Recovery Program. Although a fundamental premise of native species recovery is that restoration of predam flow regimes inevitably leads to native species recovery, such is not the case in many parts of the CRb. For example, populations of the endangered humpback chub (Gila cypha) are largest in the sediment deficit, thermally altered conditions of the Colorado River downstream from Glen Canyon Dam, but these species occur in much smaller numbers in the upper CRb even though the flow regime, sediment supply, and sediment mass balance are less perturbed. Similar contrasts in the physical and biological response of restoration of predam flow regimes occurs in floodplains dominated by nonnative tamarisk (Tamarix spp.) where reestablishment of floods has the potential to exacerbate vertical accretion processes that disconnect the floodplain from the modern flow regime. A significant challenge in restoring segments of the CRb is to describe this paradox of physical and biological response to reestablishment of pre-dam flow regimes, and to clearly identify objectives of environmentally oriented river management. In many cases, understanding the nature of the perturbation to sediment mass balance caused by dams and diversions and understanding the constraints imposed by societal commitments to provide assured water supplies and hydroelectricity constrains the opportunities for rehabilitation and limits the management objectives to focus either on restoring predam physical processes or recovering native fish fauna and/or recovering native plant communities.

[Health risks in the biotechnological industry].

PubMed

Colombi, A; Maroni, M; Foà, V

1989-01-01

Biotechnology has been defined as the application of biological organisms, systems or processes to manufacturing and service industries. In considering health aspects of biotechnological development it must be underlined that the use of microorganisms in traditional industries, such as the production of food, bread, beer and dairy products, has not added significantly to the more usual industrial hazards. The risk factors encountered in the biotechnology industry can be defined as general, i.e., common to other industrial activities, and specific, i.e., depending on the presence of microorganisms and/or their metabolic products. The specific health risks vary according to the type of process, but can be grouped into three main categories: immunological diseases, toxic effects; pathological effects of microorganisms. Allergic immunological diseases such as bronchial asthma, contact dermatitis, oculo-rhinitis and extrinsic allergic alveolitis are by far the most frequent and well known diseases occurring among workers employed on biotechnological production. Toxic effects were observed among workers employed on the production of antibiotics and hormones or single cell proteins, where absorption of endotoxins has been described. Infectious diseases may arise from uncontrolled dissemination of pathogenic microorganisms through aerosols, dusts, aqueous and semisolid sludge effluents from biotechnological plants. The greatest risks occur in the production of antiviral vaccines, in research laboratories and in waste-water treatment plants. Risk of pathogenic effects has also been speculated from exposure to engineered microorganisms in laboratory and environmental or agricultural applications. Safety precautions consisting of protective measures, and effective barriers of containment (both physical and biological) have to be advised according to the hazardous characteristics of the organisms.(ABSTRACT TRUNCATED AT 250 WORDS)

Have sex or not? Lessons from bacteria.

PubMed

Lodé, T

2012-01-01

Sex is one of the greatest puzzles in evolutionary biology. A true meiotic process occurs only in eukaryotes, while in bacteria, gene transcription is fragmentary, so asexual reproduction in this case really means clonal reproduction. Sex could stem from a signal that leads to increased reproductive output of all interacting individuals and could be understood as a secondary consequence of primitive metabolic reactions. Meiotic sex evolved in proto-eukaryotes to solve a problem that bacteria did not have, namely a large amount of DNA material, occurring in an archaic step of proto-cell formation and genetic exchanges. Rather than providing selective advantages through reproduction, sex could be thought of as a series of separate events which combines step-by-step some very weak benefits of recombination, meiosis, gametogenesis and syngamy. Copyright © 2012 S. Karger AG, Basel.

Organic-Chemical Clues to the Theory of Impacts as a Cause of Mass Extinctions

NASA Astrophysics Data System (ADS)

Sack, N. J.

1988-11-01

The reasons for the mass extinctions, which occur from time to time in Earth's history-as, e.g., the dinosaur extinction at the Cretaceous/Tertiary boundary 65 myr ago - are still not satisfactorily cleared up. A possible reason might be the impact of one or several comets of several kilometers in diameter. In this paper the astrophysical background of this hypothesis and organic-chemical processes during an impact will be discussed. Quantitative estimations are given, which show that the amount of organic substances brought to the Earth may be of the same order of magnitude as the normal biological production of organic material. Investigations are proposed to examine the organic-chemical composition of profiles of the Cretaceous/Tertiary boundary and other boundaries, at which mass extinction had occurred, in order to find anomalies as consequences of impacts.

Real-Time Single Molecule Visualization of SH2 Domain Membrane Recruitment in Growth Factor Stimulated Cells.

PubMed

Oh, Dongmyung

2017-01-01

In the last decade, single molecule tracking (SMT) techniques have emerged as a versatile tool for molecular cell biology research. This approach allows researchers to monitor the real-time behavior of individual molecules in living cells with nanometer and millisecond resolution. As a result, it is possible to visualize biological processes as they occur at a molecular level in real time. Here we describe a method for the real-time visualization of SH2 domain membrane recruitment from the cytoplasm to epidermal growth factor (EGF) induced phosphotyrosine sites on the EGF receptor. Further, we describe methods that utilize SMT data to define SH2 domain membrane dynamics parameters such as binding (τ), dissociation (k d ), and diffusion (D) rates. Together these methods may allow us to gain greater understanding of signal transduction dynamics and the molecular basis of disease-related aberrant pathways.

Theoretical Investigation of Optical Detection and Recognition of Single Biological Molecules Using Coherent Dynamics of Exciton-Plasmon Coupling

PubMed Central

Sadeghi, S. M.; Hood, B.; Patty, K. D.; Mao, C.-B.

2013-01-01

We use quantum coherence in a system consisting of one metallic nanorod and one semi-conductor quantum dot to investigate a plasmonic nanosensor capable of digital optical detection and recognition of single biological molecules. In such a sensor the adsorption of a specific molecule to the nanorod turns off the emission of the system when it interacts with an optical pulse having a certain intensity and temporal width. The proposed quantum sensors can count the number of molecules of the same type or differentiate between molecule types with digital optical signals that can be measured with high certainty. We show that these sensors are based on the ultrafast upheaval of coherent dynamics of the system and the removal of coherent blockage of energy transfer from the quantum dot to the nanorod once the adsorption process has occurred. PMID:24040424

Supported lipid bilayer/carbon nanotube hybrids

NASA Astrophysics Data System (ADS)

Zhou, Xinjian; Moran-Mirabal, Jose M.; Craighead, Harold G.; McEuen, Paul L.

2007-03-01

Carbon nanotube transistors combine molecular-scale dimensions with excellent electronic properties, offering unique opportunities for chemical and biological sensing. Here, we form supported lipid bilayers over single-walled carbon nanotube transistors. We first study the physical properties of the nanotube/supported lipid bilayer structure using fluorescence techniques. Whereas lipid molecules can diffuse freely across the nanotube, a membrane-bound protein (tetanus toxin) sees the nanotube as a barrier. Moreover, the size of the barrier depends on the diameter of the nanotube-with larger nanotubes presenting bigger obstacles to diffusion. We then demonstrate detection of protein binding (streptavidin) to the supported lipid bilayer using the nanotube transistor as a charge sensor. This system can be used as a platform to examine the interactions of single molecules with carbon nanotubes and has many potential applications for the study of molecular recognition and other biological processes occurring at cell membranes.

Chemical anesthesia of Northern sea otters (Enhydra lutris): Results of past field studies

USGS Publications Warehouse

Monson, Daniel H.; McCormick, C.; Ballachey, Brenda E.

2001-01-01

Between 1987 and 1997, we chemically immobilized 597 wild sea otters (Enhydra lutris) in Alaska for the collection of biological samples or for surgical instrumentation. One drug-related sea otter fatality occurred during this time. Fentanyl in combination with diazepam produced consistent, smooth inductions with minimal need for supplemental anesthetics during procedures lasting 30-40 min. Antagonism with naltrexone or naloxone was rapid and complete, although we observed narcotic recycling in sea otters treated with naloxone. For surgical procedures, we recommend a fentanyl target dose of 0.33 mg/kg of body mass and diazepam at 0.11 mg/kg. For nonsurgical biological sample collection procedures, we recommend fentanyl at 0.22 mg/kg and diazepam at 0.07 mg/kg. We advise the use of the opioid antagonist naltrexone at a ratio of 2:1 to the total fentanyl administered during processing.

A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution.

PubMed

Jha, Ramesh K; Bingen, Jeremy M; Johnson, Christopher W; Kern, Theresa L; Khanna, Payal; Trettel, Daniel S; Strauss, Charlie E M; Beckham, Gregg T; Dale, Taraka

2018-06-01

Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. Here we demonstrate the optimization of an Escherichia coli- based biosensor in a robust microbial strain for the catabolism of aromatic compounds, Pseudomonas putida KT2440, through a generalizable approach of modulating interactions at the protein-DNA interface in the promoter and the protein-protein dimer interface. The high-throughput biosensor optimization approach demonstrated here is readily applicable towards other allosteric regulators.

The Biology of REM Sleep

PubMed Central

Peever, John; Fuller, Patrick M.

2018-01-01

Considerable advances in our understanding of the mechanisms and functions of rapid-eye-movement (REM) sleep have occurred over the past decade. Much of this progress can be attributed to the development of new neuroscience tools that have enabled high-precision interrogation of brain circuitry linked with REM sleep control, in turn revealing how REM sleep mechanisms themselves impact processes such as sensorimotor function. This review is intended to update the general scientific community about the recent mechanistic, functional and conceptual developments in our current understanding of REM sleep biology and pathobiology. Specifically, this review outlines the historical origins of the discovery of REM sleep, the diversity of REM sleep expression across and within species, the potential functions of REM sleep (e.g., memory consolidation), the neural circuits that control REM sleep, and how dysfunction of REM sleep mechanisms underlie debilitating sleep disorders such as REM sleep behaviour disorder and narcolepsy. PMID:26766231

Profiling the Serum Protein Corona of Fibrillar Human Islet Amyloid Polypeptide.

PubMed

Pilkington, Emily H; Gustafsson, Ove J R; Xing, Yanting; Hernandez-Fernaud, Juan; Zampronio, Cleidi; Kakinen, Aleksandr; Faridi, Ava; Ding, Feng; Wilson, Paul; Ke, Pu Chun; Davis, Thomas P

2018-05-16

Amyloids may be regarded as native nanomaterials that form in the presence of complex protein mixtures. By drawing an analogy with the physicochemical properties of nanoparticles in biological fluids, we hypothesized that amyloids should form a protein corona in vivo that would imbue the underlying amyloid with a modified biological identity. To explore this hypothesis, we characterized the protein corona of human islet amyloid polypeptide (IAPP) fibrils in fetal bovine serum using two complementary methodologies developed herein: quartz crystal microbalance and "centrifugal capture", coupled with nanoliquid chromatography tandem mass spectroscopy. Clear evidence for a significant protein corona was obtained. No trends were identified for amyloid corona proteins based on their physicochemical properties, whereas strong binding with IAPP fibrils occurred for linear proteins or multidomain proteins with structural plasticity. Proteomic analysis identified amyloid-enriched proteins that are known to play significant roles in mediating cellular machinery and processing, potentially leading to pathological outcomes and therapeutic targets.

Electricity and colloidal stability: how charge distribution in the tissue can affects wound healing.

PubMed

Farber, Paulo Luiz; Hochman, Bernardo; Furtado, Fabianne; Ferreira, Lydia Masako

2014-02-01

The role of endogenous electric fields in wound healing is still not fully understood. Electric fields are of fundamental importance in various biological processes, ranging from embryonic development to disease progression, as described by many investigators in the last century. This hypothesis brings together some relevant literature on the importance of electric fields in physiology and pathology, the theory of biologically closed electric circuits, skin battery (a phenomenon that occurs after skin injury and seems to be involved in tissue repair), the relationship between electric charge and interstitial exclusion, and how skin tissues can be regarded as colloidal systems. The importance of electric charges, as established in the early works on the subject and the relevance of zeta potential and colloid stability are also analyzed, and together bring a new light for the physics involved in the wound repair of all the body tissues. Copyright © 2013 Elsevier Ltd. All rights reserved.

A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution

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

Jha, Ramesh K.; Bingen, Jeremy M.; Johnson, Christopher W.

Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. In this study, we demonstrate the optimization of an Escherichia coli-based biosensor in a robust microbial strain formore » the catabolism of aromatic compounds, Pseudomonas putida KT2440, through a generalizable approach of modulating interactions at the protein-DNA interface in the promoter and the protein-protein dimer interface. The high-throughput biosensor optimization approach demonstrated here is readily applicable towards other allosteric regulators.« less

Infant toxicology: state of the science and considerations in evaluation of safety.

PubMed

Neal-Kluever, April; Aungst, Jason; Gu, Yan; Hatwell, Karen; Muldoon-Jacobs, Kristi; Liem, Ayesha; Ogungbesan, Adejoke; Shackelford, Mary

2014-08-01

Differences in the physiology and biological susceptibilities of adults and infants have led to growing interest in safety evaluation methods for exposures from infant formula packaging. In addition to potential physiological differences, infants aged 0-6 months may consume a sole source of food, infant formula or breast milk, and consume higher amounts of food relative to body weight compared to adults. While the duration of the exposure is short compared to the expected lifespan of the individual, it occurs during a period of important developmental processes. The purpose of this document is to (1) review key biological and exposure elements that may impact the evaluation of safety for food contact products intended for use by infants, (2) summarize the current reproductive and developmental toxicity testing protocols available, and (3) identify potential data gaps concerning this period of development. Published by Elsevier Ltd.

CoPub: a literature-based keyword enrichment tool for microarray data analysis.

PubMed

Frijters, Raoul; Heupers, Bart; van Beek, Pieter; Bouwhuis, Maurice; van Schaik, René; de Vlieg, Jacob; Polman, Jan; Alkema, Wynand

2008-07-01

Medline is a rich information source, from which links between genes and keywords describing biological processes, pathways, drugs, pathologies and diseases can be extracted. We developed a publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. CoPub is freely accessible at http://services.nbic.nl/cgi-bin/copub/CoPub.pl.

Optical micromanipulation of nanoparticles and cells inside living zebrafish.

PubMed

Johansen, Patrick Lie; Fenaroli, Federico; Evensen, Lasse; Griffiths, Gareth; Koster, Gerbrand

2016-03-21

Regulation of biological processes is often based on physical interactions between cells and their microenvironment. To unravel how and where interactions occur, micromanipulation methods can be used that offer high-precision control over the duration, position and magnitude of interactions. However, lacking an in vivo system, micromanipulation has generally been done with cells in vitro, which may not reflect the complex in vivo situation inside multicellular organisms. Here using optical tweezers we demonstrate micromanipulation throughout the transparent zebrafish embryo. We show that different cells, as well as injected nanoparticles and bacteria can be trapped and that adhesion properties and membrane deformation of endothelium and macrophages can be analysed. This non-invasive micromanipulation inside a whole-organism gives direct insights into cell interactions that are not accessible using existing approaches. Potential applications include screening of nanoparticle-cell interactions for cancer therapy or tissue invasion studies in cancer and infection biology.

Beyond nC60: strategies for identification of transformation products of fullerene oxidation in aquatic and biological samples

PubMed Central

Pycke, Benny F. G.; Chao, Tzu-Chiao; Herckes, Pierre; Westerhoff, Paul

2013-01-01

Owing to their exceptional properties and versatility, fullerenes are in widespread use for numerous applications. Increased production and use of fullerenes will inevitably result in accelerated environmental release. However, study of the occurrence, fate, and transport of fullerenes in the environment is complicated because a variety of surface modifications can occur as a result of either intentional functionalization or natural processes. To gain a better understanding of the effect and risk of fullerenes on environmental health, it is necessary to acquire reliable data on the parent compounds and their congeners. Whereas currently established quantification methods generally focus on analysis of unmodified fullerenes, we discuss in this review the occurrence and analysis of oxidized fullerene congeners (i.e., their corresponding epoxides and polyhydroxylated derivatives) in the environment and in biological specimens. We present possible strategies for detection and quantification of parent nanomaterials and their various derivatives. PMID:22644149

A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution

DOE PAGES

Jha, Ramesh K.; Bingen, Jeremy M.; Johnson, Christopher W.; ...

2018-06-01

Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. In this study, we demonstrate the optimization of an Escherichia coli-based biosensor in a robust microbial strain formore » the catabolism of aromatic compounds, Pseudomonas putida KT2440, through a generalizable approach of modulating interactions at the protein-DNA interface in the promoter and the protein-protein dimer interface. The high-throughput biosensor optimization approach demonstrated here is readily applicable towards other allosteric regulators.« less

Dissipative structures and biological rhythms

NASA Astrophysics Data System (ADS)

Goldbeter, Albert

2017-10-01

Sustained oscillations abound in biological systems. They occur at all levels of biological organization over a wide range of periods, from a fraction of a second to years, and with a variety of underlying mechanisms. They control major physiological functions, and their dysfunction is associated with a variety of physiological disorders. The goal of this review is (i) to give an overview of the main rhythms observed at the cellular and supracellular levels, (ii) to briefly describe how the study of biological rhythms unfolded in the course of time, in parallel with studies on chemical oscillations, (iii) to present the major roles of biological rhythms in the control of physiological functions, and (iv) the pathologies associated with the alteration, disappearance, or spurious occurrence of biological rhythms. Two tables present the main examples of cellular and supracellular rhythms ordered according to their period, and their role in physiology and pathophysiology. Among the rhythms discussed are neural and cardiac rhythms, metabolic oscillations such as those occurring in glycolysis in yeast, intracellular Ca++ oscillations, cyclic AMP oscillations in Dictyostelium amoebae, the segmentation clock that controls somitogenesis, pulsatile hormone secretion, circadian rhythms which occur in all eukaryotes and some bacteria with a period close to 24 h, the oscillatory dynamics of the enzymatic network driving the cell cycle, and oscillations in transcription factors such as NF-ΚB and tumor suppressors such as p53. Ilya Prigogine's concept of dissipative structures applies to temporal oscillations and allows us to unify within a common framework the various rhythms observed at different levels of biological organization, regardless of their period and underlying mechanism.

Geographic variation in mimetic precision among different species of coral snake mimics.

PubMed

Akcali, C K; Pfennig, D W

2017-07-01

Batesian mimicry is widespread, but whether and why different species of mimics vary geographically in resemblance to their model is unclear. We characterized geographic variation in mimetic precision among four Batesian mimics of coral snakes. Each mimic occurs where its model is abundant (i.e. in 'deep sympatry'), rare (i.e. at the sympatry/allopatry boundary or 'edge sympatry') and absent (i.e. in allopatry). Geographic variation in mimetic precision was qualitatively different among these mimics. In one mimic, the most precise individuals occurred in edge sympatry; in another, they occurred in deep sympatry; in the third, they occurred in allopatry; and in the fourth, precise mimics were not concentrated anywhere throughout their range. Mimicry was less precise in allopatry than in sympatry in only two mimics. We present several nonmutually exclusive hypotheses for these patterns. Generally, examining geographic variation in mimetic precision - within and among different mimics - offers novel insights into the causes and consequences of mimicry. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Adsorption-desorption kinetics of soft particles onto surfaces

NASA Astrophysics Data System (ADS)

Osberg, Brendan; Gerland, Ulrich

A broad range of physical, chemical, and biological systems feature processes in which particles randomly adsorb on a substrate. Theoretical models usually assume ``hard'' (mutually impenetrable) particles, but in soft matter physics the adsorbing particles can be effectively compressible, implying ``soft'' interaction potentials. We recently studied the kinetics of such soft particles adsorbing onto one-dimensional substrates, identifying three novel phenomena: (i) a gradual density increase, or ''cramming'', replaces the usual jamming behavior of hard particles, (ii) a density overshoot, can occur (only for soft particles) on a time scale set by the desorption rate, and (iii) relaxation rates of soft particles increase with particle size (on a lattice), while hard particles show the opposite trend. The latter occurs since unjamming requires desorption and many-bodied reorganization to equilibrate -a process that is generally very slow. Here we extend this analysis to a two-dimensional substrate, focusing on the question of whether the adsorption-desorption kinetics of particles in two dimensions is similarly enriched by the introduction of soft interactions. Application to experiments, for example the adsorption of fibrinogen on two-dimensional surfaces, will be discussed.

Influence of ion size and charge on osmosis.

PubMed

Cannon, James; Kim, Daejoong; Maruyama, Shigeo; Shiomi, Junichiro

2012-04-12

Osmosis is fundamental to many processes, such as in the function of biological cells and in industrial desalination to obtain clean drinking water. The choice of solute in industrial applications of osmosis is highly important in maximizing efficiency and minimizing costs. The macroscale process of osmosis originates from the nanoscale properties of the solvent, and therefore an understanding of the mechanisms of how these properties determine osmotic strength can be highly useful. For this reason, we have undertaken molecular dynamics simulations to systematically study the influence of ion size and charge on the strength of osmosis of water through carbon nanotube membranes. Our results show that strong osmosis occurs under optimum conditions of ion placement near the region of high water density near the membrane wall and of maintenance of a strong water hydration shell around the ions. The results in turn allow greater insight into the origin of the strong osmotic strength of real ions such as NaCl. Finally, in terms of practical simulation, we highlight the importance of avoiding size effects that can occur if the simulation cell is too small.

Microwave (MW) promoted high yield expedient synthesis of steryl ferulates--A class of novel biologically active compounds: A comparative study of their antioxidant activity with that of naturally occurring γ-oryzanol.

PubMed

Begum, Ashma; Borah, Preetismita; Chowdhury, Pritish

2016-03-01

Synthetic steryl ferulates [3-O-(trans-4-feruloyl)-sterols] are currently gaining considerable importance in recent years to be used as nutraceuticals and food additives as well as in pharmaceutical applications substituting γ-oryzanol - a class of naturally occurring steryl ferulates having potent antioxidant and other organoleptic properties. Considering the importance of this class of compounds coupled with green technology associated with microwave energy (MW) in organic synthesis, we report here an expedited and high yield synthesis of steryl ferulates from abundant steroids, viz., cholesterol, cholestanol, stigmasterol, stigmastanol, β-sitosterol, β-campesterol, β-campestanol and ergosterol applying MW energy in the crucial step of esterification process of sterols with trans-4-O-acetylferulic acid to furnish their esterified products, viz., 3-O-(trans-4-O-acetylferuloyl)-sterols for their eventual deprotection to their respective steryl ferulates. We further report an efficient and scalable process of producing acetylferulic acid. Testing of synthesized steryl ferulates against antioxidant assays has also been highlighted. Copyright © 2015 Elsevier Inc. All rights reserved.

Creating biological nanomaterials using synthetic biology.

PubMed

Rice, MaryJoe K; Ruder, Warren C

2014-02-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

Chemistry in motion: tiny synthetic motors.

PubMed

Colberg, Peter H; Reigh, Shang Yik; Robertson, Bryan; Kapral, Raymond

2014-12-16

CONSPECTUS: Diffusion is the principal transport mechanism that controls the motion of solute molecules and other species in solution; however, the random walk process that underlies diffusion is slow and often nonspecific. Although diffusion is an essential mechanism for transport in the biological realm, biological systems have devised more efficient transport mechanisms using molecular motors. Most biological motors utilize some form of chemical energy derived from their surroundings to induce conformational changes in order to carry out specific functions. These small molecular motors operate in the presence of strong thermal fluctuations and in the regime of low Reynolds numbers, where viscous forces dominate inertial forces. Thus, their dynamical behavior is fundamentally different from that of macroscopic motors, and different mechanisms are responsible for the production of useful mechanical motion. There is no reason why our interest should be confined to the small motors that occur naturally in biological systems. Recently, micron and nanoscale motors that use chemical energy to produce directed motion by a number of different mechanisms have been made in the laboratory. These small synthetic motors also experience strong thermal fluctuations and operate in regimes where viscous forces dominate. Potentially, these motors could be directed to perform different transport tasks, analogous to those of biological motors, for both in vivo and in vitro applications. Although some synthetic motors execute conformational changes to effect motion, the majority do not, and, instead, they use other mechanisms to convert chemical energy into directed motion. In this Account, we describe how synthetic motors that operate by self-diffusiophoresis make use of a self-generated concentration gradient to drive motor motion. A description of propulsion by self-diffusiophoresis is presented for Janus particle motors comprising catalytic and noncatalytic faces. The properties of the dynamics of chemically powered motors are illustrated by presenting the results of particle-based simulations of sphere-dimer motors constructed from linked catalytic and noncatalytic spheres. The geometries of both Janus and sphere-dimer motors with asymmetric catalytic activity support the formation of concentration gradients around the motors. Because directed motion can occur only when the system is not in equilibrium, the nature of the environment and the role it plays in motor dynamics are described. Rotational Brownian motion also acts to limit directed motion, and it has especially strong effects for very small motors. We address the following question: how small can motors be and still exhibit effects due to propulsion, even if only to enhance diffusion? Synthetic motors have the potential to transform the manner in which chemical dynamical processes are carried out for a wide range of applications.

Gaps within the Biomedical Literature: Initial Characterization and Assessment of Strategies for Discovery

PubMed Central

Peng, Yufang; Bonifield, Gary; Smalheiser, Neil R.

2017-01-01

Within well-established fields of biomedical science, we identify “gaps”, topical areas of investigation that might be expected to occur but are missing. We define a field by carrying out a topical PubMed query, and analyze Medical Subject Headings by which the set of retrieved articles are indexed. Medical Subject headings (MeSH terms) which occur in >1% of the articles are examined pairwise to see how often they are predicted to co-occur within individual articles (assuming that they are independent of each other). A pair of MeSH terms that are predicted to co-occur in at least 10 articles, yet are not observed to co-occur in any article, are “gaps” and were studied further in a corpus of 10 disease-related article sets and 10 related to biological processes. Overall, articles that filled gaps were cited more heavily than non-gap-filling articles and were 61% more likely to be published in multidisciplinary high-impact journals. Nine different features of these “gaps” were characterized and tested to learn which, if any, correlate with the appearance of one or more articles containing both MeSH terms within the next five years. Several different types of gaps were identified, each having distinct combinations of predictive features: a) those arising as a byproduct of MeSH indexing rules; b) those having little biological meaning; c) those representing “low hanging fruit” for immediate exploitation; and d) those representing gaps across disciplines or sub-disciplines that do not talk to each other or work together. We have built a free, open tool called “Mine the Gap!” that identifies and characterizes the “gaps” for any PubMed query, which can be accessed via the Anne O’Tate value-added PubMed search interface (http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi). PMID:29271976

Normal form from biological motion despite impaired ventral stream function.

PubMed

Gilaie-Dotan, S; Bentin, S; Harel, M; Rees, G; Saygin, A P

2011-04-01

We explored the extent to which biological motion perception depends on ventral stream integration by studying LG, an unusual case of developmental visual agnosia. LG has significant ventral stream processing deficits but no discernable structural cortical abnormality. LG's intermediate visual areas and object-sensitive regions exhibit abnormal activation during visual object perception, in contrast to area V5/MT+ which responds normally to visual motion (Gilaie-Dotan, Perry, Bonneh, Malach, & Bentin, 2009). Here, in three studies we used point light displays, which require visual integration, in adaptive threshold experiments to examine LG's ability to detect form from biological and non-biological motion cues. LG's ability to detect and discriminate form from biological motion was similar to healthy controls. In contrast, he was significantly deficient in processing form from non-biological motion. Thus, LG can rely on biological motion cues to perceive human forms, but is considerably impaired in extracting form from non-biological motion. Finally, we found that while LG viewed biological motion, activity in a network of brain regions associated with processing biological motion was functionally correlated with his V5/MT+ activity, indicating that normal inputs from V5/MT+ might suffice to activate his action perception system. These results indicate that processing of biologically moving form can dissociate from other form processing in the ventral pathway. Furthermore, the present results indicate that integrative ventral stream processing is necessary for uncompromised processing of non-biological form from motion. Copyright © 2011 Elsevier Ltd. All rights reserved.

Mixed mechanisms of multi-site phosphorylation

PubMed Central

Suwanmajo, Thapanar; Krishnan, J.

2015-01-01

Multi-site phosphorylation is ubiquitous in cell biology and has been widely studied experimentally and theoretically. The underlying chemical modification mechanisms are typically assumed to be distributive or processive. In this paper, we study the behaviour of mixed mechanisms that can arise either because phosphorylation and dephosphorylation involve different mechanisms or because phosphorylation and/or dephosphorylation can occur through a combination of mechanisms. We examine a hierarchy of models to assess chemical information processing through different mixed mechanisms, using simulations, bifurcation analysis and analytical work. We demonstrate how mixed mechanisms can show important and unintuitive differences from pure distributive and processive mechanisms, in some cases resulting in monostable behaviour with simple dose–response behaviour, while in other cases generating new behaviour-like oscillations. Our results also suggest patterns of information processing that are relevant as the number of modification sites increases. Overall, our work creates a framework to examine information processing arising from complexities of multi-site modification mechanisms and their impact on signal transduction. PMID:25972433

Biological Entanglement-Like Effect After Communication of Fish Prior to X-Ray Exposure.

PubMed

Mothersill, Carmel; Smith, Richard; Wang, Jiaxi; Rusin, Andrej; Fernandez-Palomo, Cris; Fazzari, Jennifer; Seymour, Colin

2018-01-01

The phenomenon by which irradiated organisms including cells in vitro communicate with unirradiated neighbors is well established in biology as the radiation-induced bystander effect (RIBE). Generally, the purpose of this communication is thought to be protective and adaptive, reflecting a highly conserved evolutionary mechanism enabling rapid adjustment to stressors in the environment. Stressors known to induce the effect were recently shown to include chemicals and even pathological agents. The mechanism is unknown but our group has evidence that physical signals such as biophotons acting on cellular photoreceptors may be implicated. This raises the question of whether quantum biological processes may occur as have been demonstrated in plant photosynthesis. To test this hypothesis, we decided to see whether any form of entanglement was operational in the system. Fish from 2 completely separate locations were allowed to meet for 2 hours either before or after which fish from 1 location only (group A fish) were irradiated. The results confirm RIBE signal production in both skin and gill of fish, meeting both before and after irradiation of group A fish. The proteomic analysis revealed that direct irradiation resulted in pro-tumorigenic proteomic responses in rainbow trout. However, communication from these irradiated fish, both before and after they had been exposed to a 0.5 Gy X-ray dose, resulted in largely beneficial proteomic responses in completely nonirradiated trout. The results suggest that some form of anticipation of a stressor may occur leading to a preconditioning effect or temporally displaced awareness after the fish become entangled.

Metabolome analysis for discovering biomarkers of gastroenterological cancer.

PubMed

Suzuki, Makoto; Nishiumi, Shin; Matsubara, Atsuki; Azuma, Takeshi; Yoshida, Masaru

2014-09-01

Improvements in analytical technologies have made it possible to rapidly determine the concentrations of thousands of metabolites in any biological sample, which has resulted in metabolome analysis being applied to various types of research, such as clinical, cell biology, and plant/food science studies. The metabolome represents all of the end products and by-products of the numerous complex metabolic pathways operating in a biological system. Thus, metabolome analysis allows one to survey the global changes in an organism's metabolic profile and gain a holistic understanding of the changes that occur in organisms during various biological processes, e.g., during disease development. In clinical metabolomic studies, there is a strong possibility that differences in the metabolic profiles of human specimens reflect disease-specific states. Recently, metabolome analysis of biofluids, e.g., blood, urine, or saliva, has been increasingly used for biomarker discovery and disease diagnosis. Mass spectrometry-based techniques have been extensively used for metabolome analysis because they exhibit high selectivity and sensitivity during the identification and quantification of metabolites. Here, we describe metabolome analysis using liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and capillary electrophoresis-mass spectrometry. Furthermore, the findings of studies that attempted to discover biomarkers of gastroenterological cancer are also outlined. Finally, we discuss metabolome analysis-based disease diagnosis. Copyright © 2014 Elsevier B.V. All rights reserved.

Extinction and recolonization of coastal megafauna following human arrival in New Zealand

PubMed Central

Collins, Catherine J.; Rawlence, Nicolas J.; Prost, Stefan; Anderson, Christian N. K.; Knapp, Michael; Scofield, R. Paul; Robertson, Bruce C.; Smith, Ian; Matisoo-Smith, Elizabeth A.; Chilvers, B. Louise; Waters, Jonathan M.

2014-01-01

Extinctions can dramatically reshape biological communities. As a case in point, ancient mass extinction events apparently facilitated dramatic new evolutionary radiations of surviving lineages. However, scientists have yet to fully understand the consequences of more recent biological upheaval, such as the megafaunal extinctions that occurred globally over the past 50 kyr. New Zealand was the world's last large landmass to be colonized by humans, and its exceptional archaeological record documents a vast number of vertebrate extinctions in the immediate aftermath of Polynesian arrival approximately AD 1280. This recently colonized archipelago thus presents an outstanding opportunity to test for rapid biological responses to extinction. Here, we use ancient DNA (aDNA) analysis to show that extinction of an endemic sea lion lineage (Phocarctos spp.) apparently facilitated a subsequent northward range expansion of a previously subantarctic-limited lineage. This finding parallels a similar extinction–replacement event in penguins (Megadyptes spp.). In both cases, an endemic mainland clade was completely eliminated soon after human arrival, and then replaced by a genetically divergent clade from the remote subantarctic region, all within the space of a few centuries. These data suggest that ecological and demographic processes can play a role in constraining lineage distributions, even for highly dispersive species, and highlight the potential for dynamic biological responses to extinction. PMID:24827440

Recovery of elemental sulphur from anaerobic effluents through the biological oxidation of sulphides.

PubMed

de Sousa, José Tavares; Lima, Jéssyca de Freitas; da Silva, Valquíria Cordeiro; Leite, Valderi Duarte; Lopes, Wilton Silva

2017-03-01

The aim of the present study was to evaluate the biological oxidation of sulphide in two different UASB reactors by assessing the occurrence of oxidized forms of sulphur in the effluents and the amount of S 0 that could be recovered in the process. The bioreactors employed were an anaerobic hybrid (AH) reactor employing porous polyurethane foam as support media and a micro-aerated UASB reactor equipped with an aeration device above the digestion zone. The AH reactor produced a final effluent containing low concentrations of S 2- (3.87% of total sulphur load). It was achieved due to a complete oxidation of 56.1% of total sulphur. The partial biological oxidation that occurred in the AH reactor allowed the recovery of 30% of the sulphur load as S 0 . The effluent from the micro-aerated UASB reactor contained 5% of the sulphur load in the form of S 2- , while 20.9% was present as dissolved SO 4 2- and 46% was precipitated as S 0 . It is concluded that the AH reactor or micro-aeration carried out above the digestion zone of the UASB reactor favoured the biological oxidation of S 2- and the release of odourless effluents. Both technologies represent feasible and low-cost alternatives for the anaerobic treatment of domestic sewage.

Metabolite damage and repair in metabolic engineering design.

PubMed

Sun, Jiayi; Jeffryes, James G; Henry, Christopher S; Bruner, Steven D; Hanson, Andrew D

2017-11-01

The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such metabolite damage reactions are now known to occur throughout metabolism and to generate (formerly enigmatic) peaks detected in metabolomics datasets. It is also now known that metabolite damage is often countered by dedicated repair enzymes that undo or prevent it. Metabolite damage and repair are highly relevant to engineered pathway design: metabolite damage reactions can reduce flux rates and product yields, and repair enzymes can provide robust, host-independent solutions. Herein, after introducing the core principles of metabolite damage and repair, we use case histories to document how damage and repair processes affect efficient operation of engineered pathways - particularly those that are heterologous, non-natural, or cell-free. We then review how metabolite damage reactions can be predicted, how repair reactions can be prospected, and how metabolite damage and repair can be built into genome-scale metabolic models. Lastly, we propose a versatile 'plug and play' set of well-characterized metabolite repair enzymes to solve metabolite damage problems known or likely to occur in metabolic engineering and synthetic biology projects. Copyright © 2017 International Metabolic Engineering Society. All rights reserved.

Fluorescent ratiometric pH indicator SypHer2: applications in neuroscience and regenerative biology

PubMed Central

Matlashov, Mikhail E.; Bogdanova, Yulia A.; Ermakova, Galina V.; Mishina, Natalia M.; Ermakova, Yulia G.; Nikitin, Evgeny S.; Balaban, Pavel M.; Okabe, Shigeo; Lukyanov, Sergey; Enikolopov, Grigori; Zaraisky, Andrey G.; Belousov, Vsevolod V.

2015-01-01

Background SypHer is a genetically encoded fluorescent pH-indicator with a ratiometric readout, suitable for measuring fast intracellular pH shifts. However, a relatively low brightness of the indicator limits its use. Methods Here we designed a new version of pH-sensor - SypHer-2, that has up to three times brighter fluorescence signal in cultured mammalian cells compared to the SypHer. Results Using the new indicator we registered activity-associated pH oscillations in neuronal cell culture. We observed prominent temporal neuronal cytoplasm acidification that occurs in parallel with calcium entry. Furthermore, we monitored pH in presynaptic and postsynaptic termini by targeting SypHer-2 directly to these compartments and revealed marked differences in pH dynamics between synaptic boutons and dendritic spines. Finally, we were able to reveal for the first time the intracellular pH drop which occurs within an extended region of the amputated tail of the Xenopus laevis tadpole before it begins to regenerate. Conclusions SypHer2 is suitable for quantitative monitoring of pH in biological systems of different scales, from small cellular subcompartments to animal tissues in vivo. General significance The new pH-sensor will help to investigate pH-dependent processes in both in vitro and in vivo studies. PMID:26259819

Metabolite damage and repair in metabolic engineering design

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

Sun, Jiayi; Jeffryes, James G.; Henry, Christopher S.

The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such metabolite damage reactions are now known to occur throughout metabolism and to generate (formerly enigmatic) peaks detected in metabolomics datasets. It is also now known that metabolite damage is often countered by dedicated repair enzymes that undo or prevent it. Metabolite damage and repair are highly relevant to engineered pathway design: metabolite damage reactions can reduce flux rates and product yields,more » and repair enzymes can provide robust, host-independent solutions. Herein, after introducing the core principles of metabolite damage and repair, we use case histories to document how damage and repair processes affect efficient operation of engineered pathways - particularly those that are heterologous, non-natural, or cell-free. We then review how metabolite damage reactions can be predicted, how repair reactions can be prospected, and how metabolite damage and repair can be built into genome-scale metabolic models. Lastly, we propose a versatile 'plug and play' set of well-characterized metabolite repair enzymes to solve metabolite damage problems known or likely to occur in metabolic engineering and synthetic biology projects.« less

Biodegradation and attenuation of steroidal hormones and alkylphenols by stream biofilms and sediments

USGS Publications Warehouse

Writer, Jeffrey; Barber, Larry B.; Ryan, Joseph N.; Bradley, Paul M.

2011-01-01

Biodegradation of select endocrine-disrupting compounds (17β-estradiol, estrone, 17α-ethynylestradiol, 4-nonylphenol, 4-nonylphenolmonoexthoylate, and 4-nonylphenoldiethoxylate) was evaluated in stream biofilm, sediment, and water matrices collected from locations upstream and downstream from a wastewater treatment plant effluent discharge. Both biologically mediated transformation to intermediate metabolites and biologically mediated mineralization were evaluated in separate time interval experiments. Initial time intervals (0–7 d) evaluated biodegradation by the microbial community dominant at the time of sampling. Later time intervals (70 and 185 d) evaluated the biodegradation potential as the microbial community adapted to the absence of outside energy sources. The sediment matrix was more effective than the biofilm and water matrices at biodegrading 4-nonylphenol and 17β-estradiol. Biodegradation by the sediment matrix of 17α-ethynylestradiol occurred at later time intervals (70 and 185 d) and was not observed in the biofilm or water matrices. Stream biofilms play an important role in the attenuation of endocrine-disrupting compounds in surface waters due to both biodegradation and sorption processes. Because sorption to stream biofilms and bed sediments occurs on a faster temporal scale (<1 h) than the potential to biodegrade the target compounds (50% mineralization at >185 d), these compounds can accumulate in stream biofilms and sediments.

Extracellular biosynthesis of platinum nanoparticles using the fungus Fusarium oxysporum.

PubMed

Syed, Asad; Ahmad, Absar

2012-09-01

Nanoscience is a blooming field and promises a better future. In order to fabricate nanoparticles in an eco-friendly and inexpensive manner, significant efforts are being made to replace the chemical and physical methods currently being used with the biological methods. Chemical methods are toxic while the physical ones are very expensive. Biological methods, apart from being cost-effective, also provide protein capped nanoparticles which are thus very stable, have good dispersity and do not flocculate, and may find use in various applications. The present work emphasizes on platinum nanoparticles synthesis protocol which occurs at ambient conditions. The fungus Fusarium oxysporum when incubated with hexachloroplatinic acid (H(2)PtCl(6)) in ambient conditions reduces the precursor and leads to the formation of stable extracellular platinum nanoparticles. The biosynthesis of platinum nanoparticles was monitored by UV-visible spectroscopy and these nanoparticles were completely characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The nanoparticles are in the size range of 5-30 nm and are stabilized by proteins present in the solution. The reduction process is believed to occur enzymatically, thus creating the possibility of a rational, fungal-based method for the synthesis of nanoparticles over a wide range of chemical compositions. Copyright © 2012 Elsevier B.V. All rights reserved.

Fluorescent ratiometric pH indicator SypHer2: Applications in neuroscience and regenerative biology.

PubMed

Matlashov, Mikhail E; Bogdanova, Yulia A; Ermakova, Galina V; Mishina, Natalia M; Ermakova, Yulia G; Nikitin, Evgeny S; Balaban, Pavel M; Okabe, Shigeo; Lukyanov, Sergey; Enikolopov, Grigori; Zaraisky, Andrey G; Belousov, Vsevolod V

2015-11-01

SypHer is a genetically encoded fluorescent pH-indicator with a ratiometric readout, suitable for measuring fast intracellular pH shifts. However, the relatively low brightness of the indicator limits its use. Here we designed a new version of pH-sensor called SypHer-2, which has up to three times brighter fluorescence in cultured mammalian cells compared to the SypHer. Using the new indicator we registered activity-associated pH oscillations in neuronal cell culture. We observed prominent transient neuronal cytoplasm acidification that occurs in parallel with calcium entry. Furthermore, we monitored pH in presynaptic and postsynaptic termini by targeting SypHer-2 directly to these compartments and revealed marked differences in pH dynamics between synaptic boutons and dendritic spines. Finally, we were able to reveal for the first time the intracellular pH drop that occurs within an extended region of the amputated tail of the Xenopus laevis tadpole before it begins to regenerate. SypHer2 is suitable for quantitative monitoring of pH in biological systems of different scales, from small cellular subcompartments to animal tissues in vivo. The new pH-sensor will help to investigate pH-dependent processes in both in vitro and in vivo studies. Copyright © 2015 Elsevier B.V. All rights reserved.

Enhancement of radiosensitivity of melanoma cells by pegylated gold nanoparticles under irradiation of megavoltage electrons.

PubMed

Mousavi, Mehdi; Nedaei, Hassan Ali; Khoei, Samideh; Eynali, Samira; Khoshgard, Karim; Robatjazi, Mostafa; Iraji Rad, Rasoul

2017-02-01

Gold nanoparticles (GNP) have significant potential as radiosensitizer agents due to their distinctive properties. Several studies have shown that the surface modification of nanoparticles with methyl polyethylene glycol (mPEG) can increase their biocompatibility. However, the present study investigated the radiosensitization effects of mPEG-coated GNP (mPEG-GNP) in B16F10 murine melanoma cells under irradiation of 6 MeV Electron beam. The synthesized GNP were characterized by UV-Visible spectroscopy, dynamic light scattering, transmission electron microscopy, and zeta potential. Enhancement of radiosensitization was evaluated by the clonogenic assay at different radiation doses of megavoltage electron beams. It was observed that mPEG-GNP with a hydrodynamic size of approximately 50 nm are almost spherical and cellular uptake occurred at all concentrations. Both proliferation efficiency and survival fraction decreased with increasing mPEG-GNP concentration. Furthermore, significant GNP sensitization occurred with a maximum dose enhancement factor of 1.22 at a concentration of 30 μM. Pegylated-GNP are taken up by B16F10 cancer cells and cause radiosensitization in the presence of 6 MeV electrons. The radiosensitization effects of GNP may probably be due to biological processes. Therefore, the underlying biological mechanisms beyond the physical dose enhancement need to be further clarified.

Enzyme activities by indicator of quality in organic soil

NASA Astrophysics Data System (ADS)

Raigon Jiménez, Mo; Fita, Ana Delores; Rodriguez Burruezo, Adrián

2016-04-01

The analytical determination of biochemical parameters, as soil enzyme activities and those related to the microbial biomass is growing importance by biological indicator in soil science studies. The metabolic activity in soil is responsible of important processes such as mineralization and humification of organic matter. These biological reactions will affect other key processes involved with elements like carbon, nitrogen and phosphorus , and all transformations related in soil microbial biomass. The determination of biochemical parameters is useful in studies carried out on organic soil where microbial processes that are key to their conservation can be analyzed through parameters of the metabolic activity of these soils. The main objective of this work is to apply analytical methodologies of enzyme activities in soil collections of different physicochemical characteristics. There have been selective sampling of natural soils, organic farming soils, conventional farming soils and urban soils. The soils have been properly identified conserved at 4 ° C until analysis. The enzyme activities determinations have been: catalase, urease, cellulase, dehydrogenase and alkaline phosphatase, which bring together a representative group of biological transformations that occur in the soil environment. The results indicate that for natural and agronomic soil collections, the values of the enzymatic activities are within the ranges established for forestry and agricultural soils. Organic soils are generally higher level of enzymatic, regardless activity of the enzyme involved. Soil near an urban area, levels of activities have been significantly reduced. The vegetation cover applied to organic soils, results in greater enzymatic activity. So the quality of these soils, defined as the ability to maintain their biological productivity is increased with the use of cover crops, whether or spontaneous species. The practice of cover based on legumes could be used as an ideal choice for the recovery of degraded soils, because these soils have the highest levels of enzymatic activities.

Regulatory administrative databases in FDA's Center for Biologics Evaluation and Research: convergence toward a unified database.

PubMed

Smith, Jeffrey K

2013-04-01

Regulatory administrative database systems within the Food and Drug Administration's (FDA) Center for Biologics Evaluation and Research (CBER) are essential to supporting its core mission, as a regulatory agency. Such systems are used within FDA to manage information and processes surrounding the processing, review, and tracking of investigational and marketed product submissions. This is an area of increasing interest in the pharmaceutical industry and has been a topic at trade association conferences (Buckley 2012). Such databases in CBER are complex, not for the type or relevance of the data to any particular scientific discipline but because of the variety of regulatory submission types and processes the systems support using the data. Commonalities among different data domains of CBER's regulatory administrative databases are discussed. These commonalities have evolved enough to constitute real database convergence and provide a valuable asset for business process intelligence. Balancing review workload across staff, exploring areas of risk in review capacity, process improvement, and presenting a clear and comprehensive landscape of review obligations are just some of the opportunities of such intelligence. This convergence has been occurring in the presence of usual forces that tend to drive information technology (IT) systems development toward separate stovepipes and data silos. CBER has achieved a significant level of convergence through a gradual process, using a clear goal, agreed upon development practices, and transparency of database objects, rather than through a single, discrete project or IT vendor solution. This approach offers a path forward for FDA systems toward a unified database.

Probing the biology of dry biological systems to address the basis of seed longevity

USDA-ARS?s Scientific Manuscript database

Drying cells reduces molecular mobility and slows chemical and physical reactions. As a result, dry biological systems deteriorate slowly. The time course of deterioration in a population of living cells often follows a sigmoidal pattern in which aging is occurring but no changes to viability are ...

Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs

PubMed Central

2017-01-01

Mass-spectrometry-based, high-throughput proteomics experiments produce large amounts of data. While typically acquired to answer specific biological questions, these data can also be reused in orthogonal ways to reveal new biological knowledge. We here present a novel method for such orthogonal data reuse of public proteomics data. Our method elucidates biological relationships between proteins based on the co-occurrence of these proteins across human experiments in the PRIDE database. The majority of the significantly co-occurring protein pairs that were detected by our method have been successfully mapped to existing biological knowledge. The validity of our novel method is substantiated by the extremely few pairs that can be mapped to existing knowledge based on random associations between the same set of proteins. Moreover, using literature searches and the STRING database, we were able to derive meaningful biological associations for unannotated protein pairs that were detected using our method, further illustrating that as-yet unknown associations present highly interesting targets for follow-up analysis. PMID:28480704

Dynamics of the Indian-Ocean oxygen minimum zones

NASA Astrophysics Data System (ADS)

McCreary, Julian P.; Yu, Zuojun; Hood, Raleigh R.; Vinaychandran, P. N.; Furue, Ryo; Ishida, Akio; Richards, Kelvin J.

2013-05-01

In the Indian Ocean, mid-depth oxygen minimum zones (OMZs) occur in the Arabian Sea and the Bay of Bengal. The lower part of the Arabian-Sea OMZ (ASOMZ; below 400 m) intensifies northward across the basin; in contrast, its upper part (above 400 m) is located in the central/eastern basin, well east of the most productive regions along the western boundary. The Bay-of-Bengal OMZ (BBOMZ), although strong, is weaker than the ASOMZ. To investigate the processes that maintain the Indian-Ocean OMZs, we obtain a suite of solutions to a coupled biological/physical model. Its physical component is a variable-density, 61/2 >-layer model, in which each layer corresponds to a distinct dynamical regime or water-mass type. Its biological component has six compartments: nutrients, phytoplankton, zooplankton, two size classes of detritus, and oxygen. Because the model grid is non-eddy resolving (0.5°), the biological model also includes a parameterization of enhanced mixing based on the eddy kinetic energy derived from satellite observations. To explore further the impact of local processes on OMZs, we also obtain analytic solutions to a one-dimensional, simplified version of the biological model. Our control run is able to simulate basic features of the oxygen, nutrient, and phytoplankton fields throughout the Indian Ocean. The model OMZs result from a balance, or lack thereof, between a sink of oxygen by remineralization and subsurface oxygen sources due primarily to northward spreading of oxygenated water from the Southern Hemisphere, with a contribution from Persian-Gulf water in the northern Arabian Sea. The northward intensification of the lower ASOMZ results mostly from horizontal mixing since advection is weak in its depth range. The eastward shift of the upper ASOMZ is due primarily to enhanced advection and vertical eddy mixing in the western Arabian Sea, which spread oxygenated waters both horizontally and vertically. Advection carries small detritus from the western boundary into the central/eastern Arabian Sea, where it provides an additional source of remineralization that drives the ASOMZ to suboxic levels. The model BBOMZ is weaker than the ASOMZ because the Bay lacks a remote source of detritus from the western boundary. Although detritus has a prominent annual cycle, the model OMZs do not because there is not enough time for significant remineralization to occur.

Buckling condensation in constrained growth

NASA Astrophysics Data System (ADS)

Dervaux, Julien; Ben Amar, Martine

2011-03-01

The multiple complexities inherent to living objects have motivated the search for abiotic substitutes, able to mimic some of their relevant physical properties. Hydrogels provide a highly monitorable counterpart and have thus found many applications in medicine and bioengineering. Recently, it has been recognized that their ability to swell could be used to unravel some of the universal physical processes at work during biological growth. However, it is yet unknown how the microscopic distinctions between swelling and biological growth affect macroscopic changes (shape, stresses) induced by volume variations. To answer this question, we focus on a clinically motivated example of growth. Some solid tumors such as melanoma or glioblastoma undergo a shape transition during their evolution. This bifurcation appears when growth is confined at the periphery of the tumor and is concomitant with the transition from the avascular to the vascular stage of the tumor evolution. To model this phenomenon, we consider in this paper the deformation of an elastic ring enclosing a core of different stiffness. When the volume of the outer ring increases, the system develops a periodic instability. We consider two possible descriptions of the volume variation process: either by imposing a homogeneous volumetric strain (biological growth) or through migration of solvent molecules inside a solid network (swelling). For thin rings, both theories are in qualitative agreement. When the interior is soft, we predict the emergence of a large wavelength buckling. Upon increasing the stiffness of the inner disc, the wavelength of the instability decreases until a condensation of the buckles occurs at the free boundary. This short wavelength pattern is independent of the stiffness of the disc and is only limited by the presence of surface tension. For thicker rings, two scenarios emerge. When a volumetric strain is prescribed, compressive stresses accumulate in the vicinity of the core and the deformation localizes itself at the boundary between the disc and the ring. On the other hand, swelling being an instance of stress-modulated growth, elastic stretches near the core saturate and the instability occurs primarily at the free boundary. Besides its implications for the mechanical stability of avascular tumors, this work provides important results concerning layered tissues growth and the role of hydrogels as biological tissues substitutes.

Seismic and Biological Sources of Ambient Ocean Sound

NASA Astrophysics Data System (ADS)

Freeman, Simon Eric

Sound is the most efficient radiation in the ocean. Sounds of seismic and biological origin contain information regarding the underlying processes that created them. A single hydrophone records summary time-frequency information from the volume within acoustic range. Beamforming using a hydrophone array additionally produces azimuthal estimates of sound sources. A two-dimensional array and acoustic focusing produce an unambiguous two-dimensional `image' of sources. This dissertation describes the application of these techniques in three cases. The first utilizes hydrophone arrays to investigate T-phases (water-borne seismic waves) in the Philippine Sea. Ninety T-phases were recorded over a 12-day period, implying a greater number of seismic events occur than are detected by terrestrial seismic monitoring in the region. Observation of an azimuthally migrating T-phase suggests that reverberation of such sounds from bathymetric features can occur over megameter scales. In the second case, single hydrophone recordings from coral reefs in the Line Islands archipelago reveal that local ambient reef sound is spectrally similar to sounds produced by small, hard-shelled benthic invertebrates in captivity. Time-lapse photography of the reef reveals an increase in benthic invertebrate activity at sundown, consistent with an increase in sound level. The dominant acoustic phenomenon on these reefs may thus originate from the interaction between a large number of small invertebrates and the substrate. Such sounds could be used to take census of hard-shelled benthic invertebrates that are otherwise extremely difficult to survey. A two-dimensional `map' of sound production over a coral reef in the Hawaiian Islands was obtained using two-dimensional hydrophone array in the third case. Heterogeneously distributed bio-acoustic sources were generally co-located with rocky reef areas. Acoustically dominant snapping shrimp were largely restricted to one location within the area surveyed. This distribution of sources could reveal small-scale spatial ecological limitations, such as the availability of food and shelter. While array-based passive acoustic sensing is well established in seismoacoustics, the technique is little utilized in the study of ambient biological sound. With the continuance of Moore's law and advances in battery and memory technology, inferring biological processes from ambient sound may become a more accessible tool in underwater ecological evaluation and monitoring.

Evaluation of a contraction flow field on hydrodynamic damage to entomopathogenic nematodes-A biological pest control agent.

PubMed

Fife, Jane P; Derksen, Richard C; Ozkan, H Erdal; Grewal, Parwinder S; Chalmers, Jeffrey J; Krause, Charles R

2004-04-05

Mechanized production and delivery of biological pesticides presents challenges because the biological agents must remain viable during these processes. This study evaluates the effect of flow through an abrupt contraction, where flow characteristics similar to that found within bioprocesses and spray equipment are developed, on damage to a benchmark biological pest control agent, entomopathogenic nematodes (EPNs). An opposed-pistons, contraction flow device generated volumetric flow rates ranging between 8.26 cm(3)/s and 41.3 cm(3)/s. Four EPN species were evaluated: Heterorhabditis bacteriophora, Heterorhabditis megidis, Steinernema carpocapsae, and Steinernema glaseri. Damage was quantified by counting living and dead EPNs. Optical and cold field emission scanning electron microscope (CFE-SEM) images provided qualitative information to describe how the damage occurred. The experimental flow field was completely described using FLUENT, a computational fluid dynamics program. Local flow parameters computed in FLUENT were compared to EPN damage. The type and extent of damage varied between EPN species. Damaged Heterorhabditis spp. generally remained whole with an internal rupture located near the center of the body, while Steinernema spp. most often broke into several pieces. The fast-transient stress field generated at the entrance to the contraction caused a momentary tensile loading and then relaxation that damaged the EPNs. At high flow rates, the tensile stresses became large enough to cause failure of the EPN structural membrane. The relative elasticity of the EPN structural membrane may explain the differences in damage observed between the species. It is speculated that the internal rupture of the Heterorhabditis spp. occurred during the processes of stretching and relaxing at the contraction entrance. Appreciable damage was observed at lower average energy dissipation rates for H. bacteriophora (1.23E + 8 W/m(3)), H. megidis (1.72E + 8 W/m(3)), and S. glaseri (2.89E + 8 W/m(3)) compared to S. carpocapsae (3.70E + 8 W/m(3)). Energy dissipation rates within an equipment component should be kept below 1E + 8 W/m(3) to avoid hydrodynamic damage to EPNs. The relationship between average energy dissipation and EPN damage provides important information for future simulation efforts of actual spray equipment components. Copyright 2004 Wiley Periodicals, Inc.

Magic moment? Maternal marriage for children born out of wedlock.

PubMed

Gibson-Davis, Christina

2014-08-01

To test the existence of the "magic moment" for parental marriage immediately post-birth and to inform policies that preferentially encourage biological over step parent marriage, this study estimates the incidence and stability of maternal marriage for children born out of wedlock. Data came from the National Survey of Family Growth on 5,255 children born non maritally. By age 15, 29 % of children born non maritally experienced a biological-father marriage, and 36 % experienced a stepfather marriage. Stepfather marriages occurred much later in a child's life-one-half occurred after the child turned age 7-and had one-third higher odds of dissolution. Children born to black mothers had qualitatively different maternal marriage experiences than children born to white or Hispanic mothers, with less biological-parent marriage and higher incidences of divorce. Findings support the existence of the magic moment and demonstrate that biological marriages were more enduring than stepfather marriages. Yet relatively few children born out of wedlock experienced stable, biological-parent marriages as envisioned by marriage promotion programs.

Advancing Risk Assessment through the Application of Systems Toxicology

PubMed Central

Sauer, John Michael; Kleensang, André; Peitsch, Manuel C.; Hayes, A. Wallace

2016-01-01

Risk assessment is the process of quantifying the probability of a harmful effect to individuals or populations from human activities. Mechanistic approaches to risk assessment have been generally referred to as systems toxicology. Systems toxicology makes use of advanced analytical and computational tools to integrate classical toxicology and quantitative analysis of large networks of molecular and functional changes occurring across multiple levels of biological organization. Three presentations including two case studies involving both in vitro and in vivo approaches described the current state of systems toxicology and the potential for its future application in chemical risk assessment. PMID:26977253

Nitrogen on Mars: Insights from Curiosity

NASA Technical Reports Server (NTRS)

Stern, J. C.; Sutter, B.; Jackson, W. A.; Navarro-Gonzalez, Rafael; McKay, Chrisopher P.; Ming, W.; Archer, P. Douglas; Glavin, D. P.; Fairen, A. G.; Mahaffy, Paul R.

2017-01-01

Recent detection of nitrate on Mars indicates that nitrogen fixation processes occurred in early martian history. Data collected by the Sample Analysis at Mars (SAM) instrument on the Curiosity Rover can be integrated with Mars analog work in order to better understand the fixation and mobility of nitrogen on Mars, and thus its availability to putative biology. In particular, the relationship between nitrate and other soluble salts may help reveal the timing of nitrogen fixation and post-depositional behavior of nitrate on Mars. In addition, in situ measurements of nitrogen abundance and isotopic composition may be used to model atmospheric conditions on early Mars.

Information processing occurs via critical avalanches in a model of the primary visual cortex

NASA Astrophysics Data System (ADS)

Bortolotto, G. S.; Girardi-Schappo, M.; Gonsalves, J. J.; Pinto, L. T.; Tragtenberg, M. H. R.

2016-01-01

We study a new biologically motivated model for the Macaque monkey primary visual cortex which presents power-law avalanches after a visual stimulus. The signal propagates through all the layers of the model via avalanches that depend on network structure and synaptic parameter. We identify four different avalanche profiles as a function of the excitatory postsynaptic potential. The avalanches follow a size-duration scaling relation and present critical exponents that match experiments. The structure of the network gives rise to a regime of two characteristic spatial scales, one of which vanishes in the thermodynamic limit.

Visual event-related potentials to biological motion stimuli in autism spectrum disorders

PubMed Central

Bletsch, Anke; Krick, Christoph; Siniatchkin, Michael; Jarczok, Tomasz A.; Freitag, Christine M.; Bender, Stephan

2014-01-01

Atypical visual processing of biological motion contributes to social impairments in autism spectrum disorders (ASD). However, the exact temporal sequence of deficits of cortical biological motion processing in ASD has not been studied to date. We used 64-channel electroencephalography to study event-related potentials associated with human motion perception in 17 children and adolescents with ASD and 21 typical controls. A spatio-temporal source analysis was performed to assess the brain structures involved in these processes. We expected altered activity already during early stimulus processing and reduced activity during subsequent biological motion specific processes in ASD. In response to both, random and biological motion, the P100 amplitude was decreased suggesting unspecific deficits in visual processing, and the occipito-temporal N200 showed atypical lateralization in ASD suggesting altered hemispheric specialization. A slow positive deflection after 400 ms, reflecting top-down processes, and human motion-specific dipole activation differed slightly between groups, with reduced and more diffuse activation in the ASD-group. The latter could be an indicator of a disrupted neuronal network for biological motion processing in ADS. Furthermore, early visual processing (P100) seems to be correlated to biological motion-specific activation. This emphasizes the relevance of early sensory processing for higher order processing deficits in ASD. PMID:23887808

Collective dynamics during cell division

NASA Astrophysics Data System (ADS)

Zapperi, Stefano; Bertalan, Zsolt; Budrikis, Zoe; La Porta, Caterina A. M.

In order to correctly divide, cells have to move all their chromosomes at the center, a process known as congression. This task is performed by the combined action of molecular motors and randomly growing and shrinking microtubules. Chromosomes are captured by growing microtubules and transported by motors using the same microtubules as tracks. Coherent motion occurs as a result of a large collection of random and deterministic dynamical events. Understanding this process is important since a failure in chromosome segregation can lead to chromosomal instability one of the hallmarks of cancer. We describe this complex process in a three dimensional computational model involving thousands of microtubules. The results show that coherent and robust chromosome congression can only happen if the total number of microtubules is neither too small, nor too large. Our results allow for a coherent interpretation a variety of biological factors already associated in the past with chromosomal instability and related pathological conditions.

Autoheated thermophilic aerobic digestion

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

Deeny, K.; Hahn, H.; Leonhard, D.

1991-10-01

Autothermal thermophilic aerobic digestion (ATAD) is first and foremost a digestion process, the primary purpose of which is to decompose a portion of the waste organic solids generated from wastewater treatment. As a result of the high operating temperature, digestion is expected to occur within a short time period (6 days) and accomplish a high degree of pathogen reduction. ATAD systems are two-stage aerobic digestion processes that operate under thermophilic temperature conditions (40 to 80C) without supplemental heat. Like composting, the systems rely on the conservation of heat released during digestion itself to attain and sustain the desired operating temperature.more » Typical ATAD systems operate at 55C and may reach temperatures of 60 to 65C in the second-stage reactor. Perhaps because of the high operating temperature, this process has been referred to as Liquid Composting.' Major advantages associated with thermophilic operation include high biological reaction rates and a substantial degree of pathogen reduction.« less

Aroma formation by immobilized yeast cells in fermentation processes.

PubMed

Nedović, V; Gibson, B; Mantzouridou, T F; Bugarski, B; Djordjević, V; Kalušević, A; Paraskevopoulou, A; Sandell, M; Šmogrovičová, D; Yilmaztekin, M

2015-01-01

Immobilized cell technology has shown a significant promotional effect on the fermentation of alcoholic beverages such as beer, wine and cider. However, genetic, morphological and physiological alterations occurring in immobilized yeast cells impact on aroma formation during fermentation processes. The focus of this review is exploitation of existing knowledge on the biochemistry and the biological role of flavour production in yeast for the biotechnological production of aroma compounds of industrial importance, by means of immobilized yeast. Various types of carrier materials and immobilization methods proposed for application in beer, wine, fruit wine, cider and mead production are presented. Engineering aspects with special emphasis on immobilized cell bioreactor design, operation and scale-up potential are also discussed. Ultimately, examples of products with improved quality properties within the alcoholic beverages are addressed, together with identification and description of the future perspectives and scope for cell immobilization in fermentation processes. Copyright © 2014 John Wiley & Sons, Ltd.

Endogenous peptide profile for elucidating biosynthetic processing of the ghrelin precursor.

PubMed

Tsuchiya, Takashi; Iwakura, Hiroshi; Minamino, Naoto; Kangawa, Kenji; Sasaki, Kazuki

2017-09-02

Ghrelin is an orexigenic peptide primarily produced by gastric endocrine cells. The biosynthetic cleavage site of ghrelin has been well documented, but how its downstream region undergoes proteolytic processing remains poorly explored. Here, we provide the first snapshot of endogenous peptides from the ghrelin precursor by profiling the secretopeptidome of cultured mouse ghrelin-producing cells during exocytosis. Mapping of MS/MS sequenced peptides to the precursor highlighted three atypical monobasic processing sites, including the established C-terminus of ghrelin and the N-terminal cleavage site for obestatin, a putative 23-amino-acid C-terminally amidated peptide. However, we found that mouse obestatin does not occur in the form originally reported, but that a different amidation site is used to generate a shorter peptide. These data can be extended to study and characterize the precursor-derived peptides located downstream of ghrelin in different biological contexts. Copyright © 2017 Elsevier Inc. All rights reserved.

Analysis of Wastewater Treatment Efficiency in a Soft Drinks Industry

NASA Astrophysics Data System (ADS)

Boguniewicz-Zabłocka, Joanna; Capodaglio, Andrea G.; Vogel, Daniel

2017-10-01

During manufacturing processes, most industrial plants generate wastewater which could become harmful to the environment. Discharge of untreated or improperly treated industrial wastewaters into surface water could, in fact, lead to deterioration of the receiving water body's quality. This paper concerns wastewater treatment solutions used in the soft drink production industry: wastewater treatment plant effectiveness analysis was determined in terms of basic pollution indicators, such as BOD, COD, TSS and variable pH. Initially, the performance of mechanic-biological systems for the treatment of wastewater from a specific beverages production process was studied in different periods, due to wastewater flow fluctuation. The study then showed the positive effects on treatment of wastewater augmentation by methanol, nitrogen and phosphorus salts dosed into it during the treatment process. Results confirm that after implemented modification (methanol, nitrogen and phosphorus additions) pollution removal occurs mostly with higher efficiency.

Injuries and illnesses in a cohort of elite youth alpine ski racers and the influence of biological maturity and relative age: a two-season prospective study

PubMed Central

Müller, Lisa; Hildebrandt, Carolin; Müller, Erich; Oberhoffer, Renate; Raschner, Christian

2017-01-01

Background Studies on injuries and illnesses involving youth ski racers younger than 15 years are lacking in the literature. The aim of this study was prospectively to assess the incidence, prevalence, and severity of traumatic and overuse injuries, as well as illnesses of elite youth ski racers with regard to sex, biological maturity status, and relative age. Subjects and methods A prospective, longitudinal cohort design was used to monitor the anthropometrics, training characteristics, traumatic and overuse injuries, and illnesses of 82 elite youth ski racers (51 males, 31 females, age 9–14 years) over 2 consecutive years. The exact training exposure (skiing and athletic) was recorded. Relative age and estimated biological maturity status were assessed. Results Relatively low injury incidence or prevalence (traumatic, 0.86/1,000 hours of training; overuse, 0.28/1,000 hours) and comparably high illness prevalence (2.4/athlete) were reported. The knee was the most commonly affected body part (traumatic injuries 36.5%, overuse injuries 82%). A high number of bone fractures were revealed (46%), while no stress fractures occurred; 66% of the illnesses were respiratory tract infections. No differences were found between males and females, the differing maturity groups, or relative age quartiles. Early-maturing athletes had comparably low traumatic and overuse-injury rates. Relatively younger athletes had low traumatic injury rates. Conclusion The injury-prevention measures implemented in the training process of youth ski racers seem to contribute to a low incidence of injury. Biological maturity status should be considered in the training process to prevent injuries in late-maturing athletes. PMID:28546774

ROSICS: CHEMISTRY AND PROTEOMICS OF CYSTEINE MODIFICATIONS IN REDOX BIOLOGY

PubMed Central

Kim, Hee-Jung; Ha, Sura; Lee, Hee Yoon; Lee, Kong-Joo

2015-01-01

Post-translational modifications (PTMs) occurring in proteins determine their functions and regulations. Proteomic tools are available to identify PTMs and have proved invaluable to expanding the inventory of these tools of nature that hold the keys to biological processes. Cysteine (Cys), the least abundant (1–2%) of amino acid residues, are unique in that they play key roles in maintaining stability of protein structure, participating in active sites of enzymes, regulating protein function and binding to metals, among others. Cys residues are major targets of reactive oxygen species (ROS), which are important mediators and modulators of various biological processes. It is therefore necessary to identify the Cys-containing ROS target proteins, as well as the sites and species of their PTMs. Cutting edge proteomic tools which have helped identify the PTMs at reactive Cys residues, have also revealed that Cys residues are modified in numerous ways. These modifications include formation of disulfide, thiosulfinate and thiosulfonate, oxidation to sulfenic, sulfinic, sulfonic acids and thiosulfonic acid, transformation to dehydroalanine (DHA) and serine, palmitoylation and farnesylation, formation of chemical adducts with glutathione, 4-hydroxynonenal and 15-deoxy PGJ2, and various other chemicals. We present here, a review of relevant ROS biology, possible chemical reactions of Cys residues and details of the proteomic strategies employed for rapid, efficient and sensitive identification of diverse and novel PTMs involving reactive Cys residues of redox-sensitive proteins. We propose a new name, “ROSics,” for the science which describes the principles of mode of action of ROS at molecular levels. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:184–208, 2015. PMID:24916017

A probabilistic framework for identifying biosignatures using Pathway Complexity

NASA Astrophysics Data System (ADS)

Marshall, Stuart M.; Murray, Alastair R. G.; Cronin, Leroy

2017-11-01

One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes-whether those processes occur at the scale of cells or societies, they are the consequences of living systems. While these objects are not living, they cannot randomly form, as they are the product of a biological organism and hence are either technological or cultural biosignatures. A generalized approach that aims to evaluate complex objects as possible biosignatures could be useful to explore the cosmos for new life forms. However, it is not obvious how it might be possible to create such a self-contained approach. This would require us to prove rigorously that a given artefact is too complex to have formed by chance. In this paper, we present a new type of complexity measure, which we call `Pathway Complexity', that allows us not only to threshold the abiotic-biotic divide, but also to demonstrate a probabilistic approach based on object abundance and complexity which can be used to unambiguously assign complex objects as biosignatures. We hope that this approach will not only open up the search for biosignatures beyond the Earth, but also allow us to explore the Earth for new types of biology, and to determine when a complex chemical system discovered in the laboratory could be considered alive. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle.

PubMed

Mondet, Fanny; Rau, Andrea; Klopp, Christophe; Rohmer, Marine; Severac, Dany; Le Conte, Yves; Alaux, Cedric

2018-05-04

The parasite Varroa destructor represents a significant threat to honeybee colonies. Indeed, development of Varroa infestation within colonies, if left untreated, often leads to the death of the colony. Although its impact on bees has been extensively studied, less is known about its biology and the functional processes governing its adult life cycle and adaptation to its host. We therefore developed a full life cycle transcriptomic catalogue in adult Varroa females and included pairwise comparisons with males, artificially-reared and non-reproducing females (10 life cycle stages and conditions in total). Extensive remodeling of the Varroa transcriptome was observed, with an upregulation of energetic and chitin metabolic processes during the initial and final phases of the life cycle (e.g. phoretic and post-oviposition stages), whereas during reproductive stages in brood cells genes showing functions related to transcriptional regulation were overexpressed. Several neurotransmitter and neuropeptide receptors involved in behavioural regulation, as well as active compounds of salivary glands, were also expressed at a higher level outside the reproductive stages. No difference was detected between artificially-reared phoretic females and their counterparts in colonies, or between females who failed to reproduce and females who successfully reproduced, indicating that phoretic individuals can be reared outside host colonies without impacting their physiology and that mechanisms underlying reproductive failure occur before oogenesis. We discuss how these new findings reveal the remarkable adaptation of Varroa to its host biology and notably to the switch from living on adults to reproducing in sealed brood cells. By spanning the entire adult life cycle, our work captures the dynamic changes in the parasite gene expression and serves as a unique resource for deciphering Varroa biology and identifying new targets for mite control.

Simultaneous monitoring of biofilm growth, microbial activity, and inorganic deposits on surfaces with an in situ, online, real-time, non-destructive, optical sensor.

PubMed

Strathmann, Martin; Mittenzwey, Klaus-Henrik; Sinn, Gert; Papadakis, Wassilios; Flemming, Hans-Curt

2013-01-01

Deposits on surfaces in water-bearing systems, also known as 'fouling', can lead to substantial losses in the performance of industrial processes as well as a decreased product quality. Early detection and localization of such deposits can, to a considerable extent, save such losses. However, most of the surfaces that become fouled, for example, in process water pipes, membrane systems, power plants, and food and beverage industries, are difficult to access and analyses conducted on the water phase do not reveal the site or extent of deposits. Furthermore, it is of interest to distinguish biological from non-biological deposits. Although they usually occur together, different countermeasures are necessary. Therefore, sensors are required that indicate the development of surface fouling in real-time, non-destructively, and in situ, preferably allowing for discrimination between chemical and/or biological deposits. In this paper, an optical deposit sensor is presented which fulfills these requirements. Based on multiple fluorescence excitation emission matrix analysis, it detects autofluorescence of amino acids as indicators of biomass. Autofluorescence of nicotinamide adenine dinucleotide + hydrogen is interpreted as an indicator of biological activity, thus it acts as a viability marker, making the method suited for assessing the efficacy of disinfection treatments. Scattering signals from abiotic deposits such as calcium carbonate or corrosion products can clearly be distinguished from biotic substances and monitored separately. The sensor provides an early warning of fouling, allowing for timely countermeasures to be deployed. It also provides an assessment of the success of cleaning treatments and is a promising tool for integrated antifouling strategies.

Effects of biological activity, light, temperature and oxygen on phosphorus release processes at the sediment and water interface of Taihu Lake, China.

PubMed

Jiang, Xia; Jin, Xiangcan; Yao, Yang; Li, Lihe; Wu, Fengchang

2008-04-01

Effects of biological activity, light, temperature and oxygen on the phosphorus (P) release processes at the sediment and water interface of a shallow lake, Taihu Lake, China, were investigated. The results show that organisms at the sediment and water interface can stimulate P release from sediments, and their metabolism can alter the surrounding micro-environmental conditions. The extent of P release and its effects on P concentration in the overlying water were affected by factors such as light, temperature and dissolved oxygen. The organism biomass increased as temperature increased, which was beneficial for P release. Dissolved total phosphorus (DTP) and dissolved inorganic phosphorus (DIP) concentrations in the corresponding overlying water were mainly controlled by light. P release occurred in both aerobic and anoxic conditions with the presence of organisms. However in the presence of light , P release in an anoxic environment was much greater than in an aerobic environment, which may stimulate alga bloom and result in an increase in total phosphorus (TP) in the overlying water. This information aids the understanding of P biogeochemical cycling at the interface and its relationship with eutrophication in shallow lakes.

The Pathway of Oligomeric DNA Melting Investigated by Molecular Dynamics Simulations

PubMed Central

Wong, Ka-Yiu; Pettitt, B. Montgomery

2008-01-01

Details of the reaction coordinate for DNA melting are fundamental to much of biology and biotechnology. Recently, it has been shown experimentally that there are at least three states involved. To clarify the reaction mechanism of the melting transition of DNA, we perform 100-ns molecular dynamics simulations of a homo-oligomeric, 12-basepair DNA duplex, d(A12)·d(T12), with explicit salt water at 400 K. Analysis of the trajectory reveals the various biochemically important processes that occur on different timescales. Peeling (including fraying from the ends), searching for Watson-Crick complements, and dissociation are recognizable processes. However, we find that basepair searching for Watson-Crick complements along a strand is not mechanistically tied to or directly accessible from the dissociation steps of strand melting. A three-step melting mechanism is proposed where the untwisting of the duplex is determined to be the major component of the reaction coordinate at the barrier. Though the observations are limited to the characteristics of the system being studied, they provide important insight into the mechanism of melting of other more biologically relevant forms of DNA, which will certainly differ in details from those here. PMID:18952784

Comparative peptidomic profile between human hypertrophic scar tissue and matched normal skin for identification of endogenous peptides involved in scar pathology.

PubMed

Li, Jingyun; Chen, Ling; Li, Qian; Cao, Jing; Gao, Yanli; Li, Jun

2018-08-01

Endogenous peptides recently attract increasing attention for their participation in various biological processes. Their roles in the pathogenesis of human hypertrophic scar remains poorly understood. In this study, we used liquid chromatography-tandem mass spectrometry to construct a comparative peptidomic profiling between human hypertrophic scar tissue and matched normal skin. A total of 179 peptides were significantly differentially expressed in human hypertrophic scar tissue, with 95 upregulated and 84 downregulated peptides between hypertrophic scar tissue and matched normal skin. Further bioinformatics analysis (Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis) indicated that precursor proteins of these differentially expressed peptides correlate with cellular process, biological regulation, cell part, binding and structural molecule activity ribosome, and PPAR signaling pathway occurring during pathological changes of hypertrophic scar. Based on prediction database, we found that 78 differentially expressed peptides shared homology with antimicrobial peptides and five matched known immunomodulatory peptides. In conclusion, our results show significantly altered expression profiles of peptides in human hypertrophic scar tissue. These peptides may participate in the etiology of hypertrophic scar and provide beneficial scheme for scar evaluation and treatments. © 2017 Wiley Periodicals, Inc.

Planar optical waveguide based sandwich assay sensors and processes for the detection of biological targets including early detection of cancers

DOEpatents

Martinez, Jennifer S [Santa Fe, NM; Swanson, Basil I [Los Alamos, NM; Shively, John E [Arcadia, CA; Li, Lin [Monrovia, CA

2009-06-02

An assay element is described including recognition ligands adapted for binding to carcinoembryonic antigen (CEA) bound to a film on a single mode planar optical waveguide, the film from the group of a membrane, a polymerized bilayer membrane, and a self-assembled monolayer containing polyethylene glycol or polypropylene glycol groups therein and an assay process for detecting the presence of CEA is described including injecting a possible CEA-containing sample into a sensor cell including the assay element, maintaining the sample within the sensor cell for time sufficient for binding to occur between CEA present within the sample and the recognition ligands, injecting a solution including a reporter ligand into the sensor cell; and, interrogating the sample within the sensor cell with excitation light from the waveguide, the excitation light provided by an evanescent field of the single mode penetrating into the biological target-containing sample to a distance of less than about 200 nanometers from the waveguide thereby exciting any bound reporter ligand within a distance of less than about 200 nanometers from the waveguide and resulting in a detectable signal.

The advantage of being slow: The quasi-neutral contact process.

PubMed

de Oliveira, Marcelo Martins; Dickman, Ronald

2017-01-01

According to the competitive exclusion principle, in a finite ecosystem, extinction occurs naturally when two or more species compete for the same resources. An important question that arises is: when coexistence is not possible, which mechanisms confer an advantage to a given species against the other(s)? In general, it is expected that the species with the higher reproductive/death ratio will win the competition, but other mechanisms, such as asymmetry in interspecific competition or unequal diffusion rates, have been found to change this scenario dramatically. In this work, we examine competitive advantage in the context of quasi-neutral population models, including stochastic models with spatial structure as well as macroscopic (mean-field) descriptions. We employ a two-species contact process in which the "biological clock" of one species is a factor of α slower than that of the other species. Our results provide new insights into how stochasticity and competition interact to determine extinction in finite spatial systems. We find that a species with a slower biological clock has an advantage if resources are limited, winning the competition against a species with a faster clock, in relatively small systems. Periodic or stochastic environmental variations also favor the slower species, even in much larger systems.

Influence of climate on malaria transmission depends on daily temperature variation.

PubMed

Paaijmans, Krijn P; Blanford, Simon; Bell, Andrew S; Blanford, Justine I; Read, Andrew F; Thomas, Matthew B

2010-08-24

Malaria transmission is strongly influenced by environmental temperature, but the biological drivers remain poorly quantified. Most studies analyzing malaria-temperature relations, including those investigating malaria risk and the possible impacts of climate change, are based solely on mean temperatures and extrapolate from functions determined under unrealistic laboratory conditions. Here, we present empirical evidence to show that, in addition to mean temperatures, daily fluctuations in temperature affect parasite infection, the rate of parasite development, and the essential elements of mosquito biology that combine to determine malaria transmission intensity. In general, we find that, compared with rates at equivalent constant mean temperatures, temperature fluctuation around low mean temperatures acts to speed up rate processes, whereas fluctuation around high mean temperatures acts to slow processes down. At the extremes (conditions representative of the fringes of malaria transmission, where range expansions or contractions will occur), fluctuation makes transmission possible at lower mean temperatures than currently predicted and can potentially block transmission at higher mean temperatures. If we are to optimize control efforts and develop appropriate adaptation or mitigation strategies for future climates, we need to incorporate into predictive models the effects of daily temperature variation and how that variation is altered by climate change.

Sex allocation promotes the stable co-occurrence of competitive species

NASA Astrophysics Data System (ADS)

Kobayashi, Kazuya

2017-03-01

Biodiversity has long been a source of wonder and scientific curiosity. Theoretically, the co-occurrence of competitive species requires niche differentiation, and such differences are well known; however, the neutral theory, which assumes the equivalence of all individuals regardless of the species in a biological community, has successfully recreated observed patterns of biodiversity. In this research, the evolution of sex allocation is demonstrated to be the key to resolving why the neutral theory works well, despite the observed species differences. The sex allocation theory predicts that female-biased allocation evolves in species in declining density and that this allocation improves population growth, which should lead to an increase in density. In contrast, when the density increases, a less biased allocation evolves, which reduces the population growth rate and leads to decreased density. Thus, sex allocation provides a buffer against species differences in population growth. A model incorporating this mechanism demonstrates that hundreds of species can co-occur over 10,000 generations, even in homogeneous environments, and reproduces the observed patterns of biodiversity. This study reveals the importance of evolutionary processes within species for the sustainability of biodiversity. Integrating the entire biological process, from genes to community, will open a new era of ecology.

Evidence of atmospheric nanoparticle formation from emissions of marine microorganisms

NASA Astrophysics Data System (ADS)

Sellegri, K.; Pey, J.; Rose, C.; Culot, A.; DeWitt, H. L.; Mas, S.; Schwier, A. N.; Temime-Roussel, B.; Charriere, B.; Saiz-Lopez, A.; Mahajan, A. S.; Parin, D.; Kukui, A.; Sempere, R.; D'Anna, B.; Marchand, N.

2016-06-01

Earth, as a whole, can be considered as a living organism emitting gases and particles into its atmosphere, in order to regulate its own temperature. In particular, oceans may respond to climate change by emitting particles that ultimately will influence cloud coverage. At the global scale, a large fraction of the aerosol number concentration is formed by nucleation of gas-phase species, but this process has never been directly observed above oceans. Here we present, using semicontrolled seawater-air enclosures, evidence that nucleation may occur from marine biological emissions in the atmosphere of the open ocean. We identify iodine-containing species as major precursors for new particle clusters' formation, while questioning the role of the commonly accepted dimethyl sulfide oxidation products, in forming new particle clusters in the region investigated and within a time scale on the order of an hour. We further show that amines would sustain the new particle formation process by growing the new clusters to larger sizes. Our results suggest that iodine-containing species and amines are correlated to different biological tracers. These observations, if generalized, would call for a substantial change of modeling approaches of the sea-to-air interactions.

Anthropology and cultural neuroscience: creating productive intersections in parallel fields.

PubMed

Brown, R A; Seligman, R

2009-01-01

Partly due to the failure of anthropology to productively engage the fields of psychology and neuroscience, investigations in cultural neuroscience have occurred largely without the active involvement of anthropologists or anthropological theory. Dramatic advances in the tools and findings of social neuroscience have emerged in parallel with significant advances in anthropology that connect social and political-economic processes with fine-grained descriptions of individual experience and behavior. We describe four domains of inquiry that follow from these recent developments, and provide suggestions for intersections between anthropological tools - such as social theory, ethnography, and quantitative modeling of cultural models - and cultural neuroscience. These domains are: the sociocultural construction of emotion, status and dominance, the embodiment of social information, and the dual social and biological nature of ritual. Anthropology can help locate unique or interesting populations and phenomena for cultural neuroscience research. Anthropological tools can also help "drill down" to investigate key socialization processes accountable for cross-group differences. Furthermore, anthropological research points at meaningful underlying complexity in assumed relationships between social forces and biological outcomes. Finally, ethnographic knowledge of cultural content can aid with the development of ecologically relevant stimuli for use in experimental protocols.

Systems microscopy: an emerging strategy for the life sciences.

PubMed

Lock, John G; Strömblad, Staffan

2010-05-01

Dynamic cellular processes occurring in time and space are fundamental to all physiology and disease. To understand complex and dynamic cellular processes therefore demands the capacity to record and integrate quantitative multiparametric data from the four spatiotemporal dimensions within which living cells self-organize, and to subsequently use these data for the mathematical modeling of cellular systems. To this end, a raft of complementary developments in automated fluorescence microscopy, cell microarray platforms, quantitative image analysis and data mining, combined with multivariate statistics and computational modeling, now coalesce to produce a new research strategy, "systems microscopy", which facilitates systems biology analyses of living cells. Systems microscopy provides the crucial capacities to simultaneously extract and interrogate multiparametric quantitative data at resolution levels ranging from the molecular to the cellular, thereby elucidating a more comprehensive and richly integrated understanding of complex and dynamic cellular systems. The unique capacities of systems microscopy suggest that it will become a vital cornerstone of systems biology, and here we describe the current status and future prospects of this emerging field, as well as outlining some of the key challenges that remain to be overcome. Copyright 2010 Elsevier Inc. All rights reserved.

Bioactive molecules in milk and their role in health and disease: the role of transforming growth factor-beta.

PubMed

Donnet-Hughes, A; Duc, N; Serrant, P; Vidal, K; Schiffrin, E J

2000-02-01

Human breast milk is rich in nutrients, hormones, growth factors and immunoactive molecules, which influence the growth, development and immune status of the newborn infant. Although several of these factors are also present in bovine milk, the greater susceptibility of the formula-fed infant to infection and disease and the development of allergy is often attributed to the reduced level of protective factors in milk formulas. Nevertheless, modifying manufacturing processes may preserve the biological activity of some bioactive molecules in end products. Transforming growth factor (TGF)-beta is one such molecule. TGF-beta is a polypeptide, which has been described in both human and bovine milk. It is implicated in many processes, including epithelial cell growth and differentiation, development, carcinogenesis and immune regulation. The present article discusses the biological activity of TGF-beta2 that has been preserved and activated in a cow's milk-based product. More specifically, it addresses possible mechanisms of action in the intestinal lumen and speculates on how milk products containing naturally occurring TGF-beta2 could be exploited in functional foods for the infant or as therapies for specific intestinal diseases.

Aerobic and anaerobic nitrogen transformation processes in N2-fixing cyanobacterial aggregates

PubMed Central

Klawonn, Isabell; Bonaglia, Stefano; Brüchert, Volker; Ploug, Helle

2015-01-01

Colonies of N2-fixing cyanobacteria are key players in supplying new nitrogen to the ocean, but the biological fate of this fixed nitrogen remains poorly constrained. Here, we report on aerobic and anaerobic microbial nitrogen transformation processes that co-occur within millimetre-sized cyanobacterial aggregates (Nodularia spumigena) collected in aerated surface waters in the Baltic Sea. Microelectrode profiles showed steep oxygen gradients inside the aggregates and the potential for nitrous oxide production in the aggregates' anoxic centres. 15N-isotope labelling experiments and nutrient analyses revealed that N2 fixation, ammonification, nitrification, nitrate reduction to ammonium, denitrification and possibly anaerobic ammonium oxidation (anammox) can co-occur within these consortia. Thus, N. spumigena aggregates are potential sites of nitrogen gain, recycling and loss. Rates of nitrate reduction to ammonium and N2 were limited by low internal nitrification rates and low concentrations of nitrate in the ambient water. Presumably, patterns of N-transformation processes similar to those observed in this study arise also in other phytoplankton colonies, marine snow and fecal pellets. Anoxic microniches, as a pre-condition for anaerobic nitrogen transformations, may occur within large aggregates (⩾1 mm) even when suspended in fully oxygenated waters, whereas anoxia in small aggregates (<1 to ⩾0.1 mm) may only arise in low-oxygenated waters (⩽25 μM). We propose that the net effect of aggregates on nitrogen loss is negligible in NO3−-depleted, fully oxygenated (surface) waters. In NO3−-enriched (>1.5 μM), O2-depleted water layers, for example, in the chemocline of the Baltic Sea or the oceanic mesopelagic zone, aggregates may promote N-recycling and -loss processes. PMID:25575306

Aerobic and anaerobic nitrogen transformation processes in N2-fixing cyanobacterial aggregates.

PubMed

Klawonn, Isabell; Bonaglia, Stefano; Brüchert, Volker; Ploug, Helle

2015-06-01

Colonies of N(2)-fixing cyanobacteria are key players in supplying new nitrogen to the ocean, but the biological fate of this fixed nitrogen remains poorly constrained. Here, we report on aerobic and anaerobic microbial nitrogen transformation processes that co-occur within millimetre-sized cyanobacterial aggregates (Nodularia spumigena) collected in aerated surface waters in the Baltic Sea. Microelectrode profiles showed steep oxygen gradients inside the aggregates and the potential for nitrous oxide production in the aggregates' anoxic centres. (15)N-isotope labelling experiments and nutrient analyses revealed that N(2) fixation, ammonification, nitrification, nitrate reduction to ammonium, denitrification and possibly anaerobic ammonium oxidation (anammox) can co-occur within these consortia. Thus, N. spumigena aggregates are potential sites of nitrogen gain, recycling and loss. Rates of nitrate reduction to ammonium and N(2) were limited by low internal nitrification rates and low concentrations of nitrate in the ambient water. Presumably, patterns of N-transformation processes similar to those observed in this study arise also in other phytoplankton colonies, marine snow and fecal pellets. Anoxic microniches, as a pre-condition for anaerobic nitrogen transformations, may occur within large aggregates (⩾1 mm) even when suspended in fully oxygenated waters, whereas anoxia in small aggregates (<1 to ⩾0.1 mm) may only arise in low-oxygenated waters (⩽25 μM). We propose that the net effect of aggregates on nitrogen loss is negligible in NO(3)(-)-depleted, fully oxygenated (surface) waters. In NO(3)(-)-enriched (>1.5 μM), O(2)-depleted water layers, for example, in the chemocline of the Baltic Sea or the oceanic mesopelagic zone, aggregates may promote N-recycling and -loss processes.

Frontiers, Opportunities, and Challenges in Biochemical and Chemical Catalysis of CO2

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

Appel, Aaron M.; Bercaw, John E.; Bocarsly, Andrew B.

2013-08-14

Our central premise is that catalytic scientists can learn by studying how these important metabolic processes occur in nature. Complementarily, biochemists can learn by studying how catalytic scientists view these same chemical transformations promoted by synthetic catalysts. From these studies, hypotheses can be developed and tested through manipulation of enzyme structure and by synthesizing simple molecular catalysts to incorporate different structural features of the enzymes. It is hoped that these studies will lead to new and useful concepts in catalyst design for fuel production and utilization. This paper describes the results of a workshop held to explore these concepts inmore » regard to the development of new and more efficient catalytic processes for the conversion of CO2 to a variety of carbon-based fuels. The organization of this overview/review is as follows: 1) The first section briefly explores how interactions between the catalysis and biological communities have been fruitful in developing new catalysts for the reduction of protons to hydrogen, the simplest fuel generation reaction. 2) The second section assesses the state of the art in both biological and chemical reduction of CO2 by two electrons to form either carbon monoxide (CO) or formate (HCOO-). It also attempts to identify common principles between biological and synthetic catalysts and productive areas for future research. 3) The third section explores both biological and chemical processes that result in the reduction of CO2 beyond the level of CO and formate, again seeking to identify common principles and productive areas of future research. 4) The fourth section explores the formation of carbon-carbon bonds in biological and chemical systems in the same vein as the other sections. 5) A fifth section addresses the role of non-redox reactions of CO2 in biological systems and their role in carbon metabolism, with a parallel discussion of chemical systems. 6) In section 6, the topics of electrode modification, photochemical systems, and tandem catalysis are briefly discussed. These areas may be important for developing practical systems for CO2 reduction, and they share the common theme of coupling chemical reactions. 7) Section 7 describes some of the crosscutting activities that are critical for advancing the science underpinning catalyst development. 8) The last section attempts to summarize common issues in biological and chemical catalysis and to identify challenges that must be addressed to achieve practical catalysts that are suitable for the reduction of CO2 to fuels.« less