Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

International Nuclear Information System (INIS)

Stokes-Rees, Ian; Levesque, Ian; Murphy, Frank V. IV; Yang, Wei; Deacon, Ashley; Sliz, Piotr

2012-01-01

It has been difficult, historically, to manage and maintain early-stage experimental data collected by structural biologists in synchrotron facilities. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to manage collected data at synchrotrons and to facilitate the efficient and secure transfer of data to the owner's home institution. Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

Energy Technology Data Exchange (ETDEWEB)

Stokes-Rees, Ian [Harvard Medical School, Boston, MA 02115 (United States); Levesque, Ian [Harvard Medical School, Boston, MA 02115 (United States); Harvard Medical School, Boston, MA 02115 (United States); Murphy, Frank V. IV [Argonne National Laboratory, Argonne, IL 60439 (United States); Yang, Wei; Deacon, Ashley [Stanford University, Menlo Park, CA 94025 (United States); Sliz, Piotr, E-mail: piotr-sliz@hms.harvard.edu [Harvard Medical School, Boston, MA 02115 (United States)

2012-05-01

It has been difficult, historically, to manage and maintain early-stage experimental data collected by structural biologists in synchrotron facilities. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to manage collected data at synchrotrons and to facilitate the efficient and secure transfer of data to the owner's home institution. Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities.

Adaptation of sensor morphology: an integrative view of perception from biologically inspired robotics perspective

Science.gov (United States)

Nurzaman, Surya G.

2016-01-01

Sensor morphology, the morphology of a sensing mechanism which plays a role of shaping the desired response from physical stimuli from surroundings to generate signals usable as sensory information, is one of the key common aspects of sensing processes. This paper presents a structured review of researches on bioinspired sensor morphology implemented in robotic systems, and discusses the fundamental design principles. Based on literature review, we propose two key arguments: first, owing to its synthetic nature, biologically inspired robotics approach is a unique and powerful methodology to understand the role of sensor morphology and how it can evolve and adapt to its task and environment. Second, a consideration of an integrative view of perception by looking into multidisciplinary and overarching mechanisms of sensor morphology adaptation across biology and engineering enables us to extract relevant design principles that are important to extend our understanding of the unfinished concepts in sensing and perception. PMID:27499843

Maneuvering control and configuration adaptation of a biologically inspired morphing aircraft

Science.gov (United States)

Abdulrahim, Mujahid

Natural flight as a source of inspiration for aircraft design was prominent with early aircraft but became marginalized as aircraft became larger and faster. With recent interest in small unmanned air vehicles, biological inspiration is a possible technology to enhance mission performance of aircraft that are dimensionally similar to gliding birds. Serial wing joints, loosely modeling the avian skeletal structure, are used in the current study to allow significant reconfiguration of the wing shape. The wings are reconfigured to optimize aerodynamic performance and maneuvering metrics related to specific mission tasks. Wing shapes for each mission are determined and related to the seagulls, falcons, albatrosses, and non-migratory African swallows on which the aircraft are based. Variable wing geometry changes the vehicle dynamics, affording versatility in flight behavior but also requiring appropriate compensation to maintain stability and controllability. Time-varying compensation is in the form of a baseline controller which adapts to both the variable vehicle dynamics and to the changing mission requirements. Wing shape is adapted in flight to minimize a cost function which represents energy, temporal, and spatial efficiency. An optimal control architecture unifies the control and adaptation tasks.

Capturing microscopic features of bone remodeling into a macroscopic model based on biological rationales of bone adaptation.

Science.gov (United States)

Kim, Young Kwan; Kameo, Yoshitaka; Tanaka, Sakae; Adachi, Taiji

2017-10-01

To understand Wolff's law, bone adaptation by remodeling at the cellular and tissue levels has been discussed extensively through experimental and simulation studies. For the clinical application of a bone remodeling simulation, it is significant to establish a macroscopic model that incorporates clarified microscopic mechanisms. In this study, we proposed novel macroscopic models based on the microscopic mechanism of osteocytic mechanosensing, in which the flow of fluid in the lacuno-canalicular porosity generated by fluid pressure gradients plays an important role, and theoretically evaluated the proposed models, taking biological rationales of bone adaptation into account. The proposed models were categorized into two groups according to whether the remodeling equilibrium state was defined globally or locally, i.e., the global or local uniformity models. Each remodeling stimulus in the proposed models was quantitatively evaluated through image-based finite element analyses of a swine cancellous bone, according to two introduced criteria associated with the trabecular volume and orientation at remodeling equilibrium based on biological rationales. The evaluation suggested that nonuniformity of the mean stress gradient in the local uniformity model, one of the proposed stimuli, has high validity. Furthermore, the adaptive potential of each stimulus was discussed based on spatial distribution of a remodeling stimulus on the trabecular surface. The theoretical consideration of a remodeling stimulus based on biological rationales of bone adaptation would contribute to the establishment of a clinically applicable and reliable simulation model of bone remodeling.

Highly Adaptable but Not Invulnerable: Necessary and Facilitating Conditions for Research in Evolutionary Developmental Biology

NARCIS (Netherlands)

Laudel, Grit; Benninghoff, Martin; Lettkemann, Eric; Håkansson, Elias; Whitley, Richard; Gläser, Jochen

2014-01-01

Evolutionary developmental biology is a highly variable scientific innovation because researchers can adapt their involvement in the innovation to the opportunities provided by their environment. On the basis of comparative case studies in four countries, we link epistemic properties of research

Biological stress response terminology: Integrating the concepts of adaptive response and preconditioning stress within a hormetic dose-response framework

International Nuclear Information System (INIS)

Calabrese, Edward J.; Bachmann, Kenneth A.; Bailer, A. John; Bolger, P. Michael; Borak, Jonathan; Cai, Lu; Cedergreen, Nina; Cherian, M. George; Chiueh, Chuang C.; Clarkson, Thomas W.; Cook, Ralph R.; Diamond, David M.; Doolittle, David J.; Dorato, Michael A.; Duke, Stephen O.; Feinendegen, Ludwig; Gardner, Donald E.; Hart, Ronald W.; Hastings, Kenneth L.; Hayes, A. Wallace; Hoffmann, George R.; Ives, John A.; Jaworowski, Zbigniew; Johnson, Thomas E.; Jonas, Wayne B.; Kaminski, Norbert E.; Keller, John G.; Klaunig, James E.; Knudsen, Thomas B.; Kozumbo, Walter J.; Lettieri, Teresa; Liu, Shu-Zheng; Maisseu, Andre; Maynard, Kenneth I.; Masoro, Edward J.; McClellan, Roger O.; Mehendale, Harihara M.; Mothersill, Carmel; Newlin, David B.; Nigg, Herbert N.; Oehme, Frederick W.; Phalen, Robert F.; Philbert, Martin A.; Rattan, Suresh I.S.; Riviere, Jim E.; Rodricks, Joseph; Sapolsky, Robert M.; Scott, Bobby R.; Seymour, Colin; Sinclair, David A.; Smith-Sonneborn, Joan; Snow, Elizabeth T.; Spear, Linda; Stevenson, Donald E.; Thomas, Yolene; Tubiana, Maurice; Williams, Gary M.; Mattson, Mark P.

2007-01-01

Many biological subdisciplines that regularly assess dose-response relationships have identified an evolutionarily conserved process in which a low dose of a stressful stimulus activates an adaptive response that increases the resistance of the cell or organism to a moderate to severe level of stress. Due to a lack of frequent interaction among scientists in these many areas, there has emerged a broad range of terms that describe such dose-response relationships. This situation has become problematic because the different terms describe a family of similar biological responses (e.g., adaptive response, preconditioning, hormesis), adversely affecting interdisciplinary communication, and possibly even obscuring generalizable features and central biological concepts. With support from scientists in a broad range of disciplines, this article offers a set of recommendations we believe can achieve greater conceptual harmony in dose-response terminology, as well as better understanding and communication across the broad spectrum of biological disciplines

Biologically inspired control of humanoid robot arms robust and adaptive approaches

CERN Document Server

Spiers, Adam; Herrmann, Guido

2016-01-01

This book investigates a biologically inspired method of robot arm control, developed with the objective of synthesising human-like motion dynamically, using nonlinear, robust and adaptive control techniques in practical robot systems. The control method caters to a rising interest in humanoid robots and the need for appropriate control schemes to match these systems. Unlike the classic kinematic schemes used in industrial manipulators, the dynamic approaches proposed here promote human-like motion with better exploitation of the robot’s physical structure. This also benefits human-robot interaction. The control schemes proposed in this book are inspired by a wealth of human-motion literature that indicates the drivers of motion to be dynamic, model-based and optimal. Such considerations lend themselves nicely to achievement via nonlinear control techniques without the necessity for extensive and complex biological models. The operational-space method of robot control forms the basis of many of the techniqu...

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology.

Science.gov (United States)

Stokes-Rees, Ian; Levesque, Ian; Murphy, Frank V; Yang, Wei; Deacon, Ashley; Sliz, Piotr

2012-05-01

Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities.

Reproductive biology and adaptability of the invasive alien freshwater Amphipod Crangonyx floridanus (Crustacea: Amphipoda, Crangonyctidae).

Science.gov (United States)

Tojo, Koji; Tanaka, Yoshiki; Kuranishi, Ryoichi B; Kanada, Shoji

2010-06-01

We studied the reproductive biology and adaptability of the alien freshwater crangonyctid amphipod Crangonyx floridanus, currently inhabiting a large portion of Japan, both in the field and under controlled laboratory conditions. In the Chikuma River population of this alien amphipod, egg-bearing individuals were found throughout the year. In terms of egg maturation cycle, egg development (during embryogenesis), and egg count per ovipositional cycle, these amphipods display a very efficient reproductive system. This study also established their adaptability to a wide range of water temperatures (primarily 4-20 degrees C, however in some cases, these individuals are able to survive at up to 30 degrees C). C. floridanus's strong capacity to adapt to broad and variable environmental conditions is certainly contributing to its high rate of population increase, and rapid dispersion throughout Japan.

A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing.

Science.gov (United States)

Ahmad, Muneer; Jung, Low Tan; Bhuiyan, Al-Amin

2017-10-01

Digital signal processing techniques commonly employ fixed length window filters to process the signal contents. DNA signals differ in characteristics from common digital signals since they carry nucleotides as contents. The nucleotides own genetic code context and fuzzy behaviors due to their special structure and order in DNA strand. Employing conventional fixed length window filters for DNA signal processing produce spectral leakage and hence results in signal noise. A biological context aware adaptive window filter is required to process the DNA signals. This paper introduces a biological inspired fuzzy adaptive window median filter (FAWMF) which computes the fuzzy membership strength of nucleotides in each slide of window and filters nucleotides based on median filtering with a combination of s-shaped and z-shaped filters. Since coding regions cause 3-base periodicity by an unbalanced nucleotides' distribution producing a relatively high bias for nucleotides' usage, such fundamental characteristic of nucleotides has been exploited in FAWMF to suppress the signal noise. Along with adaptive response of FAWMF, a strong correlation between median nucleotides and the Π shaped filter was observed which produced enhanced discrimination between coding and non-coding regions contrary to fixed length conventional window filters. The proposed FAWMF attains a significant enhancement in coding regions identification i.e. 40% to 125% as compared to other conventional window filters tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. This study proves that conventional fixed length window filters applied to DNA signals do not achieve significant results since the nucleotides carry genetic code context. The proposed FAWMF algorithm is adaptive and outperforms significantly to process DNA signal contents. The algorithm applied to variety of DNA datasets produced noteworthy discrimination between coding and non-coding regions contrary

75 FR 8968 - Draft Guidance for Industry on Adaptive Design Clinical Trials for Drugs and Biologics; Availability

Science.gov (United States)

2010-02-26

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2010-D-0090] Draft Guidance for Industry on Adaptive Design Clinical Trials for Drugs and Biologics; Availability... familiar and less familiar approaches. As more experience is obtained with the less familiar designs...

Assessment of students’ health condition by indicators of adaptation potential, biological age and bio-energetic reserves of organism

Directory of Open Access Journals (Sweden)

O.V. Martyniuk

2015-06-01

Full Text Available Purpose: to assess students’ health condition by indicators of adaptation potential, biological age and express-assessment. Material: in the research 47 first and second year girl students participated, who belonged to main health group. Results: we distributed the girl students into three groups: 14.89% of them were included in group with “safe” health condition; 34.04% - in group of “third state”; 51.06% were related to group with “ dangerous” health condition. We established that dangerous level was characterized by energy potential of below middle and low level. It is accompanied by accelerated processes of organism’s age destructions and tension of regulation mechanisms. Conclusions: the received results permit to further develop and generalize the data of students’ health’s assessment by indicators of adaptation potentials, biological age and physical health’s condition.

Remote Sensing Dynamic Monitoring of Biological Invasive Species Based on Adaptive PCNN and Improved C-V Model

Directory of Open Access Journals (Sweden)

PENG Gang

2014-12-01

Full Text Available Biological species invasion problem bring serious damage to the ecosystem, and have become one of the six major enviromental problems that affect the future economic development, also have become one of the hot topic in domestic and foreign scholars. Remote sensing technology has been successfully used in the investigation of coastal zone resources, dynamic monitoring of the resources and environment, and other fields. It will cite a new remote sensing image change detection algorithm based on adaptive pulse coupled neural network (PCNN and improved C-V model, for remote sensing dynamic monitoring of biological species invasion. The experimental results show that the algorithm is effective in the test results of biological species invasions.

Molecular PET imaging for biology-guided adaptive radiotherapy of head and neck cancer.

Science.gov (United States)

Hoeben, Bianca A W; Bussink, Johan; Troost, Esther G C; Oyen, Wim J G; Kaanders, Johannes H A M

2013-10-01

Integration of molecular imaging PET techniques into therapy selection strategies and radiation treatment planning for head and neck squamous cell carcinoma (HNSCC) can serve several purposes. First, pre-treatment assessments can steer decisions about radiotherapy modifications or combinations with other modalities. Second, biology-based objective functions can be introduced to the radiation treatment planning process by co-registration of molecular imaging with planning computed tomography (CT) scans. Thus, customized heterogeneous dose distributions can be generated with escalated doses to tumor areas where radiotherapy resistance mechanisms are most prevalent. Third, monitoring of temporal and spatial variations in these radiotherapy resistance mechanisms early during the course of treatment can discriminate responders from non-responders. With such information available shortly after the start of treatment, modifications can be implemented or the radiation treatment plan can be adapted tailing the biological response pattern. Currently, these strategies are in various phases of clinical testing, mostly in single-center studies. Further validation in multicenter set-up is needed. Ultimately, this should result in availability for routine clinical practice requiring stable production and accessibility of tracers, reproducibility and standardization of imaging and analysis methods, as well as general availability of knowledge and expertise. Small studies employing adaptive radiotherapy based on functional dynamics and early response mechanisms demonstrate promising results. In this context, we focus this review on the widely used PET tracer (18)F-FDG and PET tracers depicting hypoxia and proliferation; two well-known radiation resistance mechanisms.

Ecological-biological Aspects of Stipa krylovii Roshev Adaptation at the Initial Stages of Ontogenesis

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N.S. Chistyakova

2016-08-01

Full Text Available Xerophytic cereal Stipa krylovii Roshev is interesting as a relic with extensive capabilities to adapt to severe climatic conditions of Eastern Zabaikal’ye, which allows it to occupy a vast areal. The species under study is characterized by distinctive ecological-biological peculiarities, which are underpinned by not only distribution, but historical establishment of the species. The primary goal of the research was to study ecological-biological peculiarities of adaptation of wild cereal Stipa krylovii to the habitat in Eastern Zabaikal’ye. According to the observations, Stipa krylovii is characterized by late development rate coinciding with the period of optimal heat and moisture availability. Seed embryos have a well-developed scutellum, distinct structures and well differentiated embryo axis. The studies identified no lateral or secondary roots in the cereal. In nature, seeds of S. krylovii are characterized by profound organic peace period, which persists in the course of sprouting under optimal conditions. Peace period of S. krylovii caryopses is likely to be due to the presence of sprouting inhibitors and is overcome in moist autumn period. Seed viability was determined under various soil moisture parameters up to its complete water capacity; the impact of moisture content on seed sprouting rate was studied. The results of the tests on caryopses sprouting with various moisture content demonstrated that at minimum moisture content (10% S. krylovii forms epidermal hairs on coleorhiza; 30% of soil water content is enough for growth activation, viability and sprouting rate of this cereal, which is due to its xerophytic nature. This morphological peculiarity is likely to ensure in nature sprouting of these species in early spring, when soil contain minimum water. Intensity of the initial growth was determined by a number of parameters: rate of change in linear growth of trunk and root parts of the embryo, growth of dry substance of

Adapting to Biology: Maintaining Container-Closure System Compatibility with the Therapeutic Biologic Revolution.

Science.gov (United States)

Degrazio, Dominick

Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to the dimension of evolving therapeutic biologics. Important concerns associated with this changeover are becoming forefront, as challenges develop of varying complexity uncommon with the synthesis and production of traditional drugs. Therefore, alternative measures must be established that aim to preserve the efficacy and functionality of a biologic that might not be implemented for small molecules. Conserving protein stability is relative to perpetuating a net equilibrium of both intrinsic and extrinsic factors. Key to sustaining this balance is the ability of container-closure systems to maintain their compatibility with the ever-changing dynamics of therapeutic biologics. Failure to recognize and adjust the material properties of packaging components to support compatibility with therapeutic biologics can compromise patient safety, drug productivity, and biological stability. This review will examine the differences between small-molecule drugs and therapeutic biologics, lay a basic foundation for understanding the stability of therapeutic biologics, and demonstrate potential sources of container-closure systems' incompatibilities with therapeutic biologics at a mechanistic level. Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to recombinantly derived therapeutic biologics. Concerns associated with this transformation are becoming prominent, as therapeutic biologics are uncharacteristic to small-molecule drugs. Maintaining the stability of a therapeutic biologic is a combination of balancing intrinsic factors and external elements within the biologic's microenvironment. An important aspect of this balance is relegated to the overall compatibility of primary, parenteral container-closure systems with therapeutic biologics

Biological invasions, ecological resilience and adaptive governance.

Science.gov (United States)

Chaffin, Brian C; Garmestani, Ahjond S; Angeler, David G; Herrmann, Dustin L; Stow, Craig A; Nyström, Magnus; Sendzimir, Jan; Hopton, Matthew E; Kolasa, Jurek; Allen, Craig R

2016-12-01

In a world of increasing interconnections in global trade as well as rapid change in climate and land cover, the accelerating introduction and spread of invasive species is a critical concern due to associated negative social and ecological impacts, both real and perceived. Much of the societal response to invasive species to date has been associated with negative economic consequences of invasions. This response has shaped a war-like approach to addressing invasions, one with an agenda of eradications and intense ecological restoration efforts towards prior or more desirable ecological regimes. This trajectory often ignores the concept of ecological resilience and associated approaches of resilience-based governance. We argue that the relationship between ecological resilience and invasive species has been understudied to the detriment of attempts to govern invasions, and that most management actions fail, primarily because they do not incorporate adaptive, learning-based approaches. Invasive species can decrease resilience by reducing the biodiversity that underpins ecological functions and processes, making ecosystems more prone to regime shifts. However, invasions do not always result in a shift to an alternative regime; invasions can also increase resilience by introducing novelty, replacing lost ecological functions or adding redundancy that strengthens already existing structures and processes in an ecosystem. This paper examines the potential impacts of species invasions on the resilience of ecosystems and suggests that resilience-based approaches can inform policy by linking the governance of biological invasions to the negotiation of tradeoffs between ecosystem services. Copyright © 2016. Published by Elsevier Ltd.

Adaption of Ulva pertusa to multiple-contamination of heavy metals and nutrients: Biological mechanism of outbreak of Ulva sp. green tide.

Science.gov (United States)

Ge, Changzi; Yu, Xiru; Kan, Manman; Qu, Chunfeng

2017-12-15

The multiple-contamination of heavy metals and nutrients worsens increasingly and Ulva sp. green tide occurs almost simultaneously. To reveal the biological mechanism for outbreak of the green tide, Ulva pertusa was exposed to seven-day-multiple-contamination. The relation between pH variation (V pH ), Chl a content, ratio of (Chl a content)/(Chl b content) (R chla/chlb ), SOD activity of U. pertusa (A SOD ) and contamination concentration is [Formula: see text] (pcontamination concentrations of seawaters where Ulva sp. green tide occurred and the contamination concentrations set in the present work, U. pertusa can adapt to multiple-contaminations in these waters. Thus, the adaption to multiple-contamination may be one biological mechanism for the outbreak of Ulva sp. green tide. Copyright © 2017 Elsevier Ltd. All rights reserved.

Adaptation in Living Systems

Science.gov (United States)

Tu, Yuhai; Rappel, Wouter-Jan

2018-03-01

Adaptation refers to the biological phenomenon where living systems change their internal states in response to changes in their environments in order to maintain certain key functions critical for their survival and fitness. Adaptation is one of the most ubiquitous and arguably one of the most fundamental properties of living systems. It occurs throughout all biological scales, from adaptation of populations of species over evolutionary time to adaptation of a single cell to different environmental stresses during its life span. In this article, we review some of the recent progress made in understanding molecular mechanisms of cellular-level adaptation. We take the minimalist (or the physicist) approach and study the simplest systems that exhibit generic adaptive behaviors, namely chemotaxis in bacterium cells (Escherichia coli) and eukaryotic cells (Dictyostelium). We focus on understanding the basic biochemical interaction networks that are responsible for adaptation dynamics. By combining theoretical modeling with quantitative experimentation, we demonstrate universal features in adaptation as well as important differences in different cellular systems. Future work in extending the modeling framework to study adaptation in more complex systems such as sensory neurons is also discussed.

ADAPT: building conceptual models of the physical and biological processes across permafrost landscapes

Science.gov (United States)

Allard, M.; Vincent, W. F.; Lemay, M.

2012-12-01

Fundamental and applied permafrost research is called upon in Canada in support of environmental protection, economic development and for contributing to the international efforts in understanding climatic and ecological feedbacks of permafrost thawing under a warming climate. The five year "Arctic Development and Adaptation to Permafrost in Transition" program (ADAPT) funded by NSERC brings together 14 scientists from 10 Canadian universities and involves numerous collaborators from academia, territorial and provincial governments, Inuit communities and industry. The geographical coverage of the program encompasses all of the permafrost regions of Canada. Field research at a series of sites across the country is being coordinated. A common protocol for measuring ground thermal and moisture regime, characterizing terrain conditions (vegetation, topography, surface water regime and soil organic matter contents) is being applied in order to provide inputs for designing a general model to provide an understanding of transfers of energy and matter in permafrost terrain, and the implications for biological and human systems. The ADAPT mission is to produce an 'Integrated Permafrost Systems Science' framework that will be used to help generate sustainable development and adaptation strategies for the North in the context of rapid socio-economic and climate change. ADAPT has three major objectives: to examine how changing precipitation and warming temperatures affect permafrost geosystems and ecosystems, specifically by testing hypotheses concerning the influence of the snowpack, the effects of water as a conveyor of heat, sediments, and carbon in warming permafrost terrain and the processes of permafrost decay; to interact directly with Inuit communities, the public sector and the private sector for development and adaptation to changes in permafrost environments; and to train the new generation of experts and scientists in this critical domain of research in Canada

Computational adaptive optics for broadband optical interferometric tomography of biological tissue.

Science.gov (United States)

Adie, Steven G; Graf, Benedikt W; Ahmad, Adeel; Carney, P Scott; Boppart, Stephen A

2012-05-08

Aberrations in optical microscopy reduce image resolution and contrast, and can limit imaging depth when focusing into biological samples. Static correction of aberrations may be achieved through appropriate lens design, but this approach does not offer the flexibility of simultaneously correcting aberrations for all imaging depths, nor the adaptability to correct for sample-specific aberrations for high-quality tomographic optical imaging. Incorporation of adaptive optics (AO) methods have demonstrated considerable improvement in optical image contrast and resolution in noninterferometric microscopy techniques, as well as in optical coherence tomography. Here we present a method to correct aberrations in a tomogram rather than the beam of a broadband optical interferometry system. Based on Fourier optics principles, we correct aberrations of a virtual pupil using Zernike polynomials. When used in conjunction with the computed imaging method interferometric synthetic aperture microscopy, this computational AO enables object reconstruction (within the single scattering limit) with ideal focal-plane resolution at all depths. Tomographic reconstructions of tissue phantoms containing subresolution titanium-dioxide particles and of ex vivo rat lung tissue demonstrate aberration correction in datasets acquired with a highly astigmatic illumination beam. These results also demonstrate that imaging with an aberrated astigmatic beam provides the advantage of a more uniform depth-dependent signal compared to imaging with a standard gaussian beam. With further work, computational AO could enable the replacement of complicated and expensive optical hardware components with algorithms implemented on a standard desktop computer, making high-resolution 3D interferometric tomography accessible to a wider group of users and nonspecialists.

[The hyperiricosuria as an indicator of derangement of biologic functions of endoecology and adaptation, biologic reactions of excretion, inflammation and arterial tension].

Science.gov (United States)

Titov, V N; Oshchepkova, E V; Dmitriev, V A; Gushchina, O V; Shiriaeva, Iu K; Iashin, A Ia

2012-04-01

--initiator of inflammation. The uric acid in the form of ion-capturers of active forms of oxygen is involved into in the formation of syndrome of compensatory anti-inflammatory defense. It may be assumed that simultaneously with post-secretory reabsorption of ions of urates in proximal tubules of nephron occurs intensification of philogenetically late post-secretory reabsorption of ions of sodium and activation of of biologic reaction of hydrodynamic and hydraulic pressure in local pool of intravascular medium i.e. arterial tension. The uric acid simultaneously participates in realization of biologic function of endoecology and adaptation, biologic reactions of excretion, inflammation and arterial tension.

SU-C-202-04: Adapting Biologically Optimized Dose Escalation Based On Mid-Treatment PET/CT for Non-Small-Cell Lung Cancer

Energy Technology Data Exchange (ETDEWEB)

Zhang, P; Kuo, L; Yorke, E; Hu, Y; Lockney, N; Mageras, G; Deasy, J; Rimner, A [Memorial Sloan Kettering Cancer Center, New York, NY (United States)

2016-06-15

Purpose: To develop a biological modeling strategy which incorporates the response observed on the mid-treatment PET/CT into a dose escalation design for adaptive radiotherapy of non-small-cell lung cancer. Method: FDG-PET/CT was acquired midway through standard fractionated treatment and registered to pre-treatment planning PET/CT to evaluate radiation response of lung cancer. Each mid-treatment PET voxel was assigned the median SUV inside a concentric 1cm-diameter sphere to account for registration and imaging uncertainties. For each voxel, the planned radiation dose, pre- and mid-treatment SUVs were used to parameterize the linear-quadratic model, which was then utilized to predict the SUV distribution after the full prescribed dose. Voxels with predicted post-treatment SUV≥2 were identified as the resistant target (response arm). An adaptive simultaneous integrated boost was designed to escalate dose to the resistant target as high as possible, while keeping prescription dose to the original target and lung toxicity intact. In contrast, an adaptive target volume was delineated based only on the intensity of mid-treatment PET/CT (intensity arm), and a similar adaptive boost plan was optimized. The dose escalation capability of the two approaches was compared. Result: Images of three patients were used in this planning study. For one patient, SUV prediction indicated complete response and no necessary dose escalation. For the other two, resistant targets defined in the response arm were multifocal, and on average accounted for 25% of the pre-treatment target, compared to 67% in the intensity arm. The smaller response arm targets led to a 6Gy higher mean target dose in the adaptive escalation design. Conclusion: This pilot study suggests that adaptive dose escalation to a biologically resistant target predicted from a pre- and mid-treatment PET/CT may be more effective than escalation based on the mid-treatment PET/CT alone. More plans and ultimately clinical

The RBE of tritium-beta exposure for the induction of the adaptive response and apoptosis; cellular defense mechanisms against the biological effects of ionizing radiation

International Nuclear Information System (INIS)

Boreham, D.R.; Bahen, M.E.; Dolling, J-A.

1997-01-01

Adaption to radiation is one of a few biological responses that has been demonstrated to occur in mammalian cells exposed to doses of ionizing radiation in the occupational exposure range. The adaptive response has been well characterized in the yeast Saccharomyces cerevisiae, although the doses required to induce the response are higher than in mammalian cells. When yeast cells are primed with sublethal doses of gamma-radiation, they subsequently undergo an adaptive response and develop resistance to radiation, heat the chemical mutagens in a time and dose dependent manner. We have used this model system to assess the relative ability of tritium-beta radiation to induce the adaptive response the examined tritium-induced radiation resistance, thermal tolerance and suppression of mutation. The results show that sublethal priming doses of tritium caused yeast cells to develop resistance to radiation, heat, and a chemical mutagen MNNG. The magnitude and kinetics of the response, per unit dose, were the same for tritium and gamma-radiation. Therefore, the relative biological effectiveness (RBE) of tritium induction of the adaptive response was about 1.0. Apoptosis is a genetically programmed cell death or cell suicide. Cells damaged by radiation can be selectively removed from the population by apoptosis and therefore eliminated as a potential cancer risk to the organism. Since we have previously shown that apoptosis is a sensitive indicator of radiation damage in human lymphocytes exposed to low doses, we have used this endpoint to investigate the potency of tritium-beta radiation. Initially, tritium was compared to X-rays for relative effectiveness at inducing apoptosis. The results showed the lymphocytes irradiated in vitro with X-rays or tritium had similar levels of apoptosis per unit dose. Therefore the relative biology effectiveness of tritium for induction of apoptosis in human lymphocytes was also about 1. In the work presented here, we have demonstrated that

Adaptive evolution in ecological communities.

Directory of Open Access Journals (Sweden)

Martin M Turcotte

Full Text Available Understanding how natural selection drives evolution is a key challenge in evolutionary biology. Most studies of adaptation focus on how a single environmental factor, such as increased temperature, affects evolution within a single species. The biological relevance of these experiments is limited because nature is infinitely more complex. Most species are embedded within communities containing many species that interact with one another and the physical environment. To understand the evolutionary significance of such ecological complexity, experiments must test the evolutionary impact of interactions among multiple species during adaptation. Here we highlight an experiment that manipulates species composition and tracks evolutionary responses within each species, while testing for the mechanisms by which species interact and adapt to their environment. We also discuss limitations of previous studies of adaptive evolution and emphasize how an experimental evolution approach can circumvent such shortcomings. Understanding how community composition acts as a selective force will improve our ability to predict how species adapt to natural and human-induced environmental change.

Two bridges between biology and learning

Directory of Open Access Journals (Sweden)

Jorun Nyléhn

2016-04-01

Full Text Available Human biology, in terms of organization of our brains and our evolutionary past, constrains and enables learning. Two examples where neurobiology and evolution influences learning are given and discussed in relation to education: mirror neurons and adaptive memory. Mirror neurons serves imitation and understanding of other peoples intentions. Adaptive memory implies that our memory is an adaptation influenced by our evolutionary past, enabling us to solve problems in the present and in the future. Additionally, the aim is to contribute to bridges between natural and social sciences in an attempt to achieve an improved understanding of learning. The relevance of perspectives on learning founded in biology are discussed, and the article argues for including biological perspectives in discussions of education and learning processes.

Teaching Mathematical Biology in High School Using Adapted Primary Literature

Science.gov (United States)

Norris, Stephen P.; Stelnicki, Nathan; de Vries, Gerda

2012-01-01

The study compared the effect of two adaptations of a scientific article on students' comprehension and use of scientific inquiry skills. One adaptation preserved as much as possible the canonical form of the original article (APL, Adapted Primary Literature) and the other was written in a more narrative mode typical of secondary literature (SL).…

The sources of adaptive variation.

Science.gov (United States)

Charlesworth, Deborah; Barton, Nicholas H; Charlesworth, Brian

2017-05-31

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed. © 2017 The Author(s).

Limitations of science and adapting to Nature

International Nuclear Information System (INIS)

Narasimhan, T N

2007-01-01

Historically, science has pursued a premise that Nature can be understood fully, its future predicted precisely, and its behavior controlled at will. However, emerging knowledge indicates that the nature of Earth and biological systems transcends the limits of science, questioning the premise of knowing, prediction, and control. This knowledge has led to the recognition that, for civilized human survival, technological society has to adapt to the constraints of these systems. Simultaneously, spurred by explosive developments in the understanding of materials (non-biological and biological), applied scientific research pursues a contrary goal of controlling the material world, with the promise of spectacular economic growth and human well-being. If adaptation to Nature is so important, why does applied research pursue a contrary course? Adapting to Nature requires a recognition of the limitations of science, and espousal of human values. Although the concept of adapting to Nature is accepted by some, especially conservation ecologists, such an acceptance may not exist in other fields. Also, in a world dominated by democratic ideals of freedom and liberty, the discipline required for adapting to Nature may often be overridden by competition among various segments of society to exercise their respective rights. In extreme cases of catastrophic failure of Earth or biological systems, the imperative for adaptation may fall victim to instinct for survival. In essence, although adequate scientific know-how and technological competence exists to facilitate adaptation to Nature, choosing between that and the pursuit of controlling Nature entails human judgment. What that choice may be when humans have to survive under severe environmental stress cannot be predicted

Limitations of science and adapting to Nature

Energy Technology Data Exchange (ETDEWEB)

Narasimhan, T N [Department of Materials Science and Engineering, Department of Environmental Science, Policy and Management, 210 Hearst Memorial Mining Building, University of California, Berkeley, CA 94720-1760 (United States)

2007-07-15

Historically, science has pursued a premise that Nature can be understood fully, its future predicted precisely, and its behavior controlled at will. However, emerging knowledge indicates that the nature of Earth and biological systems transcends the limits of science, questioning the premise of knowing, prediction, and control. This knowledge has led to the recognition that, for civilized human survival, technological society has to adapt to the constraints of these systems. Simultaneously, spurred by explosive developments in the understanding of materials (non-biological and biological), applied scientific research pursues a contrary goal of controlling the material world, with the promise of spectacular economic growth and human well-being. If adaptation to Nature is so important, why does applied research pursue a contrary course? Adapting to Nature requires a recognition of the limitations of science, and espousal of human values. Although the concept of adapting to Nature is accepted by some, especially conservation ecologists, such an acceptance may not exist in other fields. Also, in a world dominated by democratic ideals of freedom and liberty, the discipline required for adapting to Nature may often be overridden by competition among various segments of society to exercise their respective rights. In extreme cases of catastrophic failure of Earth or biological systems, the imperative for adaptation may fall victim to instinct for survival. In essence, although adequate scientific know-how and technological competence exists to facilitate adaptation to Nature, choosing between that and the pursuit of controlling Nature entails human judgment. What that choice may be when humans have to survive under severe environmental stress cannot be predicted.

Population variability in biological adaptive responses to DNA damage and the shapes of carcinogen dose-response curves

International Nuclear Information System (INIS)

Conolly, Rory B.; Gaylor, David W.; Lutz, Werner K.

2005-01-01

Carcinogen dose-response curves for both ionizing radiation and chemicals are typically assumed to be linear at environmentally relevant doses. This assumption is used to ensure protection of the public health in the absence of relevant dose-response data. A theoretical justification for the assumption has been provided by the argument that low dose linearity is expected when an exogenous agent adds to an ongoing endogenous process. Here, we use computational modeling to evaluate (1) how two biological adaptive processes, induction of DNA repair and cell cycle checkpoint control, may affect the shapes of dose-response curves for DNA-damaging carcinogens and (2) how the resulting dose-response behaviors may vary within a population. Each model incorporating an adaptive process was capable of generating not only monotonic dose-responses but also nonmonotonic (J-shaped) and threshold responses. Monte Carlo analysis suggested that all these dose-response behaviors could coexist within a population, as the spectrum of qualitative differences arose from quantitative changes in parameter values. While this analysis is largely theoretical, it suggests that (a) accurate prediction of the qualitative form of the dose-response requires a quantitative understanding of the mechanism (b) significant uncertainty is associated with human health risk prediction in the absence of such quantitative understanding and (c) a stronger experimental and regulatory focus on biological mechanisms and interindividual variability would allow flexibility in regulatory treatment of environmental carcinogens without compromising human health

The purpose of adaptation.

Science.gov (United States)

Gardner, Andy

2017-10-06

A central feature of Darwin's theory of natural selection is that it explains the purpose of biological adaptation. Here, I: emphasize the scientific importance of understanding what adaptations are for, in terms of facilitating the derivation of empirically testable predictions; discuss the population genetical basis for Darwin's theory of the purpose of adaptation, with reference to Fisher's 'fundamental theorem of natural selection'; and show that a deeper understanding of the purpose of adaptation is achieved in the context of social evolution, with reference to inclusive fitness and superorganisms.

Biologically-Inspired Adaptive Obstacle Negotiation Behavior of Hexapod Robots

DEFF Research Database (Denmark)

Goldschmidt, Dennis; Wörgötter, Florentin; Manoonpong, Poramate

2014-01-01

by these findings, we present an adaptive neural control mechanism for obstacle negotiation behavior in hexapod robots. It combines locomotion control, backbone joint control, local leg reflexes, and neural learning. While the first three components generate locomotion including walking and climbing, the neural...... learning mechanism allows the robot to adapt its behavior for obstacle negotiation with respect to changing conditions, e.g., variable obstacle heights and different walking gaits. By successfully learning the association of an early, predictive signal (conditioned stimulus, CS) and a late, reflex signal...... (unconditioned stimulus, UCS), both provided by ultrasonic sensors at the front of the robot, the robot can autonomously find an appropriate distance from an obstacle to initiate climbing. The adaptive neural control was developed and tested first on a physical robot simulation, and was then successfully...

Limitations of science and adaptive management

OpenAIRE

Narasimhan, T.N.

2001-01-01

Adaptive management consists in patterning human sustenance within the constraints of Earth and biological systems whose behavior is inherently uncertain and difficult to control. For successful adaptive management, a mind-set recognizing the limitations of science is needed.

The bottom-up approach to defining life : deciphering the functional organization of biological cells via multi-objective representation of biological complexity from molecules to cells

Directory of Open Access Journals (Sweden)

Sathish ePeriyasamy

2013-12-01

Full Text Available In silico representation of cellular systems needs to represent the adaptive dynamics of biological cells, recognizing a cell’s multi-objective topology formed by spatially and temporally cohesive intracellular structures. The design of these models needs to address the hierarchical and concurrent nature of cellular functions and incorporate the ability to self-organise in response to transitions between healthy and pathological phases, and adapt accordingly. The functions of biological systems are constantly evolving, due to the ever changing demands of their environment. Biological systems meet these demands by pursuing objectives, aided by their constituents, giving rise to biological functions. A biological cell is organised into an objective/task hierarchy. These objective hierarchy corresponds to the nested nature of temporally cohesive structures and representing them will facilitate in studying pleiotropy and polygeny by modeling causalities propagating across multiple interconnected intracellular processes. Although biological adaptations occur in physiological, developmental and reproductive timescales, the paper is focused on adaptations that occur within physiological timescales, where the biomolecular activities contributing to functional organisation, play a key role in cellular physiology. The paper proposes a multi-scale and multi-objective modelling approach from the bottom-up by representing temporally cohesive structures for multi-tasking of intracellular processes. Further the paper characterises the properties and constraints that are consequential to the organisational and adaptive dynamics in biological cells.

Entropy and Selection: Life as an Adaptation for Universe Replication

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Michael E. Price

2017-01-01

Full Text Available Natural selection is the strongest known antientropic process in the universe when operating at the biological level and may also operate at the cosmological level. Consideration of how biological natural selection creates adaptations may illuminate the consequences and significance of cosmological natural selection. An organismal trait is more likely to constitute an adaptation if characterized by more improbable complex order, and such order is the hallmark of biological selection. If the same is true of traits created by selection in general, then the more improbably ordered something is (i.e., the lower its entropy, the more likely it is to be a biological or cosmological adaptation. By this logic, intelligent life (as the least-entropic known entity is more likely than black holes or anything else to be an adaptation designed by cosmological natural selection. This view contrasts with Smolin’s suggestion that black holes are an adaptation designed by cosmological natural selection and that life is the by-product of selection for black holes. Selection may be the main or only ultimate antientropic process in the universe/multiverse; that is, much or all observed order may ultimately be the product or by-product of biological and cosmological selection.

Biologically-Inspired Adaptive Obstacle Negotiation Behavior of Hexapod Robots

Directory of Open Access Journals (Sweden)

Dennis eGoldschmidt

2014-01-01

Full Text Available Neurobiological studies have shown that insects are able to adapt leg movements and posture for obstacle negotiation in changing environments. Moreover, the distance to an obstacle where an insect begins to climb is found to be a major parameter for successful obstacle negotiation. Inspired by these findings, we present an adaptive neural control mechanism for obstacle negotiation behavior in hexapod robots. It combines locomotion control, backbone joint control, local leg reflexes, and neural learning. While the first three components generate locomotion including walking and climbing, the neural learning mechanism allows the robot to adapt its behavior for obstacle negotiation with respect to changing conditions, e.g., variable obstacle heights and different walking gaits. By successfully learning the association of an early, predictive signal (conditioned stimulus, CS and a late, reflex signal (unconditioned stimulus, UCS, both provided by ultrasonic sensors at the front of the robot, the robot can autonomously find an appropriate distance from an obstacle to initiate climbing. The adaptive neural control was developed and tested first on a physical robot simulation, and was then successfully transferred to a real hexapod robot, called AMOS II. The results show that the robot can efficiently negotiate obstacles with a height up to 85% of the robot's leg length in simulation and 75% in a real environment.

An embodied biologically constrained model of foraging: from classical and operant conditioning to adaptive real-world behavior in DAC-X.

Science.gov (United States)

Maffei, Giovanni; Santos-Pata, Diogo; Marcos, Encarni; Sánchez-Fibla, Marti; Verschure, Paul F M J

2015-12-01

Animals successfully forage within new environments by learning, simulating and adapting to their surroundings. The functions behind such goal-oriented behavior can be decomposed into 5 top-level objectives: 'how', 'why', 'what', 'where', 'when' (H4W). The paradigms of classical and operant conditioning describe some of the behavioral aspects found in foraging. However, it remains unclear how the organization of their underlying neural principles account for these complex behaviors. We address this problem from the perspective of the Distributed Adaptive Control theory of mind and brain (DAC) that interprets these two paradigms as expressing properties of core functional subsystems of a layered architecture. In particular, we propose DAC-X, a novel cognitive architecture that unifies the theoretical principles of DAC with biologically constrained computational models of several areas of the mammalian brain. DAC-X supports complex foraging strategies through the progressive acquisition, retention and expression of task-dependent information and associated shaping of action, from exploration to goal-oriented deliberation. We benchmark DAC-X using a robot-based hoarding task including the main perceptual and cognitive aspects of animal foraging. We show that efficient goal-oriented behavior results from the interaction of parallel learning mechanisms accounting for motor adaptation, spatial encoding and decision-making. Together, our results suggest that the H4W problem can be solved by DAC-X building on the insights from the study of classical and operant conditioning. Finally, we discuss the advantages and limitations of the proposed biologically constrained and embodied approach towards the study of cognition and the relation of DAC-X to other cognitive architectures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biological transportation networks: Modeling and simulation

KAUST Repository

Albi, Giacomo; Artina, Marco; Foransier, Massimo; Markowich, Peter A.

2015-01-01

We present a model for biological network formation originally introduced by Cai and Hu [Adaptation and optimization of biological transport networks, Phys. Rev. Lett. 111 (2013) 138701]. The modeling of fluid transportation (e.g., leaf venation

Adaptive leg coordination with a biologically inspired neurocontroller

Science.gov (United States)

Braught, Grant; Thomopoulos, Stelios C.

1996-10-01

Natural selection is responsible for the creation of robust and adaptive control systems. Nature's control systems are created only from primitive building blocks. Using insect neurophysiology as a guide, a neural architecture for leg coordination in a hexapod robot has been developed. Reflex chains and sensory feedback mechanisms from various insects and crustacea form the basis of a pattern generator for intra-leg coordination. The pattern generator contains neural oscillators which learn from sensory feedback to produce stepping patterns. Using sensory feedback as the source of learning information allows the pattern generator to adapt to changes in the leg dynamics due to internal or external causes. A coupling between six of the single leg pattern generators is used to produce the inter-leg coordination necessary to establish stable gaits.

Group adaptation, formal darwinism and contextual analysis.

Science.gov (United States)

Okasha, S; Paternotte, C

2012-06-01

We consider the question: under what circumstances can the concept of adaptation be applied to groups, rather than individuals? Gardner and Grafen (2009, J. Evol. Biol.22: 659-671) develop a novel approach to this question, building on Grafen's 'formal Darwinism' project, which defines adaptation in terms of links between evolutionary dynamics and optimization. They conclude that only clonal groups, and to a lesser extent groups in which reproductive competition is repressed, can be considered as adaptive units. We re-examine the conditions under which the selection-optimization links hold at the group level. We focus on an important distinction between two ways of understanding the links, which have different implications regarding group adaptationism. We show how the formal Darwinism approach can be reconciled with G.C. Williams' famous analysis of group adaptation, and we consider the relationships between group adaptation, the Price equation approach to multi-level selection, and the alternative approach based on contextual analysis. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Culture, Urbanism and Changing Human Biology.

Science.gov (United States)

Schell, L M

2014-04-03

Anthropologists have long known that human activity driven by culture changes the environment. This is apparent in the archaeological record and through the study of the modern environment. Perhaps the largest change since the paleolithic era is the organization of human populations in cities. New environments can reshape human biology through evolution as shown by the evolution of the hominid lineage. Evolution is not the only process capable of reshaping our biology. Some changes in our human biology are adaptive and evolutionary while others are pathological. What changes in human biology may be wrought by the modern urban environment? One significant new change in the environment is the introduction of pollutants largely through urbanization. Pollutants can affect human biology in myriad ways. Evidence shows that human growth, reproduction, and cognitive functioning can be altered by some pollutants, and altered in different ways depending on the pollutant. Thus, pollutants have significance for human biologists and anthropologists generally. Further, they illustrate the bio-cultural interaction characterizing human change. Humans adapt by changing the environment, a cultural process, and then change biologically to adjust to that new environment. This ongoing, interactive process is a fundamental characteristic of human change over the millennia.

Adaptation.

Science.gov (United States)

Broom, Donald M

2006-01-01

The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and

Homeoviscous adaptation and the regulation of membrane lipids

DEFF Research Database (Denmark)

Ernst, Robert; Ejsing, Christer S; Antonny, Bruno

2016-01-01

Biological membranes are complex and dynamic assemblies of lipids and proteins. Poikilothermic organisms including bacteria, fungi, reptiles, and fish do not control their body temperature and must adapt their membrane lipid composition in order to maintain membrane fluidity in the cold. This ada......Biological membranes are complex and dynamic assemblies of lipids and proteins. Poikilothermic organisms including bacteria, fungi, reptiles, and fish do not control their body temperature and must adapt their membrane lipid composition in order to maintain membrane fluidity in the cold....... This adaptive response was termed homeoviscous adaptation and has been frequently studied with a specific focus on the acyl chain composition of membrane lipids. Massspectrometry-based lipidomics can nowadays provide more comprehensive insights into the complexity of lipid remodeling during adaptive responses...... such as neurons maintain unique lipid compositions with specific physicochemical properties. To date little is known about the sensory mechanisms regulating the acyl chain profile in such specialized cells or during adaptive responses. Here we summarize our current understanding of lipid metabolic networks...

Biological sample collector

Science.gov (United States)

Murphy, Gloria A [French Camp, CA

2010-09-07

A biological sample collector is adapted to a collect several biological samples in a plurality of filter wells. A biological sample collector may comprise a manifold plate for mounting a filter plate thereon, the filter plate having a plurality of filter wells therein; a hollow slider for engaging and positioning a tube that slides therethrough; and a slide case within which the hollow slider travels to allow the tube to be aligned with a selected filter well of the plurality of filter wells, wherein when the tube is aligned with the selected filter well, the tube is pushed through the hollow slider and into the selected filter well to sealingly engage the selected filter well and to allow the tube to deposit a biological sample onto a filter in the bottom of the selected filter well. The biological sample collector may be portable.

Active materials for adaptive architectural envelopes based on plant adaptation principles

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Marlen Lopez

2015-06-01

Full Text Available In this paper, the authors present research into adaptive architectural envelopes that adapt to environmental changes using active materials, as a result of application of biomimetic principles from plants to architecture. Buildings use large amounts of energy in order to maintain their internal comfort, because conventional buildings are designed to provide a static design solution. Most of the current solutions for facades are not designed for optimum adaptation to contextual issues and needs, while biological solutions to adaptation are often complex, multi-functional and highly responsive. We focus on plant adaptations to the environment, as, due to their immobility, they have developed special means of protection against weather changing conditions. Furthermore, recent developments in new technologies are allowing the possibility to transfer these plant adaptation strategies to technical implementation. These technologies include: multi-material 3D printing, advances in materials science and new capabilities in simulation software. Unlike traditional mechanical activation used for dynamic systems in kinetic facades, adaptive architectural envelopes require no complex electronics, sensors, or actuators. The paper proposes a research of the relationship that can be developed between active materials and environmental issues in order to propose innovative and low-tech design strategies to achieve living envelopes according to plant adaptation principles.  

A model for homeopathic remedy effects: low dose nanoparticles, allostatic cross-adaptation, and time-dependent sensitization in a complex adaptive system

Directory of Open Access Journals (Sweden)

Bell Iris R

2012-10-01

Full Text Available Abstract Background This paper proposes a novel model for homeopathic remedy action on living systems. Research indicates that homeopathic remedies (a contain measurable source and silica nanoparticles heterogeneously dispersed in colloidal solution; (b act by modulating biological function of the allostatic stress response network (c evoke biphasic actions on living systems via organism-dependent adaptive and endogenously amplified effects; (d improve systemic resilience. Discussion The proposed active components of homeopathic remedies are nanoparticles of source substance in water-based colloidal solution, not bulk-form drugs. Nanoparticles have unique biological and physico-chemical properties, including increased catalytic reactivity, protein and DNA adsorption, bioavailability, dose-sparing, electromagnetic, and quantum effects different from bulk-form materials. Trituration and/or liquid succussions during classical remedy preparation create “top-down” nanostructures. Plants can biosynthesize remedy-templated silica nanostructures. Nanoparticles stimulate hormesis, a beneficial low-dose adaptive response. Homeopathic remedies prescribed in low doses spaced intermittently over time act as biological signals that stimulate the organism’s allostatic biological stress response network, evoking nonlinear modulatory, self-organizing change. Potential mechanisms include time-dependent sensitization (TDS, a type of adaptive plasticity/metaplasticity involving progressive amplification of host responses, which reverse direction and oscillate at physiological limits. To mobilize hormesis and TDS, the remedy must be appraised as a salient, but low level, novel threat, stressor, or homeostatic disruption for the whole organism. Silica nanoparticles adsorb remedy source and amplify effects. Properly-timed remedy dosing elicits disease-primed compensatory reversal in direction of maladaptive dynamics of the allostatic network, thus promoting

Biological and molecular analysis of the pathogenic variant C3 of potato spindle tuber viroid (PSTVd) evolved during adaptation to chamomile (Matricaria chamomilla)

Czech Academy of Sciences Publication Activity Database

Matoušek, Jaroslav; Stehlík, Jan; Procházková, Jitka; Orctová, Lidmila; Wullenweber, J.; Füssy, Zoltán; Kováčik, J.; Duraisamy, Ganesh Selvaraj; Ziegler, A.; Schubert, J.; Steger, G.

2012-01-01

Roč. 393, č. 7 (2012), s. 605-615 ISSN 1431-6730 R&D Projects: GA ČR GCP501/10/J018 Institutional research plan: CEZ:AV0Z50510513 Institutional support: RVO:60077344 Keywords : viroid-specific small RNA profiles * micro RNA probes * viroid adaptation * biolistic inoculation of plants * viroid pathogenesis markers Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.683, year: 2012

The role of adaptive trans-generational plasticity in biological invasions of plants.

Science.gov (United States)

Dyer, Andrew R; Brown, Cynthia S; Espeland, Erin K; McKay, John K; Meimberg, Harald; Rice, Kevin J

2010-03-01

High-impact biological invasions often involve establishment and spread in disturbed, high-resource patches followed by establishment and spread in biotically or abiotically stressful areas. Evolutionary change may be required for the second phase of invasion (establishment and spread in stressful areas) to occur. When species have low genetic diversity and short selection history, within-generation phenotypic plasticity is often cited as the mechanism through which spread across multiple habitat types can occur. We show that trans-generational plasticity (TGP) can result in pre-adapted progeny that exhibit traits associated with increased fitness both in high-resource patches and in stressful conditions. In the invasive sedge, Cyperus esculentus, maternal plants growing in nutrient-poor patches can place disproportional number of propagules into nutrient-rich patches. Using the invasive annual grass, Aegilops triuncialis, we show that maternal response to soil conditions can confer greater stress tolerance in seedlings in the form of greater photosynthetic efficiency. We also show TGP for a phenological shift in a low resource environment that results in greater stress tolerance in progeny. These lines of evidence suggest that the maternal environment can have profound effects on offspring success and that TGP may play a significant role in some plant invasions.

Emergent explosive synchronization in adaptive complex networks

Science.gov (United States)

Avalos-Gaytán, Vanesa; Almendral, Juan A.; Leyva, I.; Battiston, F.; Nicosia, V.; Latora, V.; Boccaletti, S.

2018-04-01

Adaptation plays a fundamental role in shaping the structure of a complex network and improving its functional fitting. Even when increasing the level of synchronization in a biological system is considered as the main driving force for adaptation, there is evidence of negative effects induced by excessive synchronization. This indicates that coherence alone cannot be enough to explain all the structural features observed in many real-world networks. In this work, we propose an adaptive network model where the dynamical evolution of the node states toward synchronization is coupled with an evolution of the link weights based on an anti-Hebbian adaptive rule, which accounts for the presence of inhibitory effects in the system. We found that the emergent networks spontaneously develop the structural conditions to sustain explosive synchronization. Our results can enlighten the shaping mechanisms at the heart of the structural and dynamical organization of some relevant biological systems, namely, brain networks, for which the emergence of explosive synchronization has been observed.

A case study of evolutionary computation of biochemical adaptation

International Nuclear Information System (INIS)

François, Paul; Siggia, Eric D

2008-01-01

Simulations of evolution have a long history, but their relation to biology is questioned because of the perceived contingency of evolution. Here we provide an example of a biological process, adaptation, where simulations are argued to approach closer to biology. Adaptation is a common feature of sensory systems, and a plausible component of other biochemical networks because it rescales upstream signals to facilitate downstream processing. We create random gene networks numerically, by linking genes with interactions that model transcription, phosphorylation and protein–protein association. We define a fitness function for adaptation in terms of two functional metrics, and show that any reasonable combination of them will yield the same adaptive networks after repeated rounds of mutation and selection. Convergence to these networks is driven by positive selection and thus fast. There is always a path in parameter space of continuously improving fitness that leads to perfect adaptation, implying that the actual mutation rates we use in the simulation do not bias the results. Our results imply a kinetic view of evolution, i.e., it favors gene networks that can be learned quickly from the random examples supplied by mutation. This formulation allows for deductive predictions of the networks realized in nature

Biological Systems Thinking for Control Engineering Design

Directory of Open Access Journals (Sweden)

D. J. Murray-Smith

2004-01-01

Full Text Available Artificial neural networks and genetic algorithms are often quoted in discussions about the contribution of biological systems thinking to engineering design. This paper reviews work on the neuromuscular system, a field in which biological systems thinking could make specific contributions to the development and design of automatic control systems for mechatronics and robotics applications. The paper suggests some specific areas in which a better understanding of this biological control system could be expected to contribute to control engineering design methods in the future. Particular emphasis is given to the nonlinear nature of elements within the neuromuscular system and to processes of neural signal processing, sensing and system adaptivity. Aspects of the biological system that are of particular significance for engineering control systems include sensor fusion, sensor redundancy and parallelism, together with advanced forms of signal processing for adaptive and learning control. 

Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes.

Science.gov (United States)

Christie, Joshua R; Beekman, Madeleine

2017-03-01

Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes-specifically their organization into host cells and their uniparental (maternal) inheritance-enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller's ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes-despite their asexual mode of reproduction-can readily undergo adaptive evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Adaptability and evolution.

Science.gov (United States)

Bateson, Patrick

2017-10-06

The capacity of organisms to respond in their own lifetimes to new challenges in their environments probably appeared early in biological evolution. At present few studies have shown how such adaptability could influence the inherited characteristics of an organism's descendants. In part, this has been because organisms have been treated as passive in evolution. Nevertheless, their effects on biological evolution are likely to have been important and, when they occurred, accelerated the pace of evolution. Ways in which this might have happened have been suggested many times since the 1870s. I review these proposals and discuss their relevance to modern thought.

Students' Adaptation in the Social and Cultural Dynamics

Science.gov (United States)

Sadyrin, Vladimir Vitalievich; Potapova, Marina Vladimirovna; Gnatyshina, Elena Alexandrovna; Uvarina, Nataliya Viktorovna; Danilova, Viktoriya Valerievna

2016-01-01

Modern scientific literature views issues on adaptation based on various aspects: biological, medical, pedagogical, sociological, cybernetic, interdisciplinary, etc. The given article is devoted to the analysis of the problem of adaptation as social and psychological phenomenon including peculiarities of its functioning in the conditions of social…

Development of the Biology Card Sorting Task to Measure Conceptual Expertise in Biology

Science.gov (United States)

Smith, Julia I.; Combs, Elijah D.; Nagami, Paul H.; Alto, Valerie M.; Goh, Henry G.; Gourdet, Muryam A. A.; Hough, Christina M.; Nickell, Ashley E.; Peer, Adrian G.; Coley, John D.; Tanner, Kimberly D.

2013-01-01

There are widespread aspirations to focus undergraduate biology education on teaching students to think conceptually like biologists; however, there is a dearth of assessment tools designed to measure progress from novice to expert biological conceptual thinking. We present the development of a novel assessment tool, the Biology Card Sorting Task, designed to probe how individuals organize their conceptual knowledge of biology. While modeled on tasks from cognitive psychology, this task is unique in its design to test two hypothesized conceptual frameworks for the organization of biological knowledge: 1) a surface feature organization focused on organism type and 2) a deep feature organization focused on fundamental biological concepts. In this initial investigation of the Biology Card Sorting Task, each of six analytical measures showed statistically significant differences when used to compare the card sorting results of putative biological experts (biology faculty) and novices (non–biology major undergraduates). Consistently, biology faculty appeared to sort based on hypothesized deep features, while non–biology majors appeared to sort based on either surface features or nonhypothesized organizational frameworks. Results suggest that this novel task is robust in distinguishing populations of biology experts and biology novices and may be an adaptable tool for tracking emerging biology conceptual expertise. PMID:24297290

A Critical Perspective on Synthetic Biology

OpenAIRE

Michel Morange

2009-01-01

Synthetic biology emerged around 2000 as a new biological discipline. It shares with systems biology the same modular vision of organisms, but is more concerned with applications than with a better understanding of the functioning of organisms. A herald of this new discipline is Craig Venter who aims to create an artificial microorganism with the minimal genome compatible with life and to implement into it different 'functional modules' to generate new micro-organisms adapted to specific task...

Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks

Science.gov (United States)

Fortunato, Angelo; Boddy, Amy; Mallo, Diego; Aktipis, Athena; Maley, Carlo C.; Pepper, John W.

2017-01-01

Evolution by natural selection is the conceptual foundation for nearly every branch of biology and increasingly also for biomedicine and medical research. In cancer biology, evolution explains how populations of cells in tumors change over time. It is a fundamental question whether this evolutionary process is driven primarily by natural selection and adaptation or by other evolutionary processes such as founder effects and drift. In cancer biology, as in organismal evolutionary biology, there is controversy about this question and also about the use of adaptation through natural selection as a guiding framework for research. In this review, we discuss the differences and similarities between evolution among somatic cells versus evolution among organisms. We review what is known about the parameters and rate of evolution in neoplasms, as well as evidence for adaptation. We conclude that adaptation is a useful framework that accurately explains the defining characteristics of cancer. Further, convergent evolution through natural selection provides the only satisfying explanation both for how a group of diverse pathologies have enough in common to usefully share the descriptive label of “cancer” and for why this convergent condition becomes life-threatening. PMID:28148564

Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks.

Science.gov (United States)

Fortunato, Angelo; Boddy, Amy; Mallo, Diego; Aktipis, Athena; Maley, Carlo C; Pepper, John W

2017-02-01

Evolution by natural selection is the conceptual foundation for nearly every branch of biology and increasingly also for biomedicine and medical research. In cancer biology, evolution explains how populations of cells in tumors change over time. It is a fundamental question whether this evolutionary process is driven primarily by natural selection and adaptation or by other evolutionary processes such as founder effects and drift. In cancer biology, as in organismal evolutionary biology, there is controversy about this question and also about the use of adaptation through natural selection as a guiding framework for research. In this review, we discuss the differences and similarities between evolution among somatic cells versus evolution among organisms. We review what is known about the parameters and rate of evolution in neoplasms, as well as evidence for adaptation. We conclude that adaptation is a useful framework that accurately explains the defining characteristics of cancer. Further, convergent evolution through natural selection provides the only satisfying explanation both for how a group of diverse pathologies have enough in common to usefully share the descriptive label of "cancer" and for why this convergent condition becomes life-threatening. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Hypoxia adaptation in fish of the Amazon: a never-ending task

African Journals Online (AJOL)

ance, fish of the Amazon have developed multiple adaptive solutions which occur at all biological levels. These solutions are thought to represent adaptive convergence rather than phylogenetic relatedness. Fish of the ..... these adjustments, morpho-functional adaptations of gills ..... Ecology of the flshes in the Amazon and.

Pollinator adaptation and the evolution of floral nectar sugar composition.

Science.gov (United States)

Abrahamczyk, S; Kessler, M; Hanley, D; Karger, D N; Müller, M P J; Knauer, A C; Keller, F; Schwerdtfeger, M; Humphreys, A M

2017-01-01

A long-standing debate concerns whether nectar sugar composition evolves as an adaptation to pollinator dietary requirements or whether it is 'phylogenetically constrained'. Here, we use a modelling approach to evaluate the hypothesis that nectar sucrose proportion (NSP) is an adaptation to pollinators. We analyse ~ 2100 species of asterids, spanning several plant families and pollinator groups (PGs), and show that the hypothesis of adaptation cannot be rejected: NSP evolves towards two optimal values, high NSP for specialist-pollinated and low NSP for generalist-pollinated plants. However, the inferred adaptive process is weak, suggesting that adaptation to PG only provides a partial explanation for how nectar evolves. Additional factors are therefore needed to fully explain nectar evolution, and we suggest that future studies might incorporate floral shape and size and the abiotic environment into the analytical framework. Further, we show that NSP and PG evolution are correlated - in a manner dictated by pollinator behaviour. This contrasts with the view that a plant necessarily has to adapt its nectar composition to ensure pollination but rather suggests that pollinators adapt their foraging behaviour or dietary requirements to the nectar sugar composition presented by the plants. Finally, we document unexpectedly sucrose-poor nectar in some specialized nectarivorous bird-pollinated plants from the Old World, which might represent an overlooked form of pollinator deception. Thus, our broad study provides several new insights into how nectar evolves and we conclude by discussing why maintaining the conceptual dichotomy between adaptation and constraint might be unhelpful for advancing this field. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Biologically Inspired Technology Using Electroactive Polymers (EAP)

Science.gov (United States)

Bar-Cohen, Yoseph

2006-01-01

Evolution allowed nature to introduce highly effective biological mechanisms that are incredible inspiration for innovation. Humans have always made efforts to imitate nature's inventions and we are increasingly making advances that it becomes significantly easier to imitate, copy, and adapt biological methods, processes and systems. This brought us to the ability to create technology that is far beyond the simple mimicking of nature. Having better tools to understand and to implement nature's principles we are now equipped like never before to be inspired by nature and to employ our tools in far superior ways. Effectively, by bio-inspiration we can have a better view and value of nature capability while studying its models to learn what can be extracted, copied or adapted. Using electroactive polymers (EAP) as artificial muscles is adding an important element to the development of biologically inspired technologies.

Lack of adaptation from standing genetic variation despite the presence of putatively adaptive alleles in introduced sweet vernal grass (Anthoxanthum odoratum).

Science.gov (United States)

Gould, B; Geber, M

2016-01-01

Population genetic theory predicts that the availability of appropriate standing genetic variation should facilitate rapid evolution when species are introduced to new environments. However, few tests of rapid evolution have been paired with empirical surveys for the presence of previously identified adaptive genetic variants in natural populations. In this study, we examined local adaptation to soil Al toxicity in the introduced range of sweet vernal grass (Anthoxanthum odoratum), and we genotyped populations for the presence of Al tolerance alleles previously identified at the long-term ecological Park Grass Experiment (PGE, Harpenden, UK) in the species native range. We found that markers associated with Al tolerance at the PGE were present at appreciable frequency in introduced populations. Despite this, there was no strong evidence of local adaptation to soil Al toxicity among populations. Populations demonstrated significantly different intrinsic root growth rates in the absence of Al. This suggests that selection on correlated root growth traits may constrain the ability of populations to evolve significantly different root growth responses to Al. Our results demonstrate that genotype-phenotype associations may differ substantially between the native and introduced parts of a species range and that adaptive alleles from a native species range may not necessarily promote phenotypic differentiation in the introduced range. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Ten questions about systems biology

DEFF Research Database (Denmark)

Joyner, Michael J; Pedersen, Bente K

2011-01-01

to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many......In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...

Ten questions about systems biology

DEFF Research Database (Denmark)

Joyner, Michael J; Pedersen, Bente K

2011-01-01

In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many...

Adaptive optical microscope for brain imaging in vivo

Science.gov (United States)

Wang, Kai

2017-04-01

The optical heterogeneity of biological tissue imposes a major limitation to acquire detailed structural and functional information deep in the biological specimens using conventional microscopes. To restore optimal imaging performance, we developed an adaptive optical microscope based on direct wavefront sensing technique. This microscope can reliably measure and correct biological samples induced aberration. We demonstrated its performance and application in structural and functional brain imaging in various animal models, including fruit fly, zebrafish and mouse.

Hygienic significance of radiostability as measures of adaptive feasibilities

International Nuclear Information System (INIS)

Kudritskij, Yu.K.

1987-01-01

An attempt is made to substantiate hygienic significance of radiostability analysis as measures of adaptive feasibilities variation under the low dose ionizing radiation effect (IR). Examples of this substantiation are presented. Not only biological radiation effects but social adaptivity problems may be analysed. With more information adaptive feasibilities of human body to radiation factor are extended, its radiostability increases. Analysis of the state of adaptive feasibilities and their development estimation are vital problems of radiation hygiene, the basis for regulation and normalization of radiation factor

Phenomenon of adaptive response of cells in radiobiology

International Nuclear Information System (INIS)

Fillipovich, I.V.

1991-01-01

Consideration is given to various adaptive reactions to low-level radiation, their association with an absorbed dose, dose rate, radiation quality and time-interval between exposures, as well as with a cell cycle phase. Possible mechanisms of the adaptive response and the character and role of DNA damages, that can induce gene expression of the adaptive response, are discussed. The data on the influence of a preliminary long-term exposure to low-level radiation on the radiosensitivity of biological objects are analyzed with due regard for the adaptive cell response. It is concluded that the adaptive response of cells to ionizing radiation is a particular case of the phenomenon of cell adaptation of the effect of genotoxic factors of the environment

Cellular and molecular aspects of plant adaptation to microgravity

Science.gov (United States)

Kordyum, Elizabeth; Kozeko, Liudmyla

2016-07-01

Elucidation of the range and mechanisms of the biological effects of microgravity is one of the urgent fundamental tasks of space and gravitational biology. The absence of forbidding on plant growth and development in orbital flight allows studying different aspects of plant adaptation to this factor that is directly connected with development of the technologies of bioregenerative life-support systems. Microgravity belongs to the environmental factors which cause adaptive reactions at the cellular and molecular levels in the range of physiological responses in the framework of genetically determined program of ontogenesis. It is known that cells of a multicellular organism not only take part in reactions of the organism but also carry out processes that maintain their integrity. In light of these principles, the problem of identification of biochemical, physiological and structural patterns that can have adaptive significance at the cellular and molecular levels in real and simulated microgravity is considered. It is pointed that plant cell responses in microgravity and under clinorotation vary according to growth phase, physiological state, and taxonomic position of the object. At the same time, the responses have, to some degree, a similar character reflecting the changes in the cell organelle functional load. The maintenance of the plasmalemma fluidity at the certain level, an activation of both the antioxidant system and expression of HSP genes, especially HSP70, under increasing reactive oxygen species, lipid peroxidation intensity and alteration in protein homeostasis, are a strategic paradigm of rapid (primary) cell adaptation to microgravity. In this sense, biological membranes, especially plasmalemma, and their properties and functions may be considered as the most sensitive indicators of the influence of gravity or altered gravity on a cell. The plasmalemma lipid bilayer is a border between the cell internal content and environment, so it is a mediator

Beyond borders: the need for strategic global adaptation

Energy Technology Data Exchange (ETDEWEB)

Burton, Ian

2008-12-15

The 'adaptation is local' mantra is no longer valid. Climate impacts are pervasive, inevitably crossing geographic and political boundaries. And they will be severe. Some top scientists now say we should prepare for a rise in global mean surface temperature of 4°C – even though most impact and adaptation research is based on 2°C. What will this mean for adaptation? We need to move far beyond measures like National Adaptation Plans of Action. The ramifications of this new scenario are much more than physical and biological: there are significant socioeconomic and geopolitical implications on a par with those of mitigation. Adaptation must be understood, negotiated and financed in that light.

Toluene : biological waste-gas treatment, toxicity and microbial adaptation

NARCIS (Netherlands)

Weber, F.J.

1995-01-01

Due to the increasing stringent legislation concerning the emission of volatile organic compounds, there is nowadays a growing interest to apply biological waste-gas treatment techniques for the removal of higher concentrations of specific contaminants from waste gases. Fluctuations in the

Bacterial surface adaptation

Science.gov (United States)

Utada, Andrew

2014-03-01

Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

Vestigial Biological Structures: A Classroom-Applicable Test of Creationist Hypotheses

Science.gov (United States)

Senter, Phil; Ambrocio, Zenis; Andrade, Julia B.; Foust, Katanya K.; Gaston, Jasmine E.; Lewis, Ryshonda P.; Liniewski, Rachel M.; Ragin, Bobby A.; Robinson, Khanna L.; Stanley, Shane G.

2015-01-01

Lists of vestigial biological structures in biology textbooks are so short that some young-Earth creationist authors claim that scientists have lost confidence in the existence of vestigial structures and can no longer identify any verifiable ones. We tested these hypotheses with a method that is easily adapted to biology classes. We used online…

Adaptation of the Biolog Phenotype MicroArrayTM Technology to Profile the Obligate Anaerobe Geobacter metallireducens

Energy Technology Data Exchange (ETDEWEB)

Joyner, Dominique; Fortney, Julian; Chakraborty, Romy; Hazen, Terry

2010-05-17

The Biolog OmniLog? Phenotype MicroArray (PM) plate technology was successfully adapted to generate a select phenotypic profile of the strict anaerobe Geobacter metallireducens (G.m.). The profile generated for G.m. provides insight into the chemical sensitivity of the organism as well as some of its metabolic capabilities when grown with a basal medium containing acetate and Fe(III). The PM technology was developed for aerobic organisms. The reduction of a tetrazolium dye by the test organism represents metabolic activity on the array which is detected and measured by the OmniLog(R) system. We have previously adapted the technology for the anaerobic sulfate reducing bacterium Desulfovibrio vulgaris. In this work, we have taken the technology a step further by adapting it for the iron reducing obligate anaerobe Geobacter metallireducens. In an osmotic stress microarray it was determined that the organism has higher sensitivity to impermeable solutes 3-6percent KCl and 2-5percent NaNO3 that result in osmotic stress by osmosis to the cell than to permeable non-ionic solutes represented by 5-20percent ethylene glycol and 2-3percent urea. The osmotic stress microarray also includes an array of osmoprotectants and precursor molecules that were screened to identify substrates that would provide osmotic protection to NaCl stress. None of the substrates tested conferred resistance to elevated concentrations of salt. Verification studies in which G.m. was grown in defined medium amended with 100mM NaCl (MIC) and the common osmoprotectants betaine, glycine and proline supported the PM findings. Further verification was done by analysis of transcriptomic profiles of G.m. grown under 100mM NaCl stress that revealed up-regulation of genes related to degradation rather than accumulation of the above-mentioned osmoprotectants. The phenotypic profile, supported by additional analysis indicates that the accumulation of these osmoprotectants as a response to salt stress does not

Adaptive Synchronization of Memristor-based Chaotic Neural Systems

Directory of Open Access Journals (Sweden)

Xiaofang Hu

2014-11-01

Full Text Available Chaotic neural networks consisting of a great number of chaotic neurons are able to reproduce the rich dynamics observed in biological nervous systems. In recent years, the memristor has attracted much interest in the efficient implementation of artificial synapses and neurons. This work addresses adaptive synchronization of a class of memristor-based neural chaotic systems using a novel adaptive backstepping approach. A systematic design procedure is presented. Simulation results have demonstrated the effectiveness of the proposed adaptive synchronization method and its potential in practical application of memristive chaotic oscillators in secure communication.

Biological Soft Robotics.

Science.gov (United States)

Feinberg, Adam W

2015-01-01

In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed.

Mapping biological systems to network systems

CERN Document Server

Rathore, Heena

2016-01-01

The book presents the challenges inherent in the paradigm shift of network systems from static to highly dynamic distributed systems – it proposes solutions that the symbiotic nature of biological systems can provide into altering networking systems to adapt to these changes. The author discuss how biological systems – which have the inherent capabilities of evolving, self-organizing, self-repairing and flourishing with time – are inspiring researchers to take opportunities from the biology domain and map them with the problems faced in network domain. The book revolves around the central idea of bio-inspired systems -- it begins by exploring why biology and computer network research are such a natural match. This is followed by presenting a broad overview of biologically inspired research in network systems -- it is classified by the biological field that inspired each topic and by the area of networking in which that topic lies. Each case elucidates how biological concepts have been most successfully ...

Nonequilibrium Enhances Adaptation Efficiency of Stochastic Biochemical Systems.

Directory of Open Access Journals (Sweden)

Chen Jia

Full Text Available Adaptation is a crucial biological function possessed by many sensory systems. Early work has shown that some influential equilibrium models can achieve accurate adaptation. However, recent studies indicate that there are close relationships between adaptation and nonequilibrium. In this paper, we provide an explanation of these two seemingly contradictory results based on Markov models with relatively simple networks. We show that as the nonequilibrium driving becomes stronger, the system under consideration will undergo a phase transition along a fixed direction: from non-adaptation to simple adaptation then to oscillatory adaptation, while the transition in the opposite direction is forbidden. This indicates that although adaptation may be observed in equilibrium systems, it tends to occur in systems far away from equilibrium. In addition, we find that nonequilibrium will improve the performance of adaptation by enhancing the adaptation efficiency. All these results provide a deeper insight into the connection between adaptation and nonequilibrium. Finally, we use a more complicated network model of bacterial chemotaxis to validate the main results of this paper.

From Cellular Attractor Selection to Adaptive Signal Control for Traffic Networks.

Science.gov (United States)

Tian, Daxin; Zhou, Jianshan; Sheng, Zhengguo; Wang, Yunpeng; Ma, Jianming

2016-03-14

The management of varying traffic flows essentially depends on signal controls at intersections. However, design an optimal control that considers the dynamic nature of a traffic network and coordinates all intersections simultaneously in a centralized manner is computationally challenging. Inspired by the stable gene expressions of Escherichia coli in response to environmental changes, we explore the robustness and adaptability performance of signalized intersections by incorporating a biological mechanism in their control policies, specifically, the evolution of each intersection is induced by the dynamics governing an adaptive attractor selection in cells. We employ a mathematical model to capture such biological attractor selection and derive a generic, adaptive and distributed control algorithm which is capable of dynamically adapting signal operations for the entire dynamical traffic network. We show that the proposed scheme based on attractor selection can not only promote the balance of traffic loads on each link of the network but also allows the global network to accommodate dynamical traffic demands. Our work demonstrates the potential of bio-inspired intelligence emerging from cells and provides a deep understanding of adaptive attractor selection-based control formation that is useful to support the designs of adaptive optimization and control in other domains.

The use of nuclear reactor in radiation biology

International Nuclear Information System (INIS)

Ujeno, Yowri

1991-01-01

The Kyoto University Reactor (KUR) is widely used not only in biology, but also in applied biology, today. These studies were surveyed in the present paper and the future possibility to use KUR in radiation biology was discussed. The researches on the effects of thermal neutrons on various normal tissues, the biological effects of neutrons except thermal neutrons, especially intermediate neutrons between thermal and high speed neutrons or cold neutrons, the adaptive response of cells to thermal neutron radiation, the application of nuclear reactor-produced radionuclides including 195m Pt to biology, and the mutation in botanical science and so on, should be continued using nuclear reactor. The necessity of nuclear reactor in biology and applied biology is emphasized. (author)

The use of information theory in evolutionary biology.

Science.gov (United States)

Adami, Christoph

2012-05-01

Information is a key concept in evolutionary biology. Information stored in a biological organism's genome is used to generate the organism and to maintain and control it. Information is also that which evolves. When a population adapts to a local environment, information about this environment is fixed in a representative genome. However, when an environment changes, information can be lost. At the same time, information is processed by animal brains to survive in complex environments, and the capacity for information processing also evolves. Here, I review applications of information theory to the evolution of proteins and to the evolution of information processing in simulated agents that adapt to perform a complex task. © 2012 New York Academy of Sciences.

Functional genetic divergence in high CO2 adapted Emiliania huxleyi populations.

Science.gov (United States)

Lohbeck, Kai T; Riebesell, Ulf; Collins, Sinéad; Reusch, Thorsten B H

2013-07-01

Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short-term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well-established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO2 . After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO2 -adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment "high light" did not reveal such genetic divergence whereas growth in a low-salinity environment revealed strong pleiotropic effects in high CO2 adapted populations, indicating divergent genetic bases for adaptation to high CO2 . This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

A roadmap for island biology

DEFF Research Database (Denmark)

Patino, Jairo; Whittaker, Robert J.; Borges, Paulo A.V.

2017-01-01

Aims: The 50th anniversary of the publication of the seminal book, The Theory of Island Biogeography, by Robert H. MacArthur and Edward O. Wilson, is a timely moment to review and identify key research foci that could advance island biology. Here, we take a collaborative horizon-scanning approach...... to identify 50 fundamental questions for the continued development of the field. Location: Worldwide. Methods: We adapted a well-established methodology of horizon scanning to identify priority research questions in island biology, and initiated it during the Island Biology 2016 conference held in the Azores......); global change (5); conservation and management policies (5); and invasive alien species (4). Main conclusions: Collectively, this cross-disciplinary set of topics covering the 50 fundamental questions has the potential to stimulate and guide future research in island biology. By covering fields ranging...

Biological design in science classrooms

Science.gov (United States)

Scott, Eugenie C.; Matzke, Nicholas J.

2007-01-01

Although evolutionary biology is replete with explanations for complex biological structures, scientists concerned about evolution education have been forced to confront “intelligent design” (ID), which rejects a natural origin for biological complexity. The content of ID is a subset of the claims made by the older “creation science” movement. Both creationist views contend that highly complex biological adaptations and even organisms categorically cannot result from natural causes but require a supernatural creative agent. Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges and that would not overtly rely upon biblical literalism. Scientists do not use ID to explain nature, but because it has support from outside the scientific community, ID is nonetheless contributing substantially to a long-standing assault on the integrity of science education. PMID:17494747

Methods for isolation and viability assessment of biological organisms

Science.gov (United States)

Letant, Sonia Edith; Baker, Sarah Elyse; Bond, Tiziana; Chang, Allan Shih-Ping

2015-02-03

Isolation of biological or chemical organisms can be accomplished using a surface enhanced Raman scattering (SERS) system. The SERS system can be a single or a stacked plurality of photonic crystal membranes with noble-metal lined through pores for flowing analyte potentially containing the biological or chemical organisms. The through pores can be adapted to trap individual biological or chemical organisms and emit SERS spectra, which can then be detected by a detector and further analyzed for viability of the biological or chemical organism.

Synthetic biology and its alternatives. Descartes, Kant and the idea of engineering biological machines.

Science.gov (United States)

Kogge, Werner; Richter, Michael

2013-06-01

The engineering-based approach of synthetic biology is characterized by an assumption that 'engineering by design' enables the construction of 'living machines'. These 'machines', as biological machines, are expected to display certain properties of life, such as adapting to changing environments and acting in a situated way. This paper proposes that a tension exists between the expectations placed on biological artefacts and the notion of producing such systems by means of engineering; this tension makes it seem implausible that biological systems, especially those with properties characteristic of living beings, can in fact be produced using the specific methods of engineering. We do not claim that engineering techniques have nothing to contribute to the biotechnological construction of biological artefacts. However, drawing on Descartes's and Kant's thinking on the relationship between the organism and the machine, we show that it is considerably more plausible to assume that distinctively biological artefacts emerge within a paradigm different from the paradigm of the Cartesian machine that underlies the engineering approach. We close by calling for increased attention to be paid to approaches within molecular biology and chemistry that rest on conceptions different from those of synthetic biology's engineering paradigm. Copyright © 2013 Elsevier Ltd. All rights reserved.

Degradation alternatives for a commercial fungicide in water: biological, photo-Fenton, and coupled biological photo-Fenton processes.

Science.gov (United States)

López-Loveira, Elsa; Ariganello, Federico; Medina, María Sara; Centrón, Daniela; Candal, Roberto; Curutchet, Gustavo

2017-11-01

Imazalil (IMZ) is a widely used fungicide for the post-harvest treatment of citrus, classified as "likely to be carcinogenic in humans" for EPA, that can be only partially removed by conventional biological treatment. Consequently, specific or combined processes should be applied to prevent its release to the environment. Biological treatment with adapted microorganism consortium, photo-Fenton, and coupled biological photo-Fenton processes were tested as alternatives for the purification of water containing high concentration of the fungicide and the coadjutants present in the commercial formulation. IMZ-resistant consortium with the capacity to degrade IMZ in the presence of a C-rich co-substrate was isolated from sludge coming from a fruit packaging company wastewater treatment plant. This consortium was adapted to resist and degrade the organics present in photo-Fenton-oxidized IMZ water solution. Bacteria colonies from the consortia were isolated and identified. The effect of H 2 O 2 initial concentration and dosage on IMZ degradation rate, average oxidation state (AOS), organic acid concentration, oxidation, and mineralization percentage after photo-Fenton process was determined. The application of biological treatment to the oxidized solutions notably decreased the total organic carbon (TOC) in solution. The effect of the oxidation degree, limited by H 2 O 2 concentration and dosage, on the percentage of mineralization obtained after the biological treatment was determined and explained in terms of changes in AOS. The concentration of H 2 O 2 necessary to eliminate IMZ by photo-Fenton and to reduce TOC and chemical oxygen demand (COD) by biological treatment, in order to allow the release of the effluents to rivers with different flows, was estimated.

Adaptation of Arabidopsis thaliana to the Yangtze River basin.

Science.gov (United States)

Zou, Yu-Pan; Hou, Xing-Hui; Wu, Qiong; Chen, Jia-Fu; Li, Zi-Wen; Han, Ting-Shen; Niu, Xiao-Min; Yang, Li; Xu, Yong-Chao; Zhang, Jie; Zhang, Fu-Min; Tan, Dunyan; Tian, Zhixi; Gu, Hongya; Guo, Ya-Long

2017-12-28

Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different. We sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping. A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates.

Pragmatic turn in biology: From biological molecules to genetic content operators.

Science.gov (United States)

Witzany, Guenther

2014-08-26

Erwin Schrödinger's question "What is life?" received the answer for decades of "physics + chemistry". The concepts of Alain Turing and John von Neumann introduced a third term: "information". This led to the understanding of nucleic acid sequences as a natural code. Manfred Eigen adapted the concept of Hammings "sequence space". Similar to Hilbert space, in which every ontological entity could be defined by an unequivocal point in a mathematical axiomatic system, in the abstract "sequence space" concept each point represents a unique syntactic structure and the value of their separation represents their dissimilarity. In this concept molecular features of the genetic code evolve by means of self-organisation of matter. Biological selection determines the fittest types among varieties of replication errors of quasi-species. The quasi-species concept dominated evolution theory for many decades. In contrast to this, recent empirical data on the evolution of DNA and its forerunners, the RNA-world and viruses indicate cooperative agent-based interactions. Group behaviour of quasi-species consortia constitute de novo and arrange available genetic content for adaptational purposes within real-life contexts that determine epigenetic markings. This review focuses on some fundamental changes in biology, discarding its traditional status as a subdiscipline of physics and chemistry.

Tritium biological effects and perspective of the biological study

International Nuclear Information System (INIS)

Komatsu, Kenshi

1998-01-01

Since tritium is an emitter of weak β-rays (5.7keV) and is able to bind to DNA, i.e., the most important genome component, the biological effects should be expected to be more profound than that of X-rays and γ-rays. When carcinogenesis, genetical effects and the detriments for fetus and embryo were used as a biological endpoint, most of tritium RBE (relative biological effectiveness) ranged from 1 to 2. The tritium risk in man could be calculated from these RBEs and γ-ray risk for human exposure, which are obtained mainly from the data on Atomic Bomb survivors. However, the exposure modality from environmental tritium should be a chronic irradiation with ultra low dose rate or a fractionated irradiation. We must estimate the tritium effect in man based on biological experiments alone, due to lack of such epidemiological data. Low dose rate experiment should be always accompanied by the statistical problem of data, since their biological effects are fairy low, and they should involve a possible repair system, such as adaptive response (or hormesis effect) and 'Kada effect' observed in bacteria. Here we discuss future works for the tritium assessment in man, such as (1) developing a high radiation sensitive assay system with rodent hybrid cells containing a single human chromosome and also (2) study on mammal DNA repair at molecular levels using a radiosensitive hereditary disease, Nijmegen Breakage Syndrome. (author)

Risk-adaptive optimization: Selective boosting of high-risk tumor subvolumes

International Nuclear Information System (INIS)

Kim, Yusung; Tome, Wolfgang A.

2006-01-01

Background and Purpose: A tumor subvolume-based, risk-adaptive optimization strategy is presented. Methods and Materials: Risk-adaptive optimization employs a biologic objective function instead of an objective function based on physical dose constraints. Using this biologic objective function, tumor control probability (TCP) is maximized for different tumor risk regions while at the same time minimizing normal tissue complication probability (NTCP) for organs at risk. The feasibility of risk-adaptive optimization was investigated for a variety of tumor subvolume geometries, risk-levels, and slopes of the TCP curve. Furthermore, the impact of a correlation parameter, δ, between TCP and NTCP on risk-adaptive optimization was investigated. Results: Employing risk-adaptive optimization, it is possible in a prostate cancer model to increase the equivalent uniform dose (EUD) by up to 35.4 Gy in tumor subvolumes having the highest risk classification without increasing predicted normal tissue complications in organs at risk. For all tumor subvolume geometries investigated, we found that the EUD to high-risk tumor subvolumes could be increased significantly without increasing normal tissue complications above those expected from a treatment plan aiming for uniform dose coverage of the planning target volume. We furthermore found that the tumor subvolume with the highest risk classification had the largest influence on the design of the risk-adaptive dose distribution. The parameter δ had little effect on risk-adaptive optimization. However, the clinical parameters D 5 and γ 5 that represent the risk classification of tumor subvolumes had the largest impact on risk-adaptive optimization. Conclusions: On the whole, risk-adaptive optimization yields heterogeneous dose distributions that match the risk level distribution of different subvolumes within the tumor volume

Gender Stereotypes on Biology Practical Pedagogy: A Student-Teachers' Perspective

Science.gov (United States)

Abimbola, I. O.; Dada, F. E.

2015-01-01

This study examines ideas of pre-service teachers on goals of biology practical in three purposely selected Colleges of Education. To this end, A researcher designed questionnaire which was adapted titled "views of preservice teachers on biology practical" to elicit information, and findings of a survey administered to 405 preservice…

A first attempt to bring computational biology into advanced high school biology classrooms.

Science.gov (United States)

Gallagher, Suzanne Renick; Coon, William; Donley, Kristin; Scott, Abby; Goldberg, Debra S

2011-10-01

Computer science has become ubiquitous in many areas of biological research, yet most high school and even college students are unaware of this. As a result, many college biology majors graduate without adequate computational skills for contemporary fields of biology. The absence of a computational element in secondary school biology classrooms is of growing concern to the computational biology community and biology teachers who would like to acquaint their students with updated approaches in the discipline. We present a first attempt to correct this absence by introducing a computational biology element to teach genetic evolution into advanced biology classes in two local high schools. Our primary goal was to show students how computation is used in biology and why a basic understanding of computation is necessary for research in many fields of biology. This curriculum is intended to be taught by a computational biologist who has worked with a high school advanced biology teacher to adapt the unit for his/her classroom, but a motivated high school teacher comfortable with mathematics and computing may be able to teach this alone. In this paper, we present our curriculum, which takes into consideration the constraints of the required curriculum, and discuss our experiences teaching it. We describe the successes and challenges we encountered while bringing this unit to high school students, discuss how we addressed these challenges, and make suggestions for future versions of this curriculum.We believe that our curriculum can be a valuable seed for further development of computational activities aimed at high school biology students. Further, our experiences may be of value to others teaching computational biology at this level. Our curriculum can be obtained at http://ecsite.cs.colorado.edu/?page_id=149#biology or by contacting the authors.

Quantum Information Biology: From Information Interpretation of Quantum Mechanics to Applications in Molecular Biology and Cognitive Psychology

Science.gov (United States)

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

2015-10-01

We discuss foundational issues of quantum information biology (QIB)—one of the most successful applications of the quantum formalism outside of physics. QIB provides a multi-scale model of information processing in bio-systems: from proteins and cells to cognitive and social systems. This theory has to be sharply distinguished from "traditional quantum biophysics". The latter is about quantum bio-physical processes, e.g., in cells or brains. QIB models the dynamics of information states of bio-systems. We argue that the information interpretation of quantum mechanics (its various forms were elaborated by Zeilinger and Brukner, Fuchs and Mermin, and D' Ariano) is the most natural interpretation of QIB. Biologically QIB is based on two principles: (a) adaptivity; (b) openness (bio-systems are fundamentally open). These principles are mathematically represented in the framework of a novel formalism— quantum adaptive dynamics which, in particular, contains the standard theory of open quantum systems.

Cross-category adaptation: objects produce gender adaptation in the perception of faces.

Directory of Open Access Journals (Sweden)

Amir Homayoun Javadi

Full Text Available Adaptation aftereffects have been found for low-level visual features such as colour, motion and shape perception, as well as higher-level features such as gender, race and identity in domains such as faces and biological motion. It is not yet clear if adaptation effects in humans extend beyond this set of higher order features. The aim of this study was to investigate whether objects highly associated with one gender, e.g. high heels for females or electric shavers for males can modulate gender perception of a face. In two separate experiments, we adapted subjects to a series of objects highly associated with one gender and subsequently asked participants to judge the gender of an ambiguous face. Results showed that participants are more likely to perceive an ambiguous face as male after being exposed to objects highly associated to females and vice versa. A gender adaptation aftereffect was obtained despite the adaptor and test stimuli being from different global categories (objects and faces respectively. These findings show that our perception of gender from faces is highly affected by our environment and recent experience. This suggests two possible mechanisms: (a that perception of the gender associated with an object shares at least some brain areas with those responsible for gender perception of faces and (b adaptation to gender, which is a high-level concept, can modulate brain areas that are involved in facial gender perception through top-down processes.

Cross-category adaptation: objects produce gender adaptation in the perception of faces.

Science.gov (United States)

Javadi, Amir Homayoun; Wee, Natalie

2012-01-01

Adaptation aftereffects have been found for low-level visual features such as colour, motion and shape perception, as well as higher-level features such as gender, race and identity in domains such as faces and biological motion. It is not yet clear if adaptation effects in humans extend beyond this set of higher order features. The aim of this study was to investigate whether objects highly associated with one gender, e.g. high heels for females or electric shavers for males can modulate gender perception of a face. In two separate experiments, we adapted subjects to a series of objects highly associated with one gender and subsequently asked participants to judge the gender of an ambiguous face. Results showed that participants are more likely to perceive an ambiguous face as male after being exposed to objects highly associated to females and vice versa. A gender adaptation aftereffect was obtained despite the adaptor and test stimuli being from different global categories (objects and faces respectively). These findings show that our perception of gender from faces is highly affected by our environment and recent experience. This suggests two possible mechanisms: (a) that perception of the gender associated with an object shares at least some brain areas with those responsible for gender perception of faces and (b) adaptation to gender, which is a high-level concept, can modulate brain areas that are involved in facial gender perception through top-down processes.

Quantum biology at the cellular level--elements of the research program.

Science.gov (United States)

Bordonaro, Michael; Ogryzko, Vasily

2013-04-01

Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) - a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the 'basis-dependent' nature of these concepts. We introduce the notion of 'formal superposition' and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular 'decision-making' and adaptation. We stress that the interpretation of the notion of 'formal superposition' should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., 'Basis-Dependent Selection', BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the 'evolvability mechanism' loophole are also discussed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Biology and Mechanics of Blood Flows Part I: Biology

CERN Document Server

Thiriet, Marc

2008-01-01

Biology and Mechanics of Blood Flows presents the basic knowledge and state-of-the-art techniques necessary to carry out investigations of the cardiovascular system using modeling and simulation. Part I of this two-volume sequence, Biology, addresses the nanoscopic and microscopic scales. The nanoscale corresponds to the scale of biochemical reaction cascades involved in cell adaptation to mechanical stresses among other stimuli. The microscale is the scale of stress-induced tissue remodeling associated with acute or chronic loadings. The cardiovascular system, like any physiological system, has a complicated three-dimensional structure and composition. Its time dependent behavior is regulated, and this complex system has many components. In this authoritative work, the author provides a survey of relevant cell components and processes, with detailed coverage of the electrical and mechanical behaviors of vascular cells, tissues, and organs. Because the behaviors of vascular cells and tissues are tightly coupl...

An adaptation model for trabecular bone at different mechanical levels

Directory of Open Access Journals (Sweden)

Lv Linwei

2010-07-01

Full Text Available Abstract Background Bone has the ability to adapt to mechanical usage or other biophysical stimuli in terms of its mass and architecture, indicating that a certain mechanism exists for monitoring mechanical usage and controlling the bone's adaptation behaviors. There are four zones describing different bone adaptation behaviors: the disuse, adaptation, overload, and pathologic overload zones. In different zones, the changes of bone mass, as calculated by the difference between the amount of bone formed and what is resorbed, should be different. Methods An adaptation model for the trabecular bone at different mechanical levels was presented in this study based on a number of experimental observations and numerical algorithms in the literature. In the proposed model, the amount of bone formation and the probability of bone remodeling activation were proposed in accordance with the mechanical levels. Seven numerical simulation cases under different mechanical conditions were analyzed as examples by incorporating the adaptation model presented in this paper with the finite element method. Results The proposed bone adaptation model describes the well-known bone adaptation behaviors in different zones. The bone mass and architecture of the bone tissue within the adaptation zone almost remained unchanged. Although the probability of osteoclastic activation is enhanced in the overload zone, the potential of osteoblasts to form bones compensate for the osteoclastic resorption, eventually strengthening the bones. In the disuse zone, the disuse-mode remodeling removes bone tissue in disuse zone. Conclusions The study seeks to provide better understanding of the relationships between bone morphology and the mechanical, as well as biological environments. Furthermore, this paper provides a computational model and methodology for the numerical simulation of changes of bone structural morphology that are caused by changes of mechanical and biological

Multistability in Bistable Ferroelectric Materials toward Adaptive Applications

NARCIS (Netherlands)

Ghosh, Anirban; Koster, Gertjan; Rijnders, Augustinus J.H.M.

2016-01-01

Traditionally thermodynamically bistable ferroic materials are used for nonvolatile operations based on logic gates (e.g., in the form of field effect transistors). But, this inherent bistability in these class of materials limits their applicability for adaptive operations. Emulating biological

Speech recognition employing biologically plausible receptive fields

DEFF Research Database (Denmark)

Fereczkowski, Michal; Bothe, Hans-Heinrich

2011-01-01

spectro-temporal receptive fields to auditory spectrogram input, motivated by the auditory pathway of humans, and ii) the adaptation or learning algorithms involved are biologically inspired. This is in contrast to state-of-the-art combinations of Mel-frequency cepstral coefficients and Hidden Markov...

Switching Adaptability in Human-Inspired Sidesteps: A Minimal Model.

Science.gov (United States)

Fujii, Keisuke; Yoshihara, Yuki; Tanabe, Hiroko; Yamamoto, Yuji

2017-01-01

Humans can adapt to abruptly changing situations by coordinating redundant components, even in bipedality. Conventional adaptability has been reproduced by various computational approaches, such as optimal control, neural oscillator, and reinforcement learning; however, the adaptability in bipedal locomotion necessary for biological and social activities, such as unpredicted direction change in chase-and-escape, is unknown due to the dynamically unstable multi-link closed-loop system. Here we propose a switching adaptation model for performing bipedal locomotion by improving autonomous distributed control, where autonomous actuators interact without central control and switch the roles for propulsion, balancing, and leg swing. Our switching mobility model achieved direction change at any time using only three actuators, although it showed higher motor costs than comparable models without direction change. Our method of evaluating such adaptation at any time should be utilized as a prerequisite for understanding universal motor control. The proposed algorithm may simply explain and predict the adaptation mechanism in human bipedality to coordinate the actuator functions within and between limbs.

Topics in space gerontology: Effects of altered gravity and the problem of biological age

Science.gov (United States)

Economos, A. C.

1982-01-01

The use of altered gravity experimentation as a gerontological research tool is examined and a rationale for a systems approach to the adaptation to spaceflight is presented. The dependence of adaptation capacity on biological age is also discussed.

Predicting life-history adaptations to pollutants

Energy Technology Data Exchange (ETDEWEB)

Maltby, L. [Univ. of Sheffield (United Kingdom). Dept. of Animal and Plant Sciences

1995-12-31

Animals may adapt to pollutant stress so that individuals from polluted environments are less susceptible than those from unpolluted environments. In addition to such direct adaptations, animals may respond to pollutant stress by life-history modifications; so-called indirect adaptations. This paper will demonstrate how, by combining life-history theory and toxicological data, it is possible to predict stress-induced alterations in reproductive output and offspring size. Pollutant-induced alterations in age-specific survival in favor of adults and reductions in juvenile growth, conditions are predicted to select for reduced investment in reproduction and the allocation of this investment into fewer, larger offspring. Field observations on the freshwater crustaceans, Asellus aquaticus and Gammarus pulex, support these predictions. Females from metal-polluted sites had lower investment in reproduction and produced larger offspring than females of the same species from unpolluted sites. Moreover, interpopulation differences in reproductive biology persisted in laboratory cultures indicating that they had a genetic basis and were therefore due to adaptation rather than acclimation. The general applicability of this approach will be considered.

Adaptive response to high LET radiations

International Nuclear Information System (INIS)

Dam, Annamaria; Bogdandi, E. Noemi; Polonyi, Istvan; Sardy, M. Marta; Balashazy, Imre; Palfalvy, Jozsef

2001-01-01

The biological consequences of exposure to ionizing radiation include gene mutation, chromosome aberrations, cellular transformation and cell death. These effects are attributed to the DNA damaging effects of the irradiation resulting in irreversible changes during DNA replication or during the processing of the DNA damage by enzymatic repair processes. These repair processes could initiate some adaptive mechanisms in the cell, which could lead to radioadaptive response (RAR). Adaptive responses have typically been detected by exposing cells to a low radiation dose (1-50 mGy) and then challenging the cells with a higher dose of radiation (2-4 Gy) and comparing the outcome to that seen with the challenge dose only. For adaptive response to be seen the challenge dose must be delivered within 24 hour of the inducing dose. Radio-adaptation is extensively studied for low LET radiation. Nevertheless, few data are available for high LET radiation at very low doses and dose rate. Our study was aimed to investigate the radioadaptive response to low-dose neutron irradiation by detection of the genotoxic damage i.e.: hprt-mutant colonies induced. Altered protein synthesis was also studied to identify stress proteins may responsible for radio-adaptation. New alpha particle irradiator system was also built up to study the biological effects of low dose alpha irradiation. The experiments were carried out on monolayers of human melanoma and CHO (Chines Hamster Ovary) cells irradiated by neutrons produced in the biological irradiation channel of the Research Reactor of Budapest Neutron Center. Cells were exposed to 0.5-50 mGy neutron doses with dose rates of 1.59-10 mGy/min. The challenge doses of 2-4 Gy gamma rays were administrated within 1-48 hours after priming treatment. The induced mutants at hprt locus were selected by adding 6-thioguanine and allow to grow for 10 days for expression of the phenotype. The protein synthesis was studied by PAGE, the molecular mass of specific

Biological transportation networks: Modeling and simulation

KAUST Repository

Albi, Giacomo

2015-09-15

We present a model for biological network formation originally introduced by Cai and Hu [Adaptation and optimization of biological transport networks, Phys. Rev. Lett. 111 (2013) 138701]. The modeling of fluid transportation (e.g., leaf venation and angiogenesis) and ion transportation networks (e.g., neural networks) is explained in detail and basic analytical features like the gradient flow structure of the fluid transportation network model and the impact of the model parameters on the geometry and topology of network formation are analyzed. We also present a numerical finite-element based discretization scheme and discuss sample cases of network formation simulations.

Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes

Science.gov (United States)

Christie, Joshua R.; Beekman, Madeleine

2017-01-01

Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes—specifically their organization into host cells and their uniparental (maternal) inheritance—enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller’s ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes—despite their asexual mode of reproduction—can readily undergo adaptive evolution. PMID:28025277

Adaptive treatment-length optimization in spatiobiologically integrated radiotherapy

Science.gov (United States)

Ajdari, Ali; Ghate, Archis; Kim, Minsun

2018-04-01

Recent theoretical research on spatiobiologically integrated radiotherapy has focused on optimization models that adapt fluence-maps to the evolution of tumor state, for example, cell densities, as observed in quantitative functional images acquired over the treatment course. We propose an optimization model that adapts the length of the treatment course as well as the fluence-maps to such imaged tumor state. Specifically, after observing the tumor cell densities at the beginning of a session, the treatment planner solves a group of convex optimization problems to determine an optimal number of remaining treatment sessions, and a corresponding optimal fluence-map for each of these sessions. The objective is to minimize the total number of tumor cells remaining (TNTCR) at the end of this proposed treatment course, subject to upper limits on the biologically effective dose delivered to the organs-at-risk. This fluence-map is administered in future sessions until the next image is available, and then the number of sessions and the fluence-map are re-optimized based on the latest cell density information. We demonstrate via computer simulations on five head-and-neck test cases that such adaptive treatment-length and fluence-map planning reduces the TNTCR and increases the biological effect on the tumor while employing shorter treatment courses, as compared to only adapting fluence-maps and using a pre-determined treatment course length based on one-size-fits-all guidelines.

Selective adaptation in networks of heterogeneous populations: model, simulation, and experiment.

Directory of Open Access Journals (Sweden)

Avner Wallach

2008-02-01

Full Text Available Biological systems often change their responsiveness when subject to persistent stimulation, a phenomenon termed adaptation. In neural systems, this process is often selective, allowing the system to adapt to one stimulus while preserving its sensitivity to another. In some studies, it has been shown that adaptation to a frequent stimulus increases the system's sensitivity to rare stimuli. These phenomena were explained in previous work as a result of complex interactions between the various subpopulations of the network. A formal description and analysis of neuronal systems, however, is hindered by the network's heterogeneity and by the multitude of processes taking place at different time-scales. Viewing neural networks as populations of interacting elements, we develop a framework that facilitates a formal analysis of complex, structured, heterogeneous networks. The formulation developed is based on an analysis of the availability of activity dependent resources, and their effects on network responsiveness. This approach offers a simple mechanistic explanation for selective adaptation, and leads to several predictions that were corroborated in both computer simulations and in cultures of cortical neurons developing in vitro. The framework is sufficiently general to apply to different biological systems, and was demonstrated in two different cases.

Adaptive comanagement of a marine protected area network in Fiji.

Science.gov (United States)

Weeks, Rebecca; Jupiter, Stacy D

2013-12-01

Adaptive management of natural resources is an iterative process of decision making whereby management strategies are progressively changed or adjusted in response to new information. Despite an increasing focus on the need for adaptive conservation strategies, there remain few applied examples. We describe the 9-year process of adaptive comanagement of a marine protected area network in Kubulau District, Fiji. In 2011, a review of protected area boundaries and management rules was motivated by the need to enhance management effectiveness and the desire to improve resilience to climate change. Through a series of consultations, with the Wildlife Conservation Society providing scientific input to community decision making, the network of marine protected areas was reconfigured so as to maximize resilience and compliance. Factors identified as contributing to this outcome include well-defined resource-access rights; community respect for a flexible system of customary governance; long-term commitment and presence of comanagement partners; supportive policy environment for comanagement; synthesis of traditional management approaches with systematic monitoring; and district-wide coordination, which provided a broader spatial context for adaptive-management decision making. Co-Manejo Adaptativo de una Red de Áreas Marinas Protegidas en Fiyi. © 2013 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

Comparative analysis of field-isolate and monkey-adapted Plasmodium vivax genomes.

Science.gov (United States)

Chan, Ernest R; Barnwell, John W; Zimmerman, Peter A; Serre, David

2015-03-01

Significant insights into the biology of Plasmodium vivax have been gained from the ability to successfully adapt human infections to non-human primates. P. vivax strains grown in monkeys serve as a renewable source of parasites for in vitro and ex vivo experimental studies and functional assays, or for studying in vivo the relapse characteristics, mosquito species compatibilities, drug susceptibility profiles or immune responses towards potential vaccine candidates. Despite the importance of these studies, little is known as to how adaptation to a different host species may influence the genome of P. vivax. In addition, it is unclear whether these monkey-adapted strains consist of a single clonal population of parasites or if they retain the multiclonal complexity commonly observed in field isolates. Here we compare the genome sequences of seven P. vivax strains adapted to New World monkeys with those of six human clinical isolates collected directly in the field. We show that the adaptation of P. vivax parasites to monkey hosts, and their subsequent propagation, did not result in significant modifications of their genome sequence and that these monkey-adapted strains recapitulate the genomic diversity of field isolates. Our analyses also reveal that these strains are not always genetically homogeneous and should be analyzed cautiously. Overall, our study provides a framework to better leverage this important research material and fully utilize this resource for improving our understanding of P. vivax biology.

Materials learning from life: concepts for active, adaptive and autonomous molecular systems.

Science.gov (United States)

Merindol, Rémi; Walther, Andreas

2017-09-18

Bioinspired out-of-equilibrium systems will set the scene for the next generation of molecular materials with active, adaptive, autonomous, emergent and intelligent behavior. Indeed life provides the best demonstrations of complex and functional out-of-equilibrium systems: cells keep track of time, communicate, move, adapt, evolve and replicate continuously. Stirred by the understanding of biological principles, artificial out-of-equilibrium systems are emerging in many fields of soft matter science. Here we put in perspective the molecular mechanisms driving biological functions with the ones driving synthetic molecular systems. Focusing on principles that enable new levels of functionalities (temporal control, autonomous structures, motion and work generation, information processing) rather than on specific material classes, we outline key cross-disciplinary concepts that emerge in this challenging field. Ultimately, the goal is to inspire and support new generations of autonomous and adaptive molecular devices fueled by self-regulating chemistry.

Middle-Range Theory: Coping and Adaptation with Active Aging.

Science.gov (United States)

Salazar-Barajas, Martha Elba; Salazar-González, Bertha Cecilia; Gallegos-Cabriales, Esther Carlota

2017-10-01

Various disciplines focus on a multiplicity of aspects of aging: lifestyles, personal biological factors, psychological conditions, health conditions, physical environment, and social and economic factors. The aforementioned are all related to the determinants of active aging. The aim is to describe the development of a middle-range theory based on coping and adaptation with active aging. Concepts and relationships derived from Roy's model of adaptation are included. The proposed concepts are hope, health habits, coping with aging, social relations, and active aging.

Environment, Biology, and Culture: Implications for Adolescent Development.

Science.gov (United States)

Zahn-Waxler, Carolyn

1996-01-01

Introduces this special theme issue examining the roles of socialization, biology, and culture as they affect adaptive and maladaptive developmental outcomes. Problems of adolescence addressed include antisocial behavior, depressive symptoms, substance abuse, low achievement, and eating problems. Considers factors implicated in successful…

Can we manage for biological diversity in the absence of science?

Science.gov (United States)

Trauger, D.L.; Hall, R.J.

1995-01-01

Conservation of biological diversity is dependent on sound scientific information about underlying ecological processes. Current knowledge of the composition, distribution, abundance and life cycles of most species of plants and animals is incomplete, insufficient, unreliable, or nonexistent. Contemporary managers are also confronted with additional levels of complexity related to varying degrees of knowledge and understanding about interactions of species and ecosystems. Consequently, traditional species-oriented management schemes may have unintended consequences and ecosystem-oriented management initiatives may fail in the face of inadequate or fragmentary information on the structure, function, and dynamics of biotic communities and ecological systems. Nevertheless, resource managers must make decisions and manage based on the best biological information currently available. Adaptive resource management may represent a management paradigm that allows managers to learn something about the species or systems that they are managing while they are managing, but potential pitfalls lurk for such approaches. In addition to lack of control over the primary physical, chemical, and ecological processes, managers also lack control over social, economic, and political parameters affecting resource management options. Moreover, appropriate goals may be difficult to identify and criteria for determining success may be elusive. Some management responsibilities do not lend themselves to adaptive strategies. Finally, the lessons learned from adaptive management are usually obtained from a highly situational context that may limit applicability in a wider range of situations or undermine confidence that problems and solutions were properly diagnosed and addressed. Several scenarios are critically examined where adaptive management approaches may be inappropriate or ineffective and where management for biological diversity may be infeasible or inefficient without a sound

Measurement of specimen-induced aberrations of biological samples using phase stepping interferometry.

Science.gov (United States)

Schwertner, M; Booth, M J; Neil, M A A; Wilson, T

2004-01-01

Confocal or multiphoton microscopes, which deliver optical sections and three-dimensional (3D) images of thick specimens, are widely used in biology. These techniques, however, are sensitive to aberrations that may originate from the refractive index structure of the specimen itself. The aberrations cause reduced signal intensity and the 3D resolution of the instrument is compromised. It has been suggested to correct for aberrations in confocal microscopes using adaptive optics. In order to define the design specifications for such adaptive optics systems, one has to know the amount of aberrations present for typical applications such as with biological samples. We have built a phase stepping interferometer microscope that directly measures the aberration of the wavefront. The modal content of the wavefront is extracted by employing Zernike mode decomposition. Results for typical biological specimens are presented. It was found for all samples investigated that higher order Zernike modes give only a small contribution to the overall aberration. Therefore, these higher order modes can be neglected in future adaptive optics sensing and correction schemes implemented into confocal or multiphoton microscopes, leading to more efficient designs.

Relational Analysis of High School Students' Cognitive Self-Regulated Learning Strategies and Conceptions of Learning Biology

Science.gov (United States)

Sadi, Özlem

2017-01-01

The purpose of this study was to analyze the relation between students' cognitive learning strategies and conceptions of learning biology. The two scales, "Cognitive Learning Strategies" and "Conceptions of Learning Biology", were revised and adapted to biology in order to measure the students' learning strategies and…

BIOLOGICAL CLONING OF A BOVINE CORONAVIRUS ISOLATE

OpenAIRE

Betancourt, A; Rodríguez, Edisleidy; Relova, Damarys; Barrera, Maritza

2008-01-01

Con el objetivo de obtener un aislado de Coronavirus bovino clonado biológicamente se adaptó el aislado VB73/04 a la multiplicación en la línea celular MDBK. Este aislado indujo la formación de placas, las cuales resultaron homogéneas después del clonaje biológico. La población viral obtenida fue identificada como Coronavirus bovino por RT-PCR y Seroneutralización. In order to obtain a biologically cloned bovine coronavirus isolate, the isolate VB73/04 was adapted to multiplication in MDBK...

Systems biology solutions for biochemical production challenges

DEFF Research Database (Denmark)

Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

2017-01-01

There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics...... characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity...... compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains...

Mining biological networks from full-text articles.

Science.gov (United States)

Czarnecki, Jan; Shepherd, Adrian J

2014-01-01

The study of biological networks is playing an increasingly important role in the life sciences. Many different kinds of biological system can be modelled as networks; perhaps the most important examples are protein-protein interaction (PPI) networks, metabolic pathways, gene regulatory networks, and signalling networks. Although much useful information is easily accessible in publicly databases, a lot of extra relevant data lies scattered in numerous published papers. Hence there is a pressing need for automated text-mining methods capable of extracting such information from full-text articles. Here we present practical guidelines for constructing a text-mining pipeline from existing code and software components capable of extracting PPI networks from full-text articles. This approach can be adapted to tackle other types of biological network.

Using Whole Mount in situ Hybridization to Link Molecular and Organismal Biology

OpenAIRE

Jacobs, Nicole L.; Albertson, R. Craig; Wiles, Jason R.

2011-01-01

Whole mount in situ hybridization (WISH) is a common technique in molecular biology laboratories used to study gene expression through the localization of specific mRNA transcripts within whole mount specimen. This technique (adapted from Albertson and Yelick, 2005) was used in an upper level undergraduate Comparative Vertebrate Biology laboratory classroom at Syracuse University. The first two thirds of the Comparative Vertebrate Biology lab course gave students the opportunity to study the ...

Mistranslation: from adaptations to applications.

Science.gov (United States)

Hoffman, Kyle S; O'Donoghue, Patrick; Brandl, Christopher J

2017-11-01

The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness. In studies of model organisms, mistranslation often acts as an adaptive response. These studies reveal evolutionary conserved mechanisms to maintain proteostasis even during high rates of mistranslation. This review discusses the evolutionary basis of altered genetic codes, how mistranslation is identified, and how deviations to the genetic code are exploited. We revisit early discoveries of genetic code deviations and provide examples of adaptive mistranslation events in nature. Lastly, we highlight innovations in synthetic biology to expand the genetic code. The genetic code is still evolving. Mistranslation increases proteomic diversity that enables cells to survive stress conditions or suppress a deleterious allele. Genetic code variants have been identified by genome and metagenome sequence analyses, suppressor genetics, and biochemical characterization. Understanding the mechanisms of translation and genetic code deviations enables the design of new codes to produce novel proteins. Engineering the translation machinery and expanding the genetic code to incorporate non-canonical amino acids are valuable tools in synthetic biology that are impacting biomedical research. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

Biological effects of low-dose ionizing radiation exposure

International Nuclear Information System (INIS)

Reinoehl-Kompa, Sabine; Baldauf, Daniela; Heller, Horst

2009-01-01

The report on the meeting of the Strahlenschutzkommission 2007 concerning biological effects of low-dose ionizing radiation exposure includes the following contributions: Adaptive response. The importance of DNA damage mechanisms for the biological efficiency of low-energy photons. Radiation effects in mammography: the relative biological radiation effects of low-energy photons. Radiation-induced cataracts. Carcinomas following prenatal radiation exposure. Intercellular apoptosis induction and low-dose irradiation: possible consequences for the oncogenesis control. Mechanistic models for the carcinogenesis with radiation-induced cell inactivation: application to all solid tumors in the Japanese atomic bomb survivors. Microarrays at low radiation doses. Mouse models for the analysis of biological effects of low-dose ionizing radiation. The bystander effect: observations, mechanisms and implications. Lung carcinoma risk of Majak workers - modeling of carcinogenesis and the bystander effect. Microbeam studies in radiation biology - an overview. Carcinogenesis models with radiation-induced genomic instability. Application to two epidemiological cohorts.

Radio-adaptation: cellular and molecular features of a response to low levels of ionizing radiation

International Nuclear Information System (INIS)

Rigaud, O.

1998-01-01

It is well established that sublethal doses of DNA damaging agents induce protective mechanisms against a subsequent high dose treatment ; for instance, the phenomenon of radio-adaptation in the case of ionizing radiations. Since the early observation described in 1984, numerous studies have confirmed the radio-adaptive response in terms of reduction of chromosomal breaks for varied biological models in vitro and in vivo. Evidence for an adaptive response against the induction of gene mutations and the lethal effect is clearly demonstrated. This paper reviews the experimental results describing various aspects of these adaptive responses expressed on these different biological end-points. The molecular mechanism underlying radio-adaptation still remains nuclear. The development of this phenomenon requires de novo synthesis of transcripts and proteins during the time interval between the two doses. Some data are consistent with the hypotheses that these gene products would be involved in the activation of DNA repair pathways and antioxidant systems. However, a major question still remains unanswered; indeed, it is not clear whether or not the radio-adaptation could affect the estimation of cancer risk related with low level exposure to ionizing radiation, a major concern in radioprotection. Until such data are available, it is yet unwise to evoke the beneficial effects of radio-adaptation. (authors)

Adaptation, allometry, and hypertension.

Science.gov (United States)

Weder, A B; Schork, N J

1994-08-01

Essential hypertension is a "disease of civilization" but has a clear genetic component. From an evolutionary perspective, persistence in the human genome of elements capable of raising blood pressure presupposes their adaptive significance. Recently, two hypotheses that explicitly appeal to selectionist arguments, the "slavery" and "thrifty gene" theories, have been forwarded. We find neither completely successful, and we advance an alternative explanation of the adaptive importance of genes responsible for hypertension. We propose that blood pressure rises during childhood and adolescence to subserve homeostatic needs of the organism. Specifically, we contend that blood pressure is a flexible element in the repertoire of renal homeostatic mechanisms serving to match renal function to growth. The effect of modern diet and lifestyle on human growth stimulates earlier and more vigorous development, straining biologically necessary relationships between renal and general somatic growth and requiring compensation via homeostatic mechanisms preserved during evolution. Prime among such mechanisms is blood pressure, which rises as a compensation to maintain renal function in the face of greater growth. Since virtually all members of acculturated societies share in the modern lifestyle, the demands imposed by accelerated growth and development result in a populational shift to higher blood pressures, with a consequent increase in the prevalence of hypertension. We propose that hypertension is the product of maladaptation of highly genetically conserved mechanisms subserving important biological homeostatic needs. Elucidation of the mechanisms underlying hypertension will require approaches that examine the developmental processes linking growth to blood pressure.

Molecular Signals and Skeletal Muscle Adaptation to Exercise

Directory of Open Access Journals (Sweden)

Mark Wilson

2013-09-01

Full Text Available The phenotypic plasticity of skeletal muscle affords a considerable degree of adaptability not seen in other bodily tissues. The mechanical properties of skeletal muscle are highly dependent on loading conditions. The extent of skeletal muscle plasticity is distinctly highlighted by a loss of muscle mass, or atrophy, after a period of reduced weight-bearing activity, for example during periods of extended bed rest, space flight and in spinal cord injury. On the other hand, increased mechanical loading, or resistance training, induces muscle growth, or hypertrophy. Endurance exercise performance is also dependent on the adaptability of skeletal muscle, especially muscles that contribute to posture, locomotion and the mechanics of breathing.  However, the molecular pathways governing skeletal muscle adaptations are yet to be satisfactorily delineated and require further investigation. Researchers in the areas of exercise physiology, physiotherapy and sports medicine are endeavoring to translate experimental knowledge into effective, innovative treatments and regimens in order to improve physical performance and health in both elite athletes and the general community. The efficacy of the translation of molecular biological paradigms in experimental exercise physiology has long been underappreciated. Indeed, molecular biology tools can now be used to answer questions regarding skeletal muscle adaptation in response to exercise and provide new frameworks to improve physical performance. Furthermore, transgenic animal models, knockout animal models and in vivo studies provide tools to test questions concerned with how exercise initiates adaptive changes in gene expression. In light of these perceived deficiencies, an attempt is made here to elucidate the molecular mechanisms of skeletal muscle adaptation to exercise. An examination will be made of the functional capacity of skeletal muscle to respond to a variety of exercise conditions, namely

Molecular Signals and Skeletal Muscle Adaptation to Exercise

Directory of Open Access Journals (Sweden)

Mark Wilson

2013-08-01

Full Text Available The phenotypic plasticity of skeletal muscle affords a considerable degree of adaptability not seen in other bodily tissues. The mechanical properties of skeletal muscle are highly dependent on loading conditions. The extent of skeletal muscle plasticity is distinctly highlighted by a loss of muscle mass, or atrophy, after a period of reduced weight-bearing activity, for example during periods of extended bed rest, space flight and in spinal cord injury. On the other hand, increased mechanical loading, or resistance training, induces muscle growth, or hypertrophy. Endurance exercise performance is also dependent on the adaptability of skeletal muscle, especially muscles that contribute to posture, locomotion and the mechanics of breathing. However, the molecular pathways governing skeletal muscle adaptations are yet to be satisfactorily delineated and require further investigation. Researchers in the areas of exercise physiology, physiotherapy and sports medicine are endeavoring to translate experimental knowledge into effective, innovative treatments and regimens in order to improve physical performance and health in both elite athletes and the general community. The efficacy of the translation of molecular biological paradigms in experimental exercise physiology has long been underappreciated. Indeed, molecular biology tools can now be used to answer questions regarding skeletal muscle adaptation in response to exercise and provide new frameworks to improve physical performance. Furthermore, transgenic animal models, knockout animal models and in vivo studies provide tools to test questions concerned with how exercise initiates adaptive changes in gene expression. In light of these perceived deficiencies, an attempt is made here to elucidate the molecular mechanisms of skeletal muscle adaptation to exercise. An examination will be made of the functional capacity of skeletal muscle to respond to a variety of exercise conditions, namely

Modeling of biological intelligence for SCM system optimization.

Science.gov (United States)

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Modeling of Biological Intelligence for SCM System Optimization

Directory of Open Access Journals (Sweden)

Shengyong Chen

2012-01-01

Full Text Available This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Modeling of Biological Intelligence for SCM System Optimization

Science.gov (United States)

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

Technologies for climate change adaptation. Agriculture sector

Energy Technology Data Exchange (ETDEWEB)

Zhu, X [ed.; UNEP Risoe Centre, Roskilde (Denmark); Clements, R; Quezada, A; Torres, J [Practical Action Latin America, Lima (Peru); Haggar, J [Univ. of Greenwich, London (United Kingdom)

2011-08-15

This guidebook presents a selection of technologies for climate change adaptation in the agriculture sector. A set of 22 adaptation technologies are showcased. These are based primarily on the principles of agroecology, but also include scientific technologies of climate and biological sciences complemented by important sociological and institutional capacity building processes that are required for climate change to function. The technologies cover: 1) Planning for climate change and variability. 2) Sustainable water use and management. 3) Soil management. 4) Sustainable crop management. 5) Sustainable livestock management. 6) Sustainable farming systems. 7) Capacity building and stakeholder organisation. Technologies that tend to homogenise the natural environment and agricultural production have low possibilities of success in environmental stress conditions that are likely to result from climate change. On the other hand, technologies that allow for, and promote diversity are more likely to provide a strategy which strengthens agricultural production in the face of uncertain future climate change scenarios. The 22 technologies showcased in this guidebook have been selected because they facilitate the conservation and restoration of diversity while also providing opportunities for increasing agricultural productivity. Many of these technologies are not new to agricultural production practices, but they are implemented based on the assessment of current and possible future impacts of climate change in a particular location. agroecology is an approach that encompasses concepts of sustainable production and biodiversity promotion and therefore provides a useful framework for identifying and selecting appropriate adaptation technologies for the agriculture sector. The guidebook provides a systematic analysis of the most relevant information available on climate change adaptation technologies in the agriculture sector. It has been compiled based on a literature

Studying cell biology in the skin.

Science.gov (United States)

Morrow, Angel; Lechler, Terry

2015-11-15

Advances in cell biology have often been driven by studies in diverse organisms and cell types. Although there are technical reasons for why different cell types are used, there are also important physiological reasons. For example, ultrastructural studies of vesicle transport were aided by the use of professional secretory cell types. The use of tissues/primary cells has the advantage not only of using cells that are adapted to the use of certain cell biological machinery, but also of highlighting the physiological roles of this machinery. Here we discuss advantages of the skin as a model system. We discuss both advances in cell biology that used the skin as a driving force and future prospects for use of the skin to understand basic cell biology. A unique combination of characteristics and tools makes the skin a useful in vivo model system for many cell biologists. © 2015 Morrow and Lechler. 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).

Pupil-segmentation-based adaptive optics for microscopy

Science.gov (United States)

Ji, Na; Milkie, Daniel E.; Betzig, Eric

2011-03-01

Inhomogeneous optical properties of biological samples make it difficult to obtain diffraction-limited resolution in depth. Correcting the sample-induced optical aberrations needs adaptive optics (AO). However, the direct wavefront-sensing approach commonly used in astronomy is not suitable for most biological samples due to their strong scattering of light. We developed an image-based AO approach that is insensitive to sample scattering. By comparing images of the sample taken with different segments of the pupil illuminated, local tilt in the wavefront is measured from image shift. The aberrated wavefront is then obtained either by measuring the local phase directly using interference or with phase reconstruction algorithms similar to those used in astronomical AO. We implemented this pupil-segmentation-based approach in a two-photon fluorescence microscope and demonstrated that diffraction-limited resolution can be recovered from nonbiological and biological samples.

Illuminating Cell Biology

Science.gov (United States)

2002-01-01

NASA's Ames Research Center awarded Ciencia, Inc., a Small Business Innovation Research contract to develop the Cell Fluorescence Analysis System (CFAS) to address the size, mass, and power constraints of using fluorescence spectroscopy in the International Space Station's Life Science Research Facility. The system will play an important role in studying biological specimen's long-term adaptation to microgravity. Commercial applications for the technology include diverse markets such as food safety, in situ environmental monitoring, online process analysis, genomics and DNA chips, and non-invasive diagnostics. Ciencia has already sold the system to the private sector for biosensor applications.

From biological neural networks to thinking machines: Transitioning biological organizational principles to computer technology

Science.gov (United States)

Ross, Muriel D.

1991-01-01

The three-dimensional organization of the vestibular macula is under study by computer assisted reconstruction and simulation methods as a model for more complex neural systems. One goal of this research is to transition knowledge of biological neural network architecture and functioning to computer technology, to contribute to the development of thinking computers. Maculas are organized as weighted neural networks for parallel distributed processing of information. The network is characterized by non-linearity of its terminal/receptive fields. Wiring appears to develop through constrained randomness. A further property is the presence of two main circuits, highly channeled and distributed modifying, that are connected through feedforward-feedback collaterals and biasing subcircuit. Computer simulations demonstrate that differences in geometry of the feedback (afferent) collaterals affects the timing and the magnitude of voltage changes delivered to the spike initiation zone. Feedforward (efferent) collaterals act as voltage followers and likely inhibit neurons of the distributed modifying circuit. These results illustrate the importance of feedforward-feedback loops, of timing, and of inhibition in refining neural network output. They also suggest that it is the distributed modifying network that is most involved in adaptation, memory, and learning. Tests of macular adaptation, through hyper- and microgravitational studies, support this hypothesis since synapses in the distributed modifying circuit, but not the channeled circuit, are altered. Transitioning knowledge of biological systems to computer technology, however, remains problematical.

The biological effects of low doses of ionizing radiation on adaptive possibilities of the organism

International Nuclear Information System (INIS)

Bulbuc, G.

1997-01-01

The study of adaptive possibilities and cancer risk in animals exposed at low doses of ionizing radiation was the object of the present work. The action of immunostimulating treatment on these processes was studied as well. In previously irradiated animals the diminution of adaptive possibilities and of the antitumoral resistance of the organism was observed. The stimulating action of Bufostimulin on these processes in irradiated animals was less pronounced than in unirradiated ones. (author)

Biological versus Electronic Adaptive Coloration: How Can One Inform the Other?

Science.gov (United States)

2012-01-01

electrokinetic displays (figure 5a) now provide colour quality comparable to that found in printed newspapers (specifications for newsprint advertising ...paper (e-paper) and biological organisms. Multiple colours , contrast, polarization, reflectance, diffusivity and texture must all be controlled...framework of scientific metrics. Currently the highest performance approach for both nature and technology uses colourant transposition. Three outcomes

A biological-based model that links genomic instability, bystander effects, and adaptive response

International Nuclear Information System (INIS)

Scott, B.R.

2004-01-01

This paper links genomic instability, bystander effects, and adaptive response in mammalian cell communities via a novel biological-based, dose-response model called NEOTRANS 3 . The model is an extension of the NEOTRANS 2 model that addressed stochastic effects (genomic instability, mutations, and neoplastic transformation) associated with brief exposure to low radiation doses. With both models, ionizing radiation produces DNA damage in cells that can be associated with varying degrees of genomic instability. Cells with persistent problematic instability (PPI) are mutants that arise via misrepair of DNA damage. Progeny of PPI cells also have PPI and can undergo spontaneous neoplastic transformation. Unlike NEOTRANS 2 , with NEOTRANS 3 newly induced mutant PPI cells and their neoplastically transformed progeny can be suppressed via our previously introduced protective apoptosis-mediated (PAM) process, which can be activated by low linear energy transfer (LET) radiation. However, with NEOTRANS 3 (which like NEOTRANS 2 involves cross-talk between nongenomically compromised [e.g., nontransformed, nonmutants] and genomically compromised [e.g., mutants, transformants, etc.] cells), it is assumed that PAM is only activated over a relatively narrow, dose-rate-dependent interval (D PAM ,D off ); where D PAM is a small stochastic activation threshold, and D off is the stochastic dose above which PAM does not occur. PAM cooperates with activated normal DNA repair and with activated normal apoptosis in guarding against genomic instability. Normal repair involves both error-free repair and misrepair components. Normal apoptosis and the error-free component of normal repair protect mammals by preventing the occurrence of mutant cells. PAM selectively removes mutant cells arising via the misrepair component of normal repair, selectively removes existing neoplastically transformed cells, and probably selectively removes other genomically compromised cells when it is activated

Biological origins of color categorization.

Science.gov (United States)

Skelton, Alice E; Catchpole, Gemma; Abbott, Joshua T; Bosten, Jenny M; Franklin, Anna

2017-05-23

The biological basis of the commonality in color lexicons across languages has been hotly debated for decades. Prior evidence that infants categorize color could provide support for the hypothesis that color categorization systems are not purely constructed by communication and culture. Here, we investigate the relationship between infants' categorization of color and the commonality across color lexicons, and the potential biological origin of infant color categories. We systematically mapped infants' categorical recognition memory for hue onto a stimulus array used previously to document the color lexicons of 110 nonindustrialized languages. Following familiarization to a given hue, infants' response to a novel hue indicated that their recognition memory parses the hue continuum into red, yellow, green, blue, and purple categories. Infants' categorical distinctions aligned with common distinctions in color lexicons and are organized around hues that are commonly central to lexical categories across languages. The boundaries between infants' categorical distinctions also aligned, relative to the adaptation point, with the cardinal axes that describe the early stages of color representation in retinogeniculate pathways, indicating that infant color categorization may be partly organized by biological mechanisms of color vision. The findings suggest that color categorization in language and thought is partially biologically constrained and have implications for broader debate on how biology, culture, and communication interact in human cognition.

Adaptive laboratory evolution – principles and applications for biotechnology

Science.gov (United States)

2013-01-01

Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations during long term selection under specified growth conditions. Although regularly performed for more than 25 years, the advent of transcript and cheap next-generation sequencing technologies has resulted in many recent studies, which successfully applied this technique in order to engineer microbial cells for biotechnological applications. Adaptive laboratory evolution has some major benefits as compared with classical genetic engineering but also some inherent limitations. However, recent studies show how some of the limitations may be overcome in order to successfully incorporate adaptive laboratory evolution in microbial cell factory design. Over the last two decades important insights into nutrient and stress metabolism of relevant model species were acquired, whereas some other aspects such as niche-specific differences of non-conventional cell factories are not completely understood. Altogether the current status and its future perspectives highlight the importance and potential of adaptive laboratory evolution as approach in biotechnological engineering. PMID:23815749

Gene expression and adaptive noncoding changes during human evolution.

Science.gov (United States)

Babbitt, Courtney C; Haygood, Ralph; Nielsen, William J; Wray, Gregory A

2017-06-05

Despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear. Here we present new measurements of gene expression in five tissues of humans and chimpanzees, and use them to assess this relationship. We then compare our results with previous studies of adaptive noncoding changes, analyzing correlations at the level of gene ontology groups, in order to gain statistical power to detect correlations. Consistent with previous studies, we find little correlation between gene expression and adaptive noncoding changes at the level of individual genes; however, we do find significant correlations at the level of biological function ontology groups. The types of function include processes regulated by specific transcription factors, responses to genetic or chemical perturbations, and differentiation of cell types within the immune system. Among functional categories co-enriched with both differential expression and noncoding adaptation, prominent themes include cancer, particularly epithelial cancers, and neural development and function.

Comparative Ecophysiology and Evolutionary Biology of Island and Mainland Chaparral Communities

OpenAIRE

Ramirez, Aaron Robert

2015-01-01

The unique nature of island ecosystems have fascinated generations of naturalists, ecologists, and evolutionary biologists. Studying island systems led to the development of keystone biological theories including: Darwin and Wallace's theories of natural selection, Carlquist's insights into the biology of adaptive radiations, MacArthur and Wilson's theory of island biogeography, and many others. Utilizing islands as natural laboratories allows us to discover the underlying fabric of ecology a...

Monitoring biological diversity: strategies, tools, limitations, and challenges.

Science.gov (United States)

Erik A. Beever

2006-01-01

Monitoring is an assessment of the spatial and temporal variability in one or more ecosystem properties, and is an essential component of adaptive management. Monitoring can help determine whether mandated environmental standards are being met and can provide an early-warning system of ecological change. Development of a strategy for monitoring biological diversity...

Speed adaptation in a powered transtibial prosthesis controlled with a neuromuscular model.

Science.gov (United States)

Markowitz, Jared; Krishnaswamy, Pavitra; Eilenberg, Michael F; Endo, Ken; Barnhart, Chris; Herr, Hugh

2011-05-27

Control schemes for powered ankle-foot prostheses would benefit greatly from a means to make them inherently adaptive to different walking speeds. Towards this goal, one may attempt to emulate the intact human ankle, as it is capable of seamless adaptation. Human locomotion is governed by the interplay among legged dynamics, morphology and neural control including spinal reflexes. It has been suggested that reflexes contribute to the changes in ankle joint dynamics that correspond to walking at different speeds. Here, we use a data-driven muscle-tendon model that produces estimates of the activation, force, length and velocity of the major muscles spanning the ankle to derive local feedback loops that may be critical in the control of those muscles during walking. This purely reflexive approach ignores sources of non-reflexive neural drive and does not necessarily reflect the biological control scheme, yet can still closely reproduce the muscle dynamics estimated from biological data. The resulting neuromuscular model was applied to control a powered ankle-foot prosthesis and tested by an amputee walking at three speeds. The controller produced speed-adaptive behaviour; net ankle work increased with walking speed, highlighting the benefits of applying neuromuscular principles in the control of adaptive prosthetic limbs.

Systems Biology of the Immune Response to Live and Inactivated Dengue Virus Vaccines

Science.gov (United States)

2017-09-01

AWARD NUMBER: W81XWH-16-2-0031 TITLE: Systems Biology of the Immune Response to Live and Inactivated Dengue Virus Vaccines PRINCIPAL...SUBTITLE 5a. CONTRACT NUMBER Systems Biology of the Immune Response to Live and Inactivated Dengue Virus Vaccines 5b. GRANT NUMBER W81XWH-16-2-0031 5c...adaptive (T and B cell) responses will be measured using molecular and cellular approaches and the data analyzed using a systems biology approach

Unaffected perceptual thresholds for biological and non-biological form-from-motion perception in autism spectrum conditions.

Directory of Open Access Journals (Sweden)

Ayse Pinar Saygin

2010-10-01

Full Text Available Perception of biological motion is linked to the action perception system in the human brain, abnormalities within which have been suggested to underlie impairments in social domains observed in autism spectrum conditions (ASC. However, the literature on biological motion perception in ASC is heterogeneous and it is unclear whether deficits are specific to biological motion, or might generalize to form-from-motion perception.We compared psychophysical thresholds for both biological and non-biological form-from-motion perception in adults with ASC and controls. Participants viewed point-light displays depicting a walking person (Biological Motion, a translating rectangle (Structured Object or a translating unfamiliar shape (Unstructured Object. The figures were embedded in noise dots that moved similarly and the task was to determine direction of movement. The number of noise dots varied on each trial and perceptual thresholds were estimated adaptively. We found no evidence for an impairment in biological or non-biological object motion perception in individuals with ASC. Perceptual thresholds in the three conditions were almost identical between the ASC and control groups.Impairments in biological motion and non-biological form-from-motion perception are not across the board in ASC, and are only found for some stimuli and tasks. We discuss our results in relation to other findings in the literature, the heterogeneity of which likely relates to the different tasks performed. It appears that individuals with ASC are unaffected in perceptual processing of form-from-motion, but may exhibit impairments in higher order judgments such as emotion processing. It is important to identify more specifically which processes of motion perception are impacted in ASC before a link can be made between perceptual deficits and the higher-level features of the disorder.

Modular microfluidic system for biological sample preparation

Science.gov (United States)

Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

2015-09-29

A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.

Systems biology solutions for biochemical production challenges.

Science.gov (United States)

Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus; Herrgård, Markus J

2017-06-01

There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Nanomechanical strength mechanisms of hierarchical biological materials and tissues.

Science.gov (United States)

Buehler, Markus J; Ackbarow, Theodor

2008-12-01

Biological protein materials (BPMs), intriguing hierarchical structures formed by assembly of chemical building blocks, are crucial for critical functions of life. The structural details of BPMs are fascinating: They represent a combination of universally found motifs such as alpha-helices or beta-sheets with highly adapted protein structures such as cytoskeletal networks or spider silk nanocomposites. BPMs combine properties like strength and robustness, self-healing ability, adaptability, changeability, evolvability and others into multi-functional materials at a level unmatched in synthetic materials. The ability to achieve these properties depends critically on the particular traits of these materials, first and foremost their hierarchical architecture and seamless integration of material and structure, from nano to macro. Here, we provide a brief review of this field and outline new research directions, along with a review of recent research results in the development of structure-property relationships of biological protein materials exemplified in a study of vimentin intermediate filaments.

Contribution of the modulation of intensity and the optimization to deliver a dose adapted to the biological heterogeneities

International Nuclear Information System (INIS)

Kubs, F.

2007-10-01

The recent progress in functional imaging by Positron Emission Tomography (TEP) opens new perspectives in the delineation of target volumes in radiotherapy. The functional data is major; we can intend to adapt the irradiation doses on the tumor activity (TA) and to perform a dose escalation. Our objectives were (i) to characterize the TEP threshold, by quantifying the uncertainties of the target volume contour according to the lesion size and the threshold contour level, (ii) to set up the geometry suited to perform a high-precision irradiation based on the TA, (iii) to estimate the dosimetric impact of this new protocol and (iv) to verify that dosimetry is perfectly distributed. Three original phantoms were specially created to satisfy the constraints met, as well as two virtual phantoms containing 3 dose levels (dose level 3 = TA). Our results showed the importance of the effect threshold-volume on the planning in radiotherapy. To use this irradiation method, the diameter of 1 cm for the third level was able to be reached. A dose escalation of 20 Gy was possible between the second (70 Gy) and the third level (90 Gy). The dosimetric impact estimated on two real cases was suitable - increase of COIN (conformal index) from 0.6 to 0.8 and decrease of NTCP (normal tissue complication probability) of a factor 5 -. In absolute and relative dosimetry, the clinical tolerances were respected. So all the treatment process, going from the diagnosis with the TEP to reveal the TA, to the patient treatment made beforehand on phantom, and going through the ballistic and the dose calculation, was estimated and validated according to our objective to adapt the irradiation to the biological heterogeneities. However such high doses should be carefully estimated before being prescribed clinically and progress is also expected in imaging, because the minimal size which we can irradiate is on the limit of the resolution TEP. (author)

Biology Question Generation from a Semantic Network

Science.gov (United States)

Zhang, Lishan

Science instructors need questions for use in exams, homework assignments, class discussions, reviews, and other instructional activities. Textbooks never have enough questions, so instructors must find them from other sources or generate their own questions. In order to supply instructors with biology questions, a semantic network approach was developed for generating open response biology questions. The generated questions were compared to professional authorized questions. To boost students' learning experience, adaptive selection was built on the generated questions. Bayesian Knowledge Tracing was used as embedded assessment of the student's current competence so that a suitable question could be selected based on the student's previous performance. A between-subjects experiment with 42 participants was performed, where half of the participants studied with adaptive selected questions and the rest studied with mal-adaptive order of questions. Both groups significantly improved their test scores, and the participants in adaptive group registered larger learning gains than participants in the control group. To explore the possibility of generating rich instructional feedback for machine-generated questions, a question-paragraph mapping task was identified. Given a set of questions and a list of paragraphs for a textbook, the goal of the task was to map the related paragraphs to each question. An algorithm was developed whose performance was comparable to human annotators. A multiple-choice question with high quality distractors (incorrect answers) can be pedagogically valuable as well as being much easier to grade than open-response questions. Thus, an algorithm was developed to generate good distractors for multiple-choice questions. The machine-generated multiple-choice questions were compared to human-generated questions in terms of three measures: question difficulty, question discrimination and distractor usefulness. By recruiting 200 participants from

Radiation dose response of normal lung assessed by Cone Beam CT - A potential tool for biologically adaptive radiation therapy

International Nuclear Information System (INIS)

Bertelsen, Anders; Schytte, Tine; Bentzen, Soren M.; Hansen, Olfred; Nielsen, Morten; Brink, Carsten

2011-01-01

Background: Density changes of healthy lung tissue during radiotherapy as observed by Cone Beam CT (CBCT) might be an early indicator of patient specific lung toxicity. This study investigates the time course of CBCT density changes and tests for a possible correlation with locally delivered dose. Methods: A total of 665 CBCTs in 65 lung cancer patients treated with IMRT/VMAT to 60 or 66 Gy in 2 Gy fractions were analyzed. For each patient, CBCT lung density changes during the treatment course were related to the locally delivered dose. Results: A dose response is observed for the patient population at the end of the treatment course. However, the observed dose response is highly variable among patients. Density changes at 10th and 20th fraction are clearly correlated to those observed at the end of the treatment course. Conclusions: CBCT density changes in healthy lung tissue during radiotherapy correlate with the locally delivered dose and can be detected relatively early during the treatment. If these density changes are correlated to subsequent clinical toxicity this assay could form the basis for biological adaptive radiotherapy.

The law of adaptive bone remodeling : a case for crying Newton?

NARCIS (Netherlands)

Huiskes, R.; Odgaard, A.; Weinans, H.

1995-01-01

The biological mechanisms of strain-adaptive bone remodeling are largely unknown. Yet, several authors published algorithms to mimic this process, without prior validation of its premises. Biologists are sometimes confused by this seemingly irresponsible behavior. However, this kind of inductive

Genomic scan reveals loci under altitude adaptation in Tibetan and Dahe pigs.

Directory of Open Access Journals (Sweden)

Kunzhe Dong

Full Text Available High altitude environments are of particular interest in the studies of local adaptation as well as their implications in physiology and clinical medicine in human. Some Chinese pig breeds, such as Tibetan pig (TBP that is well adapted to the high altitude and Dahe pig (DHP that dwells at the moderate altitude, provide ideal materials to study local adaptation to altitudes. Yet, it is still short of in-depth analysis and understanding of the genetic adaptation to high altitude in the two pig populations. In this study we conducted a genomic scan for selective sweeps using FST to identify genes showing evidence of local adaptations in TBP and DHP, with Wuzhishan pig (WZSP as the low-altitude reference. Totally, we identified 12 specific selective genes (CCBE1, F2RL1, AGGF1, ZFPM2, IL2, FGF5, PLA2G4A, ADAMTS9, NRBF2, JMJD1C, VEGFC and ADAM19 for TBP and six (OGG1, FOXM, FLT3, RTEL1, CRELD1 and RHOG for DHP. In addition, six selective genes (VPS13A, GNA14, GDAP1, PARP8, FGF10 and ADAMTS16 were shared by the two pig breeds. Among these selective genes, three (VEGFC, FGF10 and ADAMTS9 were previously reported to be linked to the local adaptation to high altitudes in pigs, while many others were newly identified by this study. Further bioinformatics analysis demonstrated that majority of these selective signatures have some biological functions relevant to the altitude adaptation, for examples, response to hypoxia, development of blood vessels, DNA repair and several hematological involvements. These results suggest that the local adaptation to high altitude environments is sophisticated, involving numerous genes and multiple biological processes, and the shared selective signatures by the two pig breeds may provide an effective avenue to identify the common adaptive mechanisms to different altitudes.

The role of mechanics in biological and bio-inspired systems.

Science.gov (United States)

Egan, Paul; Sinko, Robert; LeDuc, Philip R; Keten, Sinan

2015-07-06

Natural systems frequently exploit intricate multiscale and multiphasic structures to achieve functionalities beyond those of man-made systems. Although understanding the chemical make-up of these systems is essential, the passive and active mechanics within biological systems are crucial when considering the many natural systems that achieve advanced properties, such as high strength-to-weight ratios and stimuli-responsive adaptability. Discovering how and why biological systems attain these desirable mechanical functionalities often reveals principles that inform new synthetic designs based on biological systems. Such approaches have traditionally found success in medical applications, and are now informing breakthroughs in diverse frontiers of science and engineering.

An Adaptable Neuromorphic Model of Orientation Selectivity Based On Floating Gate Dynamics

Directory of Open Access Journals (Sweden)

Priti eGupta

2014-04-01

Full Text Available The biggest challenge that the neuromorphic community faces today is to build systems that can be considered truly cognitive. Adaptation and self-organization are the two basic principles that underlie any cognitive function that the brain performs. If we can replicate this behavior in hardware, we move a step closer to our goal of having cognitive neuromorphic systems. Adaptive feature selectivity is a mechanism by which nature optimizes resources so as to have greater acuity for more abundant features. Developing neuromorphic feature maps can help design generic machines that can emulate this adaptive behavior. Most neuromorphic models that have attempted to build self-organizing systems, follow the approach of modeling abstract theoretical frameworks in hardware. While this is good from a modeling and analysis perspective, it may not lead to the most efficient hardware. On the other hand, exploiting hardware dynamics to build adaptive systems rather than forcing the hardware to behave like mathematical equations, seems to be a more robust methodology when it comes to developing actual hardware for real world applications. In this paper we use a novel time-staggered Winner Take All circuit, that exploits the adaptation dynamics of floating gate transistors, to model an adaptive cortical cell that demonstrates Orientation Selectivity, a well-known biological phenomenon observed in the visual cortex. The cell performs competitive learning, refining its weights in response to input patterns resembling different oriented bars, becoming selective to a particular oriented pattern. Different analysis performed on the cell such as orientation tuning, application of abnormal inputs, response to spatial frequency and periodic patterns reveal close similarity between our cell and its biological counterpart. Embedded in a RC grid, these cells interact diffusively exhibiting cluster formation, making way for adaptively building orientation selective maps

Analysis of biological spectrum of Divčibare flora

Directory of Open Access Journals (Sweden)

Popović Ivana

2006-01-01

Full Text Available One of the essential analyses which is performed during the floristic study of a region is the analysis of the biological spectrum. The analysis of the biological spectrum of the flora includes the determination of the type of life form for each taxon described in the flora of the study region. If it is considered that life form is a specific structural-functional response to the environmental effects and the result of the adaptation during the species evolution, it is clear that the basic characteristics of the site are more or less reflected in any life form. This fact is confirmed by the analysis of the biological spectrum of Divčibare flora. The study results are in correlation with the results of the analysis of the biological spectrum of the flora of Serbia and the Balkan Peninsula.

Physiological and comparative evidence fails to confirm an adaptive role for aging in evolution.

Science.gov (United States)

Cohen, Alan A

2015-01-01

The longstanding debate about whether aging may have evolved for some adaptive reason is generally considered to pit evolutionary theory against empirical observations consistent with aging as a programmed aspect of organismal biology, in particular conserved aging genes. Here I argue that the empirical evidence on aging mechanisms does not support a view of aging as a programmed phenomenon, but rather supports a view of aging as the dysregulation of complex networks that maintain organismal homeostasis. The appearance of programming is due largely to the inadvertent activation of existing pathways during the process of dysregulation. It is argued that aging differs markedly from known programmed biological phenomena such as apoptosis in that it is (a) very heterogeneous in how it proceeds, and (b) much slower than it would need to be. Furthermore, the taxonomic distribution of aging across species does not support any proposed adaptive theories of aging, which would predict that aging rate would vary on a finer taxonomic scale depending on factors such as population density. Thus, while there are problems with the longstanding non-adaptive paradigm, current evidence does not support the notion that aging is programmed or that it may have evolved for adaptive reasons.

Understanding the role of p53 in adaptive response to radiation-induced germline mutations

International Nuclear Information System (INIS)

Langlois, N.L.; Quinn, J.S.; Somers, C.M.; Boreham, D.R.; Mitchel, R.E.J.

2003-01-01

Full text: Radiation-induced adaptive response is now a widely studied area of radiation biology. Studies have demonstrated reduced levels of radiation-induced biological damage when an 'adaptive dose' is given before a higher 'challenge dose' compared to when the challenge dose is given alone. It has been shown in some systems to be a result of inducible cellular repair systems. The adaptive response has been clearly demonstrated in many model systems, however its impact on heritable effects in the mammalian germline has never been studied. Expanded Simple Tandem Repeat (ESTR) loci have been used as markers demonstrating that induced heritable mutations in mice follow a dose-response relationship. Recent data in our laboratory show preliminary evidence of radiation-induced adaptive response suppressing germline mutations at ESTR loci in wild type mice. The frequency of heritable mutations was significantly reduced when a priming dose of 0.1 Gy was given 24 hours prior to a 1 Gy acute challenging dose. We are now conducting a follow-up study to attempt to understand the mechanism of this adaptive response. P53 is known to play a significant role in governing apoptosis, DNA repair and cancer induction. In order to determine what function p53 has in the adaptive response for heritable mutations, we have mated radiation treated Trp53+/- male mice (C57Bl) to untreated, normal females (C57Bl). Using DNA fingerprinting, we are investigating the rate of inherited radiation-induced mutations on pre- and post-meiotic radiation-treated gametocytes by examining mutation frequencies in offspring DNA. If p53 is integral in the mechanism of adaptive response, we should not see an adaptive response in radiation-induced heritable mutations in these mice. This research is significant in that it will provide insight to understanding the mechanism behind radiation-induced adaptive response in the mammalian germline

Adaptive Response- A Universal Phenomenon for Radiological Protection

International Nuclear Information System (INIS)

Streffer, C.

2004-01-01

Predominantly with cells in vitro but also with whole animals in vivo it bas been shown that small radiation doses like other stress factors can render cells or organisms to a stage of higher radioresistance. This has been demonstrated with chromosomal aberrations gene mutation, cell transformation and survival. However, it is necessary to keep the appropriate conditions in a very stringent way. This implies radiation dose ranges, time factors and others. The adaptive response is transient and keeps for about three cell cycles or two to three days for mammalian cells. Most studies have been performed with low LET radiation. From the few data with high LET radiation it can be concluded that the adaptive response is much less or does not occur at all. Cellular and molecular studies indicate that the DNA repair is most important for the induction of adaptive response although the understanding of the mechanisms is certainly incomplete. In vivo other biological phenomena like the immune system also play a significant role. A high individual variability exists with respect to the extent of the adaptive response. No adaptive response apparently occurs with cells from individuals with repair-and immune-deficiencies. Several experiments during the prenatal development indicate that there is no or only little adaptive response during wide developmental stages in utero. Therefore it must be concluded that the adaptive response has limitations and is not a universal principle. Due to these restrictions of the validity and strength of adaptive response it is doubtful whether adaptive response can generally be applied in the practice of radiological protection. (Author) 42 refs

Adaptive landscape and functional diversity of Neotropical cichlids: implications for the ecology and evolution of Cichlinae (Cichlidae; Cichliformes).

Science.gov (United States)

Arbour, J H; López-Fernández, H

2014-11-01

Morphological, lineage and ecological diversity can vary substantially even among closely related lineages. Factors that influence morphological diversification, especially in functionally relevant traits, can help to explain the modern distribution of disparity across phylogenies and communities. Multivariate axes of feeding functional morphology from 75 species of Neotropical cichlid and a stepwise-AIC algorithm were used to estimate the adaptive landscape of functional morphospace in Cichlinae. Adaptive landscape complexity and convergence, as well as the functional diversity of Cichlinae, were compared with expectations under null evolutionary models. Neotropical cichlid feeding function varied primarily between traits associated with ram feeding vs. suction feeding/biting and secondarily with oral jaw muscle size and pharyngeal crushing capacity. The number of changes in selective regimes and the amount of convergence between lineages was higher than expected under a null model of evolution, but convergence was not higher than expected under a similarly complex adaptive landscape. Functional disparity was compatible with an adaptive landscape model, whereas the distribution of evolutionary change through morphospace corresponded with a process of evolution towards a single adaptive peak. The continentally distributed Neotropical cichlids have evolved relatively rapidly towards a number of adaptive peaks in functional trait space. Selection in Cichlinae functional morphospace is more complex than expected under null evolutionary models. The complexity of selective constraints in feeding morphology has likely been a significant contributor to the diversity of feeding ecology in this clade. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Psychosocial adaptation: an evolutionary concept analysis exploring a common multidisciplinary language.

Science.gov (United States)

Londono, Yenly; McMillan, Diana E

2015-11-01

To provide the first known concept analysis of psychosocial adaptation, exploring its evolution from the concept adaptation. We also determine how psychosocial adaptation is conceptualized across nursing, health, sociobehavioural and education disciplines. Psychosocial adaptation is an important conceptual term that is poorly defined in nursing and other health, sociobehavioural and education disciplines. A thorough understanding of the concept's application in nursing and across disciplines can help to clarify its meaning, facilitate a more effective common language between disciplines and inform future psychosocial adaptation research. Rodger's evolutionary view guided this concept analysis. Peer-reviewed English and Spanish manuscripts published between 2011-2013 were retrieved from the following databases: CINAHL, Psych INFO, PubMed, Scopus and LILACS. Eighty-nine articles related to psychosocial adaptation were included in the analysis. Findings identify key attributes, antecedents and consequences associated with the use of the concept. Findings were compared vis-a-vis reported characteristics of adaptation. The attributes characterizing psychosocial adaptation are: change, process, continuity, interaction and influence. In psychosocial adaptation, new life conditions serve as antecedents, while consequences are good or bad outcomes. Important features of the evolution of this concept include its broad appropriation across the reviewed disciplines. The attributes of psychosocial adaptation, have some similarities to those of general adaptation. Both concepts include an aspect of change, but unlike adaptation, psychosocial adaptation has branched away from biological descriptors, such as homeostasis and tends to focus on relational characteristics, such as interaction and influences. © 2015 John Wiley & Sons Ltd.

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

Science.gov (United States)

Castoe, Todd A; de Koning, A P Jason; Hall, Kathryn T; Card, Daren C; Schield, Drew R; Fujita, Matthew K; Ruggiero, Robert P; Degner, Jack F; Daza, Juan M; Gu, Wanjun; Reyes-Velasco, Jacobo; Shaney, Kyle J; Castoe, Jill M; Fox, Samuel E; Poole, Alex W; Polanco, Daniel; Dobry, Jason; Vandewege, Michael W; Li, Qing; Schott, Ryan K; Kapusta, Aurélie; Minx, Patrick; Feschotte, Cédric; Uetz, Peter; Ray, David A; Hoffmann, Federico G; Bogden, Robert; Smith, Eric N; Chang, Belinda S W; Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Richardson, Michael K; Mackessy, Stephen P; Bronikowski, Anne M; Bronikowsi, Anne M; Yandell, Mark; Warren, Wesley C; Secor, Stephen M; Pollock, David D

2013-12-17

Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

Seven-day human biological rhythms: An expedition in search of their origin, synchronization, functional advantage, adaptive value and clinical relevance.

Science.gov (United States)

Reinberg, Alain E; Dejardin, Laurence; Smolensky, Michael H; Touitou, Yvan

2017-01-01

This fact-finding expedition explores the perspectives and knowledge of the origin and functional relevance of the 7 d domain of the biological time structure, with special reference to human beings. These biological rhythms are displayed at various levels of organization in diverse species - from the unicellular sea algae of Acetabularia and Goniaulax to plants, insects, fish, birds and mammals, including man - under natural as well as artificial, i.e. constant, environmental conditions. Nonetheless, very little is known about their derivation, functional advantage, adaptive value, synchronization and potential clinical relevance. About 7 d cosmic cycles are seemingly too weak, and the 6 d work/1 d rest week commanded from G-d through the Laws of Mosses to the Hebrews is too recent an event to be the origin in humans. Moreover, human and insect studies conducted under controlled constant conditions devoid of environmental, social and other time cues report the persistence of 7 d rhythms, but with a slightly different (free-running) period (τ), indicating their source is endogenous. Yet, a series of human and laboratory rodent studies reveal certain mainly non-cyclic exogenous events can trigger 7 d rhythm-like phenomena. However, it is unknown whether such triggers unmask, amplify and/or synchronize previous non-overtly expressed oscillations. Circadian (~24 h), circa-monthly (~30 d) and circannual (~1 y) rhythms are viewed as genetically based features of life forms that during evolution conferred significant functional advantage to individual organisms and survival value to species. No such advantages are apparent for endogenous 7 d rhythms, raising several questions: What is the significance of the 7 d activity/rest cycle, i.e. week, storied in the Book of Genesis and adopted by the Hebrews and thereafter the residents of nearby Mediterranean countries and ultimately the world? Why do humans require 1 d off per 7 d span? Do 7 d rhythms bestow functional

The adaptive nature of the human neurocognitive architecture: an alternative model.

Science.gov (United States)

La Cerra, P; Bingham, R

1998-09-15

The model of the human neurocognitive architecture proposed by evolutionary psychologists is based on the presumption that the demands of hunter-gatherer life generated a vast array of cognitive adaptations. Here we present an alternative model. We argue that the problems inherent in the biological markets of ancestral hominids and their mammalian predecessors would have required an adaptively flexible, on-line information-processing system, and would have driven the evolution of a functionally plastic neural substrate, the neocortex, rather than a confederation of evolutionarily prespecified social cognitive adaptations. In alignment with recent neuroscientific evidence, we suggest that human cognitive processes result from the activation of constructed cortical representational networks, which reflect probabilistic relationships between sensory inputs, behavioral responses, and adaptive outcomes. The developmental construction and experiential modification of these networks are mediated by subcortical circuitries that are responsive to the life history regulatory system. As a consequence, these networks are intrinsically adaptively constrained. The theoretical and research implications of this alternative evolutionary model are discussed.

Neural Control and Adaptive Neural Forward Models for Insect-like, Energy-Efficient, and Adaptable Locomotion of Walking Machines

DEFF Research Database (Denmark)

Manoonpong, Poramate; Parlitz, Ulrich; Wörgötter, Florentin

2013-01-01

such natural properties with artificial legged locomotion systems by using different approaches including machine learning algorithms, classical engineering control techniques, and biologically-inspired control mechanisms. However, their levels of performance are still far from the natural ones. By contrast...... on sensory feedback and adaptive neural forward models with efference copies. This neural closed-loop controller enables a walking machine to perform a multitude of different walking patterns including insect-like leg movements and gaits as well as energy-efficient locomotion. In addition, the forward models...... allow the machine to autonomously adapt its locomotion to deal with a change of terrain, losing of ground contact during stance phase, stepping on or hitting an obstacle during swing phase, leg damage, and even to promote cockroach-like climbing behavior. Thus, the results presented here show...

Defining the landscape of adaptive genetic diversity.

Science.gov (United States)

Eckert, Andrew J; Dyer, Rodney J

2012-06-01

Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.). © 2012 Blackwell Publishing Ltd.

Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli

DEFF Research Database (Denmark)

Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M.

2018-01-01

Unraveling the mechanisms of microbial adaptive evolution following genetic or environmental challenges is of fundamental interest in biological science and engineering. When the challenge is the loss of a metabolic enzyme, adaptive responses can also shed significant insight into metabolic...

Climate change adaptation benefits of potential conservation partnerships.

Science.gov (United States)

Monahan, William B; Theobald, David M

2018-01-01

We evaluate the world terrestrial network of protected areas (PAs) for its partnership potential in responding to climate change. That is, if a PA engaged in collaborative, trans-boundary management of species, by investing in conservation partnerships with neighboring areas, what climate change adaptation benefits might accrue? We consider core tenets of conservation biology related to protecting large areas with high environmental heterogeneity and low climate change velocity and ask how a series of biodiversity adaptation indicators change across spatial scales encompassing potential PA and non-PA partners. Less than 1% of current world terrestrial PAs equal or exceed the size of established and successful conservation partnerships. Partnering at this scale would increase the biodiversity adaptation indicators by factors up to two orders of magnitude, compared to a null model in which each PA is isolated. Most partnership area surrounding PAs is comprised of non-PAs (70%), indicating the importance of looking beyond the current network of PAs when promoting climate change adaptation. Given monumental challenges with PA-based species conservation in the face of climate change, partnerships provide a logical and achievable strategy for helping areas adapt. Our findings identify where strategic partnering efforts in highly vulnerable areas of the world may prove critical in safeguarding biodiversity.

Adapting social neuroscience measures for schizophrenia clinical trials, part 3: fathoming external validity.

Science.gov (United States)

Olbert, Charles M; Penn, David L; Kern, Robert S; Lee, Junghee; Horan, William P; Reise, Steven P; Ochsner, Kevin N; Marder, Stephen R; Green, Michael F

2013-11-01

It is unknown whether measures adapted from social neuroscience linked to specific neural systems will demonstrate relationships to external variables. Four paradigms adapted from social neuroscience were administered to 173 clinically stable outpatients with schizophrenia to determine their relationships to functionally meaningful variables and to investigate their incremental validity beyond standard measures of social and nonsocial cognition. The 4 paradigms included 2 that assess perception of nonverbal social and action cues (basic biological motion and emotion in biological motion) and 2 that involve higher level inferences about self and others' mental states (self-referential memory and empathic accuracy). Overall, social neuroscience paradigms showed significant relationships to functional capacity but weak relationships to community functioning; the paradigms also showed weak correlations to clinical symptoms. Evidence for incremental validity beyond standard measures of social and nonsocial cognition was mixed with additional predictive power shown for functional capacity but not community functioning. Of the newly adapted paradigms, the empathic accuracy task had the broadest external validity. These results underscore the difficulty of translating developments from neuroscience into clinically useful tasks with functional significance.

DAE-BRNS life sciences symposium on molecular biology of stress response and its applications

International Nuclear Information System (INIS)

2005-01-01

The world of living organisms is full of challenges from their surroundings and these organisms learn to adapt themselves to the changes - some transient and some permanent - in these surroundings. The demands on adaptability to stress are very strong for extremophiles that live in harsh conditions such as cold or hot temperatures, salinity and hyperbaric habitats. The stress could be biotic (e.g. infection or parasitism) or abiotic (e.g. temperature, light, salinity, heavy metals etc.) Evolutionarily living organisms have developed different shapes, coloration, habits etc. to survive in their habitats. The molecular mechanisms of these biological adaptations have become clearer only in recent years from the studies on the biological responses of an organism to stresses during its life time. Such responses are characterized by activation of certain genes and synthesis of proteins and metabolites, which facilitate amelioration of the stress. The molecular biology (biochemistry and genetics) of stress response is being constantly unravelled thanks to the availability of highly sensitive and high throughput techniques and a plethora of extremophilic experimental systems such as archaebacteria, radio resistant bacteria and midges, plants surviving in cold etc. An interesting outcome of this voluminous research has been the knowledge that responses to a group of stresses share common mechanisms, at least in part. This reflects the biologically conservationist trend among otherwise diverse organisms and stresses. In this symposium several papers and posters in the area of molecular biology of stress are presented in addition to some very interesting and promising-to-be informative and stimulating plenary lectures and invited talks from highly reputed scientists. The papers relevant to INIS are indexed separately

Why Are There Old People? Senescence as Biological and Cultural Preparedness for the Transmission of Information.

Science.gov (United States)

Mergler, N.L.; Goldstein, M.D.

1983-01-01

Biological theories of adaptation are used to generate a model of human cognitive development in which physiological and cognitive change in aged persons can be understood as an adaptive stage of development. Related literature is reviewed that focuses on the elderly as information transmitters and on the psychology of "telling."…

A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.

Science.gov (United States)

Mazandu, Gaston K; Chimusa, Emile R; Mbiyavanga, Mamana; Mulder, Nicola J

2016-02-01

Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the advantage not only of handling datasets from the current high-throughput genome-wide applications, but also allowing users to choose the most relevant semantic similarity approach for their biological applications and to adapt a given module to their needs. A-DaGO-Fun is freely available to the research community at http://web.cbio.uct.ac.za/ITGOM/adagofun. It is implemented in Linux using Python under free software (GNU General Public Licence). gmazandu@cbio.uct.ac.za or Nicola.Mulder@uct.ac.za Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Psycho-pedagogіcal characteristic of adaptive mobile games for deaf children of primary school age

Directory of Open Access Journals (Sweden)

Іvahnenko A.A.

2010-11-01

Full Text Available Conducted psycho-pedagogical and medico-biological basis of usage specially adapted mobile games in the psychophysical development of deaf children of primary school age. Determine the importance of mobile gaming as a means of physical education for this children's category. As a result of research found wellness, educational, educate and correctional importance of mobile games adapted deaf schoolchildren. Adaptive mobile games are effective media for psychophysical development of deaf children that brings to improvement of cognitions.

Parental precaution: Neurobiological means and adaptive ends

OpenAIRE

Hahn-Holbrook, Jennifer; Holbrook, Colin; Haselton, Martie G.

2010-01-01

Humans invest precious reproductive resources in just a few offspring, who remain vulnerable for an extended period of their lifetimes relative to other primates. Therefore, it is likely that humans evolved a rich precautionary psychology that assists in the formidable task of protecting offspring. In this review, we integrate precautionary behaviors during pregnancy and postpartum with the adaptive functions they may serve and what is known of their biological mediators, particularly brain s...

Some nonlinear challenges in biology

International Nuclear Information System (INIS)

Mosconi, Francesco; Julou, Thomas; Desprat, Nicolas; Sinha, Deepak Kumar; Allemand, Jean-François; Croquette, Vincent; Bensimon, David

2008-01-01

Driven by a deluge of data, biology is undergoing a transition to a more quantitative science. Making sense of the data, building new models, asking the right questions and designing smart experiments to answer them are becoming ever more relevant. In this endeavour, nonlinear approaches can play a fundamental role. The biochemical reactions that underlie life are very often nonlinear. The functional features exhibited by biological systems at all levels (from the activity of an enzyme to the organization of a colony of ants, via the development of an organism or a functional module like the one responsible for chemotaxis in bacteria) are dynamically robust. They are often unaffected by order of magnitude variations in the dynamical parameters, in the number or concentrations of actors (molecules, cells, organisms) or external inputs (food, temperature, pH, etc). This type of structural robustness is also a common feature of nonlinear systems, exemplified by the fundamental role played by dynamical fixed points and attractors and by the use of generic equations (logistic map, Fisher–Kolmogorov equation, the Stefan problem, etc.) in the study of a plethora of nonlinear phenomena. However, biological systems differ from these examples in two important ways: the intrinsic stochasticity arising from the often very small number of actors and the role played by evolution. On an evolutionary time scale, nothing in biology is frozen. The systems observed today have evolved from solutions adopted in the past and they will have to adapt in response to future conditions. The evolvability of biological system uniquely characterizes them and is central to biology. As the great biologist T Dobzhansky once wrote: 'nothing in biology makes sense except in the light of evolution'. (open problem)

Virulence comparisons of high-temperature-adapted Heterorhabditis bacteriophora, Steinernema feltiae and S. carpocapsae

Directory of Open Access Journals (Sweden)

Susurluk I. A.

2015-06-01

Full Text Available Entomopathogenic nematodes (EPNs are environmentally safe alternative control agents. Nematodes in the Heterorhabditidae and Steinernematidae families are widely used in biological control frameworks, especially for soil-inhabiting insect pests. In this experiment, Heterorhabditis bacteriophora (Poinar, 1976, Steinernema feltiae (Filipjev, 1934 and S. carpocapsae (Weiser, 1955 adapted at high temperature were assessed in order to detect differences in virulence between adapted and non-adapted populations. All species were exposed to 38 °C for 2 h. After this treatment, live infective juveniles (IJs were used to infect to last instar Galleria mellonella (Linnaeus, 1758. larvae at the following doses: 1, 2, 3, 4 and 5 IJs/larva. The LD50 and LD90 were obtained for these species. Non-adapted populations of the nematode species were used as controls for this experiment. The results indicated that differences in S. feltiae and S. carpocapsae virulence between the adapted and non-adapted populations were significant; no significant difference was observed between the adapted and non-adapted H. bacteriophora populations.

Bifurcation into functional niches in adaptation.

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White, Justin S; Adami, Christoph

2004-01-01

One of the central questions in evolutionary biology concerns the dynamics of adaptation and diversification. This issue can be addressed experimentally if replicate populations adapting to identical environments can be investigated in detail. We have studied 501 such replicas using digital organisms adapting to at least two fundamentally different functional niches (survival strategies) present in the same environment: one in which fast replication is the way to live, and another where exploitation of the environment's complexity leads to complex organisms with longer life spans and smaller replication rates. While these two modes of survival are closely analogous to those expected to emerge in so-called r and K selection scenarios respectively, the bifurcation of evolutionary histories according to these functional niches occurs in identical environments, under identical selective pressures. We find that the branching occurs early, and leads to drastic phenotypic differences (in fitness, sequence length, and gestation time) that are permanent and irreversible. This study confirms an earlier experimental effort using microorganisms, in that diversification can be understood at least in part in terms of bifurcations on saddle points leading to peak shifts, as in the picture drawn by Sewall Wright.

New insights into pancreatic cancer biology.

Science.gov (United States)

Hidalgo, M

2012-09-01

Pancreatic cancer remains a devastating disease. Over the last few years, there have been important advances in the molecular and biological understanding of pancreatic cancer. This included understanding of the genomic complexity of the disease, the role of pancreatic cancer stem cells, the relevance of the tumor microenvironment, and the unique metabolic adaptation of pancreas cancer cells to obtain nutrients under hypoxic environment. In this paper, we review the most salient developments in these few areas.

West Nile Virus: Using Adapted Primary Literature in Mathematical Biology to Teach Scientific and Mathematical Reasoning in High School

Science.gov (United States)

Norris, Stephen P.; Macnab, John S.; Wonham, Marjorie; de Vries, Gerda

2009-01-01

This paper promotes the use of adapted primary literature as a curriculum and instruction innovation for use in high school. Adapted primary literature is useful for promoting an understanding of scientific and mathematical reasoning and argument and for introducing modern science into the schools. We describe a prototype adapted from a published…

MOTHERHOOD EXPERIENCE: ADOPTIVE AND BIOLOGICAL MOTHERS

Directory of Open Access Journals (Sweden)

Yulia F. Lakhvich

2014-12-01

Full Text Available To become a mother … To be a mother … What does it mean for a woman? And what else changes her life so irreversibly, allows to see the world in a different way and discovers new, earlier unknown features? Probably, nothing does. However, there is also a question how a woman bearing a child and carrying out motherhood responsibilities and a woman who has not given life to a child, but carrying out the same responsibilities, goes through the process of motherhood. It is one of the questions that was studied in a comparative research of the adaptation process in the Belarusian adoptive and biological families in case of a child appearing in the family. The study involved 64 adoptive and 62 biological mothers.

2009 MICROBIAL POPULATION BIOLOGY GORDON RESEARCH CONFERENCES JULY 19-24,2009

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ANTHONY DEAN

2009-07-24

The 2009 Gordon Conference on Microbial Population Biology will cover a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past Conferences have covered a range of topics from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. The 2009 Conference is no exception, and will include sessions on the evolution of infectious diseases, social evolution, the evolution of symbioses, experimental evolution, adaptive landscapes, community dynamics, and the evolution of protein structure and function. While genomic approaches continue to make inroads, broadening our knowledge and encompassing new questions, the conference will also emphasize the use of experimental approaches to test hypotheses decisively. As in the past, this Conference provides young scientists and graduate students opportunities to present their work in poster format and exchange ideas with leading investigators from a broad spectrum of disciplines. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. The 2009 meeting will be no exception.

A systems biology analysis of long and short-term memories of osmotic stress adaptation in fungi

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You Tao

2012-05-01

Full Text Available Abstract Background Saccharomyces cerevisiae senses hyperosmotic conditions via the HOG signaling network that activates the stress-activated protein kinase, Hog1, and modulates metabolic fluxes and gene expression to generate appropriate adaptive responses. The integral control mechanism by which Hog1 modulates glycerol production remains uncharacterized. An additional Hog1-independent mechanism retains intracellular glycerol for adaptation. Candida albicans also adapts to hyperosmolarity via a HOG signaling network. However, it remains unknown whether Hog1 exerts integral or proportional control over glycerol production in C. albicans. Results We combined modeling and experimental approaches to study osmotic stress responses in S. cerevisiae and C. albicans. We propose a simple ordinary differential equation (ODE model that highlights the integral control that Hog1 exerts over glycerol biosynthesis in these species. If integral control arises from a separation of time scales (i.e. rapid HOG activation of glycerol production capacity which decays slowly under hyperosmotic conditions, then the model predicts that glycerol production rates elevate upon adaptation to a first stress and this makes the cell adapts faster to a second hyperosmotic stress. It appears as if the cell is able to remember the stress history that is longer than the timescale of signal transduction. This is termed the long-term stress memory. Our experimental data verify this. Like S. cerevisiae, C. albicans mimimizes glycerol efflux during adaptation to hyperosmolarity. Also, transient activation of intermediate kinases in the HOG pathway results in a short-term memory in the signaling pathway. This determines the amplitude of Hog1 phosphorylation under a periodic sequence of stress and non-stressed intervals. Our model suggests that the long-term memory also affects the way a cell responds to periodic stress conditions. Hence, during osmohomeostasis, short-term memory is

2007 Microbial Population Biology (July 22-26, 2007)

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Anthony M. Dean

2008-04-01

Microbial Population Biology covers a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past meetings have covered topics ranging from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. We anticipate the 2007 meeting being no exception. The final form of the 2007 meeting is yet to be decided, but the following topics are likely to be included: evolutionary emergence of infectious disease and antibiotic resistance, genetic architecture and implications for the evolution of microbial populations, ageing in bacteria, biogeography, evolution of symbioses, the role of microbes in ecosystem function, and ecological genomics.

Feature-based plan adaptation for fast treatment planning in scanned ion beam therapy

International Nuclear Information System (INIS)

Chen Wenjing; Gemmel, Alexander; Rietzel, Eike

2013-01-01

We propose a plan adaptation method for fast treatment plan generation in scanned ion beam therapy. Analysis of optimized treatment plans with carbon ions indicates that the particle number modulation of consecutive rasterspots in depth shows little variation throughout target volumes with convex shape. Thus, we extract a depth-modulation curve (DMC) from existing reference plans and adapt it for creation of new plans in similar treatment situations. The proposed method is tested with seven CT serials of prostate patients and three digital phantom datasets generated with the MATLAB code. Plans are generated with a treatment planning software developed by GSI using single-field uniform dose optimization for all the CT datasets to serve as reference plans and ‘gold standard’. The adapted plans are generated based on the DMC derived from the reference plans of the same patient (intra-patient), different patient (inter-patient) and phantoms (phantom-patient). They are compared with the reference plans and a re-positioning strategy. Generally, in 1 min on a standard PC, either a physical plan or a biological plan can be generated with the adaptive method provided that the new target contour is available. In all the cases, the V95 values of the adapted plans can achieve 97% for either physical or biological plans. V107 is always 0 indicating no overdosage, and target dose homogeneity is above 0.98 in all cases. The dose received by the organs at risk is comparable to the optimized plans. The plan adaptation method has the potential for on-line adaptation to deal with inter-fractional motion, as well as fast off-line treatment planning, with either the prescribed physical dose or the RBE-weighted dose. (paper)

Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy.

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Penas, David R; González, Patricia; Egea, Jose A; Doallo, Ramón; Banga, Julio R

2017-01-21

The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic models. Global optimization methods can be used to solve this type of problems but the associated computational cost is very large. Moreover, many of these methods need the tuning of a number of adjustable search parameters, requiring a number of initial exploratory runs and therefore further increasing the computation times. Here we present a novel parallel method, self-adaptive cooperative enhanced scatter search (saCeSS), to accelerate the solution of this class of problems. The method is based on the scatter search optimization metaheuristic and incorporates several key new mechanisms: (i) asynchronous cooperation between parallel processes, (ii) coarse and fine-grained parallelism, and (iii) self-tuning strategies. The performance and robustness of saCeSS is illustrated by solving a set of challenging parameter estimation problems, including medium and large-scale kinetic models of the bacterium E. coli, bakerés yeast S. cerevisiae, the vinegar fly D. melanogaster, Chinese Hamster Ovary cells, and a generic signal transduction network. The results consistently show that saCeSS is a robust and efficient method, allowing very significant reduction of computation times with respect to several previous state of the art methods (from days to minutes, in several cases) even when only a small number of processors is used. The new parallel cooperative method presented here allows the solution of medium and large scale parameter estimation problems in reasonable computation times and with small hardware requirements. Further, the method includes self-tuning mechanisms which facilitate its use by non-experts. We believe that this new method can play a key role in the development of large-scale and even whole-cell dynamic models.

Is adaptation. Truly an adaptation? Is adaptation. Truly an adaptation?

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Thais Flores Nogueira Diniz

2008-04-01

Full Text Available The article begins by historicizing film adaptation from the arrival of cinema, pointing out the many theoretical approaches under which the process has been seen: from the concept of “the same story told in a different medium” to a comprehensible definition such as “the process through which works can be transformed, forming an intersection of textual surfaces, quotations, conflations and inversions of other texts”. To illustrate this new concept, the article discusses Spike Jonze’s film Adaptation. according to James Naremore’s proposal which considers the study of adaptation as part of a general theory of repetition, joined with the study of recycling, remaking, and every form of retelling. The film deals with the attempt by the scriptwriter Charles Kaufman, cast by Nicholas Cage, to adapt/translate a non-fictional book to the cinema, but ends up with a kind of film which is by no means what it intended to be: a film of action in the model of Hollywood productions. During the process of creation, Charles and his twin brother, Donald, undergo a series of adventures involving some real persons from the world of film, the author and the protagonist of the book, all of them turning into fictional characters in the film. In the film, adaptation then signifies something different from itstraditional meaning. The article begins by historicizing film adaptation from the arrival of cinema, pointing out the many theoretical approaches under which the process has been seen: from the concept of “the same story told in a different medium” to a comprehensible definition such as “the process through which works can be transformed, forming an intersection of textual surfaces, quotations, conflations and inversions of other texts”. To illustrate this new concept, the article discusses Spike Jonze’s film Adaptation. according to James Naremore’s proposal which considers the study of adaptation as part of a general theory of repetition

A meta-analysis of local adaptation in plants.

Directory of Open Access Journals (Sweden)

Roosa Leimu

Full Text Available Local adaptation is of fundamental importance in evolutionary, population, conservation, and global-change biology. The generality of local adaptation in plants and whether and how it is influenced by specific species, population and habitat characteristics have, however, not been quantitatively reviewed. Therefore, we examined published data on the outcomes of reciprocal transplant experiments using two approaches. We conducted a meta-analysis to compare the performance of local and foreign plants at all transplant sites. In addition, we analysed frequencies of pairs of plant origin to examine whether local plants perform better than foreign plants at both compared transplant sites. In both approaches, we also examined the effects of population size, and of the habitat and species characteristics that are predicted to affect local adaptation. We show that, overall, local plants performed significantly better than foreign plants at their site of origin: this was found to be the case in 71.0% of the studied sites. However, local plants performed better than foreign plants at both sites of a pair-wise comparison (strict definition of local adaption only in 45.3% of the 1032 compared population pairs. Furthermore, we found local adaptation much more common for large plant populations (>1000 flowering individuals than for small populations (<1000 flowering individuals for which local adaptation was very rare. The degree of local adaptation was independent of plant life history, spatial or temporal habitat heterogeneity, and geographic scale. Our results suggest that local adaptation is less common in plant populations than generally assumed. Moreover, our findings reinforce the fundamental importance of population size for evolutionary theory. The clear role of population size for the ability to evolve local adaptation raises considerable doubt on the ability of small plant populations to cope with changing environments.

Third eye, the biological effects; 3. oeil, les effets biologiques

Energy Technology Data Exchange (ETDEWEB)

Anon.

2004-02-01

The discovery of a third kind of photo-receptor cell in the human eye has permitted to better understand the biological effects of lighting, not only on the vision, but also on some nervous processes, like emotion, mood, stress, biological clock, etc.. This additional dimension has led the engineers of Philips Lighting company to launch a new indoor lighting concept named 'Carpe Diem'. This concept adapts both the illuminance and the color of a lighting system according to the type of work and to the expected stimulating effect. (J.S.)

Modeling biology with HDL languages: a first step toward a genetic design automation tool inspired from microelectronics.

Science.gov (United States)

Gendrault, Yves; Madec, Morgan; Lallement, Christophe; Haiech, Jacques

2014-04-01

Nowadays, synthetic biology is a hot research topic. Each day, progresses are made to improve the complexity of artificial biological functions in order to tend to complex biodevices and biosystems. Up to now, these systems are handmade by bioengineers, which require strong technical skills and leads to nonreusable development. Besides, scientific fields that share the same design approach, such as microelectronics, have already overcome several issues and designers succeed in building extremely complex systems with many evolved functions. On the other hand, in systems engineering and more specifically in microelectronics, the development of the domain has been promoted by both the improvement of technological processes and electronic design automation tools. The work presented in this paper paves the way for the adaptation of microelectronics design tools to synthetic biology. Considering the similarities and differences between the synthetic biology and microelectronics, the milestones of this adaptation are described. The first one concerns the modeling of biological mechanisms. To do so, a new formalism is proposed, based on an extension of the generalized Kirchhoff laws to biology. This way, a description of all biological mechanisms can be made with languages widely used in microelectronics. Our approach is therefore successfully validated on specific examples drawn from the literature.

Non-Western students' causal reasoning about biologically adaptive changes in humans, other animals and plants: instructional and curricular implications

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Mbajiorgu, Ngozika; Anidu, Innocent

2017-06-01

Senior secondary school students (N = 360), 14- to 18-year-olds, from the Igbo culture of eastern Nigeria responded to a questionnaire requiring them to give causal explanations of biologically adaptive changes in humans, other animals and plants. A student subsample (n = 36) was, subsequently, selected for in-depth interviews. Significant differences were found between prompts within the prompt categories, suggesting item feature effects. However, the most coherent pattern was found within the plant category as patterns differed for the mechanistic proximate (MP) reasoning category only. Patterns also differed highly significantly between the prompt categories, with patterns for teleology, MP, mechanistic ultimate and don't know categories similar for plants and other animals but different for the human category. Both urban and rural students recognise commonalities in causality between the three prompt categories, in that their preferences for causal explanations were similar across four reasoning categories. The rural students, however, were more likely than their urban counterparts to give multiple causal explanations in the span of a single response and less likely to attribute causal agency to God. Two factors, religious belief and language, for all the students; and one factor, ecological closeness to nature, for rural students were suspected to have produced these patterns.

Unified Deep Learning Architecture for Modeling Biology Sequence.

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Wu, Hongjie; Cao, Chengyuan; Xia, Xiaoyan; Lu, Qiang

2017-10-09

Prediction of the spatial structure or function of biological macromolecules based on their sequence remains an important challenge in bioinformatics. When modeling biological sequences using traditional sequencing models, characteristics, such as long-range interactions between basic units, the complicated and variable output of labeled structures, and the variable length of biological sequences, usually lead to different solutions on a case-by-case basis. This study proposed the use of bidirectional recurrent neural networks based on long short-term memory or a gated recurrent unit to capture long-range interactions by designing the optional reshape operator to adapt to the diversity of the output labels and implementing a training algorithm to support the training of sequence models capable of processing variable-length sequences. Additionally, the merge and pooling operators enhanced the ability to capture short-range interactions between basic units of biological sequences. The proposed deep-learning model and its training algorithm might be capable of solving currently known biological sequence-modeling problems through the use of a unified framework. We validated our model on one of the most difficult biological sequence-modeling problems currently known, with our results indicating the ability of the model to obtain predictions of protein residue interactions that exceeded the accuracy of current popular approaches by 10% based on multiple benchmarks.

Toward synthesizing executable models in biology.

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Fisher, Jasmin; Piterman, Nir; Bodik, Rastislav

2014-01-01

Over the last decade, executable models of biological behaviors have repeatedly provided new scientific discoveries, uncovered novel insights, and directed new experimental avenues. These models are computer programs whose execution mechanistically simulates aspects of the cell's behaviors. If the observed behavior of the program agrees with the observed biological behavior, then the program explains the phenomena. This approach has proven beneficial for gaining new biological insights and directing new experimental avenues. One advantage of this approach is that techniques for analysis of computer programs can be applied to the analysis of executable models. For example, one can confirm that a model agrees with experiments for all possible executions of the model (corresponding to all environmental conditions), even if there are a huge number of executions. Various formal methods have been adapted for this context, for example, model checking or symbolic analysis of state spaces. To avoid manual construction of executable models, one can apply synthesis, a method to produce programs automatically from high-level specifications. In the context of biological modeling, synthesis would correspond to extracting executable models from experimental data. We survey recent results about the usage of the techniques underlying synthesis of computer programs for the inference of biological models from experimental data. We describe synthesis of biological models from curated mutation experiment data, inferring network connectivity models from phosphoproteomic data, and synthesis of Boolean networks from gene expression data. While much work has been done on automated analysis of similar datasets using machine learning and artificial intelligence, using synthesis techniques provides new opportunities such as efficient computation of disambiguating experiments, as well as the ability to produce different kinds of models automatically from biological data.

Transitions in optimal adaptive strategies for populations in fluctuating environments

Science.gov (United States)

Mayer, Andreas; Mora, Thierry; Rivoire, Olivier; Walczak, Aleksandra M.

2017-09-01

Biological populations are subject to fluctuating environmental conditions. Different adaptive strategies can allow them to cope with these fluctuations: specialization to one particular environmental condition, adoption of a generalist phenotype that compromises between conditions, or population-wise diversification (bet hedging). Which strategy provides the largest selective advantage in the long run depends on the range of accessible phenotypes and the statistics of the environmental fluctuations. Here, we analyze this problem in a simple mathematical model of population growth. First, we review and extend a graphical method to identify the nature of the optimal strategy when the environmental fluctuations are uncorrelated. Temporal correlations in environmental fluctuations open up new strategies that rely on memory but are mathematically challenging to study: We present analytical results to address this challenge. We illustrate our general approach by analyzing optimal adaptive strategies in the presence of trade-offs that constrain the range of accessible phenotypes. Our results extend several previous studies and have applications to a variety of biological phenomena, from antibiotic resistance in bacteria to immune responses in vertebrates.

Are species differences in maternal effects arising from maternal care adaptive?

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Benowitz, K M; Moody, K J; Moore, A J

2015-02-01

Parental care benefits offspring through maternal effects influencing their development, growth and survival. However, although parental care in general is likely the result of adaptive evolution, it does not follow that specific differences in the maternal effects that arise from care are also adaptive. Here, we used an interspecific cross-fostering design in the burying beetle species Nicrophorus orbicollis and N. vespilloides, both of which have elaborate parental care involving direct feeding of regurgitated food to offspring, to test whether maternal effects are optimized within a species and therefore adaptive. Using a full-factorial design, we first demonstrated that N. orbicollis care for offspring longer regardless of recipient species. We then examined offspring development and mass in offspring reared by hetero- or conspecific parents. As expected, there were species-specific direct effects independent of the maternal effects, as N. orbicollis larvae were larger and took longer to develop than N. vespilloides regardless of caregiver. We also found significant differences in maternal effects: N. vespilloides maternal care caused more rapid development of offspring of either species. Contrary to expectations if maternal effects were species-specific, there were no significant interactions between caretaker and recipient species for either development time or mass, suggesting that these maternal effects are general rather than optimized within species. We suggest that rather than coadaptation between parents and offspring performance, the species differences in maternal effects may be correlated with direct effects, and that their evolution is driven by selection on those direct effects. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Biological Effects of Ionizing Radiation

International Nuclear Information System (INIS)

Durand, J.L.

2000-01-01

The aim of this work is to verify the existence of the adaptive response phenomenon induced by low doses of ionizing radiation in living cells.A wild-type yeast Saccharomyces cerevisiae (Baker's yeast) was chosen as the biological target.As a parameter to quantify the sensibility of the target to radiation, the Lethal Dose 50 (LD50 ) was observed. In our experimental condition a value of (60 ± 1) Gy was measured for LD50 with Dose Rate of (0.44 ± 0.03) Gy/min. The method employed to show up the adaptive response phenomenon consisted in exposing the sample to low ''conditioning'' doses, which would initiate these mechanisms. Later the samples with and without conditioning were exposed to higher ''challenging'' doses (such as LD50), and the surviving fractions were compared. In order to maximize the differences, the doses and the time between irradiations were varied. The best results were obtained with both a conditioning dose of (0.44 ± 0.03) Gy and a waiting time of 2 hs until the application of the challenging dose. Following this procedures the 80% of the conditioned samples has survived, after receiving the application of the LD50. The adaptive response phenomenon was also verified for a wide range of challenging doses

Toward mechanical systems biology in bone.

Science.gov (United States)

Trüssel, Andreas; Müller, Ralph; Webster, Duncan

2012-11-01

Cyclic mechanical loading is perhaps the most important physiological factor regulating bone mass and shape in a way which balances optimal strength with minimal weight. This bone adaptation process spans multiple length and time scales. Forces resulting from physiological exercise at the organ scale are sensed at the cellular scale by osteocytes, which reside inside the bone matrix. Via biochemical pathways, osteocytes orchestrate the local remodeling action of osteoblasts (bone formation) and osteoclasts (bone resorption). Together these local adaptive remodeling activities sum up to strengthen bone globally at the organ scale. To resolve the underlying mechanisms it is required to identify and quantify both cause and effect across the different scales. Progress has been made at the different scales experimentally. Computational models of bone adaptation have been developed to piece together various experimental observations at the different scales into coherent and plausible mechanisms. However additional quantitative experimental validation is still required to build upon the insights which have already been achieved. In this review we discuss emerging as well as state of the art experimental and computational techniques and how they might be used in a mechanical systems biology approach to further our understanding of the mechanisms governing load induced bone adaptation, i.e., ways are outlined in which experimental and computational approaches could be coupled, in a quantitative manner to create more reliable multiscale models of bone.

Adaptive filters and internal models: multilevel description of cerebellar function.

Science.gov (United States)

Porrill, John; Dean, Paul; Anderson, Sean R

2013-11-01

Cerebellar function is increasingly discussed in terms of engineering schemes for motor control and signal processing that involve internal models. To address the relation between the cerebellum and internal models, we adopt the chip metaphor that has been used to represent the combination of a homogeneous cerebellar cortical microcircuit with individual microzones having unique external connections. This metaphor indicates that identifying the function of a particular cerebellar chip requires knowledge of both the general microcircuit algorithm and the chip's individual connections. Here we use a popular candidate algorithm as embodied in the adaptive filter, which learns to decorrelate its inputs from a reference ('teaching', 'error') signal. This algorithm is computationally powerful enough to be used in a very wide variety of engineering applications. However, the crucial issue is whether the external connectivity required by such applications can be implemented biologically. We argue that some applications appear to be in principle biologically implausible: these include the Smith predictor and Kalman filter (for state estimation), and the feedback-error-learning scheme for adaptive inverse control. However, even for plausible schemes, such as forward models for noise cancellation and novelty-detection, and the recurrent architecture for adaptive inverse control, there is unlikely to be a simple mapping between microzone function and internal model structure. This initial analysis suggests that cerebellar involvement in particular behaviours is therefore unlikely to have a neat classification into categories such as 'forward model'. It is more likely that cerebellar microzones learn a task-specific adaptive-filter operation which combines a number of signal-processing roles. Copyright © 2012 Elsevier Ltd. All rights reserved.

Genetic Evidence of Human Adaptation to a Cooked Diet.

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Carmody, Rachel N; Dannemann, Michael; Briggs, Adrian W; Nickel, Birgit; Groopman, Emily E; Wrangham, Richard W; Kelso, Janet

2016-04-13

Humans have been argued to be biologically adapted to a cooked diet, but this hypothesis has not been tested at the molecular level. Here, we combine controlled feeding experiments in mice with comparative primate genomics to show that consumption of a cooked diet influences gene expression and that affected genes bear signals of positive selection in the human lineage. Liver gene expression profiles in mice fed standardized diets of meat or tuber were affected by food type and cooking, but not by caloric intake or consumer energy balance. Genes affected by cooking were highly correlated with genes known to be differentially expressed in liver between humans and other primates, and more genes in this overlap set show signals of positive selection in humans than would be expected by chance. Sequence changes in the genes under selection appear before the split between modern humans and two archaic human groups, Neandertals and Denisovans, supporting the idea that human adaptation to a cooked diet had begun by at least 275,000 years ago. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A Friendly-Biological Reactor SIMulator (BioReSIM for studying biological processes in wastewater treatment processes

Directory of Open Access Journals (Sweden)

Raul Molina

2014-12-01

Full Text Available Biological processes for wastewater treatments are inherently dynamic systems because of the large variations in the influent wastewater flow rate, concentration composition and the adaptive behavior of the involved microorganisms. Moreover, the sludge retention time (SRT is a critical factor to understand the bioreactor performances when changes in the influent or in the operation conditions take place. Since SRT are usually in the range of 10-30 days, the performance of biological reactors needs a long time to be monitored in a regular laboratory demonstration, limiting the knowledge that can be obtained in the experimental lab practice. In order to overcome this lack, mathematical models and computer simulations are useful tools to describe biochemical processes and predict the overall performance of bioreactors under different working operation conditions and variations of the inlet wastewater composition. The mathematical solution of the model could be difficult as numerous biochemical processes can be considered. Additionally, biological reactors description (mass balance, etc. needs models represented by partial or/and ordinary differential equations associated to algebraic expressions, that require complex computational codes to obtain the numerical solutions. Different kind of software for mathematical modeling can be used, from large degree of freedom simulators capable of free models definition (as AQUASIM, to closed predefined model structure programs (as BIOWIN. The first ones usually require long learning curves, whereas the second ones could be excessively rigid for specific wastewater treatment systems. As alternative, we present Biological Reactor SIMulator (BioReSIM, a MATLAB code for the simulation of sequencing batch reactors (SBR and rotating biological contactors (RBC as biological systems of suspended and attached biomass for wastewater treatment, respectively. This BioReSIM allows the evaluation of simple and complex

Adaptability and climate change

International Nuclear Information System (INIS)

Sprague, M.W.

1991-01-01

The potential social, economic and environmental impacts of climate change are reviewed, with emphasis on agricultural implications. Impact analyses must be done on the scale of watersheds or river basins. For agriculture, climate change effects on water resources are likely to be more important than temperature changes, and climatic variability is also equally important. Another set of critical climatic variables are the frequencies, magnitudes and timing of extreme events such as floods, droughts, etc. A carbon dioxide enriched atmosphere will increase water use efficiency and confer increased tolerance to drought, salinity and air pollution. Better understanding and accounting is required for the effects of increased carbon dioxide on all plant life, including crops. Adaptability of agriculture to change must be taken into account in predicting impacts of climate change, with technological innovation and infrastructure giving agriculture a dynamic nature. Limitations and adaptations must be considered when formulating public policy, to ensure that marginal costs do not exceed marginal benefits. Monoculture plantation forests may be the most efficient sinks of atmospheric carbon dioxide, yet widespread reliance on them may harm biological diversity. Actions the U.S. is currently taking under a no-regrets policy are summarized

Climate change adaptation strategies for federal forests of the Pacific Northwest, USA: ecological, policy, and socio-economic perspectives

Science.gov (United States)

Thomas A. Spies; Thomas W. Giesen; Frederick J. Swanson; Jerry F. Franklin; Denise Lach; K. Norman. Johnson

2010-01-01

Conserving biological diversity in a changing climate poses major challenges for land managers and society. Effective adaptive strategies for dealing with climate change require a socioecological systems perspective. We highlight some of the projected ecological responses to climate change in the Pacific Northwest, U.S.A and identify possible adaptive actions that...

The quest for a new modelling framework in mathematical biology. Comment on "On the interplay between mathematics and biology: Hallmarks towards a new systems biology" by N. Bellomo et al.

Science.gov (United States)

Eftimie, Raluca

2015-03-01

One of the main unsolved problems of modern physics is finding a "theory of everything" - a theory that can explain, with the help of mathematics, all physical aspects of the universe. While the laws of physics could explain some aspects of the biology of living systems (e.g., the phenomenological interpretation of movement of cells and animals), there are other aspects specific to biology that cannot be captured by physics models. For example, it is generally accepted that the evolution of a cell-based system is influenced by the activation state of cells (e.g., only activated and functional immune cells can fight diseases); on the other hand, the evolution of an animal-based system can be influenced by the psychological state (e.g., distress) of animals. Therefore, the last 10-20 years have seen also a quest for a "theory of everything"-approach extended to biology, with researchers trying to propose mathematical modelling frameworks that can explain various biological phenomena ranging from ecology to developmental biology and medicine [1,2,6]. The basic idea behind this approach can be found in a few reviews on ecology and cell biology [6,7,9-11], where researchers suggested that due to the parallel between the micro-scale dynamics and the emerging macro-scale phenomena in both cell biology and in ecology, many mathematical methods used for ecological processes could be adapted to cancer modelling [7,9] or to modelling in immunology [11]. However, this approach generally involved the use of different models to describe different biological aspects (e.g., models for cell and animal movement, models for competition between cells or animals, etc.).

Behavioural biology of Chagas disease vectors.

Science.gov (United States)

Lazzari, Claudio Ricardo; Pereira, Marcos Horácio; Lorenzo, Marcelo Gustavo

2013-01-01

Many arthropod species have adopted vertebrate blood as their main food source. Blood is rich in nutrients and, except for the presence of parasites, sterile. However, this food source is not freely available, nor is obtaining it devoid of risk. It circulates inside vessels hidden underneath the skin of mobile hosts that are able to defend themselves and even predate the insects that try to feed on them. Thus, the haematophagous lifestyle is associated with major morphological, physiological and behavioural adaptations that have accumulated throughout the evolutionary history of the various lineages of blood-sucking arthropods. These adaptations have significant consequences for the evolution of parasites as well as for the epidemiology of vector-transmitted diseases. In this review article, we analyse various aspects of the behaviour of triatomine bugs to illustrate how each behavioural trait represents a particular adaptation to their close association with their hosts, which may easily turn into predators. Our aim is to offer to the reader an up-to-date integrative perspective on the behaviour of Chagas disease vectors and to propose new research avenues to encourage both young and experienced colleagues to explore this aspect of triatomine biology.

Behavioural biology of Chagas disease vectors

Directory of Open Access Journals (Sweden)

Claudio Ricardo Lazzari

2013-01-01

Full Text Available Many arthropod species have adopted vertebrate blood as their main food source. Blood is rich in nutrients and, except for the presence of parasites, sterile. However, this food source is not freely available, nor is obtaining it devoid of risk. It circulates inside vessels hidden underneath the skin of mobile hosts that are able to defend themselves and even predate the insects that try to feed on them. Thus, the haematophagous lifestyle is associated with major morphological, physiological and behavioural adaptations that have accumulated throughout the evolutionary history of the various lineages of blood-sucking arthropods. These adaptations have significant consequences for the evolution of parasites as well as for the epidemiology of vector-transmitted diseases. In this review article, we analyse various aspects of the behaviour of triatomine bugs to illustrate how each behavioural trait represents a particular adaptation to their close association with their hosts, which may easily turn into predators. Our aim is to offer to the reader an up-to-date integrative perspective on the behaviour of Chagas disease vectors and to propose new research avenues to encourage both young and experienced colleagues to explore this aspect of triatomine biology.

Ruminant Metabolic Systems Biology: Reconstruction and Integration of Transcriptome Dynamics Underlying Functional Responses of Tissues to Nutrition and Physiological Statea

Science.gov (United States)

Bionaz, Massimo; Loor, Juan J.

2012-01-01

High-throughput ‘omics’ data analysis via bioinformatics is one key component of the systems biology approach. The systems approach is particularly well-suited for the study of the interactions between nutrition and physiological state with tissue metabolism and functions during key life stages of organisms such as the transition from pregnancy to lactation in mammals, ie, the peripartal period. In modern dairy cows with an unprecedented genetic potential for milk synthesis, the nature of the physiologic and metabolic adaptations during the peripartal period is multifaceted and involves key tissues such as liver, adipose, and mammary. In order to understand such adaptation, we have reviewed several works performed in our and other labs. In addition, we have used a novel bioinformatics approach, Dynamic Impact Approach (DIA), in combination with partly previously published data to help interpret longitudinal biological adaptations of bovine liver, adipose, and mammary tissue to lactation using transcriptomics datasets. Use of DIA with transcriptomic data from those tissues during normal physiological adaptations and in animals fed different levels of energy prepartum allowed visualization and integration of most-impacted metabolic pathways around the time of parturition. The DIA is a suitable tool for applying the integrative systems biology approach. The ultimate goal is to visualize the complexity of the systems at study and uncover key molecular players involved in the tissue’s adaptations to physiological state or nutrition. PMID:22807626

Structural adaptations of proteins to different biological membranes

Science.gov (United States)

Pogozheva, Irina D.; Tristram-Nagle, Stephanie; Mosberg, Henry I.; Lomize, Andrei L.

2013-01-01

To gain insight into adaptations of proteins to their membranes, intrinsic hydrophobic thicknesses, distributions of different chemical groups and profiles of hydrogen-bonding capacities (α and β) and the dipolarity/polarizability parameter (π*) were calculated for lipid-facing surfaces of 460 integral α-helical, β-barrel and peripheral proteins from eight types of biomembranes. For comparison, polarity profiles were also calculated for ten artificial lipid bilayers that have been previously studied by neutron and X-ray scattering. Estimated hydrophobic thicknesses are 30-31 Å for proteins from endoplasmic reticulum, thylakoid, and various bacterial plasma membranes, but differ for proteins from outer bacterial, inner mitochondrial and eukaryotic plasma membranes (23.9, 28.6 and 33.5 Å, respectively). Protein and lipid polarity parameters abruptly change in the lipid carbonyl zone that matches the calculated hydrophobic boundaries. Maxima of positively charged protein groups correspond to the location of lipid phosphates at 20-22 Å distances from the membrane center. Locations of Tyr atoms coincide with hydrophobic boundaries, while distributions maxima of Trp rings are shifted by 3-4 Å toward the membrane center. Distributions of Trp atoms indicate the presence of two 5-8 Å-wide midpolar regions with intermediate π* values within the hydrocarbon core, whose size and symmetry depend on the lipid composition of membrane leaflets. Midpolar regions are especially asymmetric in outer bacterial membranes and cell membranes of mesophilic but not hyperthermophilic archaebacteria, indicating the larger width of the central nonpolar region in the later case. In artificial lipid bilayers, midpolar regions are observed up to the level of acyl chain double bonds. PMID:23811361

Hypercell : A bio-inspired information design framework for real-time adaptive spatial components

NARCIS (Netherlands)

Biloria, N.M.; Chang, J.R.

2012-01-01

Contemporary explorations within the evolutionary computational domain have been heavily instrumental in exploring biological processes of adaptation, growth and mutation. On the other hand a plethora of designers owing to the increasing sophistication in computer aided design software are equally

Interspecific competition counteracts negative effects of dispersal on adaptation of an arthropod herbivore to a new host.

Science.gov (United States)

Alzate, A; Bisschop, K; Etienne, R S; Bonte, D

2017-11-01

Dispersal and competition have both been suggested to drive variation in adaptability to a new environment, either positively or negatively. A simultaneous experimental test of both mechanisms is however lacking. Here, we experimentally investigate how population dynamics and local adaptation to a new host plant in a model species, the two-spotted spider mite (Tetranychus urticae), are affected by dispersal from a stock population (no-adapted) and competition with an already adapted spider mite species (Tetranychus evansi). For the population dynamics, we find that competition generally reduces population size and increases the risk of population extinction. However, these negative effects are counteracted by dispersal. For local adaptation, the roles of competition and dispersal are reversed. Without competition, dispersal exerts a negative effect on adaptation (measured as fecundity) to a novel host and females receiving the highest number of immigrants performed similarly to the stock population females. By contrast, with competition, adding more immigrants did not result in a lower fecundity. Females from populations with competition receiving the highest number of immigrants had a significantly higher fecundity than females from populations without competition (same dispersal treatment) and than the stock population females. We suggest that by exerting a stronger selection on the adapting populations, competition can counteract the migration load effect of dispersal. Interestingly, adaptation to the new host does not significantly reduce performance on the ancestral host, regardless of dispersal rate or competition. Our results highlight that assessments of how species can adapt to changing conditions need to jointly consider connectivity and the community context. © 2017 The Authors. Journal of Evolutionary Biology Published by John Wiley & Sons ltd on Behalf of European Society for Evolutionary Biology.

Biomimicry, Biofabrication, and Biohybrid Systems: The Emergence and Evolution of Biological Design.

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Raman, Ritu; Bashir, Rashid

2017-10-01

The discipline of biological design has a relatively short history, but has undergone very rapid expansion and development over that time. This Progress Report outlines the evolution of this field from biomimicry to biofabrication to biohybrid systems' design, showcasing how each subfield incorporates bioinspired dynamic adaptation into engineered systems. Ethical implications of biological design are discussed, with an emphasis on establishing responsible practices for engineering non-natural or hypernatural functional behaviors in biohybrid systems. This report concludes with recommendations for implementing biological design into educational curricula, ensuring effective and responsible practices for the next generation of engineers and scientists. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genomic science provides new insights into the biology of forest trees

Science.gov (United States)

Andrew Groover

2015-01-01

Forest biology is undergoing a fundamental change fostered by the application of genomic science to longstanding questions surrounding the evolution, adaptive traits, development, and environmental interactions of tree species. Genomic science has made major technical leaps in recent years, most notably with the advent of 'next generation sequencing' but...

Systems Biology of Industrial Microorganisms

Science.gov (United States)

Papini, Marta; Salazar, Margarita; Nielsen, Jens

The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

The role of adaptive trans-generational plasticity in biological invasions of plants

OpenAIRE

Dyer, Andrew R; Brown, Cynthia S; Espeland, Erin K; McKay, John K; Meimberg, Harald; Rice, Kevin J

2010-01-01

High-impact biological invasions often involve establishment and spread in disturbed, high-resource patches followed by establishment and spread in biotically or abiotically stressful areas. Evolutionary change may be required for the second phase of invasion (establishment and spread in stressful areas) to occur. When species have low genetic diversity and short selection history, within-generation phenotypic plasticity is often cited as the mechanism through which spread across multiple hab...

Adaptive force produced by stress-induced regulation of random variation intensity.

Science.gov (United States)

Shimansky, Yury P

2010-08-01

The Darwinian theory of life evolution is capable of explaining the majority of related phenomena. At the same time, the mechanisms of optimizing traits beneficial to a population as a whole but not directly to an individual remain largely unclear. There are also significant problems with explaining the phenomenon of punctuated equilibrium. From another perspective, multiple mechanisms for the regulation of the rate of genetic mutations according to the environmental stress have been discovered, but their precise functional role is not well understood yet. Here a novel mathematical paradigm called a Kinetic-Force Principle (KFP), which can serve as a general basis for biologically plausible optimization methods, is introduced and its rigorous derivation is provided. Based on this principle, it is shown that, if the rate of random changes in a biological system is proportional, even only roughly, to the amount of environmental stress, a virtual force is created, acting in the direction of stress relief. It is demonstrated that KFP can provide important insights into solving the above problems. Evidence is presented in support of a hypothesis that the nature employs KFP for accelerating adaptation in biological systems. A detailed comparison between KFP and the principle of variation and natural selection is presented and their complementarity is revealed. It is concluded that KFP is not a competing alternative, but a powerful addition to the principle of variation and natural selection. It is also shown KFP can be used in multiple ways for adaptation of individual biological organisms.

Towards Synthesizing Executable Models in Biology

Directory of Open Access Journals (Sweden)

Jasmin eFisher

2014-12-01

Full Text Available Over the last decade, executable models of biological behaviors have repeatedly provided new scientific discoveries, uncovered novel insights, and directed new experimental avenues. These models are computer programs whose execution mechanistically simulates aspects of the cell’s behaviors. If the observed behavior of the program agrees with the observed biological behavior, then the program explains the phenomena. This approach has proven beneficial for gaining new biological insights and directing new experimental avenues. One advantage of this approach is that techniques for analysis of computer programs can be applied to the analysis of executable models. For example, one can confirm that a model agrees with experiments for all possible executions of the model (corresponding to all environmental conditions, even if there are a huge number of executions. Various formal methods have been adapted for this context, for example, model checking or symbolic analysis of state spaces. To avoid manual construction of executable models, one can apply synthesis, a method to produce programs automatically from high-level specifications. In the context of biological modelling, synthesis would correspond to extracting executable models from experimental data. We survey recent results about the usage of the techniques underlying synthesis of computer programs for the inference of biological models from experimental data. We describe synthesis of biological models from curated mutation experiment data, inferring network connectivity models from phosphoproteomic data, and synthesis of Boolean networks from gene expression data. While much work has been done on automated analysis of similar datasets using machine learning and artificial intelligence, using synthesis techniques provides new opportunities such as efficient computation of disambiguating experiments, as well as the ability to produce different kinds of models automatically from biological data.

Application of Non-Kolmogorovian Probability and Quantum Adaptive Dynamics to Unconscious Inference in Visual Perception Process

Science.gov (United States)

Accardi, Luigi; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

2016-07-01

Recently a novel quantum information formalism — quantum adaptive dynamics — was developed and applied to modelling of information processing by bio-systems including cognitive phenomena: from molecular biology (glucose-lactose metabolism for E.coli bacteria, epigenetic evolution) to cognition, psychology. From the foundational point of view quantum adaptive dynamics describes mutual adapting of the information states of two interacting systems (physical or biological) as well as adapting of co-observations performed by the systems. In this paper we apply this formalism to model unconscious inference: the process of transition from sensation to perception. The paper combines theory and experiment. Statistical data collected in an experimental study on recognition of a particular ambiguous figure, the Schröder stairs, support the viability of the quantum(-like) model of unconscious inference including modelling of biases generated by rotation-contexts. From the probabilistic point of view, we study (for concrete experimental data) the problem of contextuality of probability, its dependence on experimental contexts. Mathematically contextuality leads to non-Komogorovness: probability distributions generated by various rotation contexts cannot be treated in the Kolmogorovian framework. At the same time they can be embedded in a “big Kolmogorov space” as conditional probabilities. However, such a Kolmogorov space has too complex structure and the operational quantum formalism in the form of quantum adaptive dynamics simplifies the modelling essentially.

Subattomole sensitivity in biological accelerator mass spectrometry.

Science.gov (United States)

Salehpour, Mehran; Possnert, Göran; Bryhni, Helge

2008-05-15

The Uppsala University 5 MV Pelletron tandem accelerator has been used to study (14)C-labeled biological samples utilizing accelerator mass spectrometry (AMS) technology. We have adapted a sample preparation method for small biological samples down to a few tens of micrograms of carbon, involving among others, miniaturizing of the graphitization reactor. Standard AMS requires about 1 mg of carbon with a limit of quantitation of about 10 amol. Results are presented for a range of small sample sizes with concentrations down to below 1 pM of a pharmaceutical substance in human blood. It is shown that (14)C-labeled molecular markers can be routinely measured from the femtomole range down to a few hundred zeptomole (10 (-21) mol), without the use of any additional separation methods.

Pseudorandom numbers: evolutionary models in image processing, biology, and nonlinear dynamic systems

Science.gov (United States)

Yaroslavsky, Leonid P.

1996-11-01

We show that one can treat pseudo-random generators, evolutionary models of texture images, iterative local adaptive filters for image restoration and enhancement and growth models in biology and material sciences in a unified way as special cases of dynamic systems with a nonlinear feedback.

Principles for integrating reactive species into in vivo biological processes: Examples from exercise physiology.

Science.gov (United States)

Margaritelis, Nikos V; Cobley, James N; Paschalis, Vassilis; Veskoukis, Aristidis S; Theodorou, Anastasios A; Kyparos, Antonios; Nikolaidis, Michalis G

2016-04-01

The equivocal role of reactive species and redox signaling in exercise responses and adaptations is an example clearly showing the inadequacy of current redox biology research to shed light on fundamental biological processes in vivo. Part of the answer probably relies on the extreme complexity of the in vivo redox biology and the limitations of the currently applied methodological and experimental tools. We propose six fundamental principles that should be considered in future studies to mechanistically link reactive species production to exercise responses or adaptations: 1) identify and quantify the reactive species, 2) determine the potential signaling properties of the reactive species, 3) detect the sources of reactive species, 4) locate the domain modified and verify the (ir)reversibility of post-translational modifications, 5) establish causality between redox and physiological measurements, 6) use selective and targeted antioxidants. Fulfilling these principles requires an idealized human experimental setting, which is certainly a utopia. Thus, researchers should choose to satisfy those principles, which, based on scientific evidence, are most critical for their specific research question. Copyright © 2015 Elsevier Inc. All rights reserved.

Fundamental plant biology enabled by the space shuttle.

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Paul, Anna-Lisa; Wheeler, Ray M; Levine, Howard G; Ferl, Robert J

2013-01-01

The relationship between fundamental plant biology and space biology was especially synergistic in the era of the Space Shuttle. While all terrestrial organisms are influenced by gravity, the impact of gravity as a tropic stimulus in plants has been a topic of formal study for more than a century. And while plants were parts of early space biology payloads, it was not until the advent of the Space Shuttle that the science of plant space biology enjoyed expansion that truly enabled controlled, fundamental experiments that removed gravity from the equation. The Space Shuttle presented a science platform that provided regular science flights with dedicated plant growth hardware and crew trained in inflight plant manipulations. Part of the impetus for plant biology experiments in space was the realization that plants could be important parts of bioregenerative life support on long missions, recycling water, air, and nutrients for the human crew. However, a large part of the impetus was that the Space Shuttle enabled fundamental plant science essentially in a microgravity environment. Experiments during the Space Shuttle era produced key science insights on biological adaptation to spaceflight and especially plant growth and tropisms. In this review, we present an overview of plant science in the Space Shuttle era with an emphasis on experiments dealing with fundamental plant growth in microgravity. This review discusses general conclusions from the study of plant spaceflight biology enabled by the Space Shuttle by providing historical context and reviews of select experiments that exemplify plant space biology science.

An adaptive algorithm for simulation of stochastic reaction-diffusion processes

International Nuclear Information System (INIS)

Ferm, Lars; Hellander, Andreas; Loetstedt, Per

2010-01-01

We propose an adaptive hybrid method suitable for stochastic simulation of diffusion dominated reaction-diffusion processes. For such systems, simulation of the diffusion requires the predominant part of the computing time. In order to reduce the computational work, the diffusion in parts of the domain is treated macroscopically, in other parts with the tau-leap method and in the remaining parts with Gillespie's stochastic simulation algorithm (SSA) as implemented in the next subvolume method (NSM). The chemical reactions are handled by SSA everywhere in the computational domain. A trajectory of the process is advanced in time by an operator splitting technique and the timesteps are chosen adaptively. The spatial adaptation is based on estimates of the errors in the tau-leap method and the macroscopic diffusion. The accuracy and efficiency of the method are demonstrated in examples from molecular biology where the domain is discretized by unstructured meshes.

Adapting bioinformatics curricula for big data

Science.gov (United States)

Greene, Anna C.; Giffin, Kristine A.; Greene, Casey S.

2016-01-01

Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. PMID:25829469

Low environmental radiation background impairs biological defence of the yeast Saccharomyces cerevisiae to chemical radiomimetic agents

International Nuclear Information System (INIS)

Satta, L.; Augusti-Tocco, G.; Ceccarelli, R.; Paggi, P.; Scarsella, G.; Esposito, A.; Fiore, M.; Poggesi, I.; Ricordy, R.; Cundari, E.

1995-01-01

Background radiation is likely to constitute one of the factors involved in biological evolution since radiations are able to affect biological processes. Therefore, it is possible to hypothesize that organisms are adapted to environmental background radiation and that this adaptation could increase their ability to respond to the harmful effects of ionizing radiations. In fact, adaptive responses to alkylating agents and to low doses of ionizing radiation have been found in many organisms. In order to test for effects of adaptation, cell susceptibility to treatments with high doses of radiomimetic chemical agents has been studied by growing them in a reduced environmental radiation background. The experiment has been performed by culturing yeast cells (Saccharomyces cerevisiae D7) in parallel in a standard background environment and in the underground Gran Sasso National Laboratory, with reduced environmental background radiation. After a conditioning period, yeast cells were exposed to recombinogenic doses of methyl methanesulfonate. The yeast cells grown in the Gran Sasso Laboratory showed a higher frequency of radiomimetic induced recombination as compared to those grown in the standard environment. This suggests that environmental radiation may act as a conditioning agent

Sex speeds adaptation by altering the dynamics of molecular evolution.

Science.gov (United States)

McDonald, Michael J; Rice, Daniel P; Desai, Michael M

2016-03-10

Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.

Data Requirements for Developing Adaptations to Climate Variability and Change

International Nuclear Information System (INIS)

Basher, Reid E.

1999-01-01

An extensive foundation of high quality data and information on the climate and on the biological, environmental and social systems affected by climate is required in order to understand the climate impact processes involved, to develop new adaptation practices, and to subsequently implement these practices. Experience of the impacts of current and past variability of climate and sea level is a prime source of information. Many practices are in use to reduce climate impacts, for example in engineering design, agricultural risk management and climate prediction services, though their roles as adaptations to climate change are not widely appreciated. While there are good data sets on some factors and in some regions, in many cases the databases are inadequate and there are few data sets on adaptation-specific quantities such as vulnerability, resilience and adaptation effectiveness. Current international action under the United Nations Framework Convention on Climate Change (UNFCCC) pays little attention to adaptation and its information requirements. Furthermore there are trends toward reduced data gathering and to restrictions on access to data sets, especially arising from cost and commercialisation pressures. To effectively respond to the changes in climate that are now inevitable, governments will need to more clearly identify adaptation as a central feature of climate change policy and make a renewed shared commitment to collecting and freely exchanging the necessary data. 12 refs

Plant pathology: a story about biology.

Science.gov (United States)

Gordon, Thomas R; Leveau, Johan H J

2010-01-01

Disease is a universal feature of life for multicellular organisms, and the study of disease has contributed to the establishment of key concepts in the biological sciences. This implies strong connections between plant pathology and basic biology, something that could perhaps be made more apparent to undergraduate students interested in the life sciences. To that end, we present an instructional narrative that begins with a simple question: Why are there diseases? Responses and follow-up questions can facilitate exploration of such topics as the evolution of parasitism, plant adaptations to parasitism, impacts of parasites on native plant communities, and ways in which human intervention can foster the emergence of aggressive plant pathogens. This approach may help to attract students who would not have found their way to plant pathology through traditional pathways. Packaging the narrative as a game may render it more interesting and accessible, particularly to a younger audience.

Hybrid Adaptive Flight Control with Model Inversion Adaptation

Science.gov (United States)

Nguyen, Nhan

2011-01-01

This study investigates a hybrid adaptive flight control method as a design possibility for a flight control system that can enable an effective adaptation strategy to deal with off-nominal flight conditions. The hybrid adaptive control blends both direct and indirect adaptive control in a model inversion flight control architecture. The blending of both direct and indirect adaptive control provides a much more flexible and effective adaptive flight control architecture than that with either direct or indirect adaptive control alone. The indirect adaptive control is used to update the model inversion controller by an on-line parameter estimation of uncertain plant dynamics based on two methods. The first parameter estimation method is an indirect adaptive law based on the Lyapunov theory, and the second method is a recursive least-squares indirect adaptive law. The model inversion controller is therefore made to adapt to changes in the plant dynamics due to uncertainty. As a result, the modeling error is reduced that directly leads to a decrease in the tracking error. In conjunction with the indirect adaptive control that updates the model inversion controller, a direct adaptive control is implemented as an augmented command to further reduce any residual tracking error that is not entirely eliminated by the indirect adaptive control.

Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

Science.gov (United States)

Colautti, Robert I; Lau, Jennifer A

2015-05-01

Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. © 2015 John Wiley & Sons Ltd.

Hypoxia adaptation in fish of the Amazon: a never-ending task | Val ...

African Journals Online (AJOL)

In addition to seasonal long-term changes in dissolved oxygen and carbon dioxide, water bodies of the Amazon present periodic short-term episodes of hypoxia and even anoxia. To preserve gas exchange and acid base balance, fish of the Amazon have developed multiple adaptive solutions which occur at all biological ...

A Transcriptomic Analysis of Echinococcus granulosus Larval Stages: Implications for Parasite Biology and Host Adaptation

Science.gov (United States)

Parkinson, John; Wasmuth, James D.; Salinas, Gustavo; Bizarro, Cristiano V.; Sanford, Chris; Berriman, Matthew; Ferreira, Henrique B.; Zaha, Arnaldo; Blaxter, Mark L.; Maizels, Rick M.; Fernández, Cecilia

2012-01-01

Background The cestode Echinococcus granulosus - the agent of cystic echinococcosis, a zoonosis affecting humans and domestic animals worldwide - is an excellent model for the study of host-parasite cross-talk that interfaces with two mammalian hosts. To develop the molecular analysis of these interactions, we carried out an EST survey of E. granulosus larval stages. We report the salient features of this study with a focus on genes reflecting physiological adaptations of different parasite stages. Methodology/Principal Findings We generated ∼10,000 ESTs from two sets of full-length enriched libraries (derived from oligo-capped and trans-spliced cDNAs) prepared with three parasite materials: hydatid cyst wall, larval worms (protoscoleces), and pepsin/H+-activated protoscoleces. The ESTs were clustered into 2700 distinct gene products. In the context of the biology of E. granulosus, our analyses reveal: (i) a diverse group of abundant long non-protein coding transcripts showing homology to a middle repetitive element (EgBRep) that could either be active molecular species or represent precursors of small RNAs (like piRNAs); (ii) an up-regulation of fermentative pathways in the tissue of the cyst wall; (iii) highly expressed thiol- and selenol-dependent antioxidant enzyme targets of thioredoxin glutathione reductase, the functional hub of redox metabolism in parasitic flatworms; (iv) candidate apomucins for the external layer of the tissue-dwelling hydatid cyst, a mucin-rich structure that is critical for survival in the intermediate host; (v) a set of tetraspanins, a protein family that appears to have expanded in the cestode lineage; and (vi) a set of platyhelminth-specific gene products that may offer targets for novel pan-platyhelminth drug development. Conclusions/Significance This survey has greatly increased the quality and the quantity of the molecular information on E. granulosus and constitutes a valuable resource for gene prediction on the parasite genome

Entropy as a method to investigate complex biological systems. An alternative view on the biological transition from healthy aging to frailty

Directory of Open Access Journals (Sweden)

Roberto Siciliano

2017-07-01

Full Text Available Everyone is subject to a process of progressive deterioration of control mechanisms, which supervise the complex network of human physiological functions, reducing the individual ability to adapt to emerging situations of stress or change. In the light of results obtained during the last years, it appears that some of the tools of nonlinear dynamics, first developed for the physical sciences are well suited for studies of biological systems. We believe that, considering the level of order or complexity of the anatomical apparatus by measuring a physical quantity, which is the entropy, we can evaluate the health status or vice versa fragility of a biological system. In particular, a reduction in the entropy value, indicates modification of the structural order with a progressive reduction of functional reserve of the individual, which is associated with a failure to adapt to stress conditions, difficult to be analyzed and documented with a unique traditional biochemical or biomolecular vision. Therefore, in this paper, we present a method that, conceptually combines complexity, disease and aging, alloys Poisson statistics, predictive of the personal level of health, to the entropy value indicating the status of bio-dynamic and functional body, seen as a complex and open thermodynamic system.

Physics must join with biology in better assessing risk from low-dose irradiation

International Nuclear Information System (INIS)

Feinendegen, L. E.; Neumann, R. D.

2005-01-01

This review summarises the complex response of mammalian cells and tissues to low doses of ionising radiation. This thesis encompasses induction of DNA damage, and adaptive protection against both renewed damage and against propagation of damage from the basic level of biological organisation to the clinical expression of detriment. The induction of DNA damage at low radiation doses apparently is proportional to absorbed dose at the physical/chemical level. However, any propagation of such damage to higher levels of biological organisation inherently follows a sigmoid function. Moreover, low-dose-induced inhibition of damage propagation is not linear, but instead follows a dose-effect function typical for adaptive protection, after an initial rapid rise it disappears at doses higher than ∼0.1-0.2 Gy to cells. The particular biological response duality at low radiation doses precludes the validity of the linear-no-threshold hypothesis in the attempt to relate absorbed dose to cancer. In fact, theory and observation support not only a lower cancer incidence than expected from the linear-no-threshold hypothesis, but also a reduction of spontaneously occurring cancer, a hormetic response, in the healthy individual. (authors)

Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

Science.gov (United States)

Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

2016-01-01

Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

Biological responses to low dose rate gamma radiation

International Nuclear Information System (INIS)

Magae, Junji; Ogata, Hiromitsu

2003-01-01

Linear non-threshold (LNT) theory is a basic theory for radioprotection. While LNT dose not consider irradiation time or dose-rate, biological responses to radiation are complex processes dependent on irradiation time as well as total dose. Moreover, experimental and epidemiological studies that can evaluate LNT at low dose/low dose-rate are not sufficiently accumulated. Here we analyzed quantitative relationship among dose, dose-rate and irradiation time using chromosomal breakage and proliferation inhibition of human cells as indicators of biological responses. We also acquired quantitative data at low doses that can evaluate adaptability of LNT with statistically sufficient accuracy. Our results demonstrate that biological responses at low dose-rate are remarkably affected by exposure time, and they are dependent on dose-rate rather than total dose in long-term irradiation. We also found that change of biological responses at low dose was not linearly correlated to dose. These results suggest that it is necessary for us to create a new model which sufficiently includes dose-rate effect and correctly fits of actual experimental and epidemiological results to evaluate risk of radiation at low dose/low dose-rate. (author)

Macroscopic Quantum-Type Potentials in Theoretical Systems Biology

Directory of Open Access Journals (Sweden)

Laurent Nottale

2013-12-01

Full Text Available We review in this paper the use of the theory of scale relativity and fractal space-time as a tool particularly well adapted to the possible development of a future genuine systems theoretical biology. We emphasize in particular the concept of quantum-type potentials, since, in many situations, the effect of the fractality of space—or of the underlying medium—can be reduced to the addition of such a potential energy to the classical equations of motion. Various equivalent representations—geodesic, quantum-like, fluid mechanical, stochastic—of these equations are given, as well as several forms of generalized quantum potentials. Examples of their possible intervention in high critical temperature superconductivity and in turbulence are also described, since some biological processes may be similar in some aspects to these physical phenomena. These potential extra energy contributions could have emerged in biology from the very fractal nature of the medium, or from an evolutive advantage, since they involve spontaneous properties of self-organization, morphogenesis, structuration and multi-scale integration. Finally, some examples of applications of the theory to actual biological-like processes and functions are also provided.

Biological significance of sperm whale responses to sonar: Comparison with anti-predator responses

NARCIS (Netherlands)

Curé, C.; Isojunno, S.; Visser, F.; Wensveen, P.J.; Sivle, L.D.; Kvadsheim, P.H.; Lam, F.A.; Miller, P.J.O.

2016-01-01

A key issue when investigating effects of anthropogenic noise on cetacean behavior is to identify the biological significance of the responses. Predator presence can be considered a natural high-level disturbance stimulus to which prey animals have evolved adaptive response strategies to reduce

Parameter identification of PEMFC model based on hybrid adaptive differential evolution algorithm

International Nuclear Information System (INIS)

Sun, Zhe; Wang, Ning; Bi, Yunrui; Srinivasan, Dipti

2015-01-01

In this paper, a HADE (hybrid adaptive differential evolution) algorithm is proposed for the identification problem of PEMFC (proton exchange membrane fuel cell). Inspired by biological genetic strategy, a novel adaptive scaling factor and a dynamic crossover probability are presented to improve the adaptive and dynamic performance of differential evolution algorithm. Moreover, two kinds of neighborhood search operations based on the bee colony foraging mechanism are introduced for enhancing local search efficiency. Through testing the benchmark functions, the proposed algorithm exhibits better performance in convergent accuracy and speed. Finally, the HADE algorithm is applied to identify the nonlinear parameters of PEMFC stack model. Through experimental comparison with other identified methods, the PEMFC model based on the HADE algorithm shows better performance. - Highlights: • We propose a hybrid adaptive differential evolution algorithm (HADE). • The search efficiency is enhanced in low and high dimension search space. • The effectiveness is confirmed by testing benchmark functions. • The identification of the PEMFC model is conducted by adopting HADE.

Synthetic biology regulation and governance: Lessons from TAPIC for the United States, European Union, and Singapore.

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Trump, Benjamin D

2017-11-01

Synthetic biology is an emerging technology with potential benefits to various fields, yet also contains potential risks to human and environmental health. The field remains in an emerging state with limited quantitative guidance and a small but growing population of international researchers that conduct work within this field. Given the uncertain nature of this technology, an adaptive and anticipatory governance framework may be necessary to balance the potential benefits that may accrue from the technology's continued research alongside a desire to reduce or eliminate potential risks that may arise. However, such developments must account for the unique political and institutional factors that form a government's risk culture - something that can facilitate or impede the development of adaptive synthetic biology governance moving forward. The TAPIC framework helps illustrate those factors that are essential to develop good governance for emerging technologies like synthetic biology. Specifically, an application of TAPIC to synthetic biology governance indicates that the factors of accountability, participation, and integrity must be bolstered to improve technology governance in governments like with the United States, European Union, and Singapore. Copyright © 2017. Published by Elsevier B.V.

Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor

Science.gov (United States)

Cantine, Marjorie D.; Fournier, Gregory P.

2018-03-01

Extensive fundamental molecular and biological evolution took place between the prebiotic origins of life and the state of the Last Universal Common Ancestor (LUCA). Considering the evolutionary innovations between these two endpoints from the perspective of environmental adaptation, we explore the hypothesis that LUCA was temporally, spatially, and environmentally distinct from life's earliest origins in an RNA world. Using this lens, we interpret several molecular biological features as indicating an environmental transition between a cold, radiation-shielded origin of life and a mesophilic, surface-dwelling LUCA. Cellularity provides motility and permits Darwinian evolution by connecting genetic material and its products, and thus establishing heredity and lineage. Considering the importance of compartmentalization and motility, we propose that the early emergence of cellularity is required for environmental dispersal and diversification during these transitions. Early diversification and the emergence of ecology before LUCA could be an important pre-adaptation for life's persistence on a changing planet.

Improving our legacy: Incorporation of adaptive management into state wildlife action plans

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Fontaine, J.J.

2011-01-01

The loss of biodiversity is a mounting concern, but despite numerous attempts there are few large scale conservation efforts that have proven successful in reversing current declines. Given the challenge of biodiversity conservation, there is a need to develop strategic conservation plans that address species declines even with the inherent uncertainty in managing multiple species in complex environments. In 2002, the State Wildlife Grant program was initiated to fulfill this need, and while not explicitly outlined by Congress follows the fundamental premise of adaptive management, 'Learning by doing'. When action is necessary, but basic biological information and an understanding of appropriate management strategies are lacking, adaptive management enables managers to be proactive in spite of uncertainty. However, regardless of the strengths of adaptive management, the development of an effective adaptive management framework is challenging. In a review of 53 State Wildlife Action Plans, I found a keen awareness by planners that adaptive management was an effective method for addressing biodiversity conservation, but the development and incorporation of explicit adaptive management approaches within each plan remained elusive. Only ???25% of the plans included a framework for how adaptive management would be implemented at the project level within their state. There was, however, considerable support across plans for further development and implementation of adaptive management. By furthering the incorporation of adaptive management principles in conservation plans and explicitly outlining the decision making process, states will be poised to meet the pending challenges to biodiversity conservation. ?? 2010 .

Evolution of increased adult longevity in Drosophila melanogaster populations selected for adaptation to larval crowding.

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Shenoi, V N; Ali, S Z; Prasad, N G

2016-02-01

In holometabolous animals such as Drosophila melanogaster, larval crowding can affect a wide range of larval and adult traits. Adults emerging from high larval density cultures have smaller body size and increased mean life span compared to flies emerging from low larval density cultures. Therefore, adaptation to larval crowding could potentially affect adult longevity as a correlated response. We addressed this issue by studying a set of large, outbred populations of D. melanogaster, experimentally evolved for adaptation to larval crowding for 83 generations. We assayed longevity of adult flies from both selected (MCUs) and control populations (MBs) after growing them at different larval densities. We found that MCUs have evolved increased mean longevity compared to MBs at all larval densities. The interaction between selection regime and larval density was not significant, indicating that the density dependence of mean longevity had not evolved in the MCU populations. The increase in longevity in MCUs can be partially attributed to their lower rates of ageing. It is also noteworthy that reaction norm of dry body weight, a trait probably under direct selection in our populations, has indeed evolved in MCU populations. To the best of our knowledge, this is the first report of the evolution of adult longevity as a correlated response of adaptation to larval crowding. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Modeling dynamics of biological and chemical components of aquatic ecosystems

International Nuclear Information System (INIS)

Lassiter, R.R.

1975-05-01

To provide capability to model aquatic ecosystems or their subsystems as needed for particular research goals, a modeling strategy was developed. Submodels of several processes common to aquatic ecosystems were developed or adapted from previously existing ones. Included are submodels for photosynthesis as a function of light and depth, biological growth rates as a function of temperature, dynamic chemical equilibrium, feeding and growth, and various types of losses to biological populations. These submodels may be used as modules in the construction of models of subsystems or ecosystems. A preliminary model for the nitrogen cycle subsystem was developed using the modeling strategy and applicable submodels. (U.S.)

Biological conversion of coal gas to methane

Energy Technology Data Exchange (ETDEWEB)

Barik, S; Vega, J L; Clausen, E C; Gaddy, J L

1988-08-01

Biological conversion of low-Btu coal synthesis gas to higher Btu methane was demonstrated using both pure co-cultures and/or adapted-mixed anaerobic bacteria. Peptostreptococcus productus metabolized coal gas to mainly acetate and CO/sub 2/. The co-cultures containing methanogens converted these products to methane. In mixed culture studies, CH/sub 4/ and small amounts of acetate were produced. Reactor studies using stirred-tank and immobilized cell reactors exhibited excellent potential to convert CO, CO/sub 2/ and H/sub 2/ to methane at higher gas flow rates. Gas retention times ranging from 0.7 to 2 hours and high agitation were required for 90 percent CO conversion in these systems. This paper also illustrates the potential of biological methanation and demonstrates the need for good mass transfer in converting gas phase substrates. 21 refs., 1 fig., 7 tabs.

Polymeric electrochemical element for adaptive networks: Pulse mode

International Nuclear Information System (INIS)

Smerieri, Anteo; Berzina, Tatiana; Erokhin, Victor; Fontana, M. P.

2008-01-01

An electrochemically controlled polymeric heterojunction working as a memristor, i.e., having memory properties, was investigated in pulse mode, mimicking synaptic behavior of signal transmission in biological systems. Influence of parameters such as pulse duration, interval between pulses, and value of potential base level was analyzed. Learning capabilities were shown to be reversible and repeatable for both potentiation and inhibition of signal transmission. The adaptive behavior of the element was investigated and was shown to be more efficient than the dc mode

Deciphering cancer heterogeneity: the biological space

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Stephanie eRoessler

2014-04-01

Full Text Available Most lethal solid tumors including hepatocellular carcinoma (HCC are considered incurable due to extensive heterogeneity in clinical presentation and tumor biology. Tumor heterogeneity may result from different cells of origin, patient ethnicity, etiology, underlying disease and diversity of genomic and epigenomic changes which drive tumor development. Cancer genomic heterogeneity thereby impedes treatment options and poses a significant challenge to cancer management. Studies of the HCC genome have revealed that although various genomic signatures identified in different HCC subgroups share a common prognosis, each carries unique molecular changes which are linked to different sets of cancer hallmarks whose misregulation has been proposed by Hanahan and Weinberg to be essential for tumorigenesis. We hypothesize that these specific sets of cancer hallmarks collectively occupy different tumor biological space representing the misregulation of different biological processes. In principle, a combination of different cancer hallmarks can result in new convergent molecular networks that are unique to each tumor subgroup and represent ideal druggable targets. Due to the ability of the tumor to adapt to external factors such as treatment or changes in the tumor microenvironment, the tumor biological space is elastic. Our ability to identify distinct groups of cancer patients with similar tumor biology who are most likely to respond to a specific therapy would have a significant impact on improving patient outcome. It is currently a challenge to identify a particular hallmark or a newly emerged convergent molecular network for a particular tumor. Thus, it is anticipated that the integration of multiple levels of data such as genomic mutations, somatic copy number aberration, gene expression, proteomics, and metabolomics, may help us grasp the tumor biological space occupied by each individual, leading to improved therapeutic intervention and outcome.

Adaptive Rationality, Adaptive Behavior and Institutions

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Volchik Vyacheslav, V.

2015-12-01

Full Text Available The economic literature focused on understanding decision-making and choice processes reveals a vast collection of approaches to human rationality. Theorists’ attention has moved from absolutely rational, utility-maximizing individuals to boundedly rational and adaptive ones. A number of economists have criticized the concepts of adaptive rationality and adaptive behavior. One of the recent trends in the economic literature is to consider humans irrational. This paper offers an approach which examines adaptive behavior in the context of existing institutions and constantly changing institutional environment. It is assumed that adaptive behavior is a process of evolutionary adjustment to fundamental uncertainty. We emphasize the importance of actors’ engagement in trial and error learning, since if they are involved in this process, they obtain experience and are able to adapt to existing and new institutions. The paper aims at identifying relevant institutions, adaptive mechanisms, informal working rules and practices that influence actors’ behavior in the field of Higher Education in Russia (Rostov Region education services market has been taken as an example. The paper emphasizes the application of qualitative interpretative methods (interviews and discourse analysis in examining actors’ behavior.

Bituminization of biologically harmful wastes

International Nuclear Information System (INIS)

Freund, M.; Magyar, M.; Mozes, G.; Csikos, R.; Kristof, M.; Toth, L.; Hima, G.

1977-01-01

The invention claims the bitumenization of biologically harmful wastes, such as industrial wastes containing radioactive materials. These wastes containing water are transported from sludge basins, this either by gravity or by mechanical stirrino. into a suitably adapted absorption zone or to several parallel zones filled with bitumen heated to 100 to 250 degC. An inert gas is forced into the system foaming the zone contents. The foam phase is decomposed by the action of heat while water is evaporated and condensed. Bitumen containing dry matter of the radioactive wastes is discharged from the bottom part of the absorption zone and stored in a tank. (Kr)

[THE PHYSICAL CHEMICAL, BIOLOGICAL BASICS OF CELLS ABSORPTION OF UNESTERIFIED FATTY ACIDS; ALBUMIN, CAVEOLIN, CLATHRIN AND LIPID-BINDING PROTEINS OF CYTOPLASM (THE LECTURE)].

Science.gov (United States)

Titov, V N; Shoibonov, B B

2016-03-01

From aposition of phylogenetic theory of general pathology, obesity and metabolic syndrome are pathology of fatty cells. However, the first is a pathology of phylogenetically early visceral fatty cells of omentum. They supply with substratum of energy realization of biologic function of trophology, homeostasis, endoecology and adaptation. The visceral fatty cells of omentum have no receptors to insulin and synthesize adaptively insulin and they are not characterized by biologic reaction of proliferation. The obesity is a pathology of late in phylogenesis subcutaneous adpocytes. They are insulin-dependent and supply with substratum of energy realization of one biologic function of locomotion--movement at the expense of constriction of cross-striated miocytes. The adipocytes in terms of adaptation synthesize humoral mediator adponectin and actively implement biologic function of proliferation. Under both aphysiologic conditions increases passive by gradient of concentration, absorption by cells albumin-unbound free fatty acids in unionized form in micellae's composition. The passive aphysiologic absorption of free fatty acids by cells which under intracellular compartmentalization don't oxidize mitochondria results in synthesis, accumulation of triglycerides in cytoplasm of cells which don't implement it physiologically. The aphysiologic absorption of free fatty acids by cells, their etherification in triglyceride, in particular, in phylogenetically late β-cells of islets and either late cardiomyocytes which fatty acids don't synthesize de novo results in development of aphysiologic processes and disorder of function. From position of biology, these cells in vivo are subjected to loss similar to apoptosis. The formation of corpuscles of apoptosis compromise biologic function of endoecology activating biologic reaction of inflammation.

Climate change adaptation for the US National Wildlife Refuge System

Science.gov (United States)

Griffith, Brad; Scott, J. Michael; Adamcik, Robert S.; Ashe, Daniel; Czech, Brian; Fischman, Robert; Gonzalez, Patrick; Lawler, Joshua J.; McGuire, A. David; Pidgorna, Anna

2009-01-01

Since its establishment in 1903, the National Wildlife Refuge System (NWRS) has grown to 635 units and 37 Wetland Management Districts in the United States and its territories. These units provide the seasonal habitats necessary for migratory waterfowl and other species to complete their annual life cycles. Habitat conversion and fragmentation, invasive species, pollution, and competition for water have stressed refuges for decades, but the interaction of climate change with these stressors presents the most recent, pervasive, and complex conservation challenge to the NWRS. Geographic isolation and small unit size compound the challenges of climate change, but a combined emphasis on species that refuges were established to conserve and on maintaining biological integrity, diversity, and environmental health provides the NWRS with substantial latitude to respond. Individual symptoms of climate change can be addressed at the refuge level, but the strategic response requires system-wide planning. A dynamic vision of the NWRS in a changing climate, an explicit national strategic plan to implement that vision, and an assessment of representation, redundancy, size, and total number of units in relation to conservation targets are the first steps toward adaptation. This adaptation must begin immediately and be built on more closely integrated research and management. Rigorous projections of possible futures are required to facilitate adaptation to change. Furthermore, the effective conservation footprint of the NWRS must be increased through land acquisition, creative partnerships, and educational programs in order for the NWRS to meet its legal mandate to maintain the biological integrity, diversity, and environmental health of the system and the species and ecosystems that it supports.

Robust Optimal Adaptive Control Method with Large Adaptive Gain

Science.gov (United States)

Nguyen, Nhan T.

2009-01-01

In the presence of large uncertainties, a control system needs to be able to adapt rapidly to regain performance. Fast adaptation is referred to the implementation of adaptive control with a large adaptive gain to reduce the tracking error rapidly. However, a large adaptive gain can lead to high-frequency oscillations which can adversely affect robustness of an adaptive control law. A new adaptive control modification is presented that can achieve robust adaptation with a large adaptive gain without incurring high-frequency oscillations as with the standard model-reference adaptive control. The modification is based on the minimization of the Y2 norm of the tracking error, which is formulated as an optimal control problem. The optimality condition is used to derive the modification using the gradient method. The optimal control modification results in a stable adaptation and allows a large adaptive gain to be used for better tracking while providing sufficient stability robustness. Simulations were conducted for a damaged generic transport aircraft with both standard adaptive control and the adaptive optimal control modification technique. The results demonstrate the effectiveness of the proposed modification in tracking a reference model while maintaining a sufficient time delay margin.

Adaptive radiation versus 'radiation' and 'explosive diversification': why conceptual distinctions are fundamental to understanding evolution.

Science.gov (United States)

Givnish, Thomas J

2015-07-01

Adaptive radiation is the rise of a diversity of ecological roles and role-specific adaptations within a lineage. Recently, some researchers have begun to use 'adaptive radiation' or 'radiation' as synonymous with 'explosive species diversification'. This essay aims to clarify distinctions between these concepts, and the related ideas of geographic speciation, sexual selection, key innovations, key landscapes and ecological keys. Several examples are given to demonstrate that adaptive radiation and explosive diversification are not the same phenomenon, and that focusing on explosive diversification and the analysis of phylogenetic topology ignores much of the rich biology associated with adaptive radiation, and risks generating confusion about the nature of the evolutionary forces driving species diversification. Some 'radiations' involve bursts of geographic speciation or sexual selection, rather than adaptive diversification; some adaptive radiations have little or no effect on speciation, or even a negative effect. Many classic examples of 'adaptive radiation' appear to involve effects driven partly by geographic speciation, species' dispersal abilities, and the nature of extrinsic dispersal barriers; partly by sexual selection; and partly by adaptive radiation in the classical sense, including the origin of traits and invasion of adaptive zones that result in decreased diversification rates but add to overall diversity. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

Neural Control and Adaptive Neural Forward Models for Insect-like, Energy-Efficient, and Adaptable Locomotion of Walking Machines

Directory of Open Access Journals (Sweden)

Poramate eManoonpong

2013-02-01

Full Text Available Living creatures, like walking animals, have found fascinating solutions for the problem of locomotion control. Their movements show the impression of elegance including versatile, energy-efficient, and adaptable locomotion. During the last few decades, roboticists have tried to imitate such natural properties with artificial legged locomotion systems by using different approaches including machine learning algorithms, classical engineering control techniques, and biologically-inspired control mechanisms. However, their levels of performance are still far from the natural ones. By contrast, animal locomotion mechanisms seem to largely depend not only on central mechanisms (central pattern generators, CPGs and sensory feedback (afferent-based control but also on internal forward models (efference copies. They are used to a different degree in different animals. Generally, CPGs organize basic rhythmic motions which are shaped by sensory feedback while internal models are used for sensory prediction and state estimations. According to this concept, we present here adaptive neural locomotion control consisting of a CPG mechanism with neuromodulation and local leg control mechanisms based on sensory feedback and adaptive neural forward models with efference copies. This neural closed-loop controller enables a walking machine to perform a multitude of different walking patterns including insect-like leg movements and gaits as well as energy-efficient locomotion. In addition, the forward models allow the machine to autonomously adapt its locomotion to deal with a change of terrain, losing of ground contact during stance phase, stepping on or hitting an obstacle during swing phase, leg damage, and even to promote cockroach-like climbing behavior. Thus, the results presented here show that the employed embodied neural closed-loop system can be a powerful way for developing robust and adaptable machines.

Robust Approximation to Adaptive Control by Use of Representative Parameter Sets with Particular Reference to Type 1 Diabetes

Directory of Open Access Journals (Sweden)

Anthony Shannon

2006-04-01

Full Text Available This paper describes an approach to adaptive optimal control in the presence of model parameter calculation difficulties. This has wide application in a variety of biological and biomedical research and clinical problems. To illustrate the techniques, the approach is applied to the development and implementation of a practical adaptive insulin infusion algorithm for use with patients with Type 1 diabetes mellitus.

Generative mechanistic explanation building in undergraduate molecular and cellular biology

Science.gov (United States)

Southard, Katelyn M.; Espindola, Melissa R.; Zaepfel, Samantha D.; Bolger, Molly S.

2017-09-01

When conducting scientific research, experts in molecular and cellular biology (MCB) use specific reasoning strategies to construct mechanistic explanations for the underlying causal features of molecular phenomena. We explored how undergraduate students applied this scientific practice in MCB. Drawing from studies of explanation building among scientists, we created and applied a theoretical framework to explore the strategies students use to construct explanations for 'novel' biological phenomena. Specifically, we explored how students navigated the multi-level nature of complex biological systems using generative mechanistic reasoning. Interviews were conducted with introductory and upper-division biology students at a large public university in the United States. Results of qualitative coding revealed key features of students' explanation building. Students used modular thinking to consider the functional subdivisions of the system, which they 'filled in' to varying degrees with mechanistic elements. They also hypothesised the involvement of mechanistic entities and instantiated abstract schema to adapt their explanations to unfamiliar biological contexts. Finally, we explored the flexible thinking that students used to hypothesise the impact of mutations on multi-leveled biological systems. Results revealed a number of ways that students drew mechanistic connections between molecules, functional modules (sets of molecules with an emergent function), cells, tissues, organisms and populations.

The Colorado Learning Attitudes about Science Survey (CLASS) for Use in Biology

Science.gov (United States)

Semsar, Katharine; Knight, Jennifer K.; Birol, Gülnur; Smith, Michelle K.

2011-01-01

This paper describes a newly adapted instrument for measuring novice-to-expert-like perceptions about biology: the Colorado Learning Attitudes about Science Survey for Biology (CLASS-Bio). Consisting of 31 Likert-scale statements, CLASS-Bio probes a range of perceptions that vary between experts and novices, including enjoyment of the discipline, propensity to make connections to the real world, recognition of conceptual connections underlying knowledge, and problem-solving strategies. CLASS-Bio has been tested for response validity with both undergraduate students and experts (biology PhDs), allowing student responses to be directly compared with a consensus expert response. Use of CLASS-Bio to date suggests that introductory biology courses have the same challenges as introductory physics and chemistry courses: namely, students shift toward more novice-like perceptions following instruction. However, students in upper-division biology courses do not show the same novice-like shifts. CLASS-Bio can also be paired with other assessments to: 1) examine how student perceptions impact learning and conceptual understanding of biology, and 2) assess and evaluate how pedagogical techniques help students develop both expertise in problem solving and an expert-like appreciation of the nature of biology. PMID:21885823

The Colorado Learning Attitudes about Science Survey (CLASS) for use in Biology.

Science.gov (United States)

Semsar, Katharine; Knight, Jennifer K; Birol, Gülnur; Smith, Michelle K

2011-01-01

This paper describes a newly adapted instrument for measuring novice-to-expert-like perceptions about biology: the Colorado Learning Attitudes about Science Survey for Biology (CLASS-Bio). Consisting of 31 Likert-scale statements, CLASS-Bio probes a range of perceptions that vary between experts and novices, including enjoyment of the discipline, propensity to make connections to the real world, recognition of conceptual connections underlying knowledge, and problem-solving strategies. CLASS-Bio has been tested for response validity with both undergraduate students and experts (biology PhDs), allowing student responses to be directly compared with a consensus expert response. Use of CLASS-Bio to date suggests that introductory biology courses have the same challenges as introductory physics and chemistry courses: namely, students shift toward more novice-like perceptions following instruction. However, students in upper-division biology courses do not show the same novice-like shifts. CLASS-Bio can also be paired with other assessments to: 1) examine how student perceptions impact learning and conceptual understanding of biology, and 2) assess and evaluate how pedagogical techniques help students develop both expertise in problem solving and an expert-like appreciation of the nature of biology.

Adaptive developmental delay in Chagas disease vectors: an evolutionary ecology approach.

Directory of Open Access Journals (Sweden)

Frédéric Menu

2010-05-01

Full Text Available The developmental time of vector insects is important in population dynamics, evolutionary biology, epidemiology and in their responses to global climatic change. In the triatomines (Triatominae, Reduviidae, vectors of Chagas disease, evolutionary ecology concepts, which may allow for a better understanding of their biology, have not been applied. Despite delay in the molting in some individuals observed in triatomines, no effort was made to explain this variability.We applied four methods: (1 an e-mail survey sent to 30 researchers with experience in triatomines, (2 a statistical description of the developmental time of eleven triatomine species, (3 a relationship between development time pattern and climatic inter-annual variability, (4 a mathematical optimization model of evolution of developmental delay (diapause.85.6% of responses informed on prolonged developmental times in 5(th instar nymphs, with 20 species identified with remarkable developmental delays. The developmental time analysis showed some degree of bi-modal pattern of the development time of the 5(th instars in nine out of eleven species but no trend between development time pattern and climatic inter-annual variability was observed. Our optimization model predicts that the developmental delays could be due to an adaptive risk-spreading diapause strategy, only if survival throughout the diapause period and the probability of random occurrence of "bad" environmental conditions are sufficiently high.Developmental delay may not be a simple non-adaptive phenotypic plasticity in development time, and could be a form of adaptive diapause associated to a physiological mechanism related to the postponement of the initiation of reproduction, as an adaptation to environmental stochasticity through a spreading of risk (bet-hedging strategy. We identify a series of parameters that can be measured in the field and laboratory to test this hypothesis. The importance of these findings is

Synthetic Biology and Human Health: Potential Applications for Spaceflight

Science.gov (United States)

Karouia, Fathi; Carr, Christopher; Cai, Yizhi; Chen, Y.; Grenon, Marlene; Larios-Sanz, Maia; Jones, Jeffrey A.; Santos, Orlando

2011-01-01

Human space travelers experience a unique environment that affects homeostasis and physiologic adaptation. Spaceflight-related changes have been reported in the musculo-skeletal, cardiovascular, neurovestibular, endocrine, and immune systems. The spacecraft environment further subjects the traveler to noise and gravitational forces, as well as airborne chemical, microbiological contaminants, and radiation exposure. As humans prepare for longer duration missions effective countermeasures must be developed, verified, and implemented to ensure mission success. Over the past ten years, synthetic biology has opened new avenues for research and development in areas such as biological control, biomaterials, sustainable energy production, bioremediation, and biomedical therapies. The latter in particular is of great interest to the implementation of long-duration human spaceflight capabilities. This article discusses the effects of spaceflight on humans, and reviews current capabilities and potential needs associated with the health of the astronauts where synthetic biology could play an important role in the pursuit of space exploration.

Red swamp crayfish: biology, ecology and invasion - an overview

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Tainã Gonçalves Loureiro

Full Text Available ABSTRACTAlien species have been transported and traded by humans for many centuries. However, with the era of globalization, biological invasions have reached notable magnitudes. Currently, introduction of alien species is one of the major threats to biodiversity and ecosystem functioning. The North American crayfish Procambarus clarkii is one of the most widely introduced freshwater species in the world, especially due to its high economic importance. It is responsible for great modifications in invaded environments causing irreparable ecological and economic damages. Its impressive ability to successfully colonize a wide range of environments is a consequence of its behavioural and biological characteristics that can adapt to features of the invaded location, conferring to this species a notable ecological plasticity. This review summarizes the available information regarding P. clarkii's biology and invasive dynamics around the world in order to contribute to the understanding of the threats posed by its establishment, as well as to support management and impact mitigation efforts.

Learning to Adapt. Organisational Adaptation to Climate Change Impacts

International Nuclear Information System (INIS)

Berkhout, F.; Hertin, J.; Gann, D.M.

2006-01-01

Analysis of human adaptation to climate change should be based on realistic models of adaptive behaviour at the level of organisations and individuals. The paper sets out a framework for analysing adaptation to the direct and indirect impacts of climate change in business organisations with new evidence presented from empirical research into adaptation in nine case-study companies. It argues that adaptation to climate change has many similarities with processes of organisational learning. The paper suggests that business organisations face a number of obstacles in learning how to adapt to climate change impacts, especially in relation to the weakness and ambiguity of signals about climate change and the uncertainty about benefits flowing from adaptation measures. Organisations rarely adapt 'autonomously', since their adaptive behaviour is influenced by policy and market conditions, and draws on resources external to the organisation. The paper identifies four adaptation strategies that pattern organisational adaptive behaviour

Enhancing the effectiveness of biological control programs of invasive species through a more comprehensive pest management approach.

Science.gov (United States)

DiTomaso, Joseph M; Van Steenwyk, Robert A; Nowierski, Robert M; Vollmer, Jennifer L; Lane, Eric; Chilton, Earl; Burch, Patrick L; Cowan, Phil E; Zimmerman, Kenneth; Dionigi, Christopher P

2017-01-01

Invasive species are one of the greatest economic and ecological threats to agriculture and natural areas in the US and the world. Among the available management tools, biological control provides one of the most economical and long-term effective strategies for managing widespread and damaging invasive species populations of nearly all taxa. However, integrating biological control programs in a more complete integrated pest management approach that utilizes increased information and communication, post-release monitoring, adaptive management practices, long-term stewardship strategies, and new and innovative ecological and genetic technologies can greatly improve the effectiveness of biological control. In addition, expanding partnerships among relevant national, regional, and local agencies, as well as academic scientists and land managers, offers far greater opportunities for long-term success in the suppression of established invasive species. In this paper we direct our recommendations to federal agencies that oversee, fund, conduct research, and develop classical biological control programs for invasive species. By incorporating these recommendations into adaptive management strategies, private and public land managers will have far greater opportunities for long-term success in suppression of established invasive species. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Analysis of Cell Biomechanics Response to Gravity:A Fluids for Biology Study Utilizing NASA Glenns Zero Gravity Research Facility

Science.gov (United States)

Bomani, Bilal M. M.; Kassemi, Mohammad; Neumann, Eric S.

2016-01-01

It remains unclear how biological cells sense and respond to gravitational forces. Leading scientists state that a large gap exists in the understanding of physiological and molecular adaptation that occurs as biology enters the spaceflight realm. We are seeking a method to fully understand how cells sense microgravity/gravity and what triggers their response.

Ecological adaptation of diverse honey bee (Apis mellifera) populations.

Science.gov (United States)

Parker, Robert; Melathopoulos, Andony P; White, Rick; Pernal, Stephen F; Guarna, M Marta; Foster, Leonard J

2010-06-15

Honey bees are complex eusocial insects that provide a critical contribution to human agricultural food production. Their natural migration has selected for traits that increase fitness within geographical areas, but in parallel their domestication has selected for traits that enhance productivity and survival under local conditions. Elucidating the biochemical mechanisms of these local adaptive processes is a key goal of evolutionary biology. Proteomics provides tools unique among the major 'omics disciplines for identifying the mechanisms employed by an organism in adapting to environmental challenges. Through proteome profiling of adult honey bee midgut from geographically dispersed, domesticated populations combined with multiple parallel statistical treatments, the data presented here suggest some of the major cellular processes involved in adapting to different climates. These findings provide insight into the molecular underpinnings that may confer an advantage to honey bee populations. Significantly, the major energy-producing pathways of the mitochondria, the organelle most closely involved in heat production, were consistently higher in bees that had adapted to colder climates. In opposition, up-regulation of protein metabolism capacity, from biosynthesis to degradation, had been selected for in bees from warmer climates. Overall, our results present a proteomic interpretation of expression polymorphisms between honey bee ecotypes and provide insight into molecular aspects of local adaptation or selection with consequences for honey bee management and breeding. The implications of our findings extend beyond apiculture as they underscore the need to consider the interdependence of animal populations and their agro-ecological context.

Adaptive learning by extremal dynamics and negative feedback

International Nuclear Information System (INIS)

Bak, Per; Chialvo, Dante R.

2001-01-01

We describe a mechanism for biological learning and adaptation based on two simple principles: (i) Neuronal activity propagates only through the network's strongest synaptic connections (extremal dynamics), and (ii) the strengths of active synapses are reduced if mistakes are made, otherwise no changes occur (negative feedback). The balancing of those two tendencies typically shapes a synaptic landscape with configurations which are barely stable, and therefore highly flexible. This allows for swift adaptation to new situations. Recollection of past successes is achieved by punishing synapses which have once participated in activity associated with successful outputs much less than neurons that have never been successful. Despite its simplicity, the model can readily learn to solve complicated nonlinear tasks, even in the presence of noise. In particular, the learning time for the benchmark parity problem scales algebraically with the problem size N, with an exponent k∼1.4

Monitoring biological diversity: strategies, tools, limitations, and challenges

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Beever, E.A.

2006-01-01

Monitoring is an assessment of the spatial and temporal variability in one or more ecosystem properties, and is an essential component of adaptive management. Monitoring can help determine whether mandated environmental standards are being met and can provide an early-warning system of ecological change. Development of a strategy for monitoring biological diversity will likely be most successful when based upon clearly articulated goals and objectives and may be enhanced by including several key steps in the process. Ideally, monitoring of biological diversity will measure not only composition, but also structure and function at the spatial and temporal scales of interest. Although biodiversity monitoring has several key limitations as well as numerous theoretical and practical challenges, many tools and strategies are available to address or overcome such challenges; I summarize several of these. Due to the diversity of spatio-temporal scales and comprehensiveness encompassed by existing definitions of biological diversity, an effective monitoring design will reflect the desired sampling domain of interest and its key stressors, available funding, legal requirements, and organizational goals.

A Powerful Toolkit for Synthetic Biology: Over 3.8 Billion Years of Evolution

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Rothschild, Lynn J.

2010-01-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested

Adaptive optics in spinning disk microscopy: improved contrast and brightness by a simple and fast method.

Science.gov (United States)

Fraisier, V; Clouvel, G; Jasaitis, A; Dimitrov, A; Piolot, T; Salamero, J

2015-09-01

Multiconfocal microscopy gives a good compromise between fast imaging and reasonable resolution. However, the low intensity of live fluorescent emitters is a major limitation to this technique. Aberrations induced by the optical setup, especially the mismatch of the refractive index and the biological sample itself, distort the point spread function and further reduce the amount of detected photons. Altogether, this leads to impaired image quality, preventing accurate analysis of molecular processes in biological samples and imaging deep in the sample. The amount of detected fluorescence can be improved with adaptive optics. Here, we used a compact adaptive optics module (adaptive optics box for sectioning optical microscopy), which was specifically designed for spinning disk confocal microscopy. The module overcomes undesired anomalies by correcting for most of the aberrations in confocal imaging. Existing aberration detection methods require prior illumination, which bleaches the sample. To avoid multiple exposures of the sample, we established an experimental model describing the depth dependence of major aberrations. This model allows us to correct for those aberrations when performing a z-stack, gradually increasing the amplitude of the correction with depth. It does not require illumination of the sample for aberration detection, thus minimizing photobleaching and phototoxicity. With this model, we improved both signal-to-background ratio and image contrast. Here, we present comparative studies on a variety of biological samples. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

From biological and social network metaphors to coupled bio-social wireless networks

Science.gov (United States)

Barrett, Christopher L.; Eubank, Stephen; Anil Kumar, V.S.; Marathe, Madhav V.

2010-01-01

Biological and social analogies have been long applied to complex systems. Inspiration has been drawn from biological solutions to solve problems in engineering products and systems, ranging from Velcro to camouflage to robotics to adaptive and learning computing methods. In this paper, we present an overview of recent advances in understanding biological systems as networks and use this understanding to design and analyse wireless communication networks. We expand on two applications, namely cognitive sensing and control and wireless epidemiology. We discuss how our work in these two applications is motivated by biological metaphors. We believe that recent advances in computing and communications coupled with advances in health and social sciences raise the possibility of studying coupled bio-social communication networks. We argue that we can better utilise the advances in our understanding of one class of networks to better our understanding of the other. PMID:21643462

Robustness: confronting lessons from physics and biology.

Science.gov (United States)

Lesne, Annick

2008-11-01

The term robustness is encountered in very different scientific fields, from engineering and control theory to dynamical systems to biology. The main question addressed herein is whether the notion of robustness and its correlates (stability, resilience, self-organisation) developed in physics are relevant to biology, or whether specific extensions and novel frameworks are required to account for the robustness properties of living systems. To clarify this issue, the different meanings covered by this unique term are discussed; it is argued that they crucially depend on the kind of perturbations that a robust system should by definition withstand. Possible mechanisms underlying robust behaviours are examined, either encountered in all natural systems (symmetries, conservation laws, dynamic stability) or specific to biological systems (feedbacks and regulatory networks). Special attention is devoted to the (sometimes counterintuitive) interrelations between robustness and noise. A distinction between dynamic selection and natural selection in the establishment of a robust behaviour is underlined. It is finally argued that nested notions of robustness, relevant to different time scales and different levels of organisation, allow one to reconcile the seemingly contradictory requirements for robustness and adaptability in living systems.

Aspects of the political economy of development and synthetic biology.

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Wellhausen, Rachel; Mukunda, Gautam

2009-12-01

What implications might synthetic biology's potential as a wholly new method of production have for the world economy, particularly developing countries? Theories of political economy predict that synthetic biology can shift terms of trade and displace producers in developing countries. Governments, however, retain the ability to mitigate negative changes through social safety nets and to foster adaptation to some changes through research, education and investment. We consider the effects the synthetic production of otherwise naturally derived molecules are likely to have on trade and investment, particularly in developing countries. Both rubber in Malaysia and indigo dyes in India provide historical examples of natural molecules that faced market dislocations from synthetic competitors. Natural rubber was able to maintain significant market share, while natural indigo vanished from world markets. These cases demonstrate the two extremes of the impact synthetic biology might have on naturally derived products. If developing countries can cushion the pain of technological changes by providing producers support as they retool or exit, the harmful effects of synthetic biology can be mitigated while its benefits can still be captured.

Phytomonas: trypanosomatids adapted to plant environments.

Directory of Open Access Journals (Sweden)

Eleanor Jaskowska

2015-01-01

Full Text Available Over 100 years after trypanosomatids were first discovered in plant tissues, Phytomonas parasites have now been isolated across the globe from members of 24 different plant families. Most identified species have not been associated with any plant pathology and to date only two species are definitively known to cause plant disease. These diseases (wilt of palm and coffee phloem necrosis are problematic in areas of South America where they threaten the economies of developing countries. In contrast to their mammalian infective relatives, our knowledge of the biology of Phytomonas parasites and how they interact with their plant hosts is limited. This review draws together a century of research into plant trypanosomatids, from the first isolations and experimental infections to the recent publication of the first Phytomonas genomes. The availability of genomic data for these plant parasites opens a new avenue for comparative investigations into trypanosomatid biology and provides fresh insight into how this important group of parasites have adapted to survive in a spectrum of hosts from crocodiles to coconuts.

Adapting bioinformatics curricula for big data.

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Greene, Anna C; Giffin, Kristine A; Greene, Casey S; Moore, Jason H

2016-01-01

Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. © The Author 2015. Published by Oxford University Press.

Creating biological nanomaterials using synthetic biology

International Nuclear Information System (INIS)

Rice, MaryJoe K; Ruder, Warren C

2014-01-01

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. (review)

Creating biological nanomaterials using synthetic biology.

Science.gov (United States)

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.

Biological Influence of Deuterium on Procariotic and Eukaryotic Cells

OpenAIRE

Oleg Mosin; Ignat Ignatov

2014-01-01

Biologic influence of deuterium (D) on cells of various taxonomic groups of prokaryotic and eukaryotic microorganisms realizing methylotrophic, chemoheterotrophic, photo-organotrophic, and photosynthetic ways of assimilation of carbon substrates are investigated at growth on media with heavy water (D2О). The method of step by step adaptation technique of cells to D2О was developed, consisting in plating of cells on 2 % agarose nutrient media containing increasing gradient of concentration of ...

Brain disorders and the biological role of music.

Science.gov (United States)

Clark, Camilla N; Downey, Laura E; Warren, Jason D

2015-03-01

Despite its evident universality and high social value, the ultimate biological role of music and its connection to brain disorders remain poorly understood. Recent findings from basic neuroscience have shed fresh light on these old problems. New insights provided by clinical neuroscience concerning the effects of brain disorders promise to be particularly valuable in uncovering the underlying cognitive and neural architecture of music and for assessing candidate accounts of the biological role of music. Here we advance a new model of the biological role of music in human evolution and the link to brain disorders, drawing on diverse lines of evidence derived from comparative ethology, cognitive neuropsychology and neuroimaging studies in the normal and the disordered brain. We propose that music evolved from the call signals of our hominid ancestors as a means mentally to rehearse and predict potentially costly, affectively laden social routines in surrogate, coded, low-cost form: essentially, a mechanism for transforming emotional mental states efficiently and adaptively into social signals. This biological role of music has its legacy today in the disordered processing of music and mental states that characterizes certain developmental and acquired clinical syndromes of brain network disintegration. © The Author (2014). Published by Oxford University Press.

Evolution of egg coats: linking molecular biology and ecology.

Science.gov (United States)

Shu, Longfei; Suter, Marc J-F; Räsänen, Katja

2015-08-01

One central goal of evolutionary biology is to explain how biological diversity emerges and is maintained in nature. Given the complexity of the phenotype and the multifaceted nature of inheritance, modern evolutionary ecological studies rely heavily on the use of molecular tools. Here, we show how molecular tools help to gain insight into the role of egg coats (i.e. the extracellular structures surrounding eggs and embryos) in evolutionary diversification. Egg coats are maternally derived structures that have many biological functions from mediating fertilization to protecting the embryo from environmental hazards. They show great molecular, structural and functional diversity across species, but intraspecific variability and the role of ecology in egg coat evolution have largely been overlooked. Given that much of the variation that influences egg coat function is ultimately determined by their molecular phenotype, cutting-edge molecular tools (e.g. proteomics, glycomics and transcriptomics), combined with functional assays, are needed for rigorous inferences on their evolutionary ecology. Here, we identify key research areas and highlight emerging molecular techniques that can increase our understanding of the role of egg coats in the evolution of biological diversity, from adaptation to speciation. © 2015 John Wiley & Sons Ltd.

Adaptation, plant evolution, and the fossil record

Science.gov (United States)

Knoll, A. H.; Niklas, K. J.

1987-01-01

The importance of adaptation in determining patterns of evolution has become an important focus of debate in evolutionary biology. As it pertains to paleobotany, the issue is whether or not adaptive evolution mediated by natural selection is sufficient to explain the stratigraphic distributions of taxa and character states observed in the plant fossil record. One means of addressing this question is the functional evaluation of stratigraphic series of plant organs set in the context of paleoenvironmental change and temporal patterns of floral composition within environments. For certain organ systems, quantitative estimates of biophysical performance can be made on the basis of structures preserved in the fossil record. Performance estimates for plants separated in time or space can be compared directly. Implicit in different hypotheses of the forces that shape the evolutionary record (e.g. adaptation, mass extinction, rapid environmental change, chance) are predictions about stratigraphic and paleoenvironmental trends in the efficacy of functional performance. Existing data suggest that following the evolution of a significant structural innovation, adaptation for improved functional performance can be a major determinant of evolutionary changes in plants; however, there are structural and development limits to functional improvement, and once these are reached, the structure in question may no longer figure strongly in selection until and unless a new innovation evolves. The Silurian-Devonian paleobotanical record is consistent with the hypothesis that the succession of lowland floodplain dominants preserved in the fossil record of this interval was determined principally by the repeated evolution of new taxa that rose to ecological importance because of competitive advantages conferred by improved biophysical performance. This does not seem to be equally true for Carboniferous-Jurassic dominants of swamp and lowland floodplain environments. In these cases

Adaptive value of sex in microbial pathogens.

Science.gov (United States)

Michod, Richard E; Bernstein, Harris; Nedelcu, Aurora M

2008-05-01

Explaining the adaptive value of sex is one of the great outstanding problems in biology. The challenge comes from the difficulty in identifying the benefits provided by sex, which must outweigh the substantial costs of sex. Here, we consider the adaptive value of sex in viruses, bacteria and fungi, and particularly the information available on the adaptive role of sex in pathogenic microorganisms. Our general theme is that the varied aspects of sex in pathogens illustrate the varied issues surrounding the evolution of sex generally. These include, the benefits of sex (in the short- and long-term), as well as the costs of sex (both to the host and to the pathogen). For the benefits of sex (that is, its adaptive value), we consider three hypotheses: (i) sex provides for effective and efficient recombinational repair of DNA damages, (ii) sex provides DNA for food, and (iii) sex produces variation and reduces genetic associations among alleles under selection. Although the evolution of sex in microbial pathogens illustrates these general issues, our paper is not a general review of theories for the evolution of sex in all organisms. Rather, we focus on the adaptive value of sex in microbial pathogens and conclude that in terms of short-term benefits, the DNA repair hypothesis has the most support and is the most generally applicable hypothesis in this group. In particular, recombinational repair of DNA damages may substantially benefit pathogens when challenged by the oxidative defenses of the host. However, in the long-term, sex may help get rid of mutations, increase the rate of adaptation of the population, and, in pathogens, may infrequently create new infective strains. An additional general issue about sex illustrated by pathogens is that some of the most interesting consequences of sex are not necessarily the reasons for which sex evolved. For example, antibiotic resistance may be transferred by bacterial sex, but this transfer is probably not the reason sex

Adaptive Responses to Thermal Stress in Mammals

Directory of Open Access Journals (Sweden)

Yasser Lenis Sanin

2015-12-01

Full Text Available The environment animals have to cope with is a combination of natural factors such as temperature. Extreme changes in these factors can alter homeostasis, which can lead to thermal stress. This stress can be due to either high temperatures or low temperatures. Energy transference for thermoregulation in homoeothermic animals occurs through several mechanisms: conduction, convection, radiation and evaporation. When animals are subjected to thermal stress, physiological mechanisms are activated which may include endocrine, neuroendocrine and behavioral responses. Activation of the neuroendocrine system affects the secretion of hormones and neurotransmitters which act collectively as response mechanisms that allow them to adapt to stress. Mechanisms which have developed through evolution to allow animals to adapt to high environmental temperatures and to achieve thermo tolerance include physiological and physical changes in order to reduce food intake and metabolic heat production, to increase surface area of skin to dissipate heat, to increase blood flow to take heat from the body core to the skin and extremities to dissipate the heat, to increase numbers and activity of sweat glands, panting, water intake and color adaptation of integument system to reflect heat. Chronic exposure to thermal stress can cause disease, reduce growth, decrease productive and reproductive performance and, in extreme cases, lead to death. This paper aims to briefly explain the physical and physiological responses of mammals to thermal stress, like a tool for biological environment adaptation, emphasizing knowledge gaps and offering some recommendations to stress control for the animal production system.

Noise-exploitation and adaptation in neuromorphic sensors

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Hindo, Thamira; Chakrabartty, Shantanu

2012-04-01

Even though current micro-nano fabrication technology has reached integration levels where ultra-sensitive sensors can be fabricated, the sensing performance (resolution per joule) of synthetic systems are still orders of magnitude inferior to those observed in neurobiology. For example, the filiform hairs in crickets operate at fundamental limits of noise; auditory sensors in a parasitoid fly can overcome fundamental limitations to precisely localize ultra-faint acoustic signatures. Even though many of these biological marvels have served as inspiration for different types of neuromorphic sensors, the main focus these designs have been to faithfully replicate the biological functionalities, without considering the constructive role of "noise". In man-made sensors device and sensor noise are typically considered as a nuisance, where as in neurobiology "noise" has been shown to be a computational aid that enables biology to sense and operate at fundamental limits of energy efficiency and performance. In this paper, we describe some of the important noise-exploitation and adaptation principles observed in neurobiology and how they can be systematically used for designing neuromorphic sensors. Our focus will be on two types of noise-exploitation principles, namely, (a) stochastic resonance; and (b) noise-shaping, which are unified within our previously reported framework called Σ▵ learning. As a case-study, we describe the application of Σ▵ learning for the design of a miniature acoustic source localizer whose performance matches that of its biological counterpart(Ormia Ochracea).

Driving Meaningful Adaptation Action through an Adaptation Market Mechanism

Energy Technology Data Exchange (ETDEWEB)

Butzengeiger-Geyer, Sonja; Koehler, Michel; Michaelowa, Axel

2011-07-01

Approaches and criteria for allocating adaptation funds vary significantly among current sources - UN-backed funds and bilateral cooperation - and to some extent lack transparency and consistency. Such funding risks being spent in a haphazard way that repeats many of the mistakes made in development assistance over the past decades. An Adaptation Market Mechanism (AMM) could contribute to efficient allocation of adaptation funds, promote adaptation activities by private and public actors through additional financial incentives, and raise additional and reliable adaptation money. This would help to avoid future public criticism of the effectiveness and efficiency of spending adaptation funding.The proposed AMM would specify mandatory adaptation targets, on international, regional or domestic level. Participants who achieve their targets either by generating adaptation units or by buying them in the market would incentivize private, commercial and institutional actors to develop adaptation projects that create verified adaptation units. A universally accepted and verifiable trading unit applicable to all types of adaptation activities would help to maximize the cost reduction potential for the AMM. We suggest applying net present value (NPV) for property saved; Disability Adjusted Life Years Saved (DALYS) for health benefits; and potentially a separate unit to consider the environmental benefits of an adaptation activity.(Author)

Nonlinear adaptive optimization of biomass productivity in continuous bioreactors

Energy Technology Data Exchange (ETDEWEB)

Sauvaire, P; Mellichamp, D A; Agrawal, P [California Univ., Santa Barbara, CA (United States). Dept. of Chemical and Nuclear Engineering

1991-11-01

A novel on-line adaptive optimization algorithm is developed and applied to continuous biological reactors. The algorithm makes use of a simple nonlinear estimation model that relates either the cell-mass productivity or the cell-mass concentration to the dilution rate. On-line estimation is used to recursively identify the parameters in the nonlinear process model and to periodically calculate and steer the bioreactor to the dilution rate that yields optimum cell-mass productivity. Thus, the algorithm does not require an accurate process model, locates the optimum dilution rate online, and maintains the bioreactors at this optimum condition at all times. The features of the proposed new algorithm are compared with those of other adaptive optimization techniques presented in the literature. A detailed simulation study using three different microbial system models was conducted to illustrate the performance of the optimization algorithms. (orig.).

Paradigms for adaptive statistical information designs: practical experiences and strategies.

Science.gov (United States)

Wang, Sue-Jane; Hung, H M James; O'Neill, Robert

2012-11-10

In the last decade or so, interest in adaptive design clinical trials has gradually been directed towards their use in regulatory submissions by pharmaceutical drug sponsors to evaluate investigational new drugs. Methodological advances of adaptive designs are abundant in the statistical literature since the 1970s. The adaptive design paradigm has been enthusiastically perceived to increase the efficiency and to be more cost-effective than the fixed design paradigm for drug development. Much interest in adaptive designs is in those studies with two-stages, where stage 1 is exploratory and stage 2 depends upon stage 1 results, but where the data of both stages will be combined to yield statistical evidence for use as that of a pivotal registration trial. It was not until the recent release of the US Food and Drug Administration Draft Guidance for Industry on Adaptive Design Clinical Trials for Drugs and Biologics (2010) that the boundaries of flexibility for adaptive designs were specifically considered for regulatory purposes, including what are exploratory goals, and what are the goals of adequate and well-controlled (A&WC) trials (2002). The guidance carefully described these distinctions in an attempt to minimize the confusion between the goals of preliminary learning phases of drug development, which are inherently substantially uncertain, and the definitive inference-based phases of drug development. In this paper, in addition to discussing some aspects of adaptive designs in a confirmatory study setting, we underscore the value of adaptive designs when used in exploratory trials to improve planning of subsequent A&WC trials. One type of adaptation that is receiving attention is the re-estimation of the sample size during the course of the trial. We refer to this type of adaptation as an adaptive statistical information design. Specifically, a case example is used to illustrate how challenging it is to plan a confirmatory adaptive statistical information

Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation

Directory of Open Access Journals (Sweden)

Hawdon John

2010-05-01

Full Text Available Abstract Background Hookworm infection is one of the most important neglected diseases in developing countries, with approximately 1 billion people infected worldwide. To better understand hookworm biology and nematode parasitism, the present study generated a near complete transcriptome of the canine hookworm Ancylostoma caninum to a very high coverage using high throughput technology, and compared it to those of the free-living nematode Caenorhabditis elegans and the parasite Brugia malayi. Results The generated transcripts from four developmental stages, infective L3, serum stimulated L3, adult male and adult female, covered 93% of the A. caninum transcriptome. The broad diversity among nematode transcriptomes was confirmed, and an impact of parasitic adaptation on transcriptome diversity was inferred. Intra-population analysis showed that A. caninum has higher coding sequence diversity than humans. Examining the developmental expression profiles of A. caninum revealed major transitions in gene expression from larval stages to adult. Adult males expressed the highest number of selectively expressed genes, but adult female expressed the highest number of selective parasitism-related genes. Genes related to parasitism adaptation and A. caninum specific genes exhibited more expression selectivity while those conserved in nematodes tend to be consistently expressed. Parasitism related genes were expressed more selectively in adult male and female worms. The comprehensive analysis of digital expression profiles along with transcriptome comparisons enabled identification of a set of parasitism genes encoding secretory proteins in animal parasitic nematode. Conclusions This study validated the usage of deep sequencing for gene expression profiling. Parasitic adaptation of the canine hookworm is related to its diversity and developmental dynamics. This comprehensive comparative genomic and expression study substantially improves our understanding of

Biological effects of low-dose ionizing radiation exposure; Biologische Wirkungen niedriger Dosen ionisierender Strahlung

Energy Technology Data Exchange (ETDEWEB)

Reinoehl-Kompa, Sabine; Baldauf, Daniela; Heller, Horst (comps.)

2009-07-01

The report on the meeting of the Strahlenschutzkommission 2007 concerning biological effects of low-dose ionizing radiation exposure includes the following contributions: Adaptive response. The importance of DNA damage mechanisms for the biological efficiency of low-energy photons. Radiation effects in mammography: the relative biological radiation effects of low-energy photons. Radiation-induced cataracts. Carcinomas following prenatal radiation exposure. Intercellular apoptosis induction and low-dose irradiation: possible consequences for the oncogenesis control. Mechanistic models for the carcinogenesis with radiation-induced cell inactivation: application to all solid tumors in the Japanese atomic bomb survivors. Microarrays at low radiation doses. Mouse models for the analysis of biological effects of low-dose ionizing radiation. The bystander effect: observations, mechanisms and implications. Lung carcinoma risk of Majak workers - modeling of carcinogenesis and the bystander effect. Microbeam studies in radiation biology - an overview. Carcinogenesis models with radiation-induced genomic instability. Application to two epidemiological cohorts.

A Checklist for Successful Quantitative Live Cell Imaging in Systems Biology

Science.gov (United States)

Sung, Myong-Hee

2013-01-01

Mathematical modeling of signaling and gene regulatory networks has provided unique insights about systems behaviors for many cell biological problems of medical importance. Quantitative single cell monitoring has a crucial role in advancing systems modeling of molecular networks. However, due to the multidisciplinary techniques that are necessary for adaptation of such systems biology approaches, dissemination to a wide research community has been relatively slow. In this essay, I focus on some technical aspects that are often under-appreciated, yet critical in harnessing live cell imaging methods to achieve single-cell-level understanding and quantitative modeling of molecular networks. The importance of these technical considerations will be elaborated with examples of successes and shortcomings. Future efforts will benefit by avoiding some pitfalls and by utilizing the lessons collectively learned from recent applications of imaging in systems biology. PMID:24709701

Designing Networks that are Capable of Self-Healing and Adapting

Science.gov (United States)

2017-04-01

from statistical mechanics, combinatorics, boolean networks, and numerical simulations, and inspired by design principles from biological networks, we... principles for self-healing networks, and applications, and construct an all-possible-paths model for network adaptation. 2015-11-16 UNIT CONVERSION...kg m –3 ) pound-force (lbf avoirdupois) 4.448 222 newton (N) Energy/Work/Power electron volt (eV) 1.602 177 × 10 –19 joule (J) erg 1 × 10 –7

Progressive nature of heart failure and systems biology

Directory of Open Access Journals (Sweden)

George E. Louridas

2015-01-01

Full Text Available The progressive nature of heart failure (HF is the predominant cause for the clinical course that the HF syndrome is taking. Systems biology methodology is of the utmost importance to explain and comprehend the built-in mechanisms of adverse clinical progression. Various heart diseases produce myocardial damage with subsequent left ventricular remodeling which is the principal underlying pathophysiological mechanism for the clinical progression of HF. The self-organized positive feedback stabilization mechanisms of left ventricular remodeling, adrenergic stimulation and activation of the renin-angiotensin-aldosterone system and natriuretic peptide systems, are hierarchical adaptive processes. These adaptive processes are responsible for further left ventricular remodeling with subsequent clinical deterioration and for the emergence of clinical phenotypes. These mechanisms are counteracted with angiotensin-converting enzyme inhibitors, angiotensin receptor blockers and β-blockers in an attempt to improve the adverse clinical phenomena of HF progression in a new but clinically worse stabilization level. In this review our intention is to underline the progressive nature of the HF syndrome and to demonstrate the significance of ventricular remodeling and the role of self-organized positive feedback adaptive processes.

Fundamentals of adaptive signal processing

CERN Document Server

Uncini, Aurelio

2015-01-01

This book is an accessible guide to adaptive signal processing methods that equips the reader with advanced theoretical and practical tools for the study and development of circuit structures and provides robust algorithms relevant to a wide variety of application scenarios. Examples include multimodal and multimedia communications, the biological and biomedical fields, economic models, environmental sciences, acoustics, telecommunications, remote sensing, monitoring, and, in general, the modeling and prediction of complex physical phenomena. The reader will learn not only how to design and implement the algorithms but also how to evaluate their performance for specific applications utilizing the tools provided. While using a simple mathematical language, the employed approach is very rigorous. The text will be of value both for research purposes and for courses of study.

Mothers' psychological adaptation to Duchenne/Becker muscular dystrophy

Science.gov (United States)

Peay, Holly L; Meiser, Bettina; Kinnett, Kathleen; Furlong, Pat; Porter, Kathryn; Tibben, Aad

2016-01-01

Duchenne and Becker muscular dystrophy (DBMD) cause significant emotional and care-related burden on caregivers, but no studies have evaluated predictors of positive caregiver outcomes, including disorder-specific psychological adaptation. Using a community-engaged approach focused on supporting mothers in positive aspects of caregiving, this prospective study aims to assess (i) the association between child's baseline functional status and mothers' illness perceptions, resilience, and coping self-efficacy; and (ii) predictors of mothers' psychological adaptation to caring for a child with DBMD. Biological mothers with at least one living child with DBMD completed a baseline survey (n=205) with 1-year (n=147) and 2-year (n=144) follow-up surveys. Worse child's baseline function was associated not only with increased caregiver burden and reduced maternal resilience, but also with perception of positive disease impact on the family. At two follow-ups, increased psychological adaptation to DBMD was predicted by resilience (β=0.264, P=0.001) and perceived positive impact (β=0.310, P<0.001), controlling for mother's age (β=−0.305, P<0.001) and income (β=−0.088, P=0.245). Child's functional status and caregiver burden of DBMD did not predict DBMD-specific adaptation. Though clinicians caring for families with DBMD should anticipate increased caregiver burden as the disorder progresses, interventions focused on caregiver burden are not expected to influence mothers' psychosocial adaptation. Efforts to improve mothers' well-being should focus on fostering mothers' resilience and enhancing perceptions of positive disease impact (benefit finding). Results suggest that psychosocial interventions can highlight strengths and well-being rather than burden and deficit. PMID:26306645

Adapting Activity and Participation (The ADAPT intervention program)

DEFF Research Database (Denmark)

von Bülow, Cecilie

Præsentation af et ergoterapeutisk gruppebaseret program, ADAPT programmet. ADAPT programmet er designet på baggrund af evidens samt understøttet af ergoterapeutiske teorier og modeller......Præsentation af et ergoterapeutisk gruppebaseret program, ADAPT programmet. ADAPT programmet er designet på baggrund af evidens samt understøttet af ergoterapeutiske teorier og modeller...

Biological radiation effects of Radon in Drosophila

International Nuclear Information System (INIS)

Pimentel P, A.E.

1995-01-01

In order to contribute to the knowledge on the effects of radon and its decay products, the aim of this investigation is to study the biological effects of radon using Drosophila melanogaster throught the somatic mutation and recombination test (SMART) and the analysis of some adaptative factors exposing larvaes to controlled radon atmosphers, considering that this insect could be used as biological monitor. Using the somatic mutation test a mutagenic effect was observed proportional to radon concentration, into an interval of 1 ± 0.3 to 111 ± 7.4 KBq/m 3 equivalent to doses under 0.0106 Gy. The correlation analysis gives a linear (r=0.80) relationship with a positive slope of 0.2217. The same happens when gamma rays are used in the interval of 1 to 20 Gy, given a linear dose-dependent effect (r=0.878) is obtained; nevetheless the slop is smaller (m=0.003) than for radon. Analysing the results of adaptative factors of the nine exposed generations, it was found that probably radon exposition induced dominant lethals during gametogenesis or/and a selection of the more component gamets of the treated individuals in larval state. It was reflected in the significant decrease on fecundity of the generation exposed. Nevertheless the laying eggs had an increase in egg-to-adult viability and the develop velocity was higher than in control for 3 KBq/m 3 , this suggest that radon concentrations used were able to induce repair mechanisms. These data agree with the Hormesis hypothesis that says: low doses have positive effects on health. It was not possible to obtain a dose-effect relationship except with the develop velocity where it was found a dose-effect inverse proportion. In conclusion, Drosophila melanogaster could be a good system to obtain in vivo damaged induction concentration dependent of radon and its decay products, as well as to study the effects in an exposed population by the analysis of adaptative factors. (Author)

Biomimetic molecular design tools that learn, evolve, and adapt

Science.gov (United States)

2017-01-01

A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine. PMID:28694872

Biomimetic molecular design tools that learn, evolve, and adapt

Directory of Open Access Journals (Sweden)

David A Winkler

2017-06-01

Full Text Available A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine.

Nutritional sub-fertility in the dairy cow: towards improved reproductive management through a better biological understanding

DEFF Research Database (Denmark)

Friggens, Nic; Disenhaus, C; Petit, H V

2010-01-01

for the dairy producer. In this study we focus on understanding the overall biological phenomena associated with nutritional sub-fertility rather than the underlying multiplicity of physiological interactions (already described in a number of recent studies). These phenomena are important because they represent...... the natural adaptations of the animal for dealing with variations in the nutritional environment. They can also be used to monitor and modulate reproductive performance on-farm. There is an underlying trade-off between two aspects of reproduction: investment in the viability of the current calf and investment...... embryos, which are of poorer quality, than do non-lactating cows. The same applies to high- compared to medium-genetic merit cows. Another important biological property is the adaptive use of body reserves in support of reproduction. Orchestrated endocrine changes in pregnancy and lactation facilitate...

Pareto Optimal Design for Synthetic Biology.

Science.gov (United States)

Patanè, Andrea; Santoro, Andrea; Costanza, Jole; Carapezza, Giovanni; Nicosia, Giuseppe

2015-08-01

Recent advances in synthetic biology call for robust, flexible and efficient in silico optimization methodologies. We present a Pareto design approach for the bi-level optimization problem associated to the overproduction of specific metabolites in Escherichia coli. Our method efficiently explores the high dimensional genetic manipulation space, finding a number of trade-offs between synthetic and biological objectives, hence furnishing a deeper biological insight to the addressed problem and important results for industrial purposes. We demonstrate the computational capabilities of our Pareto-oriented approach comparing it with state-of-the-art heuristics in the overproduction problems of i) 1,4-butanediol, ii) myristoyl-CoA, i ii) malonyl-CoA , iv) acetate and v) succinate. We show that our algorithms are able to gracefully adapt and scale to more complex models and more biologically-relevant simulations of the genetic manipulations allowed. The Results obtained for 1,4-butanediol overproduction significantly outperform results previously obtained, in terms of 1,4-butanediol to biomass formation ratio and knock-out costs. In particular overproduction percentage is of +662.7%, from 1.425 mmolh⁻¹gDW⁻¹ (wild type) to 10.869 mmolh⁻¹gDW⁻¹, with a knockout cost of 6. Whereas, Pareto-optimal designs we have found in fatty acid optimizations strictly dominate the ones obtained by the other methodologies, e.g., biomass and myristoyl-CoA exportation improvement of +21.43% (0.17 h⁻¹) and +5.19% (1.62 mmolh⁻¹gDW⁻¹), respectively. Furthermore CPU time required by our heuristic approach is more than halved. Finally we implement pathway oriented sensitivity analysis, epsilon-dominance analysis and robustness analysis to enhance our biological understanding of the problem and to improve the optimization algorithm capabilities.

Supporting Adaptive and Adaptable Hypermedia Presentation Semantics

NARCIS (Netherlands)

D.C.A. Bulterman (Dick); L. Rutledge (Lloyd); L. Hardman (Lynda); J.R. van Ossenbruggen (Jacco)

1999-01-01

textabstractHaving the content of a presentation adapt to the needs, resources and prior activities of a user can be an important benefit of electronic documents. While part of this adaptation is related to the encodings of individual data streams, much of the adaptation can/should be guided by the

Ecological adaptation of diverse honey bee (Apis mellifera populations.

Directory of Open Access Journals (Sweden)

Robert Parker

Full Text Available BACKGROUND: Honey bees are complex eusocial insects that provide a critical contribution to human agricultural food production. Their natural migration has selected for traits that increase fitness within geographical areas, but in parallel their domestication has selected for traits that enhance productivity and survival under local conditions. Elucidating the biochemical mechanisms of these local adaptive processes is a key goal of evolutionary biology. Proteomics provides tools unique among the major 'omics disciplines for identifying the mechanisms employed by an organism in adapting to environmental challenges. RESULTS: Through proteome profiling of adult honey bee midgut from geographically dispersed, domesticated populations combined with multiple parallel statistical treatments, the data presented here suggest some of the major cellular processes involved in adapting to different climates. These findings provide insight into the molecular underpinnings that may confer an advantage to honey bee populations. Significantly, the major energy-producing pathways of the mitochondria, the organelle most closely involved in heat production, were consistently higher in bees that had adapted to colder climates. In opposition, up-regulation of protein metabolism capacity, from biosynthesis to degradation, had been selected for in bees from warmer climates. CONCLUSIONS: Overall, our results present a proteomic interpretation of expression polymorphisms between honey bee ecotypes and provide insight into molecular aspects of local adaptation or selection with consequences for honey bee management and breeding. The implications of our findings extend beyond apiculture as they underscore the need to consider the interdependence of animal populations and their agro-ecological context.

The Virtual Cell: a software environment for computational cell biology.

Science.gov (United States)

Loew, L M; Schaff, J C

2001-10-01

The newly emerging field of computational cell biology requires software tools that address the needs of a broad community of scientists. Cell biological processes are controlled by an interacting set of biochemical and electrophysiological events that are distributed within complex cellular structures. Computational modeling is familiar to researchers in fields such as molecular structure, neurobiology and metabolic pathway engineering, and is rapidly emerging in the area of gene expression. Although some of these established modeling approaches can be adapted to address problems of interest to cell biologists, relatively few software development efforts have been directed at the field as a whole. The Virtual Cell is a computational environment designed for cell biologists as well as for mathematical biologists and bioengineers. It serves to aid the construction of cell biological models and the generation of simulations from them. The system enables the formulation of both compartmental and spatial models, the latter with either idealized or experimentally derived geometries of one, two or three dimensions.

A practical workflow for making anatomical atlases for biological research.

Science.gov (United States)

Wan, Yong; Lewis, A Kelsey; Colasanto, Mary; van Langeveld, Mark; Kardon, Gabrielle; Hansen, Charles

2012-01-01

The anatomical atlas has been at the intersection of science and art for centuries. These atlases are essential to biological research, but high-quality atlases are often scarce. Recent advances in imaging technology have made high-quality 3D atlases possible. However, until now there has been a lack of practical workflows using standard tools to generate atlases from images of biological samples. With certain adaptations, CG artists' workflow and tools, traditionally used in the film industry, are practical for building high-quality biological atlases. Researchers have developed a workflow for generating a 3D anatomical atlas using accessible artists' tools. They used this workflow to build a mouse limb atlas for studying the musculoskeletal system's development. This research aims to raise the awareness of using artists' tools in scientific research and promote interdisciplinary collaborations between artists and scientists. This video (http://youtu.be/g61C-nia9ms) demonstrates a workflow for creating an anatomical atlas.

Brillouin micro-spectroscopy through aberrations via sensorless adaptive optics

Science.gov (United States)

Edrei, Eitan; Scarcelli, Giuliano

2018-04-01

Brillouin spectroscopy is a powerful optical technique for non-contact viscoelastic characterizations which has recently found applications in three-dimensional mapping of biological samples. Brillouin spectroscopy performances are rapidly degraded by optical aberrations and have therefore been limited to homogenous transparent samples. In this work, we developed an adaptive optics (AO) configuration designed for Brillouin scattering spectroscopy to engineer the incident wavefront and correct for aberrations. Our configuration does not require direct wavefront sensing and the injection of a "guide-star"; hence, it can be implemented without the need for sample pre-treatment. We used our AO-Brillouin spectrometer in aberrated phantoms and biological samples and obtained improved precision and resolution of Brillouin spectral analysis; we demonstrated 2.5-fold enhancement in Brillouin signal strength and 1.4-fold improvement in axial resolution because of the correction of optical aberrations.

Cooperative adaptive responses in gene regulatory networks with many degrees of freedom.

Science.gov (United States)

Inoue, Masayo; Kaneko, Kunihiko

2013-04-01

Cells generally adapt to environmental changes by first exhibiting an immediate response and then gradually returning to their original state to achieve homeostasis. Although simple network motifs consisting of a few genes have been shown to exhibit such adaptive dynamics, they do not reflect the complexity of real cells, where the expression of a large number of genes activates or represses other genes, permitting adaptive behaviors. Here, we investigated the responses of gene regulatory networks containing many genes that have undergone numerical evolution to achieve high fitness due to the adaptive response of only a single target gene; this single target gene responds to changes in external inputs and later returns to basal levels. Despite setting a single target, most genes showed adaptive responses after evolution. Such adaptive dynamics were not due to common motifs within a few genes; even without such motifs, almost all genes showed adaptation, albeit sometimes partial adaptation, in the sense that expression levels did not always return to original levels. The genes split into two groups: genes in the first group exhibited an initial increase in expression and then returned to basal levels, while genes in the second group exhibited the opposite changes in expression. From this model, genes in the first group received positive input from other genes within the first group, but negative input from genes in the second group, and vice versa. Thus, the adaptation dynamics of genes from both groups were consolidated. This cooperative adaptive behavior was commonly observed if the number of genes involved was larger than the order of ten. These results have implications in the collective responses of gene expression networks in microarray measurements of yeast Saccharomyces cerevisiae and the significance to the biological homeostasis of systems with many components.

Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures.

Science.gov (United States)

Paget, Caroline Mary; Schwartz, Jean-Marc; Delneri, Daniela

2014-11-01

Temperature is one of the leading factors that drive adaptation of organisms and ecosystems. Remarkably, many closely related species share the same habitat because of their different temporal or micro-spatial thermal adaptation. In this study, we seek to find the underlying molecular mechanisms of the cold-tolerant phenotype of closely related yeast species adapted to grow at different temperatures, namely S. kudriavzevii CA111 (cryo-tolerant) and S. cerevisiae 96.2 (thermo-tolerant). Using two different systems approaches, i. thermodynamic-based analysis of a genome-scale metabolic model of S. cerevisiae and ii. large-scale competition experiment of the yeast heterozygote mutant collection, genes and pathways important for the growth at low temperature were identified. In particular, defects in lipid metabolism, oxidoreductase and vitamin pathways affected yeast fitness at cold. Combining the data from both studies, a list of candidate genes was generated and mutants for two predicted cold-favouring genes, GUT2 and ADH3, were created in two natural isolates. Compared with the parental strains, these mutants showed lower fitness at cold temperatures, with S. kudriavzevii displaying the strongest defect. Strikingly, in S. kudriavzevii, these mutations also significantly improve the growth at warm temperatures. In addition, overexpression of ADH3 in S. cerevisiae increased its fitness at cold. These results suggest that temperature-induced redox imbalances could be compensated by increased glycerol accumulation or production of cytosolic acetaldehyde through the deletion of GUT2 or ADH3, respectively. © 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

FY 1997 report on the results of the industrial technology R and D project. Development of technology to use biological resources such as the complex biological system (Development of biological use petroleum substitution fuel production technology); 1997 nendo fukugo seibutsukei nado seibutsu shigen riyo gijutsu kaihatsu seika hokokusho. Seibutsu riyo sekiyu daitai nenryo seizo gijutsu no kaihatsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-03-01

Experimental researches were conducted and the FY 1997 results were reported with the aim of establishing analytical technology for the complex biological system by which the complex biological system can be analyzed in such a state as it is using the molecular biological method. In the study of the molecular genetic analytical technology, PCR primers used for amplification of topoisomerase II genes of the whole eukaryote was designed. As to the histochemical analytical technology, a study was made on the new constitution microorganism detection method by the hybridization method and the antibody specific dyeing method, and the following were conducted: manifestation in quantity of colibacillus and the recovery, refining, and construction of peptide library by fuzzy display method. Concerning the functional analytical technology, technological researches were made such as the environmental adaptation mechanism of high thermophile and the information transfer mechanism among bacteria through cell membranes for elucidation of the special environment detection/response mechanism and the special environment adaptation/resistance mechanism. As to the separation/culture technology, various anaerobic microorganisms were separated from marine sponge for the development of a method of culturing in 3D matrices. (NEDO)

75 FR 57859 - Specially Adapted Housing and Special Home Adaptation

Science.gov (United States)

2010-09-23

... Home Adaptation AGENCY: Department of Veterans Affairs. ACTION: Final rule. SUMMARY: The Department of... specially adapted housing and special home adaptation grants. This final rule incorporates certain... regulations pertaining to eligibility for specially adapted housing (SAH) grants and special home adaptation...

The General Adaptation Syndrome: A Foundation for the Concept of Periodization.

Science.gov (United States)

Cunanan, Aaron J; DeWeese, Brad H; Wagle, John P; Carroll, Kevin M; Sausaman, Robert; Hornsby, W Guy; Haff, G Gregory; Triplett, N Travis; Pierce, Kyle C; Stone, Michael H

2018-04-01

Recent reviews have attempted to refute the efficacy of applying Selye's general adaptation syndrome (GAS) as a conceptual framework for the training process. Furthermore, the criticisms involved are regularly used as the basis for arguments against the periodization of training. However, these perspectives fail to consider the entirety of Selye's work, the evolution of his model, and the broad applications he proposed. While it is reasonable to critically evaluate any paradigm, critics of the GAS have yet to dismantle the link between stress and adaptation. Disturbance to the state of an organism is the driving force for biological adaptation, which is the central thesis of the GAS model and the primary basis for its application to the athlete's training process. Despite its imprecisions, the GAS has proven to be an instructive framework for understanding the mechanistic process of providing a training stimulus to induce specific adaptations that result in functional enhancements. Pioneers of modern periodization have used the GAS as a framework for the management of stress and fatigue to direct adaptation during sports training. Updates to the periodization concept have retained its founding constructs while explicitly calling for scientifically based, evidence-driven practice suited to the individual. Thus, the purpose of this review is to provide greater clarity on how the GAS serves as an appropriate mechanistic model to conceptualize the periodization of training.

Application of enriched stable isotopes as tracers in biological systems

DEFF Research Database (Denmark)

Stürup, Stefan; Hansen, Helle Rüsz; Gammelgaard, Bente

2008-01-01

The application of enriched stable isotopes of minerals and trace elements as tracers in biological systems is a rapidly growing research field that benefits from the many new developments in inorganic mass spectrometric instrumentation, primarily within inductively coupled plasma mass spectrometry...... (ICP-MS) instrumentation, such as reaction/collision cell ICP-MS and multicollector ICP-MS with improved isotope ratio measurement and interference removal capabilities. Adaptation and refinement of radioisotope tracer experiment methodologies for enriched stable isotope experiments......, and the development of new methodologies coupled with more advanced compartmental and mathematical models for the distribution of elements in living organisms has enabled a broader use of enriched stable isotope experiments in the biological sciences. This review discusses the current and future uses of enriched...

ADAPTATION OF THE STUDENTS' MOTIVATION TOWARDS SCIENCE LEARNING QUESTIONNAIRE TO MEASURE GREEK STUDENTS’ MOTIVATION TOWARDS BIOLOGY LEARNING

OpenAIRE

Andressa, Helen; Mavrikaki, Evangelia; Dermitzaki, Irini

2015-01-01

The purpose of this study was to investigate students’ motivation towards biology learning and to determine the factors that are related to it: students’ gender and their parents’ occupation (relevant with biology or not) were investigated. The sample of the study consisted of 360 Greek high school students of the 10th grade (178 boys and 182 girls). The data were collected through Students’ Motivation Toward Science Learning (SMTSL) questionnaire. It was found that it was a valid and reliabl...

Evolution of adaptation mechanisms: Adaptation energy, stress, and oscillating death.

Science.gov (United States)

Gorban, Alexander N; Tyukina, Tatiana A; Smirnova, Elena V; Pokidysheva, Lyudmila I

2016-09-21

In 1938, Selye proposed the notion of adaptation energy and published 'Experimental evidence supporting the conception of adaptation energy.' Adaptation of an animal to different factors appears as the spending of one resource. Adaptation energy is a hypothetical extensive quantity spent for adaptation. This term causes much debate when one takes it literally, as a physical quantity, i.e. a sort of energy. The controversial points of view impede the systematic use of the notion of adaptation energy despite experimental evidence. Nevertheless, the response to many harmful factors often has general non-specific form and we suggest that the mechanisms of physiological adaptation admit a very general and nonspecific description. We aim to demonstrate that Selye׳s adaptation energy is the cornerstone of the top-down approach to modelling of non-specific adaptation processes. We analyze Selye׳s axioms of adaptation energy together with Goldstone׳s modifications and propose a series of models for interpretation of these axioms. Adaptation energy is considered as an internal coordinate on the 'dominant path' in the model of adaptation. The phenomena of 'oscillating death' and 'oscillating remission' are predicted on the base of the dynamical models of adaptation. Natural selection plays a key role in the evolution of mechanisms of physiological adaptation. We use the fitness optimization approach to study of the distribution of resources for neutralization of harmful factors, during adaptation to a multifactor environment, and analyze the optimal strategies for different systems of factors. Copyright © 2016 Elsevier Ltd. All rights reserved.

The process of organisational adaptation through innovations, and organisational adaptability

OpenAIRE

Tikka, Tommi

2010-01-01

This study is about the process of organisational adaptation and organisational adaptability. The study generates a theoretical framework about organisational adaptation behaviour and conditions that have influence on success of organisational adaptation. The research questions of the study are: How does an organisation adapt through innovations, and which conditions enhance or impede organisational adaptation through innovations? The data were gathered from five case organisations withi...

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

DEFF Research Database (Denmark)

Utrilla, José; O'Brien, Edward J.; Chen, Ke

2016-01-01

Pleiotropic regulatory mutations affect diverse cellular processes, posing a challenge to our understanding of genotype-phenotype relationships across multiple biological scales. Adaptive laboratory evolution (ALE) allows for such mutations to be found and characterized in the context of clear se...

From “Crash!” to Crash: Adapting the Adaptation

Directory of Open Access Journals (Sweden)

Ljubica Matek

2017-12-01

Full Text Available The paper focuses on J.G. Ballard’s various adaptations of his own material related to the issue of the sexual and sensual nature of an automobile crash, and suggests that adaptation is one of the key methods in art and literature which can be used as a means of contemplating and developing various aesthetic and political ideas. Ballard’s short story “Crash!” was first published in the ICA’s (Institute of Contemporary Arts Eventsheet in February 1969, and later became a chapter of his experimental novel The Atrocity Exhibition (1970. At the same time, Ballard adapts the idea into the “Crashed Cars” exhibition (1970 in London. The short story was then adapted into a short film, Crash!, directed by Harley Cokeliss (1971 and starring Ballard himself, to be finally adapted into the novel Crash (1973. Ballard’s adaptation of his initial ideas across literary forms and media testifies to the importance of adaptation as a process and method of creating art. Thus, rather than suggesting that adaptations merely “breathe life” into the written word, the paper points to the conclusion that the form and content are mutually influential and that, in this case, the novel itself is an adaptation, rather than a hypotext (which it becomes in 1996 to David Cronenberg as he adapts it to film. The complexity of the relationship between the source text and its many adaptations has already contributed to the deconstruction, in Derrida’s terms, of the hierarchy (opposition between the original and the copy. Rather, Ballard’s crossmedial and transmedial adaptations of his own ideas show how, as Ray would suggest, an adaptation cites the source and grafts it into a new context, giving it a new function, both aesthetic and political.

How the study of Listeria monocytogenes has led to new concepts in biology.

Science.gov (United States)

Rolhion, Nathalie; Cossart, Pascale

2017-06-01

The opportunistic intracellular bacterial pathogen Listeria monocytogenes has in 30 years emerged as an exceptional bacterial model system in infection biology. Research on this bacterium has provided considerable insight into how pathogenic bacteria adapt to mammalian hosts, invade eukaryotic cells, move intracellularly, interfere with host cell functions and disseminate within tissues. It also contributed to unveil features of normal host cell pathways and unsuspected functions of previously known cellular proteins. This review provides an updated overview of our knowledge on this pathogen. In many examples, findings on L. monocytogenes provided the basis for new concepts in bacterial regulation, cell biology and infection processes.

Five Hundred Years of Mercury Exposure and Adaptation

Science.gov (United States)

Lombardi, Guido; Lanzirotti, Antonio; Qualls, Clifford; Socola, Francisco; Ali, Abdul-Mehdi; Appenzeller, Otto

2012-01-01

Mercury is added to the biosphere by anthropogenic activities raising the question of whether changes in the human chromatin, induced by mercury, in a parental generation could allow adaptation of their descendants to mercury. We review the history of Andean mining since pre-Hispanic times in Huancavelica, Peru. Despite the persistent degradation of the biosphere today, no overt signs of mercury toxicity could be discerned in present day inhabitants. However, mercury is especially toxic to the autonomic nervous system (ANS). We, therefore, tested ANS function and biologic rhythms, under the control of the ANS, in 5 Huancavelicans and examined the metal content in their hair. Mercury levels varied from none to 1.014 ppm, significantly less than accepted standards. This was confirmed by microfocused synchrotron X-ray fluorescence analysis. Biologic rhythms were abnormal and hair growth rate per year, also under ANS control, was reduced (P Peru. This would generally benefit survival in the Anthropocene, the man-made world, we now live in. PMID:22910643

Mechanisms of adaptive evolution. Darwinism and Lamarckism restated.

Science.gov (United States)

Aboitiz, F

1992-07-01

This article discusses the conceptual basis of the different mechanisms of adaptive evolution. It is argued that only two such mechanisms may conceivably exist, Lamarckism and Darwinism. Darwinism is the fundamental process generating the diversity of species. Some aspects of the gene-centered approach to Darwinism are questioned, since they do not account for the generation of biological diversity. Diversity in biological design must be explained in relation to the diversity of interactions of organisms (or other higher-level units) with their environment. This aspect is usually overlooked in gene-centered views of evolution. A variant of the gene-selectionist approach has been proposed to account for the spread of cultural traits in human societies. Alternatively, I argue that social evolution is rather driven by what I call pseudo-Lamarckian inheritance. Finally, I argue that Lamarckian and pseudo-Lamarckian inheritance are just special cases of faithful replication which are found in the development of some higher-order units, such as multicellular organisms and human societies.

On Adaptive vs. Non-adaptive Security of Multiparty Protocols

DEFF Research Database (Denmark)

Canetti, Ran; Damgård, Ivan Bjerre; Dziembowski, Stefan

2001-01-01

highlights of our results are: – - According to the definition of Dodis-Micali-Rogaway (which is set in the information-theoretic model), adaptive and non-adaptive security are equivalent. This holds for both honest-but-curious and Byzantine adversaries, and for any number of parties. – - According......Security analysis of multiparty cryptographic protocols distinguishes between two types of adversarialsettings: In the non-adaptive setting, the set of corrupted parties is chosen in advance, before the interaction begins. In the adaptive setting, the adversary chooses who to corrupt during...... the course of the computation. We study the relations between adaptive security (i.e., security in the adaptive setting) and non-adaptive security, according to two definitions and in several models of computation. While affirming some prevailing beliefs, we also obtain some unexpected results. Some...

Overlooking the smallest matter: viruses impact biological invasions.

Science.gov (United States)

Faillace, Cara A; Lorusso, Nicholas S; Duffy, Siobain

2017-04-01

Parasites and pathogens have recently received considerable attention for their ability to affect biological invasions, however, researchers have largely overlooked the distinct role of viruses afforded by their unique ability to rapidly mutate and adapt to new hosts. With high mutation and genomic substitution rates, RNA and single-stranded DNA (ssDNA) viruses may be important constituents of invaded ecosystems, and could potentially behave quite differently from other pathogens. We review evidence suggesting that rapidly evolving viruses impact invasion dynamics in three key ways: (1) Rapidly evolving viruses may prevent exotic species from establishing self-sustaining populations. (2) Viruses can cause population collapses of exotic species in the introduced range. (3) Viruses can alter the consequences of biological invasions by causing population collapses and extinctions of native species. The ubiquity and frequent host shifting of viruses make their ability to influence invasion events likely. Eludicating the viral ecology of biological invasions will lead to an improved understanding of the causes and consequences of invasions, particularly as regards establishment success and changes to community structure that cannot be explained by direct interspecific interactions among native and exotic species. © 2017 John Wiley & Sons Ltd/CNRS.

Is adaptation. Truly an adaptation?

Directory of Open Access Journals (Sweden)

Thais Flores Nogueira Diniz

2006-04-01

Full Text Available The article begins by historicizing film adaptation from the arrival of cinema, pointing out the many theoretical approaches under which the process has been seen: from the concept of “the same story told in a different medium” to a comprehensible definition such as “the process through which works can be transformed, forming an intersection of textual surfaces, quotations, conflations and inversions of other texts”. To illustrate this new concept, the article discusses Spike Jonze’s film Adaptation. according to James Naremore’s proposal which considers the study of adaptation as part of a general theory of repetition, joined with the study of recycling, remaking, and every form of retelling. The film deals with the attempt by the scriptwriter Charles Kaufman, cast by Nicholas Cage, to adapt/translate a non-fictional book to the cinema, but ends up with a kind of film which is by no means what it intended to be: a film of action in the model of Hollywood productions. During the process of creation, Charles and his twin brother, Donald, undergo a series of adventures involving some real persons from the world of film, the author and the protagonist of the book, all of them turning into fictional characters in the film. In the film, adaptation then signifies something different from itstraditional meaning.

Bacteriophage lambda: The path from biology to theranostic agent.

Science.gov (United States)

Catalano, Carlos E

2018-03-13

Viral particles provide an attractive platform for the engineering of semisynthetic therapeutic nanoparticles. They can be modified both genetically and chemically in a defined manner to alter their surface characteristics, for targeting specific cell types, to improve their pharmacokinetic features and to attenuate (or enhance) their antigenicity. These advantages derive from a detailed understanding of virus biology, gleaned from decades of fundamental genetic, biochemical, and structural studies that have provided mechanistic insight into virus assembly pathways. In particular, bacteriophages offer significant advantages as nanoparticle platforms and several have been adapted toward the design and engineering of "designer" nanoparticles for therapeutic and diagnostic (theranostic) applications. The present review focuses on one such virus, bacteriophage lambda; I discuss the biology of lambda, the tools developed to faithfully recapitulate the lambda assembly reactions in vitro and the observations that have led to cooptation of the lambda system for nanoparticle design. This discussion illustrates how a fundamental understanding of virus assembly has allowed the rational design and construction of semisynthetic nanoparticles as potential theranostic agents and illustrates the concept of benchtop to bedside translational research. This article is categorized under: Biology-Inspired Nanomaterials> Protein and Virus-Based Structures Biology-Inspired Nanomaterials> Nucleic Acid-Based Structures. © 2018 Wiley Periodicals, Inc.

Plant Biology and Biogeochemistry Department annual report 2000

DEFF Research Database (Denmark)

Kossmann, J.; Gissel Nielsen, G.; Nielsen, K.K.

2001-01-01

The Department of Plant Biology and Biogeochemistry is engaged in basic and applied research to improve the scientific basis for developing new methods and technology for an environmentally benign industrial and agricultural production in the future. TheDepartment's expertise covers a wide range...... of areas needed to develop crops that meet the demands to increase agricultural production for a growing population, to produce plants with improved nutritional value, to develop crops that deliver renewableresources to the industry, and to generate plants that are adapted to the future climate...

Adaptive Lighting

DEFF Research Database (Denmark)

Petersen, Kjell Yngve; Søndergaard, Karin; Kongshaug, Jesper

2015-01-01

Adaptive Lighting Adaptive lighting is based on a partial automation of the possibilities to adjust the colour tone and brightness levels of light in order to adapt to people’s needs and desires. IT support is key to the technical developments that afford adaptive control systems. The possibilities...... offered by adaptive lighting control are created by the ways that the system components, the network and data flow can be coordinated through software so that the dynamic variations are controlled in ways that meaningfully adapt according to people’s situations and design intentions. This book discusses...... differently into an architectural body. We also examine what might occur when light is dynamic and able to change colour, intensity and direction, and when it is adaptive and can be brought into interaction with its surroundings. In short, what happens to an architectural space when artificial lighting ceases...

Testing for local adaptation in brown trout using reciprocal transplants

Directory of Open Access Journals (Sweden)

Stelkens Rike B

2012-12-01

Full Text Available Abstract Background Local adaptation can drive the divergence of populations but identification of the traits under selection remains a major challenge in evolutionary biology. Reciprocal transplant experiments are ideal tests of local adaptation, yet rarely used for higher vertebrates because of the mobility and potential invasiveness of non-native organisms. Here, we reciprocally transplanted 2500 brown trout (Salmo trutta embryos from five populations to investigate local adaptation in early life history traits. Embryos were bred in a full-factorial design and raised in natural riverbeds until emergence. Customized egg capsules were used to simulate the natural redd environment and allowed tracking the fate of every individual until retrieval. We predicted that 1 within sites, native populations would outperform non-natives, and 2 across sites, populations would show higher performance at ‘home’ compared to ‘away’ sites. Results There was no evidence for local adaptation but we found large differences in survival and hatching rates between sites, indicative of considerable variation in habitat quality. Survival was generally high across all populations (55% ± 3%, but ranged from 4% to 89% between sites. Average hatching rate was 25% ± 3% across populations ranging from 0% to 62% between sites. Conclusion This study provides rare empirical data on variation in early life history traits in a population network of a salmonid, and large-scale breeding and transplantation experiments like ours provide powerful tests for local adaptation. Despite the recently reported genetic and morphological differences between the populations in our study area, local adaptation at the embryo level is small, non-existent, or confined to ecological conditions that our experiment could not capture.

Disparate patterns of thermal adaptation between life stages in temperate vs. tropical Drosophila melanogaster.

Science.gov (United States)

Lockwood, B L; Gupta, T; Scavotto, R

2018-02-01

Many terrestrial ectothermic species exhibit limited variation in upper thermal tolerance across latitude. However, these trends may not signify limited adaptive capacity to increase thermal tolerance in the face of climate change. Instead, thermal tolerance may be similar among populations because behavioural thermoregulation by mobile organisms or life stages may buffer natural selection for thermal tolerance. We compared thermal tolerance of adults and embryos among natural populations of Drosophila melanogaster from a broad range of thermal habitats around the globe to assess natural variation of thermal tolerance in mobile vs. immobile life stages. We found no variation among populations in adult thermal tolerance, but embryonic thermal tolerance was higher in tropical strains than in temperate strains. We further report that embryos live closer to their upper thermal limits than adults - that is, thermal safety margins are smaller for embryos than adults. F1 hybrid embryos from crosses between temperate and tropical populations had thermal tolerance that matched that of tropical embryos, suggesting the dominance of heat-tolerant alleles. Together, our findings suggest that thermal selection has led to divergence in embryonic thermal tolerance but that selection for divergent thermal tolerance may be limited in adults. Further, our results suggest that thermal traits should be measured across life stages to better predict adaptive limits. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Biologically-inspired approaches for self-organization, adaptation, and collaboration of heterogeneous autonomous systems

Science.gov (United States)

Steinberg, Marc

2011-06-01

This paper presents a selective survey of theoretical and experimental progress in the development of biologicallyinspired approaches for complex surveillance and reconnaissance problems with multiple, heterogeneous autonomous systems. The focus is on approaches that may address ISR problems that can quickly become mathematically intractable or otherwise impractical to implement using traditional optimization techniques as the size and complexity of the problem is increased. These problems require dealing with complex spatiotemporal objectives and constraints at a variety of levels from motion planning to task allocation. There is also a need to ensure solutions are reliable and robust to uncertainty and communications limitations. First, the paper will provide a short introduction to the current state of relevant biological research as relates to collective animal behavior. Second, the paper will describe research on largely decentralized, reactive, or swarm approaches that have been inspired by biological phenomena such as schools of fish, flocks of birds, ant colonies, and insect swarms. Next, the paper will discuss approaches towards more complex organizational and cooperative mechanisms in team and coalition behaviors in order to provide mission coverage of large, complex areas. Relevant team behavior may be derived from recent advances in understanding of the social and cooperative behaviors used for collaboration by tens of animals with higher-level cognitive abilities such as mammals and birds. Finally, the paper will briefly discuss challenges involved in user interaction with these types of systems.

Adapting to large-scale changes in Advanced Placement Biology, Chemistry, and Physics: the impact of online teacher communities

Science.gov (United States)

Frumin, Kim; Dede, Chris; Fischer, Christian; Foster, Brandon; Lawrenz, Frances; Eisenkraft, Arthur; Fishman, Barry; Jurist Levy, Abigail; McCoy, Ayana

2018-03-01

Over the past decade, the field of teacher professional learning has coalesced around core characteristics of high quality professional development experiences (e.g. Borko, Jacobs, & Koellner, 2010. Contemporary approaches to teacher professional development. In P. L. Peterson, E. Baker, & B. McGaw (Eds.), International encyclopedia of education (Vol. 7, pp. 548-556). Oxford: Elsevier.; Darling-Hammond, Hyler, & Gardner, 2017. Effective teacher professional development. Palo Alto, CA: Learning Policy Institute). Many countries have found these advances of great interest because of a desire to build teacher capacity in science education and across the full curriculum. This paper continues this progress by examining the role and impact of an online professional development community within the top-down, large-scale curriculum and assessment revision of Advanced Placement (AP) Biology, Chemistry, and Physics. This paper is part of a five-year, longitudinal, U.S. National Science Foundation-funded project to study the relative effectiveness of various types of professional development in enabling teachers to adapt to the revised AP course goals and exams. Of the many forms of professional development our research has examined, preliminary analyses indicated that participation in the College Board's online AP Teacher Community (APTC) - where teachers can discuss teaching strategies, share resources, and connect with each other - had positive, direct, and statistically significant association with teacher self-reported shifts in practice and with gains in student AP scores (Fishman et al., 2014). This study explored how usage of the online APTC might be useful to teachers and examined a more robust estimate of these effects. Findings from the experience of AP teachers may be valuable in supporting other large-scale curriculum changes, such as the U.S. Next Generation Science Standards or Common Core Standards, as well as parallel curricular shifts in other countries.

The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change

NARCIS (Netherlands)

Valladares, F.; Matesanz, S.; Guilhaumon, F.; Araujo, M.; Balaguer, L.; Benito-Garzon, M.; Cornwell, W.K.; Gianoli, E.; van Kleunen, M.; Naya, D.E.; Nicotra, A.B.; Poorter, H.; Zavala, M.A.

2014-01-01

Species are the unit of analysis in many global change and conservation biology studies; however, species are not uniform entities but are composed of different, sometimes locally adapted, populations differing in plasticity. We examined how intraspecific variation in thermal niches and phenotypic

Stochastic adaptation and fold-change detection: from single-cell to population behavior

Directory of Open Access Journals (Sweden)

Leier André

2011-02-01

Full Text Available Abstract Background In cell signaling terminology, adaptation refers to a system's capability of returning to its equilibrium upon a transient response. To achieve this, a network has to be both sensitive and precise. Namely, the system must display a significant output response upon stimulation, and later on return to pre-stimulation levels. If the system settles at the exact same equilibrium, adaptation is said to be 'perfect'. Examples of adaptation mechanisms include temperature regulation, calcium regulation and bacterial chemotaxis. Results We present models of the simplest adaptation architecture, a two-state protein system, in a stochastic setting. Furthermore, we consider differences between individual and collective adaptive behavior, and show how our system displays fold-change detection properties. Our analysis and simulations highlight why adaptation needs to be understood in terms of probability, and not in strict numbers of molecules. Most importantly, selection of appropriate parameters in this simple linear setting may yield populations of cells displaying adaptation, while single cells do not. Conclusions Single cell behavior cannot be inferred from population measurements and, sometimes, collective behavior cannot be determined from the individuals. By consequence, adaptation can many times be considered a purely emergent property of the collective system. This is a clear example where biological ergodicity cannot be assumed, just as is also the case when cell replication rates are not homogeneous, or depend on the cell state. Our analysis shows, for the first time, how ergodicity cannot be taken for granted in simple linear examples either. The latter holds even when cells are considered isolated and devoid of replication capabilities (cell-cycle arrested. We also show how a simple linear adaptation scheme displays fold-change detection properties, and how rupture of ergodicity prevails in scenarios where transitions between

Distinguishing Byproducts from Non-Adaptive Effects of Algorithmic Adaptations

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Justin H. Park

2007-01-01

Full Text Available I evaluate the use of the byproduct concept in psychology, particularly the adaptation-byproduct distinction that is commonly invoked in discussions of psychological phenomena. This distinction can be problematic when investigating algorithmic mechanisms and their effects, because although all byproducts may be functionless concomitants of adaptations, not all incidental effects of algorithmic adaptations are byproducts (although they have sometimes been labeled as such. I call attention to Sperber's (1994 distinction between proper domains and actual domains of algorithmic mechanisms. Extending Sperber's distinction, I propose the terms adaptive effects and non-adaptive effects, which more accurately capture the phenomena of interest to psychologists and prevent fruitless adaptation-versus-byproduct debates.

Evaluating children's conservation biology learning at the zoo.

Science.gov (United States)

Jensen, Eric

2014-08-01

Millions of children visit zoos every year with parents or schools to encounter wildlife firsthand. Public conservation education is a requirement for membership in professional zoo associations. However, in recent years zoos have been criticized for failing to educate the public on conservation issues and related biological concepts, such as animal adaptation to habitats. I used matched pre- and postvisit mixed methods questionnaires to investigate the educational value of zoo visits for children aged 7-15 years. The questionnaires gathered qualitative data from these individuals, including zoo-related thoughts and an annotated drawing of a habitat. A content analysis of these qualitative data produced the quantitative data reported in this article. I evaluated the relative learning outcomes of educator-guided and unguided zoo visits at London Zoo, both in terms of learning about conservation biology (measured by annotated drawings) and changing attitudes toward wildlife conservation (measured using thought-listing data). Forty-one percent of educator-guided visits and 34% of unguided visits resulted in conservation biology-related learning. Negative changes in children's understanding of animals and their habitats were more prevalent in unguided zoo visits. Overall, my results show the potential educational value of visiting zoos for children. However, they also suggest that zoos' standard unguided interpretive materials are insufficient for achieving the best outcomes for visiting children. These results support a theoretical model of conservation biology learning that frames conservation educators as toolmakers who develop conceptual resources to enhance children's understanding of science. © 2014 Society for Conservation Biology.

Biological psychological and social determinants of old age: Bio-psycho-social aspects of human aging

Directory of Open Access Journals (Sweden)

Małgorzata Dziechciaż

2014-11-01

Full Text Available Biological psychological and social determinants of old age: Bio-psycho-social aspects of human aging. The aging of humans is a physiological and dynamic process ongoing with time. In accordance with most gerontologists’ assertions it starts in the fourth decade of life and leads to death. The process of human aging is complex and individualized, occurs in the biological, psychological and social sphere. Biological aging is characterized by progressive age-changes in metabolism and physicochemical properties of cells, leading to impaired self-regulation, regeneration, and to structural changes and functional tissues and organs. It is a natural and irreversible process which can run as successful aging, typical or pathological. Biological changes that occur with age in the human body affect mood, attitude to the environment, physical condition and social activity, and designate the place of seniors in the family and society. Psychical ageing refers to human awareness and his adaptability to the ageing process. Among adaptation attitudes we can differentiate: constructive, dependence, hostile towards others and towards self attitudes. With progressed age, difficulties with adjustment to the new situation are increasing, adverse changes in the cognitive and intellectual sphere take place, perception process involutes, perceived sensations and information received is lowered, and thinking processes change. Social ageing is limited to the role of an old person is culturally conditioned and may change as customs change. Social ageing refers to how a human being perceives the ageing process and how society sees it.

Climate adaptation

Science.gov (United States)

Kinzig, Ann P.

2015-03-01

This paper is intended as a brief introduction to climate adaptation in a conference devoted otherwise to the physics of sustainable energy. Whereas mitigation involves measures to reduce the probability of a potential event, such as climate change, adaptation refers to actions that lessen the impact of climate change. Mitigation and adaptation differ in other ways as well. Adaptation does not necessarily have to be implemented immediately to be effective; it only needs to be in place before the threat arrives. Also, adaptation does not necessarily require global, coordinated action; many effective adaptation actions can be local. Some urban communities, because of land-use change and the urban heat-island effect, currently face changes similar to some expected under climate change, such as changes in water availability, heat-related morbidity, or changes in disease patterns. Concern over those impacts might motivate the implementation of measures that would also help in climate adaptation, despite skepticism among some policy makers about anthropogenic global warming. Studies of ancient civilizations in the southwestern US lends some insight into factors that may or may not be important to successful adaptation.

Understanding climate change adaptation and adaptive capacity: synthesis report

Energy Technology Data Exchange (ETDEWEB)

Patino, L. [Policy Research Initiative, Government of Canada, Ottawa, ON (Canada)

2010-09-15

In 2007, the Natural Resources Canada (NRCan) Climate Change Impacts and Adaptation Division (CCIAD) offered its support to research projects that were involved in understanding and improving adaptation and adaptive capacity and contributed to climate change decision-making and policy development in Canada. 20 research projects were commissioned by the CCIAD. With the collaboration of NRCan, the principal findings raised by the commissioned projects were synthesized by the Policy Research Initiative (PRI). Common themes and main messages are introduced in this synthesis report, and policy and program aspects that promote adaptive capacity to climate change in Canada are identified. Common themes and important messages emerging from the research projects, as well as the processes and barriers to adaptation and adaptive capacity identified in the commissioned projects, were discussed during a workshop held in Ottawa in 2009. Five main themes and four common barriers to adaptation were found. 25 refs.

A structure-based approach to evaluation product adaptability in adaptable design

International Nuclear Information System (INIS)

Cheng, Qiang; Liu, Zhifeng; Cai, Ligang; Zhang, Guojun; Gu, Peihua

2011-01-01

Adaptable design, as a new design paradigm, involves creating designs and products that can be easily changed to satisfy different requirements. In this paper, two types of product adaptability are proposed as essential adaptability and behavioral adaptability, and through measuring which respectively a model for product adaptability evaluation is developed. The essential adaptability evaluation proceeds with analyzing the independencies of function requirements and function modules firstly based on axiomatic design, and measuring the adaptability of interfaces secondly with three indices. The behavioral adaptability reflected by the performance of adaptable requirements after adaptation is measured based on Kano model. At last, the effectiveness of the proposed method is demonstrated by an illustrative example of the motherboard of a personal computer. The results show that the method can evaluate and reveal the adaptability of a product in essence, and is of directive significance to improving design and innovative design

Real-Time Molecular Monitoring of Chemical Environment in ObligateAnaerobes during Oxygen Adaptive Response

Energy Technology Data Exchange (ETDEWEB)

Holman, Hoi-Ying N.; Wozei, Eleanor; Lin, Zhang; Comolli, Luis R.; Ball, David. A.; Borglin, Sharon; Fields, Matthew W.; Hazen, Terry C.; Downing, Kenneth H.

2009-02-25

Determining the transient chemical properties of the intracellular environment canelucidate the paths through which a biological system adapts to changes in its environment, for example, the mechanisms which enable some obligate anaerobic bacteria to survive a sudden exposure to oxygen. Here we used high-resolution Fourier Transform Infrared (FTIR) spectromicroscopy to continuously follow cellular chemistry within living obligate anaerobes by monitoring hydrogen bonding in their cellular water. We observed a sequence of wellorchestrated molecular events that correspond to changes in cellular processes in those cells that survive, but only accumulation of radicals in those that do not. We thereby can interpret the adaptive response in terms of transient intracellular chemistry and link it to oxygen stress and survival. This ability to monitor chemical changes at the molecular level can yield important insights into a wide range of adaptive responses.

Protein stability and enzyme activity at extreme biological temperatures

International Nuclear Information System (INIS)

Feller, Georges

2010-01-01

Psychrophilic microorganisms thrive in permanently cold environments, even at subzero temperatures. To maintain metabolic rates compatible with sustained life, they have improved the dynamics of their protein structures, thereby enabling appropriate molecular motions required for biological activity at low temperatures. As a consequence of this structural flexibility, psychrophilic proteins are unstable and heat-labile. In the upper range of biological temperatures, thermophiles and hyperthermophiles grow at temperatures > 100 0 C and synthesize ultra-stable proteins. However, thermophilic enzymes are nearly inactive at room temperature as a result of their compactness and rigidity. At the molecular level, both types of extremophilic proteins have adapted the same structural factors, but in opposite directions, to address either activity at low temperatures or stability in hot environments. A model based on folding funnels is proposed accounting for the stability-activity relationships in extremophilic proteins. (topical review)

Adaptive Evolution and Demographic History of Norway Spruce (Picea Abies)

OpenAIRE

Källman, Thomas

2009-01-01

One of the major challenges in evolutionary biology is to determine the genetic basis of adaptive variation. In Norway spruce (Picea abies) the timing of bud set shows a very strong latitudinal cline despite a very low genetic differentiation between populations. The timing of bud set in Norway spruce is under strong genetic control and triggered by changes in photoperiod, but no genes controlling this response have so far been described. In this thesis we used a combination of functional stu...

Soft systems thinking and social learning for adaptive management.

Science.gov (United States)

Cundill, G; Cumming, G S; Biggs, D; Fabricius, C

2012-02-01

The success of adaptive management in conservation has been questioned and the objective-based management paradigm on which it is based has been heavily criticized. Soft systems thinking and social-learning theory expose errors in the assumption that complex systems can be dispassionately managed by objective observers and highlight the fact that conservation is a social process in which objectives are contested and learning is context dependent. We used these insights to rethink adaptive management in a way that focuses on the social processes involved in management and decision making. Our approach to adaptive management is based on the following assumptions: action toward a common goal is an emergent property of complex social relationships; the introduction of new knowledge, alternative values, and new ways of understanding the world can become a stimulating force for learning, creativity, and change; learning is contextual and is fundamentally about practice; and defining the goal to be addressed is continuous and in principle never ends. We believe five key activities are crucial to defining the goal that is to be addressed in an adaptive-management context and to determining the objectives that are desirable and feasible to the participants: situate the problem in its social and ecological context; raise awareness about alternative views of a problem and encourage enquiry and deconstruction of frames of reference; undertake collaborative actions; and reflect on learning. ©2011 Society for Conservation Biology.

Active Hearing Mechanisms Inspire Adaptive Amplification in an Acoustic Sensor System.

Science.gov (United States)

Guerreiro, Jose; Reid, Andrew; Jackson, Joseph C; Windmill, James F C

2018-06-01

Over many millions of years of evolution, nature has developed some of the most adaptable sensors and sensory systems possible, capable of sensing, conditioning and processing signals in a very power- and size-effective manner. By looking into biological sensors and systems as a source of inspiration, this paper presents the study of a bioinspired concept of signal processing at the sensor level. By exploiting a feedback control mechanism between a front-end acoustic receiver and back-end neuronal based computation, a nonlinear amplification with hysteretic behavior is created. Moreover, the transient response of the front-end acoustic receiver can also be controlled and enhanced. A theoretical model is proposed and the concept is prototyped experimentally through an embedded system setup that can provide dynamic adaptations of a sensory system comprising a MEMS microphone placed in a closed-loop feedback system. It faithfully mimics the mosquito's active hearing response as a function of the input sound intensity. This is an adaptive acoustic sensor system concept that can be exploited by sensor and system designers within acoustics and ultrasonic engineering fields.

Cell-Gazing Into the Future: What Genes, Homo heidelbergensis, and Punishment Tell Us About Our Adaptive Capacity

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Jeffrey Andrews

2013-02-01

Full Text Available If we wish to understand how our species can adapt to the coming tide of environmental change, then understanding how we have adapted throughout the course of evolution is vital. Evolutionary biologists have been exploring these questions in the last forty years, establishing a solid record of evidence that conventional, individual-based models of natural selection are insufficient in explaining social evolution. More recently, this work has supported a growing consensus that our evolution, in which we have expressed extra-ordinary adaptive capacities, can best be explained by “Multi-level Selection”, a theory that includes the influence of both genes and culture to support unique adaptive capacities premised on pro-social behaviours and group selection, not individual-level competition for survival. Applying this scholarship to contemporary concerns about adapting to environmental change may be quite fruitful for identifying sources of vulnerability and adaptive capacity, thereby informing efforts to enhance the likelihood for sustainable futures. Doing so, however, requires that we bridge the gap between evolutionary biology, and the social sciences study of sustainability.

Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach.

Science.gov (United States)

Li, Jun; Zhao, Patrick X

2016-01-01

Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

Biologically inspired autonomous structural materials with controlled toughening and healing

Science.gov (United States)

Garcia, Michael E.; Sodano, Henry A.

2010-04-01

The field of structural health monitoring (SHM) has made significant contributions in the field of prognosis and damage detection in the past decade. The advantageous use of this technology has not been integrated into operational structures to prevent damage from propagating or to heal injured regions under real time loading conditions. Rather, current systems relay this information to a central processor or human operator, who then determines a course of action such as altering the mission or scheduling repair maintenance. Biological systems exhibit advanced sensory and healing traits that can be applied to the design of material systems. For instance, bone is the major structural component in vertebrates; however, unlike modern structural materials, bone has many properties that make it effective for arresting the propagation of cracks and subsequent healing of the fractured area. The foremost goal for the development of future adaptive structures is to mimic biological systems, similar to bone, such that the material system can detect damage and deploy defensive traits to impede damage from propagating, thus preventing catastrophic failure while in operation. After sensing and stalling the propagation of damage, the structure must then be repaired autonomously using self healing mechanisms motivated by biological systems. Here a novel autonomous system is developed using shape memory polymers (SMPs), that employs an optical fiber network as both a damage detection sensor and a network to deliver stimulus to the damage site initiating adaptation and healing. In the presence of damage the fiber optic fractures allowing a high power laser diode to deposit a controlled level of thermal energy at the fractured sight locally reducing the modulus and blunting the crack tip, which significantly slows the crack growth rate. By applying a pre-induced strain field and utilizing the shape memory recovery effect, thermal energy can be deployed to close the crack and return

Accelerating Yeast Prion Biology using Droplet Microfluidics

Science.gov (United States)

Ung, Lloyd; Rotem, Assaf; Jarosz, Daniel; Datta, Manoshi; Lindquist, Susan; Weitz, David

2012-02-01

Prions are infectious proteins in a misfolded form, that can induce normal proteins to take the misfolded state. Yeast prions are relevant, as a model of human prion diseases, and interesting from an evolutionary standpoint. Prions may also be a form of epigenetic inheritance, which allow yeast to adapt to stressful conditions at rates exceeding those of random mutations and propagate that adaptation to their offspring. Encapsulation of yeast in droplet microfluidic devices enables high-throughput measurements with single cell resolution, which would not be feasible using bulk methods. Millions of populations of yeast can be screened to obtain reliable measurements of prion induction and loss rates. The population dynamics of clonal yeast, when a fraction of the cells are prion expressing, can be elucidated. Furthermore, the mechanism by which certain strains of bacteria induce yeast to express prions in the wild can be deduced. Integrating the disparate fields of prion biology and droplet microfluidics reveals a more complete picture of how prions may be more than just diseases and play a functional role in yeast.

Cloning humans? Biological, ethical, and social considerations.

Science.gov (United States)

Ayala, Francisco J

2015-07-21

There are, in mankind, two kinds of heredity: biological and cultural. Cultural inheritance makes possible for humans what no other organism can accomplish: the cumulative transmission of experience from generation to generation. In turn, cultural inheritance leads to cultural evolution, the prevailing mode of human adaptation. For the last few millennia, humans have been adapting the environments to their genes more often than their genes to the environments. Nevertheless, natural selection persists in modern humans, both as differential mortality and as differential fertility, although its intensity may decrease in the future. More than 2,000 human diseases and abnormalities have a genetic causation. Health care and the increasing feasibility of genetic therapy will, although slowly, augment the future incidence of hereditary ailments. Germ-line gene therapy could halt this increase, but at present, it is not technically feasible. The proposal to enhance the human genetic endowment by genetic cloning of eminent individuals is not warranted. Genomes can be cloned; individuals cannot. In the future, therapeutic cloning will bring enhanced possibilities for organ transplantation, nerve cells and tissue healing, and other health benefits.

Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation

Directory of Open Access Journals (Sweden)

Salzburger Walter

2011-04-01

Full Text Available Abstract Background Phenotypic evolution and its role in the diversification of organisms is a central topic in evolutionary biology. A neglected factor during the modern evolutionary synthesis, adaptive phenotypic plasticity, more recently attracted the attention of many evolutionary biologists and is now recognized as an important ingredient in both population persistence and diversification. The traits and directions in which an ancestral source population displays phenotypic plasticity might partly determine the trajectories in morphospace, which are accessible for an adaptive radiation, starting from the colonization of a novel environment. In the case of repeated colonizations of similar environments from the same source population this "flexible stem" hypothesis predicts similar phenotypes to arise in repeated subsequent radiations. The Midas Cichlid (Amphilophus spp. in Nicaragua has radiated in parallel in several crater-lakes seeded by populations originating from the Nicaraguan Great Lakes. Here, we tested phenotypic plasticity in the pharyngeal jaw of Midas Cichlids. The pharyngeal jaw apparatus of cichlids, a second set of jaws functionally decoupled from the oral ones, is known to mediate ecological specialization and often differs strongly between sister-species. Results We performed a common garden experiment raising three groups of Midas cichlids on food differing in hardness and calcium content. Analyzing the lower pharyngeal jaw-bones we find significant differences between diet groups qualitatively resembling the differences found between specialized species. Observed differences in pharyngeal jaw expression between groups were attributable to the diet's mechanical resistance, whereas surplus calcium in the diet was not found to be of importance. Conclusions The pharyngeal jaw apparatus of Midas Cichlids can be expressed plastically if stimulated mechanically during feeding. Since this trait is commonly differentiated - among

Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation.

Science.gov (United States)

Muschick, Moritz; Barluenga, Marta; Salzburger, Walter; Meyer, Axel

2011-04-30

Phenotypic evolution and its role in the diversification of organisms is a central topic in evolutionary biology. A neglected factor during the modern evolutionary synthesis, adaptive phenotypic plasticity, more recently attracted the attention of many evolutionary biologists and is now recognized as an important ingredient in both population persistence and diversification. The traits and directions in which an ancestral source population displays phenotypic plasticity might partly determine the trajectories in morphospace, which are accessible for an adaptive radiation, starting from the colonization of a novel environment. In the case of repeated colonizations of similar environments from the same source population this "flexible stem" hypothesis predicts similar phenotypes to arise in repeated subsequent radiations. The Midas Cichlid (Amphilophus spp.) in Nicaragua has radiated in parallel in several crater-lakes seeded by populations originating from the Nicaraguan Great Lakes. Here, we tested phenotypic plasticity in the pharyngeal jaw of Midas Cichlids. The pharyngeal jaw apparatus of cichlids, a second set of jaws functionally decoupled from the oral ones, is known to mediate ecological specialization and often differs strongly between sister-species. We performed a common garden experiment raising three groups of Midas cichlids on food differing in hardness and calcium content. Analyzing the lower pharyngeal jaw-bones we find significant differences between diet groups qualitatively resembling the differences found between specialized species. Observed differences in pharyngeal jaw expression between groups were attributable to the diet's mechanical resistance, whereas surplus calcium in the diet was not found to be of importance. The pharyngeal jaw apparatus of Midas Cichlids can be expressed plastically if stimulated mechanically during feeding. Since this trait is commonly differentiated--among other traits--between Midas Cichlid species, its plasticity

Considerations about expected a posteriori estimation in adaptive testing: adaptive a priori, adaptive correction for bias, and adaptive integration interval.

Science.gov (United States)

Raiche, Gilles; Blais, Jean-Guy

2009-01-01

In a computerized adaptive test, we would like to obtain an acceptable precision of the proficiency level estimate using an optimal number of items. Unfortunately, decreasing the number of items is accompanied by a certain degree of bias when the true proficiency level differs significantly from the a priori estimate. The authors suggest that it is possible to reduced the bias, and even the standard error of the estimate, by applying to each provisional estimation one or a combination of the following strategies: adaptive correction for bias proposed by Bock and Mislevy (1982), adaptive a priori estimate, and adaptive integration interval.

Epistasis can accelerate adaptive diversification in haploid asexual populations.

Science.gov (United States)

Griswold, Cortland K

2015-03-07

A fundamental goal of the biological sciences is to determine processes that facilitate the evolution of diversity. These processes can be separated into ecological, physiological, developmental and genetic. An ecological process that facilitates diversification is frequency-dependent selection caused by competition. Models of frequency-dependent adaptive diversification have generally assumed a genetic basis of phenotype that is non-epistatic. Here, we present a model that indicates diversification is accelerated by an epistatic basis of phenotype in combination with a competition model that invokes frequency-dependent selection. Our model makes use of a genealogical model of epistasis and insights into the effects of balancing selection on the genealogical structure of a population to understand how epistasis can facilitate diversification. The finding that epistasis facilitates diversification may be informative with respect to empirical results that indicate an epistatic basis of phenotype in experimental bacterial populations that experienced adaptive diversification. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Influence of neural adaptation on dynamics and equilibrium state of neural activities in a ring neural network

Science.gov (United States)

Takiyama, Ken

2017-12-01

How neural adaptation affects neural information processing (i.e. the dynamics and equilibrium state of neural activities) is a central question in computational neuroscience. In my previous works, I analytically clarified the dynamics and equilibrium state of neural activities in a ring-type neural network model that is widely used to model the visual cortex, motor cortex, and several other brain regions. The neural dynamics and the equilibrium state in the neural network model corresponded to a Bayesian computation and statistically optimal multiple information integration, respectively, under a biologically inspired condition. These results were revealed in an analytically tractable manner; however, adaptation effects were not considered. Here, I analytically reveal how the dynamics and equilibrium state of neural activities in a ring neural network are influenced by spike-frequency adaptation (SFA). SFA is an adaptation that causes gradual inhibition of neural activity when a sustained stimulus is applied, and the strength of this inhibition depends on neural activities. I reveal that SFA plays three roles: (1) SFA amplifies the influence of external input in neural dynamics; (2) SFA allows the history of the external input to affect neural dynamics; and (3) the equilibrium state corresponds to the statistically optimal multiple information integration independent of the existence of SFA. In addition, the equilibrium state in a ring neural network model corresponds to the statistically optimal integration of multiple information sources under biologically inspired conditions, independent of the existence of SFA.

Implied Movement in Static Images Reveals Biological Timing Processing

Directory of Open Access Journals (Sweden)

Francisco Carlos Nather

2015-08-01

Full Text Available Visual perception is adapted toward a better understanding of our own movements than those of non-conspecifics. The present study determined whether time perception is affected by pictures of different species by considering the evolutionary scale. Static (“S” and implied movement (“M” images of a dog, cheetah, chimpanzee, and man were presented to undergraduate students. S and M images of the same species were presented in random order or one after the other (S-M or M-S for two groups of participants. Movement, Velocity, and Arousal semantic scales were used to characterize some properties of the images. Implied movement affected time perception, in which M images were overestimated. The results are discussed in terms of visual motion perception related to biological timing processing that could be established early in terms of the adaptation of humankind to the environment.

Cytogenetic dose-response and adaptive response in cells of ungulate species exposed to ionizing radiation

International Nuclear Information System (INIS)

Ulsh, B.A.; Miller, S.M.; Mallory, F.F.; Mitchel, R.E.J.; Morrison, D.P.; Boreham, D.R.

2004-01-01

In the studies reported here, the micronucleus assay, a common cytogenetic technique, was used to examine the dose-responses in fibroblasts from three ungulate species (white-tailed deer, woodland caribou, and Indian muntjac) exposed to high doses of ionizing radiation (1-4 Gy of 60 Co gamma radiation). This assay was also used to examine the effects of exposure to low doses (1-100 mGy) typical of what these species experience in a year from natural and anthropogenic environmental sources. An adaptive response, defined as the induction of resistance to a stressor by a prior exposure to a small 'adapting' stress, was observed after exposure to low doses. This work indicates that very small doses are protective for the endpoint examined. The same level of protection was seen at all adapting doses, including 1 radiation track per cell, the lowest possible cellular dose. These results are consistent with other studies in a wide variety of organisms that demonstrate a protective effect of low doses at both cellular and whole-organism levels. This implies that environmental regulations predicated on the idea that even the smallest dose of radiation carries a quantifiable risk of direct adverse consequences to the exposed organism require further examination. Cytogenetic assays provide affordable and feasible biological effects-based alternatives that are more biologically relevant than traditional contaminant concentration-based radioecological risk assessment

Modeling adaptive and non-adaptive responses to environmental change

DEFF Research Database (Denmark)

Coulson, Tim; Kendall, Bruce E; Barthold, Julia A.

2017-01-01

, with plastic responses being either adaptive or non-adaptive. We develop an approach that links quantitative genetic theory with data-driven structured models to allow prediction of population responses to environmental change via plasticity and adaptive evolution. After introducing general new theory, we...... construct a number of example models to demonstrate that evolutionary responses to environmental change over the short-term will be considerably slower than plastic responses, and that the rate of adaptive evolution to a new environment depends upon whether plastic responses are adaptive or non-adaptive....... Parameterization of the models we develop requires information on genetic and phenotypic variation and demography that will not always be available, meaning that simpler models will often be required to predict responses to environmental change. We consequently develop a method to examine whether the full...

Camels, Cormorants, and Kangaroo Rats: Integration and Synthesis in Organismal Biology After World War II.

Science.gov (United States)

Hagen, Joel B

2015-01-01

During the decades following World War II diverse groups of American biologists established a variety of distinctive approaches to organismal biology. Rhetorically, organismal biology could be used defensively to distinguish established research traditions from perceived threats from newly emerging fields such as molecular biology. But, organismal biologists were also interested in integrating biological disciplines and using a focus on organisms to synthesize levels of organization from molecules and cells to populations and communities. Part of this broad movement was the development of an area of research variously referred to as physiological ecology, environmental physiology, or ecophysiology. This area of research was distinctive in its self-conscious blend of field and laboratory practices and its explicit integration with other areas of biology such as ecology, animal behavior, and evolution in order to study adaptation. Comparing the intersecting careers of Knut Schmidt-Nielsen and George Bartholomew highlights two strikingly different approaches to physiological ecology. These alternative approaches to studying the interactions of organisms and environments also differed in important ways from the organismal biology championed by leading figures in the modern synthesis.

Is synthetic biology mechanical biology?

Science.gov (United States)

Holm, Sune

2015-12-01

A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

The Halogenated Metabolism of Brown Algae (Phaeophyta, Its Biological Importance and Its Environmental Significance

Directory of Open Access Journals (Sweden)

Stéphane La Barre

2010-03-01

Full Text Available Brown algae represent a major component of littoral and sublittoral zones in temperate and subtropical ecosystems. An essential adaptive feature of this independent eukaryotic lineage is the ability to couple oxidative reactions resulting from exposure to sunlight and air with the halogenations of various substrates, thereby addressing various biotic and abiotic stresses i.e., defense against predators, tissue repair, holdfast adhesion, and protection against reactive species generated by oxidative processes. Whereas marine organisms mainly make use of bromine to increase the biological activity of secondary metabolites, some orders of brown algae such as Laminariales have also developed a striking capability to accumulate and to use iodine in physiological adaptations to stress. We review selected aspects of the halogenated metabolism of macrophytic brown algae in the light of the most recent results, which point toward novel functions for iodide accumulation in kelps and the importance of bromination in cell wall modifications and adhesion properties of brown algal propagules. The importance of halogen speciation processes ranges from microbiology to biogeochemistry, through enzymology, cellular biology and ecotoxicology.

Effect of rare-earth-based nanoparticles on the erythrocyte osmotic adaptation

OpenAIRE

О. К. Пакулова; В. К. Kлочков; Н. С. Кавок; И. А. Костина; А. С. Сопотова; В. А. Бондаренко

2017-01-01

Rare-earth-based nanoparticles (REB NPs) have been employed in molecular and cell biology due to their unique features. However, their interaction with biosystems and the influence on cell functioning are poorly understood. In this study effect of REB NPs (composed of dielectric nanocrystalls of cerium dioxide and orthovanadates of gadolinium and yttrium) with different form-factor as well as REB NPs-cholesterol complexes on the adaptation of human erythrocytes to hypertonic lysis (4 M NaCl) ...

NASA Biological Specimen Repository

Science.gov (United States)

McMonigal, K. A.; Pietrzyk, R. A.; Sams, C. F.; Johnson, M. A.

2010-01-01

The NASA Biological Specimen Repository (NBSR) was established in 2006 to collect, process, preserve and distribute spaceflight-related biological specimens from long duration ISS astronauts. This repository provides unique opportunities to study longitudinal changes in human physiology spanning may missions. The NBSR collects blood and urine samples from all participating ISS crewmembers who have provided informed consent. These biological samples are collected once before flight, during flight scheduled on flight days 15, 30, 60, 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days after landing. The number of in-flight sessions is dependent on the duration of the mission. Specimens are maintained under optimal storage conditions in a manner that will maximize their integrity and viability for future research The repository operates under the authority of the NASA/JSC Committee for the Protection of Human Subjects to support scientific discovery that contributes to our fundamental knowledge in the area of human physiological changes and adaptation to a microgravity environment. The NBSR will institute guidelines for the solicitation, review and sample distribution process through establishment of the NBSR Advisory Board. The Advisory Board will be composed of representatives of all participating space agencies to evaluate each request from investigators for use of the samples. This process will be consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. Operations supporting the NBSR are scheduled to continue until the end of U.S. presence on the ISS. Sample distribution is proposed to begin with selections on investigations beginning in 2017. The availability of the NBSR will contribute to the body of knowledge about the diverse factors of spaceflight on human physiology.

Adventures in human population biology.

Science.gov (United States)

Baker, P T

1996-01-01

This article is a memoir of anthropologist Paul Baker's professional life. The introduction notes that the field of anthropology was altered by the impact of World War II when physical anthropologists provided vital information to the military. After the war, the GI bill supported the undergraduate and graduate studies of veterans, including Baker. After describing his academic training at the University of New Mexico and Harvard, Baker details his research training and field work in the desert for the US Climatic Research Laboratory and his work identifying the dead in Japan for the Quartermaster unit. Baker then traces his academic career at the Pennsylvania State University during which he directed two multidisciplinary research efforts for the International Biological Programme, one that sought to understand human adaptability at high altitude in Peru and another that studied migration and modernization in Samoa. Baker's last administrative positions were as staff consultant to the Man and the Biosphere (MAB) program and as chair of the US MAB committee. Baker retired from academic life at age 60 in 1987 and has devoted his time to reading and to helping organize professional associations in anthropology, especially those devoted to furthering internationally organized scientific efforts. Baker concludes this memoir by acknowledging the growth and development of the discipline of human population biology.

Adaptive management and monitoring for birds and bats

Energy Technology Data Exchange (ETDEWEB)

Palmer, C. [Bear Mountain Wind Ltd., BC (Canada); Hemmera, Vancouver, BC (Canada)

2010-07-01

The wind power industry is still in its infancy in British Columbia, and the potential impacts to the province's environment and resources are not well-understood. This PowerPoint presentation discussed the adaptive management techniques used at the Bear Mountain Wind park. The techniques were used to address uncertainty related to mitigation needs, to reduce project costs associated with mitigation, and to provide biological data. The long-term monitoring project was conducted to address uncertainties about potential environmental impacts in the region and to reduce the potential for regulatory delays. Impacts associated with the development of a wind power plant include loss of habitat, sensory disturbances, and potential collisions with birds and bats. Mitigation strategies include the careful placement of turbines in certain areas, timing alterations, and the use of a cut-in speed. Adaptive management techniques were used to improve mitigation strategies and monitor their success. The techniques facilitated environmental assessment approvals and deferred mitigation procedures until they were needed. Bat and raptor collision data collected at the site were included. figs.

Models to Study NK Cell Biology and Possible Clinical Application.

Science.gov (United States)

Zamora, Anthony E; Grossenbacher, Steven K; Aguilar, Ethan G; Murphy, William J

2015-08-03

Natural killer (NK) cells are large granular lymphocytes of the innate immune system, responsible for direct targeting and killing of both virally infected and transformed cells. NK cells rapidly recognize and respond to abnormal cells in the absence of prior sensitization due to their wide array of germline-encoded inhibitory and activating receptors, which differs from the receptor diversity found in B and T lymphocytes that is due to the use of recombination-activation gene (RAG) enzymes. Although NK cells have traditionally been described as natural killers that provide a first line of defense prior to the induction of adaptive immunity, a more complex view of NK cells is beginning to emerge, indicating they may also function in various immunoregulatory roles and have the capacity to shape adaptive immune responses. With the growing appreciation for the diverse functions of NK cells, and recent technological advancements that allow for a more in-depth understanding of NK cell biology, we can now begin to explore new ways to manipulate NK cells to increase their clinical utility. In this overview unit, we introduce the reader to various aspects of NK cell biology by reviewing topics ranging from NK cell diversity and function, mouse models, and the roles of NK cells in health and disease, to potential clinical applications. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.

Vulnerability Assessment, Climate Change Impacts and Adaptation Measures in Slovenia

Science.gov (United States)

Cegnar, T.

2010-09-01

In relation to the priority tasks of the climate change measures, the Republic of Slovenia estimates that special attention needs to be devoted to the following sectors in general: - sectors that currently indicate a strong vulnerability for the current climate variability (for instance, agriculture), - sectors where the vulnerability for climate change is increased by current trends (for instance, urban development, use of space), - sectors where the adaptation time is the longest and the subsequent development changes are connected with the highest costs (for instance, use of space, infrastructural objects, forestry, urban development, building stock). Considering the views of Slovenia to the climate change problem in Europe and Slovenia, priority measures and emphasis on future adaptation to climate change, the Republic of Slovenia has especially exposed the following action areas: - sustainable and integrated management of water sources for water power production, prevention of floods, provision of water for the enrichment of low flow rates, and preservation of environmental function as well as provision of water for other needs; - sustainable management of forest ecosystems, adjusted to changes, for the provision of their environmental function as well as being a source of biomass, wood for products for the conservation of carbon, and carbon sinks; - spatial planning as one of the important preventive instruments for the adaptation to climate change through the processes of integral planning of spatial and urban development; - sustainable use and preservation of natural wealth and the preservation of biodiversity as well as ecosystem services with measures and policies that enable an enhanced resistance of ecosystems to climate change, and the role of biological diversity in integral adaptation measures; - informing and awareness on the consequences of climate change and adaptation possibilities. For years, the most endangered sectors have been agriculture and

Adaptation research meets adaptation decision-making. Second Nordic international conference on climate change adaption. Programme and abstracts

Energy Technology Data Exchange (ETDEWEB)

NONE

2012-07-01

Nearly two years have passed since a small team of researchers began a new chapter in Nordic co-operation on climate change by organising a conference in Stockholm, Sweden. The conference, entitled Climate Adaptation in the Nordic Countries - Science, Practice, Policy, co-ordinated by the Stockholm Environment Institute and hosted by Stockholm University in November 2010, was the first of its kind in the Nordic region. Since the European Commission adopted its White Paper on adaptation to climate change in 2009, many of that document's 33 actions have been implemented, a climate change adaptation platform, Climate-ADAPT, was launched at the European Environment Agency in March this year, and just a week before this conference the Commission concluded a public consultation of stakeholders and experts in member states designed to feed into the preparation of a European Union adaptation strategy. The 2012 conference therefore presents an ideal opportunity to take stock of ongoing efforts and to consider how adaptation research efforts are keeping pace with policy demands as well as the needs of public and private decision-makers operating at a range of scales. It brings together researchers, public and private decision- makers, as well as those who plan and realize adaptation plans. Session themes include, among others: national and local adaptation plans, climate portals and climate services, adaptation in developing countries, legal aspects of adaptation, economic appraisal of adaptation, analysing and handling risk and uncertainty, urban planning and scenarios. The contributors have very diverse backgrounds, ranging from biosciences to social sciences, economics to geo-sciences, and engineering to architecture. Interest in climate change adaptation in the Nordic region is clearly high, with over 70% of our participants drawn from the five Nordic countries, but the conference has also managed to attract participation from further afield, with registrations

Trade-offs in thermal adaptation: the need for a molecular to ecological integration.

Science.gov (United States)

Pörtner, Hans O; Bennett, Albert F; Bozinovic, Francisco; Clarke, Andrew; Lardies, Marco A; Lucassen, Magnus; Pelster, Bernd; Schiemer, Fritz; Stillman, Jonathon H

2006-01-01

Through functional analyses, integrative physiology is able to link molecular biology with ecology as well as evolutionary biology and is thereby expected to provide access to the evolution of molecular, cellular, and organismic functions; the genetic basis of adaptability; and the shaping of ecological patterns. This paper compiles several exemplary studies of thermal physiology and ecology, carried out at various levels of biological organization from single genes (proteins) to ecosystems. In each of those examples, trade-offs and constraints in thermal adaptation are addressed; these trade-offs and constraints may limit species' distribution and define their level of fitness. For a more comprehensive understanding, the paper sets out to elaborate the functional and conceptual connections among these independent studies and the various organizational levels addressed. This effort illustrates the need for an overarching concept of thermal adaptation that encompasses molecular, organellar, cellular, and whole-organism information as well as the mechanistic links between fitness, ecological success, and organismal physiology. For this data, the hypothesis of oxygen- and capacity-limited thermal tolerance in animals provides such a conceptual framework and allows interpreting the mechanisms of thermal limitation of animals as relevant at the ecological level. While, ideally, evolutionary studies over multiple generations, illustrated by an example study in bacteria, are necessary to test the validity of such complex concepts and underlying hypotheses, animal physiology frequently is constrained to functional studies within one generation. Comparisons of populations in a latitudinal cline, closely related species from different climates, and ontogenetic stages from riverine clines illustrate how evolutionary information can still be gained. An understanding of temperature-dependent shifts in energy turnover, associated with adjustments in aerobic scope and performance

Adaptive steganography

Science.gov (United States)

Chandramouli, Rajarathnam; Li, Grace; Memon, Nasir D.

2002-04-01

Steganalysis techniques attempt to differentiate between stego-objects and cover-objects. In recent work we developed an explicit analytic upper bound for the steganographic capacity of LSB based steganographic techniques for a given false probability of detection. In this paper we look at adaptive steganographic techniques. Adaptive steganographic techniques take explicit steps to escape detection. We explore different techniques that can be used to adapt message embedding to the image content or to a known steganalysis technique. We investigate the advantages of adaptive steganography within an analytical framework. We also give experimental results with a state-of-the-art steganalysis technique demonstrating that adaptive embedding results in a significant number of bits embedded without detection.

Analysis of the biological spectrum of vascular flora of Ravni Srem flood forests

Directory of Open Access Journals (Sweden)

Jurišić Branislav

2011-01-01

Full Text Available One of the essential analyses performed during the floristic study of a region is the analysis of the biological spectrum. The analysis of the biological spectrum of the flora includes the determination of the type of life form for each taxon described in the flora of the study region. If it is considered that life form is a specific structural-functional response to the environmental effects and the result of the adaptation during the species evolution, it is clear that the basic characteristics of the site are more or less reflected in any life form. This fact is confirmed by the analysis of the biological spectrum of the flora of Ravni Srem. The analysis of the Ravni Srem flora shows the domination of the hemicryptophytes and the subdomination of the phanerophytes with a considerable participation of the therophytes.

Adaptive versus Non-Adaptive Security of Multi-Party Protocols

DEFF Research Database (Denmark)

Canetti, Ran; Damgård, Ivan Bjerre; Dziembowski, Stefan

2004-01-01

Security analysis of multi-party cryptographic protocols distinguishes between two types of adversarial settings: In the non-adaptive setting the set of corrupted parties is chosen in advance, before the interaction begins. In the adaptive setting the adversary chooses who to corrupt during...... the course of the computation. We study the relations between adaptive security (i.e., security in the adaptive setting) and nonadaptive security, according to two definitions and in several models of computation....

Consortium biology in immunology: the perspective from the Immunological Genome Project.

OpenAIRE

Benoist, C; Lanier, L; Merad, M; Mathis, D; Immunological Genome Project,

2012-01-01

Although the field has a long collaborative tradition, immunology has made less use than genetics of 'consortium biology', wherein groups of investigators together tackle large integrated questions or problems. However, immunology is naturally suited to large-scale integrative and systems-level approaches, owing to the multicellular and adaptive nature of the cells it encompasses. Here, we discuss the value and drawbacks of this organization of research, in the context of the long-running 'bi...

Thermodynamics of adaptive molecular resolution.

Science.gov (United States)

Delgado-Buscalioni, R

2016-11-13

A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U (1) -U (0) The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al, J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as 'real' thermodynamic variablesThis article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Redox processes in radiation biology and cancer

International Nuclear Information System (INIS)

Greenstock, C.L.

1981-01-01

Free-radical intermediates, particularly the activated oxygen species OH, O - 2 , and 1 O 2 , are implicated in many types of radiation damage to biological systems. In addition, these same species may be formed, either directly or indirectly through biochemical redox reactions, in both essential and aberrant metabolic processes. Cell survival and adaptation to an environment containing ionizing radiation and other physical and chemical carcinogens ultimately depend upon the cell's ability to maintain optimal function in response to free-radical damage at the chemical level. Many of these feedback control mechanisms are redox controlled. Radiation chemical techniques using selective radical scavengers, such as product analysis and pulse radiolysis, enable us to generate, observe, and characterize individually the nature and reactivity of potentially damaging free radicals. From an analysis of the chemical kinetics of free-radical involvement in biological damage, redox mechanisms are proposed to describe the early processes of radiation damage, redox mechanisms are proposed to describe the early processes of radiation damage, its protection and sensitization, and the role of free radicals in radiation and chemical carcinogenesis

AID Biology: A pathological and clinical perspective.

Science.gov (United States)

Choudhary, Meenal; Tamrakar, Anubhav; Singh, Amit Kumar; Jain, Monika; Jaiswal, Ankit; Kodgire, Prashant

2018-01-02

Activation-induced cytidine deaminase (AID), primarily expressed in activated mature B lymphocytes in germinal centers, is the key factor in adaptive immune response against foreign antigens. AID is responsible for producing high-affinity and high-specificity antibodies against an infectious agent, through the physiological DNA alteration processes of antibody genes by somatic hypermutation (SHM) and class-switch recombination (CSR) and functions by deaminating deoxycytidines (dC) to deoxyuridines (dU), thereby introducing point mutations and double-stranded chromosomal breaks (DSBs). The beneficial physiological role of AID in antibody diversification is outweighed by its detrimental role in the genesis of several chronic immune diseases, under non-physiological conditions. This review offers a comprehensive and better understanding of AID biology and its pathological aspects, as well as addresses the challenges involved in AID-related cancer therapeutics, based on various recent advances and evidence available in the literature till date. In this article, we discuss ways through which our interpretation of AID biology may reflect upon novel clinical insights, which could be successfully translated into designing clinical trials and improving patient prognosis and disease management.

2010 Plant Molecular Biology Gordon Research Conference

Energy Technology Data Exchange (ETDEWEB)

Michael Sussman

2010-07-23

The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2010 conference will continue in that tradition. Emerging concerns about food security have inspired a program with three main themes: (1) genomics, natural variation and breeding to understand adaptation and crop improvement, (2) hormonal cross talk, and (3) plant/microbe interactions. There are also sessions on epigenetics and proteomics/metabolomics. Thus this conference will bring together a range of disciplines, will foster the exchange of ideas and enable participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner. In particular, this conference plays a key role in enabling students and postdocs (the next generation of research leaders) to mingle with pioneers in multiple areas of plant science.

Adapt

Science.gov (United States)

Bargatze, L. F.

2015-12-01

Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted

Resilience through adaptation.

Directory of Open Access Journals (Sweden)

Guus A Ten Broeke

Full Text Available Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS. Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations with agent-based models (ABMs provide a helpful tool. However, the value of ABMs for studying adaptation depends on the availability of methodologies for sensitivity analysis that can quantify resilience and adaptation in ABMs. In this paper we propose a sensitivity analysis methodology that is based on comparing time-dependent probability density functions of output of ABMs with and without agent adaptation. The differences between the probability density functions are quantified by the so-called earth-mover's distance. We use this sensitivity analysis methodology to quantify the probability of occurrence of critical transitions and other long-term effects of agent adaptation. To test the potential of this new approach, it is used to analyse the resilience of an ABM of adaptive agents competing for a common-pool resource. Adaptation is shown to contribute positively to the resilience of this ABM. If adaptation proceeds sufficiently fast, it may delay or avert the collapse of this system.

Resilience through adaptation.

Science.gov (United States)

Ten Broeke, Guus A; van Voorn, George A K; Ligtenberg, Arend; Molenaar, Jaap

2017-01-01

Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS). Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations with agent-based models (ABMs) provide a helpful tool. However, the value of ABMs for studying adaptation depends on the availability of methodologies for sensitivity analysis that can quantify resilience and adaptation in ABMs. In this paper we propose a sensitivity analysis methodology that is based on comparing time-dependent probability density functions of output of ABMs with and without agent adaptation. The differences between the probability density functions are quantified by the so-called earth-mover's distance. We use this sensitivity analysis methodology to quantify the probability of occurrence of critical transitions and other long-term effects of agent adaptation. To test the potential of this new approach, it is used to analyse the resilience of an ABM of adaptive agents competing for a common-pool resource. Adaptation is shown to contribute positively to the resilience of this ABM. If adaptation proceeds sufficiently fast, it may delay or avert the collapse of this system.

Science of adaptation to climate change and science for adaptation

Directory of Open Access Journals (Sweden)

Rob eSwart

2014-07-01

Full Text Available Adaptation to climate change has gained a prominent place next to mitigation on global, national and local policy agendas. However, while an abundance of adaptation strategies, plans and programmes have been developed, progress in turning these into action has been slow. The development of a sound knowledge basis to support adaptation globally is suggested to accelerate progress, but has lagged behind. The emphasis in both current and newly proposed programmes is very much on practice-oriented research with strong stakeholder participation. This paper supports such practice-oriented research, but argues that this is insufficient to support adaptation policy and practice in a productive manner. We argue that there is not only a need for science for adaptation, but also a science of adaptation. The paper argues that participatory, practice-oriented research is indeed essential, but has to be complemented by and connected to more fundamental inquiry and concept development, which takes into account knowledge that has been developed in disciplinary sciences and on issues other than climate change adaptation. At the same time, the level and method of participation in science for adaptation should be determined on the basis of the specific project context and goals. More emphasis on science of adaptation can lead to improved understanding of the conditions for successful science for adaptation.

Expressing Adaptation Strategies Using Adaptation Patterns

Science.gov (United States)

Zemirline, N.; Bourda, Y.; Reynaud, C.

2012-01-01

Today, there is a real challenge to enable personalized access to information. Several systems have been proposed to address this challenge including Adaptive Hypermedia Systems (AHSs). However, the specification of adaptation strategies remains a difficult task for creators of such systems. In this paper, we consider the problem of the definition…

Distinct biological effects of different nanoparticles commonly used in cosmetics and medicine coatings

Directory of Open Access Journals (Sweden)

Yu Julia X

2011-05-01

Full Text Available Abstract Background Metal oxides in nanoparticle form such as zinc oxide and titanium dioxide now appear on the ingredient lists of household products as common and diverse as cosmetics, sunscreens, toothpaste, and medicine. Previous studies of zinc oxide and titanium dioxide in non-nanoparticle format using animals have found few adverse effects. This has led the FDA to classify zinc oxide as GRAS (generally recognized as safe for use as a food additive. However, there is no regulation specific for the use of these chemicals in nanoparticle format. Recent studies, however, have begun to raise concerns over the pervasive use of these compounds in nanoparticle forms. Unfortunately, there is a lack of easily-adaptable screening methods that would allow for the detection of their biological effects. Results We adapted two image-based assays, a fluorescence resonance energy transfer-based caspase activation assay and a green fluorescent protein coupled-LC3 assay, to test for the biological effects of different nanoparticles in a high-throughput format. We show that zinc oxide nanoparticles are cytotoxic. We also show that titanium dioxide nanoparticles are highly effective in inducing autophagy, a cellular disposal mechanism that is often activated when the cell is under stress. Conclusion We suggest that these image-based assays provide a method of screening for the biological effects of similar compounds that is both efficient and sensitive as well as do not involve the use of animals.

Generic adaptation framework for unifying adaptive web-based systems

NARCIS (Netherlands)

Knutov, E.

2012-01-01

The Generic Adaptation Framework (GAF) research project first and foremost creates a common formal framework for describing current and future adaptive hypermedia (AHS) and adaptive webbased systems in general. It provides a commonly agreed upon taxonomy and a reference model that encompasses the

Biology of teeth and implants: Host factors - pathology, regeneration, and the role of stem cells.

Science.gov (United States)

Eggert, F-Michael; Levin, Liran

2018-01-01

In chronic periodontitis and peri-implantitis, cells of the innate and adaptive immune systems are involved directly in the lesions within the tissues of the patient. Absence of a periodontal ligament around implants does not prevent a biologic process similar to that of periodontitis from affecting osseointegration. Our first focus is on factors in the biology of individuals that are responsible for the susceptibility of such individuals to chronic periodontitis and to peri-implantitis. Genetic factors are of significant importance in susceptibility to these diseases. Genetic factors of the host affect the composition of the oral microbiome in the same manner that they influence other microbiomes, such as those of the intestines and of the lungs. Our second focus is on the central role of stem cells in tissue regeneration, in the functioning of innate and adaptive immune systems, and in metabolism of bone. Epithelial cell rests of Malassez (ERM) are stem cells of epithelial origin that maintain the periodontal ligament as well as the cementum and alveolar bone associated with the ligament. The tissue niche within which ERM are found extends into the supracrestal areas of collagen fiber-containing tissues of the gingivae above the bony alveolar crest. Maintenance and regeneration of all periodontal tissues involves the activity of a variety of stem cells. The success of dental implants indicates that important groups of stem cells in the periodontium are active to enable that biologic success. Successful replantation of avulsed teeth and auto-transplantation of teeth is comparable to placing dental implants, and so must also involve periodontal stem cells. Biology of teeth and biology of implants represents the biology of the various stem cells that inhabit specialized niches within the periodontal tissues. Diverse biologic processes must function together successfully to maintain periodontal health. Osseointegration of dental implants does not involve formation of

Typology in pollination biology: Lessons from an historical critique

Directory of Open Access Journals (Sweden)

Andreas Erhardt

2011-03-01

Full Text Available Typological schemes that describe putative floral adaptations for pollinators have played a central role in pollination biology. In 1882 the prominent German botanist and Darwinist Hermann Müller commented critically on a precursor of modern versions of such “pollination syndromes” that had been developed by his Italian colleague Federico Delpino. Delpino also was a self-proclaimed Darwinist, but in fact adhered to teleology—explanation beyond nature. As a consequence he viewed his typology as reflecting a deeper ideal and thus as rigidly true, and rejected as unimportant any visitors to flowers that it did not predict. Although Müller also classified flowers as to pollinators, he considered such schemes to be fallible, and pondered what diversity and variation in floral visitors might mean. Müller’s comments, which we translate here, are of interest given that appeals to teleology have resurfaced from time to time in discussions of pollination syndromes, and more importantly because his warning against taking typological schemes too literally remains valid. Typology is a useful tool in biology, including pollination biology, but care must be taken that it does not replace nature as perceived reality.

Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

Science.gov (United States)

2013-01-01

Background Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data. The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data. PMID:24059747

Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances.

Science.gov (United States)

Wagner, James M; Alper, Hal S

2016-04-01

Coupling the tools of synthetic biology with traditional molecular genetic techniques can enable the rapid prototyping and optimization of yeast strains. While the era of yeast synthetic biology began in the well-characterized model organism Saccharomyces cerevisiae, it is swiftly expanding to include non-conventional yeast production systems such as Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. These yeasts already have roles in the manufacture of vaccines, therapeutic proteins, food additives, and biorenewable chemicals, but recent synthetic biology advances have the potential to greatly expand and diversify their impact on biotechnology. In this review, we summarize the development of synthetic biological tools (including promoters and terminators) and enabling molecular genetics approaches that have been applied in these four promising alternative biomanufacturing platforms. An emphasis is placed on synthetic parts and genome editing tools. Finally, we discuss examples of synthetic tools developed in other organisms that can be adapted or optimized for these hosts in the near future. Copyright © 2015 Elsevier Inc. All rights reserved.

Ecological opportunity and the adaptive diversification of lineages.

Science.gov (United States)

Wellborn, Gary A; Langerhans, R Brian

2015-01-01

The tenet that ecological opportunity drives adaptive diversification has been central to theories of speciation since Darwin, yet no widely accepted definition or mechanistic framework for the concept currently exists. We propose a definition for ecological opportunity that provides an explicit mechanism for its action. In our formulation, ecological opportunity refers to environmental conditions that both permit the persistence of a lineage within a community, as well as generate divergent natural selection within that lineage. Thus, ecological opportunity arises from two fundamental elements: (1) niche availability, the ability of a population with a phenotype previously absent from a community to persist within that community and (2) niche discordance, the diversifying selection generated by the adaptive mismatch between a population's niche-related traits and the newly encountered ecological conditions. Evolutionary response to ecological opportunity is primarily governed by (1) spatiotemporal structure of ecological opportunity, which influences dynamics of selection and development of reproductive isolation and (2) diversification potential, the biological properties of a lineage that determine its capacity to diversify. Diversification under ecological opportunity proceeds as an increase in niche breadth, development of intraspecific ecotypes, speciation, and additional cycles of diversification that may themselves be triggered by speciation. Extensive ecological opportunity may exist in depauperate communities, but it is unclear whether ecological opportunity abates in species-rich communities. Because ecological opportunity should generally increase during times of rapid and multifarious environmental change, human activities may currently be generating elevated ecological opportunity - but so far little work has directly addressed this topic. Our framework highlights the need for greater synthesis of community ecology and evolutionary biology, unifying

Reservoir-based Online Adaptive Forward Models with Neural Control for Complex Locomotion in a Hexapod Robot

DEFF Research Database (Denmark)

Manoonpong, Poramate; Dasgupta, Sakyasingha; Goldschmidt, Dennis

2014-01-01

Walking animals show fascinating locomotor abilities and complex behaviors. Biological study has revealed that such complex behaviors is a result of a combination of biomechanics and neural mechanisms. While biomechanics allows for flexibility and a variety of movements, neural mechanisms generate...... locomotion, make predictions, and provide adaptation. Inspired by this finding, we present here an artificial bio-inspired walking system which combines biomechanics (in terms of its body and leg structures) and neural mechanisms. The neural mechanisms consist of 1) central pattern generator-based control...... for generating basic rhythmic patterns and coordinated movements, 2) reservoir-based adaptive forward models with efference copies for sensory prediction as well as state estimation, and 3) searching and elevation control for adapting the movement of an individual leg to deal with different environmental...

Sleep Strategies of Night-Shift Nurses on Days Off: Which Ones are Most Adaptive?

Science.gov (United States)

Petrov, Megan E; Clark, C Brendan; Molzof, Hylton E; Johnson, Russell L; Cropsey, Karen L; Gamble, Karen L

2014-01-01

To determine the off-shift sleep strategies of bi-ethnic night-shift nurses, the relationship between these sleep strategies and adaptation to shift work, and identify the participant-level characteristics associated with a given sleep strategy. African-American and non-Hispanic White female, night-shift nurses from an academic hospital were recruited to complete a survey on sleep-wake patterns (n = 213). Participants completed the standard shiftwork index and the biological clocks questionnaire to determine sleep strategies and adaptation to night-shift work. In addition, chronotype was determined quantitatively with a modified version of the Munich ChronoType Questionnaire. Most participants worked ~3 consecutive 12-h night-shifts followed by several days off. Five sleep strategies used on days off were identified: (a) night stay, (b) nap proxy, (c) switch sleeper, (d) no sleep, and (e) incomplete switcher. Nap proxy and no sleep types were associated with poorer adaptation to night-shift work. The switch sleeper and incomplete switcher types were identified as more adaptive strategies that were associated with less sleep disturbance, a later chronotype, and less cardiovascular problems. Behavioral sleep strategies are related to adaptation to a typical night-shift schedule among hospital nurses. Nurses are crucial to the safety and well-being of their patients. Therefore, adoption of more adaptive sleep strategies may reduce sleep/wake dysregulation in this population, and improve cardiovascular outcomes.

Contribution of silent mutations to thermal adaptation of RNA bacteriophage Qβ.

Science.gov (United States)

Kashiwagi, Akiko; Sugawara, Ryu; Sano Tsushima, Fumie; Kumagai, Tomofumi; Yomo, Tetsuya

2014-10-01

Changes in protein function and other biological properties, such as RNA structure, are crucial for adaptation of organisms to novel or inhibitory environments. To investigate how mutations that do not alter amino acid sequence may be positively selected, we performed a thermal adaptation experiment using the single-stranded RNA bacteriophage Qβ in which the culture temperature was increased from 37.2°C to 41.2°C and finally to an inhibitory temperature of 43.6°C in a stepwise manner in three independent lines. Whole-genome analysis revealed 31 mutations, including 14 mutations that did not result in amino acid sequence alterations, in this thermal adaptation. Eight of the 31 mutations were observed in all three lines. Reconstruction and fitness analyses of Qβ strains containing only mutations observed in all three lines indicated that five mutations that did not result in amino acid sequence changes but increased the amplification ratio appeared in the course of adaptation to growth at 41.2°C. Moreover, these mutations provided a suitable genetic background for subsequent mutations, altering the fitness contribution from deleterious to beneficial. These results clearly showed that mutations that do not alter the amino acid sequence play important roles in adaptation of this single-stranded RNA virus to elevated temperature. Recent studies using whole-genome analysis technology suggested the importance of mutations that do not alter the amino acid sequence for adaptation of organisms to novel environmental conditions. It is necessary to investigate how these mutations may be positively selected and to determine to what degree such mutations that do not alter amino acid sequences contribute to adaptive evolution. Here, we report the roles of these silent mutations in thermal adaptation of RNA bacteriophage Qβ based on experimental evolution during which Qβ showed adaptation to growth at an inhibitory temperature. Intriguingly, four synonymous mutations and

TRIBE TRITICEAE L. AND THE BIOCENOTIC MECHANISMS OF ADAPTABILITY

Directory of Open Access Journals (Sweden)

T. Z. Moskalets

2016-08-01

Full Text Available The cultural species in the process ontogenesis and phylogenesis to favorable and unfavorable environmental conditions produce a number of biological mechanisms (molecular genetic, physiological, biochemical, morphological, biocenotic, plants identification behind them reflects the degree of their ecological of adaptability, plasticity and stability. Studying the and comparison of morphological parameters and relations with consort-species and representatives of tribe Triticeae allowed to find out what plants differently realize their life potential. Which are based on structural and functional features biocenotic mechanisms that manifested in adaptive properties. On example cultural cereal species shows that the basic mechanisms of adaptability are: mechanisms of functional sustainability, morphological tolerance and ontogenetic avoidance. The first group is associated with functional parameters forming and manifestation life potential of plants (accumulation protein, accumulation gluten, duration assimilatory ability flag leaf; erection leaves the upper tier; depth of node tillering; strength of the stem, ie the, low penchant to lodging; total tillering plants; synchronicity growth of main stem; the intensity fading ear after full ripeness. The second group includes mechanisms of morphological tolerance (hairiness of leaves, stems; wax-colored bloom; plaza of leaf; type of bush; density head; beardedness; glossy coating of leaf, culm; glaucous color of leaf, culm; placing spicate of scales near granule; plant height. To mechanisms of ontogenetic avoidance relating such as mismatch of pathogen, phytophage and plant; photoperiodic sensitivity; duration interphase periods in particular florification, ripening; duration of vegetation period; duration of primary dormancy (latent period; multivariation of synontоgenesis; photoperiodic sensitivity. Knowing the biocenotic mechanisms formation of adaptability cultural species discloses up new

The brine shrimp Artemia: adapted to critical life conditions

Directory of Open Access Journals (Sweden)

Gonzalo M Gajardo

2012-06-01

Full Text Available The brine shrimp Artemia is a micro-crustacean, well adapted to the harsh conditions that severely hypersaline environments impose on survival and reproduction. Adaptation to these conditions has taken place at different functional levels or domains, from the individual (molecular-cellular-physiological to the population level. Such conditions are experienced by very few equivalent macro-planktonic organisms; thus, Artemia can be considered a model animal extremophile offering a unique suite of adaptations that are the focus of this review. The most obvious is a highly efficient osmoregulation system to withstand up to 10 times the salt concentration of ordinary seawater. Under extremely critical environmental conditions, for example when seasonal lakes dry out, Artemia takes refuge by producing a highly resistant encysted gastrula embryo (cyst capable of severe dehydration enabling an escape from population extinction. Cysts can be viewed as gene banks that store a genetic memory of historical population conditions. Their occurrence is due to the evolved ability of females to perceive forthcoming unstable environmental conditions expressed by their ability to switch reproductive mode, producing either cysts (oviparity when environmental conditions become deleterious or free-swimming nauplii (ovoviviparity that are able to maintain the population under suitable conditions.At the population level the trend is for conspecific populations to be fragmented into locally adapted populations, whereas species are restricted to salty lakes in particular regions (regional endemism. The Artemia model depicts adaptation as a complex response to critical life conditions, integrating and refining past and present experiences at all levels of organization. Although we consider an invertebrate restricted to a unique environment, the processes to be discussed are of general biological interest. Finally, we highlight the benefits of understanding the stress

Establishing elements of a synthetic biology platform for Vaccinia virus production: BioBrick™ design, serum-free virus production and microcarrier-based cultivation of CV-1 cells.

Science.gov (United States)

Liu, Shuchang; Ruban, Ludmila; Wang, Yaohe; Zhou, Yuhong; Nesbeth, Darren N

2017-02-01

Vaccinia virus (VACV) is an established vector for vaccination and is beginning to prove effective as an oncolytic agent. Industrial production of VACV stands to benefit in future from advances made by synthetic biology in genome engineering and standardisation. The CV-1 cell line can be used for VACV propagation and has been used extensively with the CRISPR/Cas9 system for making precise edits of the VACV genome. Here we take first steps toward establishing a scalable synthetic biology platform for VACV production with CV-1 cells featuring standardised biological tools and serum free cell cultivation. We propose a new BioBrick™ plasmid backbone format for inserting transgenes into VACV. We then test the performance of CV-1 cells in propagation of a conventional recombinant Lister strain VACV, VACVL-15 RFP, in a serum-free process. CV-1 cells grown in 5% foetal bovine serum (FBS) Dulbecco's Modified Eagle Medium (DMEM) were adapted to growth in OptiPRO and VP-SFM brands of serum-free media. Specific growth rates of 0.047 h -1 and 0.044 h -1 were observed for cells adapted to OptiPRO and VP-SFM respectively, compared to 0.035 h -1 in 5% FBS DMEM. Cells adapted to OptiPRO and to 5% FBS DMEM achieved recovery ratios of over 96%, an indication of their robustness to cryopreservation. Cells adapted to VP-SFM showed a recovery ratio of 82%. Virus productivity in static culture, measured as plaque forming units (PFU) per propagator cell, was 75 PFU/cell for cells in 5% FBS DMEM. VP-SFM and OptiPRO adaptation increased VACV production to 150 PFU/cell and 350 PFU/cell respectively. Boosted PFU/cell from OptiPRO-adapted cells persisted when 5% FBS DMEM or OptiPRO medium was observed during the infection step and when titre was measured using cells adapted to 5% FBS DMEM or OptiPRO medium. Finally, OptiPRO-adapted CV-1 cells were successfully cultivated using Cytodex-1 microcarriers to inform future scale up studies.

Establishing elements of a synthetic biology platform for Vaccinia virus production: BioBrick™ design, serum-free virus production and microcarrier-based cultivation of CV-1 cells

Directory of Open Access Journals (Sweden)

Shuchang Liu

2017-02-01

Full Text Available Vaccinia virus (VACV is an established vector for vaccination and is beginning to prove effective as an oncolytic agent. Industrial production of VACV stands to benefit in future from advances made by synthetic biology in genome engineering and standardisation. The CV-1 cell line can be used for VACV propagation and has been used extensively with the CRISPR/Cas9 system for making precise edits of the VACV genome. Here we take first steps toward establishing a scalable synthetic biology platform for VACV production with CV-1 cells featuring standardised biological tools and serum free cell cultivation. We propose a new BioBrick™ plasmid backbone format for inserting transgenes into VACV. We then test the performance of CV-1 cells in propagation of a conventional recombinant Lister strain VACV, VACVL-15 RFP, in a serum-free process. CV-1 cells grown in 5% foetal bovine serum (FBS Dulbecco’s Modified Eagle Medium (DMEM were adapted to growth in OptiPRO and VP-SFM brands of serum-free media. Specific growth rates of 0.047 h−1 and 0.044 h−1 were observed for cells adapted to OptiPRO and VP-SFM respectively, compared to 0.035 h−1 in 5% FBS DMEM. Cells adapted to OptiPRO and to 5% FBS DMEM achieved recovery ratios of over 96%, an indication of their robustness to cryopreservation. Cells adapted to VP-SFM showed a recovery ratio of 82%. Virus productivity in static culture, measured as plaque forming units (PFU per propagator cell, was 75 PFU/cell for cells in 5% FBS DMEM. VP-SFM and OptiPRO adaptation increased VACV production to 150 PFU/cell and 350 PFU/cell respectively. Boosted PFU/cell from OptiPRO-adapted cells persisted when 5% FBS DMEM or OptiPRO medium was observed during the infection step and when titre was measured using cells adapted to 5% FBS DMEM or OptiPRO medium. Finally, OptiPRO-adapted CV-1 cells were successfully cultivated using Cytodex-1 microcarriers to inform future scale up studies.

Developmental biology, the stem cell of biological disciplines.

Science.gov (United States)

Gilbert, Scott F

2017-12-01

Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines." Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, developmental biology remains vigorous, pluripotent, and relatively undifferentiated. In many disciplines, especially in evolutionary biology and oncology, the developmental perspective is being reasserted as an important research program.

Learning to adapt: Organisational adaptation to climate change impacts

NARCIS (Netherlands)

Berkhout, F.G.H.; Hertin, J.; Gann, D.M.

2006-01-01

Analysis of human adaptation to climate change should be based on realistic models of adaptive behaviour at the level of organisations and individuals. The paper sets out a framework for analysing adaptation to the direct and indirect impacts of climate change in business organisations with new

Relations between Intuitive Biological Thinking and Biological Misconceptions in Biology Majors and Nonmajors

Science.gov (United States)

Coley, John D.; Tanner, Kimberly

2015-01-01

Research and theory development in cognitive psychology and science education research remain largely isolated. Biology education researchers have documented persistent scientifically inaccurate ideas, often termed misconceptions, among biology students across biological domains. In parallel, cognitive and developmental psychologists have described intuitive conceptual systems—teleological, essentialist, and anthropocentric thinking—that humans use to reason about biology. We hypothesize that seemingly unrelated biological misconceptions may have common origins in these intuitive ways of knowing, termed cognitive construals. We presented 137 undergraduate biology majors and nonmajors with six biological misconceptions. They indicated their agreement with each statement, and explained their rationale for their response. Results indicate frequent agreement with misconceptions, and frequent use of construal-based reasoning among both biology majors and nonmajors in their written explanations. Moreover, results also show associations between specific construals and the misconceptions hypothesized to arise from those construals. Strikingly, such associations were stronger among biology majors than nonmajors. These results demonstrate important linkages between intuitive ways of thinking and misconceptions in discipline-based reasoning, and raise questions about the origins, persistence, and generality of relations between intuitive reasoning and biological misconceptions. PMID:25713093

Atypical visual and somatosensory adaptation in schizophrenia-spectrum disorders

Science.gov (United States)

Andrade, G N; Butler, J S; Peters, G A; Molholm, S; Foxe, J J

2016-01-01

Neurophysiological investigations in patients with schizophrenia consistently show early sensory processing deficits in the visual system. Importantly, comparable sensory deficits have also been established in healthy first-degree biological relatives of patients with schizophrenia and in first-episode drug-naive patients. The clear implication is that these measures are endophenotypic, related to the underlying genetic liability for schizophrenia. However, there is significant overlap between patient response distributions and those of healthy individuals without affected first-degree relatives. Here we sought to develop more sensitive measures of sensory dysfunction in this population, with an eye to establishing endophenotypic markers with better predictive capabilities. We used a sensory adaptation paradigm in which electrophysiological responses to basic visual and somatosensory stimuli presented at different rates (ranging from 250 to 2550 ms interstimulus intervals, in blocked presentations) were compared. Our main hypothesis was that adaptation would be substantially diminished in schizophrenia, and that this would be especially prevalent in the visual system. High-density event-related potential recordings showed amplitude reductions in sensory adaptation in patients with schizophrenia (N=15 Experiment 1, N=12 Experiment 2) compared with age-matched healthy controls (N=15 Experiment 1, N=12 Experiment 2), and this was seen for both sensory modalities. At the individual participant level, reduced adaptation was more robust for visual compared with somatosensory stimulation. These results point to significant impairments in short-term sensory plasticity across sensory modalities in schizophrenia. These simple-to-execute measures may prove valuable as candidate endophenotypes and will bear follow-up in future work. PMID:27163205

Adaptive Modular Playware

DEFF Research Database (Denmark)

Lund, Henrik Hautop; Þorsteinsson, Arnar Tumi

2011-01-01

In this paper, we describe the concept of adaptive modular playware, where the playware adapts to the interaction of the individual user. We hypothesize that there are individual differences in user interaction capabilities and styles, and that adaptive playware may adapt to the individual user...

Adaptation

International Development Research Centre (IDRC) Digital Library (Canada)

building skills, knowledge or networks on adaptation, ... the African partners leading the AfricaAdapt network, together with the UK-based Institute of Development Studies; and ... UNCCD Secretariat, Regional Coordination Unit for Africa, Tunis, Tunisia .... 26 Rural–urban Cooperation on Water Management in the Context of.

Adaptive Remodeling of Achilles Tendon: A Multi-scale Computational Model.

Directory of Open Access Journals (Sweden)

Stuart R Young

2016-09-01

Full Text Available While it is known that musculotendon units adapt to their load environments, there is only a limited understanding of tendon adaptation in vivo. Here we develop a computational model of tendon remodeling based on the premise that mechanical damage and tenocyte-mediated tendon damage and repair processes modify the distribution of its collagen fiber lengths. We explain how these processes enable the tendon to geometrically adapt to its load conditions. Based on known biological processes, mechanical and strain-dependent proteolytic fiber damage are incorporated into our tendon model. Using a stochastic model of fiber repair, it is assumed that mechanically damaged fibers are repaired longer, whereas proteolytically damaged fibers are repaired shorter, relative to their pre-damage length. To study adaptation of tendon properties to applied load, our model musculotendon unit is a simplified three-component Hill-type model of the human Achilles-soleus unit. Our model results demonstrate that the geometric equilibrium state of the Achilles tendon can coincide with minimization of the total metabolic cost of muscle activation. The proposed tendon model independently predicts rates of collagen fiber turnover that are in general agreement with in vivo experimental measurements. While the computational model here only represents a first step in a new approach to understanding the complex process of tendon remodeling in vivo, given these findings, it appears likely that the proposed framework may itself provide a useful theoretical foundation for developing valuable qualitative and quantitative insights into tendon physiology and pathology.

Neo-sex chromosomes and adaptive potential in tortricid pests

Czech Academy of Sciences Publication Activity Database

Nguyen, Petr; Sýkorová, Miroslava; Šíchová, Jindra; Kůta, Václav; Dalíková, Martina; Čapková Frydrychová, Radmila; Neven, L. G.; Sahara, K.; Marec, František

2013-01-01

Roč. 110, č. 17 (2013), s. 6931-6936 ISSN 0027-8424 R&D Projects: GA ČR GA523/09/2106; GA AV ČR IAA600960925 Grant - others:Building up Modern Biotechnologies for Agriculture project(CZ) FP7-REGPOT-2008-1; Japan Society for the Promotion of Science Grant(JP) 23380030; GA JU(CZ) 137/2010/P; International Atomic Energy Agency, Vienna(AT) Research Agreement 15838 Institutional support: RVO:60077344 Keywords : adaptive evolution * leaf-rollers * performance genes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.809, year: 2013 http://www.pnas.org/content/110/17/6931.full.pdf+html

Resilience through adaptation

NARCIS (Netherlands)

Broeke, ten Guus; Voorn, van George A.K.; Ligtenberg, Arend; Molenaar, Jaap

2017-01-01

Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS). Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations

A Brief Introduction to Chinese Biological Biological

Institute of Scientific and Technical Information of China (English)

无

2005-01-01

Chinese Biological Abstracts sponsored by the Library, the Shanghai Institutes for Biological Sciences, the Biological Documentation and Information Network, all of the Chinese Academy of Sciences, commenced publication in 1987 and was initiated to provide access to the Chinese information in the field of biology.

ENDURANCE TRAINING IN FASTING CONDITIONS: BIOLOGICAL ADAPTATIONS AND BODY WEIGHT MANAGEMENT.

Science.gov (United States)

Vicente-Salar, Néstor; Urdampilleta Otegui, Aritz; Roche Collado, Enrique

2015-12-01

in the majority of sports the athlete is required to achieve optimal conditions both at a muscular and metabolic level as well as in body composition, increasing the lean body mass and maintaining a low body fat mass. In this context, different training protocols have been proposed in order to reduce body fat content, by maximizing fat use instead of glycogen. to verify if the training while fasting favours the use of fatty acids due to the low glycogen levels, allowing an improvement in the performance ant the control of body weight. protocols have been published, differing in time periods and exercise intensity. In addition, several markers ranging from gene expression analysis to determination of circulating parameters have been assessed in order to interpret the results. Discusion: at low intensities of endurance-based exercises, adipose tissue lipolysis and muscle fat oxidation rate seem to be higher in fasting than in fed state. On the other hand, glucose metabolism is adapted in order to save glycogen stores, possibly through gluconeogenesis activation. Finally, it has been observed that protein degradation is mainly downregulated. Only one study analyses changes in body composition after fasting during long periods, thus further work is necessary to demonstrate that this is the best method to control body fat. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Mast cells: potential positive and negative roles in tumor biology.

Science.gov (United States)

Marichal, Thomas; Tsai, Mindy; Galli, Stephen J

2013-11-01

Mast cells are immune cells that reside in virtually all vascularized tissues. Upon activation by diverse mechanisms, mast cells can secrete a broad array of biologically active products that either are stored in the cytoplasmic granules of the cells (e.g., histamine, heparin, various proteases) or are produced de novo upon cell stimulation (e.g., prostaglandins, leukotrienes, cytokines, chemokines, and growth factors). Mast cells are best known for their effector functions during anaphylaxis and acute IgE-associated allergic reactions, but they also have been implicated in a wide variety of processes that maintain health or contribute to disease. There has been particular interest in the possible roles of mast cells in tumor biology. In vitro studies have shown that mast cells have the potential to influence many aspects of tumor biology, including tumor development, tumor-induced angiogenesis, and tissue remodeling, and the shaping of adaptive immune responses to tumors. Yet, the actual contributions of mast cells to tumor biology in vivo remain controversial. Here, we review some basic features of mast cell biology with a special emphasis on those relevant to their potential roles in tumors. We discuss how using in vivo tumor models in combination with models in which mast cell function can be modulated has implicated mast cells in the regulation of host responses to tumors. Finally, we summarize data from studies of human tumors that suggest either beneficial or detrimental roles for mast cells in tumors. ©2013 AACR.

Relations between intuitive biological thinking and biological misconceptions in biology majors and nonmajors.

Science.gov (United States)

Coley, John D; Tanner, Kimberly

2015-03-02

Research and theory development in cognitive psychology and science education research remain largely isolated. Biology education researchers have documented persistent scientifically inaccurate ideas, often termed misconceptions, among biology students across biological domains. In parallel, cognitive and developmental psychologists have described intuitive conceptual systems--teleological, essentialist, and anthropocentric thinking--that humans use to reason about biology. We hypothesize that seemingly unrelated biological misconceptions may have common origins in these intuitive ways of knowing, termed cognitive construals. We presented 137 undergraduate biology majors and nonmajors with six biological misconceptions. They indicated their agreement with each statement, and explained their rationale for their response. Results indicate frequent agreement with misconceptions, and frequent use of construal-based reasoning among both biology majors and nonmajors in their written explanations. Moreover, results also show associations between specific construals and the misconceptions hypothesized to arise from those construals. Strikingly, such associations were stronger among biology majors than nonmajors. These results demonstrate important linkages between intuitive ways of thinking and misconceptions in discipline-based reasoning, and raise questions about the origins, persistence, and generality of relations between intuitive reasoning and biological misconceptions. © 2015 J. D. Coley and K. Tanner. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Uncertainty in adaptive capacity; Incertitudes dans la capacite d'adaptation

Energy Technology Data Exchange (ETDEWEB)

Neil Adger, W.; Vincent, K. [East Anglia Univ., Tyndall Centre for Climate Change Research, School of Environmental Sciences, Norwich (United Kingdom)

2005-03-01

The capacity to adapt is a critical element of the process of adaptation: it is the vector of resources that represent the asset base from which adaptation actions can be made. Adaptive capacity can in theory be identified and measured at various scales, from the individual to the nation. The assessment of uncertainty within such measures comes from the contested knowledge domain and theories surrounding the nature of the determinants of adaptive capacity and the human action of adaptation. While generic adaptive capacity at the national level, for example, is often postulated as being dependent on health, governance and political rights, and literacy, and economic well-being, the determinants of these variables at national levels are not widely understood. We outline the nature of this uncertainty for the major elements of adaptive capacity and illustrate these issues with the example of a social vulnerability index for countries in Africa. (authors)

An Optimal Control Modification to Model-Reference Adaptive Control for Fast Adaptation

Science.gov (United States)

Nguyen, Nhan T.; Krishnakumar, Kalmanje; Boskovic, Jovan

2008-01-01

This paper presents a method that can achieve fast adaptation for a class of model-reference adaptive control. It is well-known that standard model-reference adaptive control exhibits high-gain control behaviors when a large adaptive gain is used to achieve fast adaptation in order to reduce tracking error rapidly. High gain control creates high-frequency oscillations that can excite unmodeled dynamics and can lead to instability. The fast adaptation approach is based on the minimization of the squares of the tracking error, which is formulated as an optimal control problem. The necessary condition of optimality is used to derive an adaptive law using the gradient method. This adaptive law is shown to result in uniform boundedness of the tracking error by means of the Lyapunov s direct method. Furthermore, this adaptive law allows a large adaptive gain to be used without causing undesired high-gain control effects. The method is shown to be more robust than standard model-reference adaptive control. Simulations demonstrate the effectiveness of the proposed method.

PROFIL KETERAMPILAN PSIKOMOTOR MAHASISWA CALON GURU BIOLOGI MELALUI PRAKTIKUM KULTIVASI MIKROORGANISME

Directory of Open Access Journals (Sweden)

Rida Oktorida Khastini

2017-01-01

Full Text Available AbstractGeneral microbiology course provide comprehensive introduction to fundamental aspects of microbial world so that student gain an insight into theory, practices and able to demonstrate in the term of knowledge skills and values to overcome problem in the environment. Therefore student should have psychomotor skill as well as cognitive. The present study aimed to identify and describe the psychomotor skills of Pre Service Biology Teacher through microorganism cultivation experiment in the laboratoratory. Data were collected from 94 Pre Service Biology Teacher who enrolled General microbiology course in the even semester of academic year 2016-2017 using psychomotor skill observation sheet. Six dimensions observed: perception, set, guided response, mechanism, adaptation and originalation. Findings indicated that student psychomotor skills was categorized as good with the value of 81,2%.

Adaptation and evolution in marine environments. Vol. 2. The impacts of global change on biodiversity

Energy Technology Data Exchange (ETDEWEB)

Verde, Cinzia; Di Prisco, Guido (eds.) [CNR, Napoli (Italy). Inst. of Protein Biochemistry

2013-02-01

Offers a regionally focussed approach. Describes research on adaptive evolution. State-of-the-art content. The second volume of ''Adaptation and Evolution in Marine Environments - The Impacts of Global Change on Biodiversity'' from the series ''From Pole to Pole'' integrates the marine biology contribution of the first tome to the IPY 2007-2009, presenting overviews of organisms (from bacteria and ciliates to higher vertebrates) thriving on polar continental shelves, slopes and deep sea. The speed and extent of warming in the Arctic and in regions of Antarctica (the Peninsula, at the present) are greater than elsewhere. Changes impact several parameters, in particular the extent of sea ice; organisms, ecosystems and communities that became finely adapted to increasing cold in the course of millions of years are now becoming vulnerable, and biodiversity is threatened. Investigating evolutionary adaptations helps to foresee the impact of changes in temperate areas, highlighting the invaluable contribution of polar marine research to present and future outcomes of the IPY in the Earth system scenario.

Radioenzymatic microassay for picogram quantities of serotonin or acetylserotonin in biological fluids and tissues

International Nuclear Information System (INIS)

Hussain, M.N.; Benedict, C.R.

1987-01-01

This paper describes several modifications of the original radioenzymatic assay for serotonin which increase the sensitivity of the assay 20-fold as well as enhance its reliability. Using this method serotonin concentrations can be directly measured in biological examples without precleaning the sample. When compared to currently available methods this assay is specific and sensitive to approximately 1 pg of serotonin and can be used to measure serotonin levels in individual brain nuclei or microliter quantities of biological fluids. This assay can be easily adapted for the direct measurement of N-acetylserotonin. A large number of samples can be assayed in a single working day

Developmental biology, the stem cell of biological disciplines

OpenAIRE

Gilbert, Scott F.

2017-01-01

Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines.” Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, ...

Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters.

Science.gov (United States)

Chiang, Austin W T; Liu, Wei-Chung; Charusanti, Pep; Hwang, Ming-Jing

2014-01-15

A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system's dynamics. We demonstrate our methodology on a prototype biological system of perfect adaptation dynamics, namely the chemotaxis model for Escherichia coli. Our results agreed well with those derived from experimental data and theoretical studies in the literature. Using this model system, we showed that there are motifs in kinetic parameters and that these motifs are governed by constraints of the specified system dynamics. A systematic approach based on enrichment statistical tests has been developed to elucidate the relationships between model parameters and the roles they play in affecting system dynamics of a prototype biological network. The proposed approach is generally applicable and therefore can find wide use in systems biology modeling research.

Adaptive Lighting

DEFF Research Database (Denmark)

Petersen, Kjell Yngve; Søndergaard, Karin; Kongshaug, Jesper

2015-01-01

the investigations of lighting scenarios carried out in two test installations: White Cube and White Box. The test installations are discussed as large-scale experiential instruments. In these test installations we examine what could potentially occur when light using LED technology is integrated and distributed......Adaptive Lighting Adaptive lighting is based on a partial automation of the possibilities to adjust the colour tone and brightness levels of light in order to adapt to people’s needs and desires. IT support is key to the technical developments that afford adaptive control systems. The possibilities...... differently into an architectural body. We also examine what might occur when light is dynamic and able to change colour, intensity and direction, and when it is adaptive and can be brought into interaction with its surroundings. In short, what happens to an architectural space when artificial lighting ceases...

Judging adaptive management practices of U.S. agencies.

Science.gov (United States)

Fischman, Robert L; Ruhl, J B

2016-04-01

All U.S. federal agencies administering environmental laws purport to practice adaptive management (AM), but little is known about how they actually implement this conservation tool. A gap between the theory and practice of AM is revealed in judicial decisions reviewing agency adaptive management plans. We analyzed all U.S. federal court opinions published through 1 January 2015 to identify the agency AM practices courts found most deficient. The shortcomings included lack of clear objectives and processes, monitoring thresholds, and defined actions triggered by thresholds. This trio of agency shortcuts around critical, iterative steps characterizes what we call AM-lite. Passive AM differs from active AM in its relative lack of management interventions through experimental strategies. In contrast, AM-lite is a distinctive form of passive AM that fails to provide for the iterative steps necessary to learn from management. Courts have developed a sophisticated understanding of AM and often offer instructive rather than merely critical opinions. The role of the judiciary is limited by agency discretion under U.S. administrative law. But courts have overturned some agency AM-lite practices and insisted on more rigorous analyses to ensure that the promised benefits of structured learning and fine-tuned management have a reasonable likelihood of occurring. Nonetheless, there remains a mismatch in U.S. administrative law between the flexibility demanded by adaptive management and the legal objectives of transparency, public participation, and finality. © 2015 Society for Conservation Biology.

Pseudomonas biofilm matrix composition and niche biology

Science.gov (United States)

Mann, Ethan E.; Wozniak, Daniel J.

2014-01-01

Biofilms are a predominant form of growth for bacteria in the environment and in the clinic. Critical for biofilm development are adherence, proliferation, and dispersion phases. Each of these stages includes reinforcement by, or modulation of, the extracellular matrix. Pseudomonas aeruginosa has been a model organism for the study of biofilm formation. Additionally, other Pseudomonas species utilize biofilm formation during plant colonization and environmental persistence. Pseudomonads produce several biofilm matrix molecules, including polysaccharides, nucleic acids, and proteins. Accessory matrix components shown to aid biofilm formation and adaptability under varying conditions are also produced by pseudomonads. Adaptation facilitated by biofilm formation allows for selection of genetic variants with unique and distinguishable colony morphology. Examples include rugose small-colony variants and wrinkly spreaders (WS), which over produce Psl/Pel or cellulose, respectively, and mucoid bacteria that over produce alginate. The well-documented emergence of these variants suggests that pseudomonads take advantage of matrix-building subpopulations conferring specific benefits for the entire population. This review will focus on various polysaccharides as well as additional Pseudomonas biofilm matrix components. Discussions will center on structure–function relationships, regulation, and the role of individual matrix molecules in niche biology. PMID:22212072

A role of the adaptive immune system in glucose homeostasis.

Science.gov (United States)

Bronsart, Laura L; Contag, Christopher H

2016-01-01

The immune system, including the adaptive immune response, has recently been recognized as having a significant role in diet-induced insulin resistance. In this study, we aimed to determine if the adaptive immune system also functions in maintaining physiological glucose homeostasis in the absence of diet-induced disease. SCID mice and immunocompetent control animals were phenotypically assessed for variations in metabolic parameters and cytokine profiles. Additionally, the glucose tolerance of SCID and immunocompetent control animals was assessed following introduction of a high-fat diet. SCID mice on a normal chow diet were significantly insulin resistant relative to control animals despite having less fat mass. This was associated with a significant increase in the innate immunity-stimulating cytokines granulocyte colony-stimulating factor, monocyte chemoattractant protein 1 (MCP1), and MCP3. Additionally, the SCID mouse phenotype was exacerbated in response to a high-fat diet as evidenced by the further significant progression of glucose intolerance. These results support the notion that the adaptive immune system plays a fundamental biological role in glucose homeostasis, and that the absence of functional B and T cells results in disruption in the concentrations of various cytokines associated with macrophage proliferation and recruitment. Additionally, the absence of functional B and T cells is not protective against diet-induced pathology.

Integrating adaptive governance and participatory multicriteria methods: a framework for climate adaptation governance

Directory of Open Access Journals (Sweden)

Stefania Munaretto

2014-06-01

Full Text Available Climate adaptation is a dynamic social and institutional process where the governance dimension is receiving growing attention. Adaptive governance is an approach that promises to reduce uncertainty by improving the knowledge base for decision making. As uncertainty is an inherent feature of climate adaptation, adaptive governance seems to be a promising approach for improving climate adaptation governance. However, the adaptive governance literature has so far paid little attention to decision-making tools and methods, and the literature on the governance of adaptation is in its infancy in this regard. We argue that climate adaptation governance would benefit from systematic and yet flexible decision-making tools and methods such as participatory multicriteria methods for the evaluation of adaptation options, and that these methods can be linked to key adaptive governance principles. Moving from these premises, we propose a framework that integrates key adaptive governance features into participatory multicriteria methods for the governance of climate adaptation.

The choice of a biological model in assessing internal dose equivalent

International Nuclear Information System (INIS)

Parodo, A.; Erre, N.

1977-01-01

Many are the biological models related to kinetic behavior of radioactive materials within the organism, or in an organ. This is true particularly for the metabolic kinetics of bone-seekers radionuclides described differently by various authors: as a consequence, different forms of the retention function have been used in calculating internal dose equivalent. In our opinion, the retention functions expressed as linear combinations of exponential terms with negative exponents are preferable. In fact, they can be obtained by coherent compartmental analysis and allow a mathematical formalism fairly well definite and easily adaptable to computers. Moreover, it is possible to make use of graphs and monograms already published. The role of the biological model in internal dosimetry, referred to the reliability of the quantitative informations on the kinetic behavior of the radionuclides in the organism and, therefrom, to the accuracy of the doses calculated, is discussed. By comparing the results obtained with different biological models, one finds that the choice of a model is less important than the choice of the value of the appropriate parameters

Applying evolutionary biology to address global challenges

Science.gov (United States)

Carroll, Scott P.; Jørgensen, Peter Søgaard; Kinnison, Michael T.; Bergstrom, Carl T.; Denison, R. Ford; Gluckman, Peter; Smith, Thomas B.; Strauss, Sharon Y.; Tabashnik, Bruce E.

2014-01-01

Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens and pests that evolve too quickly, and the second from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This review highlights both progress and gaps in genetic, developmental and environmental manipulations across the life sciences that either target the rate and direction of evolution, or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development. PMID:25213376

Climate change risks and adaptation options across Australian seafood supply chains – A preliminary assessment

Directory of Open Access Journals (Sweden)

A. Fleming

2014-01-01

Full Text Available Climate change is already impacting the biology of the oceans and some dependent industries are in turn responding to these impacts. The development of response options for users of marine resources, such as fishers, is important in guiding adaptation efforts. However, harvesting fish is only the first step in a supply chain that delivers seafood to consumers. Impacts higher up the chain have seldom been considered in fisheries-climate research yet an understanding of these impacts and how climate risks and adaptation information are interpreted and used by stakeholders across the chain is vital for developing viable and sustainable adaptation options. We examined stakeholder perceptions of points where climate change impacts and adaptations currently occur, or may occur in the future, across the supply chains of several Australian fisheries (southern rock lobster, tropical rock lobster, prawn and aquaculture sectors (oyster, aquaculture prawn. We found that climate change impacts are well understood at the harvest stage and there is evidence of potential impacts and disruption to supply chains. Yet, there currently is no strong driver for change higher up the chain. Holistic adaptation planning along the supply chain, underpinned by targeted information and policy for the catch, processing and distribution, and marketing phases is needed. This effort is needed now, as some adaptation options have long lead times, and a delay in adaptation planning may limit future options. Given potential lead times and associated uncertainty, a risk-based approach is recommended with regard to adaptation planning for Australia’s seafood sector.

Pharmacological targeting of exercise adaptations in skeletal muscle: Benefits and pitfalls.

Science.gov (United States)

Weihrauch, Martin; Handschin, Christoph

2018-01-01

Exercise exerts significant effects on the prevention and treatment of many diseases. However, even though some of the key regulators of training adaptation in skeletal muscle have been identified, this biological program is still poorly understood. Accordingly, exercise-based pharmacological interventions for many muscle wasting diseases and also for pathologies that are triggered by a sedentary lifestyle remain scarce. The most efficacious compounds that induce muscle hypertrophy or endurance are hampered by severe side effects and are classified as doping. In contrast, dietary supplements with a higher safety margin exert milder outcomes. In recent years, the design of pharmacological agents that activate the training program, so-called "exercise mimetics", has been proposed, although the feasibility of such an approach is highly debated. In this review, the most recent insights into key regulatory factors and therapeutic approaches aimed at leveraging exercise adaptations are discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

Modelling the regulation of thermal adaptation in Candida albicans, a major fungal pathogen of humans.

Directory of Open Access Journals (Sweden)

Michelle D Leach

Full Text Available Eukaryotic cells have evolved mechanisms to sense and adapt to dynamic environmental changes. Adaptation to thermal insults, in particular, is essential for their survival. The major fungal pathogen of humans, Candida albicans, is obligately associated with warm-blooded animals and hence occupies thermally buffered niches. Yet during its evolution in the host it has retained a bona fide heat shock response whilst other stress responses have diverged significantly. Furthermore the heat shock response is essential for the virulence of C. albicans. With a view to understanding the relevance of this response to infection we have explored the dynamic regulation of thermal adaptation using an integrative systems biology approach. Our mathematical model of thermal regulation, which has been validated experimentally in C. albicans, describes the dynamic autoregulation of the heat shock transcription factor Hsf1 and the essential chaperone protein Hsp90. We have used this model to show that the thermal adaptation system displays perfect adaptation, that it retains a transient molecular memory, and that Hsf1 is activated during thermal transitions that mimic fever. In addition to providing explanations for the evolutionary conservation of the heat shock response in this pathogen and the relevant of this response to infection, our model provides a platform for the analysis of thermal adaptation in other eukaryotic cells.

Atomic switch networks as complex adaptive systems

Science.gov (United States)

Scharnhorst, Kelsey S.; Carbajal, Juan P.; Aguilera, Renato C.; Sandouk, Eric J.; Aono, Masakazu; Stieg, Adam Z.; Gimzewski, James K.

2018-03-01

Complexity is an increasingly crucial aspect of societal, environmental and biological phenomena. Using a dense unorganized network of synthetic synapses it is shown that a complex adaptive system can be physically created on a microchip built especially for complex problems. These neuro-inspired atomic switch networks (ASNs) are a dynamic system with inherent and distributed memory, recurrent pathways, and up to a billion interacting elements. We demonstrate key parameters describing self-organized behavior such as non-linearity, power law dynamics, and multistate switching regimes. Device dynamics are then investigated using a feedback loop which provides control over current and voltage power-law behavior. Wide ranging prospective applications include understanding and eventually predicting future events that display complex emergent behavior in the critical regime.

Dominance as adaptive stressing and ranking of males, serving to allocate reproduction by differential self-suppressed fertility: towards a fully biological understanding of social systems.

Science.gov (United States)

Moxon, Steve

2009-07-01

Dominance is a biological concept of an asymmetric 'power' relationship between (any pair of) individuals, as a result of previous encounters with others biasing likelihood of contesting. That this requires dedicated neural structure shows that dominance is adaptive; and it is usually thought that fitness is increased through dominance (hierarchy) minimising mutually unproductive contest over resources, and/or determining access to or control over resources. But highly inconsistent data indicates that this operational definition is too wide, and given clear evidence that dominance is invariably same-sex, it would seem instead to function primarily to allocate reproduction. Dominance contest exposes individual differences in metabolic vigor especially, but also in various other, including sophisticated attributes; and by a self-organising process there is ranking of same-sex individuals in a hierarchy. But this achieves nothing in itself without an integral mechanism of corresponding individual variable self-suppression of the physiology re reproduction--and mate choice with rank as the criteria. Reproductive suppression would appear to vary along a continuum, from in some species (most 'cooperative breeders') a 100% reproductive skew with total suppression of all individuals bar the sole breeder to, in most others, a gradient down the length of the dominance hierarchy. The mechanism in most species is directly either hormonal or pheromonal, on top of an indirect consequence of the stress caused by relatively low rank. Dominance would seem to have evolved as a major instrument of the proposed 'genetic filter' function of the male, whereby in effect accumulated deleterious genetic material is 'quarantined' in the male half of the lineage from where it is purged, so as to keep this source of reproductive logjam away from females, thereby to avoid amplifying the problem of the female being necessarily the limiting factor in reproduction. The theory makes predictions

Efficient synchronization of structurally adaptive coupled Hindmarsh-Rose neurons

International Nuclear Information System (INIS)

Moujahid, A.; D'Anjou, A.; Torrealdea, F.J.; Torrealdea, F.

2011-01-01

Highlights: → Neural activity might be constrained by a requirement of energy efficiency. → Signaling in synchrony is a normal way to propagate information between neurons. → Quality of synchrony affects the capacity to exchange information and the energy cost. → Adaptive mechanism leads to high degree of synchronization between nonidentical neurons. - Abstract: The use of spikes to carry information between brain areas implies complete or partial synchronization of the neurons involved. The degree of synchronization reached by two coupled systems and the energy cost of maintaining their synchronized behavior is highly dependent on the nature of the systems. For non-identical systems the maintenance of a synchronized regime is energetically a costly process. In this work, we study conditions under which two non-identical electrically coupled neurons can reach an efficient regime of synchronization at low energy cost. We show that the energy consumption required to keep the synchronized regime can be spontaneously reduced if the receiving neuron has adaptive mechanisms able to bring its biological parameters closer in value to the corresponding ones in the sending neuron.

Nuclear microscopy of biological specimens

International Nuclear Information System (INIS)

Watt, F.; Grime, G.W.; Brook, A.J.; Gadd, G.M.; Perry, C.C.; Pearce, R.B.; Turnau, K.; Watkinson, S.C.

1991-01-01

Recent developments in technology have enabled the scanning proton microprobe to scan at submicron spatial resolution on a routine basis. The use of the powerful combination of techniques PIXE (proton induced X-ray emission), nuclear (or Rutherford) backscattering (RBS), and secondary electron detection operating at this resolution will open up new areas in many scientific disciplines. This paper describes some of the work carried out in the biological sciences over the last year, using the Oxford SPM facility. Collaborations with biological scientists have drawn attention to the wealth of information that can be derived when these techniques are applied to micro-organisms, cells and plant tissue. Briefly described here are investigations into the uptake of heavy metals by the alga Pandorina morum, the structure of the diatom Stephanopyxis turris, the presence of various types of crystal structures within the cells of Spirogyra, the heavy metal uptake of a mycorrhizal fungus present in the bracken (Pteridium aquilinum) root, the role of sphagnum moss in the absorption of inorganic elements, the measurement of heavy metals in environmentally-adapted cells of the yeast Saccharomyces cerevisiae, and the elemental distribution in the growing tip of a spore from the plant Equisetum arvense, with special emphasis placed on the visual interpretation of the elemental and secondary-electron maps provided by the nuclear microscopical techniques. (orig.)

Adaptive Multimedia Retrieval: Semantics, Context, and Adaptation

DEFF Research Database (Denmark)

This book constitutes the thoroughly refereed post-conference proceedings of the 10th International Conference on Adaptive Multimedia Retrieval, AMR 2012, held in Copenhagen, Denmark, in October 2012. The 17 revised full papers presented were carefully reviewed and selected from numerous submissi......This book constitutes the thoroughly refereed post-conference proceedings of the 10th International Conference on Adaptive Multimedia Retrieval, AMR 2012, held in Copenhagen, Denmark, in October 2012. The 17 revised full papers presented were carefully reviewed and selected from numerous...... submissions. The papers cover topics of state of the art contributions, features and classification, location context, language and semantics, music retrieval, and adaption and HCI....

Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments

DEFF Research Database (Denmark)

Fletcher, Eugene; Feizi, Amir; Bisschops, Markus M. M.

2017-01-01

Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions....... Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether...... factor in the evolutionary process since cells evolved on two different carbon sources (raffinose and glucose) generated a different set of mutations in response to the presence of lactic acid. Therefore, different strategies are required for a rational design of low pH tolerant strains depending...

Adaptivity in GRAPPLE: Adaptation in any way you like (Poster)

NARCIS (Netherlands)

De Bra, P.M.E.; Smits, D.; Pechenizkiy, M.; Vasilyeva, E.; Bonk, C.J.; et al., xx

2008-01-01

GRAPPLE is an EU funded IST FP7 project that brings together a group of researchers into adaptive learning technology and environments and developers of learning management systems (LMSs), in order to offer adaptive learning as a standard feature of future LMSs. This paper presents the adaptation

A New Perspective on Changing Arctic Marine Ecosystems: Panarchy Adaptive Cycles in Pan-Arctic Spatial and Temporal Scales

Science.gov (United States)

Wiese, F. K.; Huntington, H. P.; Carmack, E.; Wassmann, P. F. J.; Leu, E. S.; Gradinger, R.

2016-02-01

Changes in the physical/biological interactions in the Arctic are occurring across a variety of spatial and temporal scales and may be mitigated or strengthened based on varying rates of evolutionary adaptation. A novel way to view these interactions and their social relevance is through the systems theory perspective of "Panarchy" proposed by Gunderson and Holling. Panarchy is an interdisciplinary approach in which structures, scales and linkages of complex-adaptive systems, including those of nature (e.g. ocean), humans (e.g. economics), and combined social-ecological systems (e.g. institutions that govern natural resource use), are mapped across multiple space and time scales in continual and interactive adaptive cycles of growth, accumulation, restructuring and renewal. In complex-adaptive systems the dynamics at a given scale are generally dominated by a small number of key internal variables that are forced by one or more external variables. The stability of such a system is characterized by its resilience, i.e. its capacity to absorb disturbance and re-organize while undergoing change, so as to retain essentially similar function, structure, identity and feedbacks. It is in the capacity of a system to cope with pressures and adversities such as exploitation, warming, governance restrictions, competition, etc. that resilience embraces human and natural systems as complex entities continually adapting through cycles of change. In this paper we explore processes at four linked spatial domains in the Arctic Ocean and link it to ecosystem resilience and re-organization characteristics. From this we derive a series of hypotheses concerning the biological responses to future physical changes and suggest ways how Panarchy theory can be applied to observational strategies to help detect early signs of environmental shifts affecting marine system services and functions. We close by discussing possible implications of the Panarchy framework for policy and governance.

Transcultural adaptation into Portuguese of an instrument for pain evaluation based on the biopsychosocial model

Directory of Open Access Journals (Sweden)

Monique Rocha Peixoto dos Santos

Full Text Available Abstract Introduction: Pain is an individual experience influenced by multiple interacting factors. The “biopsychosocial” care model has gained popularity in response to growing research evidence indicating the influence of biological, psychological, and social factors on the pain experience. The implementation of this model is a challenge in the practice of the health professional. Objective: To perform the transcultural adaptation of the SCEBS method into Brazilian Portuguese. Methods: The instrument was translated and applied to 50 healthy subjects and 50 participants with non-specific chronic pain in the spine. The process of cross-cultural adaptation included the following steps: transcultural adaptation, content analysis of the scale, pre-test, revision, back-translation review, cross-cultural adaptation, revised text correction and final report. Results: The translated and adapted 51-item Portuguese version of the SCEBS method produced an instrument called SCEBS-BR. In the assessment by the target population, 50 adult users of the Brazilian Unified Health System answered the questionnaire and showed good understanding of the instrument on the verbal rating scale. Conclusion: The SCEBS-BR was proved to be easily understandable, showing good semantic validation regardless of schooling level or age, and can be considered adequate for clinical use.

Multifocal multiphoton microscopy with adaptive optical correction

Science.gov (United States)

Coelho, Simao; Poland, Simon; Krstajic, Nikola; Li, David; Monypenny, James; Walker, Richard; Tyndall, David; Ng, Tony; Henderson, Robert; Ameer-Beg, Simon

2013-02-01

Fluorescence lifetime imaging microscopy (FLIM) is a well established approach for measuring dynamic signalling events inside living cells, including detection of protein-protein interactions. The improvement in optical penetration of infrared light compared with linear excitation due to Rayleigh scattering and low absorption have provided imaging depths of up to 1mm in brain tissue but significant image degradation occurs as samples distort (aberrate) the infrared excitation beam. Multiphoton time-correlated single photon counting (TCSPC) FLIM is a method for obtaining functional, high resolution images of biological structures. In order to achieve good statistical accuracy TCSPC typically requires long acquisition times. We report the development of a multifocal multiphoton microscope (MMM), titled MegaFLI. Beam parallelization performed via a 3D Gerchberg-Saxton (GS) algorithm using a Spatial Light Modulator (SLM), increases TCSPC count rate proportional to the number of beamlets produced. A weighted 3D GS algorithm is employed to improve homogeneity. An added benefit is the implementation of flexible and adaptive optical correction. Adaptive optics performed by means of Zernike polynomials are used to correct for system induced aberrations. Here we present results with significant improvement in throughput obtained using a novel complementary metal-oxide-semiconductor (CMOS) 1024 pixel single-photon avalanche diode (SPAD) array, opening the way to truly high-throughput FLIM.

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach.

Science.gov (United States)

Domenyuk, Valeriy; Zhong, Zhenyu; Stark, Adam; Xiao, Nianqing; O'Neill, Heather A; Wei, Xixi; Wang, Jie; Tinder, Teresa T; Tonapi, Sonal; Duncan, Janet; Hornung, Tassilo; Hunter, Andrew; Miglarese, Mark R; Schorr, Joachim; Halbert, David D; Quackenbush, John; Poste, George; Berry, Donald A; Mayer, Günter; Famulok, Michael; Spetzler, David

2017-02-20

Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~10 11 ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 10 6 enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients.

Plant's adaptive response under UV-B-radiation influence

International Nuclear Information System (INIS)

Danil'chenko, O.A.; Grodzinskij, D.M.

2002-01-01