scholarly journals One-cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!

2016 ◽  
Author(s):  
Thurston Herricks ◽  
David J. Dilworth ◽  
Fred D. Mast ◽  
Song Li ◽  
Jennifer J. Smith ◽  
...  
Keyword(s):  
Growth Analysis ◽  
Large Scale ◽  
Quantitative Methods ◽  
Growth Parameters ◽  
Single Cells ◽  
Growth Parameter ◽  
Population Heterogeneity ◽  
Time Resolved ◽  
Solid Media ◽  
The Impact

ABSTRACTCell growth is a complex phenotype widely used in systems biology to gauge the impact of genetic and environmental perturbations. Due to the magnitude of genome-wide studies, resolution is often sacrificed in favor of throughput, creating a demand for scalable, time-resolved, quantitative methods of growth assessment. We present ODELAY (One-cell Doubling Evaluation by Living Arrays of Yeast), an automated and scalable growth analysis platform. High measurement density and single cell resolution provide a powerful tool for large-scale multiparameter growth analysis based on the modeling of microcolony expansion on solid media. Pioneered in yeast but applicable to other colony forming organisms, ODELAY extracts the three key growth parameters (lag time, doubling time, and carrying capacity) that define microcolony expansion from single cells, simultaneously permitting the assessment of population heterogeneity. The utility of ODELAY is illustrated using yeast mutants, revealing a spectrum of phenotypes arising from single and combinatorial growth parameter perturbations.

scholarly journals Cell migration guided by long-lived spatial memory

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joseph d’Alessandro ◽  
Alex Barbier--Chebbah ◽  
Victor Cellerin ◽  
Olivier Benichou ◽  
René Marc Mège ◽  
...  
Keyword(s):  
Cell Migration ◽  
Spatial Memory ◽  
Large Scale ◽  
Single Cells ◽  
Environmental Perturbations ◽  
Motile Cells ◽  
Unicellular Organisms ◽  
Biochemical Signals ◽  
The Impact ◽  
Cell Trajectories

AbstractLiving cells actively migrate in their environment to perform key biological functions—from unicellular organisms looking for food to single cells such as fibroblasts, leukocytes or cancer cells that can shape, patrol or invade tissues. Cell migration results from complex intracellular processes that enable cell self-propulsion, and has been shown to also integrate various chemical or physical extracellular signals. While it is established that cells can modify their environment by depositing biochemical signals or mechanically remodelling the extracellular matrix, the impact of such self-induced environmental perturbations on cell trajectories at various scales remains unexplored. Here, we show that cells can retrieve their path: by confining motile cells on 1D and 2D micropatterned surfaces, we demonstrate that they leave long-lived physicochemical footprints along their way, which determine their future path. On this basis, we argue that cell trajectories belong to the general class of self-interacting random walks, and show that self-interactions can rule large scale exploration by inducing long-lived ageing, subdiffusion and anomalous first-passage statistics. Altogether, our joint experimental and theoretical approach points to a generic coupling between motile cells and their environment, which endows cells with a spatial memory of their path and can dramatically change their space exploration.

scholarly journals Cell migration driven by long-lived spatial memory

2021 ◽  
Author(s):  
Joseph d’Alessandro ◽  
Alex Barbier-Chebbah ◽  
Victor Cellerin ◽  
Olivier Bénichou ◽  
René-Marc Mège ◽  
...  
Keyword(s):  
Cell Migration ◽  
Spatial Memory ◽  
Large Scale ◽  
Single Cells ◽  
Environmental Perturbations ◽  
Motile Cells ◽  
Unicellular Organisms ◽  
Biochemical Signals ◽  
The Impact ◽  
Cell Trajectories

Many living cells actively migrate in their environment to perform key biological functions – from unicellular organisms looking for food to single cells such as fibroblasts, leukocytes or cancer cells that can shape, patrol or invade tissues. Cell migration results from complex intracellular processes that enable cell self-propulsion 1,2, and has been shown to also integrate various chemical or physical extracellular signals 3,4,5. While it is established that cells can modify their environment by depositing biochemical signals or mechanically remodeling the extracellular matrix, the impact of such self-induced environmental perturbations on cell trajectories at various scales remains unexplored. Here, we show that cells remember their path: by confining cells on 1D and 2D micropatterned surfaces, we demonstrate that motile cells leave long-lived physicochemical footprints along their way, which determine their future path. On this basis, we argue that cell trajectories belong to the general class of self-interacting random walks, and show that self-interactions can rule large scale exploration by inducing long-lived ageing, subdiffusion and anomalous first-passage statistics. Altogether, our joint experimental and theoretical approach points to a generic coupling between motile cells and their environment, which endows cells with a spatial memory of their path and can dramatically change their space exploration.

scholarly journals Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign

2020 ◽  
Vol 117 (46) ◽  
pp. 28784-28794
Author(s):  
Sisi Chen ◽  
Paul Rivaud ◽  
Jong H. Park ◽  
Tiffany Tsou ◽  
Emeric Charles ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Large Scale ◽  
Probabilistic Models ◽  
Single Cells ◽  
Measurement Techniques ◽  
Patient Specific ◽  
Cell Populations ◽  
Cell Measurement ◽  
The Impact

Single-cell measurement techniques can now probe gene expression in heterogeneous cell populations from the human body across a range of environmental and physiological conditions. However, new mathematical and computational methods are required to represent and analyze gene-expression changes that occur in complex mixtures of single cells as they respond to signals, drugs, or disease states. Here, we introduce a mathematical modeling platform, PopAlign, that automatically identifies subpopulations of cells within a heterogeneous mixture and tracks gene-expression and cell-abundance changes across subpopulations by constructing and comparing probabilistic models. Probabilistic models provide a low-error, compressed representation of single-cell data that enables efficient large-scale computations. We apply PopAlign to analyze the impact of 40 different immunomodulatory compounds on a heterogeneous population of donor-derived human immune cells as well as patient-specific disease signatures in multiple myeloma. PopAlign scales to comparisons involving tens to hundreds of samples, enabling large-scale studies of natural and engineered cell populations as they respond to drugs, signals, or physiological change.

Role of Turbulence in Precessing Vortex Core Dynamics

2019 ◽  
Author(s):  
Ashwini Karmarkar ◽  
Mark Frederick ◽  
Sean Clees ◽  
Danielle Mason ◽  
Jacqueline O’Connor
Keyword(s):  
Large Scale ◽  
Swirling Flows ◽  
Base Flow ◽  
Van Der Pol Oscillator ◽  
Intensity Increase ◽  
Swirl Number ◽  
Time Resolved ◽  
Turbulent Fluctuations ◽  
Eddy Viscosity Model ◽  
The Impact

Abstract Precessing vortex cores (PVC), arising from a global instability in swirling flows, can dramatically alter the dynamics of swirl-stabilized flames. Previous study of these instabilities has identified their frequencies and potential for interaction with the shear layer instabilities also present in swirling flows. In this work, we investigate the dynamics of precessing vortex cores at a range of swirl numbers and the impact that turbulence, which tends to increase with swirl number due to the increase in mean shear, has on the dynamics of this instability. This is particularly interesting as stability predictions have previously incorporated turbulence effects using an eddy viscosity model, which only captures the impact of turbulence on the base flow, not on the instantaneous dynamics of the PVC itself. Time-resolved experimental measurements of the three-component velocity field at ten swirl numbers show that at lower swirl numbers, the PVC is affected by turbulence through the presence of vortex jitter. With increasing swirl number, the PVC jitter decreases as the PVC strength increases. There is a critical swirl number below which jitter of the PVC vortex monotonically increases with increasing swirl number, and beyond which the jitter decreases, indicating that the strength of the PVC dominates over turbulent fluctuations at higher swirl numbers, despite the fact that the turbulence intensities continue to rise with increasing swirl number. Further, we use a nonlinear van der Pol oscillator model to explain the competition between the random turbulent fluctuations and coherent oscillations of the PVC. The results of this work indicate that while both the strength of the PVC and magnitude of turbulence intensity increase with increasing swirl number, there are defined regimes where each of them hold a stronger influence on the large-scale, coherent dynamics of the flow field.

scholarly journals Embedded Academic Librarianship: A Review of the Literature

2012 ◽  
Vol 7 (4) ◽  
pp. 122 ◽  
Author(s):  
Stephanie J. Schulte
Keyword(s):  
Large Scale ◽  
Quantitative Methods ◽  
Information Science ◽  
Case Reports ◽  
Future Research ◽  
Narrative Form ◽  
Cultural Integration ◽  
High Quality Research ◽  
Embedded Librarian ◽  
The Impact

Objectives – The purpose of this review is to examine the development of embedded librarianship, its multiple meanings, and activities in practice. The review will also report on published outcomes and future research needs of embedded librarian programs. Methods – A search of current literature was conducted and summarized searching PubMed, CINAHL, Library, Information Science & Technology Abstracts (EBSCO), Academic Search Complete, and ERIC (EBSCO) through August 23, 2012. Articles were selected for inclusion in the review if they reported research findings related to embedded librarianship, if they provided unique case reports about embedded librarian programs, or if they provided substantive editorial comments on the topic. Relevant study findings were assessed for quality and presented in tabular and narrative form. Results – Currently, there is disparity in how embedded librarianship is being defined and used in common practice, ranging from embedding an online component into a single course to full physical and cultural integration into an academic college or business unit of an organization. Activities of embedded librarians include creating course integrated instruction modules for either face-to-face or online courses, providing in depth research assistance to students or faculty, and co-locating within colleges or customer units via office hours for a few hours to all hours per week. Several case reports exist in the recent literature. Few high quality research studies reporting outcomes of librarians or library programs labeled as embedded exist at this point. Some evidence suggests that embedded librarians are effective with regards to student learning of information literacy objectives. Surveys suggest that both students and faculty appreciate embedded librarian services. Conclusion – Most published accounts discuss librarians embedding content and ready access to services in an online course management system. A few notable cases describe the physical and cultural integration of librarians into the library user environs. Future research using valid quantitative methods is needed to explore the impact of large scale, customized, embedded programs.

scholarly journals THE IMPACT OF MISTRANSLATION ON PHENOTYPIC VARIABILITY AND FITNESS

2020 ◽  
Author(s):  
Laasya Samhita ◽  
Parth K Raval ◽  
Godwin Stephenson ◽  
Shashi Thutupalli ◽  
Deepa Agashe
Keyword(s):  
Phenotypic Variation ◽  
Growth Parameters ◽  
Single Cells ◽  
Phenotypic Variability ◽  
Natural Populations ◽  
Population Level ◽  
Level Variation ◽  
Growth And Survival ◽  
Translation Errors ◽  
The Impact

ABSTRACTPhenotypic variation is widespread in natural populations, and can significantly alter their ecology and evolution. Phenotypic variation often reflects underlying genetic variation, but also manifests via non-heritable mechanisms. For instance, translation errors result in about 10% of cellular proteins carrying altered sequences. Thus, proteome diversification arising from translation errors can potentially generate phenotypic variability, in turn increasing variability in the fate of cells or of populations. However, this link remains unverified. We manipulated mistranslation levels in Escherichia coli, and measured phenotypic variability between single cells (individual level variation), as well as replicate populations (population level variation). Monitoring growth and survival, we find that mistranslation indeed increases variation across E. coli cells, but does not consistently increase variability in growth parameters across replicate populations. Interestingly, although any deviation from the wild type (WT) level of mistranslation reduces fitness in an optimal environment, the increased variation is associated with a survival benefit under stress. Hence, we suggest that mistranslation-induced phenotypic variation can impact growth and survival and has the potential to alter evolutionary trajectories.

scholarly journals Prokaryotic responses to a warm temperature anomaly in northeast subarctic Pacific waters

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Sachia J. Traving ◽  
Colleen T. E. Kellogg ◽  
Tetjana Ross ◽  
Ryan McLaughlin ◽  
Brandon Kieft ◽  
...  
Keyword(s):  
Water Temperature ◽  
Large Scale ◽  
Heat Waves ◽  
Biodiversity Loss ◽  
Food Web Structure ◽  
Multivariate Statistical ◽  
Time Resolved ◽  
Subarctic Pacific ◽  
Temperature Anomalies ◽  
The Impact

AbstractRecent studies on marine heat waves describe water temperature anomalies causing changes in food web structure, bloom dynamics, biodiversity loss, and increased plant and animal mortality. However, little information is available on how water temperature anomalies impact prokaryotes (bacteria and archaea) inhabiting ocean waters. This is a nontrivial omission given their integral roles in driving major biogeochemical fluxes that influence ocean productivity and the climate system. Here we present a time-resolved study on the impact of a large-scale warm water surface anomaly in the northeast subarctic Pacific Ocean, colloquially known as the Blob, on prokaryotic community compositions. Multivariate statistical analyses identified significant depth- and season-dependent trends that were accentuated during the Blob. Moreover, network and indicator analyses identified shifts in specific prokaryotic assemblages from typically particle-associated before the Blob to taxa considered free-living and chemoautotrophic during the Blob, with potential implications for primary production and organic carbon conversion and export.

Isotopes in the Water Cycle: Regional- to Global-Scale Patterns and Applications

2019 ◽  
Vol 47 (1) ◽  
pp. 453-479 ◽  
Author(s):  
Gabriel J. Bowen ◽  
Zhongyin Cai ◽  
Richard P. Fiorella ◽  
Annie L. Putman
Keyword(s):  
Data Sharing ◽  
Large Scale ◽  
Quantitative Methods ◽  
Water Cycle ◽  
Isotope Ratios ◽  
Global Scale ◽  
Global Changes ◽  
Regional Patterns ◽  
The Past ◽  
The Impact

Stable isotope ratios of hydrogen and oxygen have been applied to water cycle research for over 60 years. Over the past two decades, however, new data, data compilations, and quantitative methods have supported the application of isotopic data to address large-scale water cycle problems. Recent results have demonstrated the impact of climate variation on atmospheric water cycling, provided constraints on continental- to global-scale land-atmosphere water vapor fluxes, revealed biases in the sources of runoff in hydrological models, and illustrated regional patterns of water use and management by people. In the past decade, global isotopic observations have spurred new debate over the role of soils in the water cycle, with potential to impact both ecological and hydrological theory. Many components of the water cycle remain underrepresented in isotopic databases. Increasing accessibility of analyses and improved platforms for data sharing will refine and grow the breadth of these contributions in the future. ▪ Isotope ratios in water integrate information on hydrological processes over scales from cities to the globe. ▪ Tracing water with isotopes helps reveal the processes that govern variability in the water cycle and may govern future global changes. ▪ Improvements in instrumentation, data sharing, and quantitative analysis have advanced isotopic water cycle science over the past 20 years.

scholarly journals Evaluation of the natural and artificial regeneration of Scots pine Pinus sylvestris L. stands in the Forest District Nowa Dęba

2019 ◽  
Vol 80 (2) ◽  
pp. 105-116
Author(s):  
Justyna Długosiewicz ◽  
Stanisław Zając ◽  
Emilia Wysocka-Fijorek
Keyword(s):  
Pinus Sylvestris ◽  
Scots Pine ◽  
Natural Regeneration ◽  
Growth Parameters ◽  
Coniferous Forest ◽  
Growth Parameter ◽  
Field Work ◽  
Artificial Regeneration ◽  
The Impact ◽  
Forest District

Abstract The main purpose of this article was to highlight the potential for enhancing positive silvicultural effects and their dependency on the management method in Scots pine Pinus sylvestris L. stands. We therefore assessed the impact of natural and artificial regeneration on vitality and health, compaction, surface coverage and seedlings height. Another important goal was to assess the severity of damage in the selected forest sites. A comparative analysis was carried out based on results from field work conducted in the autumn 2010 in the Forest District Nowa Dęba. As part of this field work, also the breeding quality of the analyzed pine renewals was assessed. The obtained results indicate that natural regeneration of Scots pine under the conditions of a fresh coniferous forest as well as a fresh mixed coniferous forest is the most reasonable management practice. In wet mixed coniferous forests however, the naturally regenerating Scots pine seedlings are of lower silvicultural quality and growth parameter values compared to those in artificially regenerated stands. In fresh mixed broadleaved forests, naturally regenerated Scot pine trees showed slightly lower silvicultural quality and vitality than artificially regenerated trees. Our results indicate furthermore that there are indeed conditions under which the restoration of Scots pine in the Nowa Dęba Forest District using natural regeneration is preferable. We also found that the employed method of renewing has a significant impact on pine growth parameters in the moist mixed coniferous forest habitat. Naturally renewing pines are characterized by a lower overall viability, but at the same time natural regeneration provides a larger number of individuals with the best viability (1st vitality class), which can be a valuable selection basis for trees used in breeding.

scholarly journals Embedded Academic Librarianship: A Review of the Literature

2012 ◽  
Vol 7 (4) ◽  
pp. 122-138
Author(s):  
Stephanie J. Schulte
Keyword(s):  
Large Scale ◽  
Quantitative Methods ◽  
Information Science ◽  
Case Reports ◽  
Future Research ◽  
Narrative Form ◽  
Cultural Integration ◽  
High Quality Research ◽  
Embedded Librarian ◽  
The Impact

Objectives – The purpose of this review is to examine the development of embedded librarianship, its multiple meanings, and activities in practice. The review will also report on published outcomes and future research needs of embedded librarian programs. Methods – A search of current literature was conducted and summarized searching PubMed, CINAHL, Library, Information Science & Technology Abstracts (EBSCO), Academic Search Complete, and ERIC (EBSCO) through August 23, 2012. Articles were selected for inclusion in the review if they reported research findings related to embedded librarianship, if they provided unique case reports about embedded librarian programs, or if they provided substantive editorial comments on the topic. Relevant study findings were assessed for quality and presented in tabular and narrative form. Results – Currently, there is disparity in how embedded librarianship is being defined and used in common practice, ranging from embedding an online component into a single course to full physical and cultural integration into an academic college or business unit of an organization. Activities of embedded librarians include creating course integrated instruction modules for either face-to-face or online courses, providing in depth research assistance to students or faculty, and co-locating within colleges or customer units via office hours for a few hours to all hours per week. Several case reports exist in the recent literature. Few high quality research studies reporting outcomes of librarians or library programs labeled as embedded exist at this point. Some evidence suggests that embedded librarians are effective with regards to student learning of information literacy objectives. Surveys suggest that both students and faculty appreciate embedded librarian services. Conclusion – Most published accounts discuss librarians embedding content and ready access to services in an online course management system. A few notable cases describe the physical and cultural integration of librarians into the library user environs. Future research using valid quantitative methods is needed to explore the impact of large scale, customized, embedded programs.

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