scholarly journals SpermQ - a simple analysis software to comprehensively study flagellar beating and sperm steering

2018 ◽  
Author(s):  
Jan N Hansen ◽  
Sebastian Rassmann ◽  
Jan F Jikeli ◽  
Dagmar Wachten
Keyword(s):  
Female Genital Tract ◽  
Time Lapse ◽  
Dark Field ◽  
Comprehensive Analysis ◽  
Analysis Software ◽  
Environmental Signals ◽  
Common Time ◽  
Flagellar Beat ◽  
Standard Tool ◽  
Motile Cilia

Motile cilia, also called flagella, drive cell motility across a broad range of species; some cilia propel prokaryotes and eukaryotic cells like sperm, while cilia on epithelial surfaces create complex fluid patterns e.g. in the brain or lung. For sperm, the picture has emerged that the motile cilium, also called flagellum, is not only a motor, but also a sensor that detects stimuli from the environment, computing the beat pattern according to the sensory input. Thereby, the flagellum of the sperm cell navigates the sperm through a complex environment like the female genital tract. However, we know very little about how environmental signals change the flagellar beat and, thereby, the swimming behaviour of sperm. It has been proposed that distinct signalling domains in the flagellum control the flagellar beat. A detailed analysis has been mainly hampered by the fact that current comprehensive analysis approaches rely on complex microscopy and analysis systems. Thus, knowledge on sperm signalling regulating the flagellar beat is based on custom quantification approaches that are limited to only a few aspects of the flagellar beat, do not resolve the kinetics of the entire flagellum, rely on manual, qualitative descriptions, and are little comparable among each other. Here, we present SpermQ, a ready-to-use and comprehensive analysis software to quantify sperm motility. SpermQ provides a detailed quantification of the flagellar beat based on common time-lapse images acquired by dark-field or epi-fluorescence microscopy, making SpermQ widely applicable. We envision SpermQ becoming a standard tool in flagellar and motile cilia research that allows to readily link studies on individual signalling components in sperm and distinct flagellar beat patterns.

scholarly journals SpermQ–A Simple Analysis Software to Comprehensively Study Flagellar Beating and Sperm Steering

Cells ◽  
2018 ◽  
Vol 8 (1) ◽  
pp. 10 ◽  
Author(s):  
Jan Hansen ◽  
Sebastian Rassmann ◽  
Jan Jikeli ◽  
Dagmar Wachten
Keyword(s):  
Female Genital Tract ◽  
Time Lapse ◽  
Dark Field ◽  
Comprehensive Analysis ◽  
Analysis Software ◽  
Environmental Signals ◽  
Common Time ◽  
Flagellar Beat ◽  
Beat Pattern ◽  
Motile Cilia

Motile cilia, also called flagella, are found across a broad range of species; some cilia propel prokaryotes and eukaryotic cells like sperm, while cilia on epithelial surfaces create complex fluid patterns e.g., in the brain or lung. For sperm, the picture has emerged that the flagellum is not only a motor but also a sensor that detects stimuli from the environment, computing the beat pattern according to the sensory input. Thereby, the flagellum navigates sperm through the complex environment in the female genital tract. However, we know very little about how environmental signals change the flagellar beat and, thereby, the swimming behavior of sperm. It has been proposed that distinct signaling domains in the flagellum control the flagellar beat. However, a detailed analysis has been mainly hampered by the fact that current comprehensive analysis approaches rely on complex microscopy and analysis systems. Thus, knowledge on sperm signaling regulating the flagellar beat is based on custom quantification approaches that are limited to only a few aspects of the beat pattern, do not resolve the kinetics of the entire flagellum, rely on manual, qualitative descriptions, and are only a little comparable among each other. Here, we present SpermQ, a ready-to-use and comprehensive analysis software to quantify sperm motility. SpermQ provides a detailed quantification of the flagellar beat based on common time-lapse images acquired by dark-field or epi-fluorescence microscopy, making SpermQ widely applicable. We envision SpermQ becoming a standard tool in flagellar and motile cilia research that allows to readily link studies on individual signaling components in sperm and distinct flagellar beat patterns.

scholarly journals Entrainment of mammalian motile cilia in the brain with hydrodynamic forces

2020 ◽  
Vol 117 (15) ◽  
pp. 8315-8325 ◽  
Author(s):  
Nicola Pellicciotta ◽  
Evelyn Hamilton ◽  
Jurij Kotar ◽  
Marion Faucourt ◽  
Nathalie Delgehyr ◽  
...  
Keyword(s):  
Hydrodynamic Forces ◽  
Coordination Mechanism ◽  
Similar Frequency ◽  
Brain Ventricles ◽  
Flagellar Beat ◽  
Multiciliated Cells ◽  
Hydrodynamic Screening ◽  
Motile Cilia ◽  
External Flows ◽  
The Brain

Motile cilia are widespread across the animal and plant kingdoms, displaying complex collective dynamics central to their physiology. Their coordination mechanism is not generally understood, with previous work mainly focusing on algae and protists. We study here the entrainment of cilia beat in multiciliated cells from brain ventricles. The response to controlled oscillatory external flows shows that flows at a similar frequency to the actively beating cilia can entrain cilia oscillations. We find that the hydrodynamic forces required for this entrainment strongly depend on the number of cilia per cell. Cells with few cilia (up to five) can be entrained at flows comparable to cilia-driven flows, in contrast with what was recently observed in Chlamydomonas. Experimental trends are quantitatively described by a model that accounts for hydrodynamic screening of packed cilia and the chemomechanical energy efficiency of the flagellar beat. Simulations of a minimal model of cilia interacting hydrodynamically show the same trends observed in cilia.

scholarly journals MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Peng Zhai ◽  
Longshu Yang ◽  
Xiao Guo ◽  
Zhe Wang ◽  
Jiangtao Guo ◽  
...  
Keyword(s):  
Comprehensive Analysis ◽  
Analysis Software ◽  
Comparative Metagenomics

A binary outcome predictor generated by time-lapse analysis software offers a limited selection advantage between blastocysts

2014 ◽  
Vol 102 (3) ◽  
pp. e283
Author(s):  
M.D. Werner ◽  
K.H. Hong ◽  
J.M. Franasiak ◽  
K. Upham ◽  
R.T. Scott
Keyword(s):  
Time Lapse ◽  
Binary Outcome ◽  
Outcome Predictor ◽  
Analysis Software

scholarly journals Positioning of the Motility Machinery in Halophilic Archaea

mBio ◽  
2019 ◽  
Vol 10 (3) ◽  
Author(s):  
Zhengqun Li ◽  
Yoshiaki Kinosita ◽  
Marta Rodriguez-Franco ◽  
Phillip Nußbaum ◽  
Frank Braun ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Halophilic Archaea ◽  
Time Lapse ◽  
Content Type ◽  
Environmental Signals ◽  
Macromolecular Assemblies ◽  
Chemical Gradients ◽  
Fluorescence And Electron Microscopy ◽  
Independent Form ◽  
Macromolecular Protein

ABSTRACTBacteria and archaea exhibit tactical behavior and can move up and down chemical gradients. This tactical behavior relies on a motility structure, which is guided by a chemosensory system. Environmental signals are sensed by membrane-inserted chemosensory receptors that are organized in large ordered arrays. While the cellular positioning of the chemotaxis machinery and that of the flagellum have been studied in detail in bacteria, we have little knowledge about the localization of such macromolecular assemblies in archaea. Although the archaeal motility structure, the archaellum, is fundamentally different from the flagellum, archaea have received the chemosensory machinery from bacteria and have connected this system with the archaellum. Here, we applied a combination of time-lapse imaging and fluorescence and electron microscopy using the model euryarchaeonHaloferax volcaniiand found that archaella were specifically present at the cell poles of actively dividing rod-shaped cells. The chemosensory arrays also had a polar preference, but in addition, several smaller arrays moved freely in the lateral membranes. In the stationary phase, rod-shaped cells became round and chemosensory arrays were disassembled. The positioning of archaella and that of chemosensory arrays are not interdependent and likely require an independent form of positioning machinery. This work showed that, in the rod-shaped haloarchaeal cells, the positioning of the archaellum and of the chemosensory arrays is regulated in time and in space. These insights into the cellular organization ofH. volcaniisuggest the presence of an active mechanism responsible for the positioning of macromolecular protein complexes in archaea.IMPORTANCEArchaea are ubiquitous single cellular microorganisms that play important ecological roles in nature. The intracellular organization of archaeal cells is among the unresolved mysteries of archaeal biology. With this work, we show that cells of haloarchaea are polarized. The cellular positioning of proteins involved in chemotaxis and motility is spatially and temporally organized in these cells. This suggests the presence of a specific mechanism responsible for the positioning of macromolecular protein complexes in archaea.

scholarly journals CalR: A Web-based Analysis Tool for Indirect Calorimetry Experiments

2017 ◽  
Author(s):  
Amir I. Mina ◽  
Raymond A. LeClair ◽  
Katherine B. LeClair ◽  
David E. Cohen ◽  
Louise Lantier ◽  
...  
Keyword(s):  
Energy Balance ◽  
Energy Expenditure ◽  
Indirect Calorimetry ◽  
Statistical Tests ◽  
General Linear Model ◽  
Analysis Tool ◽  
Analysis Software ◽  
Web Based ◽  
Standard Tool ◽  
Data Files

AbstractWe report a web-based tool for analysis of indirect calorimetry experiments which measure physiological energy balance. CalR easily imports raw data files, generates plots, and determines the most appropriate statistical tests for interpretation. Analysis with the general linear model (which includes ANOVA and ANCOVA) allows for flexibility to interpret experiments of obesity and thermogenesis. Users may also produce standardized output files of an experiment which can be shared and subsequently re-evaluated using CalR. This framework will provide the transparency necessary to enhance consistency and reproducibility in experiments of energy expenditure. CalR analysis software will greatly increase the speed and efficiency with which metabolic experiments can be organized, analyzed according to accepted norms, and reproduced—and will likely become a standard tool for the field. CalR is accessible at https://CalR.bwh.harvard.edu.Graphical Abstract

scholarly journals Pandas DataFrames for a FAST binned analysis at CMS

2019 ◽  
Vol 214 ◽  
pp. 06035
Author(s):  
Benjamin Edward Krikler ◽  
Olivier Davignon ◽  
Lukasz Kreczko ◽  
Jacob Linacre ◽  
Emmanuel Olatunji Olaiya ◽  
...  
Keyword(s):  
Machine Learning ◽  
Big Data ◽  
Easy Access ◽  
Learning Tools ◽  
Analysis Software ◽  
Data Frame ◽  
Industry Standard ◽  
Standard Tool ◽  
Scientific Libraries ◽  
Binned Data

Binned data frames are a generalisation of multi-dimensional histograms, represented in a tabular format with one category per row containing the labels, bin contents, uncertainties and so on. Pandas is an industry-standard tool, which provides a data frame implementation complete with routines for data frame manipultion, persistency, visualisation, and easy access to “big data” scientific libraries and machine learning tools. FAST (the Faster Analysis Software Taskforce) has developed a generic approach for typical binned HEP analyses, driving the summary of ROOT Trees to multiple binned DataFrames with a yaml-based analysis description. Using Continuous Integration to run subsets of the analysis, we can monitor and test changes to the analysis itself, and deploy documentation automatically. This report describes this approach using examples from a public CMS tutorial and details the benefit over traditional methods.

scholarly journals Comprehensive Analysis on Seismic Design of Tall Building Structure Method

2015 ◽  
Vol 4 (2) ◽  
pp. 20
Author(s):  
Qiong Zhang
Keyword(s):  
Seismic Design ◽  
Structure Design ◽  
Comprehensive Analysis ◽  
Engineering Practice ◽  
Building Structure ◽  
Analysis Software ◽  
High Rise ◽  
Conceptual Clarity ◽  
Measure Analysis ◽  
Structure Measure

<p class="ordinary-outputtarget-output">For a high-rise structure design, the problems encountered may be perplexing, concrete analysis of concrete problems only. Engineering practice shows that the design process of the high-rise structure, design personnel only seismic conceptual clarity, structure measure analysis software three organic combinations to achieve more satisfactory results in the process of seismic structural weight in structure calculation structure properly applying the appropriate. This paper makes a theoretical analysis of necessity for building seismic design concept, in order to explore the method of high-rise building to take the necessary anti-seismic measures.</p>

scholarly journals Multifocal imaging for precise, label-free tracking of fast biological processes in 3D

2020 ◽  
Author(s):  
Jan N. Hansen ◽  
An Gong ◽  
Dagmar Wachten ◽  
René Pascal ◽  
Alex Turpin ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
High Speed ◽  
Reconstruction Algorithm ◽  
Cost Effective ◽  
Human Sperm ◽  
Dark Field ◽  
Biological Processes ◽  
Label Free ◽  
Flagellar Beat ◽  
Dark Field Microscopy

AbstractMany biological processes happen on a nano- to millimeter scale and within milliseconds. Established methods such as confocal microscopy are suitable for precise 3D recordings but lack the temporal or spatial resolution to resolve fast 3D processes and require labeled samples. Multifocal imaging (MFI) allows high-speed 3D imaging but suffers from the compromise between spatial resolution and field-of-view (FOV), requiring bright fluorescent labels and limiting its application. Here, we present a new approach for high-resolution, label-free, high-speed MFI, based on dark-field microscopy and operative over large volumes. We introduce a 3D reconstruction algorithm that increases resolution and depth of the sampled volume without compromising speed and FOV. This allowed us to characterize the flagellar beat of human sperm and surrounding fluid flow with a precision below the Abbe limit, in a large volume, and at high speed. Our MFI concept is cost-effective, can be easily built, and does not rely on object labeling, making it broadly applicable.

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