Scale-free Vertical Tracking Microscopy: Towards Bridging Scales in Biological Oceanography

AbstractUnderstanding key biophysical phenomena in the ocean often requires one to simultaneously focus on microscale entities, such as motile plankton and sedimenting particles, while maintaining the macroscale context of vertical transport in a highly stratified environment. This poses a conundrum: How to measure single organisms, at microscale resolution, in the lab, while allowing them to freely move hundreds of meters in the vertical direction? We present a solution in the form of a scale-free, vertical tracking microscope based on a circular “hydrodynamic-treadmill”. Our technology allows us to transcend physiological and ecological scales, tracking organisms from marine zooplankton to single-cells over vertical scales of meters while resolving microflows and behavioral processes. We demonstrate measurements of sinking particles, including marine snow as they sediment tens of meters while capturing sub-particle-scale phenomena. We also demonstrate depth-patterned virtual-reality environments for novel behavioral analyses of microscale plankton. This technique offers a new experimental paradigm in microscale ocean biophysics by combining physiological-scale imaging with free movement in an ecological-scale patterned environment.One sentence summaryScale-free vertical tracking microscopy captures, for the first time, untethered behavioral dynamics at cellular resolution for marine plankton.

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COMPREHENSIVE WAY OF CALCULATING ECOLOGICAL (ENVIRONMENTAL SPACE) FACTORS OF PLANT COMMUNITIES ENVIRONMENT FOR AMPLITUDE ECOLOGICAL SCALES

Vestnik Farmacii ◽

10.52540/2074-9457.2021.2.48 ◽

2021 ◽

Vol 92 (2) ◽

pp. 48-58

Author(s):

G. N. Buzuk ◽

Keyword(s):

Plant Communities ◽

Climatic Factors ◽

Ecological Factors ◽

Indicator Method ◽

Ecological Index ◽

Ecological Scales ◽

Ecological Scale ◽

Environmental Space ◽

Instrumental Methods ◽

The Ideal

Despite intensive development of instrumental methods of environmental factors analysis for plant communities their assessment with ecological scales still remains important. The main advantage of ecological scales is their ability to reflect generalized and average characteristics of ecological regimes due to significant inertia in response of plant communities composition to the change of certain characteristics of the environment. The main ways of calculation while using ecological scales are the medium-sized method and the ideal indicator method (of linear regression) including modified algorithm of calculating the level of edaphic and climatic factors of the environment with amplitude ecological scales. The aim of this work was to improve further the method for assessing the level of ecological factors (ecological space) in plant communities. For calculations and visualization of the results obtained we used Excel and our own programs written in the Matlab media. The basis of the method is finding the factor averagely weighed for the level calculated by the traditional way and by the method of the ideal indicator. It is proposed to set the weight of factors in both methods of calculation both explicitly and depending on the ecological index reflecting correspondence (adequacy) of the plant community composition to the level of ecological factors prevailing in the habitat. They can also be calculated by linear or non-linear dependencies relative to the middle of amplitude ecological scale. The conclusion is that it is possible to predict the content of secondary metabolites in plants based on assessing the level of ecological factors for plant communities.

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Subcellular localization of Apaf-1 in apoptotic rat pituitary cells

AJP Cell Physiology ◽

10.1152/ajpcell.00331.2005 ◽

2006 ◽

Vol 290 (3) ◽

pp. C672-C677 ◽

Cited By ~ 8

Author(s):

Maja Potokar ◽

Marko Kreft ◽

Helena H. Chowdhury ◽

Nina Vardjan ◽

Robert Zorec

Keyword(s):

Cytochrome C ◽

Single Cells ◽

Cellular Level ◽

Pituitary Cells ◽

Apoptotic Pathway ◽

Proliferation And Apoptosis ◽

Rat Pituitary ◽

Before And After ◽

Rat Pituitary Cells ◽

First Time

A key step in the intrinsic apoptotic pathway is the assembly of the apoptosome complex. The apoptosome components are well known; however, the physiology of the assembly of the apoptosome complex at the cellular level is still poorly defined. The aim of this work was to study the subcellular distribution of the apoptosome scaffold protein apoptotic protease-activating factor 1 (Apaf-1) before and after triggering apoptosis in single somatotrophs. Somatotrophs are the subject of extensive pituitary tissue remodeling in different physiological situations in which the quality and the number of pituitary cells are determined by cell proliferation and apoptosis. We show herein that 2 h after triggering apoptosis with rotenone, Apaf-1 redistributed to the proximity of mitochondria. In addition, the degree of colocalization between Apaf-1 and fluorescently labeled caspase-9 significantly increased during the same period. Furthermore, we show herein for the first time in single cells that the colocalization between Apaf-1 and cytochrome c increases only transiently, indicating a transient interaction between cytochrome c and Apaf-1 during the activation of apoptosis in these cells.

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Vertical charge transport through transition metal dichalcogenides – a quantitative analysis

Nanoscale ◽

10.1039/c7nr05069k ◽

2017 ◽

Vol 9 (48) ◽

pp. 19108-19113 ◽

Cited By ~ 7

Author(s):

Yuqi Zhu ◽

Ruiping Zhou ◽

Feng Zhang ◽

Joerg Appenzeller

Keyword(s):

Quantitative Analysis ◽

Transition Metal ◽

Charge Transport ◽

Effective Mass ◽

Transition Metal Dichalcogenides ◽

Vertical Direction ◽

Metal Dichalcogenides ◽

First Time

Effective mass in the vertical direction of MoS2 and WSe2 has been extracted for the first time.

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Comparison of commonly used ecological scales with the Belgard Plant Ecomorph System

Biosystems Diversity ◽

10.15421/011843 ◽

2018 ◽

Vol 26 (4) ◽

pp. 286-291

Author(s):

B. Baranovski ◽

N. Roschina ◽

L. Karmyzova ◽

I. Ivanko

Keyword(s):

Plant Species ◽

Ecological Factors ◽

Steppe Zone ◽

Doctoral Dissertation ◽

Plant Ecology ◽

Meadow Steppe ◽

Ecological Features ◽

Ecological Scales ◽

Ecological Scale ◽

Wide Range

There are several ecological scales developed both for phytoindication of ecological factors and plant ecomorphs. Among them, the scales of Ellenberg and Tsyganov are the most commonly used. L. G. Ramensky and P. S. Pogrebnyak had developed a phytoindication method; they also were founders of first ecological scale of plant species in relation to various environmental factors. One of first ecomorph systems was developed by Alexander Lyutsianovich Belgard. In 1947, Belgard presented a tabular ecomorph system in his doctoral dissertation, and later in monograph “Forest vegetation of the South-East of Ukraine”. In the system he used abbreviated Latin names applying terminology proposed in the late 19th century by Dekandol, Warmin and other authors. He considered ecomorphs as adaptations of plants to environmental conditions in forests of the steppe zone of Ukraine where forest cenoses are exposed to processes of steppization, prairification, swamping, salinization, and thus clarification of relationships between forest, meadow, steppe, marsh and weed plant species was essential. Therefore, development and introduction of cenomorph terms as “adaptation of plant species to phytocenosis as a whole” were an absolutely new contribution to the concept of ecomorph system. In environmental factor scales of Ellenberg and other authors, environment characteristics based on phytoindication were underlined; in the Belgard Plant Ecomorph System, ecomorphs reflect ability of plant species to grow within certain ranges of a given factor. These approaches are quite comparable, and ecomorphs of the Belgard system correspond to certain grades of the Ellenberg and Tsyganov scales. The Belgard ecomorph system has been applied in a number of fundamental and applied works on plant ecology and phytocenology. It is convenient for characterizing ecological features of plant species growing in the steppe zone with a wide range of environment factors such as lighting, humidity, and soil richness. Other authors have expanded and supplemented the Belgard Plant Ecomorph System based on its strategy. A number of ecomorphs was introduced; they reflect intermediate or extreme gradations of factors. A new cenomorph – silvomargoant – has been proposed by the authors of this paper.

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Exploiting variability of single cells to uncover the in vivo hierarchy of miRNA targets

10.1101/035097 ◽

2015 ◽

Cited By ~ 2

Author(s):

Andrzej Jerzy Rzepiela ◽

Arnau Vina-Vilaseca ◽

Jeremie Breda ◽

Souvik Ghosh ◽

Afzal P Syed ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Single Cells ◽

Human Embryonic Kidney Cells ◽

Mirna Targets ◽

Wide Range ◽

Gene Expression Dynamics ◽

Cell To Cell Variability ◽

First Time

MiRNAs are post-transcriptional repressors of gene expression that may additionally reduce the cell-to-cell variability in protein expression, induce correlations between target expression levels and provide a layer through which targets can influence each other's expression as 'competing RNAs' (ceRNAs). Here we combined single cell sequencing of human embryonic kidney cells in which the expression of two distinct miRNAs was induced over a wide range, with mathematical modeling, to estimate Michaelis-Menten (KM)-type constants for hundreds of evolutionarily conserved miRNA targets. These parameters, which we inferred here for the first time in the context of the entire network of endogenous miRNA targets, vary over ~2 orders of magnitude. They reveal an in vivo hierarchy of miRNA targets, defined by the concentration of miRNA-Argonaute complexes at which the targets are most sensitively down-regulated. The data further reveals miRNA-induced correlations in target expression at the single cell level, as well as the response of target noise to the miRNA concentration. The approach is generalizable to other miRNAs and post-transcriptional regulators and provides a deeper understanding of gene expression dynamics.

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Isolation of the Ascobolus immersus spore color gene b2 and study in single cells of gene silencing by methylation induced premeiotically.

Genetics ◽

10.1093/genetics/141.4.1299 ◽

1995 ◽

Vol 141 (4) ◽

pp. 1299-1314

Author(s):

V Colot ◽

J L Rossignol

Keyword(s):

Gene Silencing ◽

Physical Mapping ◽

Meiotic Recombination ◽

Hot Spot ◽

Single Cells ◽

Model System ◽

Ascobolus Immersus ◽

First Time ◽

Mutant Rescue ◽

Color Gene

Abstract The ascomycete Ascobolus immersus has been extensively used as a model system for the genetic study of meiotic recombination. More recently, an epigenetic process, known as methylation induced premeiotically (MIP), that acts on duplicated sequences has been discovered in A. immersus and has raised a new interest in this fungus. To try and extend these studies, we have now cloned the A. immersus spore color gene b2, a well characterized recombination hot-spot. Isolation of the whole gene was verified by physical mapping of four large b2 alterations, followed by transformation and mutant rescue of a null b2 allele. Transformation was also used to duplicate b2 and subject it to MIP. As a result, we were able for the first time to observe gene silencing as early as just after meiosis and in single cells. Furthermore, we have found evidence for a modulating effect of MIP on b2 expression, depending on the region of the gene that is duplicated and hence subjected to MIP.

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First direct identification of the barlens vertical structure in galaxy models

Astronomy and Astrophysics ◽

10.1051/0004-6361/202140703 ◽

2021 ◽

Vol 648 ◽

pp. L4

Author(s):

Iliya S. Tikhonenko ◽

Anton A. Smirnov ◽

Natalia Ya. Sotnikova

Keyword(s):

Vertical Structure ◽

Vertical Direction ◽

Direct Identification ◽

Flat Structure ◽

Body Model ◽

Thick Part ◽

Different Types ◽

The Galaxy ◽

The Face ◽

First Time

Applying spectral dynamics methods to one typical N-body model with a barlens, we dissect the modelled bar into separate components supported by completely different types of orbits. We identify at least four components: a narrow elongated bar, a boxy bar, and two components contributing to the barlens. We analyse the vertical structure of all components that make up the thick part of the bar, which has a boxy/peanut shape (B/P bulge). We show that the ‘peanut’ shape is mainly due to the orbits that assemble the boxy part of the face-on bar. We associate the X-shape with the narrow and elongated bar. The wider part of the barlens with square-like isophotes contributes to the boxy shape of the B/P bulge when we observe the galaxy edge-on. However, the part of the barlens with rounded isophotes in the face-on view is a rather flat structure in the vertical direction without any significant off-centre protrusions. Thus, for the first time, we demonstrate that the rounded face-on barlens cannot be entirely associated with the B/P bulge.

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Communities with Ambrosia artemisiifolia L. in the Kursk Region

Vegetation of Russia ◽

10.31111/vegrus/2019.36.41 ◽

2019 ◽

pp. 41-58

Author(s):

L. A. Arepieva

Keyword(s):

Plant Communities ◽

Software Package ◽

Ambrosia Artemisiifolia ◽

Natural Conditions ◽

Abandoned Fields ◽

Ecological Scales ◽

Ecological Scale ◽

The City ◽

Kursk Region ◽

Hygrophilous Species

The purpose of this study is to characterize plant communities with Ambrosia artemisiifolia in the Kursk Region. The work is based on 32 relevés made by the author in the city of Kursk and few district centers of the Kursk Region in 2009–2018. Some information about natural conditions of the Kursk Region is given in Table 1. Classification is carried out according to Braun-Blanquet approach. The data were treated by IBIS 7.2 software package (Zverev, 2007). The names of the higher syntaxa follow to «Vegetation of Europe…» (Mucina et al., 2016). Synoptic tables include only species with a constancy above I. Ecological conditions (soil moisture, richness in mineral nitrogen, light) were assessed with the use of average values by H. Ellenberg et al. (1992) ecological scales while hemerobiality with use of average values by N. G. Ilminskikh (1993) ecological scale and processed by IBIS software (Zverev, 2007). 4 associations of 3 classes of vegetation were revealed. Communities with Ambrosia artemisiifolia and hygrophilous species are described in Serbia (Jarić et al., 2011) wh ere subass. Chenopodio–Ambrosietum artemisiifoliae bidentetosum Jarić et al. 2011 was recorded in abandoned fields. It is differentiated by biennials and perennials from classes Artemisietea vulgaris and Molinio-Arrhenatheretea and others (Table 10). The features of communities with Ambrosia artemisiifolia identified in this work are important for the development strategies to combat this dangerous plant.

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New IR imaging modalities for cancer detection and for intra-cell chemical mapping with a sub-diffraction mid-IR s-SNOM

Faraday Discussions ◽

10.1039/c5fd00150a ◽

2016 ◽

Vol 187 ◽

pp. 539-553 ◽

Cited By ~ 19

Author(s):

H. Amrania ◽

L. Drummond ◽

R. C. Coombes ◽

S. Shousha ◽

L. Woodley-Barker ◽

...

Keyword(s):

Human Cancer ◽

Single Cells ◽

Design Feature ◽

Chemical Mapping ◽

Technological Readiness ◽

New Family ◽

Routine Basis ◽

Cancer Biopsy ◽

First Time ◽

Detailed Chemical

We present two new modalities for generating chemical maps. Both are mid-IR based and aimed at the biomedical community, but they differ substantially in their technological readiness. The first, so-called “Digistain”, is a technologically mature “locked down” way of acquiring diffraction-limited chemical images of human cancer biopsy tissue. Although it is less flexible than conventional methods of acquiring IR images, this is an intentional, and key, design feature. It allows it to be used, on a routine basis, by clinical personnel themselves. It is in the process of a full clinical evaluation and the philosophy behind the approach is discussed. The second modality is a very new, probe-based “s-SNOM”, which we are developing in conjunction with a new family of tunable “Quantum Cascade Laser” (QCL) diode lasers. Although in its infancy, this instrument can already deliver ultra-detailed chemical images whose spatial resolutions beat the normal diffraction limit by a factor of ∼1000. This is easily enough to generate chemical maps of the insides of single cells for the first time, and a range of new possible scientific applications are explored.

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Mathematical modelling of the viable epidermis: impact of cell shape and vertical arrangement

Mathematics and Mechanics of Solids ◽

10.1177/1081286517743297 ◽

2017 ◽

Vol 25 (5) ◽

pp. 1046-1059 ◽

Cited By ~ 4

Author(s):

Rebecca Wittum ◽

Arne Naegel ◽

Michael Heisig ◽

Gabriel Wittum

Keyword(s):

Mathematical Modelling ◽

Cell Shape ◽

Vertical Direction ◽

Cell Types ◽

Stratum Granulosum ◽

Viable Epidermis ◽

Membrane Permeabilities ◽

And Function ◽

First Time ◽

In Silico Methods

In-silico methods are valuable tools for understanding the barrier function of the skin. The key benefit is that mathematical modelling allows the interplay between cell shape and function to be elucidated. This study focuses on the viable (living) epidermis. For this region, previous works suggested a diffusion model and an approximation of the cells by hexagonal prisms. The work at hand extends this in three ways. First, the extracellular space is treated with full spatial resolution. This induces a decrease of permeability by about 10%. Second, cells of tetrakaidecahedral shape are considered, in addition to the original hexagonal prisms. For both cell types, the resulting membrane permeabilities are compared. Third, for the first time, the influence of cell stacking in the vertical direction is considered. This is particularly important for the stratum granulosum, where tight junctions are present.

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