scholarly journals A versatile multivariate image analysis pipeline reveals features of Xenopus extract spindles

2016 ◽  
Vol 213 (1) ◽  
pp. 127-136 ◽  
Author(s):  
Andrew W. Grenfell ◽  
Magdalena Strzelecka ◽  
Marina E. Crowder ◽  
Kara J. Helmke ◽  
Anne-Lore Schlaitz ◽  
...  
Keyword(s):  
Quantitative Information ◽  
Analysis Pipeline ◽  
Experimental Conditions ◽  
Experimental Systems ◽  
General Utility ◽  
Segmentation Approach ◽  
Assembly Factor ◽  
Minimal Modification ◽  
Insight Into ◽  
Multivariate Image

Imaging datasets are rich in quantitative information. However, few cell biologists possess the tools necessary to analyze them. Here, we present a large dataset of Xenopus extract spindle images together with an analysis pipeline designed to assess spindle morphology across a range of experimental conditions. Our analysis of different spindle types illustrates how kinetochore microtubules amplify spindle microtubule density. Extract mixing experiments reveal that some spindle features titrate, while others undergo switch-like transitions, and multivariate analysis shows the pleiotropic morphological effects of modulating the levels of TPX2, a key spindle assembly factor. We also apply our pipeline to analyze nuclear morphology in human cell culture, showing the general utility of the segmentation approach. Our analyses provide new insight into the diversity of spindle types and suggest areas for future study. The approaches outlined can be applied by other researchers studying spindle morphology and adapted with minimal modification to other experimental systems.

scholarly journals Methane and Inflammation - A Review (Fight Fire with Fire)

2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Marietta Zita Poles ◽  
László Juhász ◽  
Mihály Boros
Keyword(s):  
Stress Responses ◽  
Nitrosative Stress ◽  
Ischemia Reperfusion ◽  
Signalling Pathways ◽  
Experimental Conditions ◽  
Neuroprotective Effects ◽  
Oxidative And Nitrosative Stress ◽  
Carbohydrate Fermentation ◽  
Insight Into

AbstractMammalian methanogenesis is regarded as an indicator of carbohydrate fermentation by anaerobic gastrointestinal flora. Once generated by microbes or released by a non-bacterial process, methane is generally considered to be biologically inactive. However, recent studies have provided evidence for methane bioactivity in various in vivo settings. The administration of methane either in gas form or solutions has been shown to have anti-inflammatory and neuroprotective effects in an array of experimental conditions, such as ischemia/reperfusion, endotoxemia and sepsis. It has also been demonstrated that exogenous methane influences the key regulatory mechanisms and cellular signalling pathways involved in oxidative and nitrosative stress responses. This review offers an insight into the latest findings on the multi-faceted organ protective activity of exogenous methane treatments with special emphasis on its versatile effects demonstrated in sepsis models.

scholarly journals Natural Variation in Plant Pluripotency and Regeneration

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1261
Author(s):  
Robin Lardon ◽  
Danny Geelen
Keyword(s):  
De Novo ◽  
Shoot Organogenesis ◽  
In Vitro Regeneration ◽  
Relative Role ◽  
Root Explants ◽  
Experimental Systems ◽  
Complex Process ◽  
Insight Into ◽  
Molecular Framework

Plant regeneration is essential for survival upon wounding and is, hence, considered to be a strong natural selective trait. The capacity of plant tissues to regenerate in vitro, however, varies substantially between and within species and depends on the applied incubation conditions. Insight into the genetic factors underlying this variation may help to improve numerous biotechnological applications that exploit in vitro regeneration. Here, we review the state of the art on the molecular framework of de novo shoot organogenesis from root explants in Arabidopsis, which is a complex process controlled by multiple quantitative trait loci of various effect sizes. Two types of factors are distinguished that contribute to natural regenerative variation: master regulators that are conserved in all experimental systems (e.g., WUSCHEL and related homeobox genes) and conditional regulators whose relative role depends on the explant and the incubation settings. We further elaborate on epigenetic variation and protocol variables that likely contribute to differential explant responsivity within species and conclude that in vitro shoot organogenesis occurs at the intersection between (epi) genetics, endogenous hormone levels, and environmental influences.

scholarly journals Altered acrylic acid concentrations in hard and soft corals exposed to deteriorating water conditions

FACETS ◽  
2017 ◽  
Vol 2 (1) ◽  
pp. 531-544 ◽  
Author(s):  
Lori S.H. Westmoreland ◽  
Jennifer N. Niemuth ◽  
Hanna S. Gracz ◽  
Michael K. Stoskopf
Keyword(s):  
Acrylic Acid ◽  
Marine Algae ◽  
Soft Coral ◽  
Resonance Spectroscopy ◽  
Additional Insight ◽  
Experimental Conditions ◽  
Animal Metabolism ◽  
Reef Decline ◽  
Reliable Marker ◽  
Insight Into

A reliable marker of early coral response to environmental stressors can help guide decision-making to mitigate global coral reef decline by detecting problems before the development of clinically observable disease. We document the accumulation of acrylic acid in two divergent coral taxa, stony small polyp coral ( Acropora sp.) and soft coral ( Lobophytum sp.), in response to deteriorating water quality characterized by moderately increased ammonia (0.25 ppm) and phosphate (0.15 ppm) concentrations and decreased calcium (360 ppm) concentration, using nuclear magnetic resonance spectroscopy (NMR)-based metabolomic techniques. Changes in acrylic acid concentration in polyp tissues free of zooxanthellae suggest that acrylic acid could be a product of animal metabolism and not exclusively a metabolic by-product of the osmolyte dimethylsulfoniopropionate (DMSP) in marine algae or bacteria. Our findings build on previously documented depletions of acrylic acid in wild coral potentially correlated to temperature stress and provide additional insight into approaches to further characterize the nature of the metabolic accumulation of acrylic acid under controlled experimental conditions.

Comparative analysis reveals gravity is involved in the MIZ1-regulated root hydrotropism

2020 ◽  
Vol 71 (22) ◽  
pp. 7316-7330
Author(s):  
Ying Li ◽  
Wei Yuan ◽  
Luocheng Li ◽  
Hui Dai ◽  
Xiaolin Dang ◽  
...  
Keyword(s):  
Water Potential ◽  
Double Mutant ◽  
Root Elongation ◽  
Vertical Orientation ◽  
Tomato Plants ◽  
Oblique Orientation ◽  
Experimental Systems ◽  
Potential Gradients ◽  
Insight Into

Abstract Hydrotropism is the directed growth of roots toward the water found in the soil. However, mechanisms governing interactions between hydrotropism and gravitropism remain largely unclear. In this study, we found that an air system and an agar–sorbitol system induced only oblique water-potential gradients; an agar–glycerol system induced only vertical water-potential gradients; and a sand system established both oblique and vertical water-potential gradients. We employed obliquely oriented and vertically oriented experimental systems to study hydrotropism in Arabidopsis and tomato plants. Comparative analyses using different hydrotropic systems showed that gravity hindered the ability of roots to search for obliquely oriented water, whilst facilitating roots’ search for vertically oriented water. We found that the gravitropism-deficient mutant aux1 showed enhanced hydrotropism in the oblique orientation but impaired root elongation towards water in the vertical orientation. The miz1 mutant exhibited deficient hydrotropism in the oblique orientation but normal root elongation towards water in the vertical orientation. Importantly, in contrast to miz1, the miz1/aux1 double mutant exhibited hydrotropic bending in the oblique orientation and attenuated root elongation towards water in the vertical orientation. Our results suggest that gravitropism is required for MIZ1-regulated root hydrotropism in both the oblique orientation and the vertical orientation, providing further insight into the role of gravity in root hydrotropism.

Teaching the renal tubular reabsorption of glucose using two classic papers by Shannon et al.

2011 ◽  
Vol 35 (2) ◽  
pp. 114-116 ◽  
Author(s):  
Valdir A. Braga
Keyword(s):  
Proximal Tubule ◽  
Tubular Reabsorption ◽  
Renal Physiology ◽  
Experimental Conditions ◽  
Glucose Reabsorption ◽  
Renal Tubular Reabsorption ◽  
Renal Tubular ◽  
Classic Papers ◽  
Classic Paper ◽  
Insight Into

Most of the transport along the nephron uses membrane proteins and exhibits the three characteristics of mediated transport: saturation, specificity, and competition. Glucose reabsorption in the nephron is an excellent example of the consequences of saturation. Two classic papers by James A. Shannon and colleagues clearly show the ability of the kidney in transporting glucose and its saturation process, providing students with examples of the handling of glucose by the kidney. In addition, these articles demonstrate how stable and reproducible is the transport maximum of glucose in the proximal tubule under different experimental conditions. One key figure from each classic paper can be used to give students insight into how glucose transport becomes saturated, resulting in the excretion of glucose in urine, and will also give students a clear example of how careful experimentation and a clear interest in renal physiology led Shannon and colleagues to advance the field.

scholarly journals Antisense Inhibition of c-fes Proto-oncogene Blocks PMA-Induced Macrophage Differentiation in HL60 and in FDC-P1/MAC-11 Cells

Blood ◽  
1997 ◽  
Vol 89 (1) ◽  
pp. 135-145 ◽  
Author(s):  
Rossella Manfredini ◽  
Raffaella Balestri ◽  
Enrico Tagliafico ◽  
Francesca Trevisan ◽  
Michela Pizzanelli ◽  
...  
Keyword(s):  
Cell Lines ◽  
Phorbol Esters ◽  
Myeloid Cell ◽  
Macrophage Differentiation ◽  
Primary Transcript ◽  
Experimental Conditions ◽  
Fibronectin Receptor ◽  
Splice Junctions ◽  
Insight Into

To gain some insight into the role of c-fes in macrophage differentiation, we have analyzed the ability of HL60 leukemic promyelocytic cells and FDC-P1/MAC-11 murine myeloid precursor cells to differentiate in response to phorbol esters after inhibition of c-fes function. Fes inactivation has been obtained by using oligodeoxynucleotides (ODN) complementary to the 5′ region of c-fes mRNA and to 5′ splice junctions of c-fes primary transcript. After 5 days (d) in culture, in several separate experiments performed with different ODN preparations, a complete inhibition of c-fes expression was observed in HL60 and in FDC-P1/MAC-11 cells. No perturbation of cell growth was evident in our experimental conditions in both cell lines after c-fes inhibition. Furthermore, in HL60 cells lacking c-fes product, an almost complete downregulation of the α4β1 fibronectin receptor occurred. However, in both cell lines, the induction of macrophage differentiation by phorbol esters resulted in an almost complete maturation arrest as evaluated by morphological, cytochemical, immunological criteria, and by the cytofluorimetric cell cycle analysis. A loss of the adhesion capacity of both myeloid cell lines, when compared to terminally differentated macrophages, was also observed. These results suggest that HL60 and FDC-P1/MAC-11 cells, when treated with phorbol 12-myristate 13-acetate, require c-fes protein expression to activate the genetic program underlying macrophage differentiation.

scholarly journals VALIDATION OF POINT CLOUDS SEGMENTATION ALGORITHMS THROUGH THEIR APPLICATION TO SEVERAL CASE STUDIES FOR INDOOR BUILDING MODELLING

2016 ◽  
Vol XLI-B5 ◽  
pp. 667-674
Author(s):  
H. Macher ◽  
T. Landes ◽  
P. Grussenmeyer
Keyword(s):  
Case Studies ◽  
Point Clouds ◽  
Building Information Modelling ◽  
Home Furnishings ◽  
Laser Scanners ◽  
Segmentation Algorithms ◽  
Building Information ◽  
Segmentation Approach ◽  
Two Phases ◽  
Insight Into

Laser scanners are widely used for the modelling of existing buildings and particularly in the creation process of as-built BIM (Building Information Modelling). However, the generation of as-built BIM from point clouds involves mainly manual steps and it is consequently time consuming and error-prone. Along the path to automation, a three steps segmentation approach has been developed. This approach is composed of two phases: a segmentation into sub-spaces namely floors and rooms and a plane segmentation combined with the identification of building elements. <br><br> In order to assess and validate the developed approach, different case studies are considered. Indeed, it is essential to apply algorithms to several datasets and not to develop algorithms with a unique dataset which could influence the development with its particularities. Indoor point clouds of different types of buildings will be used as input for the developed algorithms, going from an individual house of almost one hundred square meters to larger buildings of several thousand square meters. Datasets provide various space configurations and present numerous different occluding objects as for example desks, computer equipments, home furnishings and even wine barrels. For each dataset, the results will be illustrated. The analysis of the results will provide an insight into the transferability of the developed approach for the indoor modelling of several types of buildings.

scholarly journals A novel methodology to study nanoporous alumina by small-angle neutron scattering

2019 ◽  
Vol 52 (4) ◽  
pp. 745-754 ◽  
Author(s):  
Anastasia Christoulaki ◽  
Alexis Chennevière ◽  
Isabelle Grillo ◽  
Lionel Porcar ◽  
Emmanuelle Dubois ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Condensed Matter ◽  
Quantitative Information ◽  
Sem Analysis ◽  
Experimental Conditions ◽  
Fitting Method ◽  
Hexagonal Arrangement ◽  
Sans Data

Nanoporous anodic aluminium oxide (AAO) membranes are promising host systems for confinement of condensed matter. Characterizing their structure and composition is thus of primary importance for studying the behavior of confined objects. Here a novel methodology to extract quantitative information on the structure and composition of well defined AAO membranes by combining small-angle neutron scattering (SANS) measurements and scanning electron microscopy (SEM) imaging is reported. In particular, (i) information about the pore hexagonal arrangement is extracted from SEM analysis, (ii) the best SANS experimental conditions to perform reliable measurements are determined and (iii) a detailed fitting method is proposed, in which the probed length in the fitting model is a critical parameter related to the longitudinal pore ordering. Finally, to validate this strategy, it is applied to characterize AAOs prepared under different conditions and it is shown that the experimental SANS data can be fully reproduced by a core/shell model, indicating the existence of a contaminated shell. This original approach, based on a detailed and complete description of the SANS data, can be applied to a variety of confining media and will allow the further investigation of condensed matter under confinement.

scholarly journals Active Coacervate Droplets Are Protocells That Grow and Resist Ostwald Ripening

2021 ◽  
Author(s):  
Karina K. Nakashima ◽  
Merlijn H. I. van Haren ◽  
Alain A. M. André ◽  
Irina Robu ◽  
Evan Spruijt
Keyword(s):  
Electrostatic Interactions ◽  
Protein Concentration ◽  
Ostwald Ripening ◽  
Population Level ◽  
Cellular Growth ◽  
Droplet Growth ◽  
Experimental Conditions ◽  
Active Processes ◽  
Cellular Behaviour ◽  
Insight Into

Active coacervate droplets are liquid condensates coupled to a chemical reaction that turns over their components, keeping the droplets out of equilibrium. This turnover can be used to drive active processes such as growth, and provide an insight into the chemical requirements underlying (proto)cellular behaviour. Moreover, controlled growth is a key requirement to achieve population fitness and survival. Here we present a minimal, nucleotide-based coacervate model for active droplets, and report three key findings that make these droplets into evolvable protocells. First, we show that coacervate droplets form and grow by the fuel-driven synthesis of new coacervate material. Second, we find that these droplets do not undergo Ostwald ripening, which we attribute to the attractive electrostatic interactions within complex coacervates, active or passive. Finally, we show that the droplet growth rate reflects experimental conditions such as substrate, enzyme and protein concentration, and that a different droplet composition (addition of RNA) leads to altered growth rates and droplet fitness. These findings together make active coacervate droplets a powerful platform to mimic cellular growth at a single-droplet level, and to study fitness at a population level.<br>

Transport of pesticides via macropores (IUPAC Technical Report)

2008 ◽  
Vol 80 (1) ◽  
pp. 105-160 ◽  
Author(s):  
Werner Kördel ◽  
Hans Egli ◽  
Michael Klein
Keyword(s):  
Preferential Flow ◽  
Measurement Techniques ◽  
Quantitative Information ◽  
Macropore Flow ◽  
Experimental Conditions ◽  
Pesticide Transport ◽  
Technical Report ◽  
Matrix Flow ◽  
Specific Assessment ◽  
A Site

This report provides an overview of the transport of solutes via macropores focusing on the practical relevance of the phenomenon. After a description of matrix flow and preferential flow in soil, information related to macropores, including their formation and measurement techniques, is briefly presented. Then, the influence of experimental conditions and of environmental and agricultural factors and pesticide properties is discussed, based on a statistical evaluation of all published studies offering sufficient quantitative information. Most of the analyzed parameters do not significantly influence the experimental pesticide losses. The groundwater ubiquity score (GUS) index turned out to be the most important compound property to describe substance losses through macropore flow. In a third section, tools for modeling pesticide transport through macropores are presented and critically evaluated. Results of the computer model MACRO, which is also used in the EU pesticide registration process, are compared with experimental losses. For five out of seven investigated pesticides (A-D, F), the simulated losses are in agreement with the experimental data. However, for two compounds with very low KOC values, MACRO overestimated the losses. Finally, the significance of pesticide transport via macropores for contamination of ground and surface water is assessed. Losses caused by macropore transport may considerably exceed losses caused by matrix transport at a specific site. Therefore, a site-specific assessment of pesticide leaching is needed.

Sign in / Sign up

Export Citation Format

Share Document