scholarly journals Computational Identification and 3D Morphological Characterization of Renal Glomeruli in Optically Cleared Murine Kidneys

Sensors ◽  
2021 ◽  
Vol 21 (22) ◽  
pp. 7440
Author(s):  
Nabil Nicolas ◽  
Nour Nicolas ◽  
Etienne Roux
Keyword(s):  
Statistical Analysis ◽  
Surface Area ◽  
Light Sheet ◽  
Renal Tissue ◽  
Morphological Characterization ◽  
Capillary Endothelium ◽  
Light Sheet Microscopy ◽  
Renal Glomeruli ◽  
False Positive Identification

The aim of this study was to establish an accessible methodology for the objective identification and 3D morphological characterization of renal glomeruli in mice. 3D imaging of the renal cortex was performed by light sheet microscopy on iDISCO+ optical cleared kidneys of six C57BL/6J mice after labelling of the capillary endothelium by lectin injection. 3D images were processed with the open source software ImageJ, and statistical analysis done with GraphPad Prism. Non-visual delimitation of the external surface of the glomeruli was ensured by greyscale-based thresholding, the value of which was determined from the statistical analysis of the voxel frequency distribution. Exclusion of false-positive identification was done by successive volume- and shape-based segmentation. Renal glomeruli were characterized by their number, surface area, volume, and compactness. Average data were expressed as mean ± SD. The number of glomeruli was equal to 283 ± 35 per mm3 of renal tissue, representing 1.78 ± 0.49% of the tissue volume. The surface area, volume and compactness were equal to 20,830 ± 6200 µm², 62,280 ± 14,000 µm3 and 0.068 ± 0.026, respectively. The proposed standardized methodology allows the identification of the renal glomeruli and their 3D morphological characterization, and is easily accessible for biologists.

scholarly journals 3D Imaging and Quantitative Characterization of Mouse Capillary Coronary Network Architecture

Biology ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 306
Author(s):  
Nabil Nicolas ◽  
Etienne Roux
Keyword(s):  
Network Architecture ◽  
3D Imaging ◽  
Average Length ◽  
Visual Image ◽  
Light Sheet ◽  
Difficulty Level ◽  
Capillary Endothelium ◽  
Resolution Limit ◽  
Light Sheet Microscopy

Characterization of the cardiac capillary network structure is of critical importance to understand the normal coronary functional properties and coronary microvascular diseases. The aim of our study was to establish an accessible methodology for 3D imaging and 3D processing to quantitatively characterize the capillary coronary network architecture in mice. Experiments were done on C57BL/6J mice. 3D imaging was performed by light sheet microscopy and confocal microscopy on iDISCO+ optical cleared hearts after labelling of the capillary endothelium by lectin injection. 3D images were processed with the open source software ImageJ. Non-visual image segmentation was based of the frequency distribution of the voxel greyscale values, followed by skeletonization and distance mapping. Capillary networks in left and right ventricles and septum were characterized by the volume network density, the fractal dimension, the number of segments and nodes and their ratio, the total network length, and the average length, diameter, and tortuosity of the segments. Scale-dependent parameter values can be impacted by the resolution limit of the 3D imaging technique. The proposed standardized methodology for 3D image processing is easily accessible for a biologist in terms of investment and difficulty level, and allows the quantification of the 3D capillary architecture and its statistical comparison in different conditions.

scholarly journals Characterization of Scattering Effects in Phantom Samples using Single and Two-Photon Excitation Light Sheet Microscopy

2012 ◽  
Vol 102 (3) ◽  
pp. 195a-196a
Author(s):  
Zeno Lavagnino ◽  
Francesca Cella Zanacchi ◽  
Emiliano Ronzitti ◽  
Ivan Coto Hernandez ◽  
Alberto Diaspro
Keyword(s):  
Light Sheet ◽  
Excitation Light ◽  
Two Photon ◽  
Light Sheet Microscopy ◽  
Photon Excitation ◽  
Scattering Effects ◽  
Two Photon Excitation

scholarly journals Characterization of neurite dystrophy after trauma by high speed structured illumination microscopy and lattice light sheet microscopy

2019 ◽  
Vol 312 ◽  
pp. 154-161 ◽  
Author(s):  
Jack K. Phillips ◽  
Sydney A. Sherman ◽  
Kristen Y. Cotton ◽  
John M. Heddleston ◽  
Aaron B. Taylor ◽  
...  
Keyword(s):  
High Speed ◽  
Light Sheet ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Light Sheet Microscopy

scholarly journals Morphological and Biochemical Characterization of Wild Hop (Humulus lupulus L.) Populations from Banja Luka Area (Bosnia and Herzegovina)

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 239
Author(s):  
Danijela Kondić ◽  
Andreja Čerenak ◽  
Iztok Jože Košir ◽  
Miha Ocvirk ◽  
Tanja Krmpot ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Analysis Of Variance ◽  
Biochemical Characterization ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Morphological Characterization ◽  
Humulus Lupulus L ◽  
Banja Luka ◽  
Cone Density

This study aims to do a morphological and biochemical characterization of selected wild hop populations from the Banja Luka region, as plant material with potential value for introduction into plant selection. Female inflorescences (cones) from seven populations (DKH3, DKH5, DKH6, DKH8, DKH9, DKH10, and DKH11) were sampled in 2018 and 2019. Hop cones were collected in October 2018 and 2019 for morphological characterization, when 50 cones per population were analyzed, and also the cones were collected in mid-September in 2019 for biochemical characterization. Morphological parameters were carried out for: cone length (cm), number of nodes per cone spindle, cone density, and number of seeds per cone, all important agronomic characters in hop production. Also, 27 components of essential oil and 6 components of hop resins were analyzed. Statistical analysis of morphological characteristics was performed by factorial analysis of variance (year × population), and the significance of individual differences was determined by LSD test. The grouping of examined hop populations according to the manifested morphological characteristics was performed by cluster analysis. Statistical analysis for biochemical characteristics was performed by analysis of variance, and the significance of the differences was tested by Tukey’s statistical test. In order to determine similarities between different population multivariant statistical method Principal component analysis (PCA) was applied. According to morphological and biochemical analysis, DKH6 hop population is singled out as the most valuable for hop breeding.

Morphological Characterization of Mycobacteriophage R1

1974 ◽  
Vol 32 ◽  
pp. 254-255
Author(s):  
B. L. Soloff ◽  
T. A. Rado
Keyword(s):  
Carbon Source ◽  
Stationary Phase ◽  
Growth Phase ◽  
Minimal Medium ◽  
Morphological Characterization ◽  
Logarithmic Growth Phase ◽  
Complete Lysis ◽  
Lysogenic Culture ◽  
Logarithmic Growth

Mycobacteriophage R1 was originally isolated from a lysogenic culture of M. butyricum. The virus was propagated on a leucine-requiring derivative of M. smegmatis, 607 leu−, isolated by nitrosoguanidine mutagenesis of typestrain ATCC 607. Growth was accomplished in a minimal medium containing glycerol and glucose as carbon source and enriched by the addition of 80 μg/ ml L-leucine. Bacteria in early logarithmic growth phase were infected with virus at a multiplicity of 5, and incubated with aeration for 8 hours. The partially lysed suspension was diluted 1:10 in growth medium and incubated for a further 8 hours. This permitted stationary phase cells to re-enter logarithmic growth and resulted in complete lysis of the culture.

Morphological Characterization of Rhinacanthus Species of Sri Lanka

Planta Medica ◽  
2010 ◽  
Vol 76 (05) ◽  
Author(s):  
APPR Amarasinghe ◽  
RP Karunagoda ◽  
DSA Wijesundara
Keyword(s):  
Sri Lanka ◽  
Morphological Characterization

Density and morphological characterization of bacteria in integrated and exclusive production systems

2020 ◽  
Vol 13 (11) ◽  
pp. 1
Author(s):  
A. R. B. Zanco ◽  
A. Ferreira ◽  
G. C. M. Berber ◽  
E. N. Gonzaga ◽  
D. C. C. Sabino
Keyword(s):  
Bacterial Community ◽  
Rainy Season ◽  
Production Systems ◽  
Cropping System ◽  
Morphological Characterization ◽  
Native Forest ◽  
Exclusive Production ◽  
Colony Forming Units

The different integrated production systems can directly interfere with its bacterial community. The present study aimed to assess density, bacterial diversity and the influence of dry and rainy season in different integrated and an exclusive production system. The fallow and a native forest area was assessed to. Samples were collected in 2012 March and September. The isolation were carried out into Petri dishes containing DYGS medium. The number of colony forming units (CFU) was counted after 48 hours and. The bacterial density ranged between 106 and 107 CFU g-1 soil. The crop system affected the dynamics of the bacterial community only in the rainy season. The rainy season showed greater density of total bacteria when compared to the dry period regardless of the cropping system. The dendrograms with 80 % similarity showed thirteen and fourteen groups in the rainy and dry seasons. Isolates with the capacity to solubilize phosphate in vitro were obtained from all areas in the two seasons, but this feature has been prevalent in bacteria isolated during the rainy season

Characterization of Antibacterial-Producing Endophytic Fungi of Syzygiumpolyanthum Leaves

2020 ◽  
Vol 20 (4) ◽  
pp. 448-454
Author(s):  
Rahmita Burhamzah ◽  
Gemini Alam ◽  
Herlina Rante
Keyword(s):  
Molecular Characterization ◽  
Endophytic Fungi ◽  
Morphological Characterization ◽  
Test Method ◽  
Analysis Method ◽  
Nitrogen Base ◽  
Rdna Genes ◽  
Antibacterial Screening ◽  
Planting Method

Background: Endophytic fungi live in plants’ tissue and can produce the same bioactive compounds as its host plant produces. Syzygiumpolyanthum leaves have known to be one of the antibacterial compound producers. Aim and Objective: This study aimed to characterize morphologically, microscopically, and molecularly the antibacterial-producing endophytic fungi of Syzygiumpolyanthum leaves. Methods: The isolation of endophytic fungi was done by fragment planting method on PDA medium. The antibacterial screening was performed using the antagonistic test as the first screening followed by the disc diffusion test method. The morphological characterization was based on isolate’s mycelia color, growth pattern, margin, and surface texture of the colony, while the microscopic characterization was based on its hyphae characteristics. The molecular characterization of the isolate was done by nitrogen base sequence analysis method on nucleotide constituent of ITS rDNA genes of the isolate. Results: The results found that isolate DF1 has antibacterial activity against E.coli, S.aureus, P.acne, and P.aeruginosa, with the greatest inhibition at 10% concentration of broth fermentation extract on S.aureus with a diameter of inhibition of 13.77 mm. Conclusion: Based on macroscopic, microscopic, and molecular characterization, DF1 isolate is similar to Ceriporialacerate.

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