scholarly journals 3D-Analysis of a non-planispiral ammonoid from the Hunsrück Slate: natural or pathological variation?

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3526 ◽  
Author(s):  
Julia Stilkerich ◽  
Trisha A. Smrecak ◽  
Kenneth De Baets
Keyword(s):  
Three Dimensional ◽  
Euphotic Zone ◽  
Type Specimen ◽  
3D Analysis ◽  
Three Dimensional Model ◽  
Hunsrück Slate ◽  
Early Devonian ◽  
Holotype Specimen ◽  
New Type

We herein examine the only known non-planispirally coiled early Devonian ammonoid, the holotype specimen of Ivoites opitzi, to investigate if the host was encrusted in vivo and if these sclerobionts were responsible for the trochospiral coiling observed in this unique specimen. To test if the presence of runner-like sclerobionts infested the historically collected specimen of Ivoites opitzi during its life, we used microCT to produce a three-dimensional model of the surface of the specimen. Our results indicate that sclerobionts grew across the outer rim (venter) on both sides of the ammonoid conch at exactly the location where the deviation from the planispiral was recognized, and where subsequent ammonoid growth would likely preclude encrustation. This indicates in vivo encrustation of the I. opitzi specimen, and represents the earliest documentation of the phenomenon. Further, this suggests that non-planispiral coiling in I. opitzi was likely pathologically induced and does not represent natural morphological variation in the species. Despite the observed anomalies in coiling, the specimen reached adulthood and retains important identifying morphological features, suggesting the ammonoid was minimally impacted by encrustation in life. As such, appointing a new type specimen—as suggested by some authors—for the species is not necessary. In addition, we identify the sclerobionts responsible for modifying the coiling of this specimen as hederelloids, a peculiar group of sclerobionts likely related to phoronids. Hederelloids in the Devonian are commonly found encrusting on fossils collected in moderately deep environments within the photic zone and are rarely documented in dysphotic and aphotic samples. This indicates that when the ammonoid was encrusted it lived within the euphotic zone and supports the latest interpretations of the Hunsrück Slate depositional environment in the Bundenbach-Gemünden area.

scholarly journals 3D-Analysis of a non-planispiral ammonoid from the Hunsrück Slate: natural or pathological variation?

2016 ◽  
Author(s):  
Julia Stilkerich ◽  
Trisha A Smrecak ◽  
Kenneth De Baets
Keyword(s):  
Three Dimensional ◽  
Euphotic Zone ◽  
Type Specimen ◽  
3D Analysis ◽  
Three Dimensional Model ◽  
Hunsrück Slate ◽  
Early Devonian ◽  
Holotype Specimen ◽  
New Type

We herein examine the only known non-planispirally coiled early Devonian ammonoid, the holotype specimen of Ivoites opitzi, to investigate if the host was encrusted in vivo and if these sclerobionts were responsible for the trochospiral coiling observed on this unique specimen. To test if the presence of runner-like sclerobionts infested the historically collected specimen of Ivoites opitzi during its life, we used microCT to produce a three-dimensional model of the surface of the specimen. Our results indicate that sclerobionts grew across the outer rim (venter) on both sides of the ammonoid conch at exactly the location where the deviation from the planispiral was recognized, and where subsequent ammonoid growth would likely preclude encrustation. This indicates in vivo encrustation of the I. opitzi specimen, and represents the earliest documentation of the phenomenon. Further, this suggests that non-planispiral coiling in I. opitzi was pathologically induced and does not represent natural morphological variation in the species. Despite the observed anomalies in coiling, the specimen reached adulthood and retains important identifying morphological features, suggesting the ammonoid was minimally impacted by encrustation in life. As such, appointing a new type specimen – as suggested by some authors – for the species is not necessary. In addition, we identify the sclerobionts responsible for modifying the coiling of this specimen as hederelloids, a peculiar group of sclerobionts likely related to phoronids. Hederelloids in the Devonian are commonly found encrusting on fossils collected in moderately deep environments within the photic zone and are rarely documented in dysphotic and aphotic samples. This indicates that when the ammonoid was encrusted it lived within the euphotic zone and supports the latest interpretations of the Hunsrück Slate depositional environment.

scholarly journals 3D-Analysis of a non-planispiral ammonoid from the Hunsrück Slate: natural or pathological variation?

2017 ◽  
Author(s):  
Julia Stilkerich ◽  
Trisha A Smrecak ◽  
Kenneth De Baets
Keyword(s):  
Three Dimensional ◽  
Euphotic Zone ◽  
Type Specimen ◽  
3D Analysis ◽  
Three Dimensional Model ◽  
Hunsrück Slate ◽  
Early Devonian ◽  
Holotype Specimen ◽  
New Type

We herein examine the only known non-planispirally coiled early Devonian ammonoid, the holotype specimen of Ivoites opitzi, to investigate if the host was encrusted in vivo and if these sclerobionts were responsible for the trochospiral coiling observed on this unique specimen. To test if the presence of runner-like sclerobionts infested the historically collected specimen of Ivoites opitzi during its life, we used microCT to produce a three-dimensional model of the surface of the specimen. Our results indicate that sclerobionts grew across the outer rim (venter) on both sides of the ammonoid conch at exactly the location where the deviation from the planispiral was recognized, and where subsequent ammonoid growth would likely preclude encrustation. This indicates in vivo encrustation of the I. opitzi specimen, and represents the earliest documentation of the phenomenon. Further, this suggests that non-planispiral coiling in I. opitzi was pathologically induced and does not represent natural morphological variation in the species. Despite the observed anomalies in coiling, the specimen reached adulthood and retains important identifying morphological features, suggesting the ammonoid was minimally impacted by encrustation in life. As such, appointing a new type specimen – as suggested by some authors – for the species is not necessary. In addition, we identify the sclerobionts responsible for modifying the coiling of this specimen as hederelloids, a peculiar group of sclerobionts likely related to phoronids. Hederelloids in the Devonian are commonly found encrusting on fossils collected in moderately deep environments within the photic zone and are rarely documented in dysphotic and aphotic samples. This indicates that when the ammonoid was encrusted it lived within the euphotic zone and supports the latest interpretations of the Hunsrück Slate depositional environment.

scholarly journals 3D-Analysis of a non-planispiral ammonoid from the Hunsrück Slate: natural or pathological variation?

2017 ◽  
Author(s):  
Julia Stilkerich ◽  
Trisha A Smrecak ◽  
Kenneth De Baets
Keyword(s):  
Three Dimensional ◽  
Euphotic Zone ◽  
Type Specimen ◽  
3D Analysis ◽  
Three Dimensional Model ◽  
Hunsrück Slate ◽  
Early Devonian ◽  
Holotype Specimen ◽  
New Type

We herein examine the only known non-planispirally coiled early Devonian ammonoid, the holotype specimen of Ivoites opitzi, to investigate if the host was encrusted in vivo and if these sclerobionts were responsible for the trochospiral coiling observed on this unique specimen. To test if the presence of runner-like sclerobionts infested the historically collected specimen of Ivoites opitzi during its life, we used microCT to produce a three-dimensional model of the surface of the specimen. Our results indicate that sclerobionts grew across the outer rim (venter) on both sides of the ammonoid conch at exactly the location where the deviation from the planispiral was recognized, and where subsequent ammonoid growth would likely preclude encrustation. This indicates in vivo encrustation of the I. opitzi specimen, and represents the earliest documentation of the phenomenon. Further, this suggests that non-planispiral coiling in I. opitzi was pathologically induced and does not represent natural morphological variation in the species. Despite the observed anomalies in coiling, the specimen reached adulthood and retains important identifying morphological features, suggesting the ammonoid was minimally impacted by encrustation in life. As such, appointing a new type specimen – as suggested by some authors – for the species is not necessary. In addition, we identify the sclerobionts responsible for modifying the coiling of this specimen as hederelloids, a peculiar group of sclerobionts likely related to phoronids. Hederelloids in the Devonian are commonly found encrusting on fossils collected in moderately deep environments within the photic zone and are rarely documented in dysphotic and aphotic samples. This indicates that when the ammonoid was encrusted it lived within the euphotic zone and supports the latest interpretations of the Hunsrück Slate depositional environment.

scholarly journals Three-dimensional in situ morphometrics of Mycobacterium tuberculosis infection within lesions by optical mesoscopy and novel acid-fast staining

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Robert J. Francis ◽  
Gillian Robb ◽  
Lee McCann ◽  
Bhagwati Khatri ◽  
James Keeble ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Three Dimensional ◽  
Large Field ◽  
Staining Procedure ◽  
3D Analysis ◽  
Mycobacterium Tuberculosis Infection ◽  
In Vivo Models ◽  
Novel Approach

AbstractTuberculosis (TB) preclinical testing relies on in vivo models including the mouse aerosol challenge model. The only method of determining colony morphometrics of TB infection in a tissue in situ is two-dimensional (2D) histopathology. 2D measurements consider heterogeneity within a single observable section but not above and below, which could contain critical information. Here we describe a novel approach, using optical clearing and a novel staining procedure with confocal microscopy and mesoscopy, for three-dimensional (3D) measurement of TB infection within lesions at sub-cellular resolution over a large field of view. We show TB morphometrics can be determined within lesion pathology, and differences in infection with different strains of Mycobacterium tuberculosis. Mesoscopy combined with the novel CUBIC Acid-Fast (CAF) staining procedure enables a quantitative approach to measure TB infection and allows 3D analysis of infection, providing a framework which could be used in the analysis of TB infection in situ.

scholarly journals Effects of Shiga Toxin Type 2 on a Bioengineered Three-Dimensional Model of Human Renal Tissue

2014 ◽  
Vol 83 (1) ◽  
pp. 28-38 ◽  
Author(s):  
Teresa M. DesRochers ◽  
Erica Palma Kimmerling ◽  
Dakshina M. Jandhyala ◽  
Wassim El-Jouni ◽  
Jing Zhou ◽  
...  
Keyword(s):  
Cell Culture ◽  
Renal Failure ◽  
Shiga Toxin ◽  
Three Dimensional ◽  
Kidney Injury ◽  
Renal Tissue ◽  
Three Dimensional Model ◽  
Drug Induced ◽  
Tissue Model

Shiga toxins (Stx) are a family of cytotoxic proteins that can cause hemolytic-uremic syndrome (HUS), a thrombotic microangiopathy, following infections by Shiga toxin-producingEscherichia coli(STEC). Renal failure is a key feature of HUS and a major cause of childhood renal failure worldwide. There are currently no specific therapies for STEC-associated HUS, and the mechanism of Stx-induced renal injury is not well understood primarily due to a lack of fully representative animal models and an inability to monitor disease progression on a molecular or cellular level in humans at early stages. Three-dimensional (3D) tissue models have been shown to be morein vivo-like in their phenotype and physiology than 2D cultures for numerous disease models, including cancer and polycystic kidney disease. It is unknown whether exposure of a 3D renal tissue model to Stx will yield a morein vivo-like response than 2D cell culture. In this study, we characterized Stx2-mediated cytotoxicity in a bioengineered 3D human renal tissue model previously shown to be a predictor of drug-induced nephrotoxicity and compared its response to Stx2 exposure in 2D cell culture. Our results demonstrate that although many mechanistic aspects of cytotoxicity were similar between 3D and 2D, treatment of the 3D tissues with Stx resulted in an elevated secretion of the kidney injury marker 1 (Kim-1) and the cytokine interleukin-8 compared to the 2D cell cultures. This study represents the first application of 3D tissues for the study of Stx-mediated kidney injury.

scholarly journals Identification of Novel Recognition Motifs and Regulatory Targets for the Yeast Actin-regulating Kinase Prk1p

2003 ◽  
Vol 14 (12) ◽  
pp. 4871-4884 ◽  
Author(s):  
Bo Huang ◽  
Guisheng Zeng ◽  
Alvin Y.J. Ng ◽  
Mingjie Cai
Keyword(s):  
Actin Cytoskeleton ◽  
Phosphorylation Site ◽  
Three Dimensional ◽  
Kinase Domain ◽  
Yeast Genome ◽  
Three Dimensional Model ◽  
Recognition Sequence ◽  
Yeast Saccharomyces Cerevisiae

Prk1p is a serine/threonine kinase involved in the regulation of the actin cytoskeleton organization in the yeast Saccharomyces cerevisiae. Previously, we have identified LxxQxTG as the phosphorylation site of Prk1p. In this report, the recognition sequence for Prk1p is investigated more thoroughly. It is found that the presence of a hydrophobic residue at the position of P-5 is necessary for Prk1p phosphorylation and L, I, V, and M are all able to confer the phosphorylation at various efficiencies. The residue flexibility at P-2 has also been identified to include Q, N, T, and S. A homology-based three-dimensional model of the kinase domain of Prk1p provided some structural interpretations for these substrate specificities. The characterization of the [L/I/V/M]xx[Q/N/T/S]xTG motif led to the identification of a spectrum of potential targets for Prk1p from yeast genome. One of them, Scd5p, which contains three LxxTxTG motifs and is previously known to be important for endocytosis and actin organization, has been chosen to demonstrate its relationship with Prk1p. Phosphorylation of Scd5p by Prk1p at the three LxxTxTG motifs could be detected in vitro and in vivo, and deletion of PRK1 suppressed the defects in actin cytoskeleton and endocytosis in one of the scd5 mutants. These results allowed us to conclude that Scd5p is likely another regulatory target of Prk1p.

scholarly journals Mutagenesis and Molecular Modeling Reveal Three Key Extracellular Loops of the Membrane Receptor HasR That Are Involved in Hemophore HasA Binding

2007 ◽  
Vol 189 (14) ◽  
pp. 5379-5382 ◽  
Author(s):  
Clément Barjon ◽  
Karine Wecker ◽  
Nadia Izadi-Pruneyre ◽  
Philippe Delepelaire
Keyword(s):  
Molecular Modeling ◽  
Outer Membrane ◽  
Three Dimensional ◽  
Membrane Receptor ◽  
Dimensional Model ◽  
Outer Membrane Receptor ◽  
Three Dimensional Model ◽  
Extracellular Loops

ABSTRACT On the basis of the three-dimensional model of the heme/hemophore TonB-dependent outer membrane receptor HasR, mutants with six-residue deletions in the 11 putative extracellular loops were generated. Although all mutants continued to be active TonB-dependent heme transporters, mutations in three loops abolished hemophore HasA binding both in vivo and in vitro.

scholarly journals Substructure of crystalline peroxisomes in methanol-grown Hansenula polymorpha: evidence for an in vivo crystal of alcohol oxidase.

1981 ◽  
Vol 1 (10) ◽  
pp. 949-957 ◽  
Author(s):  
M Veenhuis ◽  
W Harder ◽  
J P van Dijken ◽  
F Mayer
Keyword(s):  
Osmotic Shock ◽  
Hansenula Polymorpha ◽  
Three Dimensional ◽  
Alcohol Oxidase ◽  
Molecular Architecture ◽  
Three Dimensional Model ◽  
Structural Element ◽  
Free Mobility ◽  
Crystalline Matrix

The substructural organization of completely crystalline peroxisomes present in Hansenula polymorpha cells grown under methanol limitation in a chemostat was investigated by different cytochemical and ultrastructural techniques. Time-dependent cytochemical staining experiments indicated that activities of the two main constituents of these organelles, namely, alcohol oxidase and catalase, were present throughout the crystalline matrix. Catalase was completely removed from isolated peroxisomes by osmotic shock treatment. After such treatment, the ultrastructure of the crystalline matrix of the organelles remained virtually intact. Because alcohol oxidase activity was still present in this matrix, it was concluded that alcohol oxidase protein is the only structural element of the peroxisomal crystalloids. The molecular architecture of the crystalloids was investigated in ultrathin cryosections which permitted recognition of individual molecules in the crystalline matrix. Depending on the plane of sectioning, different crystalline patterns were observed. Tilting experiments indicated that these images were caused by superposition of octameric alcohol oxidase molecules arranged in a tetragonal lattice. A three-dimensional model of the crystalloid is presented. The repeating unit of this structure is composed of four alcohol oxidase molecules. The crystalloid represents an open structure, which may explain the observed free mobility of catalase molecules.

Design of Hydraulic Transmission Bicycle Based on Top-Down Method

2012 ◽  
Vol 468-471 ◽  
pp. 867-870 ◽  
Author(s):  
Yan Hong Yang ◽  
Xiang Qiang Zhong
Keyword(s):  
Rapid Development ◽  
Three Dimensional ◽  
New Product ◽  
Feature Modeling ◽  
Assembly Model ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Top Down ◽  
Skeleton Model ◽  
New Type

Hydraulic transmission bicycle is a new type of vehicle. It is crucial for founding an effective method of rapid development for new product. The concept drafting of hydraulic transmission bicycle was drawn, the multiple layer assembly model was built based on parametric feature modeling technique, the skeleton model and total design of hydraulic transmission bicycle was accomplished by top-down method and drawings of relevant parts based on three-dimensional model were created. The result shows that top-down method provides a new idea to improve the rapid design of product’s updates.

scholarly journals Numerical analysis of the thermal behavior of building integrated hybrid solar wall

2019 ◽  
Vol 23 (1) ◽  
pp. 144-149
Author(s):  
Djelaili Abdelbaki ◽  
Korti Abdel Ilah Nabil
Keyword(s):  
Indoor Air ◽  
Three Dimensional ◽  
Building Design ◽  
3D Analysis ◽  
Three Dimensional Model ◽  
Sustainable Building ◽  
Proposed Model ◽  
Trombe Wall ◽  
Solar Wall ◽  
Building Designs

Abstract Building designers have to think about new strategies to achieve the best sustainable building designs. Well-planned passive solar heating strategies in building design may reduce a building’s energy consumption significantly. In this paper, a proposed design of the south façade of a room by integrating a hybrid solar wall and a window to passively heat a room is studied. The simulations for the three-dimensional model of BIPV Trombe wall system were carried out for December 10th, 2015. The temperature and velocity distribution of indoor air in different positions inside the room are obtained from the simulation results. The obtained results show that the temperature difference between the inlet and the outlet of the solar wall can reach 9°C. The 3D analysis of the proposed model clearly shows that the window’s thermal effect on the passive heating cannot be neglected. Meanwhile, the simulation’s daily electrical efficiency conversion and average indoor air temperature of this system can reach 18% and 28° C, respectively for maximum solar radiation of 470 W/m2.

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