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Three dimensional reconstructions of Nummulites tests reveal complex chamber shapes.

ABSTRACT: Larger benthic foraminifera (LBF) are important and prolific carbonate producers both in modern and ancient shallow tropical seas. During the Paleogene the genus Nummulites was particularly abundant with a global distribution, leading it to be frequently used in biostratigraphy. However, their evolution is poorly understood as classification is Europe-centered and mostly based on external characters and equatorial thin sections. New occurrences from regions outside the northern Tethys which poorly fit in thus reference frame, show that a more rigid framework for the classification of Nummulites is needed. Here we apply micro computed-tomographical scanning, a tool that recently has become available, to visualise 3D chamber shape of Nummulites djokdjokartae and compare these to traditional morphometrical characters. We find that despite the regular shape in equatorial and axial thin section the irregular 3D chamber shape is not predicted by these sections. We argue that 3D reconstructions of Nummulites tests will be a great aid in improving our understanding of lineages within the genus Nummulites, and to elucidate its evolutionary and biogeographical history.

SUBMITTER: Renema W

PROVIDER: S-EPMC4493699 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Three dimensional reconstructions of Nummulites tests reveal complex chamber shapes.

Renema Willem W Cotton Laura L

PeerJ 20150702

Larger benthic foraminifera (LBF) are important and prolific carbonate producers both in modern and ancient shallow tropical seas. During the Paleogene the genus Nummulites was particularly abundant with a global distribution, leading it to be frequently used in biostratigraphy. However, their evolution is poorly understood as classification is Europe-centered and mostly based on external characters and equatorial thin sections. New occurrences from regions outside the northern Tethys which poor ...[more]

PMID: 26157635

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Project description:BackgroundDuring liver development, intrahepatic bile ducts are thought to arise by a unique asymmetric mode of cholangiocyte tubulogenesis characterized by a series of remodeling stages. Moreover, in liver diseases, cells lining the Canals of Hering can proliferate and generate new hepatic tissue. The aim of this study was to develop protocols for three-dimensional visualization of protein expression, hepatic portal structures and human hepatic cholangiocyte tubulogenesis.ResultsProtocols were developed to digitally visualize portal vessel branching and protein expression of hepatic cell lineage and extracellular matrix deposition markers in three dimensions. Samples from human prenatal livers ranging from 7 weeks + 2 days to 15½ weeks post conception as well as adult normal and acetaminophen intoxicated liver were used. The markers included cytokeratins (CK) 7 and 19, the epithelial cell adhesion molecule (EpCAM), hepatocyte paraffin 1 (HepPar1), sex determining region Y (SRY)-box 9 (SOX9), laminin, nestin, and aquaporin 1 (AQP1).Digital three-dimensional reconstructions using CK19 as a single marker protein disclosed a fine network of CK19 positive cells in the biliary tree in normal liver and in the extensive ductular reactions originating from intrahepatic bile ducts and branching into the parenchyma of the acetaminophen intoxicated liver. In the developing human liver, three-dimensional reconstructions using multiple marker proteins confirmed that the human intrahepatic biliary tree forms through several developmental stages involving an initial transition of primitive hepatocytes into cholangiocytes shaping the ductal plate followed by a process of maturation and remodeling where the intrahepatic biliary tree develops through an asymmetrical form of cholangiocyte tubulogenesis.ConclusionsThe developed protocols provide a novel and sophisticated three-dimensional visualization of vessels and protein expression in human liver during development and disease.

Project description:Background:In plants, three-dimensional (3-D) organs such as inflorescences or fruits carry out photosynthesis and thus play a significant role in carbon assimilation and yield. However, this contribution has been poorly characterized because there is no reliable method for measuring photosynthesis by 3-D organs. One of the major challenges is ensuring the uniform irradiation of samples that are placed within a sealed chamber. Results:In this study, we developed an innovative chamber with homogeneous lighting that can be used to measure photosynthesis by large 3-D organs. It consisted of a 15-cm-long sealed transparent cylinder that was surrounded by a decagonal prismatic light source, made up of a mixture of red and blue LEDs. We characterized irradiance homogeneity within the chamber at a resolution level of 1 cm and 10°. Photosynthetic photon flux density (PPFD) along the central axis of the chamber could be set to any value between 100 and 1100 µmol m-2 s-1. The coefficient of variation for the irradiation values found throughout the chamber was 10% and that for the ratio of red-to-blue spectra was less than 1.5%. The temperature of the sample was regulated to stay within 1 °C of the target temperature, regardless of PPFD. We compared the performance of our device with that of a commercially available device employing unidirectional lighting. Specifically, we examined net photosynthesis in two sample types-wheat ears and grape clusters-at varying PPFD levels. Conclusions:The devices gave similar estimates of dark respiration, regardless of sample type or age. Conversely, net photosynthesis started to become asymptotic at lower irradiance levels in our device than in the conventional device because apparent quantum yield was three times higher. When examining the effects of irradiance heterogeneity, it was clear that biased estimates could result from systems employing unidirectional light sources. Our results also confirmed that our chamber could be a useful tool for obtaining more accurate estimates of photosynthesis by 3-D organs.

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Three dimensional reconstructions of Nummulites tests reveal complex chamber shapes.

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Three dimensional reconstructions of Nummulites tests reveal complex chamber shapes.

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