Table-top Cathodoluminescence Microscopy for Geology

2020 ◽  
Author(s):  
Toon Coenen ◽  
Albert Polman
Keyword(s):  
Electron Beam ◽  
Detection System ◽  
Energetic Electron ◽  
Numerical Aperture ◽  
Graded Index ◽  
Thermo Fisher Scientific ◽  
Deformation Features ◽  
Backscattered Electron ◽  
User Friendly ◽  
Fisher Scientific

<p>Cathodoluminescence (CL) microscopy is a well-known technique for imaging geological specimens, in which the light that is generated with an energetic electron beam is collected and analyzed with a CL detector. CL provides a unique imaging contrast that can be used for visualizing growth zonation, distinguishing cement and granular detrital material, detecting trace elements, and characterizing fractures and deformation features in a large range of rocks, to name a few examples. In its simplest form CL imaging is performed with a static electron beam in an optical microscopy system (optical CL) but for more advanced experiments CL imaging is performed in a scanning electron microscope (SEM). This enables high scan speeds, high spatial resolution (< 100 nm), and correlation with other SEM based techniques such as X-ray imaging (EDS), secondary electron (SE) and backscattered electron (BSE) imaging, and more.</p><p>Currently, SEM-based CL work is mostly performed on costly floor model SEMs that require large amounts of space, complex auxiliary support systems, and an experienced operator to run the machine. In contrast, compact, affordable, and user-friendly table-top SEMs have improved substantially in the last years but they typically lack (advanced) CL imaging capabilities. Here, we will present our progress in developing a table-top SEM based CL system that can be used for geological research amongst other applications.</p><p>In particular, we have integrated a CL collection and detection system in a Thermo Fisher Scientific/Phenom XL table-top microscope, which already is equipped with SE, BSE, and EDS imaging modalities. In this SEM, electron energies of 5 – 15 keV can be used which is appropriate for most CL imaging experiments. The CL is collected using a multimode fiber optic cable connected with a graded index lens to increase the numerical aperture of the collection. Subsequently, the light is send to a spectrometer where the CL emission spectrum can be measured for every excitation point on the sample; a technique known as hyperspectral CL  imaging. To synchronize electron beam scanning with data acquisition and for data analysis we have developed dedicated software control.</p><p>We assess the potential of table-top CL by imaging representative polished zircon and quartz samples for various beam and acquisition parameters. To benchmark the system performance we compare our experimental results with results obtained from a state-of-the-art floor model SEM (Thermo Fisher Scientific Quanta 650 SFEG) system equipped with a high-end Delmic SPARC CL system. In the future, these developments may lower the threshold for using CL imaging through cost reduction and workflow simplification, making it accessible to a larger range of users within the field of geology and beyond.</p>

scholarly journals POS0009 THE RELATIONSHIP BETWEEN DIFFERENT IGG AND IGA ANTI-MODIFIED PROTEIN AUTOANTIBODIES IN RHEUMATOID ARTHRITIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 206.1-207
Author(s):  
C. Grönwall ◽  
L. Liljefors ◽  
H. Bang ◽  
A. Hensvold ◽  
M. Hansson ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Disease Activity ◽  
Comprehensive Evaluation ◽  
Patient Characteristics ◽  
Post Translational Modifications ◽  
Cell Clones ◽  
Thermo Fisher Scientific ◽  
History Of ◽  
The Relationship ◽  
Fisher Scientific

Background:Seropositive rheumatoid arthritis (RA) is characterized by the presence of rheumatoid factor (RF) and anti-citrullinated protein autoantibodies (ACPA) with different fine-specificities. Yet, other serum anti-modified protein autoantibodies (AMPA), e.g. anti-carbamylated (Carb), anti-acetylated (KAc), and anti-malondialdehyde acetaldehyde (MAA) modified protein antibodies, have been described. By using RA patient single-cell derived monoclonal antibodies we have previously shown that individual ACPA clones recognize small distinct citrulline-containing epitopes giving them extensive multireactivity when these epitopes are found in many peptides and proteins. Moreover, certain CCP2+ multireactive ACPA clones bind also to cabamylated and acetylated autoantigens [1].Objectives:To provide a comprehensive evaluation of serum IgG and IgA autoreactivity to different post-translational modifications in RA.Methods:We analyzed 30 different IgG and IgA AMPA reactivities to modified antigens by ELISA and autoantigen arrays, in N=1985 newly diagnosed RA patients and population controls. The study utilized both previously established (i.e IgG and IgA CCP2; IgG ACPA fine-specificities; IgG anti-Carb fibrinogen and Carb FCS; IgG and IgA Cit/Carb/KAc/Orn(Ac)-vimentin), and novel assays (e.g. IgG anti-MAA and IgG anti-acetylated histones). Association with patient characteristics such as smoking and disease activity were explored. The newly developed assays were also evaluated in SLE disease controls and CCP2+ RA-risk individuals without arthritis.Results:Carb and KAc reactivities by different assays were primarily seen in patients also positive for citrulline-reactivity. Modified vimentin (mod-Vim) peptides were used for direct comparison of different AMPA reactivities, revealing that IgA AMPA recognizing mod-Vim was mainly detected in subsets of patients with high IgG anti-Cit-Vim levels and a history of smoking. IgG acetylation reactivity was mainly detected in a subset of patients with Cit and Carb reactivity. Anti-acetylated histone 2B reactivity was RA-specific and associated with high anti-CCP2 IgG levels, multiple ACPA fine-specificities, and smoking. This reactivity was also found to be present in CCP2+ RA-risk individuals without arthritis. Our data further demonstrate that IgG autoreactivity to MAA was increased in RA compared to controls with highest levels in CCP2+ RA, but was not RA-specific, and showed low correlation with other AMPA. Anti-MAA was instead associated with disease activity and was not significantly increased in CCP2+ individuals at risk of RA. Notably, RA patients could be subdivided into four different subsets based on their AMPA IgG and IgA reactivity profiles.Conclusion:We conclude that autoantibodies exhibiting different patterns of ACPA fine-specificities as well as Carb and KAc reactivity are present in RA and may be derived from multireactive B-cell clones. Anti-Carb and anti-KAc could be considered reactivities within the “Cit-umbrella” similar to ACPA fine-specificities, while MAA is distinctly different.References:[1]Sahlström P, Hansson M, Steen J, Amara K, Titcombe PJ, Forsström B, Stålesen R, Israelsson L, Piccoli L, Lundberg K, Klareskog L, Mueller DL, Catrina AI, Skriner K, Malmström V, Grönwall C. Different Hierarchies of Anti-Modified Protein Autoantibody Reactivities in Rheumatoid Arthritis. Arthritis Rheumatol. 2020 Oct;72(10):1643-1657. PMID: 32501655Caroline Grönwall: None declared, Lisa Liljefors: None declared, Holger Bang Employee of: Employee at ORGENTEC Diagnostika GmbH, Aase Hensvold: None declared, Monika Hansson: None declared, Linda Mathsson-Alm Employee of: Employee at Thermo Fisher Scientific, Lena Israelsson: None declared, Anna Svärd: None declared, Cyril CLAVEL: None declared, Elisabet Svenungsson: None declared, Iva Gunnarsson: None declared, Guy Serre: None declared, Saedis Saevarsdottir: None declared, Alf Kastbom: None declared, Lars Alfredsson: None declared, Vivianne Malmström: None declared, Johan Rönnelid: None declared, Anca Catrina: None declared, Karin Lundberg: None declared, Lars Klareskog: None declared

Évaluation du CDx90® (Microgenics Thermo Fisher Scientific) pour le dosage urinaire des drogues

2010 ◽  
Vol 25 (2) ◽  
pp. 118-122
Author(s):  
K. Barrial ◽  
T. Le Bricon ◽  
F. Courtier ◽  
M.-H. Tourvieille ◽  
S. Hilaire ◽  
...  
Keyword(s):  
Thermo Fisher Scientific ◽  
Fisher Scientific

A Simple Method for Prediction of Effective Core Area and Index of Refraction of Single-mode Graded Index Fiber in the Low V Region

2014 ◽  
Vol 35 (4) ◽  
Author(s):  
Angshuman Majumdar ◽  
Satabdi Das ◽  
Sankar Gangopadhyay
Keyword(s):  
Refractive Index ◽  
Single Mode ◽  
Index Of Refraction ◽  
Core Area ◽  
Exact Results ◽  
Simple Method ◽  
Graded Index ◽  
Core Areas ◽  
V Region ◽  
User Friendly

AbstractBased on the simple power series formulation of fundamental mode developed by Chebyshev formalism in the low V region, we prescribe analytical expression for effective core area of graded index fiber. Taking step and parabolic index fibers as examples, we estimate the effective core areas as well as effective refractive index for different normalized frequencies (V number) having low values. We also show that our estimations match excellently with the available exact results. The concerned predictions by our method require little computation. Thus, this simple but accurate formalism will be user friendly for the system engineers.

scholarly journals Study of Optical Fiber Design Parameters in Fiber Optics Communications

2017 ◽  
Vol 2 (3) ◽  
pp. 302-308 ◽  
Author(s):  
Salim Qadir Mohammed ◽  
Asaad M. Asaad M. Al-Hindawi
Keyword(s):  
Optical Fiber ◽  
Fiber Optics ◽  
Numerical Aperture ◽  
Design Parameters ◽  
Light Sources ◽  
Long Distance ◽  
Graded Index ◽  
Large Bandwidth ◽  
Telecommunication Infrastructure ◽  
Distance Communication

Fiber optics is an important part in the telecommunication infrastructure. Large bandwidth and low attenuation are features for the fiber optics to provide gigabit transmission. Nowadays, fiber optics are used widely in long distance communication and networking to provide the required information traffic for multimedia applications. In this paper, the optical fiber structure and the operation mechanism for multimode and single modes are analyzed. The design parameters such as core radius, numerical aperture, attenuation, dispersion and information capacity for step index and graded index fibers are studied, calculated and compared for different light sources.

scholarly journals Immune Repertoire Analysis of Multiple Myeloma Research Samples Using NGS Characterization of Multiple B Cell Receptors in a Single Reaction

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1881-1881
Author(s):  
Geoffrey Lowman ◽  
Landon Pastushok ◽  
Karen Mochoruk ◽  
Wayne Hill ◽  
Michelle Toro ◽  
...  
Keyword(s):  
B Cell ◽  
Light Chain ◽  
Somatic Hypermutation ◽  
Cell Receptor ◽  
Clonal Lineage ◽  
Repertoire Analysis ◽  
Targeted Ngs ◽  
Thermo Fisher Scientific ◽  
Fisher Scientific ◽  
Single Reaction

Abstract Introduction B cell repertoire analysis by next-generation sequencing (NGS) is at the forefront of leukemia and lymphoma research. Some advantages provided by NGS-based techniques include a lower limit-of-detection and simpler paths to standardization compared to other methods. Importantly, in research of post-germinal B cell disorders, such as multiple myeloma (MM), NGS methods allow for the study of clonal lineage based on somatic hypermuation patterns. Current targeted NGS assays require multiple libraries to survey each B cell receptor chain (IGH, IgK, IgL), and this fact is highlighted when initial clonality detection fails due to mutations under primer binding sites. This issue can be especially true in MM which has a high rate of SHM. To address these issues, we have developed an assay for B cell analysis, based on Ion AmpliSeq™ technology, which enables efficient detection of IGH, IgK, and IgL chain rearrangements in a single reaction. Methods The B cell pan-clonality panel (Oncomine™ BCR Pan-Clonality Assay) targets the framework 3 (FR3) portion of the variable gene and the joining gene region of heavy- and light-chain loci (IGH, IgK, IgL) for all alleles found within the IMGT database, enabling readout of the complementary-determining region 3 (CDR3) sequence of each immunoglobulin chain. To maximize sensitivity, we included primers to amplify IgK loci rearrangements involving Kappa deletion element and the constant region intron. To evaluate assay performance, we conducted reproducibility studies and clonality assessment using gDNA from a total of 45 MM research samples. All MM cases examined in this work were confirmed clonal previously by light chain restriction via flow cytometry or IHC/ISH in tissue sections - 16 of the 45 MM samples were identified as lambda light chain restricted. For comparison, a small cohort of 12 B-ALL samples were also included in the study. Sequencing and repertoire analyses were performed using the Ion GeneStudio S5 System and Ion Reporter 5.16 analysis software. Results Clonality assessment of MM clinical research samples show an 93% overall positive detection rate by an assay which combines the IGH, IgK, and IgL chains in a single reaction using published guidelines for clonality assignment. Thirty-four of 45 samples show positive detection of an IGH rearrangement, while 41 of 45 showed positive detection of at least one light chain receptor. In total, 42 of 45 samples were deemed clonal by the single tube assay based on detection for one or more receptor. Clonality results for this sample set are well correlated with orthogonal data from flow, IHC/ISH, or alternate NGS assays. A clonal lambda light chain was identified in 14 of 16 samples determined to be lambda restricted by flow cytometry. In two of the lambda restricted samples only a clonal lambda rearrangement was identified, showing the benefit of including primers targeting both the kappa and lambda light chains in a pan-clonality NGS assay. Both the MM and B-ALL cohorts were evaluated for biased IGHV gene usage. IGHV3-11 was observed in 5 of 45 MM and 5 of 12 B-ALL samples. IGHV4-34, typically linked to autoreactive antibodies and underrepresented in germinal center and memory B-cells, was nonetheless found in 5 of 45 MM samples surveyed. Estimates of somatic hypermutation rates were calculated using the BCR pan-clonality assay. Most MM samples, as expected, contained some somatic hypermutation with 6 of 45 samples showing greater than 10% mutation rates. Automated lineage analysis, based on somatic hypermuation signatures within each sample, identified 8 of 45 MM samples which contained 5 or more clones in the primary clonal lineage, with one case containing a lineage with 23 clones. Two MM samples showed no somatic hypermutation as measured using the FR3 primers contained in the BCR pan-clonality assay. These samples were also evaluated using an FR1-J targeted NGS assay, which confirmed relatively low mutation rates for these MM samples at 0.44% and 1.3%, respectively. Conclusions These results demonstrate the utility of a novel assay for combined repertoire analysis of B cell receptor heavy and light chains in a single library preparation reaction. We expect this assay to simplify laboratory workflows and including analysis tools such as automated somatic hypermutation rate calculation and clonal lineage identification may open new paths for research in lymphoid cell disorders. For research use only. Disclosures Lowman: Thermo Fisher Scientific: Current Employment. Toro: Thermo Fisher Scientific: Current Employment. Pickle: Thermo Fisher Scientific: Current Employment. Ostresh: Thermo Fisher Scientific: Current Employment. Sarda: Thermo Fisher Scientific: Current Employment. Yang: Thermo Fisher Scientific: Current Employment.

scholarly journals Does the Pre-Ovulatory Pig Oviduct Rule Sperm Capacitation In Vivo Mediating Transcriptomics of Catsper Channels?

2020 ◽  
Vol 21 (5) ◽  
pp. 1840 ◽  
Author(s):  
Cristina A. Martinez ◽  
Manuel Alvarez-Rodriguez ◽  
Dominic Wright ◽  
Heriberto Rodriguez-Martinez
Keyword(s):  
Ex Vivo ◽  
Female Genital Tract ◽  
Thermo Fisher Scientific ◽  
Positive Regulators ◽  
Porcine Gene ◽  
Single Fertilization ◽  
Boar Spermatozoa ◽  
Go Terms ◽  
Fisher Scientific

Spermatozoa need to conduct a series of biochemical changes termed capacitation in order to fertilize. In vivo, capacitation is sequentially achieved during sperm transport and interaction with the female genital tract, by mechanisms yet undisclosed in detail. However, when boar spermatozoa are stored in the tubal reservoir pre-ovulation, most appear to be in a non-capacitated state. This study aimed at deciphering the transcriptomics of capacitation-related genes in the pig pre-ovulatory oviduct, following the entry of semen or of sperm-free seminal plasma (SP). Ex-vivo samples of the utero-tubal junction (UTJ) and isthmus were examined with a microarray chip (GeneChip® Porcine Gene 1.0 ST Array, Thermo Fisher Scientific) followed by bioinformatics for enriched analysis of functional categories (GO terms) and restrictive statistics. The results confirmed that entry of semen or of relative amounts of sperm-free SP modifies gene expression of these segments, pre-ovulation. It further shows that enriched genes are differentially associated with pathways relating to sperm motility, acrosome reaction, single fertilization, and the regulation of signal transduction GO terms. In particular, the pre-ovulation oviduct stimulates the Catsper channels for sperm Ca2+ influx, with AKAPs, CATSPERs, and CABYR genes being positive regulators while PKIs and CRISP1 genes appear to be inhibitors of the process. We postulate that the stimulation of PKIs and CRISP1 genes in the pre-ovulation sperm reservoir/adjacent isthmus, mediated by SP, act to prevent premature massive capacitation prior to ovulation.

203 SINGLE-STEP GENE EDITING OF 3 XENOANTIGENS IN PORCINE FIBROBLASTS USING PROGRAMMABLE NUCLEASES

2017 ◽  
Vol 29 (1) ◽  
pp. 210 ◽  
Author(s):  
A. Perota ◽  
I. Lagutina ◽  
C. Quadalti ◽  
R. Duchi ◽  
P. Turini ◽  
...  
Keyword(s):  
Gene Editing ◽  
Magnetic Beads ◽  
Single Step ◽  
High Rate ◽  
Pcr Analysis ◽  
Thermo Fisher Scientific ◽  
Protective Genes ◽  
Pcr Products ◽  
Programmable Nucleases ◽  
Fisher Scientific

Programmable nucleases (ZFN, Tal Effector Nucleases, and CRISPR) opened a new era for mammal genome editing, in particular for the pigs used for xenotransplantation. Multiple gene editing events are required both for knockout (KO) of xenoantigens and for targeted integration of human protective genes (Perota et al. 2016 J. Genet. Genomics 43, 233–23). The objective of the present work was to edit selected pig lines to KO the enzymes coding for the most relevant xenoantigens (i.e. GGTA1, CMAH, and B4GalNT2), combining Talens and CRISPR/Cas9 technologies to magnetic beads selection (Li et al. 2013 Xenotransplantation 22, 20–31). Primary porcine adult fibroblasts were transfected using Nucleofector (V-024 program). In a single reaction 2 × 106 fibroblasts were co-transfected using 2 different sets of TALENS (4 μg/set) specific for CMAH (Conchon et al., 2013) and GGTA1 (Perota et al., 2015) genes together with B4GalNT2-specific CRISPR/Cas9 expression vector (2 μg; pX330-B4GalNT2; Estrada et al., 2015). Eight days post-transfection (DPT), Gal–/– cells were selected initially using biotin-conjugated IB4 lectin (Sigma, St. Louis, MO, USA) and magnetic beads (Dynabeads M-280, Thermo Fisher Scientific, Waltham, MA, USA). The selected cells were then plated on 150-mm Petri dishes (200 cells/dish) and cultured for 10 days. Selected colonies were expanded for PCR analysis and cryopreserved for somatic cell nuclear transfer (SCNT). All colonies were analysed by PCR for CMAH gene and their resulting products were digested with HindIII (HindIII-RFLP). Colonies that lost wild-type HindIII as a consequence of Talens effected deletion were PCR characterised for GGTA1, selecting those that had detectable Indels after gel electrophoresis and finally analysed by PCR for B4GalNT2. All PCR products were validated by sequencing for all the 3 genes of interest (TopoTA, Thermo Fisher Scientific). Selected colonies were used as nuclear donors for SCNT (Lagutina et al., 2006). Eight DPT we obtained 3.45 ×106 cells. About 6.0 × 103 Gal-negative cells (0.17%) were collected from the supernatant after magnetic beads separation. Eighteen DPT, 120 colonies were picked up and their HindIII-RFLP analyses on CMAH gene revealed that 22 colonies (18.3%) were KO for both CMAH alleles. Of these 22 colonies following electrophoretic analyses of GGTA1-PCR products, 13 colonies had detectable Indels. These 13 colonies were finally PCR analysed and sequenced for B4GalNT2 and sequenced. Final sequencing results confirmed that 2 colonies (1.6%) resulted in KO for the 3 genes. Three different zona-free SCNT experiments were done and 579 reconstructed embryos were obtained. On Day 7, 322 morulae or blastocysts (56%) were transferred in 3 synchronised sows and 2 (66%) became pregnant. In conclusion, after gene editing with programmable nucleases, combining beads-mediated selection with well-designed molecular analyses, we developed a multistep assay that can be used efficiently to detect desired gene edited events in cell colonies suitable for the SCNT. Embryos generated after SCNT were able to establish pregnancies at a high rate. This work is supported by European FP7 grants Translink (n° 603049) and Xenoislet (n° 601827).

Enhancement of image contrast for carbon nanotube and polymer composite film in scanning electron microscope

Microscopy ◽  
2020 ◽  
Vol 69 (3) ◽  
pp. 167-172
Author(s):  
Yoichiro Hashimoto ◽  
Hiroyuki Ito ◽  
Masahiro Sasajima
Keyword(s):  
Composite Film ◽  
Electron Beam Irradiation ◽  
Detection System ◽  
Energy Condition ◽  
Image Contrast ◽  
Energy Conditions ◽  
Beam Irradiation ◽  
Sem Images ◽  
Ptfe Composite ◽  
Backscattered Electron

Abstract Image contrast between carbon nanotubes (CNTs) and polytetrafluoroethylene (PTFE) in a CNT/PTFE composite film, which is difficult to obtain by conventional backscattered electron (BSE) imaging, was optimized to better elucidate the distribution of CNT in the film. Ultra-low landing energy condition (0.3 keV in this study) was used to prevent specimen damage due to electron beam irradiation. Signal acceptance maps, which represent the distributions of energy and take-off angle, were calculated to evaluate the features of the signal detection system used in this study. SEM images of this composite film were taken under several sets of conditions and analyzed using these acceptance maps. CNT and PTFE in the composite film can be clearly distinguished with material and topographic contrasts using the BSE signal under optimized energy and take-off angle ranges, even at ultra-low landing energy conditions.

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