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Nagy G, Hoffmann SV, Jones NC, Grubmüller H. Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models. Appl Spectrosc 2024:37028241239977. [PMID: 38646777 DOI: 10.1177/00037028241239977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Circular dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package, SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.
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Affiliation(s)
- Gabor Nagy
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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Meiser A, Bleichner MG. Ear-EEG compares well to cap-EEG in recording auditory ERPs: a quantification of signal loss. J Neural Eng 2022; 19. [PMID: 35316801 DOI: 10.1088/1741-2552/ac5fcb] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/22/2022] [Indexed: 11/11/2022]
Abstract
Objective:Ear-EEG (Electroencephalography) allows to record brain activity using only a few electrodes located close to the ear. Ear-EEG is comfortable and easy to apply, facilitating beyond-the-lab EEG recordings in everyday life. With the unobtrusive setup, a person wearing it can blend in, allowing unhindered EEG recordings in social situations. However, compared to classical cap-EEG, only a small part of the head is covered with electrodes. Most scalp positions that are known from established EEG research are not covered by ear-EEG electrodes, making the comparison between the two approaches difficult and might hinder the transition from cap-based lab studies to ear-based beyond-the-lab studies.Approach:We here provide a reference data-set comparing ear-EEG and cap-EEG directly for four different auditory event-related potentials (ERPs): N100, MMN, P300 and N400. We show how the ERPs are reflected when using only electrodes around the ears.Main results:We find that significant condition differences for all ERP-components could be recorded using only ear-electrodes. The effect sizes were moderate to high on the single subject level. Morphology and temporal evolution of signals recorded from around-the-ear resemble highly those from standard scalp-EEG positions. We found a reduction in effect size (signal loss) for the ear-EEG electrodes compared to cap-EEG of 21-44%. The amount of signal loss depended on the ERP-component; we observed the lowest percentage signal loss for the N400 and the highest percentage signal loss for the N100. Our analysis further shows that no single channel position around the ear is optimal for recording all ERP-components or all participants, speaking in favor of multi-channel ear-EEG solutions.Significance:Our study provides reference results for future studies employing ear-EEG.
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Affiliation(s)
- Arnd Meiser
- Department of Psychology, University of Oldenburg, Ammerländer Heerstraße 112-114, Oldenburg, 26129, GERMANY
| | - Martin Georg Bleichner
- Department of Psychology, University of Oldenburg, Ammerländer Heerstraße 112-114, Oldenburg, 26129, GERMANY
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Gervin K, Page CM, Aass HCD, Jansen MA, Fjeldstad HE, Andreassen BK, Duijts L, van Meurs JB, van Zelm MC, Jaddoe VW, Nordeng H, Knudsen GP, Magnus P, Nystad W, Staff AC, Felix JF, Lyle R. Cell type specific DNA methylation in cord blood: A 450K- reference data set and cell count-based validation of estimated cell type composition. Epigenetics 2017; 11:690-698. [PMID: 27494297 DOI: 10.1080/15592294.2016.1214782] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epigenome-wide association studies of prenatal exposure to different environmental factors are becoming increasingly common. These studies are usually performed in umbilical cord blood. Since blood comprises multiple cell types with specific DNA methylation patterns, confounding caused by cellular heterogeneity is a major concern. This can be adjusted for using reference data consisting of DNA methylation signatures in cell types isolated from blood. However, the most commonly used reference data set is based on blood samples from adult males and is not representative of the cell type composition in neonatal cord blood. The aim of this study was to generate a reference data set from cord blood to enable correct adjustment of the cell type composition in samples collected at birth. The purity of the isolated cell types was very high for all samples (>97.1%), and clustering analyses showed distinct grouping of the cell types according to hematopoietic lineage. We explored whether this cord blood and the adult peripheral blood reference data sets impact the estimation of cell type composition in cord blood samples from an independent birth cohort (MoBa, n = 1092). This revealed significant differences for all cell types. Importantly, comparison of the cell type estimates against matched cell counts both in the cord blood reference samples (n = 11) and in another independent birth cohort (Generation R, n = 195), demonstrated moderate to high correlation of the data. This is the first cord blood reference data set with a comprehensive examination of the downstream application of the data through validation of estimated cell types against matched cell counts.
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Affiliation(s)
- Kristina Gervin
- a Department of Medical Genetics , Oslo University Hospital , Oslo , Norway
| | - Christian Magnus Page
- b Division of Mental and Physical Health , Norwegian Institute of Public Health , Oslo , Norway
| | | | - Michelle A Jansen
- d The Generation R Study Group, Erasmus MC , University Medical Center Rotterdam , the Netherlands.,e Department of Pediatrics, Erasmus MC , University Medical Center Rotterdam , the Netherlands.,f Department of Immunology, Erasmus MC , University Medical Center Rotterdam , the Netherlands
| | | | | | - Liesbeth Duijts
- d The Generation R Study Group, Erasmus MC , University Medical Center Rotterdam , the Netherlands.,i Department of Pediatrics, Division of Respiratory Medicine, Erasmus MC , University Medical Center Rotterdam , the Netherlands.,j Department of Pediatrics, Division of Neonatology, Erasmus MC , University Medical Center Rotterdam , the Netherlands.,k Department of Epidemiology, Erasmus MC , University Medical Center Rotterdam , the Netherlands
| | - Joyce B van Meurs
- l Department of Internal Medicine, Erasmus MC , University Medical Center Rotterdam , the Netherlands
| | - Menno C van Zelm
- m Department of Immunology, Erasmus MC , University Medical Center Rotterdam , the Netherlands.,n Department of Immunology and Pathology, Central Clinical School , Monash University , Melbourne , Victoria , Australia
| | - Vincent W Jaddoe
- d The Generation R Study Group, Erasmus MC , University Medical Center Rotterdam , the Netherlands.,e Department of Pediatrics, Erasmus MC , University Medical Center Rotterdam , the Netherlands.,k Department of Epidemiology, Erasmus MC , University Medical Center Rotterdam , the Netherlands
| | - Hedvig Nordeng
- o Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, School of Pharmacy , University of Oslo , Norway.,p PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences , University of Oslo , Oslo , Norway
| | - Gunn Peggy Knudsen
- q Health Data and Digitalisation , Norwegian Institute of Public Health , Oslo , Norway
| | - Per Magnus
- q Health Data and Digitalisation , Norwegian Institute of Public Health , Oslo , Norway
| | - Wenche Nystad
- b Division of Mental and Physical Health , Norwegian Institute of Public Health , Oslo , Norway
| | - Anne Cathrine Staff
- g Departments of Obstetrics and Gynecology , Oslo University Hospital , Oslo , Norway.,r Faculty of Medicine , University of Oslo , Oslo , Norway
| | - Janine F Felix
- d The Generation R Study Group, Erasmus MC , University Medical Center Rotterdam , the Netherlands.,e Department of Pediatrics, Erasmus MC , University Medical Center Rotterdam , the Netherlands.,k Department of Epidemiology, Erasmus MC , University Medical Center Rotterdam , the Netherlands
| | - Robert Lyle
- a Department of Medical Genetics , Oslo University Hospital , Oslo , Norway.,o Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, School of Pharmacy , University of Oslo , Norway.,p PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences , University of Oslo , Oslo , Norway
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IJspeert H, van Schouwenburg PA, van Zessen D, Pico-Knijnenburg I, Driessen GJ, Stubbs AP, van der Burg M. Evaluation of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and Adults. Front Immunol 2016; 7:410. [PMID: 27799928 PMCID: PMC5066086 DOI: 10.3389/fimmu.2016.00410] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/22/2016] [Indexed: 12/03/2022] Open
Abstract
Upon antigen recognition via their B cell receptor (BR), B cells migrate to the germinal center where they undergo somatic hypermutation (SHM) to increase their affinity for the antigen, and class switch recombination (CSR) to change the effector function of the secreted antibodies. These steps are essential to create an antigen-experienced BR repertoire that efficiently protects the body against pathogens. At the same time, the BR repertoire should be selected to protect against responses to self-antigen or harmless antigens. Insights into the processes of SHM, selection, and CSR can be obtained by studying the antigen-experienced BR repertoire. Currently, a large reference data set of healthy children and adults, which ranges from neonates to the elderly, is not available. In this study, we analyzed the antigen-experienced repertoire of 38 healthy donors (HD), ranging from cord blood to 74 years old, by sequencing IGA and IGG transcripts using next generation sequencing. This resulted in a large, freely available reference data set containing 412,890 IGA and IGG transcripts. We used this data set to study mutation levels, SHM patterns, antigenic selection, and CSR from birth to elderly HD. Only small differences were observed in SHM patterns, while the mutation levels increase in early childhood and stabilize at 6 years of age at around 7%. Furthermore, comparison of the antigen-experienced repertoire with sequences from the naive immune repertoire showed that features associated with autoimmunity such as long CDR3 length and IGHV4-34 usage are reduced in the antigen-experienced repertoire. Moreover, IGA2 and IGG2 usage was increased in HD in higher age categories, while IGG1 usage was decreased. In addition, we studied clonal relationship in the different samples. Clonally related sequences were found with different subclasses. Interestingly, we found transcripts with the same CDR1–CDR3 sequence, but different subclasses. Together, these data suggest that a single antigen can provoke a B-cell response with BR of different subclasses and that, during the course of an immune response, some B cells change their isotype without acquiring additional SHM or can directly switch to different isotypes.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | | | - David van Zessen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands; Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Ingrid Pico-Knijnenburg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Gertjan J Driessen
- Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
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