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Zaunseder E, Teinert J, Boy N, Garbade SF, Haupt S, Feyh P, Hoffmann GF, Kölker S, Mütze U, Heuveline V. Digital-Tier Strategy Improves Newborn Screening for Glutaric Aciduria Type 1. Int J Neonatal Screen 2024; 10:83. [PMID: 39728403 DOI: 10.3390/ijns10040083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 11/20/2024] [Accepted: 12/10/2024] [Indexed: 12/28/2024] Open
Abstract
Glutaric aciduria type 1 (GA1) is a rare inherited metabolic disease increasingly included in newborn screening (NBS) programs worldwide. Because of the broad biochemical spectrum of individuals with GA1 and the lack of reliable second-tier strategies, NBS for GA1 is still confronted with a high rate of false positives. In this study, we aim to increase the specificity of NBS for GA1 and, hence, to reduce the rate of false positives through machine learning methods. Therefore, we studied NBS profiles from 1,025,953 newborns screened between 2014 and 2023 at the Heidelberg NBS Laboratory, Germany. We identified a significant sex difference, resulting in twice as many false-positives male than female newborns. Moreover, the proposed digital-tier strategy based on logistic regression analysis, ridge regression, and support vector machine reduced the false-positive rate by over 90% compared to regular NBS while identifying all confirmed individuals with GA1 correctly. An in-depth analysis of the profiles revealed that in particular false-positive results with high associated follow-up costs could be reduced significantly. In conclusion, understanding the origin of false-positive NBS and implementing a digital-tier strategy to enhance the specificity of GA1 testing may significantly reduce the burden on newborns and their families from false-positive NBS results.
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Wiegert J, Höhler D, Haag J, Stamatakis A. Predicting Phylogenetic Bootstrap Values via Machine Learning. Mol Biol Evol 2024; 41:msae215. [PMID: 39418337 PMCID: PMC11523138 DOI: 10.1093/molbev/msae215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 08/28/2024] [Accepted: 09/15/2024] [Indexed: 10/19/2024] Open
Abstract
Estimating the statistical robustness of the inferred tree(s) constitutes an integral part of most phylogenetic analyses. Commonly, one computes and assigns a branch support value to each inner branch of the inferred phylogeny. The still most widely used method for calculating branch support on trees inferred under maximum likelihood (ML) is the Standard, nonparametric Felsenstein bootstrap support (SBS). Due to the high computational cost of the SBS, a plethora of methods has been developed to approximate it, for instance, via the rapid bootstrap (RB) algorithm. There have also been attempts to devise faster, alternative support measures, such as the SH-aLRT (Shimodaira-Hasegawa-like approximate likelihood ratio test) or the UltraFast bootstrap 2 (UFBoot2) method. Those faster alternatives exhibit some limitations, such as the need to assess model violations (UFBoot2) or unstable behavior in the low support interval range (SH-aLRT). Here, we present the educated bootstrap guesser (EBG), a machine learning-based tool that predicts SBS branch support values for a given input phylogeny. EBG is on average 9.4 (σ=5.5) times faster than UFBoot2. EBG-based SBS estimates exhibit a median absolute error of 5 when predicting SBS values between 0 and 100. Furthermore, EBG also provides uncertainty measures for all per-branch SBS predictions and thereby allows for a more rigorous and careful interpretation. EBG can, for instance, predict SBS support values on a phylogeny comprising 1,654 SARS-CoV2 genome sequences within 3 h on a mid-class laptop. EBG is available under GNU GPL3.
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Han SB, Teuffel J, Mukherjee G, Wade RC. Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome P450 2B4. Protein Sci 2024; 33:e5165. [PMID: 39291728 PMCID: PMC11409197 DOI: 10.1002/pro.5165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024]
Abstract
Cytochrome P450 2B4 (CYP 2B4) is one of the best-characterized CYPs and serves as a key model system for understanding the mechanisms of microsomal class II CYPs, which metabolize most known drugs. The highly flexible nature of CYP 2B4 is apparent from crystal structures that show the active site with either a wide open or a closed heme binding cavity. Here, we investigated the conformational ensemble of the full-length CYP 2B4 in a phospholipid bilayer, using multiresolution molecular dynamics (MD) simulations. Coarse-grained MD simulations revealed two predominant orientations of CYP 2B4's globular domain with respect to the bilayer. Their refinement by atomistic resolution MD showed adaptation of the enzyme's interaction with the lipid bilayer, leading to open configurations that facilitate ligand access to the heme binding cavity. CAVER analysis of enzyme tunnels, AquaDuct analysis of water routes, and Random Acceleration Molecular Dynamics simulations of ligand dissociation support the conformation-dependent passage of molecules between the active site and the protein surroundings. Furthermore, simulation of the re-entry of the inhibitor bifonazole into the open conformation of CYP 2B4 resulted in binding at a transient hydrophobic pocket within the active site cavity that may play a role in substrate binding or allosteric regulation. Together, these results show how the open conformation of CYP 2B4 facilitates the binding of substrates from and release of products to the membrane, whereas the closed conformation prolongs the residence time of substrates or inhibitors and selectively allows the passage of smaller reactants via the solvent and water channels.
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Engelhardt S. Why thorough open data descriptions matters more than ever in the age of AI: opportunities for cardiovascular research. EUROPEAN HEART JOURNAL. DIGITAL HEALTH 2024; 5:507-508. [PMID: 39318694 PMCID: PMC11417475 DOI: 10.1093/ehjdh/ztae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
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Kwon H, Kamboj O, Song A, Alarcón-Correa M, Remke J, Moafian F, Miksch B, Goyal R, Kim DY, Hamprecht FA, Fischer P. Scalable Optical Nose Realized with a Chemiresistively Modulated Light-Emitter Array. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2402287. [PMID: 38696529 DOI: 10.1002/adma.202402287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/10/2024] [Indexed: 05/04/2024]
Abstract
Biological olfaction relies on a large number of receptors that function as sensors to detect gaseous molecules. It is challenging to realize artificial olfactory systems that contain similarly large numbers of sensory materials. It is shown that combinatorial materials processing with vapor deposition can be used to fabricate large arrays of distinct chemiresistive sensing materials. By combining these with light-emitting diodes, an array of chemiresistively-modulated light-emitting diodes, or ChemLEDs, that permit a simultaneous optical read-out in response to an analyte is obtained. The optical nose uses a common voltage source and ground for all sensing elements and thus eliminates the need for complex wiring of individual sensors. This optical nose contains one hundred ChemLEDs and generates unique light patterns in response to gases and their mixtures. Optical pattern recognition methods enable the quantitative prediction of the corresponding concentrations and compositions, thereby paving the way for massively parallel artificial olfactory systems. ChemLEDs open the possibility to explore demanding gas sensing applications, including in environmental, food quality monitoring, and potentially diagnostic settings.
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Morel B, Williams TA, Stamatakis A, Szöllősi GJ. AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss. Bioinformatics 2024; 40:btae162. [PMID: 38514421 PMCID: PMC10990685 DOI: 10.1093/bioinformatics/btae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/30/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
MOTIVATION Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics. Ideally, phylogenetic methods should not only model substitutions along gene trees, which explain differences between homologous gene sequences, but also the processes that generate the gene trees themselves along a shared species tree. To conduct accurate inferences, one needs to account for uncertainty at both levels, that is, in gene trees estimated from inherently short sequences and in their diverse evolutionary histories along a shared species tree. RESULTS We present AleRax, a software that can infer reconciled gene trees together with a shared species tree using a simple, yet powerful, probabilistic model of gene duplication, transfer, and loss. A key feature of AleRax is its ability to account for uncertainty in the gene tree and its reconciliation by using an efficient approximation to calculate the joint phylogenetic-reconciliation likelihood and sample reconciled gene trees accordingly. Simulations and analyses of empirical data show that AleRax is one order of magnitude faster than competing gene tree inference tools while attaining the same accuracy. It is consistently more robust than species tree inference methods such as SpeciesRax and ASTRAL-Pro 2 under gene tree uncertainty. Finally, AleRax can process multiple gene families in parallel thereby allowing users to compare competing phylogenetic hypotheses and estimate model parameters, such as duplication, transfer, and loss probabilities for genome-scale datasets with hundreds of taxa. AVAILABILITY AND IMPLEMENTATION GNU GPL at https://github.com/BenoitMorel/AleRax and data are made available at https://cme.h-its.org/exelixis/material/alerax_data.tar.gz.
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Wang C, Karl R, Sharan L, Grizelj A, Fischer S, Karck M, De Simone R, Romano G, Engelhardt S. Surgical training of minimally invasive mitral valve repair on a patient-specific simulator improves surgical skills. Eur J Cardiothorac Surg 2024; 65:ezad387. [PMID: 37988128 DOI: 10.1093/ejcts/ezad387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/05/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023] Open
Abstract
OBJECTIVES Minimally invasive mitral valve repair (MVR) is considered one of the most challenging operations in cardiac surgery and requires much practice and experience. Simulation-based surgical training might be a method to support the learning process and help to flatten the steep learning curve of novices. The purpose of this study was to show the possible effects on learning of surgical training using a high-fidelity simulator with patient-specific mitral valve replicas. METHODS Twenty-five participants were recruited to perform MVR on anatomically realistic valve models during different training sessions. After every session their performance was evaluated by a surgical expert regarding accuracy and duration for each step. A second blinded rater similarly assessed the performance after the study. Through repeated documentation of those parameters, their progress in learning was analysed, and gains in proficiency were evaluated. RESULTS Participants showed significant performance enhancements in terms of both accuracy and time. Their surgical skills showed sizeable improvements after only 1 session. For example, the time to implant neo-chordae decreased by 24.64% (354 s-264 s, P < 0.001) and the time for annuloplasty by 4.01% (54 s-50 s, P = 0.165), whereas the number of irregular stitches for annuloplasty decreased from 52% to 24%.The significance of simulation-based surgical training as a tool for acquiring and training surgical skills was reviewed positively. CONCLUSIONS The results of this study indicate that simulation-based surgical training is a valuable and effective method for learning reconstructive techniques of minimally invasive MVR and overall general dexterity.The novel learning and training options should be implemented in the surgical traineeship for systematic teaching of various surgical skills.
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Sun Y, Piechotta M, Naarmann-de Vries I, Dieterich C, Ehrenhofer-Murray A. Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing. Nucleic Acids Res 2023; 51:11197-11212. [PMID: 37811872 PMCID: PMC10639084 DOI: 10.1093/nar/gkad826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023] Open
Abstract
Queuosine (Q) is a complex tRNA modification found in bacteria and eukaryotes at position 34 of four tRNAs with a GUN anticodon, and it regulates the translational efficiency and fidelity of the respective codons that differ at the Wobble position. In bacteria, the biosynthesis of Q involves two precursors, preQ0 and preQ1, whereas eukaryotes directly obtain Q from bacterial sources. The study of queuosine has been challenging due to the limited availability of high-throughput methods for its detection and analysis. Here, we have employed direct RNA sequencing using nanopore technology to detect the modification of tRNAs with Q and Q precursors. These modifications were detected with high accuracy on synthetic tRNAs as well as on tRNAs extracted from Schizosaccharomyces pombe and Escherichia coli by comparing unmodified to modified tRNAs using the tool JACUSA2. Furthermore, we present an improved protocol for the alignment of raw sequence reads that gives high specificity and recall for tRNAs ex cellulo that, by nature, carry multiple modifications. Altogether, our results show that 7-deazaguanine-derivatives such as queuosine are readily detectable using direct RNA sequencing. This advancement opens up new possibilities for investigating these modifications in native tRNAs, furthering our understanding of their biological function.
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de Buhr S, Gräter F. Myristoyl's dual role in allosterically regulating and localizing Abl kinase. eLife 2023; 12:e85216. [PMID: 37843155 PMCID: PMC10619977 DOI: 10.7554/elife.85216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 10/15/2023] [Indexed: 10/17/2023] Open
Abstract
c-Abl kinase, a key signaling hub in many biological processes ranging from cell development to proliferation, is tightly regulated by two inhibitory Src homology domains. An N-terminal myristoyl modification can bind to a hydrophobic pocket in the kinase C-lobe, which stabilizes the autoinhibitory assembly. Activation is triggered by myristoyl release. We used molecular dynamics simulations to show how both myristoyl and the Src homology domains are required to impose the full inhibitory effect on the kinase domain and reveal the allosteric transmission pathway at residue-level resolution. Importantly, we find myristoyl insertion into a membrane to thermodynamically compete with binding to c-Abl. Myristoyl thus not only localizes the protein to the cellular membrane, but membrane attachment at the same time enhances activation of c-Abl by stabilizing its preactivated state. Our data put forward a model in which lipidation tightly couples kinase localization and regulation, a scheme that currently appears to be unique for this non-receptor tyrosine kinase.
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Trendel J, Boileau E, Jochem M, Dieterich C, Krijgsveld J. PEPseq quantifies transcriptome-wide changes in protein occupancy and reveals selective translational repression after translational stress. Nucleic Acids Res 2023; 51:e79. [PMID: 37395449 PMCID: PMC10415142 DOI: 10.1093/nar/gkad557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/24/2023] [Accepted: 06/30/2023] [Indexed: 07/04/2023] Open
Abstract
Post-transcriptional gene regulation is accomplished by the interplay of the transcriptome with RNA-binding proteins, which occurs in a dynamic manner in response to altered cellular conditions. Recording the combined occupancy of all proteins binding to the transcriptome offers the opportunity to interrogate if a particular treatment leads to any interaction changes, pointing to sites in RNA that undergo post-transcriptional regulation. Here, we establish a method to monitor protein occupancy in a transcriptome-wide fashion by RNA sequencing. To this end, peptide-enhanced pull-down for RNA sequencing (or PEPseq) uses metabolic RNA labelling with 4-thiouridine (4SU) for light-induced protein-RNA crosslinking, and N-hydroxysuccinimide (NHS) chemistry to isolate protein-crosslinked RNA fragments across all long RNA biotypes. We use PEPseq to investigate changes in protein occupancy during the onset of arsenite-induced translational stress in human cells and reveal an increase of protein interactions in the coding region of a distinct set of mRNAs, including mRNAs coding for the majority of cytosolic ribosomal proteins. We use quantitative proteomics to demonstrate that translation of these mRNAs remains repressed during the initial hours of recovery after arsenite stress. Thus, we present PEPseq as a discovery platform for the unbiased investigation of post-transcriptional regulation.
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Schoettler JJ, Sandrio S, Boesing C, Bauer L, Miethke T, Thiel M, Krebs J. Bacterial Co- or Superinfection in Patients Treated in Intensive Care Unit with COVID-19- and Influenza-Associated Pneumonia. Pathogens 2023; 12:927. [PMID: 37513774 PMCID: PMC10385659 DOI: 10.3390/pathogens12070927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Viral pneumonia is frequently complicated by bacterial co- or superinfection (c/s) with adverse effects on patients' outcomes. However, the incidence of c/s and its impact on the outcomes of patients might be dependent on the type of viral pneumonia. We performed a retrospective observational study in patients with confirmed COVID-19 pneumonia (CP) or influenza pneumonia (IP) from 01/2009 to 04/2022, investigating the incidence of c/s using a competing risk model and its impact on mortality in these patients in a tertiary referral center using multivariate logistic regressions. Co-infection was defined as pulmonary pathogenic bacteria confirmed in tracheal aspirate or bronchoalveolar lavage within 48 h after hospitalization. Superinfection was defined as pulmonary pathogenic bacteria detected in tracheal aspirate or bronchoalveolar lavage 48 h after hospitalization. We examined 114 patients with CP and 76 patients with IP. Pulmonary bacterial co-infection was detected in 15 (13.2%), and superinfection was detected in 50 (43.9%) of CP patients. A total of 5 (6.6%) co-infections (p = 0.2269) and 28 (36.8%) superinfections (p = 0.3687) were detected in IP patients. The overall incidence of c/s did not differ between CP and IP patients, and c/s was not an independent predictor for mortality in a study cohort with a high disease severity. We found a significantly higher probability of superinfection for patients with CP compared to patients with IP (p = 0.0017).
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Gaißler A, Bochem J, Spreuer J, Ottmann S, Martens A, Amaral T, Wagner NB, Claassen M, Meier F, Terheyden P, Garbe C, Eigentler T, Weide B, Pawelec G, Wistuba-Hamprecht K. Early decrease of blood myeloid-derived suppressor cells during checkpoint inhibition is a favorable biomarker in metastatic melanoma. J Immunother Cancer 2023; 11:e006802. [PMID: 37286306 PMCID: PMC10254874 DOI: 10.1136/jitc-2023-006802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND The need for reliable clinical biomarkers to predict which patients with melanoma will benefit from immune checkpoint blockade (ICB) remains unmet. Several different parameters have been considered in the past, including routine differential blood counts, T cell subset distribution patterns and quantification of peripheral myeloid-derived suppressor cells (MDSC), but none has yet achieved sufficient accuracy for clinical utility. METHODS Here, we investigated potential cellular biomarkers from clinical routine blood counts as well as several myeloid and T cell subsets, using flow cytometry, in two independent cohorts of a total of 141 patients with stage IV M1c melanoma before and during ICB. RESULTS Elevated baseline frequencies of monocytic MDSCs (M-MDSC) in the blood were confirmed to predict shorter overall survival (OS) (HR 2.086, p=0.030) and progression-free survival (HR 2.425, p=0.001) in the whole patient cohort. However, we identified a subgroup of patients with highly elevated baseline M-MDSC frequencies that fell below a defined cut-off during therapy and found that these patients had a longer OS that was similar to that of patients with low baseline M-MDSC frequencies. Importantly, patients with high M-MDSC frequencies exhibited a skewed baseline distribution of certain other immune cells but these did not influence patient survival, illustrating the paramount utility of MDSC assessment. CONCLUSION We confirmed that in general, highly elevated frequencies of peripheral M-MDSC are associated with poorer outcomes of ICB in metastatic melanoma. However, one reason for an imperfect correlation between high baseline MDSCs and outcome for individual patients may be the subgroup of patients identified here, with rapidly decreasing M-MDSCs on therapy, in whom the negative effect of high M-MDSC frequencies was lost. These findings might contribute to developing more reliable predictors of late-stage melanoma response to ICB at the individual patient level. A multifactorial model seeking such markers yielded only MDSC behavior and serum lactate dehydrogenase as predictors of treatment outcome.
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Naujokaitis T, Khoramnia R, Łabuz G, Choi CY, Auffarth GU, Tandogan T. Imaging Function and Relative Light Transmission of Explanted Opacified Hydrophilic Acrylic Intraocular Lenses. Diagnostics (Basel) 2023; 13:diagnostics13101804. [PMID: 37238287 DOI: 10.3390/diagnostics13101804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
We evaluated the influence of intraocular lens (IOL) opacification on the optical performance of explanted hydrophilic acrylic IOLs. We performed a laboratory analysis of 32 Lentis LS-502-1 (Oculentis GmbH, Berlin, Germany) IOLs, explanted due to opacification, in comparison with six clear unused samples of the same IOL model. Using an optical bench setup, we obtained modulation transfer function (MTF), Strehl ratio, two-dimensional MTF, and United States Air Force (USAF) chart images. In addition, we assessed light transmission through the IOLs. The MTF values of opacified IOLs at 3-mm aperture were similar to those of clear lenses, with the median (interquartile range) values of 0.74 (0.01) vs. 0.76 (0.03) at the spatial frequency of 50 line pairs per millimeter in clear and opacified IOLs, respectively. The Strehl ratio of opacified lenses was not lower than that of clear lenses. The USAF-chart analysis showed a considerable reduction in brightness in opacified IOLs. The median (interquartile range) relative light transmission of opacified IOLs in comparison to clear lenses was 55.6% (20.8%) at the aperture size of 3 mm. In conclusion, the explanted opacified IOLs had comparable MTF values to those of clear lenses but significantly reduced light transmission.
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Khoramnia R, Baur ID, Yan W, Łabuz G, Auffarth GU. Comparison of a Presbyopia-Correcting Supplementary Intraocular Lens Combination and a Capsular-Bag Lens: An In Vitro Study. Diagnostics (Basel) 2023; 13:diagnostics13081482. [PMID: 37189583 DOI: 10.3390/diagnostics13081482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 05/17/2023] Open
Abstract
We evaluated the optical quality of two approaches to trifocality: polypseudophakia versus monopseudophakia. The combination (polypseudophakia) of a monofocal Basis Z B1AWY0 and AddOn Trifocal A4DW0M intraocular lens (IOL) was compared to using one Basis Z Trifocal B1EWYN IOL, all from 1stQ GmbH. In both approaches, we measured modulation transfer function (MTF) and Strehl Ratio (SR) values at 3.0 and 4.5 mm pupil sizes. We determined the through-focus (TF) MTF at 25, 50 and 100 lp/mm for the 3 mm aperture. United States Air Force (USAF) target images were recorded. MTF measurement of the trifocal lens and the combined monofocal and trifocal AddOn IOL showed good performance at the far and near focus for the 3 mm aperture. For the 4.5 mm aperture the MTF improved for the far focus but decreased for the intermediate and near focus. TF MTF showed better contrast at the far focus for the polypseudophakic setup but at the expense of the efficiency at the near focus. However, the USAF chart images revealed only minimal differences between both approaches. The optical quality of the polypseudophakic approach was not affected by the presence of two IOLs instead of one and proved to be comparable with the performance of one capsular-bag-fixated trifocal IOL. Differences between the single vs. two-lens approach seen in the TF MTF analysis could be attributed to the optical design that varied between the trifocal models.
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Baur ID, Auffarth GU, Yan W, Łabuz G, Khoramnia R. Visualization of Ray Propagation through Extended Depth-of-Focus Intraocular Lenses. Diagnostics (Basel) 2022; 12:2667. [PMID: 36359510 PMCID: PMC9689910 DOI: 10.3390/diagnostics12112667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 10/14/2023] Open
Abstract
Extended depth-of-focus (EDoF) presbyopia-correcting intraocular lens (IOL) models differ in their optical design and performance. In the laboratory, we compared the ray propagation and light intensity profiles of four IOLs: the non-diffractive AcrySof IQ Vivity (Alcon Inc., Fort Worth, TX, USA) and two diffractive models, Symfony ZXR00 (Johnson & Johnson Vision, Jacksonville, FL, USA) and AT Lara 829 MP (Carl Zeiss Meditec, Berlin, Germany). A fourth lens, the monofocal AcrySof IQ SN60WF (Alcon Inc.) acted as the control. We projected a 520 nm laser light through each submerged lens in a bath of fluorescein solution. A camera mounted on a microscope captured the light that emerged from the IOL. We recorded the IOLs' point spread function (PSF) to determine the presence of unwanted visual effects. The ray propagation visualization and light intensity profile of the monofocal control showed one distinct focus, while the AcrySof IQ Vivity demonstrated an extended focus area. We observed two distinct foci with each diffractive IOL. We found a lower level of light spread beyond the PSF center for the AcrySof IQ Vivity compared to the diffractive IOLs. In conclusion, we could confirm the extended range of focus for all the EDoF IOL models. However, the non-diffractive AcrySof IQ Vivity appears to have a smoother transition from a far to an intermediate range. We discuss whether, in clinical use, the higher level of spurious light we found in the diffractive designs may translate into increased dysphotopsia.
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Turova V, Kovtanyuk A, Pykhteev O, Sidorenko I, Lampe R. Glycocalyx Sensing with a Mathematical Model of Acoustic Shear Wave Biosensor. Bioengineering (Basel) 2022; 9:462. [PMID: 36135008 PMCID: PMC9495919 DOI: 10.3390/bioengineering9090462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/22/2022] Open
Abstract
The article deals with an idea of exploiting an acoustic shear wave biosensor for investigating the glycocalyx, a polysaccharide polymer molecule layer on the endothelium of blood vessels that, according to recent studies, plays an important role in protecting against diseases. To test this idea, a mathematical model of an acoustic shear wave sensor and corresponding software developed earlier for proteomic applications are used. In this case, the glycocalyx is treated as a layer homogenized over the thin polymer "villi". Its material characteristics depend on the density, thickness, and length of the villi and on the viscous properties of the surrounding liquid (blood plasma). It is proved that the model used has a good sensitivity to the above parameters of the villi and blood plasma. Numerical experiments performed using real data collected retrospectively from premature infants show that the use of acoustic shear wave sensors may be a promising approach to investigate properties of glycocalyx-like structures and their role in prematurity.
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Eriksson O, Bhalla US, Blackwell KT, Crook SM, Keller D, Kramer A, Linne ML, Saudargienė A, Wade RC, Hellgren Kotaleski J. Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. eLife 2022; 11:e69013. [PMID: 35792600 PMCID: PMC9259018 DOI: 10.7554/elife.69013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/13/2022] [Indexed: 12/22/2022] Open
Abstract
Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system works or why certain phenomena are observed. Data-driven modeling, on the other hand, follows a more unbiased approach, with model construction informed by the computationally intensive use of data. At the same time, researchers employ models at different biological scales and at different levels of abstraction. Combining these models while validating them against experimental data increases understanding of the multiscale brain. However, a lack of interoperability, transparency, and reusability of both models and the workflows used to construct them creates barriers for the integration of models representing different biological scales and built using different modeling philosophies. We argue that the same imperatives that drive resources and policy for data - such as the FAIR (Findable, Accessible, Interoperable, Reusable) principles - also support the integration of different modeling approaches. The FAIR principles require that data be shared in formats that are Findable, Accessible, Interoperable, and Reusable. Applying these principles to models and modeling workflows, as well as the data used to constrain and validate them, would allow researchers to find, reuse, question, validate, and extend published models, regardless of whether they are implemented phenomenologically or mechanistically, as a few equations or as a multiscale, hierarchical system. To illustrate these ideas, we use a classical synaptic plasticity model, the Bienenstock-Cooper-Munro rule, as an example due to its long history, different levels of abstraction, and implementation at many scales.
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Sprengholz P, Henkel L, Betsch C. Payments and freedoms: Effects of monetary and legal incentives on COVID-19 vaccination intentions in Germany. PLoS One 2022; 17:e0268911. [PMID: 35609052 PMCID: PMC9129024 DOI: 10.1371/journal.pone.0268911] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Monetary and legal incentives have been proposed to promote COVID-19 vaccination uptake. To evaluate the suitability of incentives, an experiment with German participants examined the effects of payments (varied within subjects: 0 to 10,000 EUR) and freedoms (varied between subjects: vaccination leading vs. not leading to the same benefits as a negative test result) on the vaccination intentions of previously unvaccinated individuals (n = 782) in April 2021. While no effect could be found for freedoms, the share of participants willing to be vaccinated increased with the payment amount. However, a significant change required large rewards of 3,250 EUR or more. While monetary incentives could increase vaccination uptake by a few percentage points, the high costs of implementation challenge the efficiency of the measure and call for alternatives. As the data suggest that considering vaccination as safe, necessary, and prosocial increases an individual's likelihood of wanting to get vaccinated without payment, interventions should focus on these features when promoting vaccination against COVID-19.
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Bochem J, Zelba H, Spreuer J, Amaral T, Wagner NB, Gaissler A, Pop OT, Thiel K, Yurttas C, Soffel D, Forchhammer S, Sinnberg T, Niessner H, Meier F, Terheyden P, Königsrainer A, Garbe C, Flatz L, Pawelec G, Eigentler TK, Löffler MW, Weide B, Wistuba-Hamprecht K. Early disappearance of tumor antigen-reactive T cells from peripheral blood correlates with superior clinical outcomes in melanoma under anti-PD-1 therapy. J Immunother Cancer 2021; 9:jitc-2021-003439. [PMID: 34933966 PMCID: PMC8693089 DOI: 10.1136/jitc-2021-003439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 01/03/2023] Open
Abstract
Background Anti-programmed cell death protein 1 (PD-1) antibodies are now routinely administered for metastatic melanoma and for increasing numbers of other cancers, but still only a fraction of patients respond. Better understanding of the modes of action and predictive biomarkers for clinical outcome is urgently required. Cancer rejection is mostly T cell-mediated. We previously showed that the presence of NY-ESO-1-reactive and/or Melan-A-reactive T cells in the blood correlated with prolonged overall survival (OS) of patients with melanoma with a heterogeneous treatment background. Here, we investigated whether such reactive T cells can also be informative for clinical outcomes in metastatic melanoma under PD-1 immune-checkpoint blockade (ICB). Methods Peripheral blood T cell stimulation by NY-ESO-1 and Melan-A overlapping peptide libraries was assessed before and during ICB in two independent cohorts of a total of 111 patients with stage IV melanoma. In certain cases, tumor-infiltrating lymphocytes could also be assessed for such responses. These were characterized using intracellular cytokine staining for interferon gamma (IFN-γ), tumor negrosis factor (TNF) and CD107a. Digital pathology analysis was performed to quantify NY-ESO-1 and Melan-A expression by tumors. Endpoints were OS and progression-free survival (PFS). Results The initial presence in the circulation of NY-ESO-1- or Melan-A-reactive T cells which became no longer detectable during ICB correlated with validated, prolonged PFS (HR:0.1; p>0.0001) and OS (HR:0.2; p=0.021). An evaluation of melanoma tissue from selected cases suggested a correlation between tumor-resident NY-ESO-1- and Melan-A-reactive T cells and disease control, supporting the notion of a therapy-associated sequestration of cells from the periphery to the tumor predominantly in those patients benefitting from ICB. Conclusions Our findings suggest a PD-1 blockade-dependent infiltration of melanoma-reactive T cells from the periphery into the tumor and imply that this seminally contributes to effective treatment.
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MESH Headings
- Aged
- Aged, 80 and over
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- Biomarkers, Tumor/immunology
- Biomarkers, Tumor/metabolism
- CD8-Positive T-Lymphocytes/immunology
- Female
- Follow-Up Studies
- Humans
- Immune Checkpoint Inhibitors/therapeutic use
- Leukocytes, Mononuclear/drug effects
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Leukocytes, Mononuclear/pathology
- Lymphocytes, Tumor-Infiltrating/immunology
- MART-1 Antigen/immunology
- MART-1 Antigen/metabolism
- Male
- Melanoma/drug therapy
- Melanoma/immunology
- Melanoma/mortality
- Melanoma/pathology
- Membrane Proteins/immunology
- Membrane Proteins/metabolism
- Middle Aged
- Prognosis
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Survival Rate
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Hübner L, Kozlov AM, Hespe D, Sanders P, Stamatakis A. Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG. Bioinformatics 2021; 37:4056-4063. [PMID: 34037680 PMCID: PMC9502163 DOI: 10.1093/bioinformatics/btab399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/10/2021] [Accepted: 05/25/2021] [Indexed: 11/18/2022] Open
Abstract
MOTIVATION Phylogenetic trees are now routinely inferred on large scale high performance computing systems with thousands of cores as the parallel scalability of phylogenetic inference tools has improved over the past years to cope with the molecular data avalanche. Thus, the parallel fault tolerance of phylogenetic inference tools has become a relevant challenge. To this end, we explore parallel fault tolerance mechanisms and algorithms, the software modifications required and the performance penalties induced via enabling parallel fault tolerance by example of RAxML-NG, the successor of the widely used RAxML tool for maximum likelihood-based phylogenetic tree inference. RESULTS We find that the slowdown induced by the necessary additional recovery mechanisms in RAxML-NG is on average 1.00 ± 0.04. The overall slowdown by using these recovery mechanisms in conjunction with a fault-tolerant Message Passing Interface implementation amounts to on average 1.7 ± 0.6 for large empirical datasets. Via failure simulations, we show that RAxML-NG can successfully recover from multiple simultaneous failures, subsequent failures, failures during recovery and failures during checkpointing. Recoveries are automatic and transparent to the user. AVAILABILITY AND IMPLEMENTATION The modified fault-tolerant RAxML-NG code is available under GNU GPL at https://github.com/lukashuebner/ft-raxml-ng. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Garnier S, Harakalova M, Weiss S, Mokry M, Regitz-Zagrosek V, Hengstenberg C, Cappola TP, Isnard R, Arbustini E, Cook SA, van Setten J, Calis JJA, Hakonarson H, Morley MP, Stark K, Prasad SK, Li J, O'Regan DP, Grasso M, Müller-Nurasyid M, Meitinger T, Empana JP, Strauch K, Waldenberger M, Marguiles KB, Seidman CE, Kararigas G, Meder B, Haas J, Boutouyrie P, Lacolley P, Jouven X, Erdmann J, Blankenberg S, Wichter T, Ruppert V, Tavazzi L, Dubourg O, Roizes G, Dorent R, de Groote P, Fauchier L, Trochu JN, Aupetit JF, Bilinska ZT, Germain M, Völker U, Hemerich D, Raji I, Bacq-Daian D, Proust C, Remior P, Gomez-Bueno M, Lehnert K, Maas R, Olaso R, Saripella GV, Felix SB, McGinn S, Duboscq-Bidot L, van Mil A, Besse C, Fontaine V, Blanché H, Ader F, Keating B, Curjol A, Boland A, Komajda M, Cambien F, Deleuze JF, Dörr M, Asselbergs FW, Villard E, Trégouët DA, Charron P. Genome-wide association analysis in dilated cardiomyopathy reveals two new players in systolic heart failure on chromosomes 3p25.1 and 22q11.23. Eur Heart J 2021; 42:2000-2011. [PMID: 33677556 PMCID: PMC8139853 DOI: 10.1093/eurheartj/ehab030] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/13/2020] [Accepted: 01/14/2021] [Indexed: 12/31/2022] Open
Abstract
AIMS Our objective was to better understand the genetic bases of dilated cardiomyopathy (DCM), a leading cause of systolic heart failure. METHODS AND RESULTS We conducted the largest genome-wide association study performed so far in DCM, with 2719 cases and 4440 controls in the discovery population. We identified and replicated two new DCM-associated loci on chromosome 3p25.1 [lead single-nucleotide polymorphism (SNP) rs62232870, P = 8.7 × 10-11 and 7.7 × 10-4 in the discovery and replication steps, respectively] and chromosome 22q11.23 (lead SNP rs7284877, P = 3.3 × 10-8 and 1.4 × 10-3 in the discovery and replication steps, respectively), while confirming two previously identified DCM loci on chromosomes 10 and 1, BAG3 and HSPB7. A genetic risk score constructed from the number of risk alleles at these four DCM loci revealed a 3-fold increased risk of DCM for individuals with 8 risk alleles compared to individuals with 5 risk alleles (median of the referral population). In silico annotation and functional 4C-sequencing analyses on iPSC-derived cardiomyocytes identify SLC6A6 as the most likely DCM gene at the 3p25.1 locus. This gene encodes a taurine transporter whose involvement in myocardial dysfunction and DCM is supported by numerous observations in humans and animals. At the 22q11.23 locus, in silico and data mining annotations, and to a lesser extent functional analysis, strongly suggest SMARCB1 as the candidate culprit gene. CONCLUSION This study provides a better understanding of the genetic architecture of DCM and sheds light on novel biological pathways underlying heart failure.
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Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki EG, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A. Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult. Mol Biol Evol 2021; 38:1777-1791. [PMID: 33316067 PMCID: PMC7798910 DOI: 10.1093/molbev/msaa314] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.
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Boujemaa-Paterski R, Martins B, Eibauer M, Beales CT, Geiger B, Medalia O. Talin-activated vinculin interacts with branched actin networks to initiate bundles. eLife 2020; 9:e53990. [PMID: 33185186 PMCID: PMC7682986 DOI: 10.7554/elife.53990] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 11/12/2020] [Indexed: 12/18/2022] Open
Abstract
Vinculin plays a fundamental role in integrin-mediated cell adhesion. Activated by talin, it interacts with diverse adhesome components, enabling mechanical coupling between the actin cytoskeleton and the extracellular matrix. Here we studied the interactions of activated full-length vinculin with actin and the way it regulates the organization and dynamics of the Arp2/3 complex-mediated branched actin network. Through a combination of surface patterning and light microscopy experiments we show that vinculin can bundle dendritic actin networks through rapid binding and filament crosslinking. We show that vinculin promotes stable but flexible actin bundles having a mixed-polarity organization, as confirmed by cryo-electron tomography. Adhesion-like synthetic design of vinculin activation by surface-bound talin revealed that clustered vinculin can initiate and immobilize bundles from mobile Arp2/3-branched networks. Our results provide a molecular basis for coordinate actin bundle formation at nascent adhesions.
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Turova V, Sidorenko I, Eckardt L, Rieger-Fackeldey E, Felderhoff-Müser U, Alves-Pinto A, Lampe R. Machine learning models for identifying preterm infants at risk of cerebral hemorrhage. PLoS One 2020; 15:e0227419. [PMID: 31940391 PMCID: PMC6961932 DOI: 10.1371/journal.pone.0227419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/18/2019] [Indexed: 11/18/2022] Open
Abstract
Intracerebral hemorrhage in preterm infants is a major cause of brain damage and cerebral palsy. The pathogenesis of cerebral hemorrhage is multifactorial. Among the risk factors are impaired cerebral autoregulation, infections, and coagulation disorders. Machine learning methods allow the identification of combinations of clinical factors to best differentiate preterm infants with intra-cerebral bleeding and the development of models for patients at risk of cerebral hemorrhage. In the current study, a Random Forest approach is applied to develop such models for extremely and very preterm infants (23-30 weeks gestation) based on data collected from a cohort of 229 individuals. The constructed models exhibit good prediction accuracy and might be used in clinical practice to reduce the risk of cerebral bleeding in prematurity.
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Feldman-Salit A, Veith N, Wirtz M, Hell R, Kummer U. Distribution of control in the sulfur assimilation in Arabidopsis thaliana depends on environmental conditions. THE NEW PHYTOLOGIST 2019; 222:1392-1404. [PMID: 30681147 DOI: 10.1111/nph.15704] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/13/2019] [Indexed: 05/24/2023]
Abstract
Sulfur assimilation is central to the survival of plants and has been studied under different environmental conditions. Multiple studies have been published trying to determine rate-limiting or controlling steps in this pathway. However, the picture remains inconclusive with at least two different enzymes proposed to represent such rate-limiting steps. Here, we used computational modeling to gain an integrative understanding of the distribution of control in the sulfur assimilation pathway of Arabidopsis thaliana. For this purpose, we set up a new ordinary differential equation (ODE)-based, kinetic model of sulfur assimilation encompassing all biochemical reactions directly involved in this process. We fitted the model to published experimental data and produced a model ensemble to deal with parameter uncertainties. The ensemble was validated against additional published experimental data. We used the model ensemble to subsequently analyse the control pattern and robustly identified a set of processes that share the control in this pathway under standard conditions. Interestingly, the pattern of control is dynamic and not static, that is it changes with changing environmental conditions. Therefore, while adenosine-5'-phosphosulfate reductase (APR) and sulfite reductase (SiR) share control under standard laboratory conditions, APR takes over an even more dominant role under sulfur starvation conditions.
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