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Developing a pipeline for identification,characterization and molecular editing of cis-regulatory elements:a case study in potato

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aBIOTECH 2025年第1期6卷 91-96页

作者： Min Wan Handan Xie Hongwei Guo Shenglin Jing Deying Zeng Bing Li Bo Zhu Zixian Zeng Department of Biological Science College of Life SciencesSichuan Normal UniversityChengdu 610101China Plant Functional Genomics and Bioinformatics Research Center Sichuan Normal UniversityChengdu 610101China Crop Research Institute Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan ProvinceSichuan Academy of Agricultural SciencesChengdu 610066China

Crop breeding requires a balance of tradeoffs among key agronomic traits caused by gene *** molecular manipulation of genes can effectively improve target traits,but this may not reduce gene pleiotropy,potentially leading to undesirable traits or even lethal ***,molecular editing of cis-regulatory elements(CREs)of target genes may facilitate the dissection of gene pleiotropy to fine-tune gene *** this study,we developed a pipeline,in potato,which employs open chromatin to predict candidate CREs,along with both transient and genetic assays to validate the function of CREs and CRISPR/Cas9 to edit candidate *** used StCDF1 as an example,a key gene for potato tuberization and identified a 288 bp-core promoter region,which showed photoperiodic inducibility.A homozygous CRISPR/Cas9-editing line was established,with two deletions in the core promoter,which displayed a reduced expression level,resulting in late tuberization under both longday and short-day *** pipeline provides an alternative pathway to improve a specific trait with limited downside on other phenotypes.

关键词： Cis-regulatory element Potato CRISPR Genome-editing

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Two iPSC lines with a heterozygous frameshift mutation in the floating-harbour syndrome locus of the SRCAP gene

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Stem Cell Research 2025年 86卷 103730页

作者： J. Rhode S. Edwards A. Tzvetkova L.R. Jensen M.F. Hossain B. Nowack L. Hagenau A.W. Kuss Human Molecular Genetics Group Department of Functional Genomics Interfaculty Institute for Genetics and Functional Genomics University Medicine Greifswald Greifswald Germany Institute of Bioinformatics University Medicine Greifswald Greifswald Germany SensID GmbH Rostock Germany

We present two CRISPR/Cas9-modified human iPSC lines with a heterozygous frameshift mutation (NM_006662.3:c.7300_7301insA) in the FLHS-locus of the SRCAP gene, which is associated with Floating-Harbor syndrome, a congenital neurodevelopmental disorder with symptoms including short stature and intellectual disability. The iPSCs express the pluripotency markers OCT4, SOX2, NANOG and TRA 1-60. They show differentiation into cells from all 3 germ layers, no chromosomal abnormalities and no off-target mutations in the tested regions. The mutation leads to a stop codon previously found in patients. Thus, either cell line can serve as disease-specific model for studying SRCAP in the context of FLHS.

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Tracking multiple particles in fluorescence time-lapse microscopy images via probabilistic data association

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IEEE Transactions on Medical Imaging 2015年第2期34卷 415-432页

作者： Godinez, William J. Rohr, Karl Department Bioinformatics and Functional Genomics Biomedical Computer Vision Group University of Heidelberg Heidelberg69120 Germany

Tracking subcellular structures as well as viral structures displayed as 'particles' in fluorescence microscopy images yields quantitative information on the underlying dynamical processes. We have developed an approach for tracking multiple fluorescent particles based on probabilistic data association. The approach combines a localization scheme that uses a bottom-up strategy based on the spot-enhancing filter as well as a top-down strategy based on an ellipsoidal sampling scheme that uses the Gaussian probability distributions computed by a Kalman filter. The localization scheme yields multiple measurements that are incorporated into the Kalman filter via a combined innovation, where the association probabilities are interpreted as weights calculated using an image likelihood. To track objects in close proximity, we compute the support of each image position relative to the neighboring objects of a tracked object and use this support to recalculate the weights. To cope with multiple motion models, we integrated the interacting multiple model algorithm. The approach has been successfully applied to synthetic 2-D and 3-D images as well as to real 2-D and 3-D microscopy images, and the performance has been quantified. In addition, the approach was successfully applied to the 2-D and 3-D image data of the recent Particle Tracking Challenge at the IEEE International Symposium on Biomedical Imaging (ISBI) 2012. © 2014 IEEE.

关键词： Fluorescence

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Characterizing somatic mutations in ovarian cancer germline risk regions

Communications Biology

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Communications Biology 2025年第1期8卷 1-9页

作者： Lai, Ping-Hung Tyrer, Jonathan P. Pharoah, Paul Gayther, Simon A. Jones, Michelle R. Peng, Pei-Chen Department of Computational Biomedicine Cedars-Sinai Medical Center West Hollywood CA United States CR-UK Department of Oncology University of Cambridge Strangeways Research Laboratory Cambridge United Kingdom Center for Inherited Oncogenesis Department of Medicine UT Health San Antonio San Antonio TX United States Center for Bioinformatics and Functional Genomics Department of Biomedical Sciences Cedars-Sinai Medical Center Los Angeles CA United States

Epithelial ovarian cancer (EOC) genetics research has been focused on germline or somatic mutations independently. Emerging evidence suggests that the somatic mutational landscape can be shaped by the germline genetic background. In this study, we aim to unravel the role of somatic alterations within EOC germline susceptibility regions by incorporating functional annotations. We investigate somatic events, including mutational signatures, point mutations, copy number alterations, and transcription factor binding disruptions, within 33 EOC germline susceptibility regions. Our analysis identifies significant associations between candidate germline susceptibility genes and somatic mutational signatures known to be key risk factors for EOC, such as mismatch repair deficiency, age-related mutagenesis, and homologous recombination deficiency. In addition, we find somatic point mutations and copy number alterations are significantly enriched in histotype-specific active enhancers and promoters within EOC risk loci. Furthermore, we examine the impact of germline variants and somatic mutations on transcription factor binding sites, identifying cancer developmental transcription factor motifs frequently affected by both types of mutations. Overall, our study highlights the importance of integrating germline and somatic mutations with regulatory and epigenomic data to gain insights into the genetic basis of EOC. © The Author(s) 2025.

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Integrating genomic and transcriptomic data into graph based approaches for defining essential reactions in the metabolic network of escherichia coli

Integrating genomic and transcriptomic data into graph based...

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Workshop on Learning, Knowledge, and Adaptivity, LWA 2007

作者： Plaimas, Kitiporn Oswald, Marcus Eils, Roland König, Rainer Germany Department of Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology Germany Interdisciplinary Center for Scientific Computing University of Heidelberg Germany

ISBN: (纸本)9783860109076

The genomic data that presently is available enables an in silico representation of the metabolic network that can be enriched with a wide range of experimentally determined attributes. We integrated biochemical knowledge with genomic and transcriptomic data by establishing a simple machine learning tool to define the essentiality of single enzymes in the metabolic network of Escherichia coli. We collected characteristics of each single reaction based not only on network topology but also on genomic and transcriptomic characteristics. The metabolic network was investigated when blocking each single reaction, respectively. A reaction was marked to be essential when basically the mutated network could not deliver the products of the knocked out reaction from the upstream substrates of the knocked out reaction. Furthermore, we calculated characteristics of the network topology including choke points, clustering coefficients, comparisons to genome neighbourhoods and gene expression coregulation of the genes that encode the corresponding enzymes. We fed the data into a machine learning system and yielded an accuracy of about 90%, when comparing our results to an experimentally performed genome wide knock-out screen. This study showed that our tool can effectively determine the biochemical lethality of enzymes in metabolic networks. The method can readily be used for pathogenic organisms to find potential drug targets.

关键词： Genome

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Probabilistic tracking of virus particles in fluorescence microscopy image sequences

Probabilistic tracking of virus particles in fluorescence mi...

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Workshops Bildverarbeitung fur die Medizin: Algorithmen - Systeme - Anwendungen, BVM 2008 - Workshop on Image Processing for Medicine: Algorithms - Systems - Applications, BVM 2008

作者： Godinez, W.J. Lampe, M. Wörz, S. Müller, B. Eils, R. Rohr, K. BIOQUANT IPMB University of Heidelberg Germany Dept. of Bioinformatics and Functional Genomics DKFZ Heidelberg Germany Department of Virology University of Heidelberg Germany

ISBN: (纸本)9783540786399

Fluorescence time-lapse microscopy is a powerful technique for observing the spatial-temporal behavior of viruses. To quantitatively analyze the exhibited dynamical relationships, tracking of viruses over time is required. We developed probabilistic approaches based on particle filters for tracking multiple virus particles in time-lapse fluorescence microscopy images. We employed a mixture of particle filters as well as independent particle filters. For the latter, we have developed a penalization strategy to maintain the identity of the tracked objects in cases where objects are in close proximity. We have applied the approaches to synthetic images and quantified their performance. We have also successfully applied the approaches to real microscopy images of HIV-1 particles and have compared the tracking results with ground truth from manual tracking.

关键词： Viruses

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Hybrid spline-based multimodal registration using a local measure for mutual information

Hybrid spline-based multimodal registration using a local me...

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Workshops Bildverarbeitung fur die Medizin: Algorithmen - Systeme - Anwendungen, BVM 2009 - Workshop on Image Processing for Medicine: Algorithms - Systems - Applications, BVM 2009

作者： Biesdorf, Andreas Wörz, Stefan Kaiser, Hans-Jürgen Rohr, Karl University of Heidelberg Dept. Bioinformatics and Functional Genomics Biomedical Computer Vision Group Germany University Hospital RWTH Aachen University Department of Nuclear Medicine Germany

ISBN: (纸本)9783540938590

We introduce a new hybrid approach for spline-based elastic registration of multimodal medical images. The approach uses point landmarks as well as intensity information based on local analytic measures for mutual information. The intensity similarity metrics are computationally efficient and can be optimized independently for each voxel. We have successfully applied our approach to synthetic images, brain phantom images, as well as real multimodal medical images.

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Engagement of sialylated glycans with Siglec receptors on suppressive myeloid cells inhibits anticancer immunity via CCL2

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Cellular & Molecular Immunology 2024年第5期21卷 495-509页

作者： Ronja Wieboldt Michael Sandholzer Emanuele Carlini Chia-wei Lin Anastasiya Börsch Andreas Zingg Didier Lardinois Petra Herzig Leyla Don Alfred Zippelius Heinz Läubli Natalia Rodrigues Mantuano Laboratory for Cancer Immunotherapy Department of BiomedicineUniversity Hospital and University of BaselBaselSwitzerland. Functional Genomics Center Zurich ETH ZurichZurichSwitzerland. Bioinformatics Core Facility Department of BiomedicineUniversity of Basel and Swiss Institute of BioinformaticsBaselSwitzerland. Department of Thoracic Surgery University Hospital BaselBaselSwitzerland. Laboratory of Cancer Immunology Department of BiomedicineUniversity Hospital and University of BaselBaselSwitzerland. Division of Oncology University Hospital BaselBaselSwitzerland.

The overexpression of sialic acids on glycans,called hypersialylation,is a common alteration found in cancer *** glycans can enhance immune evasion by interacting with sialic acid-binding immunoglobulin-like lectin(Siglec)receptors on tumorinfiltrating immune ***,we investigated the effect of sialylated glycans and their interaction with Siglec receptors on myeloid-derived suppressor cells(MDSCs).We found that MDSCs derived from the blood of lung cancer patients and tumor-bearing mice strongly express inhibitory Siglec receptors and are highly *** murine cancer models of emergency myelopoiesis,Siglec-E knockout in myeloid cells resulted in prolonged survival and increased tumor infiltration of activated T *** suppressive myeloid cells by blocking Siglec receptors or desialylation strongly reduced their suppressive *** further identified CCL2 as a mediator involved in T-cell suppression upon interaction between sialoglycans and Siglec receptors on *** results demonstrated that sialylated glycans inhibit anticancer immunity by modulating CCL2 expression.

关键词： sialoglycans Sialic acid-binding immunoglobulin-like lectin tumor microenvironment myeloid derived suppressor cells

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Revelation of potential antiviral activity of Azadirachta indica against Zika virus protease: An integrated molecular docking and dynamic simulation approach

Computational and Structural Biotechnology Reports

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Computational and Structural Biotechnology Reports 2025年 2卷

作者： Md. Habib Ullah Masum Rehana Parvin Syed Mohammad Lokman Zarin Tasnim Md. Mazharul Alam Jannatul Ferdous Department of Genomics and Bioinformatics Faculty of Biotechnology and Genetic Engineering Chattogram Veterinary and Animal Sciences University Khulshi 4225 Bangladesh Department of Pathology and Parasitology Faculty of Veterinary Medicine Chattogram Veterinary and Animal Sciences University Khulshi 4225 Bangladesh Asian University for Women (AUW) Chattogram 4000 Bangladesh Department of Industrial Biotechnology Faculty of Biotechnology and Genetic Engineering Chattogram Veterinary and Animal Sciences University Khulshi 4225 Bangladesh Functional Genomics and Proteomics Laboratory (FGPL) Department of Genetic Engineering and Biotechnology Faculty of Biological Sciences University of Chittagong Chattogram 4331 Bangladesh Department of Obstetrics and Gynecology Chittagong Medical College Hospital Chattogram 4203 Bangladesh

The Zika virus (ZIKV) is an RNA virus that mostly affects humans and primates and is transmitted via Aedes mosquitoes . The emergence of ZIKV has intensified global health concerns, emphasizing the urgent need for effective antiviral therapies. As a vital enzyme in the replication of ZIKV, the NS2B-NS3 protease offers a promising therapeutic target. This study leverages computer-aided drug design to identify bioactive compounds capable of inhibiting the ZIKV NS2B-NS3 protease, thereby disrupting viral replication. Bioactive compounds from Azadirachta indica were screened through virtual approaches, resulting in six with exceptional docking scores (<-5.5 kcal/mol). Analyses of the physicochemical properties validated the drug-like traits of the IMPHY014854 and IMPHY014908, conveying suitable hydrogen bonding profiles and moderate solubility (Log S: −2.22 to −3.60). Evaluations of pharmacokinetics suggested significant gastrointestinal absorption while exposing no permeability across the blood-brain barrier, thereby reducing interactions with the central nervous system. Toxicity evaluations revealed limited toxic effects, while several bioactive compounds exhibited particular toxicological issues. Molecular dynamics simulations further revealed the stability and interaction dynamics of ZIKV protease-ligand complexes, where the IMPHY014854 and IMPHY014908 exhibited significant residue flexibility, compactness, and solvent accessibility profiles over a 100 ns simulation. Principal component analysis revealed conformational distinctions, while Gibbs's free energy analysis demonstrated greater stability for the ZIKV protease-IMPHY014908 complex. This integrative computational strategy highlights the potential of phytochemicals as the ZIKV protease inhibitors and provides a foundation for developing effective antiviral drugs. Further, in vivo studies must be implemented to validate these findings and advance therapeutic prospects against ZIKV.

关键词： Mosquito-borne Phytodynamics Biocomputational Neem plant Protease inhibitor Antiviral drug

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Comparison of self-similarity measures for multi-modal non-rigid registration of 3D-PLI brain images

Comparison of self-similarity measures for multi-modal non-r...

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Workshop on Bildverarbeitung fur die Medizin, 2018

作者： Ali, Sharib Lin, Dehui Axer, Markus Rohr, Karl Department of Bioinformatics and Functional Genomics Biomedical Computer Vision Group BIOQUANT IPMB DKFZ University of Heidelberg Heidelberg Germany Institute of Neuroscience and Medicine 1 Research Centre Jülich Jülich Germany

ISBN: (纸本)9783662580950

We introduce self-similarity measures in a spline-based nonrigid registration method. We applied our method to register multimodal 3D polarized light imaging and blockface image data of human and rat brain sections. Quantitative evaluations demonstrate that using self-similarity measures increases the accuracy and robustness compared to a traditional mutual information measure. © Springer-Verlag GmbH Deutschland 2018.

关键词： Brain mapping

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